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1
Ungar, B., M. Yavzori, E. Fudim, O. Picard, U. Kopylov, R. Eliakim, D. Shouval, et al. "P032 Host transcriptome signatures in human fecal-washes predict histological remission in IBD patients." Journal of Crohn's and Colitis 16, Supplement_1 (January 1, 2022): i152—i153. http://dx.doi.org/10.1093/ecco-jcc/jjab232.161.
Abstract:
Abstract Background Colonoscopy is the gold standard for evaluation of inflammation in inflammatory bowel diseases (IBD), yet entails cumbersome preparations and risks of injury. Existing non-invasive prognostic tools are limited in their diagnostic power. Moreover, transcriptomics of colonic biopsies have been inconclusive in their association with clinical features. Our aim was to assess the utility of host transcriptomics of fecal wash samples of IBD patients compared to controls. Methods In this prospective cohort study, we obtained biopsies and fecal-wash samples from IBD patients and controls undergoing lower endoscopy. We performed RNAseq of biopsies and matching fecal-washes, and associated them with endoscopic and histological inflammation status. We also performed fecal mass-spectrometry proteomics on a subset of samples. We inferred cell compositions using computational deconvolution and used classification algorithms to identify informative genes. Results We analyzed biopsies and fecal washes from 39 patients (19 IBD, 20 controls). Host fecal-transcriptome carried information that was distinct from biopsy RNAseq and fecal proteomics. Transcriptomics of fecal washes, yet not of biopsies, from patients with histological inflammation were significantly correlated to one another (p=5.3*10–12). Fecal-transcriptome was significantly more powerful in identifying histological inflammation compared to transcriptome of intestinal biopsies (150 genes with area-under-the-curve >0.9 in fecal samples versus 10 genes in biopsy RNAseq). Fecal samples were enriched in inflammatory monocytes, regulatory T cells, natural killer-cells and innate lymphoid cells. Figure 1 - Fecal-wash host transcriptome predicts histological inflammation. A) Study layout, B) Clustergram of fecal-wash host cell mRNA signatures, demonstrating that patients with histological inflammation (red) are clustered when measuring fecal wash transcriptome yet not biopsy transcriptomes. C-D) Principle Component Analysis demonstrating improved separation of inflamed patients based on fecal host transcriptomes. E, F) Expression of host genes in fecal washes has higher statistical power (Area under the Curve, AUC) in classifying histological inflammation compared to biopsies. D shows NFKBIA as an example, E shows the AUC of the 5% best classifying genes, F shows the overall AUC based on biopsies or washes. Gray areas have AUC>0.9. G) UMAP of cells obtained from scRNAseq of mouse small intestine fecal washes. Conclusion Fecal wash host transcriptome is a powerful biomarker reflecting histological inflammation. Furthermore, it opens the way to identifying important correlates and therapeutic targets that may be obscure using biopsy transctriptomics.
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Dan, S., B. Ungar, S. Ben-Moshe, K. Bahar Halpern, M. Yavzori, E. Fudim, O. Picard, et al. "P017 Fecal wash host transcriptomics identifies inflammation throughout the colon and terminal ileum." Journal of Crohn's and Colitis 17, Supplement_1 (January 30, 2023): i188. http://dx.doi.org/10.1093/ecco-jcc/jjac190.0147.
Abstract:
Abstract Background Non-invasive modalities for assessing active endoscopic and histological inflammation in Crohn’s disease and Ulcerative Colitis patients are critically needed. Fecal wash host transcriptomics has been shown to be a robust classifier of endoscopic and histological inflammation in inflammatory bowel disease (IBD) patients with distal colitis. Whether such fecal washes can inform on inflammatory processes occurring in more proximal intestinal segments is currently unknown. Methods Crohn's disease and Ulcerative Colitis patients as well as healthy controls were prospectively enrolled. Host transcriptomes of biopsies and fecal washes obtained during colonoscopy at predefined locations throughout the colon and terminal ileum were analyzed and associated with same time-point clinical, endoscopic and histological parameters. Results 59 IBD patients and 50 controls were prospectively enrolled. Biospies and fecal washes from the distal, proximal colon and terminal ileum were compared. We find that host transcriptomics of distal fecal washes robustly classify histological inflammation in ileal and proximal colonic Crohn’s disease, even without distal colonic involvement. Receiver operating characteristic (ROC) curve analysis demonstrated significantly higher classification power based on the fecal wash transcriptomics compared to biopsies: Area Under the Curve, AUC=0.94+-0.07 for UC distal fecal washes and AUC=0.94+-0.09 for distal fecal washes of CD patients without distal colonic involvement, as compared to all distal biopsies AUC= 0.82+-0.20. We further demonstrate that fecal washes consist of modules of co-expressed immune, stromal and epithelial genes. Fecal wash expression of gene modules previously associated with lack of response to biological therapies correlates with disease severity. Figure 1 - Host transcriptomics of fecal washes from different intestinal segments captures information that is distinct from same – segment biopsy transcriptomics. A) Experimental layout. B) Clustergram of transcriptomes of biopsies (purple) and fecal washes (yellow). C) Principal component analysis (PCA) of biopsies (purple) and fecal washes (yellow). Black circles highlight inflamed samples. D) Spearman correlations between the transcriptomes of pairs of either biopsies or fecal washes that are both annotated as inflamed and mixed pairs (one annotated as inflamed and the other not). (A) Created with BioRender.com. TI – terminal ileum, P – proximal colon, D – distal colon. Conclusion Our study establishes the power of colonic fecal washes for identifying pathological processes throughout the ileal-colonic axis.
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Voutetakis, Konstantinos, Aristotelis Chatziioannou, Efstathios S. Gonos, and Ioannis P. Trougakos. "Comparative Meta-Analysis of Transcriptomics Data during Cellular Senescence andIn VivoTissue Ageing." Oxidative Medicine and Cellular Longevity 2015 (2015): 1–17. http://dx.doi.org/10.1155/2015/732914.
Abstract:
Several studies have employed DNA microarrays to identify gene expression signatures that mark human ageing; yet the features underlying this complicated phenomenon remain elusive. We thus conducted a bioinformatics meta-analysis on transcriptomics data from human cell- and biopsy-based microarrays experiments studying cellular senescence orin vivotissue ageing, respectively. We report that coregulated genes in the postmitotic muscle and nervous tissues are classified into pathways involved in cancer, focal adhesion, actin cytoskeleton, MAPK signalling, and metabolism regulation. Genes that are differentially regulated during cellular senescence refer to pathways involved in neurodegeneration, focal adhesion, actin cytoskeleton, proteasome, cell cycle, DNA replication, and oxidative phosphorylation. Finally, we revealed genes and pathways (referring to cancer, Huntington’s disease, MAPK signalling, focal adhesion, actin cytoskeleton, oxidative phosphorylation, and metabolic signalling) that are coregulated during cellular senescence andin vivotissue ageing. The molecular commonalities between cellular senescence and tissue ageing are also highlighted by the fact that pathways that were overrepresented exclusively in the biopsy- or cell-based datasets are modules either of the same reference pathway (e.g., metabolism) or of closely interrelated pathways (e.g., thyroid cancer and melanoma). Our reported meta-analysis has revealed novel age-related genes, setting thus the basis for more detailed future functional studies.
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Dinis Fernandes, Catarina, Annekoos Schaap, Joan Kant, Petra van Houdt, Hessel Wijkstra, Elise Bekers, Simon Linder, et al. "Radiogenomics Analysis Linking Multiparametric MRI and Transcriptomics in Prostate Cancer." Cancers 15, no. 12 (June 6, 2023): 3074. http://dx.doi.org/10.3390/cancers15123074.
Abstract:
Prostate cancer (PCa) is a highly prevalent cancer type with a heterogeneous prognosis. An accurate assessment of tumor aggressiveness can pave the way for tailored treatment strategies, potentially leading to better outcomes. While tumor aggressiveness is typically assessed based on invasive methods (e.g., biopsy), radiogenomics, combining diagnostic imaging with genomic information can help uncover aggressive (imaging) phenotypes, which in turn can provide non-invasive advice on individualized treatment regimens. In this study, we carried out a parallel analysis on both imaging and transcriptomics data in order to identify features associated with clinically significant PCa (defined as an ISUP grade ≥ 3), subsequently evaluating the correlation between them. Textural imaging features were extracted from multi-parametric MRI sequences (T2W, DWI, and DCE) and combined with DCE-derived parametric pharmacokinetic maps obtained using magnetic resonance dispersion imaging (MRDI). A transcriptomic analysis was performed to derive functional features on transcription factors (TFs), and pathway activity from RNA sequencing data, here referred to as transcriptomic features. For both the imaging and transcriptomic features, different machine learning models were separately trained and optimized to classify tumors in either clinically insignificant or significant PCa. These models were validated in an independent cohort and model performance was used to isolate a subset of relevant imaging and transcriptomic features to be further investigated. A final set of 31 imaging features was correlated to 33 transcriptomic features obtained on the same tumors. Five significant correlations (p < 0.05) were found, of which, three had moderate strength (|r| ≥ 0.5). The strongest significant correlations were seen between a perfusion-based imaging feature—MRDI A median—and the activities of the TFs STAT6 (−0.64) and TFAP2A (−0.50). A higher-order T2W textural feature was also significantly correlated to the activity of the TF STAT6 (−0.58). STAT6 plays an important role in controlling cell proliferation and migration. Loss of the AP2alpha protein expression, quantified by TFAP2A, has been strongly associated with aggressiveness and progression in PCa. According to our findings, a combination of texture features extracted from T2W and DCE, as well as perfusion-based pharmacokinetic features, can be considered for the prediction of clinically significant PCa, with the pharmacokinetic MRDI A feature being the most correlated with the underlying transcriptomic information. These results highlight a link between quantitative imaging features and the underlying transcriptomic landscape of prostate tumors.
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Cherry, Hannah, Joe Rastrick, Joanna Jacków, Maddy Parsons, and John McGrath. "O22 Unravelling the pathophysiology of KLICK syndrome to identify therapeutically targetable pathways." British Journal of Dermatology 190, no. 6 (May 17, 2024): e78-e79. http://dx.doi.org/10.1093/bjd/ljae105.022.
Abstract:
Abstract Introduction and aims Keratosis linearis with ichthyosis congenita and sclerosing keratoderma (KLICK) syndrome is an ultrarare genodermatosis associated with a homozygous pathogenic variant, c.-95delC in POMP, which encodes for proteasome maturation protein. Clinical manifestations include linear hyperkeratotic papules in the flexures, palmoplantar keratoderma and pseudoainhum. The pathophysiology of KLICK syndrome is poorly understood, resulting in nonspecific, limited treatment options. The aim of this work is to characterize KLICK syndrome at the cellular and molecular level, with the utilization of transcriptomic techniques for potential drug repurposing. Methods A lesional skin biopsy was obtained, following informed consent, from a 32-year-old female patient with KLICK syndrome. Histology and immunostaining were used to characterize the disrupted skin architecture. RNA sequencing was used to identify key dysregulated pathways and the L1000FWD reverse transcriptomics tool enabled the generation of a shortlist of potential therapeutics for KLICK syndrome. CRISPR editing techniques and induced pluripotent stem cell (iPSC) reprogramming Methods were used to generate cellular based models carrying the pathogenic POMP variant in order to support evaluation of the shortlisted therapeutic options. Results KLICK syndrome skin histology featured hyperkeratosis, hypergranulosis and delayed cellular flattening. Consistent with pathological features, pathway analysis of transcriptomic data revealed keratinocyte differentiation and epidermis development as key upregulated pathways in KLICK syndrome. Interestingly, the Panther pathway analysis tool suggested dysregulation in epidermal growth factor receptor (EGFR) signalling, and reverse transcriptomics identified erlotinib, an EGFR inhibitor, as a potential therapeutic treatment for KLICK syndrome. HaCaT keratinocytes were successfully edited using CRISPR-Cas9 to carry the KLICK patient POMP variant and a KLICK patient iPSC line was generated to support in vitro KLICK syndrome modelling. Conclusions KLICK syndrome is a hyperproliferative inflammatory skin disorder associated with a pathogenic variant in POMP. Reverse transcriptomics is a useful tool for shortlisting drugs with biologically relevant mechanisms of action with potential for treatment of rare genetic diseases such as KLICK syndrome.
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Boldanova, Tuyana, Geoffrey Fucile, Jan Vosshenrich, Aleksei Suslov, Caner Ercan, Mairene Coto-Llerena, Luigi M. Terracciano, et al. "Supervised learning based on tumor imaging and biopsy transcriptomics predicts response of hepatocellular carcinoma to transarterial chemoembolization." Cell Reports Medicine 2, no. 11 (November 2021): 100444. http://dx.doi.org/10.1016/j.xcrm.2021.100444.
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Zhang, Yueyun, Carlos Henrique Venturi Ronchi, Giovanna Ambrosini, Yuanlong Liu, Patrick Aouad, Daria Matvienko, Christoph Merten, and Cathrin Brisken. "Abstract PO5-14-06: Transcriptomics-based drug screening in 3D ex vivo patient-drived breast cancer model and patient biopsy for personalized therapy." Cancer Research 84, no. 9_Supplement (May 2, 2024): PO5–14–06—PO5–14–06. http://dx.doi.org/10.1158/1538-7445.sabcs23-po5-14-06.
Abstract:
Abstract Breast cancer is a leading cause of cancer-related mortality for women worldwide. Hormone receptor-positive (HR+) breast tumors, which represent 70% of all breast cancer cases, are treated with endocrine therapy. However, not all patients benefit from this treatment regimen because of patient-to-patient variation. Therefore, high throughput drug screening system is warranted to enable personalized medicine. Patient-derived organoids, which serve as a screening platform, lose their hormone receptors and response upon ex vivo culturing, and may not be adequate models for HR+ breast tumors. Moreover, unidentified biological components in the widely-used basement membrane matrix, Matrigel, result in high batch-to-batch variations and poor reproducibility in organoid cultures. Here, we propose a hydrogel-based 3D ex vivo model with defined structural and chemical properties to test hormone and drug sensitivity of HR+ breast tumors from patient-derived xenografts (PDXs) and patient tumor biopsies using microfluidics. Our data demonstrate the feasibility of this model to preserve cell proliferation and hormone receptor expression over 7 days. We also demonstrate that responses to hormones and FDA-approved drugs are faithfully maintained in this model. Finally, to establish a high throughput hormone and drug testing workflow with transcriptomic readout, we multiplexed barcoded- and drug-treated tumor samples in a single experiment with bulk RNA-sequencing. Our preliminary data demonstrate patient-specific responses to hormones and drugs that correspond to patient genetic mutation profiles, treatment history, disease stages and subtypes. This platform also enables testing of drugs in clinical trials that shows promising therapeutic outcomes for breast cancer, such as CDK4/6i, AKTi, PARPi, mTORi and their combination with endocrine therapy, thanks to the high throughput of the screening system and the low consumption of patient-derived or patient tissue. Given the capability of combining this physiologically-relevant 3D ex vivo model with RNA-seq for HR+ breast tumors, this platform holds potential for high throughput compound testing and transcriptomic profiling of patient biopsies for personalized medicine. Citation Format: Yueyun Zhang, Carlos Henrique Venturi Ronchi, Giovanna Ambrosini, Yuanlong Liu, Patrick Aouad, Daria Matvienko, Christoph Merten, Cathrin Brisken. Transcriptomics-based drug screening in 3D ex vivo patient-drived breast cancer model and patient biopsy for personalized therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-14-06.
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Cimadamore, Alessia, Silvia Gasparrini, Francesco Massari, Matteo Santoni, Liang Cheng, Antonio Lopez-Beltran, Marina Scarpelli, and Rodolfo Montironi. "Emerging Molecular Technologies in Renal Cell Carcinoma: Liquid Biopsy." Cancers 11, no. 2 (February 7, 2019): 196. http://dx.doi.org/10.3390/cancers11020196.
Abstract:
: Liquid biopsy, based on the circulating tumor cells (CTCs) and cell-free nucleic acids has potential applications at multiple points throughout the natural course of cancer, from diagnosis to follow-up. The advantages of doing ctDNA assessment vs. tissue-based genomic profile are the minimal procedural risk, the possibility to serial testing in order to monitor disease-relapse and response to therapy over time and to reduce hospitalization costs during the entire process. However, some critical issues related to ctDNA assays should be taken into consideration. The sensitivity of ctDNA assays depends on the assessment technique and genetic platforms used, on tumor-organ, stage, tumor heterogeneity, tumor clonality. The specificity is usually very high, whereas the concordance with tumor-based biopsy is generally low. In patients with renal cell carcinoma (RCC), qualitative analyses of ctDNA have been performed with interesting results regarding selective pressure from therapy, therapeutic resistance, exceptional treatment response to everolimus and mutations associated with aggressive behavior. Quantitative analyses showed variations of ccfDNA levels at different tumor stage. Compared to CTC assay, ctDNA is more stable than cells and easier to isolate. Splice variants, information at single-cell level and functional assays along with proteomics, transcriptomics and metabolomics studies can be performed only in CTCs.
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Das, Sreyashi, Mohan Kumar Dey, Ram Devireddy, and Manas Ranjan Gartia. "Biomarkers in Cancer Detection, Diagnosis, and Prognosis." Sensors 24, no. 1 (December 20, 2023): 37. http://dx.doi.org/10.3390/s24010037.
Abstract:
Biomarkers are vital in healthcare as they provide valuable insights into disease diagnosis, prognosis, treatment response, and personalized medicine. They serve as objective indicators, enabling early detection and intervention, leading to improved patient outcomes and reduced costs. Biomarkers also guide treatment decisions by predicting disease outcomes and facilitating individualized treatment plans. They play a role in monitoring disease progression, adjusting treatments, and detecting early signs of recurrence. Furthermore, biomarkers enhance drug development and clinical trials by identifying suitable patients and accelerating the approval process. In this review paper, we described a variety of biomarkers applicable for cancer detection and diagnosis, such as imaging-based diagnosis (CT, SPECT, MRI, and PET), blood-based biomarkers (proteins, genes, mRNA, and peptides), cell imaging-based diagnosis (needle biopsy and CTC), tissue imaging-based diagnosis (IHC), and genetic-based biomarkers (RNAseq, scRNAseq, and spatial transcriptomics).
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van Bergen, Cornelis A. M., Marvyn T. Koning, Edwin Quinten, Agnieszka Mykowiecka, Julieta Sepulveda, Ramin Monajemi, Ruben A. L. De Groen, et al. "High-Throughput BCR Sequencing and Single-Cell Transcriptomics Reveal Distinct Transcriptional Profiles Associated with Subclonal Evolution of Follicular Lymphoma." Blood 134, Supplement_1 (November 13, 2019): 298. http://dx.doi.org/10.1182/blood-2019-130508.
Abstract:
Objectives: Follicular lymphoma (FL) typically originates from premalignant mature B cells that carry the founder t(14;18) BCL2 translocation. Mutations in epigenetic modifiers and acquisition of N-glycosylation sites in CDR regions of the B-cell receptor (BCR) are recurrent secondary events in FL pathogenesis. Despite these oncogenic drivers, FL can remain indolent and clinically stable for years. The molecular events driving subclonal evolution into symptomatic progression and eventual transformation to aggressive lymphoma are insufficiently understood. FL cells are frozen in their B-cell development at the germinal center stage and undergo continuous somatic hypermutation mediated by expression of activation-induced deaminase (AID). We aim to identify crucial drivers of subclonal FL evolution by high-throughput mapping at single-cell resolution. Methods: Viable FL cells were isolated and cryopreserved from 23 histologically or immunocytologically confirmed FL samples from 13 patients with informed consent. Full-length VDJ/VJ transcripts were isolated by unbiased template-switching ARTISAN PCR and massive parallel NGS sequencing on the PacBio platform. The clonal primordial FL BCR (pBCR) was reconstructed from unmutated IGV/IGJ sequences with the CDR3 of the least mutated BCR. Since the IgTree program was unable to process the obtained numbers of BCR sequences, we developed the WILLOW algorithm for analysis of BCR evolution based on the principle of maximum parsimony and on distance from the pBCR. Intraclonal BCR variability was quantified by Shannon's diversity index. 5' single cell transcriptomics and VDJ/VJ sequencing was performed on 2 pools of highly purified FL cells from 5 lymph node biopsies on the 10x Genomics platform. Data were deconvoluted based on expressed variants by the Single Cell Sample Matcher (SCSM) algorithm. Clustering based on gene expression profiles was performed by shared nearest neighbour (SNN) modularity optimization within the R Seurat package. Genes whose expression differed significantly (adjusted p<0.05) between clusters were assigned to gene ontology terms. Results: ARTISAN PCR/PacBio NGS yielded a median of 743 full-length VDJ and VJ sequences (range 62-12782) per BCR chain with expected high intraclonal diversity (median 200 subclones, range 15-3301). WILLOW revealed dominant FL subclones with a subclonal hierarchy wherein multiple routes converged to offspring nodes with identical additional mutations rather than tree-like branching (Figure). In serial samples of 4 patients, lymph node biopsies had only marginally higher subclonal diversity than blood or bone marrow samples (p=0,055; Wilcoxon's matched-pairs signed rank test). Overall BCR mutational burden increased over time in sequential biopsies. Two cases of histological FL transformation were dominated by a single subclone (65% and 80% of all VDJ/VJ sequences, respectively) that was rare in the preceding FL BCR network (0.2% and 1.8%). Pooled transcriptomics data from 6050-6500 cells were assigned to individual samples by SCSM and revealed up to seven transcriptional clusters per FL. In 9 of 10 FL, genes assigned to immune function strongly contributed to separation into one or more clusters. Single cell VDJ/VJ sequencing yielded combined heavy and light chain BCR sequences for a median of 502 FL cells per biopsy (range 22 - 1919) that permitted mapping of subclonal evolution by WILLOW based on complete BCR information. Transcriptome clusters were not distributed evenly throughout the WILLOW FL BCR networks but rather statistically associated with distinct major FL subclones. Vice versa, major FL subclones within the same biopsy were distinguished by particular gene expression profiles. Conclusions: WILLOW facilitates mapping of subclonal FL evolution based on high-throughput BCR sequencing. FL evolution proceeds in networks rather than tree-like branching, whereby acquisition of certain combinations of several BCR mutations can occur in parallel in different trajectories. Transcriptomic profiling of single FL cells identifies distinct clusters within a single biopsy. Mapping of these clusters to the FL cell position in the subclonal FL evolutionary network identifies putative mechanisms that are associated with subclonal progression. These mechanisms involve physiological B-cell signalling pathways. Figure Disclosures No relevant conflicts of interest to declare.
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Kersch, Cymon, Cheryl Claunch, Prakash Ambady, Elmar Bucher, Daniel Schwartz, Ramon Barajas, Jeffrey Iliff, Laura Heiser, Leslie Muldoon, and Edward Neuwelt. "PATH-63. TRANSCRIPTIONAL SIGNATURES IN HISTOLOGIC STRUCTURES WITHIN GLIOBLASTOMA TUMORS MAY PREDICT PERSONALIZED TREATMENT SENSITIVITY AND SURVIVAL." Neuro-Oncology 21, Supplement_6 (November 2019): vi157. http://dx.doi.org/10.1093/neuonc/noz175.658.
Abstract:
Abstract OBJECTIVE Personalized treatment strategies in Glioblastoma multiforme (GBM) has been hampered by intra-tumoral heterogeneity. The goals of this study were to (1) determine the impact of intra-tumoral heterogeneity on established predictive and prognostic transcriptional signatures in human GBM, and (2) develop methods to mitigate the impact of tissue heterogeneity on transcriptomic-based patient stratification. METHODS We analyzed transcriptional profiles of GBM histological structures from the open-source Ivy Glioblastoma Atlas Project. To generate these data, infiltrative tumor, leading edge, cellular tumor [CT], perinecrotic zones, pseudopalisading cells, hyperplastic blood vessels and microvascular proliferation were microdissected from 34 newly diagnosed GBM and underwent RNA sequencing. Data from The Cancer Genome Atlas were used for validation. Principle component analysis, network analysis and gene set enrichment analysis were used to probe gene expression patterns. RESULTS Distinct biological networks were enriched in each tumor histological structure. Classification of patients into GBM molecular subtypes varied based on the structure assessed, with many patients classified as every subtype depending on the structure analyzed. Using only CT to classify subtypes, we identified biologically unique patterns suggesting that proneural and mesenchymal tumors may be more sensitive to chemoradiotherapy and immunotherapy, respectively. Survival outcome predicted by an established multigene panel was confounded by histologic structure. Utilizing CT transcriptomics we developed a novel survival prediction gene signature that identified the highest-risk GBM patients in both CT and bulk tissue gene expression profiles. CONCLUSIONS Histologic structures contribute to intra-tumoral heterogeneity in GBM. Using mixed-structure biopsy samples could incorrectly subtype tumors and produce invalid patient stratification. Limiting transcriptomic analysis to the CT allowed us to develop a new survival prediction gene signature that appears accurate even in mixed tissue samples. The biological patterns uncovered in the subtypes and risk-stratified groups have important implications for guiding the development of precision medicine in GBM.
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Lee, Irene Tai-Lin, Chin-Hsuan Shen, Feng-Chiao Tsai, Chun-Bing Chen, and Kevin Sheng-Kai Ma. "Cancer-Derived Extracellular Vesicles as Biomarkers for Cutaneous Squamous Cell Carcinoma: A Systematic Review." Cancers 14, no. 20 (October 18, 2022): 5098. http://dx.doi.org/10.3390/cancers14205098.
Abstract:
Cutaneous squamous cell carcinoma (cSCC) as one of the most prevalent cancers worldwide is associated with significant morbidity and mortality. Full-body skin exam and biopsy is the gold standard for cSCC diagnosis, but it is not always feasible given constraints on time and costs. Furthermore, biopsy fails to reflect the dynamic changes in tumor genomes, which challenges long-term medical treatment in patients with advanced diseases. Extracellular vesicle (EV) is an emerging biological entity in oncology with versatile clinical applications from screening to treatment. In this systematic review, pre-clinical and clinical studies on cSCC-derived EVs were summarized. Seven studies on the genomics, transcriptomics, and proteomics of cSCC-derived EVs were identified. The contents in cSCC-derived EVs may reflect the mutational landscape of the original cancer cells or be selectively enriched in EVs. Desmoglein 2 protein (Dsg2) is an important molecule in the biogenesis of cSCC-derived EVs. Ct-SLCO1B3 mRNA, and CYP24A1 circular RNA (circRNA) are enriched in cSCC-derived EVs, suggesting potentials in cSCC screening and diagnosis. p38 inhibited cSCC-associated long intergenic non-coding RNA (linc-PICSAR) and Dsg2 involved in EV-mediated tumor invasion and drug resistance served as prognostic and therapeutic predictors. We also proposed future directions to devise EV-based cSCC treatment based on these molecules and preliminary studies in other cancers.
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Kretschmer-Kazemi Far, Rosel, Kirsten Frank, and Georg Sczakiel. "Sampling, Logistics, and Analytics of Urine for RT-qPCR-based Diagnostics." Cancers 13, no. 17 (August 30, 2021): 4381. http://dx.doi.org/10.3390/cancers13174381.
Abstract:
Body fluids in the context of cancer diagnosis are the primary source of liquid biopsy, i.e., biomarker detection that includes blood and serum, urine, and saliva. RNA represents a particular class of biomarkers because it is thought to monitor the current status of gene expression in humans, in organs, and if present, also in tumors. In case of bladder cancer, we developed a scheme that describes, in detail, all steps from the collection of urine samples from patients, stabilization of samples, their transportation, storage, and marker analysis by qPCR-based technology. We find that urine samples prepared according to this protocol show stability of RNA over more than 10 days at unchilled temperatures during shipping. A specific procedure of primer design and amplicon evaluation allows a specific assignment of PCR products to human genomics and transcriptomics data collections. In summary, we describe a technical option for the robust acquisition of urine samples and the quantitative detection of RNA-based tumor markers in case of bladder cancer patients. This protocol is for general use, and we describe that it works for any RNA-based tumor marker in urine of cancer patients.
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Cook, Daniel, Dorys Lopez, Anu K. Antony, The SimBioSys Team, and John A. Cole. "Multimodal approach to capture spatially resolved single-cell tumor heterogeneity in breast cancer." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e12597-e12597. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e12597.
Abstract:
e12597 Background: Tumor heterogeneity is known to play a key role in drug response and resistance. However, knowledge of tumor heterogeneity is largely limited to genetics and biopsy samples representing one region of the tumor. The study of spatial tumor heterogeneity is gaining more interest as researchers and clinicians realize that biopsies might miss biomarker information. Although several approaches like single-cell RNA seq and multiplex IHC/IF are used to study spatial heterogeneity, these methods tend to be costly and time consuming. Additionally, there is no consensus on how to interpret these results for optimizing therapy, making it harder to implement these approaches in the clinic. Methods: Here we present a state-of-the-art technique to characterize tumor heterogeneity within individual patient tumors by integrating single cell RNA-seq data with biophysical modeling, using SimBioSys’ TumorScope (TS) – a biophysical modeling platform. As a proof of concept, we compared intra-tumoral heterogeneity from experimental single cell RNA-seq studies from TNBC patients (n=8) to to simulated intra-tumoral heterogeneity within TNBC patients from the ISPY-1 trial (n = 10). We also compared simulated vs. experimentally measured bulk transcriptional profiles within individual patients. Results: We found that the correlation between individual single-cell transcriptomes to biopsy transcriptomes was low (median Spearman correlation ̃ 0.5). However, using TS to predict single-cell scale transcriptomics within a tumor based on biophysical characteristics of the tumor resulted in correlations of ̃ 0.86, between simulated and experimentally measured transcriptomes (range = 0.85 - 0.87). TS allowed the simulated single-cell RNA-seq data to create spatially resolved single-cell maps that quantify the spatial expression of key tumor biomarkers across the whole tumor including Ki67, HER2 and PDL1. The spatial distribution of these biomarkers can have important implications for therapy and patient prognosis. A more comprehensive understanding of the distribution of these molecular markers across the tumor could inform if some tumors deserved a different Ki67 score, if some patients are not receiving HER2-targeted therapy because of HER2 uneven expression across the tumor, and if PD-L1 could improve as a biomarker by considering its spatial expression. Conclusions: In summary, we present a novel approach to characterize spatial tumor heterogeneity directly from patient MRIs using the TS biophysical modeling platform. This technology is less time consuming and less costly than other approaches, making it accessible for use in hospitals at a larger scale.
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Cook, Daniel, Dorys Lopez, Anu K. Antony, The SimBioSys Team, and John A. Cole. "Multimodal approach to capture spatially resolved single-cell tumor heterogeneity in breast cancer." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): e12597-e12597. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e12597.
Abstract:
e12597 Background: Tumor heterogeneity is known to play a key role in drug response and resistance. However, knowledge of tumor heterogeneity is largely limited to genetics and biopsy samples representing one region of the tumor. The study of spatial tumor heterogeneity is gaining more interest as researchers and clinicians realize that biopsies might miss biomarker information. Although several approaches like single-cell RNA seq and multiplex IHC/IF are used to study spatial heterogeneity, these methods tend to be costly and time consuming. Additionally, there is no consensus on how to interpret these results for optimizing therapy, making it harder to implement these approaches in the clinic. Methods: Here we present a state-of-the-art technique to characterize tumor heterogeneity within individual patient tumors by integrating single cell RNA-seq data with biophysical modeling, using SimBioSys’ TumorScope (TS) – a biophysical modeling platform. As a proof of concept, we compared intra-tumoral heterogeneity from experimental single cell RNA-seq studies from TNBC patients (n=8) to to simulated intra-tumoral heterogeneity within TNBC patients from the ISPY-1 trial (n = 10). We also compared simulated vs. experimentally measured bulk transcriptional profiles within individual patients. Results: We found that the correlation between individual single-cell transcriptomes to biopsy transcriptomes was low (median Spearman correlation ̃ 0.5). However, using TS to predict single-cell scale transcriptomics within a tumor based on biophysical characteristics of the tumor resulted in correlations of ̃ 0.86, between simulated and experimentally measured transcriptomes (range = 0.85 - 0.87). TS allowed the simulated single-cell RNA-seq data to create spatially resolved single-cell maps that quantify the spatial expression of key tumor biomarkers across the whole tumor including Ki67, HER2 and PDL1. The spatial distribution of these biomarkers can have important implications for therapy and patient prognosis. A more comprehensive understanding of the distribution of these molecular markers across the tumor could inform if some tumors deserved a different Ki67 score, if some patients are not receiving HER2-targeted therapy because of HER2 uneven expression across the tumor, and if PD-L1 could improve as a biomarker by considering its spatial expression. Conclusions: In summary, we present a novel approach to characterize spatial tumor heterogeneity directly from patient MRIs using the TS biophysical modeling platform. This technology is less time consuming and less costly than other approaches, making it accessible for use in hospitals at a larger scale.
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Gjyrezi, Ada, Charalampos Skarlis, Paul Zumbo, Doron Betel, Ioanna E. Stergiou, Michael Voulgarelis, Clio P. Mavragani, and Paraskevi Giannakakou. "Abstract 1404: Blood-based transcriptomics provides novel insights into Sjögren's syndrome-associated lymphomagenesis." Cancer Research 84, no. 6_Supplement (March 22, 2024): 1404. http://dx.doi.org/10.1158/1538-7445.am2024-1404.
Abstract:
Abstract Sjögren's syndrome (SS) is a debilitating autoimmune disorder that carries the highest risk of progressing to lymphoma among all autoimmune diseases, with up to 10% of patients developing SS-associated lymphoma. However, the underlying mechanisms are unknown, and there are currently no actionable targets for prevention and therapeutic intervention.To elucidate the mechanisms associated with SS-lymphoma, we performed RNA-Seq in peripheral blood from SS patients without (n=11) or with lymphoma (n=8). Differential gene expression and pathway analysis identified TNF-α signaling via NF-κB, inflammatory response and interferon gamma (IFN-γ) response as the top pathways enriched in SS-lymphoma patients. Interestingly, the enriched IFN-γ response pathway is consistent with our published work identifying elevated IFN-γ transcript levels in salivary gland tissues from SS patients with lymphoma. Central to SS pathogenesis is the elevation of TNF-α signaling, triggering NF-κB pathway activation and subsequent inflammation, along with inflammasome activation, in line with prior observations. Our data reveal significant upregulation of these pathways in SS-lymphoma patients, which together with the inflammatory response and IFN-γ pathway enrichment, support the idea that persistent autoimmune-related chronic inflammation fosters a microenvironment conducive to lymphomagenesis.Next, we sought to assess the impact of SS immune landscape in SS-lymphoma by performing an immune modular analysis using an established framework of 97 whole blood transcriptomics modules (Pascual), derived from transcripts co-expressed in blood across various autoimmune conditions. This analysis revealed a significant downregulation of T-cell and enrichment of B-cell modules in SS-lymphoma compared to SS patients. These findings are consistent with our biopsy results, showing lower T cell counts in high-grade vs. low-grade SS patients. As patients with high-grade SS are more likely to develop SS-lymphoma, these data possibly suggest that suppressed T-cell responses are involved in lymphomagenesis. In addition, the significant enrichment in B-cell transcriptional modules mirrors the observed clinical increase in B cell counts during the transition to SS-lymphoma. Germline mutations in B-cells are thought to drive the clonal expansion of malignant B cells, which may contribute to the observed increase of B cell transcriptomes in SS patients developing lymphoma. We are currently investigating the gene mutation landscape in these datasets to better understand their contribution to SS- lymphomagenesis.This study provides preliminary evidence that chronic inflammation along with dysregulation of T and B compartments in SS significantly contributes to lymphoma progression, emphasizing the need for further research to uncover the molecular basis and develop early diagnostic/intervention tools. Citation Format: Ada Gjyrezi, Charalampos Skarlis, Paul Zumbo, Doron Betel, Ioanna E. Stergiou, Michael Voulgarelis, Clio P. Mavragani, Paraskevi Giannakakou. Blood-based transcriptomics provides novel insights into Sjögren's syndrome-associated lymphomagenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1404.
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Yohihara, R., H. Tsuchiya, Y. Omata, H. Takahashi, S. Nakajima, H. Mizuhara, A. Uchio, et al. "POS1014 INVESTIGATING THE SYNOVIAL PATHOLOGY RELATED TO TREATMENT RESISTANCE IN JAPANESE RHEUMATOID ARTHRITIS PATIENTS USING SINGLE-CELL ANALYSIS." Annals of the Rheumatic Diseases 82, Suppl 1 (May 30, 2023): 823.1–823. http://dx.doi.org/10.1136/annrheumdis-2023-eular.1112.
Abstract:
BackgroundDespite of recent developments in therapeutic agents for rheumatoid arthritis (RA) patients[1], it is reported that half of the patients are unable to achieve remission even with existing drugs[2]. Therefore, there is an urgent need to gain mechanistic insight into treatment resistance. Nowadays, single-cell RNA sequencing (scRNA-seq) technology have dramatically improved our understanding of the heterogeneity in synovial cells. However, it has not been fully elucidated how the cell clusters are related to treatment response, especially in Asian races[3].ObjectivesWe intend to analyze the RA synovium from Japanese patients based on single-cell transcriptomics to explore the pathological key players related to treatment resistance.MethodsSynovial specimens were collected from 31 RA patients using an ultrasound-guided needle biopsy. The proportion of 5 immune cell subsets (CD4+T cells, CD8+T cells, B cells, NK cells, monocytes) and mesenchymal cells (synovial fibroblasts (SF), endothelial cells, mural cells) were analyzed by flow cytometry. CD45+and CD45-live cells were isolated, and scRNA-seq libraries were prepared using the 10x chromium system.ResultsWe classified the patients into the following three groups based on treatment status at the time of biopsy; treatment-naïve, inadequate response to conventional synthetic disease-modifying antirheumatic drugs (csDMARDs-IR), or biological DMARDs (bDMARDs-IR). The proportion of CD8+T cells, especiallyGZMB+GZMK+CD8+T cells, was significantly lower in csDMARDs-IR patients compared to treatment-naïve patients. This population was characterized by enhanced expression ofIFNGandGZMK, the cooperative inducers of IL-6 production from SF. Meanwhile, an increased proportion of SF, especiallyTHY1lowsublining andCD34+sublining, was observed in csDMARDs-IR and bDMARDs-IR patients. Intriguingly, by integrating gene set variation analysis (GSVA) with transcriptomic data of cytokine-stimulated SFin vitro4,THY1lowsublining was indicated to be activated independently of the effects of inflammatory cytokines (e.g., TNF-α, IL-1β, IFNs) (Figure 1). Collectively, this SF subpopulation was inferred to be less susceptible to cytokine-blocking agents such as IL-6 receptor or TNF-α inhibitors.ConclusionThe synovial analysis has the potential to be useful in parsing the mechanism of treatment resistance in Japanese RA patients, and gaining insights into novel therapeutic targets.References[1] Tan Y, Buch MH. ‘Difficult to treat’ rheumatoid arthritis: current position and considerations for next steps. RMD Open. 2022 Jul;8(2):e002387.[2] Burmester GR, Bijlsma JWJ, Cutolo M, et al. Managing rheumatic and musculoskeletal diseases - past, present and future. Nat Rev Rheumatol. 2017 Jul;13(7):443-448.[3] Chang F, Wei K, Slowikowski K, et al. Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nat Immunol. 2019;20(7):928-42.[4] Tsuchiya H, Ota M, Sumitomo S, et al. Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis. Ann Rheum Dis. 2021 Apr;80(4):440-450.Figure 1.Acknowledgements:NIL.Disclosure of InterestsNone Declared.
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Orsini, Arianna, Chiara Diquigiovanni, and Elena Bonora. "Omics Technologies Improving Breast Cancer Research and Diagnostics." International Journal of Molecular Sciences 24, no. 16 (August 11, 2023): 12690. http://dx.doi.org/10.3390/ijms241612690.
Abstract:
Breast cancer (BC) has yielded approximately 2.26 million new cases and has caused nearly 685,000 deaths worldwide in the last two years, making it the most common diagnosed cancer type in the world. BC is an intricate ecosystem formed by both the tumor microenvironment and malignant cells, and its heterogeneity impacts the response to treatment. Biomedical research has entered the era of massive omics data thanks to the high-throughput sequencing revolution, quick progress and widespread adoption. These technologies—liquid biopsy, transcriptomics, epigenomics, proteomics, metabolomics, pharmaco-omics and artificial intelligence imaging—could help researchers and clinicians to better understand the formation and evolution of BC. This review focuses on the findings of recent multi-omics-based research that has been applied to BC research, with an introduction to every omics technique and their applications for the different BC phenotypes, biomarkers, target therapies, diagnosis, treatment and prognosis, to provide a comprehensive overview of the possibilities of BC research.
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Miller, Dulaney, Kyle Manning, Shuran Xing, T. Jeffrey Cole, Christopher J. Benway, Elena M. Cortizas, J. Christian J. Ray, et al. "Stratification of patients with prostate cancer using a comprehensive multiomic approach: Integrating extracellular vesicle transcriptomics profiling with cfDNA methylation in urine-based liquid biopsy." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): e17095-e17095. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e17095.
Abstract:
e17095 Background: Prostate cancer (PCa) ranks as the second most frequently diagnosed cancer and the sixth most prevalent cause of cancer-related mortality in men globally. Here, we employ a multiomic approach that utilizes both urine cfDNA and extracellular vesicle (EV) RNA-derived analytes to improve the risk stratification of individuals with PCa. Methods: Samples were collected from 106 individuals with elevated PSA levels (median: 6.5 ng/ml) who underwent urine collection before biopsy and MRI for comparative analysis. Within the cohort, 51 were diagnosed with high-grade prostate cancer (≥GG3), 11 were classified as intermediate risk (GG2), and 44 showed no or low-grade prostate cancer (≤GG1). EV-RNA and cfDNA were concurrently isolated from each urine specimen to exploit complementary data within the same sample. We developed an EV-RNA sequencing platform targeting mRNAs and lncRNAs and targeted 50 million reads per sample; cfDNA methylome profiling reached an equivalent sequencing depth. Expression of EV-RNA and splice variant Differential Transcript Usage (DTU) in addition to cfDNA methylation patterns were analyzed using Bio-Techne’s multiomic platform. Machine learning-based feature selection algorithms identified biomarker signatures from each analyte. Receiver-operator characteristic curves (ROC) were generated utilizing leave-one-out cross-validation of naïve Bayes classifier models to compute the area under the curve (AUC). Individual signatures were integrated to generate a multiomic classifier. Results: Differential gene expression (DEx) analysis identified DEx genes between low and high-risk patients with known and novel implications in PCa. Tissue deconvolution analysis revealed a high representation of testis, prostate, kidney, and lymphocyte in the EV-RNA samples. Additionally, splice variant analysis unveiled several genes previously implicated in PCa with DTU. Over 18,000 differentially methylated bases were detected between high and low-risk PCa patients and subsequent segmentation of the genome elucidated highly variable segments. Following feature selection analysis, AUCs obtained from top features of EV-RNA expression, splice variants, and cfDNA methylation, demonstrated an integrative multi-analyte signature with an AUC surpassing any individual analyte and MRI PI-RADS. While signatures obtained from each analyte resulted in the effective stratification of PCa risk, the multiomic signature further improved discriminatory power, highlighting the complementary nature of the signals. Thus, a multiomic strategy leveraging cfDNA and EV cargo exhibits significant potential as a next generation risk assessment tool for high-grade PCa. This approach has the capacity to facilitate more informed decision-making in disease management.
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Quek, Camelia, Aditya Pratapa, Ines Pires da Silva, Ghamdan Al-Eryani, Aaron Mayer, Nenad Bartonicek, Kate Harvey, et al. "Abstract 4621: Distinct spatial and molecular maps in the tumour microenvironment of resistant melanoma patients treated with checkpoint inhibitor immunotherapy." Cancer Research 83, no. 7_Supplement (April 4, 2023): 4621. http://dx.doi.org/10.1158/1538-7445.am2023-4621.
Abstract:
Abstract Background: Checkpoint-based immunotherapies can achieve durable clinical responses in a variety of advanced cancers, including melanoma. However, clinical responses are not universal and there is still a substantial gap in understanding the mechanistic insights of immunotherapy resistance. This study aims to better understand patients’ resistance to immune checkpoint therapies by dissecting and tracing individual tumour and immune cell clones. Methods: Melanoma tumour dissociates and lesion matched formalin-fixed paraffin-embedded tissue samples were collected from patients with advanced melanoma receiving ipilimumab in combination with nivolumab; 2 patients were long-term responders, 2 had innate resistance and 1 acquired resistance. The molecular characteristics and spatial cellular relations associated with tumour and immune subsets in response to treatment were identified using single-cell indexing of transcriptomes and epitopes by sequencing and CODEX (CO-Detection by indEXing) multiplexed tissue imaging. Integration of spatial and molecular information was performed by combining reference-based phenotyping, Louvain clustering, and a mutual nearest neighbours-based transfer learning algorithm. Results: Pre-treatment melanoma biopsies from 5 patients (3 responding and 2 non-responding) along with a subsequent acquired resistance biopsy from an initially responding patient were analysed. Comparisons of cellular phenotypes identified higher proportions of gamma delta T cells (1.98% versus 0.2%) and enriched memory T cell profiles (CD3E, CD44, CD45RO, CD8) in responding compared to non-responding pre-treatment biopsies. Fibroblast from non-responding lesions overexpressed stromal related cytokine, IL1A (log2 fold change (FC) = 3.3) and CXCL1 (log2 FC = 1.4), which were enrichment at the tumour margin compared to responding lesions. Comparisons of a patient’s pre-treatment biopsy that initially responded to a subsequent progressing biopsy with acquired resistance had altered expression of transcript factor, ZFX (log2 FC = -1.59; adjusted p = 0.0119), and MBD2 (log2 FC = -1.5; adjusted p = 0.0225) within the patient’s memory T-cells. Conclusion: The combination of high dimensional single cell transcriptomics and spatial tissue imaging are effective tools to identify specific changes in cell phenotypes, intracellular signalling, and spatial location. This analysis identified reduced memory T cells, increased fibroblast, and altered cellular signalling were associated with resistance to immunotherapies. Citation Format: Camelia Quek, Aditya Pratapa, Ines Pires da Silva, Ghamdan Al-Eryani, Aaron Mayer, Nenad Bartonicek, Kate Harvey, Oliver Braubach, Robyn P.M. Saw, Jonathan Stretch, Kerwin F. Shannon, Alexander M. Menzies, Richard A. Scolyer, Georgina V. Long, Alexander Swarbrick, James S. Wilmott. Distinct spatial and molecular maps in the tumour microenvironment of resistant melanoma patients treated with checkpoint inhibitor immunotherapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4621.
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FRENEL, Jean Sebastien, Fadoua Ben Azzouz, Frederic Bigot, Jonathan Dauve, Marie Francoise Heymann, Wilfried Gouraud, Catherine Guette, et al. "Abstract P5-02-37: Multi-omics approach to identify markers of resistance to endocrine therapy + CDK4/6 inhibitors in first line HR+/HER2- metastatic breast cancer (MBC) patients." Cancer Research 83, no. 5_Supplement (March 1, 2023): P5–02–37—P5–02–37. http://dx.doi.org/10.1158/1538-7445.sabcs22-p5-02-37.
Abstract:
Abstract CONTEXT: Endocrine therapy combined with CDK4/6 inhibitor is the standard frontline treatment for the vast majority of HR+/HER2- MBC patients. Despite an overall survival benefit, patients eventually progress and mechanisms of resistance to this combination are not well identified. METHODS: EPICURE is an ongoing pilot prospective cohort study of heterogeneous and massive data integration, ie. multi-omics approach in MBC patients. The present study aims at identifying progression markers in patients with HR+/HER2- MBC receiving frontline endocrine therapy+iCDK4/6 by means of transcriptomics, genomics and proteomics data. All patients had a tumor biopsy at the entry in the study (B1) and a biopsy was repeated at progression if feasible (B2). Transcriptomic (RNAseq: NextSeq550, Illumina), genomic (whole exome sequencing: NextSeq550, Illumina) and proteomic (DIA mass spectrometry: TimsTOFPro2, Bruker) were performed on B1 and B2 according to available tumor tissue. RESULTS: Fifty-one patients matching inclusion criteria were included. B1 was done at inclusion for all patients (B1) (n = 51) and B2 was performed in 8 patients. (B2) (n = 8). Eight metastatic sites were biopsied: node (n = 17); liver (n = 16); bone (n = 8); breast local recurrence (n = 5); chest wall (n = 5); skin (n = 4); pleural (n = 3); ovary (n = 1). Transcriptomic, genomic and proteomic analysis of paired biopsies (B1 and B2) was performed in parallel and separately for 8, 7 and 2 patients, respectively. Exploratory data analysis of transcriptomic and proteomic data showed that liver biopsies clustered together. In order to eliminate this anatomic bias, specific genes and proteins of liver metastases were identified by means of DESeq2 analysis (12 liver vs 39 other sites) for transcriptomic data (n = 2654) and LIMMA (4 liver vs 14 other sites) for proteomic data (n = 227), and excluded for the rest of the analysis. Differential analyses (ie. gene expression, non-synonymous mutations and protein expression) between B1 and B2 were performed for each patient. These three kind of lists were finally submitted to ToppGene, DAVID and GOrilla for Gene Ontology terms enrichment analyses. Transcriptomic analyses of the 8 paired biopsies highlighted immune response (IR) in seven B1, IR in four B2 and neurogenesis in three B2. Genomics data evaluation between B1 and B2 pointed out “transposon integration” as an important pathway. Proteomic data of the 2 paired biopsies analysed underlined high immune response in B1, and muscle development/contraction and response to tumor necrosis factor in B2 for one patient. For the second one, liver metabolism in B1 and extracellular matrix and p38 MAPK cascade were emphasised. CONCLUSION: This preliminary study based on transcriptomic, genomic and proteomic data represents an encouraging first step of the EPICURE project. In a near future, additional paired biopsies and other kinds of omics data (epigenetics, radiomics, microbiomics, exposomics) will be available. Furthermore, omics data will be analysed in an integrated manner (ie. artificial intelligence), which will make it possible to detect synergies across the different omics data. Citation Format: Jean Sebastien FRENEL, Fadoua Ben Azzouz, Frederic Bigot, Jonathan Dauve, Marie Francoise Heymann, Wilfried Gouraud, Catherine Guette, Hamza Lasla, Bertrand Michel, Alain Morel, Anne Patsouris, Marie Robert, Grégoire Siekaniec, Mathilde Colombie, Pascal Jézéquel, Mario Campone. Multi-omics approach to identify markers of resistance to endocrine therapy + CDK4/6 inhibitors in first line HR+/HER2- metastatic breast cancer (MBC) patients. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-37.
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Neagu, Anca-Narcisa, Danielle Whitham, Pathea Bruno, Hailey Morrissiey, Celeste A. Darie, and Costel C. Darie. "Omics-Based Investigations of Breast Cancer." Molecules 28, no. 12 (June 14, 2023): 4768. http://dx.doi.org/10.3390/molecules28124768.
Abstract:
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three ”big omics”, based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein–protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Chang, Ming-Ling, and Sien-Sing Yang. "Metabolic Signature of Hepatic Fibrosis: From Individual Pathways to Systems Biology." Cells 8, no. 11 (November 12, 2019): 1423. http://dx.doi.org/10.3390/cells8111423.
Abstract:
Hepatic fibrosis is a major cause of morbidity and mortality worldwide, as it ultimately leads to cirrhosis, which is estimated to affect up to 2% of the global population. Hepatic fibrosis is confirmed by liver biopsy, and the erroneous nature of this technique necessitates the search for noninvasive alternatives. However, current biomarker algorithms for hepatic fibrosis have many limitations. Given that the liver is the largest organ and a major metabolic hub in the body, probing the metabolic signature of hepatic fibrosis holds promise for the discovery of new markers and therapeutic targets. Regarding individual metabolic pathways, accumulating evidence shows that hepatic fibrosis leads to alterations in carbohydrate metabolism, as aerobic glycolysis is aggravated in activated hepatic stellate cells (HSCs) and the whole fibrotic liver; in amino acid metabolism, as Fischer’s ratio (branched-chain amino acids/aromatic amino acids) decreases in patients with hepatic fibrosis; and in lipid metabolism, as HSCs lose vitamin A-containing lipid droplets during transdifferentiation, and cirrhotic patients have decreased serum lipids. The current review also summarizes recent findings of metabolic alterations relevant to hepatic fibrosis based on systems biology approaches, including transcriptomics, proteomics, and metabolomics in vitro, in animal models and in humans.
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Du, Mulong. "Prospective of Mitochondrial DNA Variations in Cancer on Genomic Medicine." Cancer Epidemiology, Biomarkers & Prevention 33, no. 6 (June 3, 2024): 766–68. http://dx.doi.org/10.1158/1055-9965.epi-24-0233.
Abstract:
Abstract Mitochondrial DNA (mtDNA) has emerged as a pivotal component in understanding the etiology and susceptibility of cancer. A recent study by Chen and colleagues delineated the germline genetic effect of mtDNA single-nucleotide polymorphisms (SNP) and haplogroups across pan-cancer risk. They identified a subset of mtSNPs and the corresponding risk score, as well as haplogroups A and M7 alongside their genetic interactions, conferring a protective effect against various cancers. These findings underscored the value of mtDNA variations as biomarkers for cancer etiology and as tools for cancer risk stratification. Future investigations are encouraged to integrate comprehensive omics data of genomics, transcriptomics, proteomics, and metabolomics, etc., from nuclear DNA with mtDNA variations, alongside single-cell and spatial technologies, to unravel the tumor mechanism and identify the drug targets. Moreover, the incorporation of polygenic risk score, that included mtDNA variations with both rare and common frequencies, and liquid biopsy-based biomarkers would enhance the predictive performance of cancer risk assessment and refine the risk stratification of population-based cancer screening. This commentary advocates for the validation across diverse populations to harness the full potential of mitochondrial genomics, and ultimately paves the prospective way for advancements in personalized cancer therapeutics and prevention strategies. See related article by Chen and colleagues, Cancer Epidemiol Biomarkers Prev 2024;33:381–8
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Reis Nisa, P. I., C. Mahony, C. Smith, C. D. Buckley, K. Raza, A. Filer, D. Windell, M. Coles, and A. Croft. "OP0094 SPATIAL POSITIONING AND MATRIX PROGRAMS OF SYNOVIAL FIBROBLASTS UNDERPIN IMMUNE CELL ORGANISATION AND SYNOVIAL TISSUE PATHOTYPE." Annals of the Rheumatic Diseases 82, Suppl 1 (May 30, 2023): 64.2–64. http://dx.doi.org/10.1136/annrheumdis-2023-eular.6114.
Abstract:
BackgroundRheumatoid arthritis (RA) is highly heterogenous with distinct cellular and molecular tissue pathotypes that associate with disease outcome[1]. The synovial membrane is the primary target tissue and undergoes significant architectural re-modelling in response to inflammation. While fibroblasts are known to shape immune cell compartmentalisation in secondary lymphoid organs, by producing distinct sets of chemokines and remodelling extracellular matrix (ECM)[2], the mechanisms underlying immune cell localisation in the synovium are poorly understood.ObjectivesTo define the functional zonation of the inflamed synovium at the single cell and regional tissue level using spatial transcriptomics and multiplex imaging.MethodsWe performed oligonucleotide probe-based spatially resolved transcriptomics on synovial tissue samples obtained by minimally invasive, ultrasound guided synovial tissue biopsies performed in patients with both rheumatoid arthritis (RA) and osteoarthritis (OA) using the 10x Visium platform. A total of 27 tissue biopsies processed sequencing 34170 spot transcriptomes. Each tissue section was composed on 1-8 fragments of synovial tissue from the same donor biopsy sample within each capture area, to maximise tissue representation and account for sampling variability. Cellular deconvolution of spot transcriptomes was performed using single cell reference datasets. Multiplex imaging was obtained to confirm gene profiles and cell types associated with the specific zonation patterns.ResultsWe identified six spatially resolved tissue niches (or zones) within synovial membrane defined by gene expression and comprised of distinct populations of stromal and immune cells. Specific patterns of gene expression were observed in each of these sub-synovial tissue zones that link to functions of immune infiltrate recruitment and organisation. This zonation pattern is maintained across pathotypes (Fibroid, Lymphocytic) and spatial gene expression analysis revealed that RA is associated with specific synovial re-modelling and the formation of lymphocytic niches when compared to OA synovial tissue. We next defined zonation areas by manually annotating immune infiltrates (as aggregates) and vasculature, based on histology. From these, we selected fibroblasts specific to immune aggregate zones and peri-vascular zones (Figure 1). We have identified differences in gene expression between these fibroblasts based on their anatomical location.Peri-vascular fibroblasts have gene expression profiles related to myofibroblast differentiation, ECM deposition and modulation (COMP), but also immune cell recruitment (PLA2G2A), cell activation (FOS & FOSB), and lipid metabolism (APOD), also associated with OA synovium. These fibroblasts display either a TGF-β response or NOTCH3 activated[3]gene expression program and are expanded in the fibroid pauci-Immune) tissue pathotype. Immune interacting (peri-aggregate) fibroblasts in contrast, show specific gene expression profiles linked to ECM regulation (POSTN), degradation (MMP3) and co-ordination of ECM remodelling to recruit immune cells (SPARC), and permit aggregate formation. These fibroblasts display a T-cell interacting[4]and IFN-γ gene expression program and along with IL-1β and TNF-α activated lining layer fibroblasts dominate the stromal cell landscape of the lymphoid tissue pathotype.ConclusionWe demonstrate that cytokine directed fibroblast-immune cell crosstalk, positional identity, and matrix specific, fibroblast gene expression programs are responsible for localising infiltrating immune cells to specific niches within the tissue and defining functional tissue zonation. These data identify novel therapeutically tractable disease pathways that underpin the pathogenicity of synovial tissue fibroblasts in RA.References[1]Lewis et al. Cell Reports 2019;28:2455-2470[2]Bajénoff M et al. Immunity 2006;25:989–1001[3]Wei K et al. Nature 2020;582:259-264.[4]Korsunsky I et al. Med (N Y) 2022;3:481-518.e14Acknowledgements:NIL.Disclosure of InterestsNone Declared.
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Lin, Pei-Hsuan, Wan-Ping Su, Chia-Jung Li, Li-Te Lin, Jim Jinn-Chyuan Sheu, Zhi-Hong Wen, Jiin-Tsuey Cheng, and Kuan-Hao Tsui. "Investigating the Role of Ferroptosis-Related Genes in Ovarian Aging and the Potential for Nutritional Intervention." Nutrients 15, no. 11 (May 25, 2023): 2461. http://dx.doi.org/10.3390/nu15112461.
Abstract:
With advancing age, women experience irreversible deterioration in the quality of their oocytes, resulting in reduced fertility. To gain a deeper understanding of the influence of ferroptosis-related genes on ovarian aging, we employed a comprehensive approach encompassing spatial transcriptomics, single-cell RNA sequencing, human ovarian pathology, and clinical biopsy. This investigation revealed the intricate interactions between ferroptosis and cellular energy metabolism in aging germ cells, shedding light on the underlying mechanisms. Our study involved 75 patients with ovarian senescence insufficiency, and we utilized multi-histological predictions of ferroptosis-related genes. Following a two-month supplementation period with DHEA, Ubiquinol CoQ10, and Cleo-20 T3, we examined the changes in hub genes. Our results showed that TFRC, NCOA4, and SLC3A2 were significantly reduced and GPX4 was increased in the supplement group, confirming our prediction based on multi-omic analysis. Our hypothesis is that supplementation would enhance the mitochondrial tricarboxylic acid cycle (TCA) or electron transport chain (ETC), resulting in increased levels of the antioxidant enzyme GPX4, reduced lipid peroxide accumulation, and reduced ferroptosis. Overall, our results suggest that supplementation interventions have a notable positive impact on in vitro fertilization (IVF) outcomes in aging cells by improving metal ion and energy metabolism, thereby enhancing oocyte quality in older women.
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Sitnikova, Suzanne Isabelle, Sophie Munnings-Tomes, Elena Galvani, Stacy Kentner, Kathy Mulgrew, Chris Rands, Judit España Agustí, et al. "Novel non-terminal tumor sampling procedure using fine needle aspiration supports immuno-oncology biomarker discovery in preclinical mouse models." Journal for ImmunoTherapy of Cancer 9, no. 6 (June 2021): e002894. http://dx.doi.org/10.1136/jitc-2021-002894.
Abstract:
BackgroundImmuno-oncology therapies are now part of the standard of care for cancer in many indications. However, durable objective responses remain limited to a subset of patients. As such, there is a critical need to identify biomarkers that can predict or enrich for treatment response. So far, the majority of putative biomarkers consist of features of the tumor microenvironment (TME). However, in preclinical mouse models, the collection of tumor tissue for this type of analysis is a terminal procedure, obviating the ability to directly link potential biomarkers to long-term treatment outcomes.MethodsTo address this, we developed and validated a novel non-terminal tumor sampling method to enable biopsy of the TME in mouse models based on fine needle aspiration.ResultsWe show that this technique enables repeated in-life sampling of subcutaneous flank tumors and yields sufficient material to support downstream analyses of tumor-infiltrating immune cells using methods such as flow cytometry and single-cell transcriptomics. Moreover, using this technique we demonstrate that we can link TME biomarkers to treatment response outcomes, which is not possible using the current method of terminal tumor sampling.ConclusionThus, this minimally invasive technique is an important refinement for the pharmacodynamic analysis of the TME facilitating paired evaluation of treatment response biomarkers with outcomes and reducing the number of animals used in preclinical research.
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Imai, Mitsuho, Jinyeong Lim, Naoko Iida, Hiromichi Ebi, Wataru Okamoto, Takeshi Kato, Taito Esaki, et al. "Deciphering tumor microenvironment dynamics in HER2-amplified refractory metastatic colorectal cancer in the TRIUMPH trial." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): 3564. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.3564.
Abstract:
3564 Background: Approximately 2-4% of patients with metastatic colorectal cancer (mCRC) harbor HER2 amplification, a subset notorious for poor response rates following conventional treatments. The TRIUMPH trial introduces anti-HER2 therapy, combining trastuzumab and pertuzumab. Despite its potential, the observed response rate stands at 30%, accompanied by an early recurrence within 3.5 months with acquired resistance, which emphasizes the need for further investigations into resistance mechanisms within this patient population. Here, we delineate the dynamic changes in both the tumor and its microenvironment in response to treatment and mechanisms of acquired resistance using spatial transcriptomics. Methods: Within the TRIUMPH trial, a total of 20 formalin-fixed paraffin-embedded (FFPE) biopsy slides from 13 patients were collected before and after treatment or at one time. Utilizing these FFPE slides, we employed imaging-based single-cell spatial transcriptomics, using a custom panel tailored for the tumor and its microenvironment. This panel includes gene sets related to tumor growth, drug resistance, and immune response. Results: To comprehend the complexities of the tumor and its surroundings, we categorized tumor tissue into distinct sections, encompassing tumor, stromal, and immune-enriched areas based on their neighbor cells. Remarkably, we noted a substantial rise in the infiltration of T cells and myeloid cells into tumor-enriched regions post-treatment. T cells increased from a median of 1.5% to 2.2%, and myeloid cells from 4.3% to 7.4%, particularly in patients showing a response. Additionally, ERBB2 expression in tumor cells was high, whereas the non-response group exhibited lower expression levels. Prior to treatment, fibroblast and endothelial cells were intricately intertwined with tumor cells. However, subsequent to treatment, these cells segregated into stromal regions, exhibiting an increase in their proportions. Notably, angiogenic tumor-associated macrophage (angio-TAM), expressing SPP1 and VEGFA, were localized at the interface of tumors and stromal cells and proliferated following disease progression. This spatial reorganization signifies dynamic alterations within the tumor microenvironment following treatment. Conclusions: Our study on HER2-amplified metastatic colorectal cancer in the TRIUMPH trial uncovers intriguing spatial changes post anti-HER2 therapy. Notably, dynamic reorganization of fibroblast and endothelial cells into stromal regions suggest complex treatment responses. Identification of angio-TAM expressing SPP1 and VEGFA adds depth to understanding the contribution of tumor microenvironment to the resistance mechanism. These findings highlight the intricate tumor microenvironment shifts, urging further exploration for optimized therapeutic strategies.
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Naing, Aung, Hirva Mamdani, Minal A. Barve, Melissa Lynne Johnson, Sam Darko, Julie A. Murphy, Lauren Trogun, et al. "Investigation of a potential protein biomarker signature that may predict clinical benefit of NT-I7 and pembrolizumab in patients with cold gastrointestinal tumors." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): 2563. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.2563.
Abstract:
2563 Background: Microsatellite stable colorectal (MSS-CRC) and pancreatic cancer (PDAC) are immunologically cold tumors due to low immunogenicity and lack of genomic diversity. NT-I7, a long-acting IL-7, and pembrolizumab (pembro) show efficacy in these hard-to-treat indications. While a limited set of patients (pts) achieve objective response, frequency and duration of the disease control rate point to a larger subset obtaining clinical benefit. To identify novel predictive biomarkers, we analyzed baseline peripheral and biopsy samples from pts based on treatment duration. Methods: Open-label Phase 2a study in pts with relapsed/refractory checkpoint inhibitor-naïve MSS-CRC and PDAC; NT-I7 1200 µg/kg IM every 6 weeks (Q6W), pembro 200 mg IV Q3W. Subjects were grouped by treatment duration, measured in NT-I7 doses administered before treatment discontinuation for any cause: 1 dose was short (ST), 2-3 doses medium (MT) and ≥4 doses long (LT). Correlative studies included peripheral (proteomics, T cell receptor sequencing [TCRseq], single cell RNA sequencing [scRNAseq]), and biopsy (genomics, transcriptomics, TCRseq). Results: As of 02OCT2023, 53 evaluable pts completed or discontinued treatment; 5 are still on follow up. ST group included 21 pts, MT 22 and LT 10 (including all 5 partial responders). Tumor biopsies were confirmed MSS with low tumor mutational burden (TMB). LT pts had similar age (59.0 [53.0-71.5] vs 66.0 [47.3-73.5]; ST vs LT) and lower baseline tumor burden (81.0 mm vs 58.0 mm; ST vs LT, p = 0.022). Biopsy analysis showed LT pts had, at baseline, upregulated pathways related to immune activity despite confirmed cold tumor status. Baseline scRNAseq in peripheral blood showed that stem-like CD8 T cells (precursors of exhausted [TPEX] and stem-cell memory [TSCM]) had a differential activation pattern in LT pts; those pathways were enriched in memory effector subsets in ST pts. Preserved antigen-specific stemness may be needed for NT-I7 + pembro efficacy. Baseline concentrations of 3 proteins that can be produced by growing tumors were significantly increased in ST pts. Pts were classified based on elevated levels of these potential biomarkers: POSITIVE (≥2 biomarkers; 20 pts) and NEGATIVE (≤1 biomarker; 33 pts). Pts with NEGATIVE signature at baseline had significantly higher overall survival, regardless of ST, MT or LT status (13.2 vs 8.9 months, p = 0.030). Conclusions: Preserved tumor-specific TPEX activity may be required for NT-I7 + pembro activity based on its presence in LT pts, who remained on treatment the longest. According to this analysis, there are 3 potentially predictive protein biomarkers that may help identify a pt subset more likely to experience clinical benefits from the combination treatment of NT-I7 + pembro. Further verification of the predictive nature of this signature in independent cohorts is ongoing. Clinical trial information: NCT04332653 .
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Tesfaye, D., N. Ghanem, F. Rings, E. Tholen, C. Phatsara, K. Schellander, and M. Hoelker. "196 EMBRYO BIOPSY TRANSCRIPTOMICS: A POTENTIAL TOOL TO IDENTIFY TRANSCRIPTS DIRECTLY RELATED TO THE ABILITY OF THE EMBRYO TO INDUCE PREGNANCY AFTER TRANSFER." Reproduction, Fertility and Development 21, no. 1 (2009): 196. http://dx.doi.org/10.1071/rdv21n1ab196.
Abstract:
The incidence of pregnancy loss due to embryonic mortality in cattle is one of the major causes of reproductive failure. The early embryonic loss can be due to problems with the embryo itself, the uterine environment, or interactions between the embryo and the uterus. So, this study was conducted to investigate the gene expression profile of bovine embryo biopsies produced in vivo and in vitro that resulted in different pregnancy outcomes. For this, biopsies representing 30 to 40% of the intact in vitro and in vivo blastocysts were taken, and 60 to 70% part was allowed to re-expand prior to transfer to recipients. Based on the pregnancy outcome after transfer, biopsies (n = 10 per pool) were grouped into 3 distinct phenotypes: those that resulted in no pregnancy, those that resulted in resorption, and those that resulted in successful pregnancy and subsequent calf delivery. A bovine cDNA microarray with 2000 clones was used to analyze the gene expression profiles of 3 replicates from each embryo biopsy group. Array data analysis revealed a total of 50 and 52 genes to be differentially expressed between biopsies derived from in vivo blastocysts that resulted in no pregnancy v. calf delivery and resorption v. calf delivery, respectively. Similarly, a total of 52 and 58 transcripts were differentially expressed between biopsies derived from in vitro-produced blastocysts that resulted in no pregnancy v. calf delivery and resorption v. calf delivery, respectively. Quantitative real-time PCR has confirmed the expression profile of 6 selected candidate genes. A distinct set of genes were found to be commonly expressed between in vitro- and in vivo-derived blastocyst biopsies, which ended up with the same pregnancy outcome. Biopsies, which ended up with calf delivery, were found to be enriched with transcripts involved in nucleosome assembly (KRT8), translation (RPLPO), electron transport (COX-2), and placenta specific (PLAC8). On the other hand, transcripts regulating immune response (TNFa), response to stress (HSPD1), and cell adhesion (CD9) were up-regulated in embryos that resulted in no pregnancy or resorption. Differences in transcript abundance of some genes have been seen between biopsies derived from in vitro and in vivo blastocysts. Biopsies from in vivo-derived blastocysts and that ended up with resorption were found to be enriched with transcripts regulating calcium-binding protein (S100A10, S100A14). Transcription factor-related transcripts (CDX2, HOXB7) were up-regulated in vitro-derived blastocyst biopsies that resulted in no pregnancy. In conclusion, the results evidenced that embryos derived from either in vitro or in vivo have more similarities than differences in their transcript abundance with respect to the ability in initiating pregnancy.
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Bojmar, Linda, Constantinos P. Zambirinis, Jonathan Hernandez, Jayasree Chakraborty, Samer Hanna, Diane Simeone, David Kelsen, et al. "Abstract PR012: Perioperative liver biopsy captures features of the liver pre-metastatic niche and predicts metastatic outcome after pancreatic cancer resection." Cancer Research 82, no. 22_Supplement (November 15, 2022): PR012. http://dx.doi.org/10.1158/1538-7445.panca22-pr012.
Abstract:
Abstract Pancreatic cancer (PC) has a high propensity for liver metastasis (LM), a rapidly lethal event, often seen early after resection of the primary tumor. Mounting pre-clinical evidence implicates the establishment of microenvironmental alterations in the liver or other target organs prior to emergence of clinically evident metastases, termed “pre-metastatic niches”, which is a crucial first step in metastatic progression. To determine the translational relevance of these findings, we evaluated liver biopsies from PC patients obtained during pancreatectomy to characterize the cellular, molecular and metabolic features that define the pre-metastatic niche and that may, in turn, be used as biomarkers to stratify the metastatic risk, and as therapeutic targets to interrupt the metastatic cascade. Thus, liver biopsies from 49 patients with localized PC were analyzed by transcriptomics, metabolomics, histopathology, flow cytometry, and in selected patients by single cell RNA sequencing. Patients underwent routine surveillance in a prospective manner to determine which patients developed early (<6 months) or late (>6 months) LM, extrahepatic metastasis, or remained disease-free. Eighteen patients with non-cancerous pancreatic lesions undergoing pancreatectomy were used as controls (non-PC). Single cell transcriptomics analyses and immuno-profiling revealed that, in contrast to non-PC livers, tumor-free, pre-metastatic livers from PC patients exhibited enhanced inflammation evidenced by enrichment of neutrophils, CD11B+ cells, and CD3+ T cells, as well as expansion and activation of a CD11B+ subset of NK cells. Furthermore, immune and metabolic profiling of PC pre-metastatic livers identified features that predicted future patterns of metastasis: high Ki67 proliferation index, neutrophil extracellular trap (NET) formation, and upregulated sortilin-1 gene expression, all of which correlated with earlier LM. Conversely, widespread lobular inflammation, with abundant lobular CD3+ T cells, as well as intact creatine metabolism and steatosis associated with no recurrence, isolated extrahepatic recurrence or later LM. We combined the above variables to develop a decision tree-based prediction model, which performed best for identification of early LM (AUC 0.85). Taken together, these data demonstrate that in patients with apparently localized PC, pre-treatment liver biopsies may confirm the presence of human hepatic pre-metastatic niche and reveal features that correlate with timing and patterns of recurrence (early or late LM, extrahepatic, or no recurrence), after resection of PC. These liver profiles represent novel biomarkers that may be used to provide prognostic information and guide subsequent treatment of PC. Citation Format: Linda Bojmar, Constantinos P. Zambirinis, Jonathan Hernandez, Jayasree Chakraborty, Samer Hanna, Diane Simeone, David Kelsen, Haiying Zhang, Irina R Matei, Per Sandström, Robert Schwartz, William R. Jarnagin, David Lyden. Perioperative liver biopsy captures features of the liver pre-metastatic niche and predicts metastatic outcome after pancreatic cancer resection [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR012.
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Treaba, Diana O., Dennis M. Bonal, Anna D. Chorzalska, Christoph Schorl, Kelsey Hopkins, John L. Reagan, Peter Rintels, Peter J. Quesenberry, and Patrycja M. Dubielecka. "Levels of Osteopontin (SPP1), Osteonectin (SPARC) and Biglycan (BGN) in Acute Myeloid Leukemia Bone Marrow Biopsies Post-Induction Therapy Define the Status of Osteogenic Niche and Show Inverse Correlation with Therapeutic Response." Blood 136, Supplement 1 (November 5, 2020): 29–30. http://dx.doi.org/10.1182/blood-2020-142604.
Abstract:
Background: Acute Myeloid Leukemia (AML) has a five-year survival rate of 25% and its high mortality is linked to poor response to treatment and relapse. Our understanding of the molecular mechanisms controlling relapse and AML progression is limited. Animal models indicate that AML cells significantly modulate their bone marrow microenvironment inducing gradual loss of endosteal and vascular niches, both playing critical roles in support and maintenance of normal hematopoiesis. The goal of this study was to determine microenvironmental factors driving the gradual retraction of endosteal and vascular niches directly in the AML core bone marrow biopsies, and assess the treatment effect on hematopoietic and non-hematopoietic cells. Methods: Transcriptomics and histopathologic evaluations of matched human AML core bone marrow biopsies obtained at diagnosis (n=12) and day 14 post-induction therapy (n=12) with daunorubicin and cytarabine (7+3) were performed. Based on post-treatment frequency of blasts in the AML bone marrow aspirate, patients were classified as responders (<5% blasts) or non-responders (> 5% blasts). Three of 6 responders (3 men, 3 women, average age 59 yrs) had normal karyotype, and three of 6 non-responders (1 man, 5 women, average age 52.6 yrs), had normal karyotype. RNA was isolated from the core bone marrow biopsies and subjected to Clariom D Human Affymetrix arrays. Transcriptomics data were analyzed using Affymetrix Transcriptome Analysis Console with LIMMA R package and Gene Set Enrichment Analysis (GSEA). H&E stained bone marrow biopsy slides were subjected to blinded histopathological assessment. Results: Transcriptomic data analysis of responder vs. non-responder samples at diagnosis indicated significant loss of transcripts associated with heme metabolism (HBB, HBD, GYPE, CA1) suggesting decrease in frequency of erythroid progenitors (Fig.A). Trends of decreased frequency of erythroid progenitors were noted in both bone marrow biopsies and aspirates of diagnostic non-responder samples (Fig.B). Decreased frequency of lymphoid cells was also noted (Fig.B). Interestingly, while post-treatment we noted a relative increase in frequencies of lymphoid cells in both responder and non-responder samples, the increase was more prominent in responders (Fig.B). Trilineage hematopoiesis appeared affected more in diagnostic and post-treatment responder samples. Transcriptome analyses of diagnostic vs. post-treatment responder samples indicated significant increase in transcripts associated with activity within endosteal niche (SPARC, SPP1, DCN, VCAN, BGN) and significant loss of transcripts associated with DNA replication (TOP2, HELLS, E2F8) (Fig.C), the latter was consistent with treatment-related loss of cellularity. Only modest increase in SPARC, SPP1 or BGN levels and no significant decrease in DNA-replication associated transcripts were noted in non-responder post-treatment samples (Fig.1D). These data indicate greater loss of AML cells and greater activity within the endosteal niche in responder in comparison to non-responder samples. Finally, analyses performed on post-treatment responder vs. non-responder samples showed significant decrease in SPARC, SPP1, DCN, VCAN, BGN in non-responder post-treatment samples (Fig.E, F). Endosteal niche in histopathologic evaluation at diagnosis was generally unremarkable in both responder and non-responder samples with only rare osteoblasts present. In contrast, post-treatment, we found an elevated number of osteoblasts in responders in comparison to non-responder samples (Fig.G, H). Conclusions: Transcriptomic and histopathologic analyses of AML bone marrow biopsies procured at diagnosis and post-treatment from responder or non-responders indicate inverse correlation between the activity of endosteal niche and levels of transcripts involved in osteoblast maturation and homeostasis. Significant suppression of mesenchymal/osteoblast component of the niche is observed in non-responder samples. To our knowledge this is a first report showing the correlation between levels of osteopontin (SPP1), osteonectin (SPARC) and biglycan (BGN) and response to chemotherapy directly in the AML core bone marrow biopsies. Our data suggest that osteo-stimulatory factors could be used to achieve better therapeutic outcomes in AML. Disclosures No relevant conflicts of interest to declare.
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Nikfar, Mehdi, Haoyang Mi, Chang Gong, Holly Kimko, and Aleksander S. Popel. "Quantifying Intratumoral Heterogeneity and Immunoarchitecture Generated In-Silico by a Spatial Quantitative Systems Pharmacology Model." Cancers 15, no. 10 (May 13, 2023): 2750. http://dx.doi.org/10.3390/cancers15102750.
Abstract:
Spatial heterogeneity is a hallmark of cancer. Tumor heterogeneity can vary with time and location. The tumor microenvironment (TME) encompasses various cell types and their interactions that impart response to therapies. Therefore, a quantitative evaluation of tumor heterogeneity is crucial for the development of effective treatments. Different approaches, such as multiregional sequencing, spatial transcriptomics, analysis of autopsy samples, and longitudinal analysis of biopsy samples, can be used to analyze the intratumoral heterogeneity (ITH) and temporal evolution and to reveal the mechanisms of therapeutic response. However, because of the limitations of these data and the uncertainty associated with the time points of sample collection, having a complete understanding of intratumoral heterogeneity role is challenging. Here, we used a hybrid model that integrates a whole-patient compartmental quantitative-systems-pharmacology (QSP) model with a spatial agent-based model (ABM) describing the TME; we applied four spatial metrics to quantify model-simulated intratumoral heterogeneity and classified the TME immunoarchitecture for representative cases of effective and ineffective anti-PD-1 therapy. The four metrics, adopted from computational digital pathology, included mixing score, average neighbor frequency, Shannon’s entropy and area under the curve (AUC) of the G-cross function. A fifth non-spatial metric was used to supplement the analysis, which was the ratio of the number of cancer cells to immune cells. These metrics were utilized to classify the TME as “cold”, “compartmentalized” and “mixed”, which were related to treatment efficacy. The trends in these metrics for effective and ineffective treatments are in qualitative agreement with the clinical literature, indicating that compartmentalized immunoarchitecture is likely to result in more efficacious treatment outcomes.
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Clemenceau, Jean R., Paola Suarez Meade, Mark E. Jentoft, Alfredo Quiñones-Hinojosa, and Tae Hyun Hwang. "Abstract 144: Spatial transcriptomic landscape of the primary and recurrent glioblastoma tumor microenvironment." Cancer Research 83, no. 7_Supplement (April 4, 2023): 144. http://dx.doi.org/10.1158/1538-7445.am2023-144.
Abstract:
Abstract Differences in clonality, genomic and epigenetic alterations are known to occur between primary Glioblastoma (pGBM) and recurrent (rGBM), but this has been insufficient to yield a promising therapeutic approach. Recent studies show that the GBM tumor microenvironment (TME), composed of reactive glial cells, microglial subtypes, neuronal activity, myeloid cells, lymphocytes, etc., plays a crucial role in the invasiveness and evolution of the glioma cells. Nevertheless, how the spatial architecture and interplay among these cells facilitates GBM resurgence is largely unknown. To this point, we developed a pipeline for characterizing the TME changes using single nucleus and spatial transcriptomics (ST). We retrospectively collected matched, fresh-frozen, IDH-wildtype pGBM and rGBM samples (n=14, 7 patients) from the Mayo Clinic Neuroscience Biobank. Single nucleus RNA sequencing was performed using the 10x Chromium platform. Matched FFPE blocks from 8 samples were collected from the Mayo Clinic pathology department for 4 of the 7 patients. A region of interest was identified from the corresponding histopathology slide by a pathologist, avoiding areas of necrosis and hemorrhage. The region was collected from the block using a 5mm biopsy punch. The tissue was re-paraffinized, and a 5µm thick section was used to perform ST with the 10x Visium for FFPE platform. We performed transcriptomic and image texture-based clustering of capture dots along with differential gene expression analysis. Based on gene expression, we identified and characterized conserved regions across samples. We used single nucleus data to infer cell composition. Spatial correlation and autocorrelation statistics were calculated on features, such as gene expression, gene set scores, cell type prediction, and antibody capture. The features’ relative spatial changes were compared between pGBM and rGBM. Our analyses showed high heterogeneity within and across samples, but we found higher molecular and textural heterogeneity in rGBM samples compared to pGBM. We found higher androgen response activity (p < 0.001) presents diffusely (I: 0.09) throughout rGBM tissue but localized to mesenchymal-like regions in pGBM (I: 0.15). KRAS signaling signature was decreased in pGBM (p < 0.01) and increased in rGBM (p < 0.01). This increase was significantly overexpressed in cluster 0 for rGBM (p=0.02), which is an area characterized by neural progenitor signature. No significant difference in KRAS or EGFR magnitude or distribution of expression was present for either GBM type, indicating an independent mechanism for pGBM. We established a pipeline for assessing the spatio-temporal changes of the GBM TME. We found evidence indicating differences in the type of growth signaling, the cells bing targeted, and their distribution across the TME between pGBM and rGBM. Our work suggests how ST can help us better understand the intricate dynamics of GBM. Citation Format: Jean R. Clemenceau, Paola Suarez Meade, Mark E. Jentoft, Alfredo Quiñones-Hinojosa, Tae Hyun Hwang. Spatial transcriptomic landscape of the primary and recurrent glioblastoma tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 144.
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Anderson, Chiron J., and Stephan Schmitz-Esser. "41 Differential Gene Expression of the Bovine Rumen Epithelial Microbiota During a Sub-acute Ruminal Acidosis (SARA) Challenge." Journal of Animal Science 100, Supplement_2 (April 12, 2022): 12. http://dx.doi.org/10.1093/jas/skac064.018.
Abstract:
Abstract Sub-Acute Ruminal Acidosis (SARA) is a metabolic disorder in dairy cattle characterized by a lowered ruminal pH, as a result of high grain diets. Dairy cows experiencing SARA show decreased milk production and impaired health; thus, SARA has major economic impacts. SARA has been associated with changes in the rumen epithelial microbiota. Previously, we performed meta-transcriptome sequencing on rumen epithelial biopsy samples from 3 fistulated Holstein cows before (baseline) and after switching to high concentrate feed to induce SARA to analyze the gene expression of the rumen epithelial microbiota. In this previous analysis, 1,607 features were detected using the KEGG Ontology reference database, including a wide variety of metabolic genes, as well as stress response, motility, and other functions. However, only 3 features were differentially expressed between baseline and SARA conditions using this approach. Here, we present a re-analysis of the meta-transcriptomics data using an improved bioinformatics pipeline to reveal additional genetic diversity and differentially expressed genes. We performed a de novo transcriptome co-assembly with Trinity, mapped reads to the assembled contigs, used RSEM to determine read counts, and DESEQ2 for detection of differentially expressed genes (Q < 0.05). Features were annotated using EggNOG, providing taxonomic predictions and GO, COG, and KEGG-based functional prediction. Using this method, a total of 76,861 transcripts were assembled, and 4,935 genes were differentially expressed between baseline and SARA conditions, representing a substantial improvement over the previous analysis. Our preliminary analysis indicates high expression levels of central metabolism and housekeeping genes, as well as oxidative stress response genes, and outer membrane proteins among rumen epithelial bacteria. Differentially expressed archaeal genes were primarily upregulated under SARA conditions and included genes involved in methanogenesis. Further analyses are ongoing and will provide insight into gene expression of the rumen epithelial microbiota, and their association with SARA.
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Lopez-Escalera, Silvia, Mari L. Lund, Gerben D. A. Hermes, Béatrice S. Y. Choi, Kei Sakamoto, and Anja Wellejus. "In Vitro Screening for Probiotic Properties of Lactobacillus and Bifidobacterium Strains in Assays Relevant for Non-Alcoholic Fatty Liver Disease Prevention." Nutrients 15, no. 10 (May 18, 2023): 2361. http://dx.doi.org/10.3390/nu15102361.
Abstract:
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial metabolic disorder that poses health challenges worldwide and is expected to continue to rise dramatically. NAFLD is associated with metabolic syndrome, type 2 diabetes mellitus, and impaired gut health. Increased gut permeability, caused by disturbance of tight junction proteins, allows passage of damaging microbial components that, upon reaching the liver, have been proposed to trigger the release of inflammatory cytokines and generate cellular stress. A growing body of research has suggested the utilization of targeted probiotic supplements as a preventive therapy to improve gut barrier function and tight junctions. Furthermore, specific microbial interactions and metabolites induce the secretion of hormones such as GLP-1, resulting in beneficial effects on liver health. To increase the likelihood of finding beneficial probiotic strains, we set up a novel screening platform consisting of multiple in vitro and ex vivo assays for the screening of 42 bacterial strains. Analysis of transepithelial electrical resistance response via co-incubation of the 42 bacterial strains with human colonic cells (Caco-2) revealed improved barrier integrity. Then, strain-individual metabolome profiling was performed revealing species-specific clusters. GLP-1 secretion assay with intestinal secretin tumor cell line (STC-1) found at least seven of the strains tested capable of enhancing GLP-1 secretion in vitro. Gene expression profiling in human biopsy-derived intestinal organoids was performed using next generation sequencing transcriptomics post bacterial co-incubation. Here, different degrees of immunomodulation by the increase in certain cytokine and chemokine transcripts were found. Treatment of mouse primary hepatocytes with selected highly produced bacterial metabolites revealed that indole metabolites robustly inhibited de novo lipogenesis. Collectively, through our comprehensive bacterial screening pipeline, not previously ascribed strains from both Lactobacillus and Bifidobacterium genera were proposed as potential probiotics based on their ability to increase epithelial barrier integrity and immunity, promote GLP-1 secretion, and produce metabolites relevant to liver health.
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Kugler, M., M. Dellinger, F. Kartnig, L. Müller, T. Preglej, L. Heinz, E. Simader, et al. "AB0056 CYTOKINE-DIRECTED CELLULAR CROSSTALK IMPRINTS SYNOVIAL PATHOTYPES IN RHEUMATOID ARTHRITIS." Annals of the Rheumatic Diseases 82, Suppl 1 (May 30, 2023): 1207.2–1207. http://dx.doi.org/10.1136/annrheumdis-2023-eular.6440.
Abstract:
BackgroundThe chronic inflammatory disease Rheumatoid Arthritis (RA) is characterized by synovial inflammation promoting cartilage and bone degradation when left untreated. Interaction between infiltrating immune cells, such as CD4+ T cells and activated fibroblast-like synoviocytes (FLS) might contribute to joint inflammation ultimately amplifying progressive joint destruction.ObjectivesTo elucidate the interaction of stimulated FLS and CD4+ T cells within an inflammatory environment and to define its impact on synovial inflammation.MethodsTo define the effect of inflammatory mediators, FLS were stimulated with different pro- and anti-inflammatory cytokines. Transcriptomic changes were measured using RNA sequencing (RNA-seq). Co-cultures of cytokine pre-treated FLS and fluorescence activated cell sorting (FACS)-purified naïve CD4+ T cells were established. Using high-content fluorescence microscopy combined with bioinformatic image analysis, cell-cell interactions were visualized and quantified. The consequence of FLS co-culturing on CD4+ T-cell development was addressed by flow cytometry of re-isolated CD4+ T-cells.ResultsRNA-seq on cytokine-stimulated FLS revealed cytokine-specific gene expression profiles. In line, we observed cytokine-specific patterns of interaction with CD4+ T-cells which could be further observed in flow cytometry data of T cell activation, proliferation and differentiation. Cytokine-stimulated FLS signatures could be detected in transcriptomic data of RA patient synovial tissue samples.ConclusionIn this study, we highlight the role of FLS in orchestrating inflammation-associated synovial tissue remodeling and how cytokine induced CD4+ T cells – FLS interactions impact on T-cell development.References[1]Zhang F, Wei K, Slowikowski K, Fonseka CY, Rao DA, Kelly S, et al. Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. Nat Immunol. 2019.[2]Smolen JS, Aletaha D, Barton A, Burmester GR, Emery P, Firestein GS, et al. Rheumatoid arthritis. Nat Rev Dis Primers. 2018;4:18001.[3]Smolen JS, Aletaha D, McInnes IB. Rheumatoid arthritis. The Lancet. 2016;388(10055):2023-38.[4]Lewis MJ, Barnes MR, Blighe K, Goldmann K, Rana S, Hackney JA, et al. Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Rep. 2019 Aug 27;28(9):2455-2470.[5]Rivellese F, Surace AEA, Goldmann K, Sciacca E, Çubuk C, Giorli G, et al. R4RA collaborative group. Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial. Nat Med. 2022 Jun;28(6):1256-1268.Acknowledgements:NIL.Disclosure of InterestsMaximilian Kugler: None declared, Mirjam Dellinger: None declared, Felix Kartnig: None declared, Lena Müller: None declared, Teresa Preglej: None declared, Leonhard Heinz: None declared, Elisabeth Simader: None declared, Lisa Göschl: None declared, Stephan Puchner: None declared, Sebastian Weiss: None declared, Giulio Superi-Furga: None declared, Josef S. Smolen Consultant of: AbbVie, Astra-Zeneca, Lilly, Novartis, Amgen, Astro, Bristol-Myers Squibb, Celgene, Celltrion, Chugai, Gilead, ILTOO, Janssen, Merck Sharp & Dohme, Novartis-Sandoz, Pfizer, Roche, Samsung and UCB, Grant/research support from: AbbVie, Astra-Zeneca, Lilly, Novartis, Amgen, Astro, Bristol-Myers Squibb, Celgene, Celltrion, Chugai, Gilead, ILTOO, Janssen, Merck Sharp & Dohme, Novartis-Sandoz, Pfizer, Roche, Samsung and UCB, Günter Steiner: None declared, Daniel Aletaha Consultant of: AbbVie, Amgen, Lilly, Merck, Novartis, Pfizer, Roche, Sandoz, Grant/research support from: AbbVie, Amgen, Lilly, Merck, Novartis, Pfizer, Roche, Sandoz, Hans Kiener: None declared, Anela Tosevska: None declared, Thomas Maria Karonitsch: None declared, Michael Bonelli Consultant of: Eli-Lilly, Grant/research support from: Galapagos.
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Ring, Alexander, Daniel Campo, Tania B. Porras, Pushpinder Kaur, Victoria A. Forte, Debu Tripathy, Janice Lu, et al. "Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer." Annals of Surgical Oncology 29, no. 5 (January 9, 2022): 2882–94. http://dx.doi.org/10.1245/s10434-021-11135-2.
Abstract:
Abstract Background Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases. Methods We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix microfluidics system to isolate cells based on size and deformability, independent of a priori knowledge of cell surface marker expression. Results Gene expression separated CTCs, metastatic biopsies, and PB into distinct groups despite heterogeneity between patients and sample types. CTCs showed higher expression of immune oncology targets compared with corresponding metastases and PB. Predictive biomarker (n = 64) expression was highly concordant for CTCs and metastases. Repeat observation data post-treatment demonstrated changes in the activation of different biological pathways. Somatic single nucleotide variant analysis showed increasing mutational complexity over time. Conclusion We demonstrate that RNA-Seq of CTCs could serve as a surrogate biomarker for breast cancer macrometastasis and yield clinically relevant insights into disease biology and clinically actionable targets.
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Chen, L., C. Zhang, R. Niu, R. Mao, Y. Qiu, and R. Feng. "P915 Multi-Omics Biomarkers for the Prediction of Response to Biologics in Patients with Inflammatory Bowel Disease." Journal of Crohn's and Colitis 18, Supplement_1 (January 1, 2024): i1670—i1671. http://dx.doi.org/10.1093/ecco-jcc/jjad212.1045.
Abstract:
Abstract Background The treatment concept for inflammatory bowel disease (IBD) has been transformed with biologics now recommended as the first-line therapy for moderate-to-severe patients. However, the significant heterogeneity among IBD patients has limited the efficacy of selected biologics based on traditional clinical factors. Therefore, it is imperative to molecularly stratify patients to match them with the most appropriate biologics. In this study, we systematically reviewed baseline omics biomarkers that have the potential to predict response to biological therapies, aiming to facilitate precision medicine in IBD. Methods We conducted a comprehensive literature search using PubMed by which we included studies that explore the role of omics biomarkers in predicting the efficacy of various biologics including anti-TNFα, anti-integrin, anti-IL-12/23P40 and anti-IL-23 P19 in patients with IBD. Results Our review included 110 studies. Of these, 86 studies focused on anti-TNFα, 17 focused on anti-integrin and 7 focused on anti-IL-12/23P40 and/or anti-IL-23P19. These studies investigated multi-levels baseline biomarkers, including genomics, transcriptomics (bulk RNA and sc-RNA sequence), proteomics, microbiome, and metabolomics (derived from serum, urine, or stool). Furthermore, recent studies already focused on integrating multiple omics analysis and showed that the predictive model based on multi-omics data could significantly enhance their performance. Among the available biomarkers, mucosal transcription of OSM (AUROC = 0.83), IL-13RA2 (AUROC = 0.90), and TREM-1 transcription in mucosal biopsy (AUROC = 0.77) as well as in PBMC ( AUROC varies between 0.78 and 0.94) could accurately predict the response to anti-TNFα. The mucosal IL-23A transcription could discriminate responders from non-responders to anti-IL-12/23P40 with an AUROC of 0.90. OSM, biomarkers of intestinal collagen turnover like C4M, IL-17, IL-22, and TNFα in serum also showed significant potential in predicting the response to anti-TNFα, anti-integrin and anti-IL-12/23P40. In addition, single-cell molecular signatures with sc-RNA sequencing provided more profound insights into predicting the response to biologics. The lack of reproducibility in results across different groups may be due to the disparity in patient selection, methodology, and study designs among different investigations. Conclusion Numerous omics markers have shown great potential in predicting the efficacy of biologics. However, it is crucial to explore and validate these novel biomarkers in larger cohorts using harmonized protocols to facilitate their evaluation into actual clinical practice, especially for newer biologics like anti-IL-12/23P40 and anti-IL-23P19.
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Patil, Madhuri. "What is the Optimum Endometrium Needed for Implantation?" Fertility & Reproduction 05, no. 04 (December 2023): 290. http://dx.doi.org/10.1142/s2661318223741048.
Abstract:
Implantation most critical step in reproduction. A complex process where blastocyst becomes intimately connected with maternal endometrium/decidua and requires; Competent embryo at blastocyst stage Receptive endometrium Synchronized dialogue between maternal and embryonic tissues Endometrial Changes for Implantation include architectural, morphological, cytochemical, molecular and genetic. These Changes Induce Endometrial receptivity, which is endometrial lining in a state of readiness for blastocyst implantation. It involves acquisition of adhesion ligands and loss of inhibitory components that may act as a barrier to an attaching embryo. Receptive endometrium is capable of selecting good quality embryos and reject the incompetent embryos. Endometrial Evaluation includes 1. Non-Invasive Assessment of Endometrial Receptivity by USG 2. Detection of abnormal Uterine cavity by 3D USG/SIS, HSG and Hysteroscopy 3. Diagnose Chronic Endometritis by hysteroscopy and Molecular tests? 4. Endometrial Microbiome by molecular tests 5. Endometrial asynchrony - Proteomics and transcriptomics 2D and 3D Ultrasound can Identify patients with poor implantation prognosis but has low predictive value in determining endometrial receptivity and IVF outcome. Ideal endometrial thickness for optimal outcome is between 7-14 mm. No Association was seen between clinical pregnancy rates (CPR) and endometrial pattern for women undergoing in IVF with fresh ET and FET. Minimum Endometrial Volume associated with pregnancy is 1.59 mL – 3D. But most pregnancies occur in volumes of 2-13 mL. Evaluation of endometrial volume is particularly useful in synechiae, adenomyosis and uterine anomalies. Vascularity demonstrated within Zone 3 or within Zones 3 and 4 prior to transfer is associated with good implantation rate. Presence of >3 peristaltic contractions of the sub endometrial myometrium/2 minutes interval on Day of hCG administration associated with poor implantation. Diagnosis of chronic endometritis is based on hysteroscopy, endometrial biopsy with plasma cells being identified histologically and specific treatment is determined based on microbial culture. Existence of non-Lactobacillus bacteria in the endometrium is correlated with negative impacts on reproductive function and should be considered as an emerging cause of implantation failure and pregnancy loss. Endometrial Receptivity Array (ERA) is validated for analysing the expression of 238 genes that are intimately related to endometrial receptivity. Abnormality in endometrial receptivity is displayed a specific gene expression profile. Intrauterine secretory profile directly linked to successful implantation and evaluation of endometrial fluid for cytokine, interleukin and growth factor secretions can be used to assess the endometrium. Conclusion: Identification of one or more of endometrial parameters that definitely indicate receptivity for implantation remains an elusive goal. None of the endometrial receptivity markers have sufficient discriminatory value to act as a diagnostic test for endometrial receptivity based on their ability to predict clinical pregnancy. Due to the dynamic, cyclic nature of the endometrium it may be difficult, to reliably assess endometrial function on the basis of a single test.
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Yu, Liping. "Abstract 1393: A Novel platform providing automated, consistent and gentle cell isolation from tissues for downstream applications." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1393. http://dx.doi.org/10.1158/1538-7445.am2022-1393.
Abstract:
Abstract Tumor biologists have long studied tumor tissue to understand cancer progression and to ultimately treat the disease. The gold standard would be to analyze tumor and immune cells from the same sample, providing purified cells that are interacting within the tumor. Many tissue homogenization techniques have been developed to release cells for downstream analysis, however, an automated and gentle process of purifying multiple cell types from the same processed tissue has remained elusive. The industry-standard workflows, such as centrifugation, have presented long-standing performance issues in terms of low cell recovery and inefficient removal of molecular debris, which often leads to sequencing results that are difficult to interpret. To ensure the quality of sequencing data from tissues, upstream processes need to improve to get the most from the precious patient tissue. Applied Cells has developed an integrated system based on multiple physics principles to achieve cell wash, concentration, and target cell isolation, with high recovery at an unprecedented flow rate. This platform combines tunable, acoustic cell purification and in-flow, column-free immuno-magnetic separation technologies, enabling automation of the entire cell sample preparation workflow for genomics and transcriptomics analysis. By harnessing the power and precision of acoustic cell manipulation, the MARS System can process a variety of samples including dissociated solid tissue in enzymatic buffer with high cell recovery and superior molecular debris removal compared to standard methods. For instance, when purifying leukocytes from a lung cancer biopsy tissue samples, MARS can remove 99.50% debris and 91% of dead cells in one single step, which is supreme than the conventional centrifuge cell wash while having >90% leukocyte recovery at 1mL/min flow rate. The in-flow microfluidics design drastically reduces residual DNA and RNA fragments that are difficult to remove using centrifuge wash methods. Furthermore, the system enables parallel cell purification and concentration for high throughput sample processing. Tumor or TIL cells can be further enriched by means of positive magnetic selection for genomic or cell biology applications. This novel platform allows improved tumor and TIL recovery in a gentle, consistent manner while having minimal interference with downstream applications, all from a single source starting material. Citation Format: Liping Yu. A Novel platform providing automated, consistent and gentle cell isolation from tissues for downstream applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1393.
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Bahrambeigi, Vahid, Jaewon J. Lee, Kimal I. Rajapakshe, Bret M. Stephens, Jason T. Henry, Sarah Dhebat, Mark W. Hurd, et al. "Abstract PR013: Transcriptomic profiling of liquid biopsy in colorectal cancer." Cancer Research 82, no. 23_Supplement_1 (December 1, 2022): PR013. http://dx.doi.org/10.1158/1538-7445.crc22-pr013.
Abstract:
Abstract Objective: Consensus molecular subtype (CMS) is a predictive factor for treatment outcomes of chemotherapies for metastatic colorectal cancer (CRC). CMS classification is based on transcriptomic profiles of CRC specimens obtained by tumor biopsy. Tumor biopsy often provides limited information due to the heterogeneity within tumor and spatial heterogeneity between the primary tumor and distant metastases. In addition, repeated tissue biopsy to monitor the treatment response is not practical. Liquid biopsy is a minimally invasive method for the real-time monitoring of cancer-derived biomarkers. Among liquid biopsy biomarkers, extracellular vesicles (EVs) have a unique potential because they possess nucleic acids. We explored the use of CRC plasma EVs in predicting the molecular subtype of CRCs using RNA-seq. Methods: EVs were isolated from 10 different CMS-stratified colorectal cancer cell lines and a normal control. Whole transcriptome RNA-seq on cellular RNA (cRNA) and cell-derived evRNA was done to determine if EVs could be used to predict the CMS subtype of their cells of origin. We then sought to perform molecular subtyping of plasma EVs from patients with CRC. RNA-seq was performed on tumor tissues and matched plasma EVs from 46 patients with CRC and 59 healthy controls (age/gender matched). The bulk transcriptome from CRC plasma EVs was deconvoluted to predict the cancer percentage (CIBERSORTx) and to utilize cancer-specific transcriptome for CMS subtyping (DeMixT). Artificial neural network (ANN)-based CMS subtype classifier was used to classify molecular subtypes. Results: There was 100% concordance between CMS subtype of evRNA with that of the cRNA. We showed that, RNA mixtures containing as low as 1% cancer cell RNA could be accurately classified into the correct CMS class. Imputed proportions of cancer in plasma of CRC patients ranged from 0.89% to 2.08%. Receiver operating characteristic (ROC) curve showed area under the curve of 0.961 with specificity and sensitivity of 0.96 and 0.9, respectively. Plasma evRNA was classified into CMS classes and there was 67% (31/46) concordance between the predicted subtype of liquid biopsies and the tumor samples. In patients with tumor purity greater than 10%, the concordance was higher at 75% (27/36). Conclusions: EVs could be used to accurately predict CMS subtypes of their cells of origin. We created a pipeline using low-input RNA library preparation from plasma EV to estimate the cancer RNA portion present in the bulk transcriptome and predict the molecular subtypes of colorectal cancers. Molecular subtyping of evRNA may help to track CMS changes of the tumor in patients undergoing treatment. Citation Format: Vahid Bahrambeigi, Jaewon J. Lee, Kimal I. Rajapakshe, Bret M. Stephens, Jason T. Henry, Sarah Dhebat, Mark W. Hurd, Ryan Sun, Scott Kopetz, Anirban Maitra, Paola A. Guerrero. Transcriptomic profiling of liquid biopsy in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR013.
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Iwamoto, F., O. Al Dalahmah, K. Manjrekar, C. Levrero, R. Michel, A. Bargo, S. Kaesshaefer, et al. "P11.82.A TARGETING THE GLIOBLASTOMA MASTER REGULATOR C/EBPß: A PHARMACOKINETIC AND PHARMACODYNAMIC NEOADJUVANT STUDY OF ST101." Neuro-Oncology 25, Supplement_2 (September 1, 2023): ii95. http://dx.doi.org/10.1093/neuonc/noad137.316.
Abstract:
Abstract BACKGROUND The vast amounts of genomics, epigenomics and transcriptomics data in glioblastoma (GBM) have yet to translate into better outcomes to most patients. One of the main challenges is to how to best integrate these diverse layers of omics to personalize and improve the treatment of glioblastomas. Cancer master regulators are often transcription factors (TFs), which control the expression of many genes and considered promising antitumor targets. CCAAT/enhancer-binding protein β (C/EBPβ) is an abundantly-expressed transcription factor (Zahnow 2009). C/EBPβ was previously described as a master regulator in GBM (Carro 2010). ST101 is a first-in-class cell-penetrating peptide antagonist of C/EBPβ with known ability to cross the blood-brain barrier. We have demonstrated potent anti-tumor activity with ST101 in multiple in vivo models including glioblastoma. Based on early efficacy data on the initial clinical study including objective responses in GBM, we designed this surgical study to further understand the antitumor mechanisms of ST101. METHODS we will recruit total of 12 newly diagnosed GBM and 6 recurrent patients. Recurrent GBM patients who are deemed surgical candidates will be treated with ST101 at the RP2D of 500 mg IV weekly for 2 to 4 weeks and then undergo standard of care surgical resection. After recovery from surgery, patients will continue ST101 until there is significant toxicity or tumor progression. 12 patients with newly diagnosed GBM who had undergone a prior biopsy or partial resection, and that upon further neurosurgical evaluation have an indication for additional debulking surgery will be eligible for this study. Patients will be treated with ST101 at the recommended phase 2 dose for 2 weeks and then undergo standard of care surgical resection. Patients will undergo standard of care treatment with radiation and temozolomide and continue ST101 after recovery from surgery. ST101 plasma concentration will be correlated with ST101 drug levels in enhancing and non-enhancing tumor tissue of recurrent and newly diagnosed patients. We will compare the molecular abnormalities in the post-treatment tissue through deep bulk whole-exome sequencing and mRNAseq against the intra-patient baseline tissue. Pharmacodynamics evaluation will focus on the expression of genes regulated by the transcription factor CEBPβ, such as BCL2, cyclins and cyclin-dependent kinases and inhibition of differentiation genes. Due to the diversity of cell types in the tumor microenvironment and the early data that ST101 can also reprogram M2 macrophages to M1 in addition to its direct antitumor effects, we will perform single nucleus RNAseq on these surgical specimens. Enrollment has started in January 2023 and 6 recurrent and 2 newly diagnosed patients have been accrued.
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Hasanov, Elshad, Lesley Flynt, Rebecca Tidwell, Hyunsoo Hwang, Roserika Brooks, Lauren Michelle Wood, Travis Solley, et al. "Phase 1b/2 study of combination 177Lu girentuximab plus cabozantinib and nivolumab in treatment naive patients with advanced clear cell RCC." Journal of Clinical Oncology 42, no. 4_suppl (February 1, 2024): TPS496. http://dx.doi.org/10.1200/jco.2024.42.4_suppl.tps496.
Abstract:
TPS496 Background: Complete response (CR) is still a rare event in patients with advanced clear cell renal cell carcinoma (ccRCC). The combination of nivolumab plus cabozantinib was recently approved for the first-line treatment of ccRCC based on the CheckMate 9ER phase 3 study demonstrating improved progression-free survival (PFS) & objective response rate (ORR) in comparison to sunitinib. However, the CR rate was only 9%. Since the anti-tumor effects of immune checkpoint inhibitors are dependent on the presence of activated tumor-infiltrating T cells, drugs that could synergize with T cells' anti-tumor activity can allow us to improve CR rates. Activation of the cGAS-STING pathway which is induced by radiation-induced DNA damage, is one promising mechanism that has been investigated. Many studies have shown that radiation treatment augments immune checkpoint inhibition. However, it is not always possible to radiate all metastatic lesions. Therefore, targeted peptide receptor radionuclide therapies, have been developed by conjugating radioisotopes to receptor binding analogs targeting specific cancer cell surface proteins, thereby delivering targeted radiation to cancer cells in the body with minimal damage to surrounding healthy cells. 177Lu girentuximab is the first antibody-radioisotope designed for ccRCC, targeting carbonic anhydrase 9-expressing cells, which includes > 90% of ccRCC. It has been tested in metastatic ccRCC as a single agent & shown to be safe and effective in stabilizing disease in 57% of pts. In this study, we hypothesize 177Lu girentuximab-induced DNA damage will potentiate the STING pathway, and this activation will synergize with nivolumab and cabozantinib to promote trafficking and infiltration of activated T cells to tumors and achieve higher CR rates. Methods: Up to 100 patients with treatment na'i"ve, biopsy-proven ccRCC with adequate organ/marrow function with 1 evaluable lesion by RECIST 1.1 will be enrolled. A 5-patient safety lead-in will evaluate myelosuppression. Ongoing safety, & futility monitoring will employ a Bayesian approach. The sample size was chosen for reasonable operating characteristics to distinguish a CR rate (primary endpoint) of 18% as better than 9% using a beta(0.09, 0.91) prior. Secondary endpoints are ORR, PFS by RECIST 1.1, and overall survival. 177Lu-girentuximab 1480 MBq/m2 (61% of single agent MTD) will be administered every 12 weeks for up to 3 cycles. Starting with the 2nd cycle, nivolumab & cabozantinib will be added at standard dose. To explore the effects of the treatment on inducing activated T cell infiltration, patients will undergo pre/post-treatment PET scan with [18F]F-AraG radiotracer as well as biopsies for single cell, spatial transcriptomics and proteomics studies. Clinical trial information: NCT05239533 .
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Jonasch, Eric, Elshad Hasanov, Lesley Flynt, Hyunsoo Hwang, Rebecca Slack Tidwell, Roserika Brooks, Lauren Michelle Wood, et al. "Phase 1b/2 study of combination 177Lu girentuximab plus cabozantinib and nivolumab in treatment naive patients with advanced clear cell RCC." Journal of Clinical Oncology 42, no. 16_suppl (June 1, 2024): TPS4610. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.tps4610.
Abstract:
TPS4610 Background: Complete response (CR) is still a rare event in patients with advanced clear cell renal cell carcinoma (ccRCC). The combination of nivolumab plus cabozantinib was recently approved for the first-line treatment of ccRCC based on the CheckMate 9ER phase 3 study demonstrating improved progression-free survival (PFS) and objective response rate (ORR) in comparison to sunitinib. However, the CR rate was only 9%. Since the anti-tumor effects of immune checkpoint inhibitors are dependent on the presence of activated tumor-infiltrating T cells, drugs that could synergize with T cells' anti-tumor activity can allow us to improve CR rates. Activation of the cGAS-STING pathway which is induced by radiation-induced DNA damage, is one promising mechanism that has been investigated. Many studies have shown that radiation treatment augments immune checkpoint inhibition. However, it is not always possible to radiate all metastatic lesions. Therefore, targeted peptide receptor radionuclide therapies, have been developed by conjugating radioisotopes to receptor binding analogs targeting specific cancer cell surface proteins, thereby delivering targeted radiation to cancer cells in the body with minimal damage to surrounding healthy cells. 177Lu girentuximab is the first antibody-radioisotope designed for ccRCC, targeting carbonic anhydrase 9-expressing cells, which includes >90% of ccRCC. It has been tested in metastatic ccRCC as a single agent and shown to be safe and effective in stabilizing disease in 57% of pts. In this study, we hypothesize that 177Lu girentuximab-induced DNA damage will potentiate the STING pathway, and this activation will synergize with nivolumab and cabozantinib to promote trafficking and infiltration of activated T cells to tumors and achieve higher CR rates. Methods: Up to 100 patients with treatment naive, biopsy-proven ccRCC with adequate organ/marrow function with 1 evaluable lesion by RECIST 1.1 will be enrolled. A 5-patient safety lead-in will evaluate myelosuppression. Ongoing safety, and futility monitoring will employ a Bayesian approach. The sample size was chosen for reasonable operating characteristics to distinguish a CR rate (primary endpoint) of 18% as better than 9% using a beta(0.09, 0.91) prior. Secondary endpoints are ORR, PFS by RECIST 1.1, and overall survival. 177Lu-girentuximab 1480 MBq/m2 (61% of single agent MTD) will be administered every 12 weeks for up to 3 cycles. Starting with the second cycle, nivolumab and cabozantinib will be added at standard dose. To explore the effects of the treatment on inducing activated T cell infiltration, patients will undergo pre/post-treatment PET scan with 18F-AraG radiotracer as well as biopsies for single cell, spatial transcriptomics and proteomics studies. Clinical trial information: NCT05663710 .
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Campbell, Katie M., Zaid Bustami, Daniel G. Chen, Egmidio Medina, Cynthia R. Gonzalez, Nataly Naser Aldeen, Ignacio Baselga-Carretero, et al. "Abstract 6550: Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory melanoma." Cancer Research 84, no. 6_Supplement (March 22, 2024): 6550. http://dx.doi.org/10.1158/1538-7445.am2024-6550.
Abstract:
Abstract Background: The phase II randomized trial S1616 (NCT03033576) showed that patients with melanoma refractory to anti-PD-1-based therapy had improved progression free survival (HR=0.63, p=0.037) and objective response (28% vs 9%) to the combination of ipilimumab with nivolumab compared to ipilimumab. Here, we report molecular and spatial proteomic features of biopsies collected from patients on S1616, both prior to and during therapy. Methods: Biopsies collected from patients from both arms at baseline (N=68 patients total) and early on-therapy (N=51; 43 with paired timepoints) were analyzed by whole exome sequencing (n=185 samples), RNA sequencing (n=105), histopathologic staining (n=149), and multiplexed ion beam imaging (n=45). Multiple biopsies were available for some patients. Mutations, gene expression, and tumor microenvironment were compared across timepoints and response to combination (N=18 responders [CR/PR], N=44 nonresponders [SD/PD]). Results: Baseline biopsies from patients responsive to combination had increased expression of genes (n=482, FDR<0.05) associated with coagulation and complement, fatty acid metabolism, oxidative phosphorylation, hypoxia, and interferon gamma response gene sets (FDR<0.05), compared to nonresponsive biopsies. Baseline biopsies from responders also had low levels of effector CD8 T cells (PD1+, TIM-3+, GZMB+, Ki67+) colocalized with tumor cells and myeloid populations expressing higher levels of MHC Class II. On-therapy biopsies from responders showed decreased detection of driver mutations by genomics, reduced gene expression of pathways enriched at baseline (oxidative phosphorylation, complement) by transcriptomics, and increased CD8 T cell to tumor cell ratios by histopathology, supporting observations of tumor regression. On-therapy biopsies from responders also had increased gene expression of genes related to inflammatory cytokine signaling. This correlated with increased proportions of effector CD8 T cells, compared to paired baseline or nonresponding biopsies, and increased organization of nonactivated CD8 T cells near mature endothelial structures (SMA+, CD31+ regions) adjacent to tumor. Biopsies from nonresponders did not demonstrate these dynamics and instead contained exhausted CD8 T cells (PD1+, TIM-3+, granzyme B-, Ki67-) colocalized with FOXP3+, CD4+ Tregs and CD163+, PD-L1+ M2 macrophages, both at baseline and on-therapy. Conclusion: In patients with melanoma refractory to anti-PD-1, addition of anti-CTLA-4 facilitates tumor-reactive CD8 T-cell infiltration and decreased suppressor cell dynamics, resulting in regression of some tumors with distinct transcriptome features. Conversely, biopsies from patients whose tumors progress on combination therapy lack expression of metabolic pathways and show CD8 T-cells restricted in proximity to M2 macrophages and Tregs. Citation Format: Katie M. Campbell, Zaid Bustami, Daniel G. Chen, Egmidio Medina, Cynthia R. Gonzalez, Nataly Naser Aldeen, Ignacio Baselga-Carretero, Agustin Vega-Crespo, Jessica Maxey, Jia M. Chen, Lawrence F. Kuklinski, Kari L. Kendra, Bartosz Chmielowski, Thach-Giao Truong, Nikhil I. Khushalani, Frances Collichio, Alexandra Ikeguchi, Adrienne I. Victor, Kim Margolin, Jeffrey A. Sosman, Sapna P. Patel, Siwen Hu-Lieskovan, James Moon, Shay Bellasea, Daniel K. Wells, Christine N. Spencer, Marshall A. Thompson, Michael Wu, Philip O. Scumpia, Ari VanderWalde, Antoni Ribas. Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6550.
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Genta, Sofia, Ming Sound Tsao, Ben X. Wang, Aaron Richard Hansen, Trevor John Pugh, Mathieu Lupien, Bryan Coburn, et al. "Immune Resistance Interrogation Study (IRIS): A prospective comprehensive multi-omic analysis in patients with intrinsic and acquired resistance to immunotherapy." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): TPS2679. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.tps2679.
Abstract:
TPS2679 Background: Immune checkpoint inhibitors (ICI) have demonstrated efficacy in a wide variety of cancers. Nevertheless, only a small proportion of patients derive a durable benefit. Mechanisms underlying primary and acquired resistance are still incompletely understood. They comprise tumor-intrinsic factors such as genomic and transcriptomic changes; upregulation of immunosuppressive subsets; T cell exhaustion; and promotion of an immune-tolerant tumor microenvironment. The collection of tumor biopsy at disease progression (PD) is challenging both in clinical and research settings as this often occurs at the time of treatment discontinuation. However, the analysis of these samples can lead to novel strategies to prevent or reverse immune resistance. Thus, the current approach to begin a profiling study with patients at the time of PD on ICI enables access and interrogation of such samples. Methods: IRIS is a prospective, investigator-initiated trial at the Princess Margaret Cancer Centre that aims to extensively characterize the genomic, transcriptomic, epigenetic and immunophenotypic profiles of tumors with primary versus acquired resistance to ICI-based therapy. Primary resistance is defined as PD at the first on-treatment imaging, whereas acquired resistance is defined as PD occurring after an initial partial or complete response or following disease stability lasting ≥6 months. Additional objectives include the evaluation of radiomic parameters on standard radiological imaging, investigation of fecal microbiome, generation of patient-derived organoids and facilitation of data and sample sharing with the research community. The planned samples size is 100 patients. A one-time fresh tumor biopsy, blood and stool samples and archival tissue (when available) are collected at the time of PD on ICI (baseline) from all the participants. Longitudinal blood samples are obtained every 2-3 months (around the time of tumor imaging) until PD in patients receiving a subsequent treatment. Subjects who are not amenable for therapy undergo blood collections at the time of further PD. Molecular characterization of tumor samples includes: DNA/RNA sequencing, Assay of Transposase Accessible Chromatin (ATAC)-sequencing, Cellular Indexing of Transcriptomes and Epitopes (CITE)-sequencing, multiplexed immunohistochemistry and flow cytometry. Results of NGS performed on the first biopsy core are returned to patient and physician. Key eligibility criteria include diagnosis of solid tumor, progression to ICI as the most recent line of treatment and disease amenable to core needle biopsy. The IRIS trial, activated in October 2020, is currently open to enrollment. As of January 2021, 21 patients have been enrolled and a total of 92 tissue cores, 42 blood and 20 stool samples have been collected. Clinical trial information: NCT04243720.
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Hasanov, Elshad, Lesley Flynt, Rebecca Slack Tidwell, Hyunsoo Hwang, Roserika Brooks, Lauren Michelle Wood, Travis Solley, et al. "Phase 1b/2 study of combination 177Lu girentuximab plus cabozantinib and nivolumab in treatment naïve patients with advanced clear cell RCC." Journal of Clinical Oncology 41, no. 16_suppl (June 1, 2023): TPS4605. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.tps4605.
Abstract:
TPS4605 Background: Complete response (CR) is still a rare event in patients with advanced clear cell renal cell carcinoma (ccRCC). The combination of nivolumab plus cabozantinib was recently approved for the first-line treatment of ccRCC based on the CheckMate 9ER phase III study demonstrating improved progression-free survival (PFS) and objective response rate (ORR) in comparison to sunitinib. However, the CR rate was only 9%. Since the anti-tumor effects of immune checkpoint inhibitors are dependent on the presence of activated tumor-infiltrating T cells, drugs that could synergize with T cells’ anti-tumor activity can allow us to improve CR rates. Activation of the cGAS-STING pathway, the master regulator of anti-tumor immunity which is induced by radiation-induced DNA damage, is one promising mechanism that has been investigated. Many studies have shown that radiation treatment augments immune checkpoint inhibition. However, it is not always possible to radiate all metastatic lesions. Therefore, targeted peptide receptor radionuclide therapies (PRRT), have been developed by conjugating radioisotopes to receptor binding analogs targeting specific cancer cell surface proteins, thereby delivering targeted radiation to cancer cells in the body with minimal damage to surrounding healthy cells. 177Lu girentuximab is the first antibody-radioisotope designed for ccRCC, targeting carbonic anhydrase IX-expressing cells, which includes > 90% of ccRCC. It has been tested in metastatic ccRCC as a single agent and shown to be safe and effective in stabilizing disease in 57% of pts. In this study, we hypothesize that 177Lu girentuximab-induced DNA damage will potentiate the STING pathway, and this activation will synergize with nivolumab and cabozantinib to promote trafficking and infiltration of activated T cells to tumors and achieve higher CR rates. Methods: Up to 100 patients with treatment naïve, biopsy-proven ccRCC with adequate organ/marrow function with ≥1 evaluable lesion by RECIST 1.1 will be enrolled. A 5-patient safety lead-in will evaluate myelosuppression. Ongoing safety, and futility monitoring will employ a Bayesian approach. The sample size was chosen for reasonable operating characteristics to distinguish a CR rate of 18% as better than 9% using a beta(0.09, 0.91) prior. Secondary endpoints are objective response, PFS by RECIST 1.1, and overall survival. 177Lu-girentuximab 1480 MBq/m2 (61% of single agent MTD) will be administered every 12 weeks for up to 3 treatment cycles. After the first cycle, nivolumab and cabozantinib will be added starting with the second cycle at standard dose. To explore the effects of the combination therapy on inducing activated T cell infiltration, patients will undergo pre/post-treatment PET scan with [18F]F-AraG radiotracer as well as biopsies for single cell, spatial transcriptomics and proteomics studies.
49
Hasanov, Elshad, Lesley Flynt, Rebecca Slack Tidwell, Hyunsoo Hwang, Roserika Brooks, Lauren Michelle King, Travis Solley, et al. "Phase 1b/2 study of combination 177Lu girentuximab plus cabozantinib and nivolumab in treatment naïve patients with advanced clear cell RCC." Journal of Clinical Oncology 41, no. 6_suppl (February 20, 2023): TPS749. http://dx.doi.org/10.1200/jco.2023.41.6_suppl.tps749.
Abstract:
TPS749 Background: Complete response (CR) is still a rare event in patients with advanced clear cell renal cell carcinoma (ccRCC). The combination of nivolumab plus cabozantinib was recently approved for the first-line treatment of ccRCC based on the CheckMate 9ER phase 3 study demonstrating improved progression-free survival (PFS) and objective response rate (ORR) in comparison to sunitinib. However, the CR rate was only 9%. Since the anti-tumor effects of immune checkpoint inhibitors are dependent on the presence of activated tumor-infiltrating T cells, drugs that could synergize with T cells’ anti-tumor activity can allow us to improve CR rates. Activation of the cGAS-STING pathway which is induced by radiation-induced DNA damage, is one promising mechanism that has been investigated. Many studies have shown that radiation treatment augments immune checkpoint inhibition. However, it is not always possible to radiate all metastatic lesions. Therefore, targeted peptide receptor radionuclide therapies, have been developed by conjugating radioisotopes to receptor binding analogs targeting specific cancer cell surface proteins, thereby delivering targeted radiation to cancer cells in the body with minimal damage to surrounding healthy cells. 177Lu girentuximab is the first antibody-radioisotope designed for ccRCC, targeting carbonic anhydrase 9-expressing cells, which includes >90% of ccRCC. It has been tested in metastatic ccRCC as a single agent and shown to be safe and effective in stabilizing disease in 57% of pts. In this study, we hypothesize that 177Lu girentuximab-induced DNA damage will potentiate the STING pathway, and this activation will synergize with nivolumab and cabozantinib to promote trafficking and infiltration of activated T cells to tumors and achieve higher CR rates. Methods: Up to 100 patients with treatment naïve, biopsy-proven ccRCC with adequate organ/marrow function with ≥1 evaluable lesion by RECIST 1.1 will be enrolled. A 5-patient safety lead-in will evaluate myelosuppression. Ongoing safety, and futility monitoring will employ a Bayesian approach. The sample size was chosen for reasonable operating characteristics to distinguish a CR rate (primary endpoint) of 18% as better than 9% using a beta(0.09, 0.91) prior. Secondary endpoints are ORR, PFS by RECIST 1.1, and overall survival. 177Lu-girentuximab 1480 MBq/m2 (61% of single agent MTD) will be administered every 12 weeks for up to 3 cycles. Starting with the second cycle, nivolumab and cabozantinib will be added at standard dose. To explore the effects of the treatment on inducing activated T cell infiltration, patients will undergo pre/post-treatment PET scan with [18F]F-AraG radiotracer as well as biopsies for single cell, spatial transcriptomics and proteomics studies. This investigator initiated trial is supported by Telix Pharmaceuticals and DOD grant W81XWH-22-1-0456.
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Hasanov, Elshad, Lesley Flynt, Rebecca Slack Tidwell, Hyunsoo Hwang, Roserika Brooks, Lauren King, Travis Solley, et al. "STARLITE 1: Phase 1b/2 study of combination 177Lu girentuximab plus cabozantinib and nivolumab in treatment naïve patients with advanced clear cell RCC." Oncologist 28, Supplement_1 (August 23, 2023): S13. http://dx.doi.org/10.1093/oncolo/oyad216.021.
Abstract:
Abstract Background Complete response (CR) is still a rare event in patients with advanced clear cell renal cell carcinoma (ccRCC). The combination of nivolumab plus cabozantinib was recently approved for the first-line treatment of ccRCC based on the CheckMate 9ER phase 3 study demonstrating improved progression-free survival (PFS) and objective response rate (ORR) in comparison to sunitinib. However, the CR rate was only 9%. Since the anti-tumor effects of immune checkpoint inhibitors are dependent on the presence of activated tumor-infiltrating T cells, drugs that could synergize with T cells’ anti-tumor activity can allow us to improve CR rates. Activation of the cGAS-STING pathway, the master regulator of anti-tumor immunity which is induced by radiation-induced DNA damage, is one promising mechanism that has been investigated. Many studies have shown that radiation treatment augments immune checkpoint inhibition. However, it is not always possible to radiate all metastatic lesions. Therefore, targeted peptide receptor radionuclide therapies (PRRT), have been developed by conjugating radioisotopes to receptor binding analogs targeting specific cancer cell surface proteins, thereby delivering targeted radiation to cancer cells in the body with minimal damage to surrounding healthy cells. 177Lu girentuximab is the first antibody-radioisotope designed for ccRCC, targeting carbonic anhydrase IX-expressing cells, which includes >90% of ccRCC. It has been tested in metastatic ccRCC as a single agent and shown to be safe and effective in stabilizing disease in 57% of pts. In this study, we hypothesize that 177Lu girentuximab-induced DNA damage will potentiate the STING pathway, and this activation will synergize with nivolumab and cabozantinib to promote trafficking and infiltration of activated T cells to tumors and achieve higher CR rates. Methods Up to 100 patients with treatment naïve, biopsy-proven ccRCC with adequate organ/marrow function with ≥1 evaluable lesion by RECIST 1.1 will be enrolled. A 5-patient safety lead-in will evaluate myelosuppression. Ongoing safety, and futility monitoring will employ a Bayesian approach. The sample size was chosen for reasonable operating characteristics to distinguish a CR rate (primary endpoint) of 18% as better than 9% using a beta(0.09, 0.91) prior. Secondary endpoints are objective response, PFS by RECIST 1.1, and overall survival. 177Lu-girentuximab 1480 MBq/m2 (61% of single agent MTD) will be administered every 12 weeks for up to 3 treatment cycles. Starting with the second cycle, nivolumab and cabozantinib will be added at standard dose. To explore the effects of the combination therapy on inducing activated T cell infiltration, patients will undergo pre/post-treatment PET scan with [18F]F-AraG radiotracer as well as biopsies for single cell, spatial transcriptomics and proteomics studies. This is an investigator initiated trial. Telix Pharmaceuticals provided drug and funding support. Also supported by DOD grant W81XWH-22-1-0456 CDMRP DOD Funding: yes