1
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SoRelle ED, Dai J, Bonglack EN, Heckenberg EM, Zhou JY, Giamberardino SN, Bailey JA, Gregory SG, Chan C, Luftig MA. Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. eLife 2021; 10:62586. [PMID: 33501914 PMCID: PMC7867410 DOI: 10.7554/elife.62586] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) are generated by transforming primary B cells with Epstein–Barr virus (EBV) and are used extensively as model systems in viral oncology, immunology, and human genetics research. In this study, we characterized single-cell transcriptomic profiles of five LCLs and present a simple discrete-time simulation to explore the influence of stochasticity on LCL clonal evolution. Single-cell RNA sequencing (scRNA-seq) revealed substantial phenotypic heterogeneity within and across LCLs with respect to immunoglobulin isotype; virus-modulated host pathways involved in survival, activation, and differentiation; viral replication state; and oxidative stress. This heterogeneity is likely attributable to intrinsic variance in primary B cells and host–pathogen dynamics. Stochastic simulations demonstrate that initial primary cell heterogeneity, random sampling, time in culture, and even mild differences in phenotype-specific fitness can contribute substantially to dynamic diversity in populations of nominally clonal cells.
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Affiliation(s)
- Elliott D SoRelle
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, United States
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
| | - Emmanuela N Bonglack
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Emma M Heckenberg
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
| | - Jeffrey Y Zhou
- Department of Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Stephanie N Giamberardino
- Duke Molecular Physiology Institute and Department of Neurology, Duke University School of Medicine, Durham, United States
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States
| | - Simon G Gregory
- Duke Molecular Physiology Institute and Department of Neurology, Duke University School of Medicine, Durham, United States
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, United States
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
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2
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Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research. Sci Rep 2019; 9:4889. [PMID: 30894562 PMCID: PMC6426863 DOI: 10.1038/s41598-019-40897-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Genotyped human B-lymphoblastoid cell lines (LCLs) are widely used models in mapping quantitative trait loci for chromatin features, gene expression, and drug response. The extent of genotype-independent functional genomic variability of the LCL model, although largely overlooked, may inform association study design. In this study, we use flow cytometry, chromatin immunoprecipitation sequencing and mRNA sequencing to study surface marker patterns, quantify genome-wide chromatin changes (H3K27ac) and transcriptome variability, respectively, among five isogenic LCLs derived from the same individual. Most of the studied LCLs were non-monoclonal and had mature B cell phenotypes. Strikingly, nearly one-fourth of active gene regulatory regions showed significantly variable H3K27ac levels, especially enhancers, among which several were classified as clustered enhancers. Large, contiguous genomic regions showed signs of coordinated activity change. Regulatory differences were mirrored by mRNA expression changes, preferentially affecting hundreds of genes involved in specialized cellular processes including immune and drug response pathways. Differential expression of DPYD, an enzyme involved in 5-fluorouracil (5-FU) catabolism, was associated with variable LCL growth inhibition mediated by 5-FU. The extent of genotype-independent functional genomic variability might highlight the need to revisit study design strategies for LCLs in pharmacogenomics.
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3
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Akhtari FS, Havener TM, Fukudo M, Jack JR, McLeod HL, Wiltshire T, Motsinger-Reif AA. The influence of Neanderthal alleles on cytotoxic response. PeerJ 2018; 6:e5691. [PMID: 30386687 PMCID: PMC6202974 DOI: 10.7717/peerj.5691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.
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Affiliation(s)
- Farida S Akhtari
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
| | - Tammy M Havener
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | | | - John R Jack
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
| | - Howard L McLeod
- The DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Tim Wiltshire
- Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America.,Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Alison A Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America.,Department of Statistics, North Carolina State University, Raleigh, NC, United States of America
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4
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Abstract
PURPOSE OF REVIEW The goal of this review is to summarize current understanding of pharmacogenetics and pharmacogenomics in chemotherapy-induced cardiotoxicity. RECENT FINDINGS Most of the studies rely on in vitro cytotoxic assays. There have been several smaller scale candidate gene approaches and a handful of genome-wide studies linking genetic variation to susceptibility to chemotherapy-induced cardiotoxicity. Currently, pharmacogenomic testing of all childhood cancer patients with an indication for doxorubicin or daunorubicin therapy for RARG rs2229774, SLC28A3 rs7853758, and UGT1A6*4 rs17863783 variants is recommended. There is no recommendation regarding testing in adults. There is clear evidence pointing to the role of pharmacogenetics and pharmacogenomics in cardiotoxicity susceptibility to chemotherapeutic agents. Larger scale studies are needed to further identify susceptibility markers and to develop pharmacogenomics-based risk profiling to improve quality of life and life expectancy in cancer survivors.
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Affiliation(s)
- Vivian Y Chang
- Department of Pediatrics, Division of Hematology/Oncology, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA
| | - Jessica J Wang
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA.
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5
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Stark AL, Madian AG, Williams SW, Chen V, Wing C, Hause RJ, To LA, Gill AL, Myers JL, Gorsic LK, Ciaccio MF, White KP, Jones RB, Dolan ME. Identification of Novel Protein Expression Changes Following Cisplatin Treatment and Application to Combination Therapy. J Proteome Res 2017; 16:4227-4236. [DOI: 10.1021/acs.jproteome.7b00576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy L. Stark
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ashraf G. Madian
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sawyer W. Williams
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Vincent Chen
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Claudia Wing
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ronald J. Hause
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lida Anita To
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Amy L. Gill
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jamie L. Myers
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lidija K. Gorsic
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mark F. Ciaccio
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kevin P. White
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Richard B. Jones
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - M. Eileen Dolan
- Department of Medicine, ‡Committee on Clinical Pharmacology
and Pharmacogenomics, ∥Ben May Department
for Cancer Research; ⊥Committee on Genetics, Genomics and Systems Biology; #The Institute for Genomics and Systems
Biology; ∇Committee on Cancer Biology; and □Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, United States
- College of Arts and
Letters, University of Notre Dame, Notre Dame, Indiana 46556, United States
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6
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Gurwitz D. Human iPSC-derived neurons and lymphoblastoid cells for personalized medicine research in neuropsychiatric disorders. DIALOGUES IN CLINICAL NEUROSCIENCE 2017. [PMID: 27757061 PMCID: PMC5067144 DOI: 10.31887/dcns.2016.18.3/dgurwitz] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development and clinical implementation of personalized medicine crucially depends on the availability of high-quality human biosamples; animal models, although capable of modeling complex human diseases, cannot reflect the large variation in the human genome, epigenome, transcriptome, proteome, and metabolome. Although the biosamples available from public biobanks that store human tissues and cells may represent the large human diversity for most diseases, these samples are not always sufficient for developing biomarkers for patient-tailored therapies for neuropsychiatric disorders. Postmortem human tissues are available from many biobanks; nevertheless, collections of neuronal human cells from large patient cohorts representing the human diversity remain scarce. Two tools are gaining popularity for personalized medicine research on neuropsychiatric disorders: human induced pluripotent stem cell-derived neurons and human lymphoblastoid cell lines. This review examines and contrasts the advantages and limitations of each tool for personalized medicine research.
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Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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7
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Free KE, Greene AM, Bondi CO, Lajud N, de la Tremblaye PB, Kline AE. Comparable impediment of cognitive function in female and male rats subsequent to daily administration of haloperidol after traumatic brain injury. Exp Neurol 2017; 296:62-68. [PMID: 28698031 DOI: 10.1016/j.expneurol.2017.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/06/2017] [Accepted: 07/07/2017] [Indexed: 01/09/2023]
Abstract
Antipsychotic drugs, such as haloperidol (HAL), are prescribed in the clinic to manage traumatic brain injury (TBI)-induced agitation. While preclinical studies have consistently shown that once-daily administration of HAL hinders functional recovery after TBI in male rats, its effects in females are unknown. Hence, the objective of this study was to directly compare neurobehavioral and histological outcomes in both sexes to determine whether the reported deleterious effects of HAL extend to females. Anesthetized adult female and male rats received either a controlled cortical impact (CCI) or sham injury and then were randomly assigned to a dosing regimen of HAL (0.5mg/kg, i.p.) or vehicle (VEH; 1mL/kg, i.p.) that was initiated 24h after injury and continued once daily for 19 consecutive days. Motor function was tested using established beam-balance/walk protocols on post-operative days 1-5 and acquisition of spatial learning was assessed with a well-validated Morris water maze task on days 14-19. Cortical lesion volume was quantified at 21days. No statistical differences were revealed between the HAL and VEH-treated sham groups and thus they were pooled for each sex. HAL only impaired motor recovery in males (p<0.05), but significantly diminished spatial learning in both sexes (p<0.05). Females, regardless of treatment, exhibited smaller cortical lesions vs VEH-treated males (p<0.05). Taken together, the data show that daily HAL does not prohibit motor recovery in females, but does negatively impact cognition. These task-dependent differential effects of HAL in female vs male rats may have clinical significance as they can direct therapy.
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Affiliation(s)
- Kristin E Free
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Anna M Greene
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Corina O Bondi
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States; Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, United States; Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, United States; Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Naima Lajud
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States; División de Neurociencias, Centro de Investigación Biomédica de Michoacán, Instituto Mexicano del Seguro Social Morelia, Mexico
| | - Patricia B de la Tremblaye
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Anthony E Kline
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA 15213, United States; Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA 15213, United States; Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15213, United States; Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA 15213, United States; Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States; Psychology, University of Pittsburgh, Pittsburgh, PA 15213, United States.
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8
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Lenkala D, Gamazon ER, LaCroix B, Im HK, Huang RS. MicroRNA biogenesis and cellular proliferation. Transl Res 2015; 166:145-51. [PMID: 25724890 PMCID: PMC4509805 DOI: 10.1016/j.trsl.2015.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/26/2015] [Accepted: 01/30/2015] [Indexed: 12/22/2022]
Abstract
Given the fundamental roles of microRNAs (miRNAs) in physiological, developmental, and pathologic processes, we hypothesized that genes involved in miRNA biogenesis contribute to human complex traits. For 13 such genes, we evaluated the relationship between transcription and 2 classes of complex traits, namely cellular growth and sensitivity to various chemotherapeutic agents in a set of lymphoblastoid cell lines. We found a highly significant correlation between argonaute RNA-induced silencing complex catalytic component 2 (AGO2) expression and cellular growth rate (Bonferroni-adjusted P < 0.05), and report additional miRNA biogenesis genes with suggestive associations with either cellular growth rate or chemotherapeutic sensitivity. AGO2 expression was found to be correlated with multiple drug sensitivity phenotypes. Furthermore, small interfering RNA knockdown of AGO2 resulted in cellular growth inhibition in an ovarian cancer cell line (OVCAR-3), supporting the role of this miRNA biogenesis gene in cell proliferation in cancer cells. Expression quantitative trait loci mapping indicated that genetic variation (in the form of both single-nucleotide polymorphisms and copy number variations) that may regulate the expression of AGO2 can have downstream effects on cellular growth-dependent complex phenotypes.
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Affiliation(s)
- Divya Lenkala
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Ill
| | - Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Ill; Division of Genetic Medicine, Vanderbilt University, Nashville, Tenn
| | - Bonnie LaCroix
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Ill
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Ill
| | - R Stephanie Huang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Ill.
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9
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Abdo N, Xia M, Brown CC, Kosyk O, Huang R, Sakamuru S, Zhou YH, Jack JR, Gallins P, Xia K, Li Y, Chiu WA, Motsinger-Reif AA, Austin CP, Tice RR, Rusyn I, Wright FA. Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:458-66. [PMID: 25622337 PMCID: PMC4421772 DOI: 10.1289/ehp.1408775] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/12/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Understanding of human variation in toxicity to environmental chemicals remains limited, so human health risk assessments still largely rely on a generic 10-fold factor (10½ each for toxicokinetics and toxicodynamics) to account for sensitive individuals or subpopulations. OBJECTIVES We tested a hypothesis that population-wide in vitro cytotoxicity screening can rapidly inform both the magnitude of and molecular causes for interindividual toxicodynamic variability. METHODS We used 1,086 lymphoblastoid cell lines from the 1000 Genomes Project, representing nine populations from five continents, to assess variation in cytotoxic response to 179 chemicals. Analysis included assessments of population variation and heritability, and genome-wide association mapping, with attention to phenotypic relevance to human exposures. RESULTS For about half the tested compounds, cytotoxic response in the 1% most "sensitive" individual occurred at concentrations within a factor of 10½ (i.e., approximately 3) of that in the median individual; however, for some compounds, this factor was > 10. Genetic mapping suggested important roles for variation in membrane and transmembrane genes, with a number of chemicals showing association with SNP rs13120371 in the solute carrier SLC7A11, previously implicated in chemoresistance. CONCLUSIONS This experimental approach fills critical gaps unaddressed by recent large-scale toxicity testing programs, providing quantitative, experimentally based estimates of human toxicodynamic variability, and also testable hypotheses about mechanisms contributing to interindividual variation.
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Affiliation(s)
- Nour Abdo
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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10
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Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet 2015; 11:e1005216. [PMID: 25950834 PMCID: PMC4423863 DOI: 10.1371/journal.pgen.1005216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/13/2015] [Indexed: 11/18/2022] Open
Abstract
Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCL cultures from six unrelated donors to iPSCs on the ensuing gene expression patterns within and between individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures, increasing the number of genes with a detectable donor effect by an order of magnitude. The proportion of variation in gene expression statistically attributed to donor increases from 6.9% in LCLs to 24.5% in iPSCs (P < 10-15). Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in iPSCs than in LCLs. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.
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Affiliation(s)
- Samantha M. Thomas
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Courtney Kagan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Bryan J. Pavlovic
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan Burnett
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Yoav Gilad
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
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11
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Chouchana L, Fernández-Ramos AA, Dumont F, Marchetti C, Ceballos-Picot I, Beaune P, Gurwitz D, Loriot MA. Molecular insight into thiopurine resistance: transcriptomic signature in lymphoblastoid cell lines. Genome Med 2015; 7:37. [PMID: 26015807 PMCID: PMC4443628 DOI: 10.1186/s13073-015-0150-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/03/2015] [Indexed: 12/15/2022] Open
Abstract
Background There has been considerable progress in the management of acute lymphoblastic leukemia (ALL) but further improvement is needed to increase long-term survival. The thiopurine agent 6-mercaptopurine (6-MP) used for ALL maintenance therapy has a key influence on clinical outcomes and relapse prevention. Genetic inheritance in thiopurine metabolism plays a major role in interindividual clinical response variability to thiopurines; however, most cases of thiopurine resistance remain unexplained. Methods We used lymphoblastoid cell lines (LCLs) from healthy donors, selected for their extreme thiopurine susceptibility. Thiopurine metabolism was characterized by the determination of TPMT and HPRT activity. We performed genome-wide expression profiling in resistant and sensitive cell lines with the goal of elucidating the mechanisms of thiopurine resistance. Results We determined a higher TPMT activity (+44%; P = 0.024) in resistant compared to sensitive cell lines, although there was no difference in HPRT activity. We identified a 32-gene transcriptomic signature that predicts thiopurine resistance. This signature includes the GTPBP4 gene coding for a GTP-binding protein that interacts with p53. A comprehensive pathway analysis of the genes differentially expressed between resistant and sensitive cell lines indicated a role for cell cycle and DNA mismatch repair system in thiopurine resistance. It also revealed overexpression of the ATM/p53/p21 pathway, which is activated in response to DNA damage and induces cell cycle arrest in thiopurine resistant LCLs. Furthermore, overexpression of the p53 target gene TNFRSF10D or the negative cell cycle regulator CCNG2 induces cell cycle arrest and may also contribute to thiopurine resistance. ARHGDIA under-expression in resistant cell lines may constitute a novel molecular mechanism contributing to thiopurine resistance based on Rac1 inhibition induced apoptosis and in relation with thiopurine pharmacodynamics. Conclusion Our study provides new insights into the molecular mechanisms underlying thiopurine resistance and suggests a potential research focus for developing tailored medicine. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0150-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurent Chouchana
- INSERM UMR-S 1147, 45 rue des Saints-Pères, Paris, 75006 France ; Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France
| | - Ana Aurora Fernández-Ramos
- INSERM UMR-S 1147, 45 rue des Saints-Pères, Paris, 75006 France ; Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France
| | - Florent Dumont
- Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France ; INSERM U1016, Institut Cochin, 22 Rue Mechain, Paris, 75014 France
| | - Catherine Marchetti
- INSERM UMR-S 1147, 45 rue des Saints-Pères, Paris, 75006 France ; Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France
| | - Irène Ceballos-Picot
- Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France ; Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Biochimie Métabolique, 149 Rue de Sèvres, Paris, 75015 France
| | - Philippe Beaune
- INSERM UMR-S 1147, 45 rue des Saints-Pères, Paris, 75006 France ; Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France ; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Biochimie Pharmacogénétique et Oncologie Moléculaire, 20 rue Leblanc, Paris, 75015 France
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marie-Anne Loriot
- INSERM UMR-S 1147, 45 rue des Saints-Pères, Paris, 75006 France ; Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, Paris, 75006 France ; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Biochimie Pharmacogénétique et Oncologie Moléculaire, 20 rue Leblanc, Paris, 75015 France
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Brown CC, Havener TM, Medina MW, Jack JR, Krauss RM, McLeod HL, Motsinger-Reif AA. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Pharmacogenomics 2015; 15:137-46. [PMID: 24444404 DOI: 10.2217/pgs.13.213] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Association mapping with lymphoblastoid cell lines (LCLs) is a promising approach in pharmacogenomics research, and in the current study we utilized LCLs to perform association mapping for 29 chemotherapy drugs. MATERIALS & METHODS Currently, we use LCLs to perform genome-wide association mapping of the cytotoxic response of 520 European-Americans to 29 different anticancer drugs; the largest LCL study to date. A novel association approach using a multivariate analysis of covariance design was employed with the software program MAGWAS, testing for differences in the dose-response profiles between genotypes without making assumptions about the response curve or the biologic mode of association. Additionally, by classifying 25 of the 29 drugs into eight families according to structural and mechanistic relationships, MAGWAS was used to test for associations that were shared across each drug family. Finally, a unique algorithm using multivariate responses and multiple linear regressions across pairs of response curves was used for unsupervised clustering of drugs. RESULTS Among the single-drug studies, suggestive associations were obtained for 18 loci, 12 within/near genes. Three of these, MED12L, CHN2 and MGMT, have been previously implicated in cancer pharmacogenomics. The drug family associations resulted in four additional suggestive loci (three contained within/near genes). One of these genes, HDAC4, associated with the DNA alkylating agents, shows possible clinical interactions with temozolomide. For the drug clustering analysis, 18 of 25 drugs clustered into the appropriate family. CONCLUSION This study demonstrates the utility of LCLs in identifying genes that have clinical importance in drug response and for assigning unclassified agents to specific drug families, and proposes new candidate genes for follow-up in a large number of chemotherapy drugs.
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Affiliation(s)
- Chad C Brown
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
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13
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Chhibber A, Kroetz DL, Tantisira KG, McGeachie M, Cheng C, Plenge R, Stahl E, Sadee W, Ritchie MD, Pendergrass SA. Genomic architecture of pharmacological efficacy and adverse events. Pharmacogenomics 2014; 15:2025-48. [PMID: 25521360 PMCID: PMC4308414 DOI: 10.2217/pgs.14.144] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The pharmacokinetic and pharmacodynamic disciplines address pharmacological traits, including efficacy and adverse events. Pharmacogenomics studies have identified pervasive genetic effects on treatment outcomes, resulting in the development of genetic biomarkers for optimization of drug therapy. Pharmacogenomics-based tests are already being applied in clinical decision making. However, despite substantial progress in identifying the genetic etiology of pharmacological response, current biomarker panels still largely rely on single gene tests with a large portion of the genetic effects remaining to be discovered. Future research must account for the combined effects of multiple genetic variants, incorporate pathway-based approaches, explore gene-gene interactions and nonprotein coding functional genetic variants, extend studies across ancestral populations, and prioritize laboratory characterization of molecular mechanisms. Because genetic factors can play a key role in drug response, accurate biomarker tests capturing the main genetic factors determining treatment outcomes have substantial potential for improving individual clinical care.
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Affiliation(s)
- Aparna Chhibber
- Department of Bioengineering & Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA,USA
| | - Deanna L Kroetz
- Department of Bioengineering & Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA,USA
| | - Kelan G Tantisira
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Michael McGeachie
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Cheng Cheng
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert Plenge
- Division of Rheumatology, Immunology & Allergy, Division of Genetics, Brigham & Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Eli Stahl
- Department of Genetics & Genomic Sciences, Mount Sinai Hospital, New York, NY, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Marylyn D Ritchie
- Department of Biochemistry & Molecular Biology, Center for Systems Genomics, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16801, USA
| | - Sarah A Pendergrass
- Department of Biochemistry & Molecular Biology, Center for Systems Genomics, Eberly College of Science, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16801, USA
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Patrick CJ. Genetics, neuroscience, and psychopathology: Clothing the emperor. Psychophysiology 2014; 51:1333-4. [DOI: 10.1111/psyp.12356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Bernig T, Richter N, Volkmer I, Staege MS. Functional analysis and molecular characterization of spontaneously outgrown human lymphoblastoid cell lines. Mol Biol Rep 2014; 41:6995-7007. [PMID: 25037273 DOI: 10.1007/s11033-014-3587-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/05/2014] [Indexed: 01/14/2023]
Abstract
In vitro, the infection of human B-cells with the lymphotropic gammaherpesvirus Epstein-Barr virus (EBV) induces formation of permanently growing lymphoblastoid cell lines (LCL). In a spontaneously outgrown LCL (cell line CSIII), we detected nucleotide sequence variations of the EBV nuclear antigen 1 (EBNA1) RNA that was different from the reference sequence of EBNA1 in the prototypic EBV strain B95-8. In the present study, we molecularly and functionally characterized this virus isolate in comparison to LCL with the prototypic nucleotide sequence. Although we detected high functional similarity between CSIII and the other LCL, our data suggest that the lytic cycle might be ineffective in the CSIII LCL. DNA microarray analysis indicated that RNA binding motif, single stranded interacting protein 1 (RBMS1), which is typically expressed in latency III of EBV to prevent the lytic cycle, was the most overexpressed gene in CSIII LCL.
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Affiliation(s)
- Toralf Bernig
- Department of Pediatrics, Children's Cancer Research Centre, Martin Luther University Halle-Wittenberg, Ernst-Grube Str. 40, D-06097, Halle, Germany
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Lenkala D, LaCroix B, Gamazon ER, Geeleher P, Im HK, Huang RS. The impact of microRNA expression on cellular proliferation. Hum Genet 2014; 133:931-8. [PMID: 24609542 PMCID: PMC4677487 DOI: 10.1007/s00439-014-1434-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/24/2014] [Indexed: 12/12/2022]
Abstract
As an important class of non-coding regulatory RNAs, microRNAs (miRNAs) play a key role in a range of biological processes. These molecules serve as post-transcriptional regulators of gene expression and their regulatory activity has been implicated in disease pathophysiology and pharmacological traits. We sought to investigate the impact of miRNAs on cellular proliferation to gain insight into the molecular basis of complex traits that depend on cellular growth, including, most prominently, cancer. We examined the relationship between miRNA expression and intrinsic cellular growth (iGrowth) in the HapMap lymphoblastoid cell lines derived from individuals of different ethnic backgrounds. We found a substantial enrichment for miRNAs (53 miRNAs, FDR < 0.05) correlated with cellular proliferation in pooled CEU (Caucasian of northern and western European descent) and YRI (individuals from Ibadan, Nigeria) samples. Specifically, 119 miRNAs (59 %) were significantly correlated with iGrowth in YRI; of these miRNAs, 18 were correlated with iGrowth in CEU. To gain further insight into the effect of miRNAs on cellular proliferation in cancer, we showed that over-expression of miR-22, one of the top iGrowth-associated miRNAs, leads to growth inhibition in an ovarian cancer cell line (SKOV3). Furthermore, over-expression of miR-22 down-regulates the expression of its target genes (MXI1 and SLC25A37) in this ovarian cancer cell line, highlighting an miRNA-mediated regulatory network potentially important for cellular proliferation. Importantly, our study identified miRNAs that can be used as molecular targets in cancer therapy.
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Affiliation(s)
- Divya Lenkala
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Bonnie LaCroix
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Paul Geeleher
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Hae Kyung Im
- Department of Health Studies, The University of Chicago, Chicago, IL 60637, USA
| | - R. Stephanie Huang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
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Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis. Proc Natl Acad Sci U S A 2014; 111:E1823-32. [PMID: 24757057 DOI: 10.1073/pnas.1401182111] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The capacity to repair different types of DNA damage varies among individuals, making them more or less susceptible to the detrimental health consequences of damage exposures. Current methods for measuring DNA repair capacity (DRC) are relatively labor intensive, often indirect, and usually limited to a single repair pathway. Here, we describe a fluorescence-based multiplex flow-cytometric host cell reactivation assay (FM-HCR) that measures the ability of human cells to repair plasmid reporters, each bearing a different type of DNA damage or different doses of the same type of DNA damage. FM-HCR simultaneously measures repair capacity in any four of the following pathways: nucleotide excision repair, mismatch repair, base excision repair, nonhomologous end joining, homologous recombination, and methylguanine methyltransferase. We show that FM-HCR can measure interindividual DRC differences in a panel of 24 cell lines derived from genetically diverse, apparently healthy individuals, and we show that FM-HCR may be used to identify inhibitors or enhancers of DRC. We further develop a next-generation sequencing-based HCR assay (HCR-Seq) that detects rare transcriptional mutagenesis events due to lesion bypass by RNA polymerase, providing an added dimension to DRC measurements. FM-HCR and HCR-Seq provide powerful tools for exploring relationships among global DRC, disease susceptibility, and optimal treatment.
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18
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Genetic variation is the major determinant of individual differences in leukocyte endothelial adhesion. PLoS One 2014; 9:e87883. [PMID: 24520339 PMCID: PMC3919726 DOI: 10.1371/journal.pone.0087883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/06/2014] [Indexed: 12/13/2022] Open
Abstract
Objective To determine the genetic contribution to leukocyte endothelial adhesion. Methods Leukocyte endothelial adhesion was assessed through a novel cell-based assay using human lymphoblastoid cell lines. A high-throughput screening method was developed to evaluate the inter-individual variability in leukocyte endothelial adhesion using lymphoblastoid cell lines derived from different donors. To assess heritability, ninety-two lymphoblastoid cell lines derived from twenty-three monozygotic twin pairs and twenty-three sibling pairs were compared. These lymphoblastoid cell lines were plated with the endothelial cell line EA.hy926 and labeled with Calcein AM dye. Fluorescence was assessed to determine endothelial cell adhesion to each lymphoblastoid cell line. Intra-pair similarity was determined for monozygotic twins and siblings using Pearson pairwise correlation coefficients. Results A leukocyte endothelial adhesion assay for lymphoblastoid cell lines was developed and optimized (CV = 8.68, Z′-factor = 0.67, SNR = 18.41). A higher adhesion correlation was found between the twins than that between the siblings. Intra-pair similarity for leukocyte endothelial adhesion in monozygotic twins was 0.60 compared to 0.25 in the siblings. The extent to which these differences are attributable to underlying genetic factors was quantified and the heritability of leukocyte endothelial adhesion was calculated to be 69.66% (p-value<0.0001). Conclusions There is a heritable component to leukocyte endothelial adhesion. Underlying genetic predisposition plays a significant role in inter-individual variability of leukocyte endothelial adhesion.
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Comprehensive genetic analysis of cytarabine sensitivity in a cell-based model identifies polymorphisms associated with outcome in AML patients. Blood 2013; 121:4366-76. [PMID: 23538338 DOI: 10.1182/blood-2012-10-464149] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A whole-genome approach was used to investigate the genetic determinants of cytarabine-induced cytotoxicity. We performed a meta-analysis of genome-wide association studies involving 523 lymphoblastoid cell lines (LCLs) from individuals of European, African, Asian, and African American ancestry. Several of the highest-ranked single-nucleotide polymorphisms (SNPs) were within the mutated in colorectal cancers (MCC) gene. MCC expression was induced by cytarabine treatment from 1.7- to 26.6-fold in LCLs. A total of 33 SNPs ranked at the top of the meta-analysis (P < 10(-5)) were successfully tested in a clinical trial of patients randomized to receive low-dose or high-dose cytarabine plus daunorubicin and etoposide; of these, 18 showed association (P < .05) with either cytarabine 50% inhibitory concentration in leukemia cells or clinical response parameters (minimal residual disease, overall survival (OS), and treatment-related mortality). This count (n = 18) was significantly greater than expected by chance (P = .016). For rs1203633, LCLs with AA genotype were more sensitive to cytarabine-induced cytotoxicity (P = 1.31 × 10(-6)) and AA (vs GA or GG) genotype was associated with poorer OS (P = .015), likely as a result of greater treatment-related mortality (P = .0037) in patients with acute myeloid leukemia (AML). This multicenter AML02 study trial was registered at www.clinicaltrials.gov as #NCT00136084.
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Brown CC, Havener TM, Medina MW, Krauss RM, McLeod HL, Motsinger‐Reif AA. Multivariate methods and software for association mapping in dose-response genome-wide association studies. BioData Min 2012; 5:21. [PMID: 23234571 PMCID: PMC3661384 DOI: 10.1186/1756-0381-5-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large sample sizes, freedom of ethical restrictions and ease of repeated measurements make cytotoxicity assays of immortalized lymphoblastoid cell lines a powerful new in vitro method in pharmacogenomics research. However, previous studies may have over-simplified the complex differences in dose-response profiles between genotypes, resulting in a loss of power. METHODS The current study investigates four previously studied methods, plus one new method based on a multivariate analysis of variance (MANOVA) design. A simulation study was performed using differences in cancer drug response between genotypes for biologically meaningful loci. These loci also showed significance in separate genome-wide association studies. This manuscript builds upon a previous study, where differences in dose-response curves between genotypes were constructed using the hill slope equation. CONCLUSION Overall, MANOVA was found to be the most powerful method for detecting real signals, and was also the most robust method for detection using alternatives generated with the previous simulation study. This method is also attractive because test statistics follow their expected distributions under the null hypothesis for both simulated and real data. The success of this method inspired the creation of the software program MAGWAS. MAGWAS is a computationally efficient, user-friendly, open source software tool that works on most platforms and performs GWASs for individuals having multivariate responses using standard file formats.
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Affiliation(s)
- Chad C Brown
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Tammy M Havener
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marisa Wong Medina
- , Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Ronald M Krauss
- , Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Howard L McLeod
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alison A Motsinger‐Reif
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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Vincent M, Oved K, Morag A, Pasmanik-Chor M, Oron-Karni V, Shomron N, Gurwitz D. Genome-wide transcriptomic variations of human lymphoblastoid cell lines: insights from pairwise gene-expression correlations. Pharmacogenomics 2012; 13:1893-904. [DOI: 10.2217/pgs.12.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aims: Human lymphoblastoid cell lines (LCLs) are a rich resource of information on human interindividual genomic, transcriptomic, proteomic and phenomic variations, and are therefore gaining popularity for pharmacogenomic studies. In the present study we demonstrate that genome-wide transcriptomic data from a small LCL panel from unrelated individuals is sufficient for detecting pairs of genes that exhibit highly correlated expression levels and may thus convey insights about coregulated genes. Materials & methods: RNA samples were prepared from LCLs representing 12 unrelated healthy adult female Caucasian donors. Transcript levels were determined with the Affymetrix Human Gene arrays. Expression-level correlations were searched using Partek® Genomics Suite™ and the R environment. Sequences of detected correlated gene pairs were compared for shared conserved 3´-UTR miRNA binding. Results: Most of the approximately 33,000 transcripts covered by the Affymetrix arrays showed closely similar expression levels in LCLs from unrelated donors. However, the expression levels of some transcripts showed large inter-individual variations. When comparing the expression levels of each of the top 1000 genes showing the largest interindividual expression variations against the others, two sets containing 156 and 4438 correlated gene pairs with false-discovery rates of 0.01 and 0.05 were detected, respectively. Similar analysis of another gene-expression data set from LCLs (GSE11582) indicated that 61 and 39% of identified pairs matched the pairs detected from our transcriptomic data, respectively. Shared conserved 3´-UTR miRNA binding sites were noted for 14–17% of the top 100 gene pairs, suggesting that regulation by miRNA may contribute to their coordinated expression. Conclusion: Probing genome-wide transcriptomic data sets of LCLs from unrelated individuals may detect coregulated genes, adding insights on cellular regulation by miRNAs. Original submitted 11 July 2012; Revision submitted 4 September 2012
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Affiliation(s)
- Marc Vincent
- Université Paris Descartes, INSERM UMRS775, Paris, France
| | - Keren Oved
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Ayelet Morag
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Varda Oron-Karni
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Noam Shomron
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - David Gurwitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 2012. [PMID: 23204130 DOI: 10.1158/1078-0432.ccr-12-2618] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE We sought to show the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results. EXPERIMENTAL DESIGN A GWAS of paclitaxel-induced cytotoxicity was conducted in 247 LCLs from the HapMap Project and compared with a GWAS of sensory peripheral neuropathy in patients with breast cancer (n = 855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis. RESULTS We observed an enrichment of LCL cytotoxicity-associated single-nucleotide polymorphisms (SNP) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTL), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of Neuroscreen-1(NS-1; rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel. CONCLUSIONS The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients.
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Affiliation(s)
- Heather E Wheeler
- Sections of Hematology/Oncology and Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer. Pharmacogenet Genomics 2012; 22:105-16. [PMID: 22173087 DOI: 10.1097/fpc.0b013e32834dd7e2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Gemcitabine is widely used to treat non-small cell lung cancer (NSCLC). The aim of this study was to assess the pharmacogenomic effects of the entire gemcitabine metabolic pathway, we genotyped single nucleotide polymorphisms (SNPs) within the 17 pathway genes using DNA samples from patients with NSCLC treated with gemcitabine to determine the effect of genetic variants within gemcitabine pathway genes on overall survival (OS) of patients with NSCLC after treatment of gemcitabine. METHODS Eight of the 17 pathway genes were resequenced with DNA samples from Coriell lymphoblastoid cell lines (LCLs) using Sanger sequencing for all exons, exon-intron junctions, and 5'-, 3'-UTRs. A total of 107 tagging SNPs were selected on the basis of the resequencing data for the eight genes and on HapMap data for the remaining nine genes, followed by successful genotyping of 394 NSCLC patient DNA samples. Association of SNPs/haplotypes with OS was performed using the Cox regression model, followed by functional studies performed with LCLs and NSCLC cell lines. RESULTS Five SNPs in four genes (CDA, NT5C2, RRM1, and SLC29A1) showed associations with OS of those patients with NSCLC, as well as nine haplotypes in four genes (RRM1, RRM2, SLC28A3, and SLC29A1) with a P value of less than 0.05. Genotype imputation using the LCLs was performed for a region of 200 kb surrounding those SNPs, followed by association studies with gemcitabine cytotoxicity. Functional studies demonstrated that downregulation of SLC29A1, NT5C2, and RRM1 in NSCLC cell lines altered cell susceptibility to gemcitabine. CONCLUSION These studies help in identifying biomarkers to predict gemcitabine response in NSCLC, a step toward the individualized chemotherapy of lung cancer.
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Morag A, Oved K, Gurwitz D. Sex differences in human lymphoblastoid cells sensitivities to antipsychotic drugs. J Mol Neurosci 2012; 49:554-8. [PMID: 22760742 DOI: 10.1007/s12031-012-9852-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 06/26/2012] [Indexed: 12/30/2022]
Abstract
Adverse drug reactions (ADRs) are a major concern in pharmacotherapy and are more common among women. Immortalized human lymphoblastoid cell lines (LCLs) are emerging as a novel tool for studying interindividual variability in drug response, including ADRs. In the present study, we compared sensitivities of LCLs from unrelated healthy male and female donors to growth inhibition by a panel of common drugs. We observed large interindividual drug sensitivity variations with similar mean sensitivities recorded for LCLs from male and female donors for most tested drugs. A notable exception was observed for the typical antipsychotic haloperidol and the atypical antipsychotic risperidone, which exhibited, on average, more robust in vitro growth inhibition in male as compared with female LCLs. An opposite finding was observed for the antidepressant paroxetine, which was more potent for inhibiting the growth of female as compared with male LCLs. These observations are discussed in the context of the higher incidence of dystonia reported for male schizophrenia patients treated with haloperidol and the higher efficacy of paroxetine in female major depression patients.
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Affiliation(s)
- Ayelet Morag
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
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Holzinger ER, Ritchie MD. Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies. Pharmacogenomics 2012; 13:213-22. [PMID: 22256870 DOI: 10.2217/pgs.11.145] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The current paradigm of human genetics research is to analyze variation of a single data type (i.e., DNA sequence or RNA levels) to detect genes and pathways that underlie complex traits such as disease state or drug response. While these studies have detected thousands of variations that associate with hundreds of complex phenotypes, much of the estimated heritability, or trait variability due to genetic factors, remain unexplained. We may be able to account for a portion of the missing heritability if we incorporate a systems biology approach into these analyses. Rapid technological advances will make it possible for scientists to explore this hypothesis via the generation of high-throughput omics data - transcriptomic, proteomic and methylomic to name a few. Analyzing this 'meta-dimensional' data will require clever statistical techniques that allow for the integration of qualitative and quantitative predictor variables. For this article, we examine two major categories of approaches for integrated data analysis, give examples of their use in experimental and in silico datasets, and assess the limitations of each method.
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Affiliation(s)
- Emily R Holzinger
- Center for Human Genetics Research, Vanderbilt University, Department of Molecular Physiology & Biophysics, Nashville, TN, USA
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Wheeler HE, Dolan ME. Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. Pharmacogenomics 2012; 13:55-70. [PMID: 22176622 DOI: 10.2217/pgs.11.121] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The ability to predict how an individual patient will respond to a particular treatment is the ambitious goal of personalized medicine. The genetic make up of an individual has been shown to play a role in drug response. For pharmacogenomic studies, human lymphoblastoid cell lines (LCLs) comprise a useful model system for identifying genetic variants associated with pharmacologic phenotypes. The availability of extensive genotype data for many panels of LCLs derived from individuals of diverse ancestry allows for the study of genetic variants contributing to interethnic and interindividual variation in susceptibility to drugs. Many genome-wide association studies for drug-induced phenotypes have been performed in LCLs, often incorporating gene-expression data. LCLs are also being used in follow-up studies to clinical findings to determine how an associated variant functions to affect phenotype. This review describes the most recent pharmacogenomic findings made in LCLs, including the translation of some findings to clinical cohorts.
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Affiliation(s)
- Heather E Wheeler
- Section of Hematology/Oncology, Department of Medicine, 900 East 57th St, University of Chicago, Chicago, IL 60637, USA
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Gamazon ER, Ziliak D, Im HK, LaCroix B, Park DS, Cox NJ, Huang RS. Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am J Hum Genet 2012; 90:1046-63. [PMID: 22658545 DOI: 10.1016/j.ajhg.2012.04.023] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 04/19/2012] [Accepted: 04/28/2012] [Indexed: 12/12/2022] Open
Abstract
We sought to comprehensively and systematically characterize the relationship between genetic variation, miRNA expression, and mRNA expression. Genome-wide expression profiling of samples of European and African ancestry identified in each population hundreds of miRNAs whose increased expression is correlated with correspondingly reduced expression of target mRNAs. We scanned 3' UTR SNPs with a potential functional effect on miRNA binding for cis-acting expression quantitative trait loci (eQTLs) for the corresponding proximal target genes. To extend sequence-based, localized analyses of SNP effect on miRNA binding, we proceeded to dissect the genetic basis of miRNA expression variation; we mapped miRNA expression levels-as quantitative traits-to loci in the genome as miRNA eQTLs, demonstrating that miRNA expression is under significant genetic control. We found that SNPs associated with miRNA expression are significantly enriched with those SNPs already shown to be associated with mRNA. Moreover, we discovered that many of the miRNA-associated genetic variations identified in our study are associated with a broad spectrum of human complex traits from the National Human Genome Research Institute catalog of published genome-wide association studies. Experimentally, we replicated miRNA-induced mRNA expression inhibition and the cis-eQTL relationship to the target gene for several identified relationships among SNPs, miRNAs, and mRNAs in an independent set of samples; furthermore, we conducted miRNA overexpression and inhibition experiments to functionally validate the miRNA-mRNA relationships. This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated.
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Affiliation(s)
- Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL 60637, USA
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Abstract
The amazing successes in cure rates for children with cancer over the last century have come in large part from identifying clinical, genetic, and molecular variables associated with response to therapy in large cooperative clinical trials and stratifying therapies according to the predicted risk of relapse. There is an expanding interest in identifying germline genomic variants, as opposed to genetic variants within the tumor, that are associated with susceptibility to toxicity and for risk of relapse. This review highlights the most important germline pharmacogenetic and pharmacogenomic studies in pediatric oncology. Incorporating germline genomics into risk-adapted therapies will likely lead to safer and more effective treatments for children with cancer.
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Affiliation(s)
- Navin Pinto
- Department of Pediatrics and Medicine, and Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois 60637, USA.
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Mixed effects modeling of proliferation rates in cell-based models: consequence for pharmacogenomics and cancer. PLoS Genet 2012; 8:e1002525. [PMID: 22346769 PMCID: PMC3276560 DOI: 10.1371/journal.pgen.1002525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/20/2011] [Indexed: 11/19/2022] Open
Abstract
The International HapMap project has made publicly available extensive genotypic data on a number of lymphoblastoid cell lines (LCLs). Building on this resource, many research groups have generated a large amount of phenotypic data on these cell lines to facilitate genetic studies of disease risk or drug response. However, one problem that may reduce the usefulness of these resources is the biological noise inherent to cellular phenotypes. We developed a novel method, termed Mixed Effects Model Averaging (MEM), which pools data from multiple sources and generates an intrinsic cellular growth rate phenotype. This intrinsic growth rate was estimated for each of over 500 HapMap cell lines. We then examined the association of this intrinsic growth rate with gene expression levels and found that almost 30% (2,967 out of 10,748) of the genes tested were significant with FDR less than 10%. We probed further to demonstrate evidence of a genetic effect on intrinsic growth rate by determining a significant enrichment in growth-associated genes among genes targeted by top growth-associated SNPs (as eQTLs). The estimated intrinsic growth rate as well as the strength of the association with genetic variants and gene expression traits are made publicly available through a cell-based pharmacogenomics database, PACdb. This resource should enable researchers to explore the mediating effects of proliferation rate on other phenotypes. Cell-based models provide a convenient system to conduct studies that would be impossible to apply to human subjects, but the phenotypes measured on these models can be marred with biological noise. We propose a method (MEM) to address this issue by statistically combining data from various sources, and we apply it to the proliferation rates of cell lines collected as part of the International HapMap project. We show that the proliferation rate computed using our method is a better measure of the true proliferation rate of the cells and produces a much stronger association with gene expression phenotypes on the same cell lines: more than 30% of the genes tested were significantly associated with proliferation rate. We also demonstrate that genetic variants have an effect on growth rate. Finally, we make these intrinsic proliferation rates and the strength of the association with gene expression phenotypes public, which should allow other researchers to explore the mediating effects of proliferation on other phenotypes.
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Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet 2012; 21:2111-23. [PMID: 22286170 PMCID: PMC3315207 DOI: 10.1093/hmg/dds021] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the ‘missing heritability problem’. Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. The goal of our study was to explore a complimentary approach, which combines GWAS results with functional data in order to identify novel genetic associations with small effect sizes. To do so, we conducted a GWAS for lymphocyte count, a physiologic quantitative trait associated with asthma, in 462 Hutterites. In parallel, we performed a genome-wide gene expression study in lymphoblastoid cell lines from 96 Hutterites. We found significant support for genetic associations using the GWAS data when we considered variants near the 193 genes whose expression levels across individuals were most correlated with lymphocyte counts. Interestingly, these variants are also enriched with signatures of an association with asthma susceptibility, an observation we were able to replicate. The associated loci include genes previously implicated in asthma susceptibility as well as novel candidate genes enriched for functions related to T cell receptor signaling and adenosine triphosphate synthesis. Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility.
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31
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O'Donnell PH, Stark AL, Gamazon ER, Wheeler HE, McIlwee BE, Gorsic L, Im HK, Huang RS, Cox NJ, Dolan ME. Identification of novel germline polymorphisms governing capecitabine sensitivity. Cancer 2012; 118:4063-73. [PMID: 22864933 DOI: 10.1002/cncr.26737] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND Capecitabine, an oral 5-fluorouracil (5-FU) prodrug, is widely used in the treatment of breast, colorectal, and gastric cancers. To guide the selection of patients with potentially the greatest benefit of experiencing antitumor efficacy, or, alternatively, of developing toxicities, identifying genomic predictors of capecitabine sensitivity could permit its more informed use. METHODS The objective of this study was to perform capecitabine sensitivity genome-wide association studies (GWAS) using 503 well genotyped human cell lines from individuals representing multiple different world populations. A meta-analysis that included all ethnic populations then enabled the identification of novel germline determinants (single nucleotide polymorphisms [SNPs]) of capecitabine susceptibility. RESULTS First, an intrapopulation GWAS of Caucasian individuals identified reference SNP 4702484 (rs4702484) (within adenylate cyclase 2 [ADCY2]) at a level reaching genome-wide significance (P = 5.2 × 10(-8) ). This SNP is located upstream of the 5 methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) gene, and it is known that the enzyme for MTRR is involved in the methionine-folate biosynthesis and metabolism pathway, which is the primary target of 5-FU-related compounds, although the authors were unable to identify a direct relation between rs4702484 and MTRR expression in a tested subset of cells. In the meta-analysis, 4 SNPs comprised the top hits, which, again, included rs4702484 and 3 additional SNPs (rs8101143, rs576523, and rs361433) that approached genome-wide significance (P values from 1.9 × 10(-7) to 8.8 × 10(-7) ). The meta-analysis also identified 1 missense variant (rs11722476; serine to asparagine) within switch/sucrose nonfermentable-related, matrix-associated, actin-dependent regulator of chromatin (SMARCAD1), a novel gene for association with capecitabine/5-FU susceptibility. CONCLUSIONS Toward the goal of individualizing cancer chemotherapy, the current study identified novel SNPs and genes associated with capecitabine sensitivity that are potentially informative and testable in any patient regardless of ethnicity.
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Affiliation(s)
- Peter H O'Donnell
- Section of Hematology-Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
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Brown C, Havener TM, Everitt L, McLeod H, Motsinger-Reif AA. A comparison of association methods for cytotoxicity mapping in pharmacogenomics. Front Genet 2011; 2:86. [PMID: 22303380 PMCID: PMC3268638 DOI: 10.3389/fgene.2011.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/15/2011] [Indexed: 02/03/2023] Open
Abstract
Cytotoxicity assays of immortalized lymphoblastoid cell lines (LCLs) represent a promising new in vitro approach in pharmacogenomics research. However, previous studies employing LCLs in gene mapping have used simple association methods, which may not adequately capture the true differences in non-linear response profiles between genotypes. Two common approaches summarize each dose-response curve with either the IC50 or the slope parameter estimates from a hill slope fit and treat these estimates as the response in a linear model. The current study investigates these two methods, as well as four novel methods, and compares their power to detect differences between the response profiles of genotypes under a variety of different alternatives. The four novel methods include two methods that summarize each dose-response by its area under the curve, one method based off of an analysis of variance (ANOVA) design, and one method that compares hill slope fits for all individuals of each genotype. The power of each method was found to depend not only on the choice of alternative, but also on the choice for the set of dosages used in cytotoxicity measurements. The ANOVA-based method was found to be the most robust across alternatives and dosage sets for power in detecting differences between genotypes.
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Affiliation(s)
- Chad Brown
- Department of Statistics, North Carolina State UniversityRaleigh, NC, USA
| | - Tammy M. Havener
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - Lorraine Everitt
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - Howard McLeod
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - Alison A. Motsinger-Reif
- Department of Statistics, North Carolina State UniversityRaleigh, NC, USA
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, NC, USA
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Wen Y, Gorsic LK, Wheeler HE, Ziliak DM, Huang RS, Dolan ME. Chemotherapeutic-induced apoptosis: a phenotype for pharmacogenomics studies. Pharmacogenet Genomics 2011; 21:476-88. [PMID: 21642893 PMCID: PMC3134538 DOI: 10.1097/fpc.0b013e3283481967] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To determine whether cellular apoptosis is a suitable phenotypic trait for pharmacogenomics studies by evaluating caspase 3/7-mediated activity in lymphoblastoid cell lines after treatment with six chemotherapeutic agents: 5'-deoxyfluorouridine, pemetrexed, cytarabine, paclitaxel, carboplatin, and cisplatin. MATERIALS AND METHODS Using monozygotic twin pair and sibling pair lymphoblastoid cell lines, we identified conditions for measurement of caspase 3/7 activity in lymphoblastoid cell lines. Genome-wide association studies were performed with over 2 million single nucleotide polymorphisms (SNPs) and cisplatin-induced apoptosis in HapMap CEU cell lines (n=77). RESULTS Although treatment with 5'-deoxyfluorouridine and pemetrexed for up to 24 h resulted in low levels of apoptosis or interindividual variation in caspase-dependent cell death; paclitaxel, cisplatin, carboplatin, and cytarabine treatment for 24 h resulted in 9.4-fold, 9.1-fold, 7.0-fold, and 6.0-fold increases in apoptosis relative to control, respectively. There was a weak correlation between caspase activity and cytotoxicity (r(2)=0.03-0.29) demonstrating that cytotoxicity and apoptosis are two distinct phenotypes that may produce independent genetic associations. Estimated heritability (h(2)) for apoptosis was 0.57 and 0.29 for cytarabine (5 and 40 μmol/l, respectively), 0.22 for paclitaxel (12.5 nmol/l), and 0.34 for cisplatin (5 μmol/l). In the genome-wide association study using the HapMap CEU panel, we identified a significant enrichment of cisplatin-induced cytotoxicity SNPs within the significant cisplatin-induced apoptosis SNPs and an enrichment of expression quantitative trait loci (eQTL). Among these eQTLs, we identified several eQTLs with known function related to apoptosis and/or cytotoxicity. CONCLUSION Our study identifies apoptosis as a phenotype for pharmacogenomic studies in lymphoblastoid cell lines after treatment with paclitaxel, cisplatin, carboplatin, and cytarabine that may have utility for discovering biomarkers to predict response to certain chemotherapeutics.
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Affiliation(s)
| | | | - Heather E. Wheeler
- Section of Hematology/Oncology, Department of Medicine, the University of Chicago, Chicago, IL 60637, USA
| | - Dana M. Ziliak
- Section of Hematology/Oncology, Department of Medicine, the University of Chicago, Chicago, IL 60637, USA
| | - R. Stephanie Huang
- Section of Hematology/Oncology, Department of Medicine, the University of Chicago, Chicago, IL 60637, USA
| | - M. Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, the University of Chicago, Chicago, IL 60637, USA
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Watson VG, Hardison NE, Harris T, Motsinger-Reif A, McLeod HL. Genomic profiling in CEPH cell lines distinguishes between the camptothecins and indenoisoquinolines. Mol Cancer Ther 2011; 10:1839-45. [PMID: 21750217 DOI: 10.1158/1535-7163.mct-10-0872] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have attempted to use a familial genetics strategy to study mechanisms of topoisomerase 1 (Top1) inhibition. Investigations have steadily been chipping away at the pathways involved in cellular response following Top1 inhibition for more than 20 years. Our system-wide approach, which phenotypes a collection of genotyped human cell lines for sensitivity to compounds and interrogates all genes and molecular pathways simultaneously. Previously, we characterized the in vitro sensitivity of 15 families of Centre d'Etude Polymorphisme Humain (CEPH) cell lines (n = 142) to 9 camptothecin analogues. Linkage analysis revealed a pattern of 7 quantitative trait loci (QTL) shared by all of the camptothecins. To identify which, if any, QTLs are related to the general mechanism of Top1 inhibition or should be considered camptothecin specific, we characterized the in vitro sensitivity of the same panel of CEPH cell lines to the indenisoquinolones, a structurally distinct class of Top1 inhibitors. Four QTLs on chromosomes 1, 5, 11, and 16 were shared by both the camptothecins and the indenoisoquinolines and are considered associated with the general mechanism of Top1 inhibition. The remaining 3 QTLs (chromosomes 6 and 20) are considered specific to camptothecin-induced cytotoxicity. Finally, 8 QTLs were identified, which were unique to the indenoisoquinolines.
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Affiliation(s)
- Venita Gresham Watson
- UNC Institute for Pharmacogenomics and Individualized Therapy, Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, Dolan ME. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 2011; 6:e21920. [PMID: 21755009 PMCID: PMC3130766 DOI: 10.1371/journal.pone.0021920] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/08/2011] [Indexed: 12/31/2022] Open
Abstract
Chemotherapeutic agents are used in the treatment of many cancers, yet variable resistance and toxicities among individuals limit successful outcomes. Several studies have indicated outcome differences associated with ancestry among patients with various cancer types. Using both traditional SNP-based and newly developed gene-based genome-wide approaches, we investigated the genetics of chemotherapeutic susceptibility in lymphoblastoid cell lines derived from 83 African Americans, a population for which there is a disparity in the number of genome-wide studies performed. To account for population structure in this admixed population, we incorporated local ancestry information into our association model. We tested over 2 million SNPs and identified 325, 176, 240, and 190 SNPs that were suggestively associated with cytarabine-, 5'-deoxyfluorouridine (5'-DFUR)-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-4)). Importantly, some of these variants are found only in populations of African descent. We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Using a gene-based genome-wide association approach, we identified 26, 11, 20, and 41 suggestive candidate genes for association with cytarabine-, 5'-DFUR-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-3)). Fourteen of these genes showed evidence of association with their respective chemotherapeutic phenotypes in the Yoruba from Ibadan, Nigeria (p<0.05), including TP53I11, COPS5 and GAS8, which are known to be involved in tumorigenesis. Although our results require further study, we have identified variants and genes associated with chemotherapeutic susceptibility in African Americans by using an approach that incorporates local ancestry information.
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Affiliation(s)
- Heather E. Wheeler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Marleen Welsh
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Amy L. Stark
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - M. Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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36
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Maranville JC, Luca F, Richards AL, Wen X, Witonsky DB, Baxter S, Stephens M, Di Rienzo A. Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet 2011; 7:e1002162. [PMID: 21750684 PMCID: PMC3131293 DOI: 10.1371/journal.pgen.1002162] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 05/15/2011] [Indexed: 01/14/2023] Open
Abstract
Glucocorticoids (GCs) mediate physiological responses to environmental stress and are commonly used as pharmaceuticals. GCs act primarily through the GC receptor (GR, a transcription factor). Despite their clear biomedical importance, little is known about the genetic architecture of variation in GC response. Here we provide an initial assessment of variability in the cellular response to GC treatment by profiling gene expression and protein secretion in 114 EBV-transformed B lymphocytes of African and European ancestry. We found that genetic variation affects the response of nearby genes and exhibits distinctive patterns of genotype-treatment interactions, with genotypic effects evident in either only GC-treated or only control-treated conditions. Using a novel statistical framework, we identified interactions that influence the expression of 26 genes known to play central roles in GC-related pathways (e.g. NQO1, AIRE, and SGK1) and that influence the secretion of IL6.
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Affiliation(s)
- Joseph C. Maranville
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Francesca Luca
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Allison L. Richards
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Xiaoquan Wen
- Department of Statistics, The University of Chicago, Chicago, Illinois, United States of America
| | - David B. Witonsky
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Shaneen Baxter
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, The University of Chicago, Chicago, Illinois, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
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Matsson P, Yee SW, Markova S, Morrissey K, Jenkins G, Xuan J, Jorgenson E, Kroetz DL, Giacomini KM. Discovery of regulatory elements in human ATP-binding cassette transporters through expression quantitative trait mapping. THE PHARMACOGENOMICS JOURNAL 2011; 12:214-26. [PMID: 21383772 PMCID: PMC3325368 DOI: 10.1038/tpj.2011.8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ATP-Binding Cassette (ABC) membrane transporters determine the disposition of many drugs, metabolites and endogenous compounds. Coding region variation in ABC transporters is the cause of many genetic disorders, but much less is known about the genetic basis and functional outcome of ABC transporter expression level variation. We used genotype and mRNA transcript level data from human lymphoblastoid cell lines to assess population and gender differences in ABC transporter expression, and to guide the discovery of genomic regions involved in transcriptional regulation. Nineteen of 49 ABC genes were differentially expressed between individuals of African, Asian and European descent suggesting an important influence of race on expression level of ABC transporters. Twenty-four significant associations were found between transporter transcript levels and proximally located genetic variants. Several of the associations were experimentally validated in reporter assays. Through influencing ABC expression levels, these SNPs may affect disease susceptibility and response to drugs.
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Affiliation(s)
- P Matsson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
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Gamazon ER, Im HK, O'Donnell PH, Ziliak D, Stark AL, Cox NJ, Dolan ME, Huang RS. Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity. Mol Cancer Ther 2011; 10:472-80. [PMID: 21252287 DOI: 10.1158/1535-7163.mct-10-0910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Using a genome-wide gene expression data set generated from Affymetrix GeneChip Human Exon 1.0ST array, we comprehensively surveyed the role of 322 X chromosome gene expression traits on cellular sensitivity to cisplatin and carboplatin. We identified 31 and 17 X chromosome genes whose expression levels are significantly correlated (after multiple testing correction) with sensitivity to carboplatin and cisplatin, respectively, in the combined HapMap CEU (Utah residents with ancestry from northern and western Europe) and YRI (Yoruba in Ibahan, Nigeria) populations (false discovery rate, FDR < 0.05). Of those, 14 overlap for both cisplatin and carboplatin. Using an independent gene expression quantification method, the Illumina Sentrix Human-6 Expression BeadChip, measured on the same HapMap cell lines, we found that 4 and 2 of these genes are significantly associated with carboplatin and cisplatin sensitivity, respectively, in both analyses. Two genes, CTPS2 and DLG3, were identified by both genome-wide gene expression analyses as correlated with cellular sensitivity to both platinating agents. The expression of DLG3 gene was also found to correlate with cellular sensitivity to platinating agents in NCI-60 cancer cell lines. In addition, we evaluated whether the expression of X chromosome genes contributed to the observed differences in sensitivity to the platinums between CEU and YRI-derived cell lines. Of the 34 distinct genes significantly correlated with either carboplatin or cisplatin sensitivity, 14 are differentially expressed (defined as P < 0.05) between CEU and YRI. Thus, sex chromosome genes play a role in cellular sensitivity to platinating agents and differences in the expression level of these genes are an important source of variation that should be included in comprehensive pharmacogenomic studies.
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Affiliation(s)
- Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, 900 E. 57 street, KCBD room 7148, Chicago, IL 60637, USA
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Stark AL, Zhang W, Zhou T, O'Donnell PH, Beiswanger CM, Huang RS, Cox NJ, Dolan ME. Population differences in the rate of proliferation of international HapMap cell lines. Am J Hum Genet 2010; 87:829-33. [PMID: 21109222 DOI: 10.1016/j.ajhg.2010.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/01/2010] [Accepted: 10/18/2010] [Indexed: 11/28/2022] Open
Abstract
The International HapMap Project is a resource for researchers containing genotype, sequencing, and expression information for EBV-transformed lymphoblastoid cell lines derived from populations across the world. The expansion of the HapMap beyond the four initial populations of Phase 2, referred to as Phase 3, has increased the sample number and ethnic diversity available for investigation. However, differences in the rate of cellular proliferation between the populations can serve as confounders in phenotype-genotype studies using these cell lines. Within the Phase 2 populations, the JPT and CHB cell lines grow faster (p < 0.0001) than the CEU or YRI cell lines. Phase 3 YRI cell lines grow significantly slower than Phase 2 YRI lines (p < 0.0001), with no widespread genetic differences based on common SNPs. In addition, we found significant growth differences between the cell lines in the Phase 2 ASN populations and the Han Chinese from the Denver metropolitan area panel in Phase 3 (p < 0.0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration.
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Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010; 6:e1000888. [PMID: 20369019 PMCID: PMC2848547 DOI: 10.1371/journal.pgen.1000888] [Citation(s) in RCA: 928] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 02/25/2010] [Indexed: 12/12/2022] Open
Abstract
Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. Using a web site we developed to serve results of expression quantitative trait locus (eQTL) studies in lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), we show that single nucleotide polymorphisms (SNPs) associated with complex traits (from http://www.genome.gov/gwastudies/) are significantly more likely to be eQTLs than minor-allele-frequency–matched SNPs chosen from high-throughput GWAS platforms. These findings are robust across a range of thresholds for establishing eQTLs (p-values from 10−4–10−8), and a broad spectrum of human complex traits. Analyses of GWAS data from the Wellcome Trust studies confirm that annotating SNPs with a score reflecting the strength of the evidence that the SNP is an eQTL can improve the ability to discover true associations and clarify the nature of the mechanism driving the associations. Our results showing that trait-associated SNPs are more likely to be eQTLs and that application of this information can enhance discovery of trait-associated SNPs for complex phenotypes raise the possibility that we can utilize this information both to increase the heritability explained by identifiable genetic factors and to gain a better understanding of the biology underlying complex traits. We show here that single nucleotide polymorphisms (SNPs) associated with complex traits (as identified in the catalog of results from genome-wide association studies http://www.genome.gov/gwastudies/) are more likely than other SNPs chosen from high-throughput genotyping platforms to predict expression levels of genes. These observations confirm that genetic risk factors for complex traits will often affect phenotype by altering the amount or timing of protein production, rather than by changing the type of protein produced. This knowledge can be used to improve our ability to discover genetic risk factors for complex traits and to improve our understanding of their underlying biology.
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Affiliation(s)
- Dan L. Nicolae
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Eric Gamazon
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Wei Zhang
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Shiwei Duan
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - M. Eileen Dolan
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Nancy J. Cox
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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