1
|
Wang J, Thomas HR, Chen Y, Percival SM, Waldrep SC, Ramaker RC, Thompson RG, Cooper SJ, Chong Z, Parant JM. Reduced sister chromatid cohesion acts as a tumor penetrance modifier. PLoS Genet 2022; 18:e1010341. [PMID: 35994499 PMCID: PMC9436123 DOI: 10.1371/journal.pgen.1010341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/01/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Sister chromatid cohesion (SCC) is an important process in chromosome segregation. ESCO2 is essential for establishment of SCC and is often deleted/altered in human cancers. We demonstrate that esco2 haploinsufficiency results in reduced SCC and accelerates the timing of tumor onset in both zebrafish and mouse p53 heterozygous null models, but not in p53 homozygous mutant or wild-type animals. These data indicate that esco2 haploinsufficiency accelerates tumor onset in a loss of heterozygosity (LOH) sensitive background. Analysis of The Cancer Genome Atlas (TCGA) confirmed ESCO2 deficient tumors have elevated number of LOH events throughout the genome. Further, we demonstrated heterozygous loss of sgo1, important in maintaining SCC, also results in reduced SCC and accelerated tumor formation in a p53 heterozygous background. Surprisingly, while we did observe elevated levels of chromosome missegregation and micronuclei formation in esco2 heterozygous mutant animals, this chromosomal instability did not contribute to the accelerated tumor onset in a p53 heterozygous background. Interestingly, SCC also plays a role in homologous recombination, and we did observe elevated levels of mitotic recombination derived p53 LOH in tumors from esco2 haploinsufficient animals; as well as elevated levels of mitotic recombination throughout the genome of human ESCO2 deficient tumors. Together these data suggest that reduced SCC contributes to accelerated tumor penetrance through elevated mitotic recombination. Tumorigenesis often involves the inactivation of tumor suppressor genes. This often encompasses an inactivation mutation in one allele and loss of the other wild-type allele, referred to as loss of heterozygosity (LOH). The rate at which the cells lose the wild-type allele can influence the timing of tumor onset, and therefore an indicator of a patient’s risk of cancer. Factors that influence this process could be used as a predictive indicator of cancer risk, however these factors are still unclear. We demonstrate that partial impairment of sister chromatid cohesion (SCC), a fundamental component of the chromosome segregation in mitosis and homologous recombination repair, enhanced tumorigenesis. Our data suggest this is through elevated levels of mitotic recombination derived p53 LOH. This study emphasizes the importance of understanding how impaired SCC, mitotic recombination rates, and LOH rates influence cancer risk.
Collapse
Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Yu Chen
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - Stefanie M. Percival
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Ryne C. Ramaker
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Sara J. Cooper
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Zechen Chong
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
2
|
Ramaker RC, Hardigan AA, Gordon ER, Wright CA, Myers RM, Cooper SJ. Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition. BMC Cancer 2021; 21:632. [PMID: 34049503 PMCID: PMC8164247 DOI: 10.1186/s12885-021-08388-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 05/17/2021] [Indexed: 01/05/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) patients suffer poor outcomes, including a five-year survival of below 10%. Poor outcomes result in part from therapeutic resistance that limits the impact of cytotoxic first-line therapy. Novel therapeutic approaches are needed, but currently no targeted therapies exist to treat PDAC. Methods To assess cellular resistance mechanisms common to four cytotoxic chemotherapies (gemcitabine, 5-fluorouracil, irinotecan, and oxaliplatin) used to treat PDAC patients, we performed four genome-wide CRISPR activation (CRISPRact) and CRISPR knock-out (CRISPRko) screens in two common PDAC cell lines (Panc-1 and BxPC3). We used pathway analysis to identify gene sets enriched among our hits and conducted RNA-sequencing and chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize top hits from our screen. We used scratch assays to assess changes in cellular migration with HDAC1 overexpression. Results Our data revealed activation of ABCG2, a well-described efflux pump, as the most consistent mediator of resistance in each of our screens. CRISPR-mediated activation of genes involved in transcriptional co-repressor complexes also conferred resistance to multiple drugs. Expression of many of these genes, including HDAC1, is associated with reduced survival in PDAC patients. Up-regulation of HDAC1 in vitro increased promoter occupancy and expression of several genes involved in the epithelial-to-mesenchymal transition (EMT). These cells also displayed phenotypic changes in cellular migration consistent with activation of the EMT pathway. The expression changes resulting from HDAC1 activation were also observed with activation of several other co-repressor complex members. Finally, we developed a publicly available analysis tool, PancDS, which integrates gene expression profiles with our screen results to predict drug sensitivity in resected PDAC tumors and cell lines. Conclusion Our results provide a comprehensive resource for identifying cellular mechanisms of drug resistance in PDAC, mechanistically implicate HDAC1, and co-repressor complex members broadly, in multi-drug resistance, and provide an analytical tool for predicting treatment response in PDAC tumors and cell lines. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08388-1.
Collapse
Affiliation(s)
- Ryne C Ramaker
- University of Alabama-Birmingham, Birmingham, AL, 35294, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Andrew A Hardigan
- University of Alabama-Birmingham, Birmingham, AL, 35294, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Emily R Gordon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Carter A Wright
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,University of Alabama - Huntsville, Huntsville, AL, 35899, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| |
Collapse
|
3
|
Hiatt SM, Lawlor JM, Handley LH, Ramaker RC, Rogers BB, Partridge EC, Boston LB, Williams M, Plott CB, Jenkins J, Gray DE, Holt JM, Bowling KM, Bebin EM, Grimwood J, Schmutz J, Cooper GM. Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders. HGG Adv 2021; 2:100023. [PMID: 33937879 PMCID: PMC8087252 DOI: 10.1016/j.xhgg.2021.100023] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. Here, we describe a genomic analysis using Pacific Biosciences circular consensus sequencing (CCS) reads, which are both long (>10 kb) and accurate (>99% bp accuracy). We used CCS on six proband-parent trios with NDDs that were unexplained despite extensive testing, including genome sequencing with short reads. We identified variants and created de novo assemblies in each trio, with global metrics indicating these datasets are more accurate and comprehensive than those provided by short-read data. In one proband, we identified a likely pathogenic (LP), de novo L1-mediated insertion in CDKL5 that results in duplication of exon 3, leading to a frameshift. In a second proband, we identified multiple large de novo structural variants, including insertion-translocations affecting DGKB and MLLT3, which we show disrupt MLLT3 transcript levels. We consider this extensive structural variation likely pathogenic. The breadth and quality of variant detection, coupled to finding variants of clinical and research interest in two of six probands with unexplained NDDs, support the hypothesis that long-read genome sequencing can substantially improve rare disease genetic discovery rates.
Collapse
Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35924, USA
| | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David E. Gray
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James M. Holt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kevin M. Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35924, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | |
Collapse
|
4
|
Partridge EC, Chhetri SB, Prokop JW, Ramaker RC, Jansen CS, Goh ST, Mackiewicz M, Newberry KM, Brandsmeier LA, Meadows SK, Messer CL, Hardigan AA, Coppola CJ, Dean EC, Jiang S, Savic D, Mortazavi A, Wold BJ, Myers RM, Mendenhall EM. Occupancy maps of 208 chromatin-associated proteins in one human cell type. Nature 2020; 583:720-728. [PMID: 32728244 PMCID: PMC7398277 DOI: 10.1038/s41586-020-2023-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/09/2020] [Indexed: 01/02/2023]
Abstract
Transcription factors are DNA-binding proteins that have key roles in gene regulation1,2. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes3–6. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP–seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium. ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.
Collapse
Affiliation(s)
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Camden S Jansen
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Say-Tar Goh
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - C Luke Messer
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candice J Coppola
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Emma C Dean
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shan Jiang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Daniel Savic
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. .,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA.
| |
Collapse
|
5
|
Breitbach ME, Ramaker RC, Roberts K, Kimberly RP, Absher D. Population-Specific Patterns of Epigenetic Defects in the B Cell Lineage in Patients With Systemic Lupus Erythematosus. Arthritis Rheumatol 2019; 72:282-291. [PMID: 31430064 DOI: 10.1002/art.41083] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine the stage of B cell development at which a systemic lupus erythematosus (SLE)-associated DNA methylation signature originates in African American (AA) and European American (EA) subjects, and to assess whether epigenetic defects in B cell development patterns could be predictive of SLE status in individual and mixed immune cell populations. METHODS B cells from AA patients (n = 31) and EA patients (n = 49) with or without SLE were sorted using fluorescence-activated cell sorting into 5 B cell subsets. DNA methylation, measured at ~460,000 CpG sites, was interrogated in each subset. Enrichment analysis of transcription factor interaction at SLE-associated methylation sites was performed. A random forests algorithm was used to identify an epigenetic signature of SLE in the B cell subsets, which was then validated in an independent cohort of AA and EA patients and healthy controls. RESULTS Regression analysis across all B cell stages resulted in identification of 60 CpGs that reached genome-wide significance for SLE-associated methylation differences (P ≤ 1.07 × 10-7 ). Interrogation of ethnicity-specific CpGs associated with SLE revealed a hypomethylated pattern that was enriched for interferon (IFN)-regulated genes and binding of EBF1 in AA patients (each P < 0.001). AA patients with SLE could be distinguished from healthy controls when the predictive model developed with the transitional B cell subset was applied to other B cell subsets (mean receiver operating characteristic [ROC] area under the curve [AUC] 0.98), and when applied to CD19+ pan-B cells (mean ROC AUC 0.95) and CD4+ pan-T cells (mean ROC AUC 0.97) from the independent validation cohort. CONCLUSION These results indicate that SLE-specific methylation patterns are ethnicity dependent. A pattern of epigenetic changes near IFN-regulated genes early in B cell development is a hallmark of SLE in AA female subjects. EBF1 binding sites are highly enriched for significant methylation changes, implying that this may be a potential regulator of SLE-associated epigenetic changes.
Collapse
Affiliation(s)
- Megan E Breitbach
- University of Alabama at Huntsville and HudsonAlpha Institute for Biotechnology
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, and University of Alabama at Birmingham
| | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| |
Collapse
|
6
|
Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM. CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries. Nucleic Acids Res 2019; 47:e84. [PMID: 31165880 PMCID: PMC6698666 DOI: 10.1093/nar/gkz425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/19/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.
Collapse
Affiliation(s)
- Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| |
Collapse
|
7
|
Ramaker RC, Gordon ER, Cooper SJ. R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. Bioinformatics 2019; 34:1789-1791. [PMID: 29280991 DOI: 10.1093/bioinformatics/btx825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022] Open
Abstract
Summary Comprehensive 2D gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds, but produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. Very few existing tools address this aspect of analysis and those that do have shortfalls in usability or performance. We have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering and provides compatibility with multiple peak quantification methods. We demonstrate that our package's performance compares favorably to existing tools on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines. Availability and implementation R2DGC can be downloaded at https://github.com/rramaker/R2DGC or installed via the Comprehensive R Archive Network (CRAN). Contact sjcooper@hudsonalpha.org. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Emily R Gordon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| |
Collapse
|
8
|
Ramaker RC, Hardigan AA, Gordon ER, Myers RM, Cooper SJ. Abstract 5135: Genome-wide CRISPR-based screening reveals ABCG2 as a novel drug resistance gene in pancreatic cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-5135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly cancers and incidence is increasing due to the increase in risk factors such as diabetes and obesity. One reason for the high mortality rate associated with this cancer is the high rate of resistance to commonly used chemotherapies. Our previous work showed a link between patient survival and expression of drug resistance genes, thus we undertook genome-wide CRISPR knockout and activation screens to identify genes conferring resistance to cytotoxic chemotherapies in two pancreatic cancer cell lines. Our screen revealed hundreds of genes with potential roles in drug resistance, many of which have expression levels that correlate with patient survival. We have validated our top candidates by stably expressing individual guide RNAs in each of three pancreatic cell lines, Panc-1, BxPC-3 and MiaPaCa-2 and screening for viability following treatment with three chemotherapeutic agents, oxaliplatin, gemcitabine, and irinotecan. ABCG2, an ABC transporter, was revealed as our top hit, conferring resistance to multiple drugs in multiple cell lines. Our results would suggest that repression of ABCG2 might improve sensitivity to cytotoxic chemotherapies. We test this hypothesis using an ABCG2 inhibitor and demonstrate the effect of this inhibitor on cell viability, drug sensitivity and transcriptomic profiles in the context of cell lines with variable ABCG2 expression.
Note: This abstract was not presented at the meeting.
Citation Format: Ryne C. Ramaker, Andrew A. Hardigan, Emily R. Gordon, Richard M. Myers, Sara J. Cooper. Genome-wide CRISPR-based screening reveals ABCG2 as a novel drug resistance gene in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5135.
Collapse
|
9
|
Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
Collapse
Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
| |
Collapse
|
10
|
Roberts BS, Hardigan AA, Moore DE, Ramaker RC, Jones AL, Fitz-Gerald MB, Cooper GM, Wilcox CM, Kimberly RP, Myers RM. Discovery and Validation of Circulating Biomarkers of Colorectal Adenoma by High-Depth Small RNA Sequencing. Clin Cancer Res 2018; 24:2092-2099. [PMID: 29490987 PMCID: PMC5932113 DOI: 10.1158/1078-0432.ccr-17-1960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/02/2018] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
Purpose: Colorectal cancer is the third most common cancer worldwide, causing approximately 700,000 deaths each year. The majority of colorectal cancers begin as adenomas. Definitive screening for colorectal adenomas is currently accomplished through colonoscopy but, owing largely to costs and invasiveness, is typically limited to patient groups at higher risk by virtue of age or family history. We sought to determine if blood-based small RNA markers could detect colorectal adenoma.Experimental Design: We applied high-depth small RNA sequencing to plasma from a large (n = 189) cohort of patients, balanced for age, sex, and ancestry. Our analytical methodology allowed for the detection of both microRNAs and other small RNA species. We replicated sequencing results by qPCR on plasma samples from an independent cohort (n = 140).Results: We found several small RNA species with significant associations to colorectal adenoma, including both microRNAs and non-microRNA small RNAs. These associations were robust to correction for patient covariates, including age. Among the adenoma-associated small RNAs, two, a miR-335-5p isoform and an un-annotated small RNA, were validated by qPCR in an independent cohort. A classifier trained on measures of these two RNAs in the discovery cohort yields an AUC of 0.755 (0.775 with age) for adenoma detection in the independent cohort. This classifier accurately detects adenomas in patients under 50 and is robust to sex or ancestry.Conclusions: Circulating small RNAs (including but not limited to miRNAs) discovered by sequencing and validated by qPCR identify patients with colorectal adenomas effectively. Clin Cancer Res; 24(9); 2092-9. ©2018 AACR.
Collapse
Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.
| |
Collapse
|
11
|
Alonso A, Lasseigne BN, Williams K, Nielsen J, Ramaker RC, Hardigan AA, Johnston B, Roberts BS, Cooper SJ, Marsal S, Myers RM. aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments. Bioinformatics 2018; 33:1727-1729. [PMID: 28108448 PMCID: PMC5447234 DOI: 10.1093/bioinformatics/btx023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Summary The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis. Availability and documentation https://github.com/HudsonAlpha/aRNAPipe ; DOI: 10.5281/zenodo.202950. Contact rmyers@hudsonalpha.org. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Arnald Alonso
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | | | - Kelly Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Josh Nielsen
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bobbi Johnston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| |
Collapse
|
12
|
Ramaker RC, Lasseigne BN, Hardigan AA, Palacio L, Gunther DS, Myers RM, Cooper SJ. RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature. Oncotarget 2017; 8:38668-38681. [PMID: 28454104 PMCID: PMC5503562 DOI: 10.18632/oncotarget.16961] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023] Open
Abstract
Despite advances in cancer diagnosis and treatment strategies, robust prognostic signatures remain elusive in most cancers. Cell proliferation has long been recognized as a prognostic marker in cancer, but the generation of comprehensive, publicly available datasets allows examination of the links between cell proliferation and cancer characteristics such as mutation rate, stage, and patient outcomes. Here we explore the role of cell proliferation across 19 cancers (n = 6,581 patients) by using tissue-based RNA sequencing data from The Cancer Genome Atlas Project and calculating a 'proliferative index' derived from gene expression associated with Proliferating Cell Nuclear Antigen (PCNA) levels. This proliferative index is significantly associated with patient survival (Cox, p-value < 0.05) in 7 of 19 cancers, which we have defined as "proliferation-informative cancers" (PICs). In PICs, the proliferative index is strongly correlated with tumor stage and nodal invasion. PICs demonstrate reduced baseline expression of proliferation machinery relative to non-PICs. Additionally, we find the proliferative index is significantly associated with gross somatic mutation burden (Spearman, p = 1.76 x 10-23) as well as with mutations in individual driver genes. This analysis provides a comprehensive characterization of tumor proliferation indices and their association with disease progression and prognosis in multiple cancer types and highlights specific cancers that may be particularly susceptible to improved targeting of this classic cancer hallmark.
Collapse
Affiliation(s)
- Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laura Palacio
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| |
Collapse
|
13
|
Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM. Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer 2017; 17:273. [PMID: 28412973 PMCID: PMC5392915 DOI: 10.1186/s12885-017-3252-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. METHODS We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. RESULTS We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. CONCLUSIONS DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.
Collapse
Affiliation(s)
- Marie K. Kirby
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: TRM Oncology, 5901-C Peachtree Dunwoody Rd, Suite 200, Atlanta, GA 30328 USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Genetics, Kaul Human Genetics Building, Suite 230, 720 20th Street South, Birmingham, AL 35294 USA
| | - Brian S. Roberts
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | | | - David S. Gunther
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: University of Southern California, University Park, Los Angeles, CA 90089 USA
| | - Todd C. Burwell
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Boeing Co., 499 Boeing Blvd, SW, Huntsville, AL 35824 USA
| | - Nicholas S. Davis
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Duke University, 101 Science Drive, Durham, NC 27708 USA
| | - Zulfiqar G. Gulzar
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
- Present Address: NuGEN technologies, 201 Industrial Rd #310, San Carlos, CA 94070 USA
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - James D. Brooks
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| |
Collapse
|
14
|
McDaniel JM, Varley KE, Gertz J, Savic DS, Roberts BS, Bailey SK, Shevde LA, Ramaker RC, Lasseigne BN, Kirby MK, Newberry KM, Partridge EC, Jones AL, Boone B, Levy SE, Oliver PG, Sexton KC, Grizzle WE, Forero A, Buchsbaum DJ, Cooper SJ, Myers RM. Genomic regulation of invasion by STAT3 in triple negative breast cancer. Oncotarget 2017; 8:8226-8238. [PMID: 28030809 PMCID: PMC5352396 DOI: 10.18632/oncotarget.14153] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. Immunohistochemical detection of ER, PR, and HER2 receptors/proteins is a critical step in breast cancer diagnosis and guided treatment. Breast tumors that do not express these proteins are known as "triple negative breast cancer" (TNBC) and are typically basal-like. TNBCs are the most aggressive subtype, with the highest mortality rates and no targeted therapy, so there is a pressing need to identify important TNBC tumor regulators. The signal transducer and activator of transcription 3 (STAT3) transcription factor has been previously implicated as a constitutively active oncogene in TNBC. However, its direct regulatory gene targets and tumorigenic properties have not been well characterized. By integrating RNA-seq and ChIP-seq data from 2 TNBC tumors and 5 cell lines, we discovered novel gene signatures directly regulated by STAT3 that were enriched for processes involving inflammation, immunity, and invasion in TNBC. Functional analysis revealed that STAT3 has a key role regulating invasion and metastasis, a characteristic often associated with TNBC. Our findings suggest therapies targeting STAT3 may be important for preventing TNBC metastasis.
Collapse
Affiliation(s)
- Joy M McDaniel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Daniel S Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sarah K Bailey
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL 35294, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | | | - Marie K Kirby
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Patsy G Oliver
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Katherine C Sexton
- University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL 35294, USA
| | - William E Grizzle
- University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL 35294, USA
| | - Andres Forero
- University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL 35294, USA
| | - Donald J Buchsbaum
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| |
Collapse
|
15
|
Cohen JL, Ata AE, Jackson NL, Rahn EJ, Ramaker RC, Cooper S, Kerman IA, Clinton SM. Differential stress induced c-Fos expression and identification of region-specific miRNA-mRNA networks in the dorsal raphe and amygdala of high-responder/low-responder rats. Behav Brain Res 2016; 319:110-123. [PMID: 27865919 DOI: 10.1016/j.bbr.2016.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/19/2016] [Accepted: 11/08/2016] [Indexed: 01/03/2023]
Abstract
Chronic stress triggers a variety of physical and mental health problems, and how individuals cope with stress influences risk for emotional disorders. To investigate molecular mechanisms underlying distinct stress coping styles, we utilized rats that were selectively-bred for differences in emotionality and stress reactivity. We show that high novelty responding (HR) rats readily bury a shock probe in the defensive burying test, a measure of proactive stress coping behavior, while low novelty responding (LR) rats exhibit enhanced immobility, a measure of reactive coping. Shock exposure in the defensive burying test elicited greater activation of HR rats' caudal dorsal raphe serotonergic cells compared to LRs, but lead to more pronounced activation throughout LRs' amygdala (lateral, basolateral, central, and basomedial nuclei) compared to HRs. RNA-sequencing revealed 271 mRNA transcripts and 33 microRNA species that were differentially expressed in HR/LR raphe and amygdala. We mapped potential microRNA-mRNA networks by correlating and clustering mRNA and microRNA expression and identified networks that differed in either the HR/LR dorsal raphe or amygdala. A dorsal raphe network linked three microRNAs which were down-regulated in LRs (miR-206-3p, miR-3559-5p, and miR-378a-3p) to repression of genes related to microglia and immune response (Cd74, Cyth4, Nckap1l, and Rac2), the genes themselves were up-regulated in LR dorsal raphe. In the amygdala, another network linked miR-124-5p, miR-146a-5p, miR-3068-3p, miR-380-5p, miR-539-3p, and miR-7a-1-3p with repression of chromatin remodeling-related genes (Cenpk, Cenpq, Itgb3bp, and Mis18a). Overall this work highlights potential drivers of gene-networks and downstream molecular pathways within the raphe and amygdala that contribute to individual differences in stress coping styles and stress vulnerabilities.
Collapse
Affiliation(s)
- Joshua L Cohen
- Medical Scientist Training Program, University of Alabama-Birmingham, USA
| | - Anooshah E Ata
- University of Alabama-Birmingham School of Medicine, USA
| | - Nateka L Jackson
- Department of Neurobiology, University of Alabama-Birmingham, USA
| | - Elizabeth J Rahn
- Department of Neurobiology, University of Alabama-Birmingham, USA
| | - Ryne C Ramaker
- Medical Scientist Training Program, University of Alabama-Birmingham, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ilan A Kerman
- School of Neuroscience, Virginia Tech University, USA; Department of Psychiatry & Behavioral Medicine, Carilion Clinic, Virginia Tech Carilion School of Medicine, USA
| | | |
Collapse
|
16
|
Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM. RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4. Mol Oncol 2016; 10:1169-82. [PMID: 27282075 PMCID: PMC5423196 DOI: 10.1016/j.molonc.2016.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/25/2016] [Accepted: 05/17/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma patients have low survival rates due to late-stage diagnosis and high rates of cancer recurrence even after surgical resection. It is important to understand the molecular characteristics associated with survival differences in pancreatic adenocarcinoma tumors that may inform patient care. RESULTS RNA sequencing was performed for 51 patient tumor tissues extracted from patients undergoing surgical resection, and expression was associated with overall survival time from diagnosis. Our analysis uncovered 323 transcripts whose expression correlates with survival time in our pancreatic patient cohort. This genomic signature was validated in an independent RNA-seq dataset of 68 additional patients from the International Cancer Genome Consortium. We demonstrate that this transcriptional profile is largely independent of markers of cellular division and present a 19-transcript predictive model built from a subset of the 323 transcripts that can distinguish patients with differing survival times across both the training and validation patient cohorts. We present evidence that a subset of the survival-associated transcripts is associated with resistance to gemcitabine treatment in vitro, and reveal that reduced expression of one of the survival-associated transcripts, Angiopoietin-like 4, impairs growth of a gemcitabine-resistant pancreatic cancer cell line. CONCLUSIONS Gene expression patterns in pancreatic adenocarcinoma tumors can distinguish patients with differing survival outcomes after undergoing surgical resection, and the survival difference could be associated with the intrinsic gemcitabine sensitivity of primary patient tumors. Thus, these transcriptional differences may impact patient care by distinguishing patients who would benefit from a non-gemcitabine based therapy.
Collapse
Affiliation(s)
- Marie K Kirby
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jason Gertz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Patsy G Oliver
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - James A Posey
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| |
Collapse
|
17
|
Ghatalia P, Yang ES, Lasseigne BN, Ramaker RC, Cooper SJ, Chen D, Sudarshan S, Wei S, Guru AS, Zhao A, Cooper T, Della Manna DL, Naik G, Myers RM, Sonpavde G. Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets. PLoS One 2016; 11:e0160924. [PMID: 27574806 PMCID: PMC5004806 DOI: 10.1371/journal.pone.0160924] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/27/2016] [Indexed: 01/05/2023] Open
Abstract
Kinases are therapeutically actionable targets. Kinase inhibitors targeting vascular endothelial growth factor receptors (VEGFR) and mammalian target of rapamycin (mTOR) improve outcomes in metastatic clear cell renal cell carcinoma (ccRCC), but are not curative. Metastatic tumor tissue has not been comprehensively studied for kinase gene expression. Paired intra-patient kinase gene expression analysis in primary tumor (T), matched normal kidney (N) and metastatic tumor tissue (M) may assist in identifying drivers of metastasis and prioritizing therapeutic targets. We compared the expression of 519 kinase genes using NanoString in T, N and M in 35 patients to discover genes over-expressed in M compared to T and N tissue. RNA-seq data derived from ccRCC tumors in The Cancer Genome Atlas (TCGA) were used to demonstrate differential expression of genes in primary tumor tissue from patients that had metastasis at baseline (n = 79) compared to those that did not develop metastasis for at least 2 years (n = 187). Functional analysis was conducted to identify key signaling pathways by using Ingenuity Pathway Analysis. Of 10 kinase genes overexpressed in metastases compared to primary tumor in the discovery cohort, 9 genes were also differentially expressed in TCGA primary tumors with metastasis at baseline compared to primary tumors without metastasis for at least 2 years: EPHB2, AURKA, GSG2, IKBKE, MELK, CSK, CHEK2, CDC7 and MAP3K8; p<0.001). The top pathways overexpressed in M tissue were pyridoxal 5'-phosphate salvage, salvage pathways of pyrimidine ribonucleotides, NF-kB signaling, NGF signaling and cell cycle control of chromosomal replication. The 9 kinase genes validated to be over-expressed in metastatic ccRCC may represent currently unrecognized but potentially actionable therapeutic targets that warrant functional validation.
Collapse
Affiliation(s)
- Pooja Ghatalia
- Department of Internal Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, United States of America
| | - Eddy S. Yang
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | | | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, UAB, Birmingham, AL, United States of America
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Dongquan Chen
- UAB Department of Preventive Medicine, Birmingham, AL, United States of America
| | - Sunil Sudarshan
- UAB Department of Urology, Birmingham, AL, United States of America
| | - Shi Wei
- UAB Department of Urologic Pathology, Birmingham, AL, United States of America
| | - Arjun S. Guru
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | - Amy Zhao
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | - Tiffiny Cooper
- Department of Radiation Oncology, UAB, Birmingham, AL, United States of America
| | | | - Gurudatta Naik
- UAB Department of Medicine, Section of Hematology-Oncology and the UAB Comprehensive Cancer Center, Birmingham, AL, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Guru Sonpavde
- UAB Department of Medicine, Section of Hematology-Oncology and the UAB Comprehensive Cancer Center, Birmingham, AL, United States of America
- * E-mail:
| |
Collapse
|
18
|
Savic D, Ramaker RC, Roberts BS, Dean EC, Burwell TC, Meadows SK, Cooper SJ, Garabedian MJ, Gertz J, Myers RM. Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation. Genome Med 2016; 8:74. [PMID: 27401066 PMCID: PMC4940857 DOI: 10.1186/s13073-016-0328-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/14/2016] [Indexed: 12/28/2022] Open
Abstract
Background The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intriguingly, recent studies suggest that these metabolic regulators also impact tumor cell proliferation. However, a comprehensive temporal molecular characterization of the LXR and PPARG gene regulatory responses in tumor cells is still lacking. Methods To better define the underlying molecular processes governing the genetic control of cellular growth in response to extracellular metabolic signals, we performed a comprehensive, genome-wide characterization of the temporal regulatory cascades mediated by LXR and PPARG signaling in HT29 colorectal cancer cells. For this analysis, we applied a multi-tiered approach that incorporated cellular phenotypic assays, gene expression profiles, chromatin state dynamics, and nuclear receptor binding patterns. Results Our results illustrate that the activation of both nuclear receptors inhibited cell proliferation and further decreased glutathione levels, consistent with increased cellular oxidative stress. Despite a common metabolic reprogramming, the gene regulatory network programs initiated by these nuclear receptors were widely distinct. PPARG generated a rapid and short-term response while maintaining a gene activator role. By contrast, LXR signaling was prolonged, with initial, predominantly activating functions that transitioned to repressive gene regulatory activities at late time points. Conclusions Through the use of a multi-tiered strategy that integrated various genomic datasets, our data illustrate that distinct gene regulatory programs elicit common phenotypic effects, highlighting the complexity of the genome. These results further provide a detailed molecular map of metabolic reprogramming in cancer cells through LXR and PPARG activation. As ligand-inducible TFs, these nuclear receptors can potentially serve as attractive therapeutic targets for the treatment of various cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0328-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Emma C Dean
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Todd C Burwell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Michael J Garabedian
- Departments of Microbiology and Urology, New York University, New York, NY, 10016, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| |
Collapse
|
19
|
Coppola CJ, C Ramaker R, Mendenhall EM. Identification and function of enhancers in the human genome. Hum Mol Genet 2016; 25:R190-R197. [PMID: 27402881 DOI: 10.1093/hmg/ddw216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022] Open
Abstract
The study of gene regulation has rapidly advanced by leveraging next-generation sequencing to identify and characterize the cis and trans elements that are critical for defining cell identity. These advances have paralleled a movement towards whole genome sequencing in clinics. These two tracks have increasingly synergized to underscore the importance of cis-regulatory elements in development as well produce countless studies implicating these elements in human disease. Other studies have emphasized the clinical phenotypes associated with variation or mutations in trans factors, including non-coding RNAs and chromatin regulators. These studies highlight the importance of obtaining a comprehensive understanding of mammalian gene regulation for predicting the impact of genetic variation on patient phenotypes. Currently lagging behind the generation of vast datasets and annotations is our ability to examine these putative elements in the dynamic context of a developing organism.
Collapse
Affiliation(s)
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eric M Mendenhall
- University of Alabama in Huntsville, Huntsville, AL, USA HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| |
Collapse
|