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Heward, Joanne, and Stephen C. L. Gough. "Genetic Susceptibility to the Development of Autoimmune Disease." Clinical Science 93, no. 6 (December 1, 1997): 479–91. http://dx.doi.org/10.1042/cs0930479.
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1. Autoimmune diseases are common conditions which appear to develop in genetically susceptible individuals, with expression of disease being modified by permissive and protective environments. Familial clustering and data from twin studies provided the impetus for the search for putative loci. Both the candidate gene approach in population-based case-control studies and entire genome screening in families have helped identify susceptibility genes in a number of autoimmune diseases. 2. After the first genome screen in type 1 (insulin-dependent) diabetes mellitus it seems likely that most autoimmune diseases are polygenic with no single gene being either necessary or sufficient for disease development. Of the organ-specific autoimmune diseases, genome screens have now been completed in insulin-dependent diabetes mellitus and multiple sclerosis. Furthermore, the clustering of autoimmune diseases within the same individuals suggests that the same genes may be involved in the different diseases. This is supported by data showing that both HLA (human leucocyte antigen) and CTLA-4 (cytotoxic T-lymphocyte-associated-4) appear to be involved in the development of insulin-dependent diabetes mellitus and Graves' disease. 3. Genome screens have also been completed in some of the non-organ-specific autoimmune diseases including rheumatoid arthritis, inflammatory bowel disease and psoriasis. Many candidate genes have also been investigated although these are predominantly in population-based case-control studies. 4. Substantial progress has been made in recent years towards the identification of susceptibility loci in autoimmune diseases. The inconsistencies seen between case-control studies may largely be due to genetic mismatching between cases and controls in small datasets. Family-based association studies are being increasingly used to confirm genetic linkages and help with fine mapping strategies. It will, however, require a combination of biology and genetics, as has been necessary with the major histocompatibility complex in insulin-dependent diabetes mellitus, to identify primary aetiological mutations.
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Bischof, Jocelyn M., and Rachel Wevrick. "Genome-wide analysis of gene transcription in the hypothalamus." Physiological Genomics 22, no. 2 (July 14, 2005): 191–96. http://dx.doi.org/10.1152/physiolgenomics.00071.2005.
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As the genomic regions containing loci predisposing to obesity-related traits are mapped in human population screens and mouse genetic studies, identification of susceptibility genes will increasingly be facilitated by bioinformatic methods. We hypothesized that candidate genes can be prioritized by their expression levels in tissues of central importance in obesity. Our objective was to develop a combined bioinformatics and molecular paradigm to identify novel genes as candidates for murine or human obesity genetic modifiers based on their differential expression patterns in the hypothalamus compared with other murine tissues. We used bioinformatics tools to search publicly available gene expression databases using criteria designed to identify novel genes differentially expressed in the hypothalamus. We used RNA methods to determine their expression sites and levels of expression in the hypothalamus of the murine brain. We identified the chromosomal location of the novel genes in mice and in humans and compared these locations with those of genetic loci predisposing to obesity-related traits. We developed a search strategy that correctly identified a set of genes known to be important in hypothalamic function as well as a candidate gene for Prader-Willi syndrome that was not previously identified as differentially expressed in the hypothalamus. Using this same strategy, we identified and characterized a set of 11 genes not previously known to be differentially expressed in the murine hypothalamus. Our results demonstrate the feasibility of combined bioinformatics and molecular approaches to the identification of genes that are candidates for obesity-related disorders in humans and mice.
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Kim, Stuart K., Condor Nguyen, Andrew L. Avins, and Geoffrey D. Abrams. "Three genes associated with anterior and posterior cruciate ligament injury." Bone & Joint Open 2, no. 6 (June 1, 2021): 414–21. http://dx.doi.org/10.1302/2633-1462.26.bjo-2021-0040.r1.
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Aims The aim of this study was to screen the entire genome for genetic markers associated with risk for anterior cruciate ligament (ACL) and posterior cruciate ligament (PCL) injury. Methods Genome-wide association (GWA) analyses were performed using data from the Kaiser Permanente Research Board (KPRB) and the UK Biobank. ACL and PCL injury cases were identified based on electronic health records from KPRB and the UK Biobank. GWA analyses from both cohorts were tested for ACL and PCL injury using a logistic regression model adjusting for sex, height, weight, age at enrolment, and race/ethnicity using allele counts for single nucleotide polymorphisms (SNPs). The data from the two GWA studies were combined in a meta-analysis. Candidate genes previously reported to show an association with ACL injury in athletes were also tested for association from the meta-analysis data from the KPRB and the UK Biobank GWA studies. Results There was a total of 2,214 cases of ACL and PCL injury and 519,869 controls within the two cohorts, with three loci demonstrating a genome-wide significant association in the meta-analysis: INHBA, AEBP2, and LOC101927869. Of the eight candidate genes previously studied in the literature, six were present in the current dataset, and only COL3A1 (rs1800255) showed a significant association (p = 0.006). Conclusion Genetic markers in three novel loci in this study and one previously-studied candidate gene were identified as potential risk factors for ACL and PCL injury and deserve further validation and investigation of molecular mechanisms. Cite this article: Bone Jt Open 2021;2(6):414–421.
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Mescheriakova, Julia Y., Annemieke JMH Verkerk, Najaf Amin, André G. Uitterlinden, Cornelia M. van Duijn, and Rogier Q. Hintzen. "Linkage analysis and whole exome sequencing identify a novel candidate gene in a Dutch multiple sclerosis family." Multiple Sclerosis Journal 25, no. 7 (June 6, 2018): 909–17. http://dx.doi.org/10.1177/1352458518777202.
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Background: Multiple sclerosis (MS) is a complex disease resulting from the joint effect of many genes. It has been speculated that rare variants might explain part of the missing heritability of MS. Objective: To identify rare coding genetic variants by analyzing a large MS pedigree with 11 affected individuals in several generations. Methods: Genome-wide linkage screen and whole exome sequencing (WES) were performed to identify novel coding variants in the shared region(s) and in the known 110 MS risk loci. The candidate variants were then assessed in 591 MS patients and 3169 controls. Results: Suggestive evidence for linkage was obtained to 7q11.22-q11.23. In WES data, a rare missense variant p.R183C in FKBP6 was identified that segregated with the disease in this family. The minor allele frequency was higher in an independent cohort of MS patients than in healthy controls (1.27% vs 0.95%), but not significant (odds ratio (OR) = 1.33 (95% confidence interval (CI): 0.8–2.4), p = 0.31). Conclusion: The rare missense variant in FKBP6 was identified in a large Dutch MS family segregating with the disease. This association to MS was not found in an independent MS cohort. Overall, genome-wide studies in larger cohorts are needed to adequately investigate the role of rare variants in MS risk.
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Samuel, Nardin, and Ivan Radovanovic. "Genetic basis of intracranial aneurysm formation and rupture: clinical implications in the postgenomic era." Neurosurgical Focus 47, no. 1 (July 2019): E10. http://dx.doi.org/10.3171/2019.4.focus19204.
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OBJECTIVEDespite the prevalence and impact of intracranial aneurysms (IAs), the molecular basis of their pathogenesis remains largely unknown. Moreover, there is a dearth of clinically validated biomarkers to efficiently screen patients with IAs and prognosticate risk for rupture. The aim of this study was to survey the literature to systematically identify the spectrum of genetic aberrations that have been identified in IA formation and risk of rupture.METHODSA literature search was performed using the Medical Subject Headings (MeSH) system of databases including PubMed, EMBASE, and Google Scholar. Relevant studies that reported on genetic analyses of IAs, rupture risk, and long-term outcomes were included in the qualitative analysis.RESULTSA total of 114 studies were reviewed and 65 were included in the qualitative synthesis. There are several well-established mendelian syndromes that confer risk to IAs, with variable frequency. Linkage analyses, genome-wide association studies, candidate gene studies, and exome sequencing identify several recurrent polymorphic variants at candidate loci, and genes associated with the risk of aneurysm formation and rupture, including ANRIL (CDKN2B-AS1, 9p21), ARGHEF17 (11q13), ELN (7q11), SERPINA3 (14q32), and SOX17 (8q11). In addition, polymorphisms in eNOS/NOS3 (7q36) may serve as predictive markers for outcomes following intracranial aneurysm rupture. Genetic aberrations identified to date converge on posited molecular mechanisms involved in vascular remodeling, with strong implications for an associated immune-mediated inflammatory response.CONCLUSIONSComprehensive studies of IA formation and rupture have identified candidate risk variants and loci; however, further genome-wide analyses are needed to identify high-confidence genetic aberrations. The literature supports a role for several risk loci in aneurysm formation and rupture with putative candidate genes. A thorough understanding of the genetic basis governing risk of IA development and the resultant aneurysmal subarachnoid hemorrhage may aid in screening, clinical management, and risk stratification of these patients, and it may also enable identification of putative mechanisms for future drug development.
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Jensen, Lea Møller, Barbara Ann Halkier, and Meike Burow. "How to discover a metabolic pathway? An update on gene identification in aliphatic glucosinolate biosynthesis, regulation and transport." Biological Chemistry 395, no. 5 (May 1, 2014): 529–43. http://dx.doi.org/10.1515/hsz-2013-0286.
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Abstract Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all biosynthetic genes, as well as the first sets of regulators and transporters, have been identified. An array of approaches, i.e. classical mapping, quantitative trait loci (QTL) mapping, eQTL mapping, co-expression, genome wide association studies (GWAS), mutant screens and phylogenetic analyses, has been exploited to increase the number of identified genes. Here we summarize the lessons learned from the different approaches used over the years with the aim to help designing and combining new approaches in the future.
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Webster, Hollie, Gabriel Keeble, Bernard Dell, John Fosu-Nyarko, Y. Mukai, Paula Moolhuijzen, Matthew Bellgard, et al. "Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance." Functional Plant Biology 39, no. 7 (2012): 569. http://dx.doi.org/10.1071/fp12083.
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In wheat (Triticum aestivum L.) drought-induced pollen sterility is a major contributor to grain yield loss and is caused by the downregulation of the cell wall invertase gene IVR1. The IVR1 gene catalyses the irreversible hydrolysis of sucrose to glucose and fructose, the essential energy substrates which support pollen development. Downregulation of IVR1 in response to drought is isoform specific and shows variation in temporal and tissue-specific expression. IVR1 is now prompting interest as a candidate gene for molecular marker development to screen wheat germplasm for improved drought tolerance. The aim of this study was to define the family of IVR1 genes to enable: (1) individual isoforms to be assayed in gene expression studies; and (2) greater accuracy in IVR1 mapping to the wheat genetic map and drought tolerance QTL analysis. Using a cell wall invertase-specific motif as a probe, wheat genomics platforms were screened for the presence of unidentified IVR1 isoforms. Wheat genomics platforms screened included the IWGSC wheat survey sequence, the wheat D genome donor sequence from Aegilops tauschii Coss, and the CCG wheat chromosome 3B assembly: contig506. Chromosome-specific sequences homologous to the query motif were isolated and characterised. Sequence annotation results showed five previously unidentified IVR1 isoforms exist on multiple chromosome arms and on all three genomes (A, B and D): IVR1–3A, IVR1–4A, IVR1–5B, IVR1.2–3B and IVR1-5D. Including three previously characterised IVR1 isoforms (IVR1.1–1A, IVR1.2–1A and IVR1.1–3B), the total number of isoform gene family members is eight. The IVR1 isoforms contain two motifs common to cell wall invertase (NDPN and WECPDF) and a high degree of conservation in exon 4, suggesting conservation of functionality. Sequence divergence at a primary structure level in other regions of the gene was evident amongst the isoforms, which likely contributes to variation in gene regulation and expression in response to water deficit within this subfamily of IVR1 isoforms in wheat.
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Sheffer, Michal, Yiguo Hu, Ophir Shalem, Neville Sanjana, Eugen Dhimolea, Subhashis Sarkar, Megan A. Bariteau, et al. "Genome-Scale Crispr-Cas9 Knockout Studies Reveal Mutifactorial and Functionally Overlapping Mechanisms of Myeloma Cell Resistance to Proteasome Inhibition." Blood 124, no. 21 (December 6, 2014): 273. http://dx.doi.org/10.1182/blood.v124.21.273.273.
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Abstract Acquired or de novo resistance to established and investigational therapies represents a major clinical challenge for multiple myeloma (MM) and other neoplasias. Despite extensive efforts, clinically-validated molecular markers that predict for proteasome inhibitor (PSI) resistance in most MM patients remain elusive. This challenge is partly due to limited availability so far of molecular data on MM patients before the start of PSI treatment vs. immediately after resistance to it develops; this challenge may also reflect the heterogeneity of the complex molecular mechanisms regulating MM cell response to PSIs. We hypothesized that resistance to PSIs can be mediated by disruption of several functionally overlapping genes, and that the prevalence of any of these lesions may be too low to detect in datasets available thus far. To examine this latter hypothesis, we performed a genome-wide screen for genes whose loss confers to MM cells resistance against bortezomib, through the use of the CRISPR (clustered regularly interspaced short palindromic repeats)–associated nuclease Cas9 system. Specifically RPMI-8226 MM cells were transduced with lentiviral construct for Cas9 nuclease, followed by lentiviral delivery of a genome-scale pooled library of 123,411 single-guide RNAs (sgRNAs), which selectively align to target sequences at the 5′ constitutive exons of 18,080 genes and direct the Cas9 nuclease to cause double-stranded cleavage and loss of function of the respective gene. From the pool of MM cells transduced with the sgRNA library and treated with bortezomib, treatment-resistant cells were processed for deep sequencing, to identify enriched sgRNAs and their corresponding genes. We identified that loss-of-function of 33 candidate genes is associated with bortezomib resistance. We observed a high level of consistency between independent sgRNAs targeting the same gene, as well as a high rate of hit confirmation across different biological replicates. Notably, this set of candidate bortezomib-resistance genes was distinct from the "hits" we identified through a parallel CRISPR screen on the same cell line for resistance to a different targeted therapy (namely the bromodomain inhibitor JQ1), supporting the ability of this approach to identify treatment-specific resistance genes. These candidate bortezomib-resistance genes have documented or presumed roles in the regulation of extrinsic and intrinsic apoptotic cascades, autophagy, Toll-like receptor and NF-kappaB signaling, aggresome function, heat shock protein expression, chromatin remodeling, nutrient sensing, and tumor suppressor gene networks. Importantly, information from several publically available molecular profiling datasets converge to support the putative clinical relevance of these genes. For instance, gene expression data from tumor cells of bortezomib-naive patients with advanced MM revealed several transcriptional signatures of these candidate genes (defined by low transcript levels for any of the genes in the signature) which correlated with shorter time to disease progression after treatment with bortezomib (p<0.01, log-rank test), but not dexamethasone (p>0.426). Congruent with these findings, the highly bortezomib-responsive clinical setting of newly-diagnosed MM is associated with low cumulative frequency of mutations of these bortezomib-resistance genes (e.g. cumulative mutation rate of 3.9%, 95% confidence interval [CI] 1.25-6.55%). Notably, in other malignancies that are typically PSI-resistant, a higher cumulative frequency of such lesions is observed (average of ~28%, range 0-76%, 95% CI 22.46-32.70%; 57 datasets from 20+ neoplasias examined). In summary, this first application of the CRISPR/Cas9-based technology in MM illustrates its power to interrogate gene function on a genome-wide scale. This approach identifies bortezomib-resistance genes that are associated with pathways linked with the regulation of proteasome inhibitor response. Results from molecularly-annotated clinical samples converge to support a possible role for these genes in bortezomib resistance. This experience supports the value of CRISPR/Cas9-based studies to dissect the molecular mechanisms of treatment resistance in MM and other hematologic neoplasias (* equal contribution of M.S. and Y.H.). Disclosures Shalem: Broad Institute: Patent application for CRISPR technology Patents & Royalties. Sanjana:Broad Institute: Patent application for CRISPR technology Patents & Royalties. Zhang:Broad Institute: Patent application for CRISPR technology Patents & Royalties. Mitsiades:Johnson & Johnson: Research Funding; Amgen: Research Funding; Celgene: Consultancy, Honoraria; Millennium Pharmaceuticals: Consultancy, Honoraria.
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DOU, BINGDE, BEIWEI HOU, HAIMING XU, XIANGYANG LOU, XIAOFEI CHI, JINBIN YANG, FANG WANG, ZHONGFU NI, and QIXIN SUN. "Efficient mapping of a female sterile gene in wheat (Triticum aestivum L.)." Genetics Research 91, no. 5 (October 2009): 337–43. http://dx.doi.org/10.1017/s0016672309990218.
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SummaryStudies on inheritance of fertility are of great importance in wheat breeding. Although substantial progress has been achieved in molecular characterization of male sterility and fertility restoration recently, little effort has been devoted to female sterility. To identify the gene(s) controlling female sterility in wheat efficiently, an investigation was conducted for the seed setting ratio using a set of F2 populations derived from the cross between a female sterile line XND126 and an elite cultivar Gaocheng 8901. Bulked segregation analysis (BSA) method and recessive class approach were adopted to screen for SSR markers potentially linked to female fertility gene loci in 2005. Out of 1080 SSRs in wheat genome, eight markers on chromosome 2D showed a clear difference between two disparate bulks and small recombination frequency values, suggesting a strong linkage signal to the sterility gene. Based on the candidate linked markers, partial linkage maps were constructed with Mapmaker 3.0 (EXP) instead of whole genome maps, and quantitative trait locus (QTL) mapping was implemented with software QTLNetwork 2.0. A major gene locus designated as taf1, was located on chromosome 2DS. The above result was confirmed by the analysis for 2007 data, and taf1 was identified on the same chromosome 2DS with a confidence interval of 2·4 cM, which could explain 44·99% of phenotypic variation. These results provided fundamental information for fine mapping studies and laid the groundwork for wheat fertility genetic studies.
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Slof-Op ‘t Landt, Margarita C. T., Eric F. van Furth, Ingrid Meulenbelt, P. Eline Slagboom, Meike Bartels, Dorret I. Boomsma, and Cynthia M. Bulik. "Eating Disorders: From Twin Studies to Candidate Genes and Beyond." Twin Research and Human Genetics 8, no. 5 (October 1, 2005): 467–82. http://dx.doi.org/10.1375/twin.8.5.467.
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AbstractSubstantial effort has been put into the exploration of the biological background of eating disorders, through family, twin and molecular genetic studies. Family studies have shown that anorexia (AN) and bulimia nervosa (BN) are strongly familial, and that familial etiologic factors appear to be shared by both disorders. Twin studies often focus on broader phenotypes or subthreshold eating disorders. These studies consistently yielded moderate to substantial heritabilities. In addition, there has been a proliferation of molecular genetic studies that focused on Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV; American Psychiatric Association, 1994) AN and BN. Seven linkage regions have been identified in genome-wide screens. Many genetic association studies have been performed, but no consistent association between a candidate gene and AN or BN has been reported. Larger genetic association studies and collaborations are needed to examine the involvement of several candidate genes and biological pathways in eating disorders. In addition, twin studies should be designed to assist the molecular work by further exploring genetic determinants of endophenotypes, evaluating the magnitude of contribution to liability of measured genotypes as well as environmental risk factors related to eating disorders. In this manner twin and molecular studies can move the field forward in a mutually informative way.
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Ballering, Katie S., Christopher J. Kristich, Suzanne M. Grindle, Ana Oromendia, David T. Beattie, and Gary M. Dunny. "Functional Genomics of Enterococcus faecalis: Multiple Novel Genetic Determinants for Biofilm Formation in the Core Genome." Journal of Bacteriology 191, no. 8 (February 13, 2009): 2806–14. http://dx.doi.org/10.1128/jb.01688-08.
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ABSTRACT The ability of Enterococcus faecalis to form robust biofilms on host tissues and on abiotic surfaces such as catheters likely plays a major role in the pathogenesis of opportunistic antibiotic-resistant E. faecalis infections and in the transfer of antibiotic resistance genes. We have carried out a comprehensive analysis of genetic determinants of biofilm formation in the core genome of E. faecalis. Here we describe 68 genetic loci predicted to be involved in biofilm formation that were identified by recombinase in vivo expression technology (RIVET); most of these genes have not been studied previously. Differential expression of a number of these determinants during biofilm growth was confirmed by quantitative reverse transcription-PCR, and genetic complementation studies verified a role in biofilm formation for several candidate genes. Of particular interest was genetic locus EF1809, predicted to encode a regulatory protein of the GntR family. We isolated 14 independent nonsibling clones containing the putative promoter region for this gene in the RIVET screen; EF1809 also showed the largest increase in expression during biofilm growth of any of the genes tested. Since an in-frame deletion of EF1809 resulted in a severe biofilm defect that could be complemented by the cloned wild-type gene, we have designated EF1809 ebrA (enterococcal biofilm regulator). Most of the novel genetic loci identified in our studies are highly conserved in gram-positive bacterial pathogens and may thus constitute a pool of uncharacterized genes involved in biofilm formation that may be useful targets for drug discovery.
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Kim, Rachel, Alla Trubetskoy, Takeshi Suzuki, Nancy A. Jenkins, Neal G. Copeland, and Jack Lenz. "Genome-Based Identification of Cancer Genes by Proviral Tagging in Mouse Retrovirus-Induced T-Cell Lymphomas." Journal of Virology 77, no. 3 (February 1, 2003): 2056–62. http://dx.doi.org/10.1128/jvi.77.3.2056-2062.2003.
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ABSTRACT The identification of tumor-inducing genes is a driving force for elucidating the molecular mechanisms underlying cancer. Many retroviruses induce tumors by insertion of viral DNA adjacent to cellular oncogenes, resulting in altered expression and/or structure of the encoded proteins. The availability of the mouse genome sequence now allows analysis of retroviral common integration sites in murine tumors to be used as a genetic screen for identification of large numbers of candidate cancer genes. By positioning the sequences of inverse PCR-amplified, virus-host junction fragments within the mouse genome, 19 target genes were identified in T-cell lymphomas induced by the retrovirus SL3-3. The candidate cancer genes included transcription factors (Fos, Gfi1, Lef1, Myb, Myc, Runx3, and Sox3), all three D cyclins, Ras signaling pathway components (Rras2/TC21 and Rasgrp1), and Cmkbr7/CCR7. The most frequent target was Rras2. Insertions as far as 57 kb away from the transcribed portion were associated with substantially increased transcription of Rras2, and no coding sequence mutations, including those typically involved in Ras activation, were detected. These studies demonstrate the power of genome-based analysis of retroviral insertion sites for cancer gene discovery, identify several new genes worth examining for a role in human cancer, and implicate the pathways in which those genes act in lymphomagenesis. They also provide strong genetic evidence that overexpression of unmutated Rras2 contributes to tumorigenesis, thus suggesting that it may also do so if it is inappropriately expressed in human tumors.
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Barrows, Nicholas J., Caroline Le Sommer, Mariano A. Garcia-Blanco, and James L. Pearson. "Factors Affecting Reproducibility between Genome-Scale siRNA-Based Screens." Journal of Biomolecular Screening 15, no. 7 (July 12, 2010): 735–47. http://dx.doi.org/10.1177/1087057110374994.
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RNA interference-based screening is a powerful new genomic technology that addresses gene function en masse. To evaluate factors influencing hit list composition and reproducibility, the authors performed 2 identically designed small interfering RNA (siRNA)–based, whole-genome screens for host factors supporting yellow fever virus infection. These screens represent 2 separate experiments completed 5 months apart and allow the direct assessment of the reproducibility of a given siRNA technology when performed in the same environment. Candidate hit lists generated by sum rank, median absolute deviation, z-score, and strictly standardized mean difference were compared within and between whole-genome screens. Application of these analysis methodologies within a single screening data set using a fixed threshold equivalent to a p-value ≤0.001 resulted in hit lists ranging from 82 to 1140 members and highlighted the tremendous impact analysis methodology has on hit list composition. Intra- and interscreen reproducibility was significantly influenced by the analysis methodology and ranged from 32% to 99%. This study also highlighted the power of testing at least 2 independent siRNAs for each gene product in primary screens. To facilitate validation, the authors conclude by suggesting methods to reduce false discovery at the primary screening stage. In this study, they present the first comprehensive comparison of multiple analysis strategies and demonstrate the impact of the analysis methodology on the composition of the “hit list.” Therefore, they propose that the entire data set derived from functional genome-scale screens, especially if publicly funded, should be made available as is done with data derived from gene expression and genome-wide association studies.
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Yan, Kexin, Yutao Wang, Yining Shao, and Ting Xiao. "Gene Instability-Related lncRNA Prognostic Model of Melanoma Patients via Machine Learning Strategy." Journal of Oncology 2021 (May 25, 2021): 1–22. http://dx.doi.org/10.1155/2021/5582920.
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Background. Melanoma is a common tumor characterized by a high mortality rate in its late stage. After metastasis, current treatment methods are relatively ineffective. Many studies have shown that long noncoding RNA (lncRNA) may participate in gene mutation and genomic instability in cancer. Methods. We downloaded transcriptome data, mutation data, and clinical follow-up data of melanoma patients from The Cancer Genome Atlas. We divided samples into groups according to the number of somatic cell mutations and then performed a differential analysis to screen out the differentially expressed genes. We then divided samples into genomic unstable and genomic stable groups. We compared lncRNA expression profiles in these groups and constructed a protein-coding genes network coexpressed with selected lncRNA to analyze the pathways enriched by these genes. Two machine learning methods, least absolute shrinkage and selector operation (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), were applied to conduct the lncRNA-related prognostic model. Afterward, we performed survival analysis, risk correlation analysis, independent prognostic analysis, and clinical subgroup model validation. Finally, through wound healing assay and transwell assay, the function of AATBC was verified by A375 cell lines. Results. We screened 61 prognostic-related lncRNAs and constructed an lncRNA-mRNA coexpression network based on these lncRNAs. Seven lncRNAs were selected as common characteristic factors based on the two machine learning methods. The model formula was as follows: risk score = 0.085 ∗ AATBC + 0.190 ∗ AC026689.1−0.117 ∗ AC083799.1 + 0.036 ∗ AC091544.6−0.039 ∗ LINC01287−0.291 ∗ SPRY4.AS1 + 0.056 ∗ ZNF667.AS1. The seven lncRNAs in this formula are key candidates. Cell experiments have verified that knocking down AATBC in A375 cell lines can reduce the proliferation and invasion ability of melanoma cells. Conclusion. The lncRNA we identified provides a new way to study lncRNA’s role in the genomic instability of melanoma. Our findings may provide essential candidate biomarkers for the diagnosis and treatment of melanoma.
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LIMVIPHUVADH, VACHIRANEE, LING LING CHUA, FRANK EISENHABER, SHARMILA ADHIKARI, and SEBASTIAN MAURER-STROH. "IS LGI2 THE CANDIDATE GENE FOR PARTIAL EPILEPSY WITH PERICENTRAL SPIKES?" Journal of Bioinformatics and Computational Biology 08, no. 01 (February 2010): 117–27. http://dx.doi.org/10.1142/s0219720010004550.
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Partial epilepsy with pericentral spikes (PEPS) is a familial epilepsy with disease locus mapped to human chromosome region 4p15; yet, the causative gene is unknown. In this work, arguments based on protein sequence analysis and patient-specific chromosomal deletions are provided for LGI2 as the prime candidate gene for PEPS among the 52 genes known at the genome locus 4p15. Furthermore, we suggest that two reports of patients that were not classified as PEPS but show very similar phenotypes and deletions in the PEPS disease locus, could in fact describe the same disease. To test this hypothesis, patients with diagnosed PEPS or the described similar phenotypes could be screened for mutations in LGI2 and other shortlisted candidate genes. The linkage between PEPS and its disease causing gene(s) would allow diagnosis of the disease based on genetic screening as well as hereditary studies. Furthermore, previous knowledge on molecular disease mechanisms of related LGI proteins, for example LGI1 and autosomal dominant lateral temporal epilepsy, could be applied to deepen the understanding of the PEPS disease mechanism at the molecular level, which may facilitate therapeutic intervention in the future. Supplementary Table is available at .
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Qi, Xiaoguang, Chunyan Qi, Xindan Kang, Yi Hu, and Weidong Han. "Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma." PeerJ 8 (June 17, 2020): e9362. http://dx.doi.org/10.7717/peerj.9362.
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Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicator in lung adenocarcinoma. Moreover, the prognosis of patients with different forms of lung adenocarcinoma was associated with differences in mutations and pathways in potential hub genes. Conclusions PDL1-positive lung adenocarcinoma and PDL1-negative lung adenocarcinoma might be different subtypes of lung adenocarcinoma. The hub genes might play an important role in PDL1 regulatory pathways. Further studies on hub genes are warranted to reveal new mechanisms underlying the regulation of PDL1 expression. These results are crucial for understanding and applying precision immunotherapy for lung adenocarcinoma.
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Westrick, Randal Joseph, Guojing Zhu, Jishu Xu, Audrey C. A. Cleuren, Angela Yang, David R. Siemieniak, Kart Tomberg, Weiping Peng, Jun Z. Li, and David Ginsburg. "Whole-Exome Sequencing to Identify Mutations in Thrombosis Modifier Genes Isolated From a Factor V Leiden-Dependent Sensitized ENU Suppressor Screen in the Mouse." Blood 118, no. 21 (November 18, 2011): 1183. http://dx.doi.org/10.1182/blood.v118.21.1183.1183.
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Abstract Abstract 1183 Only ∼10% of individuals carrying the common venous thrombosis risk factor, Factor V Leiden (FVL) will develop venous thrombosis in their lifetime. In order to identify potential FVL modifier genes, we performed a sensitized dominant ENU mutagenesis screen, based on the perinatal synthetic lethal thrombus previously observed in mice homozygous for FVL (FVQ/Q) and hemizygous for tissue factor pathway inhibitor deficiency (Tfpi+/−). The genome-wide ENU mutagenesis screen was performed by crossing ENU-treated male FVQ/Q mice with FVQ/+ Tfpi+/− females. Surviving G1 offspring were analyzed to identify survivors with the otherwise lethal FVQ/Q Tfpi+/− genotype. As proof of concept, we demonstrated that reduced tissue factor (Tf+/−) suppresses the lethal FVQ/Q Tfpi+/− phenotype, suggesting that mutations at Tf should be among the suppressor genes identified by our screen. Analysis of 7,128 G1 offspring (∼2X genome coverage) identified 98 FVQ/Q Tfpi+/− mice that survived to weaning. Fourteen FVQ/Q Tfpi+/− G1 mice exhibited successful transmission of a putative suppressor mutation to two or more FVQ/Q Tfpi+/− G2 offspring. Extensive genotyping of mice from an expanded genetic cross from one of these lines mapped a candidate suppressor locus to a chromosome 3 region encompassing the TF gene (LOD=4.93). With continued improvements in next generation sequencing technologies, we have now applied whole exome sequencing to analysis of 8 of the remaining 13 lines. The entire DNA coding region (the “exome”, totaling 49.6 Mb of DNA sequence) from a progeny-tested member of each line was captured using the Agilent SureSelect mouse exome capture system. Whole-exome sequencing using the Illumina HiSeq high-throughput sequencer yielded 12–15 gigabases of sequence data per sample, corresponding to an average of ∼200 fold sequencing coverage for each nucleotide position. Variant analysis using the Gene Analysis Toolkit revealed the presence of a small number of high confidence novel heterozygous (dominant) variants in each sample. Each of these heterozygous variants is a candidate suppressor mutation and these are presently being tested in remaining FVQ/Q Tfpi+/− mice from each respective line. Based on previous studies where ENU-induced mutations in mice have been identified, we anticipate the identification of putative exomic mutations in approximately 80% of tested suppressor lines. Identification of these mutations should provide candidate modifier genes for FVL and other human hemostatic disorders. Disclosures: Ginsburg: Portola Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Catalyst Biosciences: Membership on an entity's Board of Directors or advisory committees; Shire Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees.
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Corbi, Sâmia Cruz Tfaile, Alliny Souza Bastos, Rafael Nepomuceno, Thamiris Cirelli, Raquel Alves dos Santos, Catarina Satie Takahashi, Cristiane S. Rocha, Silvana Regina Perez Orrico, Claudia V. Maurer-Morelli, and Raquel Mantuaneli Scarel-Caminaga. "Expression Profile of Genes Potentially Associated with Adequate Glycemic Control in Patients with Type 2 Diabetes Mellitus." Journal of Diabetes Research 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/2180819.
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Despite increasing research in type 2 diabetes mellitus (T2D), there are few studies showing the impact of the poor glycemic control on biological processes occurring in T2D. In order to identify potential genes related to poorly/well-controlled patients with T2D, our strategy of investigation included a primary screen by microarray (Human Genome U133) in a small group of individuals followed by an independent validation in a greater group using RT-qPCR. Ninety patients were divided as follows: poorly controlled T2D (G1), well-controlled T2D (G2), and normoglycemic individuals (G3). After using affy package in R, differentially expressed genes (DEGs) were prospected as candidate genes potentially relevant for the glycemic control in T2D patients. After validation by RT-qPCR, the obtained DEGs were as follows—G1 + G2 versus G3: HLA-DQA1, SOS1, and BRCA2; G2 versus G1: ENO2, VAMP2, CCND3, CEBPD, LGALS12, AGBL5, MAP2K5, and PPAP2B; G2 versus G3: HLA-DQB1, MCM4, and SEC13; and G1 versus G3: PPIC. This demonstrated a systemic exacerbation of the gene expression related to immune response in T2D patients. Moreover, genes related to lipid metabolisms and DNA replication/repair were influenced by the glycemic control. In conclusion, this study pointed out candidate genes potentially associated with adequate glycemic control in T2D patients, contributing to the knowledge of how the glycemic control could systemically influence gene expression.
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Tang, Huihui, Ricardo De Matos Simoes, Ryosuke Shirasaki, Olga Dashevsky, Brian Glassner, Sondra L. Downey-Kopyscinski, Sara Gandolfi, et al. "CRISPR Activation Screen for Drivers of MM Cell Proliferation." Blood 132, Supplement 1 (November 29, 2018): 3197. http://dx.doi.org/10.1182/blood-2018-99-118712.
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Abstract CRISPR/Cas9-based gene editing has become a powerful tool for loss-of-function (LOF) studies and has allowed us to systematically interrogate the function of genes regulating the survival and proliferation of multiple myeloma (MM) cells in vitro, in vivo and in the context of treatment resistance (e.g. De Matos Simoes et al., Shirasaki et al., and Gandolfi et al. ASH 2017). We reasoned, however, that important additional information can be obtained from CRISPR-based gain-of-function (GOF) approaches which can achieve transcriptional activation at endogenous genomic loci. We thus performed genome-scale CRISPR activation studies using the dCas9-P65-HSF transcriptional activation system (in which a Cas9 variant lacking nuclease activity [dCas9] confers P65-HSF-mediated activation of genes recognized by sgRNAs against their promoter regions). Specifically, MM.1S cells were transduced with the dCas9-P65-HSF system and pooled lentiviral particles of the Calabrese CRISPR activation sgRNA library, consisting of 2 pooled sgRNA sub-libraries (total of ~110,000 sgRNAs targeting ~18000 genes, at initial coverage of 800 cells/sgRNA). Cells were cultured for 12 weeks and harvested at baseline and various intervals, e.g. 4 and 12 weeks of culture. Next generation sequencing of genomic DNA quantified the abundance of sgRNAs in the tumor cell population and genes were ranked (with rank aggregation algorithms) in terms of their sgRNA enrichment or depletion. These analyses allowed us to observe a series of genes with statistically significant sgRNA enrichment and known or presumed roles in MM biology, including key MM transcription factors such as IRF4, the thalidomide derivative targets IKZF3 and IKZF1, and the co-factor POU2AF1; known oncogenes, e.g. KRAS and MYC; NF-kappaB pathway members, e.g. RELA; and signal transduction regulators, e.g. IGF1R and its downstream effectors IRS1 and AKT2. These results are consistent with the major depletion of sgRNAs for these genes in loss-of-function (LOF) CRISPR knockout studies. However, several other genes with significant sgRNA enrichment in CRISPR activation studies did not exhibit major sgRNA depletion in CRISPR knockout studies, including the B/plasma cell transcription factor POU2F2 (Oct2), for which high protein expression correlates with reduced survival in MM (Toman I. et al 2011); the transcription factor PAX2, the TRAF interacting protein TIFA, or the Toll-like receptor TLR4. Interestingly, significant depletion of sgRNAs was observed for several genes with known or proposed tumor suppressive properties including YAP1 (an oncogene for solid tumors, but reported as tumor suppressor for MM and other blood cancers); the pro-death TNFRSF10A (TRAIL receptor DR4), TP73, CDKN1A, the negative regulator of c-Myc MXI1, or the pro-apoptotic Bcl2 family member BAK1. Depletion or enrichment of sgRNAs for most of the aforementioned genes was detectable by 4 weeks of culture, while more pronounced changes and detection of additional statistically-significant hits was observed in later time-points. For genes with significant sgRNA enrichment in our CRISPR activation study, we examined a series of molecular alterations, including transcript overexpression in MM cell lines or patient-derived samples vs. normal plasma cells, or relapsed/refractory MM vs. earlier disease MM stages; mutational status; correlation of transcript levels with clinical outcome in MM; and extent of open chromatin (based on H3K27Ac chromatin marks) within or proximal to each gene in MM cell lines. Some "hits" from our screen exhibited at least one of these molecular alterations, but most genes harbored no such alterations or their magnitude or frequency ranked outside the top 50-100 genes. These results suggest that CRISPR activation studies can identify important putative regulators of MM biology, which may not be readily detectable based on known annotations of the MM cell genome, transcriptome, or epigenome. Genome-scale CRISPR-based transcriptional activation are an important gain-of-function system to uncover genes which induce vs. suppress tumor cell survival and proliferation, and provide information orthogonal to those yielded by other CRISPR-based approaches that involve loss-of-function interventions. Our use of CRISPR activation allowed us to both validate previously known genes and identify promising new candidate regulators of MM cell biology. Disclosures Mitsiades: EMD Serono: Research Funding; Abbvie: Research Funding; Takeda: Other: employment of a relative; TEVA: Research Funding; Janssen/ Johnson & Johnson: Research Funding.
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Westrick, Randal J., Sara L. Manning, Sarah L. Dobies, Abigail L. Peterson, David R. Siemieniak, Lindsey M. Korepta, and David Ginsburg. "A Sensitized Genome-Wide ENU Mutagenesis Screen in the Mouse to Identify Genetic Modifiers of Thrombosis." Blood 104, no. 11 (November 16, 2004): 2. http://dx.doi.org/10.1182/blood.v104.11.2.2.
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Abstract Factor V Leiden, (FVL) is the most common known inherited thrombotic risk factor and is present in approximately 5% of most Western populations and 25–50% of patients presenting with venous thrombosis. However, FVL is incompletely penetrant, with only approximately 10% of FVL carriers developing thrombosis in their lifetimes. Though interactions between FVL and other known prothrombotic mutations have been documented in a few cases, the genetic factors responsible for the incomplete penetrance of FVL remain largely unknown. We previously reported a remarkable synthetic lethality in mice carrying the FVL mutation and partial deficiency of a key coagulation component, tissue factor pathway inhibitor (TFPI). Complete TFPI deficiency in mice is embryonic lethal, whereas heterozygosity is compatible with normal survival. However, homozygosity for FVL (FvQ/Q) in the context of heterozygosity for TFPI (Tfpi+/−) is uniformly lethal due to disseminated perinatal thrombosis. In order to identify potential modifier genes contributing to FVL penetrance, we have utilized this lethal genetic interaction as a phenotyping tool for a sensitized ENU mutagenesis screen in laboratory mice. We hypothesize that dominant mutations in key components of the coagulation system will improve hemostatic balance and allow survival in mice carrying the lethal FvQ/Q Tfpi+/− genotype combination. As an example, we propose that loss of one tissue factor allele might compensate for reduced TFPI and rescue FvQ/Q Tfpi+/− . To test this hypothesis, we bred tissue factor heterozygous mice (Tf+/−) with FvQ/Q Tfpi+/− mice and observed complete rescue, with normal survival and the expected number (8 of 57) of FvQ/Q Tfpi+/− Tf+/− mice from a FvQ/+ Tfpi+/− Tf+/−x FvQ/Q cross. In order to identify candidate modifier genes, we performed a whole genome mutagenesis screen. In this screen, male FvQ/Q mice were mutagenized with ENU and bred to FvQ/+ Tfpi+/− double heterozygous females. DNAs from surviving offspring were PCR assayed to identify rescued mice with the FvQ/Q Tfpi+/− genotype. Analysis of 2250 offspring, corresponding to approximately half genome coverage, has identified 15 mice that survived to weaning. Heritability was demonstrated for the 5 mutant lines subjected to progeny testing to date. Genetic crosses are in progress to map the mutant genes in 3 of the 5 progeny tested lines. These preliminary results demonstrate the feasibility of this sensitized screen for the identification of dominant suppressors of thrombosis. Based on our data, we estimate that there are likely 10–20 mammalian genes for which a <50% reduction in expression could result in a major shift in hemostatic balance sufficient to rescue the lethal thrombosis associated with the FvQ/Q Tfpi+/− lethal genotype. Each of these loci represent a candidate for a human modifier gene in patients with FVL and other thrombophilic mutations. Finally, the biologic pathways uncovered by these studies should provide new insights into the overall regulation of hemostatic balance and identify potential new targets for therapeutic intervention.
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Mao, Yongcai, Nicole R. London, Li Ma, Daniel Dvorkin, and Yang Da. "Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model." Physiological Genomics 28, no. 1 (December 2006): 46–52. http://dx.doi.org/10.1152/physiolgenomics.00096.2006.
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Epistasis effects (gene interactions) have been increasingly recognized as important genetic factors underlying complex traits. The existence of a large number of single nucleotide polymorphisms (SNPs) provides opportunities and challenges to screen DNA variations affecting complex traits using a candidate gene analysis. In this article, four types of epistasis effects of two candidate gene SNPs with Hardy-Weinberg disequilibrium (HWD) and linkage disequilibrium (LD) are considered: additive × additive, additive × dominance, dominance × additive, and dominance × dominance. The Kempthorne genetic model was chosen for its appealing genetic interpretations of the epistasis effects. The method in this study consists of extension of Kempthorne's definitions of 35 individual genetic effects to allow HWD and LD, genetic contrasts of the 35 extended individual genetic effects to define the 4 epistasis effects, and a linear model method for testing epistasis effects. Formulas to predict statistical power (as a function of contrast heritability, sample size, and type I error) and sample size (as a function of contrast heritability, type I error, and type II error) for detecting each epistasis effect were derived, and the theoretical predictions agreed well with simulation studies. The accuracy in estimating each epistasis effect and rates of false positives in the absence of all or three epistasis effects were evaluated using simulations. The method for epistasis testing can be a useful tool to understand the exact mode of epistasis, to assemble genome-wide SNPs into an epistasis network, and to assemble all SNP effects affecting a phenotype using pairwise epistasis tests.
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Bajaj, Jeevisha, James Scott-Browne, Kyle Spinler, and Tannishtha Reya. "An In Vivo Genome-Wide CRISPR Screen Identifies Novel Dependencies for Blast Crisis Chronic Myelogenous Leukemia." Blood 132, Supplement 1 (November 29, 2018): 1727. http://dx.doi.org/10.1182/blood-2018-99-119178.
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Abstract Poorly differentiated aggressive myeloid diseases such as Acute Myelogenous Leukemia (AML) and blast crisis Chronic Myelogenous Leukemia (bcCML) are often resistant to standard therapy and associated with significantly poor survival in both children and adults. There is thus a significant need for a better understanding of the mechanisms that drive disease progression and for finding novel therapeutic targets. Thus, to determine the molecular effectors of myeloid leukemia growth in vivo, we carried out a genome-wide CRISPR/Cas9 dropout screen using the lentiviral Brie gRNA library. This library targets 19,674 genes, and has on average 3 gRNAs for each gene, and 1000 control non-targeting gRNAs. We carried out this whole-genome screen in a mouse model of Cas9+ blast crisis CML (bcCML) driven by BCR-ABL/ NUP98-HOXA9 since this represents a very aggressive phase of myeloid cancer where 90% of the leukemic blasts are undifferentiated and cancer stem cell-like. This in vivo screen led to the identification of 3636 genes essential for leukemic growth and propagation in the bone marrow of recipient mice, constituting pathways such as metabolism, protein translation and DNA replication. The genes that were significantly depleted included known drivers of myeloid cancer progression and regulators of myeloid cancer stem cells (for example, Brd4, Kdm1a, Pafah1b1/Lis1, Rptor), indicating that our screening strategy can successfully identify functional drivers of cancer growth. While intrinsic signals that drive myeloid cancer progression are well described, little is known about how interactions with the surrounding microenvironment can control leukemic growth and propagation. Our whole-genome screen identified ~130 cell surface genes that are significantly depleted in the bcCML stem cells transplanted in vivo. Since environmental factors commonly signal through receptors on the surface of leukemic cells, this subset is likely to include most, if not all, genetic effectors of niche driven signals required for in vivo growth and propagation of aggressive myeloid leukemia cells. Of these 130 genes, several have earlier been shown by us and others to be essential for myeloid cancer progression including Itgb1, Cxcr4 and Cd44. We are currently testing the functional contribution of novel candidate cell surface molecules, which can integrate signals from the environment, on the in vivo growth and progression of myeloid malignancies. We anticipate that these studies will provide a basis for testing antibody-mediated therapeutic inhibition of specific microenvironmental signals on myeloid leukemia growth and propagation. Disclosures No relevant conflicts of interest to declare.
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Sadhukhan, Tamal, Mansi Vishal, Gautami Das, Aanchal Sharma, Arijit Mukhopadhyay, Shyamal K. Das, Kunal Ray, and Jharna Ray. "Evaluation of the Role of LRRK2 Gene in Parkinson’s Disease in an East Indian Cohort." Disease Markers 32, no. 6 (2012): 355–62. http://dx.doi.org/10.1155/2012/895065.
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Leucine rich repeat kinase 2 (LRRK2)gene defects cause Parkinson's disease (PD). Recently,LRRK2has also been shown by genome wide association (GWA) studies to be a susceptibility gene for the disease. In India mutations inLRRK2is a rare cause of PD. We, therefore, genotyped 64 SNPs acrossLRRK2in 161 control samples and finally studied 6 haplotype tagging SNPs for association-based study on 300 cases and 446 ethnically matched controls to explore the potential role ofLRRK2as a susceptibility gene in PD for East Indians. We did not find any significant allele/ genotype or haplotype associations with PD suggesting that common genetic variants withinLRRK2play limited role in modulating PD among East Indians. In addition, we also screened for the common mutations (viz. p.R1441C, p.R1441G, p.R1441H, p.Y1699C, p.G2019S), and a risk variant common among Asians (p.G2385R) but did not observe any of the above mentioned variants in our cohort. Our study, therefore, strongly suggests thatLRRK2has minimal role as a candidate and susceptibility gene in PD pathogenesis among East Indians.
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Ji, Chen, Yuming Li, Kai Yang, Yanwei Gao, Yan Sha, Dong Xiao, Xiaohong Liang, and Zhongqin Cheng. "Identification of four genes associated with cutaneous metastatic melanoma." Open Medicine 15, no. 1 (June 11, 2020): 531–39. http://dx.doi.org/10.1515/med-2020-0190.
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AbstractBackgroundCutaneous melanoma is an aggressive cancer with increasing incidence and mortality rates worldwide. Metastasis is one of the primary elements that influence the prognosis of patients with cutaneous melanoma. This study aims to clarify the potential mechanism underlying the low survival rate of metastatic melanoma and to search for novel target genes to improve the survival rate of patients with metastatic tumors.MethodsGene expression dataset and clinical data were downloaded from The Cancer Genome Atlas portal. Differentially expressed genes (DEGs) were identified, and their functions were studied through gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Survival and multivariate Cox regression analyses were used to screen out candidate genes that could affect the prognosis of patients with metastatic melanoma.ResultsAfter a series of comprehensive statistical analysis, 464 DEGs were identified between primary tumor tissues and metastatic tissues. Survival and multivariate Cox regression analyses revealed four vital genes, namely, POU2AF1, ITGAL, CXCR2P1, and MZB1, that affect the prognosis of patients with metastatic melanoma.ConclusionThis study provides a new direction for studying the pathogenesis of metastatic melanoma. The genes related to cutaneous metastatic melanoma that affect the overall survival time of patients were identified.
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Ma, Haiyu, Chao Fang, Lingling Liu, Qiong Wang, Jueken Aniwashi, Yiming Sulaiman, Kezierkailedi Abudilaheman, and Wujun Liu. "Identification of novel genes associated with litter size of indigenous sheep population in Xinjiang, China using specific-locus amplified fragment sequencing technology." PeerJ 7 (November 26, 2019): e8079. http://dx.doi.org/10.7717/peerj.8079.
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Background There are abundant sheep breed resources in the Xinjiang region of China attributing to its diverse ecological system, which include several high-litter size sheep populations. Previous studies have confirmed that the major high prolificacy gene cannot be used to detect high litter size. Our research team found a resource group in Pishan County, southern Xinjiang. It showed high fertility with an average litter size of two to four in one birth, excellent breast development, and a high survival rate of lambs. In the present study, we used this resource as an ideal sample for studying the genetic mechanisms of high prolificacy in sheep. Methods Indigenous sheep populations from Xinjiang, with different litter sizes, were selected for the research, and specific-locus amplified fragment sequencing (SLAF-seq) technology was used to comprehensively screen single nucleotide polymorphisms (SNPs) from the whole genome that may cause differences in litter size. Novel genes associated with litter size of sheep were detected using genome-wide association studies (GWAS), providing new clues revealing the regulation mechanism of sheep fecundity. Candidate genes related to ovulation and litter size were selected for verification using Kompetitive Allele Specific polymerase chain reaction (KASP) cluster analysis. Results We identified 685,300 SNPs using the SLAF-seq technique for subsequent genome-wide analysis. Subsequently, 155 SNPs were detected at the genome-wide level. Fourteen genes related to sheep reproduction were notated: COIL, SLK, FSHR, Plxna3, Ddx24, CXCL12, Pla2g7, ATP5F1A, KERA, GUCY1A1, LOC101107541, LOC101107119, LOC101107809, and BRAF. Based on literature reports, 30 loci of seven genes and candidate genes (CXCL12, FSHR, SLK, GUCY1A1, COIL, LOC101107541, and LOC101107119) related to ovulation and litter size were selected for verification using KASP cluster analysis. Among them, nine loci of three genes were successfully genotyped. Three loci of FSHR (GenBank ID: 443299, g. 75320741G>A site), GUCY1A1 (GenBank ID: 101110000, g. 43266624C>T site), and COIL (GenBank ID: 101123134, g. 7321466C>G site) were found to be significantly or extremely significantly associated with litter size. These three loci are expected to be used as molecular markers to determine differences in litter size in sheep.
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Mathews, Carol A., and Victor I. Reus. "Genetic Linkage in Bipolar Disorder." CNS Spectrums 8, no. 12 (December 2003): 891–904. http://dx.doi.org/10.1017/s1092852900028686.
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AbstractBipolar disorder is an etiologically complex syndrome that is dearly heritable. Multiple, genes, working singly or in concert, are likely to cause susceptibility to bipolar disorder. Bipolar disorder genetics has progressed rapidly in the last few decades. However, specific causal genetic mutations for bipolar disorder have not been identified. Both candidate gene studies and complete genome screens have been conducted. They have provided compelling evidence for several potential bipolar disorder susceptibility loci in several regions of the genome. The strongest evidence suggests that bipolar disorder susceptibility loci may lie in one or more genomic regions on chromosomes 18, 4, and 21. Other regions of interest, including those on chromosomes 5 and 8, are also under investigation. New approaches, such as the use of genetically isolated populations and the use of endophenotypes for bipolar disorder, hold promise for continued advancement in the search to identify specific bipolar disorder genes.
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De Matos Simoes, Ricardo, Geoffrey M. Matthews, Yiguo Hu, Brian Glassner, Megan A. Bariteau, Michal Sheffer, Ryosuke Shirasaki, and Constantine S. Mitsiades. "Integrated Evaluation of Results from Genome-Wide Association Studies and Crispr/Cas9-Based Functional Genomics in Myeloma: Implications for Cell-Autonomous Vs. Non-Autonomous Role of Candidate Genes in Myeloma Pathophysiology." Blood 128, no. 22 (December 2, 2016): 486. http://dx.doi.org/10.1182/blood.v128.22.486.486.
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Abstract Genome wide association studies (GWAS) in multiple myeloma (MM), and other neoplasias, have provided important insights into candidate germline variations, which may influence the risk of an individual to develop a given cancer, experience adverse clinical outcomes or develop side effects after treatment. However, it has been typically challenging to pursue further mechanistic evaluation of all these germline variants. Consequently, the role of many such variants in myeloma biology and clinical behavior often remains to be elucidated. We reasoned that recently developed functional genomics platforms, such as the CRISPR/Cas9 gene editing methodology, could provide insight into the role of GWAS-derived germline variants in MM. Specifically, we hypothesized that at least some germline variants previously proposed to correlate with higher risk for development of MM or its adverse clinical outcome could reside in or be proximal to genes which influence the proliferation and survival of MM cells. To address this hypothesis, we examined the results from our genome-wide CRISPR/Cas9-based gene editing screens in 2 MM cell lines (MM1.S and RPMI-8226; using the GeCKOv2 library of single guide RNAs [sgRNAs]), as well as additional results from other in-house or publicly available genome-wide CRISPR/Cas9 gene editing studies in 50 cell lines from other hematologic malignancies and 8 different types of solid tumors. In this functional genomic dataset, we examined the performance of 50 genes located in close proximity to over 60 risk loci identified in 6 different previously published GWAS studies for MM. Many of these genes had plausible potential involvement in MM/tumor biology, given their participation in transcriptional control or epigenetic regulation (e.g. CBX7, ASXL2, LCOR, MED24, SMARCD3, POU5F1); immunoglobulin secretion in plasma cells (ELL2), cell-to-cell adhesion (e.g. CDH12, CDH13); DNA repair (e.g. POLQ). We determined whether sgRNAs against these genes exhibited statistically significant (for 3 or more sgRNAs/gene, FDR=0.05) depletion or enrichment among the MM or non-MM cell lines of our study. While 14 and 6 of these genes exhibited statistically significant depletion (FDR=0.05) of their sgRNAs (3 or more per gene) in RPMI8226 and MM.1S cells, respectively, almost all of these genes were not ranked within the top 2000 genes with the most pronounced sgRNA depletion (in terms of log2 fold change and number of depleted sgRNAs/gene) in either MM or non-MM cell lines. Similarly, statistically significant sgRNA enrichment was not observed for the overwhelming majority of the genes in question in MM or non-MM cell lines. Interestingly, however, several genes showed a statistically significant association with clinical outcome in at least one clinically annotated gene expression profiling dataset in MM (e.g. correlation of ELL2, CDH13 transcript levels with clinical outcome of bortezomib-treated MM patients). These results taken together suggest that the majority of genes identified through prior GWAS studies for MM risk or adverse clinical outcome in this disease may have modest, if any, impact of the proliferation or survival of MM cells, as well as many other types of non-MM tumor cells, in CRISPR/Cas9-based screens conducted in cell-autonomous assay systems. In turn, these observations imply that, if these candidate genes are validated to play important roles in the pathophysiology of MM cells in vivo, this may likely involve cell-nonautonomous roles of these genes, e.g. in regulating tumor cell interaction with non-malignant cells in the local microenvironment or immune evasion. Our results highlight the value of a previously underappreciated approach in integrating genome-wide CRISPR/Cas9 in vitro genomic results with GWAS studies, in order to more comprehensively examine the putative roles of candidate germline variants and their proximal genes in the pathophysiology of myeloma and other neoplasias. Disclosures No relevant conflicts of interest to declare.
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Rodrigues, Marcelo, Birgit Lengerer, Thomas Ostermann, and Peter Ladurner. "Molecular biology approaches in bioadhesion research." Beilstein Journal of Nanotechnology 5 (July 8, 2014): 983–93. http://dx.doi.org/10.3762/bjnano.5.112.
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The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.
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Vecchione, Loredana, Valentina Gambino, Giovanni d'Ario, Sun Tian, Iris Simon, Vlad Calin Popovici, Mauro Delorenzi, Rene Bernards, and Sabine Tejpar. "Identification of synthetic lethal interactions with the BRAF oncogene in colorectal cancer." Journal of Clinical Oncology 31, no. 4_suppl (February 1, 2013): 403. http://dx.doi.org/10.1200/jco.2013.31.4_suppl.403.
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403 Background: Approximately 8-15% of colorectal (CRC) patients carry an activating mutation in BRAF. This CRC subtype is associated with poor outcome and with resistance, both to chemotherapeutic treatments and to tailored drugs. We recently showed that BRAF (V600E) colon cancers (CCs) have a characteristic gene expression signature (1, 2) which is found also in subsets of KRAS mutant and KRAS-BRAF wild type (WT2) tumors. Tumors having this gene signature, referred as “BRAF-like”, have a similar poor prognosis irrespective of the presence of the BRAF (V600E) mutation. By using a shRNA-based genetic screen in BRAF mutant CC cell lines we aimed to identify genes and pathways necessary for survival and growth of BRAFmutant CC. Such studies may reveal additional targets for therapy and potentially provide new biomarkers for patient stratification Methods: We identified 363 genes that are selectively overexpressed in BRAF mutant tumors as compared to WT2 type tumors, based on gene expression profiles of the PETACC3 (1) and Agendia (2) datasets. The TRC human genome-wide shRNA collection (TRC-Hs1.0) was used to generate a 1815 hairpins sub-library targeting those identified genes (BRAF library). BRAF(V600E) CC cell lines were infected with the BRAF library and screened for shRNAs that cause lethality. LIM1215 CC cell line (WT2) was used as a control. Cells stably expressing the shRNA library were cultured for 13 days, after which shRNAs were recovered by PCR. Deep sequencing was applied to determine the specific depletion of shRNA in BRAF(V600E) cells as compared to LIM1215 cells Results: Candidate genes were identified by using following filtering criteria: depletion in BRAF(V600E) cells by at least 50% and depletion in BRAF(V600E) cells 1, 5-fold higher than in control cells with the corresponding p-value to be ≤ 0.1. A total of 34 genes met our criteria of which 6 genes were presented with more than one hairpin and were concordant across the cell lines selected for validation. Conclusions: We identified candidate synthetic lethal genes in BRAF mutant CC cell lines. Functional analysis is ongoing. Data will be presented. References 1. J Clin Oncol 2012 Apr 20;30(12):1288-9 2. Gut (2012). doi:10.1136/gutjnl-2012-302423
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Gan, Olga I., Michael Milyavsky, Mark F. van Delft, Alla Buzina, Irina Kalatskaya, Troy Ketela, Lincoln Stein, Jason Moffat, and John E. Dick. "Genome-Wide shRNA Screen for DNA Damage Response Regulators in Human Hematopoietic Stem and Progenitor Cells." Blood 118, no. 21 (November 18, 2011): 1289. http://dx.doi.org/10.1182/blood.v118.21.1289.1289.
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Abstract Abstract 1289 Hematopoietic stem cells due to their life-long function should protect genome integrity to avoid accumulation of genetic aberrations leading to malignant transformation or bone marrow failure. We reported recently that human HSC of cord blood origin are exquisitely sensitive to DNA damage-induced apoptosis. Thus, following 3Gy of ionizing radiation HSC show evidence of persistent DNA damage response and greater p53-dependent apoptosis in comparison with commited myeloid progenitors. To elucidate the molecular basis of these observations we carried out a genome-wide loss-of-function genetic screen using a library of 80 000 shRNA vectors targeting more than 16 000 human genes. A screen was performed on immortalized (by TLS-ERG infection) cord blood cells (TEX), which radio-sensitivity is similar to early hematopoietic cells. To find out the radio-protective hits we exposed infected cells to four rounds of 4Gy irradiation in three independent experiments. TEX cells exhibited steady increase of their proliferative potential after each irradiation exposure. Cells were gathered after each irradiation round and their DNA was subjected to sequencing to determine protective hits. Upon the analysis we recognized known regulators of DNA damage response (e.g. p53) and identified many genes that previously were not connected to genotoxic stress response. Thus, the knockdown of these genes was at least as effective as p53 knockdown in protection of TEX cells against gamma-irradiation. The validation of the chosen hits on TEX cells showed that about half of them indeed mediate the protection against irradiation. Further validation included real-time PCR of infected cells to ensure the absence of off-target effect along with Western blot analysis of affected protein. We followed up the investigation of chosen hits on primary human lineage-negative cord blood cells and observed that only few candidates were mediating the same effect on HSC/progenitors cells as on TEX cells. To further validate the effect of the most prominently effective hits we employed several shRNA vectors for the same target gene. Following this step of validation, we choose to investigate the knockdown of CHEK2, the gene with reported role in DNA damage response in several murine tissues. Our preliminary studies in long-term cytokine-supplemented cultures demonstrated that CHEK2 is involved in DNA damage response of human HSC and progenitors. The further investigation of the effect of CHEK2 knockdown on repopulating human HSC is currently underway. An integrated analysis of our observations revealed several putative CHEK2-centered molecular networks, which connect DNA damage response to HSC function. Disclosures: No relevant conflicts of interest to declare.
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Matthews, Geoffrey M., Ricardo De Matos Simoes, Yiguo Hu, Michal Sheffer, Eugen Dhimolea, Paul J. Hengeveld, Megan A. Bariteau, et al. "Characterization of Lineage Vs. Context-Dependent Essential Genes in Multiple Myeloma Using Crispr/Cas9 Genome Editing." Blood 128, no. 22 (December 2, 2016): 119. http://dx.doi.org/10.1182/blood.v128.22.119.119.
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Abstract Multiple Myeloma (MM) remains an incurable malignancy in part because of an incomplete understanding of which genes are critically responsible for MM cell survival and proliferation. To address this unmet need, and building on our recent functional genomics studies with the CRISPR/Cas9 gene editing platform (ASH 2015; Int. MM Workshop, Rome 2015), we reasoned that quantification of sgRNA depletion in the absence of any treatment could identify genes essential for the survival or proliferation of MM cells and better define their role as candidate therapeutic targets. To this end, we transduced Cas9-expressing RPMI-8226 and MM.1S cells with the lentiviral genome-scale GeCKO pooled library of sgRNAs. After culture of these cell lines for 2, 6, 8 or 12 weeks without any treatment, we identified, based on next generation sequencing for the sgRNA sequences, genes with significantly depleted sgRNAs (4-6 sgRNAs/gene, >2-fold average depletion, FDR=0.05, based on MAGECK algorithm) in Cas9+ cells compared to their initial sgRNA plasmid pools, baseline cultures, or isogenic parental Cas9-negative cells. These results were confirmed for each cell line with a 2nd independent genome-wide analysis and with a focused sgRNA library containing a subset of candidates defined by the genome-wide analyses. We compared these results with data from our in-house or publicly available CRISPR/Cas9 gene editing studies, involving a total of 50 cell lines from other hematologic malignancies (leukemia, lymphoma) and from 8 different types of solid tumors. We identified 3 broad categories of essential genes in MM cells: a) core essential genes, with sgRNA depletion across the majority of MM and non-MM lines of our study, representing cellular processes critical for practically all lineages (e.g. genes involved in regulation of basic transcription factor complexes, ribosomal function, proteasome, spliceosome, structural proteins for mitochondria and other key organelles, et.c.); b) genes selectively essential for MM cell lines, but not for the overwhelming majority of leukemia, lymphoma or solid tumor cell lines; c) genes with a role in small subset(s) of cell lines, across diseases, which harbor defined genetic features correlating with this dependency. We integrated our CRISPR/Cas9-based data on MM-selective essential genes with a reanalysis of the Achilles Heel shRNA screen in MM and non-MM cell lines (10 and 493, respectively) of the Cell Line Encyclopedia Program (CCLE) program. We applied a series of statistical tests (e.g. Wilcoxon rank test or marker selection feature of GENE-E algorithm with 1000 permutation tests) to identify genes with a significantly lower rank in sgRNA or shRNA depletion in MM vs. non-MM cell lines, across different specific thresholds for fold change and statistical significance. We identified more than 50 high-value candidate target genes with preferential essentiality in MM, compared to non-MM cell lines of diverse lineages. Prominent examples of such MM-selective, essential genes included: transcription factors (e.g. IRF4, CCND2, MAF, NFKB1, NFKB2, RELA, RELB); otherNF-kB-related genes (e.g. IKBKB); PIM2 (but not PIM1 or PIM3 in this cell line panel); regulators of protein homeostasis, including diverse E2 and E3 ubiquitin ligases; and several other known or biologically-plausible dependencies which are under further evaluation. Many of these MM-selective dependencies exhibited significantly higher expression in MM, compared to non-MM cells, both in cell lines (based on the CCLE dataset) and patient-derived samples (comparison of Broad/MMRF vs. TCGA datasets, respectively). Notable observations of context-dependent essential genes include ARID1A in MM.1S cells (plausibly due to deficiency in its paralog ARID1B); and cases of both MM and non-MM cells with RAS mutations but lack of dependency on that gene. Targeting of lineage-specific dependencies (e.g. ER or AR in breast or prostate Ca, respectively) has provided major clinical benefit in some tumors; while context-specific dependencies are a cornerstone of molecularly-guided individualized treatments. Therefore, by identifying lineage- and context-dependent essential genes for MM, our integrated genome-wide CRISPR/Cas9 and shRNA analyses in molecularly annotated panels of MM vs. non-MM cell lines provide an attractive framework towards designing novel therapies for MM. Disclosures No relevant conflicts of interest to declare.
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Goldin, Lynn R., and Susan L. Slager. "Familial CLL: Genes and Environment." Hematology 2007, no. 1 (January 1, 2007): 339–45. http://dx.doi.org/10.1182/asheducation-2007.1.339.
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Abstract Families with multiple individuals affected with chronic lymphocytic leukemia (CLL) and other related B-cell tumors have been described in the literature. Familial CLL does not appear to differ from sporadic CLL in terms of prognostic markers and clinical outcome. While some environmental factors (such as farming-related exposures and occupational chemicals) may increase risk of CLL, results of epidemiologic studies have been generally inconsistent. Rates of CLL in the population show significant international variation, with the highest rates in the U.S. and Europe and the lowest rates in Asia. Migrants from Asia to the U.S. also have low rates of CLL, which supports a greater role for genetic compared with environmental risk factors. Large, population-based case-control and cohort studies have also shown significant familial aggregation of CLL and related conditions including non-Hodgkin and Hodgkin lymphoma. Monoclonal B-cell lymphocytosis also aggregates in families with CLL. However, the clinical implication of familial aggregation is minimal given the overall rarity of CLL. Linkage studies have been conducted in high-risk CLL families to screen the whole genome for loci that contribute to susceptibility, but no gene mutations have yet been identified by this method. Association studies of candidate genes have implicated immune function and other genes, but more studies are needed to verify these findings. The ability to conduct large-scale genomic studies will play an important role in detecting susceptibility genes for CLL over the next few years and thereby help to delineate etiologic pathways.
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Xiao Zhu, Yuan, Laura Bruins, Chang-Xin Shi, Jessica Schmidt, Chris Sereduk, Mia Champion, Esteban Braggio, Holly Yin, and A. Keith Stewart. "A Synthetic Lethality Druggable Genome RNAi Screen Identifies Genes Mediating Sensitivity To Lenalidomide In Multiple Myeloma Including RSK2." Blood 122, no. 21 (November 15, 2013): 3084. http://dx.doi.org/10.1182/blood.v122.21.3084.3084.
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Abstract Immunomodulatory drugs (IMiDs) are widely used in the treatment of patients with Multiple Myeloma (MM) however, only 30% of relapsed MM patients respond to single agent therapy and most patients eventually develop drug resistance. The molecular target of IMiDs in MM is cereblon but other parallel pathways or downstream events which enhance or preclude drug responsiveness are unknown. We therefore conducted a genome scale small interfering RNA (siRNA) lethality study in MM in the presence of increasing concentrations of lenalidomide. Primary screening was performed in a single-siRNA-per-well format with the human druggable genome siRNA set V4 comprising four siRNAs targeting each of 6,992 genes (total 27968 siRNAs). Lenalidomide was added 24 hours post transfection and cell viability was measured by ATP-dependent luminescence at 144 hours after transfection. Primary screen data was rigorously evaluated for multiple quality control metrics and found to exceed all expected performance parameters with >98% global transfection efficiency, <0.25 CV values, and minimal plate-to-plate and set-to-set variations observed. Hit selection was performed by analysis of IC50 value shift in the presence of each testing siRNA compared with three different control siRNA oligos. 160 candidate genes that enhance lenalidomide sensitivity upon silencing (sensitizers) were selected and re-screened with four siRNA oligos targeting each gene. 50 genes were identified as reproducible lenalidomide sensitizers including three Peroxisome (PEX) family proteins (PEX1, PEX10 and PEX7) and seven RAB family proteins (RAB17, RAB1A, RAB26, RAB30, RAB36, RAB4A and RAB8A). Four kinase genes were also identified in sensitizer hits and two of these, I-Kappa-B Kinase-Alpha (IKK1 or CHUK) and ribosomal protein S6 kinase (RPS6KA3 or RSK2), encode proteins that associate with significance together with a phosphorylation dependent transcription factor (CREB1) in Toll signaling pathways (p-value 0.0068). RSK2 is a serine/threonine-protein kinase that acts downstream of oncogenic FGFR3 mediated signaling and is phosphorylated by ERK (MAPK1/ERK2 and MAPK3/ERK1 signaling) during hematopoietic transformation. Phosphorylated RSK2 was previously reported to be frequently expressed in myeloma cell lines and primary myeloma cells. Using lentiviral shRNA expression, we demonstrated that knockdown of RSK2 in three genetically variable MM cell lines induced cyctocytoxiticy and consistently sensitized to lenalidomide. Two selective small molecular inhibitors of RSK2 (SL 0101-1 and BI-D1870) were then demonstrated to synergize with lenalidomide to induce myeloma cell cytotoxicixity. To further understand the mechanism underlying sensitization, immunoblotting analysis was performed to look at downstream changes after either RSK2 knockdown or RSK2 inhibition by BI-D1870. We found that both RSK2 knockdown and BI-D1870 treatment, mimicking lenalidomide treatment or cereblon inhibition, induced downregulation of both IRF4 and MYC in MM cells. The combination of lenalidomide and BI-D1870 not only produced a substantial synergistic effect inducing MM cytotoxicity, but also demonstrated a significant enhancement of downregulation of IRF4 and MYC. Forced overexpression of RSK2 attenuated the synergistic effects of lenalidomide and BI-D1870. In summary, our high throughput screen identified multiple gene targets that associate with increasing sensitivity to IMiDs in MM cells, of which, RSK2 was further validated by both shRNA silencing and specific inhibitors as an effective target to cooperate with IMiDs to induce myeloma cytotoxicity. Clinical studies of RSK2 inhibition in concert with IMiD (cereblon inhibitor) therapy would be appropriate. Disclosures: Stewart: Onyx: Consultancy, Research Funding; Millennium: Honoraria, Research Funding; Celgene: Honoraria; BMS: Honoraria.
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Desai, Ankit A., Homaa Ahmad, Tong Zhou, Wei Zhang, Sharon Trevino, Michael Wade, Nalini Raghavachari, et al. "Integration of Genomic and Genetic Approaches Highlight a Novel Validated Gene Signature for Pulmonary Hypertension Associated with Sickle Cell Disease." Blood 118, no. 21 (November 18, 2011): 511. http://dx.doi.org/10.1182/blood.v118.21.511.511.
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Abstract Abstract 511 Background: Pulmonary hypertension (PH) is a serious complication of sickle cell disease (SCD) associated with increased mortality. Gene expression profiles of peripheral blood mononuclear cells (PBMC) and genetic strategies have been studied in pulmonary arterial hypertension and in SCD. We hypothesized that a PBMC-derived gene signature in SCD patients may be utilized as a PH biomarker which may be further validated using integrated genomic and genetic strategies. Methods & Results: Twenty-seven patients with homozygous SCD underwent transthoracic echocardiography and PBMC isolation for genome—wide expression profiling. An independent SCD cohort (n=132) was genotyped using Affymetrix 6.0 SNP array and also underwent TTE. PH was defined as estimated right ventricular systolic pressure (RVSP)>30 mmHg with a peak tricuspid regurgitation velocity (TRV)>2.5m/s. Genome-wide mRNA and miRNA expression profiles were correlated against PH severity using RVSP (correlation coefficient ρR) and TRV (ρT) as surrogates. Utilizing a correlation threshold (ρR2>0.15, ρT2>0.15) for prioritization yielded 631 transcripts and 12 miRNAs. A support vector machine analysis on the transcripts identified a 10 gene signature which discriminated patients with and without echo-defined PH with 100% accuracy. This gene signature was then validated in an independent cohort of SCD patients with PH confirmed by right heart catheterization (n=10) and without PH (n=10) with 90% accuracy. In silico analyses of the top PH-related miRNAs revealed strong binding predictions of miR-301a to polypeptide N-acetylgalactosaminyltransferase 13 (GALNT13), a PH signature gene, which was further validated by microarray data confirming correlation between miR-301a and GALNT13 expression (p=0.024). Genome-wide association study in 132 adult SCD patients comparing echo-defined PH (n=51) versus no PH (n=81) revealed 12 significant SNPs, which were within or upstream to the PH signature genes (Table 1, P<0.01). Seven of the 12 SNPs were associated with GALNT13, further validating this top candidate PH signature gene. Integrating all available genomic and genetic information from a sub-population of 24 patients with SCD revealed significant expression quantitative trait loci (eQTLs) associated with echo-defined PH. Within our PH signature genes, we found four trans-acting eQTLs, based on a FDR<5% with Bonferroni-Holm correction (p=2.1 e-07 for all four) and 1 cis-acting eQTL (p=0.6e-04) upstream of the adenosine A2B receptor gene (ADORA2B) based on a nominal p value 1e–03. Conclusion: These genomic signatures are potential biomarkers to screen at-risk populations in SCD for the presence of PH. Integrative analyses with genomic and genetic analyses highlight ADORA2B and GALNT13, a glycosyltransferase enzyme, as potential candidate genes in SCD-related PH. Disclosures: No relevant conflicts of interest to declare.
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Messick, Troy E., Samantha S. Soldan, Julianna Deakyne, and Paul M. Lieberman. "Development of a small molecule drug for EBV-associated gastric cancers." Journal of Clinical Oncology 35, no. 4_suppl (February 1, 2017): 63. http://dx.doi.org/10.1200/jco.2017.35.4_suppl.63.
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63 Background: Worldwide, EBV is associated with ~10% of gastric cancer. Currently, no pharmaceutical-based therapies exist that selectively target EBV associated gastric cancers. EBV, in its latent oncogenic form, is dependent on the continuous expression of Epstein-Barr Nuclear Antigen 1 (EBNA1), a multifunctional dimeric protein critical for viral replication, genome maintenance and viral gene expression. Methods: The aim of this program is to advance the development of a New Chemical Entity (NCE) for latent infection of Epstein-Barr Virus (EBV) to treat EBV-associated gastric cancer. We have used structure-based drug design and medicinal chemistry methods to identify and develop a small molecule clinical candidate that selectively inhibits the DNA-binding activity of EBNA1. Results: The clinical candidate inhibits EBNA1 function with nanomolar potency in biochemical assays and low micromolecular activity in several cell-based assays. We demonstrate that our clinical candidate provides protection in 4 different xenograft models of EBV-driven tumor growth, including patient-derived xenografts. Furthermore, RNA analysis experiments confirm in vivo target engagement by the elimination of EBV in treated tumor tissue. The clinical candidate is selective, showing no activity in an EBV-negative xenograft experiments. The clinical candidate has met industry-accepted criteria for drug suitability, safety and toxicology including physicochemical properties, metabolic stability, selectivity in broad-based screens and bioavailability, and lack in vivoliabilities, including genotoxicity and 14-day toxicity studies. Conclusions: IND-enabling studies including safety pharmacology and toxicology and GMP manufacturing have begun with a projected First-In-Human clinical trial in Q4 2017. These data establish proof-of-concept for targeting EBNA1—a protein previously thought to be undruggable.
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Duggan, Shane P., Sinead Phipps, Fiona Behan, Catherine Garry, and Dermot P. Kelleher. "Dissecting the invasive potential of esophageal cancer by siRNA library screening." Journal of Clinical Oncology 33, no. 3_suppl (January 20, 2015): 86. http://dx.doi.org/10.1200/jco.2015.33.3_suppl.86.
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86 Background: The low survival for esophageal cancer is in part attributed to its high invasive potential and distant metastasis. In cancer, abnormal cell migration is an essential component of metastasis, and it is reasonable to consider that the conversion between different forms of morphology permits tumor cells to metastasise. Discovering regulators of esophageal cancer morphogenesis may aid in the development of novel targeted therapies that limit metastatic potential. Methods: GOhTRT cells were seeded and treated with siRNA (Human Druggable Genome, Dharmacon) by reverse transfection. Cells were fixed, immunostained for DNA, tubulin and actin and imaged with automated microscope. Cell images were processed using the InCell Analyzer software and the R statistical software systems CellHTS2 and RNAither. The effect of RNAi knockdown on cell viability and cell motility were assessed using MTT cell proliferation assay and scratch wound assay. Results: 127 gene candidates greatly exhibited effects on F-actin and α-tubulin area staining. This list was refined to six high quality candidates (RRM2, ITGB8, GPS1, SPRY1, NOL1 and MYO9B). Silencing of GPS1, MYO9B and SPRY1 increased the rate of migration in a scratch wound assay, with 86.98% ± 3.097%, 75.78% ±5.454% and 72.97% ± 5.463% (p =0.0022) respectively. There was no significant difference in cell viability absorbance values for siGPS1 (0.9037 ± 0.06575; p =0.1905) and siSPRY1 (0.9088 ± 0.09849; p =0.2985), which suggests that the increased rate of wound closure previously seen is by virtue of migratory signalling as oppose to an increase in cell proliferation. Cell viability was decreased considerably in siRRM2 cells (0.2492 ± 0.02798; p <0.0001) and siMYO9B (0.4048 ± 0.04663; p<0.0001) in comparison to siNT cells (1.046 ± 0.07712). Conclusions: In summary, this screen successfully identified high confidence hits associated with cytoskeletal remodelling, some of which are already associated with metastasis in literature and database searches. Further mechanistic studies and gene pathway analysis of candidate genes will provide novel therapeutic targets which can be utilised to block the spread of cancer in patients.
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Veo, Bethany, Etienne Danis, Susan Fosmire, Dong Wang, Angela Pierce, Nathan Dahl, Sana Karam, Natalie Serkova, Sujatha Venkataraman, and Rajeev Vibhakar. "MBRS-26. CDK7 MEDIATED TRANSCRIPTIONAL PROCESSIVITY OF DNA REPAIR NETWORKS REGULATES SENSITIVITY TO RADIATION IN MYC DRIVEN MEDULLOBLASTOMA." Neuro-Oncology 22, Supplement_3 (December 1, 2020): iii403. http://dx.doi.org/10.1093/neuonc/noaa222.541.
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Abstract Myc-driven Medulloblastoma remains a major therapeutic challenge due to frequent metastasis and a poor 5-year survival rate. Myc overexpression results in transcriptional dysregulation, proliferation, and survival of malignant cells. To identify therapeutic targets in Myc-amplified medulloblastoma we performed a CRISPR-Cas9 essentiality screen targeting 1140 genes annotated as the druggable genome. The cyclin-dependent kinase, CDK7, was identified as a top candidate. CDK7 phosphorylates the c-terminal domain of RNA Pol II facilitating transcriptional initiation and elongation. We subjected Myc-amplified cells treated with CDK7 inhibitors to whole transcriptomic analysis. The resultant data revealed gene networks mediating DNA repair were functionally repressed. Consistent with this data, ChIP-sequencing showed the most significant reduction in RNA Pol II and Myc promoter occupancy within a subset of DNA repair genes including BRCA2 and RAD51 but not across the whole genome. These data suggest that inhibition of CDK7 mechanistically limits Myc driven transcriptional processivity of DNA repair networks. Further, evaluation of genes mediating DNA repair show a muted response to DNA damage and increased cell death with CDK7 inhibition. We next evaluated Myc-amplified MB cell response to ionizing radiation in vitro and in vivo with CDK7 inhibition. Inhibition of CDK7 enhanced radiation sensitivity of Myc MB cells by potentiating DNA damage. Further, cotreatment produced decreased MRI T2 tumor volumes and enhanced survival benefit in orthotopic PDX xenografted mice compared to radiation alone. Our studies establish a mechanism for selective inhibition of Myc-driven MB by CDK7 inhibition combined with radiation as a viable therapeutic strategy for Myc-amplified medulloblastoma.
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Gandolfi, Sara, Michal Sheffer, Emily Lowry, Olga Dashevsky, Ryosuke Shirasaki, Ricardo De Matos Simoes, and Constantine S. Mitsiades. "Identification of Molecular Markers of Tumor Cell Sensitivity and Resistance to Natural Killer Cells through Genome-Wide CRISPR Activation and CRISPR Editing Screens in Multiple Myeloma Cell Lines: Implications for Anti-Myeloma Immunotherapy." Blood 132, Supplement 1 (November 29, 2018): 1115. http://dx.doi.org/10.1182/blood-2018-99-118736.
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Abstract Natural killer (NK) cells represent a promising immunotherapeutic approach as they can potently kill tumor cells without triggering graft-versus-host reactions. Indeed, infusion of high numbers of NK cells, either autologous or allogeneic, after their ex vivo expansion and activation, has been feasible and safe in clinical studies. However, prior studies and early clinical trials indicate that tumor cells can exhibit decreased response to NK due to the protective effect of nonmalignant mesenchymal stromal cells; and depending on the genetic background of the tumor cells. To our knowledge, since earlier subgenome-scale RNAi-based studies, there have been no genome-wide CRISPR-based screens to identify candidate markers conferring tumor cell resistance or sensitivity to NK cells in multiple myeloma (MM). To address this void, and building on a recent loss-of-function (LOF) study by our group on solid tumors, we sought to identify genes regulating the response of MM cells to the cytotoxic activity of NK cells by conducting a genome-wide CRISPR/Cas9-based gene editing (Brunello library of sgRNA) and gene activation (Calabrese library of sgRNA) screens in MM.1S cells co-cultured with primary NK (pNK) cells (effector-to-target [E:T] ratio of 3.75:1) derived from healthy donor peripheral blood mononuclear cells (PBMCs) cultured in vitro in GMP SCGM medium with IL-2. Briefly, MM.1S cells engineered to stably express the nuclease SpCas9 (Brunello) or a catalytically inactive programmable RNA-dependent DNA-binding protein (dCas9)-VP64 (Calabrese) were also transduced with lentiviral particles for a pool of ~70,000 (Brunello library) or ~120,000 (Calabrese) sgRNAs, targeting exons of ~20,000 genes (plus non-targeting control sgRNAs), under conditions of transduction which allow for an average of no more than 1 sgRNA to be incorporated in a given cell. This allowed us to convert the initial population of MM.1S cells into heterogeneous pools in which each gene is subject to individual LOF or gain-of-function (GOF), due to Cas9-mediated editing, by only 1 sgRNA. Flow cytometry was performed to verify pNK viability, purity (CD56 and CD3), and expression of p46 receptor, surrogate marker of NK cell activity. These screens identified genes whose knock-out (Brunello sgRNA library) or activation (Calabrese sgRNA library) led to NK cells resistance or potential sensitivity. The hits observed in the current MM-oriented study exhibited, compared to our similar studies in solid tumor model, substantial gene level differences, but notable overlap at the pathway level (including death receptor pathways, NK activating pathways), which suggests that mechanisms determining tumor cell response vs. resistance to NK cells operate through modules consistent across tumors, but manifested through potentially different members of the respective pathways in different neoplasms. For instance, in this MM-oriented study, we identified that NK cell sensitivity of tumor cells is modulating by activation of several metabolic and homeostatic genes, receptor kinases, and interestingly membrane-bound proteins of the mucin family, e.g. MUC1, and MUC4, which have been reported to play a role in NK-mediated tumor killing in other types of cancer. MUC1 in particular has a clinical relevance as a small molecule inhibitor with prior preclinical studies in MM is available. Interestingly, our GOF screen identified as potential NK cell sensitizers TNFRSF10B, a death receptor related to TNFRSF10A (a hit identified in our studies in solid tumors), the putative death receptor adaptor TRADD, and the NK ligands PVR and ULBP1. Interestingly, genes such as PTEN and TP53, commonly associated with high-risk MM, didn't affect the response to NK cell, suggesting that NK cell-based therapies may potentially have a role in treatment of MM patients with high-risk clinical or biological features. In conclusion, this is the first study applying both LOF and GOF genome-wide screens to NK cell response in MM. The combination of such screens performed in parallel provide complementary and orthogonal information that allows us to identify genes that might not have been appreciated if only either LOF or GOF alone screens had been performed. We envision that the methodology and results presented herein will provide a framework towards validation of molecular markers which can help to optimize and individualize the use of NK cell-based therapy in MM. Disclosures Mitsiades: Abbvie: Research Funding; TEVA: Research Funding; EMD Serono: Research Funding; Janssen/ Johnson & Johnson: Research Funding; Takeda: Other: employment of a relative.
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Yu, Lijun, Meiyan Wei, and Fengyan Li. "Longitudinal Analysis of Gene Expression Changes During Cervical Carcinogenesis Reveals Potential Therapeutic Targets." Evolutionary Bioinformatics 16 (January 2020): 117693432092057. http://dx.doi.org/10.1177/1176934320920574.
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Despite advances in the treatment of cervical cancer (CC), the prognosis of patients with CC remains to be improved. This study aimed to explore candidate gene targets for CC. CC datasets were downloaded from the Gene Expression Omnibus database. Genes with similar expression trends in varying steps of CC development were clustered using Short Time-series Expression Miner (STEM) software. Gene functions were then analyzed using the Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Protein interactions among genes of interest were predicted, followed by drug-target genes and prognosis-associated genes. The expressions of the predicted genes were determined using real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting. Red and green profiles with upward and downward gene expressions, respectively, were screened using STEM software. Genes with increased expression were significantly enriched in DNA replication, cell-cycle-related biological processes, and the p53 signaling pathway. Based on the predicted results of the Drug-Gene Interaction database, 17 drug-gene interaction pairs, including 3 red profile genes (TOP2A, RRM2, and POLA1) and 16 drugs, were obtained. The Cancer Genome Atlas data analysis showed that high POLA1 expression was significantly correlated with prolonged survival, indicating that POLA1 is protective against CC. RT-qPCR and Western blotting showed that the expressions of TOP2A, RRM2, and POLA1 gradually increased in the multistep process of CC. TOP2A, RRM2, and POLA1 may be targets for the treatment of CC. However, many studies are needed to validate our findings.
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Burgos, Hector L., Emanuel F. Burgos, Andrew J. Steinberger, Garret Suen, and Mark J. Mandel. "Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions." mSystems 5, no. 6 (December 15, 2020): e00846-20. http://dx.doi.org/10.1128/msystems.00846-20.
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ABSTRACTBeneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces.IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes—both beneficial and pathogenic—colonize specific animal hosts.
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Kotini, Andriana, Jeffrey J. Delrow, Timothy A. Graubert, Stephen Nimer, and Eirini P. Papapetrou. "Functional Dissection of Chromosome 7q Loss and Haploinsufficient Gene Discovery Using iPSC Models of MDS." Blood 124, no. 21 (December 6, 2014): 524. http://dx.doi.org/10.1182/blood.v124.21.524.524.
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Abstract Somatic loss of one copy of the long arm of chromosome 7 [del(7q)] is a characteristic cytogenetic abnormality in MDS and other myeloid malignancies, well-recognized for decades and associated with unfavorable prognosis. Despite compelling clinical evidence that the del(7q) holds a key to the pathogenesis of MDS, the mechanism remains elusive. Gene haploinsufficiency has been proposed as a plausible mechanism, but definitive evidence is lacking. Narrowing down the responsible region and identifying the critical genes has proved challenging with existing approaches. Chr7q deletions are typically very large and modeling in the mouse is problematic, as the genomic regions syntenic to the human chr7q are dispersed into 4 different mouse chromosomes. More than one commonly deleted regions (CDRs) have been proposed by physical mapping studies in patient cells. A handful of genes on chr7q have been implicated through candidate gene approaches and knockout studies in the mouse. However, despite the intense efforts, the contribution of the del(7q) to the disease phenotype and the critical gene or genes on chr7q that mediate it remain unclear. To overcome the limitations of existing tools (primary patient cells, mouse models) to study del(7q)-MDS, we developed a new model harnessing reprogramming and genome editing technologies. First we derived del(7q)-, in parallel with isogenic karyotypically normal induced pluripotent stem cells (iPSCs) from bone marrow hematopoietic cells of two MDS patients. By whole exome sequencing, we were able to identify somatic variants of the MDS clone and show that they are present in the del(7q)-MDS-iPSCs, but not in the karyotypically normal iPSCs, which therefore unambiguously originate from residual normal cells. We used these isogenic and fully genetically characterized patient-derived iPSCs to characterize disease-relevant cellular phenotypes specific to the MDS-iPSCs, which included severely reduced hematopoietic potential and clonogenicity and increased apoptosis. We next found that iPSC clones spontaneously acquiring a second copy of chr7q had an in vitro growth advantage, which enabled us to isolate one clone that completely rescued its hematopoietic differentiation ability upon restoration of a diploid dosage of a ~30Mb chr7q telomeric region. This result provides the first definitive evidence that the del(7q) abnormality confers a profound loss of hematopoietic potential and that this defect is mediated through reduced dosage, consistent with haploinsufficiency of one or more genes. To further narrow down the critical region, we developed genome editing technologies to engineer large chromosomal deletions for the first time in human cells. Combining gene targeting with a modified Cre-loxP approach and the CRISPR/Cas9 endonuclease technology, we were able to generate a panel of 12 iPSC lines harboring hemizygous deletions of various defined segments spanning the entire long arm of chr7. By asking which of them recapitulate the MDS hematopoietic phenotype, we were able to “functionally map” the critical segment in a region spanning cytobands q32.3 - q36.1. To identify critical gene(s) on chr7q, we designed a phenotype-rescue screen. We selected 62 candidate haploinsufficient genes on the basis of significantly reduced expression in del(7q)- compared to isogenic normal iPSCs. We constructed a barcoded lentiviral library of these ORFs and performed a pooled library screen for rescue of hematopoiesis in del(7q)-MDS-iPSCs, i.e. enrichment in CD45+ hematopoietic progenitors. We selected the top 6 genes within our region that were found recurrently enriched in at least 2 independent experiments. Four of them could be individually validated: dosage complementation partially rescued hematopoiesis and knockdown studies mimicking haploinsufficiency (50% knockdown) in normal primary CD34+ hematopoietic progenitor cells had a detrimental effect in hematopoiesis. The four genes include EZH2 and LUC7L2 – two genes found to harbor recurrent heterozygous loss-of-function mutations in MDS – as well as two genes with no previously known role in MDS, located in close genomic proximity to the former two. This approach, constituting a new paradigm of functional human genetics with patient-specific iPSCs, can be more broadly applicable to the study of the phenotypic consequences of segmental chromosomal deletions and to haploinsufficient gene discovery. Disclosures No relevant conflicts of interest to declare.
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Ventosa, Maria, Padma Kadiyala, Stephen Carney, Maria Castro, and Pedro Lowenstein. "GENE-32. SYNTHETIC LETHAL INTERACTIONS WITH IDH1R132H IN GLIOMA STEM-LIKE CELLS." Neuro-Oncology 21, Supplement_6 (November 2019): vi104. http://dx.doi.org/10.1093/neuonc/noz175.434.
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Abstract Gliomas are the most frequently diagnosed human primary brain tumors. Mutations in Isocitrate Dehydrogenase (IDH) 1 occur in the vast majority of low grade gliomas and secondary high grade glioblastomas. A single amino acid missense mutation in IDH1 at arginine 132 (R132H) is an early event in tumor development. IDH1R132H leads to the production of the oncometabolite 2-R-2-hydroxyglutarate. However the exact roles played by IDH1R132H in the development and malignant transformation of the tumors remain unclear. Further studies are required to determine optimal therapeutic strategies to target the IDH1 mutated subsets of gliomas. New generation high-throughput genetic perturbation technologies make it possible to systematically identify the genes and pathways required for the survival and proliferation of mammalian cells. Herein, we present preliminary results from a CRISPR-dCas9 derived activation to drive the transcriptional activation of more than 23,000 coding genes in both wild type and mutant IDH1 patient-derived pediatric glioma cells. Based on an average of three viability screens per cell type, we analyzed the sgRNA library representation in the IDH1 mutated and non-mutated glioma cultures after the genome wide activation. We identified 1553 candidate genes that upon gain of function trigger the death of glioma cells harboring the IDH1 mutation. The analysis of these results further pinpoints the activation of the Cyclin E1 (CCNE1), the BCL2 Antagonist/Killer 1 (BAK1) and the Homeobox B13 (HOXB13) as the most significant synthetic lethal targets in IDH1R132H glioma cells. Interestingly, results from RNAseq showed a decreased expression of these genes in IDH1 mutated compared to non-mutated glioma cells. Thus, this viability screening aims to elucidate genes that interact with IDH1R123H and play a role in tumor cell fitness. The functional analysis of these candidate genes will allow us to uncover their contribution to the progression of IDH1 mutated gliomas.
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Cullum, Richard L., Lauren M. Lucas, Jared I. Senfeld, John T. Piazza, Logan T. Neel, Kanupriya Whig, Ling Zhai, et al. "Development and application of high-throughput screens for the discovery of compounds that disrupt ErbB4 signaling: Candidate cancer therapeutics." PLOS ONE 15, no. 12 (December 30, 2020): e0243901. http://dx.doi.org/10.1371/journal.pone.0243901.
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Whereas recent clinical studies report metastatic melanoma survival rates high as 30–50%, many tumors remain nonresponsive or become resistant to current therapeutic strategies. Analyses of The Cancer Genome Atlas (TCGA) skin cutaneous melanoma (SKCM) data set suggests that a significant fraction of melanomas potentially harbor gain-of-function mutations in the gene that encodes for the ErbB4 receptor tyrosine kinase. In this work, a drug discovery strategy was developed that is based on the observation that the Q43L mutant of the naturally occurring ErbB4 agonist Neuregulin-2beta (NRG2β) functions as a partial agonist at ErbB4. NRG2β/Q43L stimulates tyrosine phosphorylation, fails to stimulate ErbB4-dependent cell proliferation, and inhibits agonist-induced ErbB4-dependent cell proliferation. Compounds that exhibit these characteristics likely function as ErbB4 partial agonists, and as such hold promise as therapies for ErbB4-dependent melanomas. Consequently, three highly sensitive and reproducible (Z’ > 0.5) screening assays were developed and deployed for the identification of small-molecule ErbB4 partial agonists. Six compounds were identified that stimulate ErbB4 phosphorylation, fail to stimulate ErbB4-dependent cell proliferation, and appear to selectively inhibit ErbB4-dependent cell proliferation. Whereas further characterization is needed to evaluate the full therapeutic potential of these molecules, this drug discovery platform establishes reliable and scalable approaches for the discovery of ErbB4 inhibitors.
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Gonzalez-Jaramillo, Valentina, Eliana Portilla-Fernandez, Marija Glisic, Trudy Voortman, Mohsen Ghanbari, Wichor Bramer, Rajiv Chowdhury, et al. "Epigenetics and Inflammatory Markers: A Systematic Review of the Current Evidence." International Journal of Inflammation 2019 (May 8, 2019): 1–14. http://dx.doi.org/10.1155/2019/6273680.
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Epigenetic mechanisms have been suggested to play a role in the genetic regulation of pathways related to inflammation. Therefore, we aimed to systematically review studies investigating the association between DNA methylation and histone modifications with circulatory inflammation markers in blood. Five bibliographic databases were screened until 21 November of 2017. We included studies conducted on humans that examined the association between epigenetic marks (DNA methylation and/or histone modifications) and a comprehensive list of inflammatory markers. Of the 3,759 identified references, 24 articles were included, involving, 17,399 individuals. There was suggestive evidence for global hypomethylation but better-quality studies in the future have to confirm this. Epigenome-wide association studies (EWAS) (n=7) reported most of the identified differentially methylated genes to be hypomethylated in inflammatory processes. Candidate genes studies reported 18 differentially methylated genes related to several circulatory inflammation markers. There was no overlap in the methylated sites investigated in candidate gene studies and EWAS, except for TMEM49, which was found to be hypomethylated with higher inflammatory markers in both types of studies. The relation between histone modifications and inflammatory markers was assessed by one study only. This review supports an association between epigenetic marks and inflammation, suggesting hypomethylation of the genome. Important gaps in the quality of studies were reported such as inadequate sample size, lack of adjustment for relevant confounders, and failure to replicate the findings. While most of the studies have been focused on C-reactive protein, further efforts should investigate other inflammatory markers.
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Fang, Peihong, Paul Arens, Xintong Liu, Xin Zhang, Deepika Lakwani, Fabrice Foucher, Jérémy Clotault, et al. "Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs." Theoretical and Applied Genetics 134, no. 8 (May 2, 2021): 2495–515. http://dx.doi.org/10.1007/s00122-021-03838-7.
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Abstract Key message Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Abstract Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certain MLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, these MLO genes are called susceptibility genes. We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data. We identified 19 MLO genes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicot MLO susceptibility genes. We detected a total of 198 different allelic variants in the set of Rosa species and accessions, corresponding to 5–15 different alleles for each of the genes. Some diploid Rosa species shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the four RhMLO genes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them, RhMLO1 and RhMLO2, are required for infection by P. pannosa and suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.
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Oravecz, Tamas, Alex Turner, Philip Brown, Brian Zambrowicz, and Gerd Blobel. "Genetic Modeling of Chemical Antagonists: Genome Scale Validation of Hematopoietic Disease Drug Targets by In Vivo Functional Analysis." Blood 104, no. 11 (November 16, 2004): 2577. http://dx.doi.org/10.1182/blood.v104.11.2577.2577.
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Abstract Clinical management remains elusive for a large number of patients with hematological and other disorders necessitating the development of new, more effective pharmaceutical agents. While the sequencing of the human genome has provided a list of all drug targets that will ever exist, in order to improve the speed and cost of drug development there is a critical need to identify the small subset of these targets whose modulation will lead to therapeutic outcomes. As a genetic model of a perfectly selective and potent chemical antagonist, the analysis of the phenotypes of knockout mice allows one to predict the mechanism based efficacy and side effect profile of modulators of a particular target in a physiologic mammalian setting without having to first develop a candidate drug with which to validate the target. The power of this approach has been demonstrated by studies examining the targets of the best-selling drugs and current pharmaceutical pipelines. These analyses have confirmed a strong (~85%) correlation between the target’s knockout phenotype and the efficacy and/or side effects of drugs that modulate them. We have implemented this target validation approach by developing systems and infrastructure to generate and comprehensively phenotype mutant mice at a rate of more than fifteen novel lines per week. The battery of tests encompassed by our analysis have been specifically selected to reveal those genes that encode key control points in mammalian physiology whose modulation may be used to treat major disease processes including hematologic disorders. Tests to detect hematologic phenotypes include complete blood count; immunophenotyping; blood chemistry; analysis of soluble factors (immunoglobulins, cytokines and inflammatory mediators); full histopathologic examination, and various in vivo and in vitro immune challenge and cell activation assays. In addition, selected lines are subjected to more extensive analyses including additional challenge assays, gene expression profiling, and bone marrow transplantation. Data will be presented describing one of the lines analyzed in this screen, the Abl2 knockout, which has an increased mean total white blood count relative to wild-type littermates, as well as smaller body size (decreased length and weight). In parallel with the identification of therapeutically relevant proteins, we are actively exploring pharmacologic methods, both with small molecules and therapeutic antibodies, to modify the function of these novel gene targets, and ultimately to treat human disease.
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Schieber, Michael, and John D. Crispino. "FBXO11 Is a Candidate Tumor Suppressor in the Transformation of MDS to Secondary AML." Blood 134, Supplement_1 (November 13, 2019): 4217. http://dx.doi.org/10.1182/blood-2019-124007.
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Myelodysplastic syndrome (MDS) is a heterogenous myeloid lineage malignancy characterized by blood cell morphological dysplasia, ineffective clonal hematopoiesis, and risk of secondary transformation to acute myeloid leukemia (sAML). Genomic sequencing of large MDS cohorts has led to the identification of recurrent genetic abnormalities that carry independent prognostic significance and overlap with mutational changes in sAML. However, no set of mutations is sufficient to predict the transformation of MDS raising the question of how an identical genotype produces MDS in one patient and sAML in another? We hypothesize there are therapeutically targetable cellular processes altered by the initiating genetic changes in MDS that predict transformation to sAML. To uncover novel cellular pathways involved in MDS transformation, we performed an unbiased genome-wide CRISPR/Cas9 in the human MDS-L cell line. MDS-L was established from bone marrow mononuclear cells in a 52-year-old male patient and requires IL3-containing media for growth in vitro (Figure 1A). GFP expressing MDS-L cells were transduced with Cas9 and a sgRNA against GFP to confirm functional Cas9 expression in MDS-L (Figures 1B and C). In Cas9 expressing MDS-L cells, we then transduced the Brunello sgRNA CRISPR library and subjected the cells to IL-3 starvation for 4 weeks. Cells surviving IL-3 starvation were then expanded and harvested for genomic DNA. High throughput sequencing of the barcoded DNA produced raw reads that were analyzed using the PinAPL-Py web-based software. sgRNAs appearing in duplicate with absolute read counts over 1000 or in triplicate over 100 were considered significant. We identified 5 genes that conferred resistance to IL-3 starvation, which included FBXO11 (Figure 1D). The Fbox protein FBXO11 is a component of the SCF ubiquitin ligase complex and regulates its substrates via ubiquitination and proteasomal degradation. FBXO11 is mutated in up to 20% of diffuse large B-cell lymphomas and its loss in breast cancer models leads to increased metastases. Therefore, we hypothesized FBXO11 may also function as a tumor suppressor in the transformation of MDS to AML. We confirmed in the Bloodspot gene expression database that there are decreased levels of FBXO11 in a variety of AML samples, including complex karyotype, compared to normal HSCs. To validate the results of the screen, we synthesized two sgRNAs targeting FBXO11, transduced these into MDS-L cells, and detected reduced FBXO11 expression (Figure 1E). Loss of FBXO11 expression promoted survival in IL-3 free media, confirming the selection readout of the screen (Figure 1F). We then designed a silent mutation in the shorter isoform of FBXO11 (FBXO11v1sm1) that rendered resistance to CRISPR/Cas9 (Figure 1G) and observed that overexpression of FBXO11v1sm1 re-sensitized cells to cytokine starvation (Figure 1H). Whether there are different functions between FBXO11 variant 1 and 4 are currently being explored. We are actively performing RNA sequencing and ubiquitin proteomics in FBXO11 knockout cells to identify its downstream targets and assaying for reduced expression of FBXO11 in primary patient MDS and AML samples. Based on our studies, we predict that SCF ubiquitin ligase component FBXO11 is a tumor suppressor regulating the transformation of MDS to secondary AML. Figure 1 Disclosures Crispino: Sierra Oncology: Consultancy; MPN Research Foundation: Membership on an entity's Board of Directors or advisory committees; Forma Therapeutics: Research Funding; Scholar Rock: Research Funding.
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Lathen, Daniel R., Collin B. Merrill, and Adrian Rothenfluh. "Flying Together: Drosophila as a Tool to Understand the Genetics of Human Alcoholism." International Journal of Molecular Sciences 21, no. 18 (September 11, 2020): 6649. http://dx.doi.org/10.3390/ijms21186649.
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Alcohol use disorder (AUD) exacts an immense toll on individuals, families, and society. Genetic factors determine up to 60% of an individual’s risk of developing problematic alcohol habits. Effective AUD prevention and treatment requires knowledge of the genes that predispose people to alcoholism, play a role in alcohol responses, and/or contribute to the development of addiction. As a highly tractable and translatable genetic and behavioral model organism, Drosophila melanogaster has proven valuable to uncover important genes and mechanistic pathways that have obvious orthologs in humans and that help explain the complexities of addiction. Vinegar flies exhibit remarkably strong face and mechanistic validity as a model for AUDs, permitting many advancements in the quest to understand human genetic involvement in this disease. These advancements occur via approaches that essentially fall into one of two categories: (1) discovering candidate genes via human genome-wide association studies (GWAS), transcriptomics on post-mortem tissue from AUD patients, or relevant physiological connections, then using reverse genetics in flies to validate candidate genes’ roles and investigate their molecular function in the context of alcohol. (2) Utilizing flies to discover candidate genes through unbiased screens, GWAS, quantitative trait locus analyses, transcriptomics, or single-gene studies, then validating their translational role in human genetic surveys. In this review, we highlight the utility of Drosophila as a model for alcoholism by surveying recent advances in our understanding of human AUDs that resulted from these various approaches. We summarize the genes that are conserved in alcohol-related function between humans and flies. We also provide insight into some advantages and limitations of these approaches. Overall, this review demonstrates how Drosophila have and can be used to answer important genetic questions about alcohol addiction.
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Gandolfi, Sara, Michal Sheffer, Olli Dufva, Khalid Saeed, Emily Lowry, Olga Dashevsky, Ryosuke Shirasaki, et al. "Heterogeneity of Molecular Mechanisms Determining Blood Cancer Cell Lines Resistance to Natural Killer Cells in the Context of Tumor-Stromal Interactions: Insights from Studies of Pooled "DNA-Barcoded" Cell Line Panels." Blood 134, Supplement_1 (November 13, 2019): 620. http://dx.doi.org/10.1182/blood-2019-130793.
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Immunotherapy has remarkably changed the treatment paradigm in hematologic malignancies and natural killer (NK) cell therapy represents an attractive option, as it has been feasible and safe in early clinical trials, without graft-versus-host effects. Nevertheless, the molecular markers determining cancer cell sensitivity or resistance to NK cells, especially in the context of tumor cell interaction with the bone marrow (BM) stromal microenvironment remain incompletely understood, but have major translational relevance since these tumor-stromal interactions have been known to attenuate the response of blood cancer cells to diverse classes of pharmacological agents. To address these questions, we performed NK cell treatment of a series of cell lines from hematologic malignancies by applying a pooled "DNA-barcoded" format of these cell lines (PRISM system). We specifically quantified the dose-dependent responses to primary NK cells for 70 molecularly-annotated blood cancer cell lines, including myeloid and lymphoblastic leukemia, diffuse large B cell lymphoma and 15 multiple myeloma (MM) lines, either in presence or in absence of BM stromal cells (BMSCs) and interferon gamma (IFNg), followed by integrated computational analyses to identify candidate molecular markers correlating with tumor cell sensitivity or resistance to NK cells. NK cell cytotoxicity, quantified by the relative abundance of barcodes in treated cells compared to controls, was correlated with the transcriptional, mutational and other molecular features of each of the 70 cell lines from publicly available databases. Furthermore, data from MM cell lines were compared to our genome-wide loss of function (LOF) and gain of function (GOF) CRISPR screen data in the MM cell line MM.1S. Two distinct clusters of cell lines, sensitive and resistant to NK cell treatment, were identified. Such clusters retained distinct pattern of in vitro resistance in the presence of stroma, while showing an overall markedly decreased NK cell responsiveness, which underscores the protective effect of stromal microenvironment in blood malignancies, regardless of the addition of IFNg. RNA-seq data showed no differences in dependencies between the two clusters and no distinct gene expression patterns at baseline that clearly allows to predict NK cell response, which underscores the heterogeneity of resistance patterns at single gene level, across different hematologic malignancies. However, when comparing baseline RNAseq data to data obtained from previous GOF and LOF CRISPR screens in MM.1S, surface antigens such as PVR, ULBP1, ULBP3 were more frequently downregulated, whereas MUC1 was upregulated in resistant cells clusters. An important observation is that gene lesions such as TP53, PTEN, MMSET, commonly associated with high-risk diseases, do not affect NK cell responses in the cell lines tested. Interestingly, a gene set enrichment analysis (GSEA) showed that the cluster of resistant cells displays upregulation of class I MHC complex, class II MHC complex binding, IL7 pathway and a downregulation of transmembrane receptor protein serine/threonine kinase signaling pathway. GSEA also showed that baseline state of IFN-JAK-STAT signaling correlates with BMSCs-induced NK cell resistance, a result further confirmed by addition of IFNgto tumor-NK cocultures in the absence of BMSCs. No significant differences in NK cell response were observed when comparing cell lines of different hematologic neoplasms, suggesting that candidate markers from these studies may be relevant across different hematologic malignancies. In conclusion, this is the first study of this size correlating the molecular annotation of different concurrently-treated hematologic cell lines with their response to a NK-based treatment in the context of BMSC interaction. This study of a large panel of pooled "DNA-barcoded" cell lines provided complementary and orthogonal information to our LOF and GOF screens, expanding our potential to identify and validate molecular markers for individualized use of NK cell-based therapies in hematologic malignancies. Disclosures Mustjoki: BMS: Honoraria, Research Funding; Novartis: Research Funding; Pfizer: Research Funding. Mitsiades:EMD Serono: Research Funding; Abbvie: Research Funding; Karyopharm: Research Funding; Sanofi: Research Funding; Arch Oncology: Research Funding; Fate Therapeutics: Honoraria; Ionis Pharmaceuticals: Honoraria; Takeda: Other: employment of a relative ; Janssen/Johnson & Johnson: Research Funding; TEVA: Research Funding.
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Schneider, Eberhard, Nady El Hajj, Fabian Müller, Bianca Navarro, and Thomas Haaf. "Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers." Cytogenetic and Genome Research 146, no. 1 (2015): 19–27. http://dx.doi.org/10.1159/000435778.
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The epigenome is thought to mediate between genes and the environment, particularly in response to adverse life experiences. Similar to other psychiatric diseases, the suicide liability of an individual appears to be influenced by many genetic factors of small effect size as well as by environmental stressors. To identify epigenetic marks associated with suicide, which is considered the endpoint of complex gene-environment interactions, we compared the cortex DNA methylation patterns of 6 suicide completers versus 6 non-psychiatric sudden-death controls, using Illumina 450K methylation arrays. Consistent with a multifactorial disease model, we found DNA methylation changes in a large number of genes, but no changes with large effects reaching genome-wide significance. Global methylation of all analyzed CpG sites was significantly (0.25 percentage point) lower in suicide than in control brains, whereas the vast majority (97%) of the top 1,000 differentially methylated regions (DMRs) were higher methylated (0.6 percentage point) in suicide brains. Annotation analysis of the top 1,000 DMRs revealed an enrichment of differentially methylated promoters in functional categories associated with transcription and expression in the brain. In addition, we performed a comprehensive literature research to identify suicide genes that have been replicated in independent genetic association, brain methylation and/or expression studies. Although, in general, there was no significant overlap between different published data sets or between our top 1,000 DMRs and published data sets, our methylation screen strengthens a number of candidate genes (APLP2, BDNF, HTR1A, NUAK1, PHACTR3, MSMP, SLC6A4, SYN2, and SYNE2) and supports a role for epigenetics in the pathophysiology of suicide.