Academic literature on the topic 'Spatial omic'
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Journal articles on the topic "Spatial omic"
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Xu, Tinghui, and Kris Sankaran. "Interactive visualization of spatial omics neighborhoods." F1000Research 11 (July 18, 2022): 799. http://dx.doi.org/10.12688/f1000research.122113.1.
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Dimensionality reduction of spatial omic data can reveal shared, spatially structured patterns of expression across a collection of genomic features. We studied strategies for discovering and interactively visualizing low-dimensional structure in spatial omic data based on the construction of neighborhood features. We designed quantile and network-based spatial features that result in spatially consistent embeddings. A simulation compares embeddings made with and without neighborhood-based featurization, and a re-analysis of Keren et al., 2019 illustrates the overall workflow. We provide an R package, NBFvis, to support computation and interactive visualization for the proposed dimensionality reduction approach. Code and data for reproducing experiments and analysis are available on GitHub.
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Liu, Hailong, Xiaoguang Qiu, and Tao Jiang. "TAMI-74. SPATIOTEMPORAL MULTI-OMIC LANDSCAPE OF HUMAN MEDULLOBLASTOMA AT SINGLE CELL RESOLUTION." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi213—vi214. http://dx.doi.org/10.1093/neuonc/noab196.856.
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Abstract Medulloblastoma is the most common malignant childhood tumor type with distinct molecular subgroups. While advances in the comprehensive treatment have been made, the mortality in the high-risk group is still very high, driven by an incomplete understanding of cellular diversity. Here we use single-nucleus RNA expression, chromatin accessibility and spatial transcriptomic profiling to generate an integrative multi-omic map in 40 human medulloblastomas spanning all molecular subgroups and human postnatal cerebella, which is supplemented by the bulk whole genome and RNA sequences across 300 cases. This approach provides spatially resolved insights into the medulloblastoma and cerebellum transcriptome and epigenome with identification of distinct cell-type in the tumor microenvironment. Medulloblastoma exhibited three tumor subpopulations including the quiescent, the differentiated, and a stem-like (proliferating) population unique to cancer, which localized to an immunosuppressive-vascular niche. We identified and validated mechanisms of stem-like to differentiated process among the malignant cells that drive tumor progression. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing stem-like malignant cells as a hub for intercellular communication. Multiple features of potential immunosuppression and angiogenesis were observed, including Treg cells and endothelial cells co-localization in compartmentalized tumor stroma. Collectively, our study provides an integrative molecular landscape of human medulloblastoma and represents a reference to advance mechanistic and therapeutic studies of pediatric neuro-oncological disease.
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Kwon, Sang Ho, Madhavi Tippani, Abby Spangler, Heena Divecha, Kelsey Montgomery, Charles Bruce, Stephen Williams, et al. "Multi-Omic Approaches for Spatial and Pathological Registration of Gene Expression in Human Cortex." Biological Psychiatry 91, no. 9 (May 2022): S85—S86. http://dx.doi.org/10.1016/j.biopsych.2022.02.230.
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Gonçalves, Juliana P. L., Christine Bollwein, and Kristina Schwamborn. "Mass Spectrometry Imaging Spatial Tissue Analysis toward Personalized Medicine." Life 12, no. 7 (July 12, 2022): 1037. http://dx.doi.org/10.3390/life12071037.
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Novel profiling methodologies are redefining the diagnostic capabilities and therapeutic approaches towards more precise and personalized healthcare. Complementary information can be obtained from different omic approaches in combination with the traditional macro- and microscopic analysis of the tissue, providing a more complete assessment of the disease. Mass spectrometry imaging, as a tissue typing approach, provides information on the molecular level directly measured from the tissue. Lipids, metabolites, glycans, and proteins can be used for better understanding imbalances in the DNA to RNA to protein translation, which leads to aberrant cellular behavior. Several studies have explored the capabilities of this technology to be applied to tumor subtyping, patient prognosis, and tissue profiling for intraoperative tissue evaluation. In the future, intercenter studies may provide the needed confirmation on the reproducibility, robustness, and applicability of the developed classification models for tissue characterization to assist in disease management.
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Hsieh, James J., Natalia Miheecheva, Akshaya Ramachandran, Yang Lyu, Ilia Galkin, Viktor Svekolkin, Ekaterina Postovalova, et al. "Integrated single-cell spatial multi-omics of intratumor heterogeneity in renal cell carcinoma." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): e17106-e17106. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e17106.
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e17106 Background: Clear cell renal cell carcinoma (ccRCC) exhibits conspicuous intratumor heterogeneity (ITH) - a driver of tumor evolution and metastasis. ITH in RCC has been studied extensively with bulk tumor DNA sequencing, which lacks the ability to integrate single cell resolution data, spatial architecture, and microenvironment composition. Therefore, we analyzed primary ccRCC tumors at multiple biopsy sites with CyTOF, multiplex immunofluorescence (MxIF), whole exome sequencing (WES), RNA sequencing (RNA-seq), single nuclei RNA-seq (snRNA-seq), and whole genome bisulfite sequencing (WGBS). Methods: Primary ccRCC tumors collected from 6 patients (pts) were biopsied at multiple locations and subjected to CyTOF (n = 21 sites, 6 pts), MxIF (20 markers, n = 8 sites, 3 pts), WES (n = 8 sites, 3 pts), RNA-seq (n = 8 sites, 3 pts), snRNA-seq (n = 8 sites, 3 pts), and WGBS (n = 8 sites, 3 pts), enabling integrated multi-omics analysis. MxIF, CyTOF, and genomic/transcriptomic analyses were performed by BostonGene. Results: Genomic intratumor (IT) evolution of ccRCC cells was tracked with WES, and subclonal distribution of SETD2, STAG2, TSC2 and PBRM1 mutations was observed in different IT regions. Different regions of the same tumor were similar, whereas individual patient tumors were distinct according to tumor microenvironment cellular composition measured by CyTOF or deconvoluted from RNA-seq. The cellular deconvolution of the ccRCC tumors reconstructed from RNA-seq correlated with CyTOF, snRNA-seq and WGBS, showing high concordance among the methods. The promoter CpG island methylation levels, averaged across all genes, positively correlated with ccRCC grade. MxIF revealed spatial IT heterogeneity in the distribution of immune infiltrate components. Macrophages and T cells dispersed among malignant cells; whereas, T cells formed clusters at unique tumor margins. Conclusions: The utilization of multi-omics methods produced a high-resolution portrait of the ccRCC tumor composition and identified differential ITH among regions within the primary tumors or among individual primary tumors. This study demonstrated strong concordance among the different technologies, suggesting that tumor deconvolution by bulk RNA-seq might be clinically applicable for ccRCC tumors. MxIF analysis enabled a fine elucidation of the spatial relationships among the tumor and the immune and stromal cells, missed by common omic platforms. Integrated single cell multi-omics could render specific pathobiological and therapeutic insights that impact treatment decisions.
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Kulasinghe, Arutha, James Monkman, Honesty Kim, Aaron Mayer, Ahmed Mehdi, Nicholas Matigian, Marie Cumberbatch, et al. "Abstract 2036: Multi-omic dissection of immunotherapy response groups in non-small cell lung cancer (NSCLC)." Cancer Research 82, no. 12_Supplement (June 15, 2022): 2036. http://dx.doi.org/10.1158/1538-7445.am2022-2036.
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Abstract Immunotherapies have led to long term benefits in a subset of non-small cell lung cancer (NSCLC) patients. Developing predictive biomarkers of response to therapy is currently an unmet clinical need. The composition of the cellular content of the tumour microenvironment (TME) is an important characteristic driving treatment resistance. In this study, we utilised spatial transcriptomics methods, including Nanostring digital spatial profiling (DSP) and multiplex IHC, to define the tumour/stroma (compartment) specific proteome and transcriptome from a cohort of 2nd line immunotherapy treated NSCLC patients. We identified by mIHC that CD68+ macrophages with PD1+, FoxP3+ cells is significantly enriched in immunotherapy resistant tumours (p=0.012). Moreover, IL2 mRNA (p=0.001) in the stromal compartment was significantly increased in patients that were sensitive to ICI therapy, whilst CTLA-4 and IDO-1 were suppressed in responsive patients. Tumour compartment localised CD44 was depleted in the responder group and corresponded inversely with higher stromal expression of one of its ligands, SPP1 (p=0.008). Orthogonal validation of CD44 by multiplex immunofluorescence confirmed both its association with response and localisation to tumour cells rather than immune cell infiltrate. Cox survival analysis showed that tumour compartment CD44 expression was associated with a poorer prognosis (HR=1.61, p=0.01) whilst stromal localisation of CTLA-4 (HR=1.78, p=0.003) and ARG1 (HR=2.37, p=0.01) were associated with poorer outcome. Through a multi-omics approach, we demonstrate the utility of spatial mapping of NSCLC tumours and provide evidence for the role of a number of compartment-specific biomarkers which may aid in identifying those likely to respond to immunotherapy. Citation Format: Arutha Kulasinghe, James Monkman, Honesty Kim, Aaron Mayer, Ahmed Mehdi, Nicholas Matigian, Marie Cumberbatch, Milan Bhagat, Rahul Ladwa, Scott Mueller, Mark Adams, Ken O'Byrne. Multi-omic dissection of immunotherapy response groups in non-small cell lung cancer (NSCLC) [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 2036.
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Lou, Emil, Katherine Ladner, Kerem Wainer-Katsir, Karina Deniz, Yaara Porat, Boris Brant, Shiri Davidi, et al. "Abstract 2037: Spatial omic changes of malignant pleural mesothelioma following treatment using tumor-treating fields." Cancer Research 82, no. 12_Supplement (June 15, 2022): 2037. http://dx.doi.org/10.1158/1538-7445.am2022-2037.
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Abstract Background: Application of alternating-electric fields as cancer-directed therapy known as Tumor-Treating Fields (TTFields) has been shown to be effective by exerting dipole alignment forces on polar microtubule subunits and dielectrophoretic forces in the cytokinetic furrow. This effect results in disruption of mitosis at the cellular level, and at the clinical level with significantly prolonged overall survival of patients with glioblastoma and malignant pleural mesothelioma (MPM). The molecular alterations that occur at the genomic and transcriptomic levels following TTFields treatment are unknown. We applied a spatial omics approach to elucidate spatial intratumoral effects of TTFields at the molecular level in regions of interest (ROI) in a mouse model of MPM. Methods: Eight Balb/C mice were injected with AB1 MPM cells until sizable tumors were observed (2-3 weeks). TTFields were applied, with heat sham used as a negative control. After 14 days (6 days of treatment, 2 days of rest, then 6 more days of treatment) tumors were resected, fixed and paraffin embedded. Following the Nanostring GeoMx protocol, thin sections of all eight tumors were placed on a slide, and incubated with both Ki-67 antibodies, and a GeoMx Mouse Cancer Transcriptome Atlas RNA probe set. Using Ki-67 staining as a guide, 12 ROIs were selected across each tumor to capture intratumoral heterogeneity, including the core and periphery of each tumor The DSP barcoded RNA probes were cleaved, sequenced and analyzed. We compared differential expression of subset gene classes of TTFields vs heat sham treated tumors; results were further stratified into Ki-67 high and low subsets for each sample. Results were assessed by Gene Set Enrichment. Results: Sham-treated tumors grew to over 300 mm3; TTFields-treated tumors averaged 100 mm3, confirming anti-tumor effect. Gene Set Enrichment Analysis uncovered upregulation of genes associated with interferon-alpha and -gamma responses in TTFields-treated tumors, which also displayed downregulation of pathway components associated with glycolysis, mTOR signaling, oxidative phosphorylation, cell invasion, hypoxia, and TNF-alpha signaling. Spatial analysis detected a heterogeneous response and differential expression between different portions of tumors. Conclusions: TTFields application induces clear patterns of differential expression in the transcriptome of treated tumors, including an increasingly immune-stimulated tumor microenvironment that also affects molecular pathways critical to cellular proliferation and invasion. These findings point the way toward improved understanding of timing and sequences of TTFields in relation to systemic cytotoxic, targeted, and immune modulation forms of therapeutic strategies. Our finding of upregulated immune response implicates TTFields as a potential synergistic tactic when coupled with immunotherapeutic approaches. Citation Format: Emil Lou, Katherine Ladner, Kerem Wainer-Katsir, Karina Deniz, Yaara Porat, Boris Brant, Shiri Davidi, Yuki Padmanabhan, Phillip Wong, Amrinder Nain, Clifford J. Steer, Moshe Giladi. Spatial omic changes of malignant pleural mesothelioma following treatment using tumor-treating fields [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 2037.
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Johnson, Brett E., Allison L. Creason, Jayne M. Stommel, Jamie M. Keck, Swapnil Parmar, Courtney B. Betts, Aurora Blucher, et al. "An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer." Cell Reports Medicine 3, no. 2 (February 2022): 100525. http://dx.doi.org/10.1016/j.xcrm.2022.100525.
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Langston, Jordan C., Michael T. Rossi, Qingliang Yang, William Ohley, Edwin Perez, Laurie E. Kilpatrick, Balabhaskar Prabhakarpandian, and Mohammad F. Kiani. "Omics of endothelial cell dysfunction in sepsis." Vascular Biology 4, no. 1 (May 1, 2022): R15—R34. http://dx.doi.org/10.1530/vb-22-0003.
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During sepsis, defined as life-threatening organ dysfunction due to dysregulated host response to infection, systemic inflammation activates endothelial cells and initiates a multifaceted cascade of pro-inflammatory signaling events, resulting in increased permeability and excessive recruitment of leukocytes. Vascular endothelial cells share many common properties but have organ-specific phenotypes with unique structure and function. Thus, therapies directed against endothelial cell phenotypes are needed to address organ-specific endothelial cell dysfunction. Omics allow for the study of expressed genes, proteins and/or metabolites in biological systems and provide insight on temporal and spatial evolution of signals during normal and diseased conditions. Proteomics quantifies protein expression, identifies protein–protein interactions and can reveal mechanistic changes in endothelial cells that would not be possible to study via reductionist methods alone. In this review, we provide an overview of how sepsis pathophysiology impacts omics with a focus on proteomic analysis of mouse endothelial cells during sepsis/inflammation and its relationship with the more clinically relevant omics of human endothelial cells. We discuss how omics has been used to define septic endotype signatures in different populations with a focus on proteomic analysis in organ-specific microvascular endothelial cells during sepsis or septic-like inflammation. We believe that studies defining septic endotypes based on proteomic expression in endothelial cell phenotypes are urgently needed to complement omic profiling of whole blood and better define sepsis subphenotypes. Lastly, we provide a discussion of how in silico modeling can be used to leverage the large volume of omics data to map response pathways in sepsis.
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O'Byrne, Kenneth John, James Monkman, Honesty Kim, Marie Cumberbatch, Milan Bhagat, Rahul Ladwa, Mark N. Adams, and Arutha Kulasinghe. "Multi-omic and spatial dissection of immunotherapy response groups in non–small cell lung cancer (NSCLC)." Journal of Clinical Oncology 40, no. 16_suppl (June 1, 2022): 8544. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.8544.
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8544 Background: Immune checkpoint inhibitors (ICI) have shown durable benefit in a subset of non-small cell lung cancer (NSCLC) patients. The composition of the tumour microenvironment (TME) is becomingly increasingly recognised as an important factor to predict response to therapy. Methods: Here, we applied digital spatial profiling of the tumour and stromal compartments from a 2nd line NSCLC ICI-treated cohort (n = 41 patient) and standard of care (SOC), platinum treated NSCLC cohort (n = 47), to identify tissue-based signatures of response to therapy. Results: We demonstrate by mIHC that the interaction of CD68+ macrophages with PD1+, FoxP3+ cells is significantly enriched in ICI refractory tumours (p = 0.012). Patients sensitive to ICI therapy expressed higher levels of IL2 receptor alpha (CD25, p = 0.028) within the tumour compartments, which corresponded with the increased expression of IL2 mRNA (p = 0.001) within their stroma. Immuno-inhibitory markers CTLA-4 (p = 0.021) and IDO-1 (p = 0.023) were supressed in ICI-responsive patients. Tumour CD44 (p = 0.02) was depleted in the response group and corresponded inversely with significantly higher stromal expression of one of its ligands, SPP1 (osteopontin, p = 0.008). Analysis of dysregulated transcripts indicated the potential inhibition of stromal interferon-gamma (IFNγ) activity, estrogen-receptor and Wnt-1 signalling activity within the tumour cells of ICI responsive patients. Cox survival analysis indicated tumour CD44 expression was associated with poorer prognosis (HR = 1.61, p = 0.01), consistent with its depletion in ICI sensitive patients. Similarly, stromal CTLA-4 (HR = 1.78, p = 0.003) and MDSC/M2 macrophage marker ARG1 (HR = 2.37, p = 0.01) were associated with poorer outcome while BAD (HR = 0.5, p = 0.01) appeared protective. The SOC cohort paralleled similar roles for immune checkpoints and pro-apoptotic markers, with LAG3 (HR = 3.81, p = 0.04) indicating poorer outcome, and BIM (HR = 0.16, p = 0.014) with improved outcome. Interestingly, stromal mRNA for E-selectin (HR = 652, p = 0.001), CCL17 (HR = 70, p = 0.006) and MTOR (HR = 1065, p = 0.008) were highly associated with poorer outcome in ICI treated patients, indicating pro-tumourigenic features in the tumour microenvironment that may facilitate ICI resistance. Conclusions: Through multi-modal approaches, we have dissected the characteristics of NSCLC treatment groups and provide evidence for the role of several markers including IL2, CD25, CD44 and SPP1 in the efficacy of current generations of ICI therapy.
Dissertations / Theses on the topic "Spatial omic"
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DENTI, VANNA. "Development of multi-omic mass spectrometry imaging approaches to assist clinical investigations." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/365169.
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Con il termine di –omica spaziale si intende l’insieme di diverse tecniche che consentono di rilevare alterazioni significative delle biomolecole all’interno dei loro tessuti d’origine o delle strutture cellulari, permettendo quindi di integrare ed ampliare la comprensione dei cambiamenti biologici che si verificano in tessuti patologici complessi ed eterogenei, come il cancro. Tuttavia, per comprendere appieno la complessità e le dinamiche al di là delle condizioni patologiche, è necessario studiare e integrare diverse analisi molecolari, come quelle di lipidi e glicani, in modo da ottenere un’istantanea molecolare il più completa ed estesa possibile della malattia. Tra le tecniche di -omica spaziale, quella di desorbimento e ionizzazione laser assistiti da matrice (MALDI) abbinata alla spettrometria di massa imaging (MSI), permette lo studio della componente molecolare del tessuto patologico tramite un approccio multiplex, che permette di esaminare diverse centinaia di biomolecole in una singola analisi. Pertanto, l’analisi MALDI-MSI viene utilizzata per studi -omici spaziali di proteine, peptidi e N-glicani su campioni di tessuti clinici fissati in formalina e inclusi in paraffina (FFPE). Per quanto riguarda i lipidi, invece, questo tipo di analisi è sempre stato considerato poco efficace su campioni FFPE a causa della perdita di una grande quantità di contenuto lipidico durante le fasi di lavaggio con solventi organici, mentre i restanti lipidi resistenti ai solventi sono inaccessibili poiché trattenuti nei legami incrociati della formalina.
In questi tre anni di dottorato, abbiamo sviluppato nuovi approcci MALDI-MSI per l'analisi spaziale multi-omica su campioni di tessuto clinico FFPE.
Le prime tre pubblicazioni riportate in questa tesi si sono concentrate sullo sviluppo di protocolli MALDI-MSI per lipidi in campioni FFPE. In particolare, due di essi descrivono il metodo di preparazione del campione per la rilevazione di ioni di fosfolipidi carichi positivamente, principalmente fosfatidilcoline (PC), in campioni clinici di carcinoma renale a cellule chiare (ccRCC) e in un modello di xenotrapianto di cancro al seno. La terza pubblicazione riporta la possibilità di utilizzare ioni di fosfolipidi carichi negativamente, principalmente fosfatidilinositoli (PI), per definire firme lipidiche in grado di distinguere i gradi di tumore del colon-retto che presentano diverse quantità di linfociti infiltranti il tumore (TIL).
Il lavoro finale propone un originale metodo MALDI-MSI multi-omico per l'analisi sequenziale di lipidi, N-glicani e peptidi triptici su una singola sezione FFPE. In particolare, il metodo è stato inizialmente implementato su replicati tecnici di cervello murino e successivamente utilizzato su campioni di ccRCC, come ulteriore prova, ottenendo una caratterizzazione più completa del tessuto tumorale grazie alla combinazione delle informazioni molecolari.
Complessivamente, questi risultati aprono la strada a un nuovo approccio multi-omico spaziale basato sulla spettrometria di massa imaging (MSI) che è in grado di restituire un ritratto molecolare più ampio e più preciso della malattia.The field of spatial omics defines the gathering of different techniques that allow the detection of significant alterations of biomolecules in the context of their native tissue or cellular structures. As such, they extend the landscape of biological changes occurring in complex and heterogeneous pathological tissues, such as cancer. However, additional molecular levels, such as lipids and glycans, must be studied to define a more comprehensive molecular snapshot of disease and fully understand the complexity and dynamics beyond pathological condition. Among the spatial-omics techniques, matrix-assisted laser desorption/ionisation (MALDI)-mass spectrometry imaging (MSI) offers a powerful insight into the chemical biology of pathological tissues in a multiplexed approach where several hundreds of biomolecules can be examined within a single experiment. Thus, MALDI-MSI has been readily employed for spatial omics studies of proteins, peptides and N-Glycans on clinical formalin-fixed paraffin-embedded (FFPE) tissue samples. Conversely, MALDI-MSI analysis of lipids has always been considered not feasible on FFPE samples due to the loss of a great amount of lipid content during washing steps with organic solvents, with the remaining solvent-resistant lipids being involved in the formalin cross-links. In this three-year thesis work, novel MALDI-MSI approaches for spatial multi-omics analysis on clinical FFPE tissue samples were developed. The first three publications reported in this thesis focused on the development of protocols for MALDI-MSI of lipids in FFPE samples. In particular, two of them describe a sample preparation method for the detection of positively charged phospholipids ions, mainly phosphatidylcholines (PCs), in clinical clear cell Renal Cell Carcinoma (ccRCC) samples and in a xenograft model of breast cancer. The third publication reports the possibility to use negatively charged phospholipids ions, mainly phosphatidylinositols (PIs), to define lipid signatures able to distinguish colorectal cancers with different amount of tumour infiltrating lymphocytes (TILs). The final work proposes a unique multi-omic MALDI-MSI method for the sequential analysis of lipids, N-Glycans and tryptic peptides on a single FFPE section. Specifically, the method feasibility was first established on murine brain technical replicates. The method was consequently used on ccRCC samples, as a proof of concept, assessing a more comprehensive characterisation of the tumour tissue when combining the multi-level molecular information. Altogether, these findings pave the way for new MSI-based spatial multi-omics approach aiming at an extensive and more precise molecular portrait of disease.
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van, den Bruck David. "Spatial omics in neuronal cells - what goes where and why?" Doctoral thesis, Humboldt-Universität zu Berlin, 2019. http://dx.doi.org/10.18452/20232.
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Intrazelluläre Protein- und RNA-Lokalisation ist ein lebenswichtiger molekularer Mechanismus. Ihm unterliegen sowohl die äußere Gestaltung der Zellform, Zellagilität, zelluläre Differenzierung sowie die intra- sowie interzelluläre Kommunikation. Diverse Krankheiten werden mit Fehlfunktionen des intrazellulären Molekültransportes assoziiert und es existieren unzählige Beispiele für bekannte Wege des intrazellulären Protein- und RNA-Transportes. Allerdings ist die globale Komposition lokaler Protein- und RNA-Reservoirs bisher kaum wissenschaftlich erforscht worden.
In dieser Studie beschreibe ich die Protein- sowie RNA-Kompositionen subzellulärer Fraktionen zweier neuronaler Zelltypen. Die Neuriten und Somata von Neuroblastoma-Zellen (N1E-115) und Ascl1 induzierten Neuronen (beides Mauszellen) wurden mechanisch voneinander separiert und mittels RNA-Sequenzierung und Massenspektrometrie auf ihre Bestandteile untersucht.
Die Verteilung von mRNAs korreliert signifikant mit der Verteilung der entsprechenden Proteine in Ascl1-iNs während in der Neuroblastoma Zelllinie N1E-115 kein solcher Trend nachgewiesen werden konnte. Der Vergleich zu Datensätzen von anderen Zellsystemen und Methoden zeigt, dass das lokale Proteom sowie das lokale Transkriptome und Translatome stark Zelltyp spezifisch ist.
Um den Einfluss lokaler Proteinbiosynthese auf die Komposition subzellulärer Proteinpools zu erheben, habe ich die Lokalisation neu synthetisierter Proteine untersucht. Es scheint, als sei die RNA-Lokalisation und lokale Translation von hoher Relevanz für die Protein-Lokalisation in diesen stark polarisierten Zellsystemen.
Des Weiteren stelle ich eine Methode vor, um de novo „zip codes“ in diesen neuronalen Zellsystemen zu identifizieren. Diese könnte ein elementar wichtiger Schritt sein, um Fehlfunktionen im interzellulären Molekültransport zu verstehen.Intracellular protein and RNA localization is one of the mayor players in the formation of cell shape, enabling cell agility, cellular differentiation and cell signaling. Various diseases are associated with malfunctions of intracellular molecule transport. There are many known pathways of how and why proteins and RNAs are transported within the cell and where they are located, though there is not much known about the global distribution of proteins and RNAs within the cell. In this study I apply a subcellular fractionation method coupled to multiple omics approaches to investigate the global distribution of mRNAs, noncoding RNAs and proteins in neuronal cells. Neurites and soma from mouse neuroblastoma cells (N1E-115) as well as from Ascl1 induced neurons (Ascl1-iNs) were isolated and the composition of the spatial proteome and transcriptome was examined. The localization of mRNAs correlates significantly with the localization of their corresponding protein products in Ascl1-iNs whereas it does not in the mouse neuroblastoma cell line N1E-115. Comparing these datasets with recently published data of other cell lines and methods it is clear, that the local proteome, transcriptome and translatome of neuronal cells is highly cell type specific. To investigate how spatial protein pools are established I analyzed local pools of newly synthesized proteins revealing that many proteins are synthesized on the spot. RNA localization therefore plays a crucial role in generating local protein pools in these highly polarized cell systems. Additionally, I propose a method to identify on a global scale de novo “zip codes” in these cell systems which would be a great step towards understanding malfunctions in molecule transport.
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Schmitz-Linneweber, Christian [Gutachter], Marina [Gutachter] Chekulaeva, and Matthias [Gutachter] Selbach. "Spatial omics in neuronal cells - what goes where and why? / Gutachter: Christian Schmitz-Linneweber, Marina Chekulaeva, Matthias Selbach." Berlin : Humboldt-Universität zu Berlin, 2019. http://d-nb.info/1200026233/34.
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Devaux, Stéphanie. "Spatio-temporal studies of the spinal cord injury through OMICs and physiological approaches." Thesis, Lille 1, 2016. http://www.theses.fr/2016LIL10073/document.
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Les lésions de la moelle épinière (LME) appartiennent aux troubles incurables du système nerveux central. Les symptômes cliniques sont la conséquence des modifications dégénératives liées principalement à une inflammation aiguë, à la démyélinisation des axones et la formation d’une cavité qui perturbe les voies axonales. Nous mimons la LME grâce à la technique de ballon compression au niveau thoracique Th8-9 chez le rat. Une première étude a montré une régionalisation des protéines sécrétées 3 jours après lésion avec au niveau rostral un profil neuroprotecteur et au niveau caudal un profil neuroinflammatoire et apoptotique. Une étude spatio-temporelle a ensuite été mené pour compléter ces premiers résultats. Nous avons mis en évidence une symétrie entre les segments rostral et caudal avec la présence de facteurs neurotrophiques mais également d’inhibiteur de croissance neuritique au niveau caudal (lectines et RhoA). Des immunoglobulines ont été identifiés et semblent être colocalisées avec certains neurones. L’utilisation de biomatériaux injectés au niveau de la lésion permet de combler la cavité mais aussi de servir de réseau pour une future croissance axonale. Les alginates ont la capacité de libérer des facteurs qui permettront de moduler l’inflammation et de promouvoir la repousse neuritique. Les premiers résultats concernant l’injection de l’inhibiteur de RhoA tendent à montrer une augmentation de la repousse neuritique et des vésicules synaptiques au sein de la lésion. L’ensemble de ces résultats ont clairement démontré une évolution spatio-temporelle du profil moléculaire et ont défini le segment caudal comme étant une potentielle cible de traitementSpinal cord injury (SCI) belongs to incurable disorders of the CNS. Primary damage and axonal disruption are followed by progressive cascade of secondary deleterious reactions. Although axonal regeneration is initiated, it is quickly repressed due to severe inflammation, lack of trophic support and inhibitory environment. In a balloon-compression SCI rat model the secretomes of the lesion segment and adjacent segments 3 days after SCI were studied and a regionalization of inflammatory and neurotrophic response between the rostral and caudal segments was highlighted. These results were complemented with spatiotemporal study of SCI. Rostral and caudal segments have shown the ability to regenerate due to the presence of immune cells with an anti-inflammatory and neurotrophic phenotype. However, a time lag occurs between segments, with a caudal segment near the lesion expressing inflammatory and apoptotic phenotype. This segment appears to be a potential target for future treatment. Indeed, this segment shows the presence of lectins and RhoA proteins but also the presence of antibodies colocalized with neurons. Therapeutic strategies have focused on the inhibition of these factors in addition to the use of biomaterials. Alginates fill the cavity and create a network facilitating axonal regrowth and have the ability to release factors which would modulate inflammation and stimulate regeneration. These data established spatiotemporal evolution and indicate that we can initiate regenerative processes in the caudal segment if trophic factors are added
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Buchard, Virginie. "Caractérisation du contenu atmosphérique en ozone et en aérosols au moyen de mesures spectrales dans l'UV : validation de l'instrument spatial OMI / AURA." Thesis, Lille 1, 2009. http://www.theses.fr/2009LIL10025/document.
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Depuis la découverte d'une diminution de la quantité d'ozone stratosphérique au milieu des années 1980, une surveillance de la couche d'ozone et de l'éclairement UV s'est mise en place à l'aide d'instruments au sol et spatiaux. Les mesures de rayonnement UV permettent d'une part de surveiller l'intensité de ce rayonnement arrivant au sol, et d'autre part de caractériser certains composés atmosphériques comme la quantité d'ozone et les aérosols. L'essentiel de ce travail concerne l'analyse et l'utilisation des mesures d'éclairement UV spectral effectuées sur deux sites de mesures au sol, à Villeneuve d'Ascq (VdA) et à Briançon. Nous avons poursuivi la restitution de la colonne totale d'ozone, ce qui nous a permis de disposer d'une série temporelle de plusieurs années. Nous avons également déterminé deux paramètres aérosols, l'épaisseur optique (AOT) et l'albédo de diffusion simple; les comparaisons avec les mesures photométriques du réseau AERONET/PHOTONS se sont révélées très satisfaisantes. Les données obtenues à partir de septembre 2004 nous ont permis de participer dans le cadre d'un projet de l'ESA, à la validation de l'instrument spatial OMI, destiné à effectuer une surveillance globale de l'ozone et de l'UV. Ce travail a permis d'établir que les produits ozone d'OMI sont bien restitués, alors que les éclairements UV spectral et érythémateux sont à utiliser avec précaution. A VdA, les comparaisons entre les AOT-OMI et les AOT restituées au sol sont peu satisfaisantes. De meilleurs accords ont été obtenus sur les sites photométriques impliqués dans la campagne AMMA en Afrique de l'Ouest, cette région étant sous l'influence de contenus élevés en aérosols absorbantsSince the discovery of the stratospheric ozone reduction in the middle of the 1980's, a monitoring of the ozone layer and UV irradiance was organized, using ground-based and satellite instruments. Measurements of UV radiation allow both to monitor the intensity of this radiation reaching the surface and to retrieve atmospheric compounds as content of ozone and aerosol characteristics. The main part of this work concerns the analysis and the use of UV spectral measurements performed at Villeneuve d'Ascq (VdA) and at Briançon. We continued the restitution of the total column of ozone that provides a multi-year record of this quantity. We determined two aerosol parameters, the aerosol optical thickness (AOT) and the single scattering albedo; comparisons with photometric measurements from the AERONET/PHOTONS network appeared very good. The data obtained from September 2004 enabled us to be involved within the framework of an ESA project in the validation of the OMI/AURA instrument, which is dedicated to a global monitoring of ozone and UV. We have established that the OMI ozone products are very well retrieved, whereas spectral and erythemal dose UV have to be used with caution. At VdA, the comparisons between OMI-AOT and those derived fram graund-based measurements are not satisfying. Better results were obtained at six sites located in WesternAfrica region during the AMMA campaign, this region being influenced by high loads of absorbing aerasols
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Chang, Chih-Wei, and 張至為. "Spatially resolved omics via photoredox catalysis." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/57mpy4.
Full textBooks on the topic "Spatial omic"
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Mcgourty, Kieran. Spatial Omics: Methods for Reconstructing the Spatial Heterogeneity of Biological Tissue. Elsevier Science & Technology Books, 2023.
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Siegel, Tiffany Porta. MALDI Mass Spectrometry Imaging: From Fundamentals to Spatial Omics. Royal Society of Chemistry, The, 2021.
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Siegel, Tiffany Porta. MALDI Mass Spectrometry Imaging: From Fundamentals to Spatial Omics. Royal Society of Chemistry, The, 2021.
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Siegel, Tiffany Porta. MALDI Mass Spectrometry Imaging: From Fundamentals to Spatial Omics. Royal Society of Chemistry, The, 2021.
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Pineda, Jesús, and Nathalie Reyns, eds. Larval Transport in the Coastal Zone: Biological and Physical Processes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198786962.003.0011.
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Larval transport is fundamental to several ecological processes, yet it remains unresolved for the majority of systems. We define larval transport, and describe its components, namely, larval behavior and the physical transport mechanisms accounting for advection, diffusion, and their variability. We then discuss other relevant processes in larval transport, including swimming proficiency, larval duration, accumulation in propagating features, episodic larval transport, and patchiness and spatial variability in larval abundance. We address challenges and recent approaches associated with understanding larval transport, including autonomous sampling, imaging, -omics, and the exponential growth in the use of poorly tested numerical simulation models to examine larval transport and population connectivity. Thus, we discuss the promises and pitfalls of numerical modeling, concluding with recommendations on moving forward, including a need for more process-oriented understanding of the mechanisms of larval transport and the use of emergent technologies.
Conference papers on the topic "Spatial omic"
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Martinez Martinez, Damian C., and Margarita S. Narducci. "Spatial Variation Prediction and Mapping of Soil Temperature." In 2020 Virtual Symposium in Plant Omics Sciences (OMICAS). IEEE, 2020. http://dx.doi.org/10.1109/omicas52284.2020.9535656.
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Schütt, Annette, Gerrit Kuhlmann, Ying Zhu, and Mark Wenig. "Analysis of temporal and spatial patterns of OMI NO2 data." In Hyperspectral Imaging and Sounding of the Environment. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/hise.2016.hm4e.2.
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Shepherd, Douglas. "Spatial '-omics' in large samples using high numerical aperture oblique plane microscopy." In Virtual 12th Light Sheet Fluorescence Microscopy Conference 2020. Royal Microscopical Society, 2020. http://dx.doi.org/10.22443/rms.lsfm2020.42.
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Anand, Jasdeep S., Roland J. Leigh, and Paul S. Monks. "High spatial resolution NO2tropospheric slant columns retrieved from OMI spatial-zoom spectra using an earthshine reference." In Second International Conference on Remote Sensing and Geoinformation of the Environment (RSCy2014), edited by Diofantos G. Hadjimitsis, Kyriacos Themistocleous, Silas Michaelides, and Giorgos Papadavid. SPIE, 2014. http://dx.doi.org/10.1117/12.2066154.
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Wenqi, Gao, Tan Suqing, and Zhou Jin. "Computer-generated hologram for reconstruction of unusual mode image." In Diffractive Optics and Micro-Optics. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/domo.1996.jtub.26.
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Usually in reconstruction of Fourier computer-generated hologram[FCGH] the lens is necessary to make imaging at finite distance instead of imaging at infinite originally. The reconstructed images are mutual inverted ( one upright image,another inverted image) both appear in a same plane. Whether the imaging lens in reconstruction FCGH will be able to omit? Whether two reconstructed images will be able to separate in spatial? Whether two images have an identical direction and different shape in the same plane? It is the motivation for us to do this study. Through theoretic analysis and experimental reconstruction these assume can be realized essentially.
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Eng, Christine L., Joe P. Yeong, Andy Nguyen, Amanda Y. Guo, Brenda Tay, Mei Mei Chang, Sherlly Lim, et al. "Abstract 3872: Spatial and multi-omics characterization of the tumor microenvironment in colorectal cancer." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-3872.
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Jie Jiang and Yong Zha. "Temporal-spatial distribution of tropospheric NO2 in China using OMI NO2 column measurements." In 2011 International Conference on Remote Sensing, Environment and Transportation Engineering (RSETE). IEEE, 2011. http://dx.doi.org/10.1109/rsete.2011.5964631.
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Bordignon, Pino, Alice Comberlato, Saska Brajkovic, and Diego Dupouy. "38 Fully automated spatial multi-omics analysis to map the tumor microenvironment with single-cell resolution." In SITC 37th Annual Meeting (SITC 2022) Abstracts. BMJ Publishing Group Ltd, 2022. http://dx.doi.org/10.1136/jitc-2022-sitc2022.0038.
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Madissoon, Elo, Amanda Oliver, Vitalii Kleshchevnikov, Anna Wilbrey-Clark, Krzysztof Polnski, Lira Mamanova, Liam Bolt, et al. "The multi-omics spatial lung atlas reveales new cell states and their functions in airway mesenchyme." In ERS Lung Science Conference 2022 abstracts. European Respiratory Society, 2022. http://dx.doi.org/10.1183/23120541.lsc-2022.260.
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Phan, Phong, David Highton, Ilias Tachtsidis, Martin Smith, and Clare Elwell. "A New Multichannel Broadband Near Infrared Spectroscopy System to Measure the Spatial Distribution of Cytochrome-c-Oxidase and Tissue Oxygenation." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/ots.2016.om4c.3.
Full textReports on the topic "Spatial omic"
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Pokrzywinski, Kaytee, Kaitlin Volk, Taylor Rycroft, Susie Wood, Tim Davis, and Jim Lazorchak. Aligning research and monitoring priorities for benthic cyanobacteria and cyanotoxins : a workshop summary. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41680.
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In 2018, the US Army Engineer Research and Development Center partnered with the US Army Corps of Engineers–Buffalo District, the US Environmental Protection Agency, Bowling Green State University, and the Cawthron Institute to host a workshop focused on benthic and sediment-associated cyanobacteria and cyanotoxins, particularly in the context of harmful algal blooms (HAB). Technical sessions on the ecology of benthic cyanobacteria in lakes and rivers; monitoring of cyanobacteria and cyanotoxins; detection of benthic and sediment-bound cyanotoxins; and the fate, transport, and health risks of cyanobacteria and their associated toxins were presented. Research summaries included the buoyancy and dispersal of benthic freshwater cyanobacteria mats, the fate and quantification of cyanotoxins in lake sediments, and spatial and temporal variation of toxins in streams. In addition, summaries of remote sensing methods, omic techniques, and field sampling techniques were presented. Critical research gaps identified from this workshop include (1) ecology of benthic cyanobacteria, (2) identity, fate, transport, and risk of cyanotoxins produced by benthic cyanobacteria, (3) standardized sampling and analysis protocols, and (4) increased technical cooperation between government, academia, industry, nonprofit organizations, and other stakeholders. Conclusions from this workshop can inform monitoring and management efforts for benthic cyanobacteria and their associated toxins.
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Fait, Aaron, Grant Cramer, and Avichai Perl. Towards improved grape nutrition and defense: The regulation of stilbene metabolism under drought. United States Department of Agriculture, May 2014. http://dx.doi.org/10.32747/2014.7594398.bard.
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The goals of the present research proposal were to elucidate the physiological and molecular basis of the regulation of stilbene metabolism in grape, against the background of (i) grape metabolic network behavior in response to drought and of (ii) varietal diversity. The specific objectives included the study of the physiology of the response of different grape cultivars to continuous WD; the characterization of the differences and commonalities of gene network topology associated with WD in berry skin across varieties; the study of the metabolic response of developing berries to continuous WD with specific attention to the stilbene compounds; the integration analysis of the omics data generated; the study of isolated drought-associated stress factors on the regulation of stilbene biosynthesis in plantaand in vitro. Background to the topic Grape quality has a complex relationship with water input. Regulated water deficit (WD) is known to improve wine grapes by reducing the vine growth (without affecting fruit yield) and boosting sugar content (Keller et al. 2008). On the other hand, irregular rainfall during the summer can lead to drought-associated damage of fruit developmental process and alter fruit metabolism (Downey et al., 2006; Tarara et al., 2008; Chalmers et al., 792). In areas undergoing desertification, WD is associated with high temperatures. This WD/high temperature synergism can limit the areas of grape cultivation and can damage yields and fruit quality. Grapes and wine are the major source of stilbenes in human nutrition, and multiple stilbene-derived compounds, including isomers, polymers and glycosylated forms, have also been characterized in grapes (Jeandet et al., 2002; Halls and Yu, 2008). Heterologous expression of stilbenesynthase (STS) in a variety of plants has led to an enhanced resistance to pathogens, but in others the association has not been proven (Kobayashi et al., 2000; Soleas et al., 1995). Tomato transgenic plants harboring a grape STS had increased levels of resveratrol, ascorbate, and glutathione at the expense of the anthocyanin pathways (Giovinazzo et al. 2005), further emphasizing the intermingled relation among secondary metabolic pathways. Stilbenes are are induced in green and fleshy parts of the berries by biotic and abiotic elicitors (Chong et al., 2009). As is the case for other classes of secondary metabolites, the biosynthesis of stilbenes is not very well understood, but it is known to be under tight spatial and temporal control, which limits the availability of these compounds from plant sources. Only very few studies have attempted to analyze the effects of different environmental components on stilbene accumulation (Jeandet et al., 1995; Martinez-Ortega et al., 2000). Targeted analyses have generally shown higher levels of resveratrol in the grape skin (induced), in seeded varieties, in varieties of wine grapes, and in dark-skinned varieties (Gatto et al., 2008; summarized by Bavaresco et al., 2009). Yet, the effect of the grape variety and the rootstock on stilbene metabolism has not yet been thoroughly investigated (Bavaresco et al., 2009). The study identified a link between vine hydraulic behavior and physiology of stress with the leaf metabolism, which the PIs believe can eventually lead to the modifications identified in the developing berries that interested the polyphenol metabolism and its regulation during development and under stress. Implications are discussed below.