1
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Pang L, Cai C, Aggarwal P, Wang D, Vijay V, Bagam P, Blamer J, Matter A, Turner A, Ren L, Papineau K, Srinivasasainagendra V, Tiwari HK, Yang X, Schnackenberg L, Mattes W, Broeckel U. Predicting oncology drug-induced cardiotoxicity with donor-specific iPSC-CMs-a proof-of-concept study with doxorubicin. Toxicol Sci 2024; 200:79-94. [PMID: 38547396 PMCID: PMC11199917 DOI: 10.1093/toxsci/kfae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024] Open
Abstract
Many oncology drugs have been found to induce cardiotoxicity in a subset of patients, which significantly limits their clinical use and impedes the benefit of lifesaving anticancer treatments. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carry donor-specific genetic information and have been proposed for exploring the interindividual difference in oncology drug-induced cardiotoxicity. Herein, we evaluated the inter- and intraindividual variability of iPSC-CM-related assays and presented a proof of concept to prospectively predict doxorubicin (DOX)-induced cardiotoxicity (DIC) using donor-specific iPSC-CMs. Our findings demonstrated that donor-specific iPSC-CMs exhibited greater line-to-line variability than the intraindividual variability in impedance cytotoxicity and transcriptome assays. The variable and dose-dependent cytotoxic responses of iPSC-CMs resembled those observed in clinical practice and largely replicated the reported mechanisms. By categorizing iPSC-CMs into resistant and sensitive cell lines based on their time- and concentration-related phenotypic responses to DOX, we found that the sensitivity of donor-specific iPSC-CMs to DOX may predict in vivo DIC risk. Furthermore, we identified a differentially expressed gene, DND microRNA-mediated repression inhibitor 1 (DND1), between the DOX-resistant and DOX-sensitive iPSC-CMs. Our results support the utilization of donor-specific iPSC-CMs in assessing interindividual differences in DIC. Further studies will encompass a large panel of donor-specific iPSC-CMs to identify potential novel molecular and genetic biomarkers for predicting DOX and other oncology drug-induced cardiotoxicity.
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Affiliation(s)
- Li Pang
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Chengzhong Cai
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Praful Aggarwal
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Dong Wang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Vikrant Vijay
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Prathyusha Bagam
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Jacob Blamer
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Andrea Matter
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Amy Turner
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Lijun Ren
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Katy Papineau
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Xi Yang
- Division of Pharmacology & Toxicology, Office of Cardiology, Hematology, Endocrinology, & Nephrology, Office of New Drug, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, USA
| | - Laura Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - William Mattes
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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2
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Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype × environment interactions in gene regulation and complex traits. Nat Genet 2024; 56:1057-1068. [PMID: 38858456 DOI: 10.1038/s41588-024-01776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Genotype × environment interactions (GxE) have long been recognized as a key mechanism underlying human phenotypic variation. Technological developments over the past 15 years have dramatically expanded our appreciation of the role of GxE in both gene regulation and complex traits. The richness and complexity of these datasets also required parallel efforts to develop robust and sensitive statistical and computational approaches. Although our understanding of the genetic architecture of molecular and complex traits has been maturing, a large proportion of complex trait heritability remains unexplained. Furthermore, there are increasing efforts to characterize the effect of environmental exposure on human health. We therefore review GxE in human gene regulation and complex traits, advocating for a comprehensive approach that jointly considers genetic and environmental factors in human health and disease.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Ali Ranjbaran
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, US.
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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3
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McIntire E, Barr KA, Gonzales NM, Gilad Y. Guided Differentiation of Pluripotent Stem Cells for Cardiac Cell Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.21.550072. [PMID: 37502898 PMCID: PMC10370173 DOI: 10.1101/2023.07.21.550072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We have developed a guided differentiation protocol for induced pluripotent stem cells (iPSCs) that rapidly generates a temporally and functionally diverse set of cardiac-relevant cell types. By leveraging techniques used in embryoid body and cardiac organoid generation, we produce both progenitor and terminal cardiac cell types concomitantly in just 10 days. Our results show that guided differentiation generates functionally relevant cardiac cell types that closely align with the transcriptional profiles of cells from differentiation time-course collections, mature cardiac organoids, and in vivo heart tissue. Guided differentiation prioritizes simplicity by minimizing the number of reagents and steps required, thereby enabling rapid and cost-effective experimental throughput. We expect this approach will provide a scalable cardiac model for population-level studies of gene regulatory variation and gene-by-environment interactions.
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Affiliation(s)
- Erik McIntire
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Natalia M Gonzales
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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4
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Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. eLife 2024; 13:e85235. [PMID: 38334359 PMCID: PMC10901511 DOI: 10.7554/elife.85235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2024] [Indexed: 02/10/2024] Open
Abstract
Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
- Department of Biology, University of Rome Tor VergataRomeItaly
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5
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Matthews ER, Johnson OD, Horn KJ, Gutiérrez JA, Powell SR, Ward MC. Anthracyclines induce cardiotoxicity through a shared gene expression response signature. PLoS Genet 2024; 20:e1011164. [PMID: 38416769 PMCID: PMC10927150 DOI: 10.1371/journal.pgen.1011164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/11/2024] [Accepted: 01/31/2024] [Indexed: 03/01/2024] Open
Abstract
TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.
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Affiliation(s)
- E. Renee Matthews
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Omar D. Johnson
- Biochemistry, Cellular and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kandace J. Horn
- John Sealy School of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - José A. Gutiérrez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Simon R. Powell
- Neuroscience Graduate Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle C. Ward
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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6
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Thomas D, Manhas A, Sayed N. Harnessing iPSCs to Dissect Causality in Anthracycline-Induced Cardiotoxicity: All That Fits Are Not Hits. JACC CardioOncol 2024; 6:51-54. [PMID: 38510297 PMCID: PMC10950438 DOI: 10.1016/j.jaccao.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Amit Manhas
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
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7
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Abstract
Anthracycline-induced cardiotoxicity (AIC) is a serious and common side effect of anthracycline therapy. Identification of genes and genetic variants associated with AIC risk has clinical potential as a cardiotoxicity predictive tool and to allow the development of personalized therapies. In this review, we provide an overview of the function of known AIC genes identified by association studies and categorize them based on their mechanistic implication in AIC. We also discuss the importance of functional validation of AIC-associated variants in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to advance the implementation of genetic predictive biomarkers. Finally, we review how patient-specific hiPSC-CMs can be used to identify novel patient-relevant functional targets and for the discovery of cardioprotectant drugs to prevent AIC. Implementation of functional validation and use of hiPSC-CMs for drug discovery will identify the next generation of highly effective and personalized cardioprotectants and accelerate the inclusion of approved AIC biomarkers into clinical practice.
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Affiliation(s)
- Romina B Cejas
- Department of Pharmacology and Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA;
| | - Kateryna Petrykey
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Paul W Burridge
- Department of Pharmacology and Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA;
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8
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Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol 2024; 25:28. [PMID: 38254214 PMCID: PMC10801966 DOI: 10.1186/s13059-023-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
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Affiliation(s)
- Benjamin J Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Joshua Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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9
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Seah C, Signer R, Deans M, Bader H, Rusielewicz T, Hicks EM, Young H, Cote A, Townsley K, Xu C, Hunter CJ, McCarthy B, Goldberg J, Dobariya S, Holtzherimer PE, Young KA, Noggle SA, Krystal JH, Paull D, Girgenti MJ, Yehuda R, Brennand KJ, Huckins LM. Common genetic variation impacts stress response in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573459. [PMID: 38234801 PMCID: PMC10793429 DOI: 10.1101/2023.12.27.573459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
To explain why individuals exposed to identical stressors experience divergent clinical outcomes, we determine how molecular encoding of stress modifies genetic risk for brain disorders. Analysis of post-mortem brain (n=304) revealed 8557 stress-interactive expression quantitative trait loci (eQTLs) that dysregulate expression of 915 eGenes in response to stress, and lie in stress-related transcription factor binding sites. Response to stress is robust across experimental paradigms: up to 50% of stress-interactive eGenes validate in glucocorticoid treated hiPSC-derived neurons (n=39 donors). Stress-interactive eGenes show brain region- and cell type-specificity, and, in post-mortem brain, implicate glial and endothelial mechanisms. Stress dysregulates long-term expression of disorder risk genes in a genotype-dependent manner; stress-interactive transcriptomic imputation uncovered 139 novel genes conferring brain disorder risk only in the context of traumatic stress. Molecular stress-encoding explains individualized responses to traumatic stress; incorporating trauma into genomic studies of brain disorders is likely to improve diagnosis, prognosis, and drug discovery.
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10
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Snijders GJLJ, de Paiva Lopes K, Sneeboer MAM, Muller BZ, Gigase FAJ, Vialle RA, Missall R, Kubler R, Raj T, Humphrey J, de Witte LD. The human microglia responsome: a resource to better understand microglia states in health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562067. [PMID: 37873223 PMCID: PMC10592813 DOI: 10.1101/2023.10.12.562067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Microglia, the immune cells of the brain, are increasingly implicated in neurodegenerative disorders through genetic studies. However, how genetic risk factors for these diseases are related to microglial gene expression, microglial function, and ultimately disease, is still largely unknown. Microglia change rapidly in response to alterations in their cellular environment, which is regulated through changes in transcriptional programs, which are as yet poorly understood. Here, we compared the effects of a set of inflammatory and restorative stimuli (lipopolysaccharide, interferon-gamma, resiquimod, tumor necrosis factor-alpha, adenosine triphosphate, dexamethasone, and interleukin-4) on human microglial cells from 67 different donors (N = 398 samples) at the gene and transcript level. We show that microglia from different anatomical brain regions show distinct responses to inflammatory stimuli. We observed a greater overlap between human stimulated microglia and human monocytes than with mouse microglia. We define specific microglial signatures across conditions which are highly relevant for a wide range of biological functions and complex human diseases. Finally, we used our stimulation signatures to interpret associations from Alzheimer's disease (AD) genetic studies and microglia by integrating our inflammatory gene expression profiles with common genetic variants to map cis -expression QTLs (eQTLs). Together, we provide the most comprehensive transcriptomic database of the human microglia responsome. Highlights RNA-sequencing of 398 human microglial samples exposed to six different triggers.Microglia from different anatomical regions show distinct stimulation responses.Responses in human microglia show a greater overlap with human monocytes than murine microglia.Mapping of response Quantitative Trait Loci identifies interactions between genotype and effect of stimulation on gene expression.Our atlas provides a reference map for interpreting microglia signatures in health and disease.
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11
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Arzt M, Gao B, Mozneb M, Pohlman S, Cejas RB, Liu Q, Huang F, Yu C, Zhang Y, Fan X, Jenkins A, Giuliano AE, Burridge PW, Cui X, Sharma A. Protein-encapsulated doxorubicin reduces cardiotoxicity in hiPSC-cardiomyocytes and cardiac spheroids while maintaining anticancer efficacy. Stem Cell Reports 2023; 18:1913-1924. [PMID: 37657447 PMCID: PMC10656302 DOI: 10.1016/j.stemcr.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023] Open
Abstract
The chemotherapeutic doxorubicin (DOX) detrimentally impacts the heart during cancer treatment. This necessitates development of non-cardiotoxic delivery systems that retain DOX anticancer efficacy. We used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), endothelial cells (hiPSC-ECs), cardiac fibroblasts (hiPSC-CFs), multi-lineage cardiac spheroids (hiPSC-CSs), patient-specific hiPSCs, and multiple human cancer cell lines to compare the anticancer efficacy and reduced cardiotoxicity of single protein encapsulated DOX (SPEDOX-6), to standard unformulated (UF) DOX. Cell viability assays and immunostaining in human cancer cells, hiPSC-ECs, and hiPSC-CFs revealed robust uptake of SPEDOX-6 and efficacy in killing these proliferative cell types. In contrast, hiPSC-CMs and hiPSC-CSs exhibited substantially lower cytotoxicity during SPEDOX-6 treatment compared with UF DOX. SPEDOX-6-treated hiPSC-CMs and hiPSC-CSs maintained their functionality, as indicated by sarcomere contractility assessment, calcium imaging, multielectrode arrays, and RNA sequencing. This study demonstrates the potential of SPEDOX-6 to alleviate cardiotoxic side effects associated with UF DOX, while maintaining its anticancer potency.
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Affiliation(s)
- Madelyn Arzt
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bowen Gao
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Maedeh Mozneb
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephany Pohlman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; CIRM Bridges to Stem Cell Research Program, California State University, Channel Islands, CA, USA
| | - Romina B Cejas
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qizhi Liu
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Changjun Yu
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA; Sunstate Biosciences LLC, Monrovia, CA, USA
| | - Yi Zhang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xuemo Fan
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amelia Jenkins
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Armando E Giuliano
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xiaojiang Cui
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Arun Sharma
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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12
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Kang JB, Raveane A, Nathan A, Soranzo N, Raychaudhuri S. Methods and Insights from Single-Cell Expression Quantitative Trait Loci. Annu Rev Genomics Hum Genet 2023; 24:277-303. [PMID: 37196361 PMCID: PMC10784788 DOI: 10.1146/annurev-genom-101422-100437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution. Compared with bulk RNA sequencing, which averages gene expression across cell types and cell states, single-cell assays capture the transcriptional states of individual cells, including fine-grained, transient, and difficult-to-isolate populations at unprecedented scale and resolution. Single-cell eQTL (sc-eQTL) mapping can identify context-dependent eQTLs that vary with cell states, including some that colocalize with disease variants identified in genome-wide association studies. By uncovering the precise contexts in which these eQTLs act, single-cell approaches can unveil previously hidden regulatory effects and pinpoint important cell states underlying molecular mechanisms of disease. Here, we present an overview of recently deployed experimental designs in sc-eQTL studies. In the process, we consider the influence of study design choices such as cohort, cell states, and ex vivo perturbations. We then discuss current methodologies, modeling approaches, and technical challenges as well as future opportunities and applications.
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Affiliation(s)
- Joyce B Kang
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | | | - Aparna Nathan
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | - Nicole Soranzo
- Human Technopole, Milan, Italy; ,
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- British Heart Foundation Centre of Research Excellence and Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Raychaudhuri
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, United Kingdom
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13
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Wu EY, Singh NP, Choi K, Zakeri M, Vincent M, Churchill GA, Ackert-Bicknell CL, Patro R, Love MI. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty. Genome Biol 2023; 24:165. [PMID: 37438847 PMCID: PMC10337143 DOI: 10.1186/s13059-023-03003-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to groups by transcription start site. The aggregation strategies strengthen the signal for transcripts with high uncertainty. The SEESAW suite of methods is shown to have higher power than other allelic imbalance methods when there is isoform-level allelic imbalance. We also introduce a new test for detecting imbalance that varies across a covariate, such as time.
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Affiliation(s)
- Euphy Y Wu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Noor P Singh
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | - Mohsen Zakeri
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | | | | | - Cheryl L Ackert-Bicknell
- Department of Orthopedics, School of Medicine, University of Colorado, Anschutz Campus, Aurora, CO, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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14
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Ceballos JA, Jaramillo-Isaza S, Calderón JC, Miranda PB, Giraldo MA. Doxorubicin Interaction with Lipid Monolayers Leads to Decreased Membrane Stiffness when Experiencing Compression-Expansion Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37320858 DOI: 10.1021/acs.langmuir.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Physical membrane models permit to study and quantify the interactions of many external molecules with monitored and simplified systems. In this work, we have constructed artificial Langmuir single-lipid monolayers with dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylethanolamine (DPPE), dipalmitoylphosphatidylserine (DPPS), or sphingomyelin to resemble the main lipid components of the mammalian cell membranes. We determined the collapse pressure, minimum area per molecule, and maximum compression modulus (Cs-1) from surface pressure measurements in a Langmuir trough. Also, from compression/expansion isotherms, we estimated the viscoelastic properties of the monolayers. With this model, we explored the membrane molecular mechanism of toxicity of the well-known anticancer drug doxorubicin, with particular emphasis in cardiotoxicity. The results showed that doxorubicin intercalates mainly between DPPS and sphingomyelin, and less between DPPE, inducing a change in the Cs-1 of up to 34% for DPPS. The isotherm experiments suggested that doxorubicin had little effect on DPPC, partially solubilized DPPS lipids toward the bulk of the subphase, and caused a slight or large expansion in the DPPE and sphingomyelin monolayers, respectively. Furthermore, the dynamic viscoelasticity of the DPPE and DPPS membranes was greatly reduced (by 43 and 23%, respectively), while the reduction amounted only to 12% for sphingomyelin and DPPC models. In conclusion, doxorubicin intercalates into the DPPS, DPPE, and sphingomyelin, but not into the DPPC, membrane lipids, inducing a structural distortion that leads to decreased membrane stiffness and reduced compressibility modulus. These alterations may constitute a novel, early step in explaining the doxorubicin mechanism of action in mammalian cancer cells or its toxicity in non-cancer cells, with relevance to explain its cardiotoxicity.
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Affiliation(s)
- Jorge A Ceballos
- Biophysics Group, Institute of Physics, University of Antioquia, Medellin 050010, Colombia
- School of Health Sciences, Pontifical Bolivarian University, Medellin 050031, Colombia
- Sao Carlos Physics Institute, University of Sao Paulo, P.O. Box 369, Sao Carlos, SP 13560-970, Brazil
| | | | - Juan C Calderón
- Physiology and Biochemistry Research Group-PHYSIS, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia
| | - Paulo B Miranda
- Sao Carlos Physics Institute, University of Sao Paulo, P.O. Box 369, Sao Carlos, SP 13560-970, Brazil
| | - Marco A Giraldo
- Biophysics Group, Institute of Physics, University of Antioquia, Medellin 050010, Colombia
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15
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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16
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Hicks EM, Seah C, Cote A, Marchese S, Brennand KJ, Nestler EJ, Girgenti MJ, Huckins LM. Integrating genetics and transcriptomics to study major depressive disorder: a conceptual framework, bioinformatic approaches, and recent findings. Transl Psychiatry 2023; 13:129. [PMID: 37076454 PMCID: PMC10115809 DOI: 10.1038/s41398-023-02412-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Major depressive disorder (MDD) is a complex and heterogeneous psychiatric syndrome with genetic and environmental influences. In addition to neuroanatomical and circuit-level disturbances, dysregulation of the brain transcriptome is a key phenotypic signature of MDD. Postmortem brain gene expression data are uniquely valuable resources for identifying this signature and key genomic drivers in human depression; however, the scarcity of brain tissue limits our capacity to observe the dynamic transcriptional landscape of MDD. It is therefore crucial to explore and integrate depression and stress transcriptomic data from numerous, complementary perspectives to construct a richer understanding of the pathophysiology of depression. In this review, we discuss multiple approaches for exploring the brain transcriptome reflecting dynamic stages of MDD: predisposition, onset, and illness. We next highlight bioinformatic approaches for hypothesis-free, genome-wide analyses of genomic and transcriptomic data and their integration. Last, we summarize the findings of recent genetic and transcriptomic studies within this conceptual framework.
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Affiliation(s)
- Emily M Hicks
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Carina Seah
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Alanna Cote
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Shelby Marchese
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA.
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Departments of Psychiatry and of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA.
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17
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Seah C, Huckins LM, Brennand KJ. Stem Cell Models for Context-Specific Modeling in Psychiatric Disorders. Biol Psychiatry 2023; 93:642-650. [PMID: 36658083 DOI: 10.1016/j.biopsych.2022.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies reveal the complex polygenic architecture underlying psychiatric disorder risk, but there is an unmet need to validate causal variants, resolve their target genes(s), and explore their functional impacts on disorder-related mechanisms. Disorder-associated loci regulate transcription of target genes in a cell type- and context-specific manner, which can be measured through expression quantitative trait loci. In this review, we discuss methods and insights from context-specific modeling of genetically and environmentally regulated expression. Human induced pluripotent stem cell-derived cell type and organoid models have uncovered context-specific psychiatric disorder associations by investigating tissue-, cell type-, sex-, age-, and stressor-specific genetic regulation of expression. Techniques such as massively parallel reporter assays and pooled CRISPR (clustered regularly interspaced short palindromic repeats) screens make it possible to functionally fine-map genome-wide association study loci and validate their target genes at scale. Integration of disorder-associated contexts with these patient-specific human induced pluripotent stem cell models makes it possible to uncover gene by environment interactions that mediate disorder risk, which will ultimately improve our ability to diagnose and treat psychiatric disorders.
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Affiliation(s)
- Carina Seah
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
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18
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D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. Nat Commun 2023; 14:1132. [PMID: 36854752 PMCID: PMC9975214 DOI: 10.1038/s41467-023-36638-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. We identify 2,578 eQTLs associated with a specific developmental stage-, tissue- and/or cell type. Colocalization between eQTL and GWAS signals of five cardiac traits identified variants with high posterior probabilities for being causal in 210 GWAS loci. Pulse pressure GWAS loci are enriched for colocalization with fetal- and smooth muscle- eQTLs; pulse rate with adult- and cardiac muscle- eQTLs; and atrial fibrillation with cardiac muscle- eQTLs. Fine mapping identifies 79 credible sets with five or fewer SNPs, of which 15 were associated with spatiotemporal eQTLs. Our study shows that many cardiac GWAS variants impact traits and disease in a developmental stage-, tissue- and/or cell type-specific fashion.
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Affiliation(s)
- Matteo D'Antonio
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
| | - Jennifer P Nguyen
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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19
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Resztak JA, Choe J, Nirmalan S, Wei J, Bruinsma J, Houpt R, Alazizi A, Mair-Meijers HE, Wen X, Slatcher RB, Zilioli S, Pique-Regi R, Luca F. Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma. Nat Commun 2023; 14:230. [PMID: 36646693 PMCID: PMC9842661 DOI: 10.1038/s41467-022-35742-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Puberty is an important developmental period marked by hormonal, metabolic and immune changes. Puberty also marks a shift in sex differences in susceptibility to asthma. Yet, little is known about the gene expression changes in immune cells that occur during pubertal development. Here we assess pubertal development and leukocyte gene expression in a longitudinal cohort of 251 children with asthma. We identify substantial gene expression changes associated with age and pubertal development. Gene expression changes between pre- and post-menarcheal females suggest a shift from predominantly innate to adaptive immunity. We show that genetic effects on gene expression change dynamically during pubertal development. Gene expression changes during puberty are correlated with gene expression changes associated with asthma and may explain sex differences in prevalence. Our results show that molecular data used to study the genetics of early onset diseases should consider pubertal development as an important factor that modifies the transcriptome.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Jane Choe
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julian Bruinsma
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Russell Houpt
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | | | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, MI, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
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20
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Zhong Y, De T, Mishra M, Avitia J, Alarcon C, Perera MA. Leveraging drug perturbation to reveal genetic regulators of hepatic gene expression in African Americans. Am J Hum Genet 2023; 110:58-70. [PMID: 36608685 PMCID: PMC9892765 DOI: 10.1016/j.ajhg.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Expression quantitative locus (eQTL) studies have paved the way in identifying genetic variation impacting gene expression levels. African Americans (AAs) are disproportionately underrepresented in eQTL studies, resulting in a lack of power to identify population-specific regulatory variants especially related to drug response. Specific drugs are known to affect the biosynthesis of drug metabolism enzymes as well as other genes. We used drug perturbation in cultured primary hepatocytes derived from AAs to determine the effect of drug treatment on eQTL mapping and to identify the drug response eQTLs (reQTLs) that show altered effect size following drug treatment. Whole-genome genotyping (Illumina MEGA array) and RNA sequencing were performed on 60 primary hepatocyte cultures after treatment with six drugs (Rifampin, Phenytoin, Carbamazepine, Dexamethasone, Phenobarbital, and Omeprazole) and at baseline (no treatment). eQTLs were mapped by treatment and jointly with Meta-Tissue. We found varying transcriptional changes across different drug treatments and identified Nrf2 as a potential general transcriptional regulator. We jointly mapped eQTLs with gene expression data across all drug treatments and baseline, which increased our power to detect eQTLs by 2.7-fold. We also identified 2,988 reQTLs (eQTLs with altered effect size after drug treatment). reQTLs were more likely to overlap transcription factor binding sites, and we uncovered reQTLs for drug metabolizing genes such as CYP3A5. Our results provide insights into the genetic regulation of gene expression in hepatocytes through drug perturbation and provide insight into SNPs that effect the liver's ability to respond to transcription upregulation.
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Affiliation(s)
- Yizhen Zhong
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tanima De
- Integrative Translational Genetic, Regeneron Genetic Center, Tarrytown, NY 10591, USA
| | - Mrinal Mishra
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Juan Avitia
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Cristina Alarcon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Minoli A Perera
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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21
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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22
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Wu X, Shen F, Jiang G, Xue G, Philips S, Gardner L, Cunningham G, Bales C, Cantor E, Schneider BP. A non-coding GWAS variant impacts anthracycline-induced cardiotoxic phenotypes in human iPSC-derived cardiomyocytes. Nat Commun 2022; 13:7171. [PMID: 36418322 PMCID: PMC9684507 DOI: 10.1038/s41467-022-34917-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Anthracyclines, widely used to treat breast cancer, have the potential for cardiotoxicity. We have previously identified and validated a germline single nucleotide polymorphism, rs28714259, associated with an increased risk of anthracycline-induced heart failure. We now provide insights into the mechanism by which rs28714259 might confer increased risk of cardiac damage. Using hiPSC-derived cardiomyocyte cell lines with either intrinsic polymorphism or CRISPR-Cas9-mediated deletion of rs28714259 locus, we demonstrate that glucocorticoid receptor signaling activated by dexamethasone pretreatment prior to doxorubicin exposure preserves cardiomyocyte viability and contractility in cardiomyocytes containing the major allele. Homozygous loss of the rs28714259 major allele diminishes dexamethasone's protective effect. We further demonstrate that the risk allele of rs28714259 disrupts glucocorticoid receptor and rs28714259 binding affinity. Finally, we highlight the activation of genes and pathways involved in cardiac hypertrophy signaling that are blocked by the risk allele, suggesting a decreased adaptive survival response to doxorubicin-related stress.
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Affiliation(s)
- Xi Wu
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Fei Shen
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Guanglong Jiang
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Gloria Xue
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Santosh Philips
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Laura Gardner
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Geneva Cunningham
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Casey Bales
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Erica Cantor
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Bryan Paul Schneider
- Department of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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23
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Mullen M, Wen Tan WL, Rhee JW, Wu JC. Modeling Susceptibility to Cardiotoxicity in Cancer Therapy Using Human iPSC-Derived Cardiac Cells and Systems Biology. Heart Fail Clin 2022; 18:335-347. [PMID: 35718410 DOI: 10.1016/j.hfc.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of human-induced pluripotent stem cell-derived cardiac cell types has created a new paradigm in assessing drug-induced cardiotoxicity. Advances in genomics and epigenomics have also implicated several genomic loci and biological pathways that may contribute to susceptibility to cancer therapies. In this review, we first provide a brief overview of the cardiotoxicity associated with chemotherapy. We then provide a detailed summary of systems biology approaches being applied to elucidate potential molecular mechanisms involved in cardiotoxicity. Finally, we discuss combining systems biology approaches with iPSC technology to help discover molecular mechanisms associated with cardiotoxicity.
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Affiliation(s)
- McKay Mullen
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - Wilson Lek Wen Tan
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - June-Wha Rhee
- Department of Medicine, City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA 91010, USA.
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University; Department of Radiology, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA.
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24
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Flynn E, Lappalainen T. Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci 2022; 5:119-139. [PMID: 35483347 DOI: 10.1146/annurev-biodatasci-122120-010010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thousands of common genetic variants in the human population have been associated with disease risk and phenotypic variation by genome-wide association studies (GWAS). However, the majority of GWAS variants fall into noncoding regions of the genome, complicating our understanding of their regulatory functions, and few molecular mechanisms of GWAS variant effects have been clearly elucidated. Here, we set out to review genetic variant effects, focusing on expression quantitative trait loci (eQTLs), including their utility in interpreting GWAS variant mechanisms. We discuss the interrelated challenges and opportunities for eQTL analysis, covering determining causal variants, elucidating molecular mechanisms of action, and understanding context variability. Addressing these questions can enable better functional characterization of disease-associated loci and provide insights into fundamental biological questions of the noncoding genetic regulatory code and its control of gene expression. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Elise Flynn
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA.,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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25
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Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans. Genes (Basel) 2022; 13:genes13020235. [PMID: 35205280 PMCID: PMC8871770 DOI: 10.3390/genes13020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The discovery of expression quantitative trait loci (eQTLs) and their target genes (eGenes) has not only compensated for the limitations of genome-wide association studies for complex phenotypes but has also provided a basis for predicting gene expression. Efforts have been made to develop analytical methods in statistical genetics, a key discipline in eQTL analysis. In particular, mixed model– and deep learning–based analytical methods have been extremely beneficial in mapping eQTLs and predicting gene expression. Nevertheless, we still face many challenges associated with eQTL discovery. Here, we discuss two key aspects of these challenges: 1, the complexity of eTraits with various factors such as polygenicity and epistasis and 2, the voluminous work required for various types of eQTL profiles. The properties and prospects of statistical methods, including the mixed model method, Bayesian inference, the deep learning method, and the integration method, are presented as future directions for eQTL discovery. This review will help expedite the design and use of efficient methods for eQTL discovery and eTrait prediction.
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26
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McKennan C, Nicolae D. Estimating and accounting for unobserved covariates in high-dimensional correlated data. J Am Stat Assoc 2022; 117:225-236. [PMID: 35615339 PMCID: PMC9126075 DOI: 10.1080/01621459.2020.1769635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput 'omic' data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high dimensional data with correlated or nonexchangeable residuals. We demonstrate each method's superior performance compared to other state of the art methods by analyzing simulated multi-tissue gene expression data and identifying sex-associated DNA methylation sites in a real, longitudinal twin study.
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Affiliation(s)
| | - Dan Nicolae
- Department of Statistics, University of Chicago
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27
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Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T. Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet 2022; 18:e1009719. [PMID: 35100260 PMCID: PMC8830792 DOI: 10.1371/journal.pgen.1009719] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/10/2022] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tens of thousands of genetic variants associated with gene expression (cis-eQTLs) have been discovered in the human population. These eQTLs are active in various tissues and contexts, but the molecular mechanisms of eQTL variability are poorly understood, hindering our understanding of genetic regulation across biological contexts. Since many eQTLs are believed to act by altering transcription factor (TF) binding affinity, we hypothesized that analyzing eQTL effect size as a function of TF level may allow discovery of mechanisms of eQTL variability. Using GTEx Consortium eQTL data from 49 tissues, we analyzed the interaction between eQTL effect size and TF level across tissues and across individuals within specific tissues and generated a list of 10,098 TF-eQTL interactions across 2,136 genes that are supported by at least two lines of evidence. These TF-eQTLs were enriched for various TF binding measures, supporting with orthogonal evidence that these eQTLs are regulated by the implicated TFs. We also found that our TF-eQTLs tend to overlap genes with gene-by-environment regulatory effects and to colocalize with GWAS loci, implying that our approach can help to elucidate mechanisms of context-specificity and trait associations. Finally, we highlight an interesting example of IKZF1 TF regulation of an APBB1IP gene eQTL that colocalizes with a GWAS signal for blood cell traits. Together, our findings provide candidate TF mechanisms for a large number of eQTLs and offer a generalizable approach for researchers to discover TF regulators of genetic variant effects in additional QTL datasets.
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Affiliation(s)
- Elise D. Flynn
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Athena L. Tsu
- New York Genome Center, New York, New York, United States of America
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Silva Kasela
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Sarah Kim-Hellmuth
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kristin G. Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Harmen J. Bussemaker
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (PM); (TL)
| | - Tuuli Lappalainen
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (PM); (TL)
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28
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Masui A, Hirai T, Gotoh S. Perspectives of future lung toxicology studies using human pluripotent stem cells. Arch Toxicol 2022; 96:389-402. [PMID: 34973109 PMCID: PMC8720162 DOI: 10.1007/s00204-021-03188-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/02/2021] [Indexed: 12/17/2022]
Abstract
The absence of in vitro platforms for human pulmonary toxicology studies is becoming an increasingly serious concern. The respiratory system has a dynamic mechanical structure that extends from the airways to the alveolar region. In addition, the epithelial, endothelial, stromal, and immune cells are highly organized in each region and interact with each other to function synergistically. These cells of varied lineage, particularly epithelial cells, have been difficult to use for long-term culture in vitro, thus limiting the development of useful experimental tools. This limitation has set a large distance between the bench and the bedside for analyzing the pathogenic mechanisms, the efficacy of candidate therapeutic agents, and the toxicity of compounds. Several researchers have proposed solutions to these problems by reporting on methods for generating human lung epithelial cells derived from pluripotent stem cells (PSCs). Moreover, the use of organoid culture, organ-on-a-chip, and material-based techniques have enabled the maintenance of functional PSC-derived lung epithelial cells as well as primary cells. The aforementioned technological advances have facilitated the in vitro recapitulation of genetic lung diseases and the detection of ameliorating or worsening effects of genetic and chemical interventions, thus indicating the future possibility of more sophisticated preclinical compound assessments in vitro. In this review, we will update the recent advances in lung cell culture methods, principally focusing on human PSC-derived lung epithelial organoid culture systems with the hope of their future application in toxicology studies.
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Affiliation(s)
- Atsushi Masui
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Nogi, Tochigi, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shimpei Gotoh
- Department of Drug Discovery for Lung Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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29
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Huang MF, Pang LK, Chen YH, Zhao R, Lee DF. Cardiotoxicity of Antineoplastic Therapies and Applications of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Cells 2021; 10:2823. [PMID: 34831045 PMCID: PMC8616116 DOI: 10.3390/cells10112823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
The therapeutic landscape for the treatment of cancer has evolved significantly in recent decades, aided by the development of effective oncology drugs. However, many cancer drugs are often poorly tolerated by the body and in particular the cardiovascular system, causing adverse and sometimes fatal side effects that negate the chemotherapeutic benefits. The prevalence and severity of chemotherapy-induced cardiotoxicity warrants a deeper investigation of the mechanisms and implicating factors in this phenomenon, and a consolidation of scientific efforts to develop mitigating strategies. Aiding these efforts is the emergence of induced pluripotent stem cells (iPSCs) in recent years, which has allowed for the generation of iPSC-derived cardiomyocytes (iPSC-CMs): a human-based, patient-derived, and genetically variable platform that can be applied to the study of chemotherapy-induced cardiotoxicity and beyond. After surveying chemotherapy-induced cardiotoxicity and the associated chemotherapeutic agents, we discuss the use of iPSC-CMs in cardiotoxicity modeling, drug screening, and other potential applications. Improvements to the iPSC-CM platform, such as the development of more adult-like cardiomyocytes and ongoing advances in biotechnology, will only enhance the utility of iPSC-CMs in both basic science and clinical applications.
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Affiliation(s)
- Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Lon Kai Pang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Hung Chen
- Department and Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (M.-F.H.); (L.K.P.)
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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30
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-meijers HE, Wu P, Slatcher RB, Zhou X, Luca F, Pique-regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.. [PMID: 35313584 PMCID: PMC8936121 DOI: 10.1101/2021.09.30.462672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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31
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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32
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Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses. PLoS Genet 2021; 17:e1009493. [PMID: 34570765 PMCID: PMC8509894 DOI: 10.1371/journal.pgen.1009493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/12/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.
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Affiliation(s)
- Anthony S. Findley
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Yen Lung Lin
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Cynthia A. Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Luis Barreiro
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
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33
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Andrysiak K, Stępniewski J, Dulak J. Human-induced pluripotent stem cell-derived cardiomyocytes, 3D cardiac structures, and heart-on-a-chip as tools for drug research. Pflugers Arch 2021; 473:1061-1085. [PMID: 33629131 PMCID: PMC8245367 DOI: 10.1007/s00424-021-02536-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/13/2022]
Abstract
Development of new drugs is of high interest for the field of cardiac and cardiovascular diseases, which are a dominant cause of death worldwide. Before being allowed to be used and distributed, every new potentially therapeutic compound must be strictly validated during preclinical and clinical trials. The preclinical studies usually involve the in vitro and in vivo evaluation. Due to the increasing reporting of discrepancy in drug effects in animal and humans and the requirement to reduce the number of animals used in research, improvement of in vitro models based on human cells is indispensable. Primary cardiac cells are difficult to access and maintain in cell culture for extensive experiments; therefore, the human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) became an excellent alternative. This technology enables a production of high number of patient- and disease-specific cardiomyocytes and other cardiac cell types for a large-scale research. The drug effects can be extensively evaluated in the context of electrophysiological responses with a use of well-established tools, such as multielectrode array (MEA), patch clamp, or calcium ion oscillation measurements. Cardiotoxicity, which is a common reason for withdrawing drugs from marketing or rejection at final stages of clinical trials, can be easily verified with a use of hiPSC-CM model providing a prediction of human-specific responses and higher safety of clinical trials involving patient cohort. Abovementioned studies can be performed using two-dimensional cell culture providing a high-throughput and relatively lower costs. On the other hand, more complex structures, such as engineered heart tissue, organoids, or spheroids, frequently applied as co-culture systems, represent more physiological conditions and higher maturation rate of hiPSC-derived cells. Furthermore, heart-on-a-chip technology has recently become an increasingly popular tool, as it implements controllable culture conditions, application of various stimulations and continuous parameters read-out. This paper is an overview of possible use of cardiomyocytes and other cardiac cell types derived from hiPSC as in vitro models of heart in drug research area prepared on the basis of latest scientific reports and providing thorough discussion regarding their advantages and limitations.
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Affiliation(s)
- Kalina Andrysiak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Jacek Stępniewski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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34
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Sobreira DR, Joslin AC, Zhang Q, Williamson I, Hansen GT, Farris KM, Sakabe NJ, Sinnott-Armstrong N, Bozek G, Jensen-Cody SO, Flippo KH, Ober C, Bickmore WA, Potthoff M, Chen M, Claussnitzer M, Aneas I, Nóbrega MA. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. Science 2021; 372:1085-1091. [PMID: 34083488 PMCID: PMC8386003 DOI: 10.1126/science.abf1008] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/28/2021] [Indexed: 12/11/2022]
Abstract
Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the FTO gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting IRX3 and IRX5 from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
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Affiliation(s)
- Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Amelia C Joslin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Qi Zhang
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University, Stanford 94305 CA, USA
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Grazyna Bozek
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Sharon O Jensen-Cody
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kyle H Flippo
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Matthew Potthoff
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Melina Claussnitzer
- Metabolism Program and Cardiovascular Disease Initiative, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02131, USA
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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35
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Scott EN, Wright GEB, Drögemöller BI, Hasbullah JS, Gunaretnam EP, Miao F, Bhavsar AP, Shen F, Schneider BP, Carleton BC, Ross CJD. Transcriptome-wide association study uncovers the role of essential genes in anthracycline-induced cardiotoxicity. NPJ Genom Med 2021; 6:35. [PMID: 34021165 PMCID: PMC8140137 DOI: 10.1038/s41525-021-00199-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
Anthracyclines are highly effective chemotherapeutic agents; however, their clinical utility is limited by severe anthracycline-induced cardiotoxicity (ACT). Genome-wide association studies (GWAS) have uncovered several genetic variants associated with ACT, but the impact of these findings requires further elucidation. We conducted a transcriptome-wide association study (TWAS) using our previous GWAS summary statistics (n = 280 patients) to identify gene expression-related associations with ACT. We identified a genetic association between decreased expression of GDF5 and ACT (Z-score = -4.30, P = 1.70 × 10-5), which was replicated in an independent cohort (n = 845 patients, P = 3.54 × 10-3). Additionally, cell viability of GDF5-silenced human cardiac myocytes was significantly decreased in response to anthracycline treatment. Subsequent gene set enrichment and pathway analyses of the TWAS data revealed that genes essential for survival, cardioprotection and response to anthracyclines, as well as genes involved in ribosomal, spliceosomal and cardiomyopathy pathways are important for the development of ACT.
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Affiliation(s)
- Erika N Scott
- Faculty of Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Galen E B Wright
- Faculty of Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Britt I Drögemöller
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jafar S Hasbullah
- Faculty of Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Erandika P Gunaretnam
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fudan Miao
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Amit P Bhavsar
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.,Faculty of Medicine & Dentistry, Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, Canada
| | - Fei Shen
- Division of Hematology/Oncology, Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Bryan P Schneider
- Division of Hematology/Oncology, Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Bruce C Carleton
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Pharmaceutical Outcomes Programme, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Colin J D Ross
- Faculty of Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. .,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada. .,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
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36
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Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S, Wen X, Lanfear DE, Pique-Regi R, Gilad Y, Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. eLife 2021; 10:e67077. [PMID: 33988505 PMCID: PMC8248987 DOI: 10.7554/elife.67077] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type, and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average, half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease.
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Affiliation(s)
- Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Alan Monziani
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Katherine Rhodes
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Michelle C Ward
- Department of Medicine, University of ChicagoChicagoUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | | | - Sriram Sankararaman
- Department of Computer Science, UCLALos AngelesUnited States
- Department of Human Genetics, UCLALos AngelesUnited States
- Department of Computational Medicine, UCLALos AngelesUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research, Henry Ford HospitalDetroitUnited States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Yoav Gilad
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Department of Medicine, University of ChicagoChicagoUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
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37
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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38
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Keung W, Cheung YF. Human Pluripotent Stem Cells for Modeling of Anticancer Therapy-Induced Cardiotoxicity and Cardioprotective Drug Discovery. Front Pharmacol 2021; 12:650039. [PMID: 33953683 PMCID: PMC8090862 DOI: 10.3389/fphar.2021.650039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022] Open
Abstract
Anticancer chemotherapies have been shown to produce severe side effects, with cardiotoxicity from anthracycline being the most notable. Identifying risk factors for anticancer therapy-induced cardiotoxicity in cancer patients as well as understanding its underlying mechanism is essential to improving clinical outcomes of chemotherapy treatment regimens. Moreover, cardioprotective agents against anticancer therapy-induced cardiotoxicity are scarce. Human induced pluripotent stem cell technology offers an attractive platform for validation of potential single nucleotide polymorphism with increased risk for cardiotoxicity. Successful validation of risk factors and mechanism of cardiotoxicity would aid the development of such platform for novel drug discovery and facilitate the practice of personalized medicine.
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Affiliation(s)
- Wendy Keung
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yiu-Fai Cheung
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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39
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Lam CK, Wu JC. Clinical Trial in a Dish: Using Patient-Derived Induced Pluripotent Stem Cells to Identify Risks of Drug-Induced Cardiotoxicity. Arterioscler Thromb Vasc Biol 2021; 41:1019-1031. [PMID: 33472401 PMCID: PMC11006431 DOI: 10.1161/atvbaha.120.314695] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Drug-induced cardiotoxicity is a significant clinical issue, with many drugs in the market being labeled with warnings on cardiovascular adverse effects. Treatments are often prematurely halted when cardiotoxicity is observed, which limits their therapeutic potential. Moreover, cardiotoxicity is a major reason for abandonment during drug development, reducing available treatment options for diseases and creating a significant financial burden and disincentive for drug developers. Thus, it is important to minimize the cardiotoxic effects of medications that are in use or in development. To this end, identifying patients at a higher risk of developing cardiovascular adverse effects for the drug of interest may be an effective strategy. The discovery of human induced pluripotent stem cells has enabled researchers to generate relevant cell types that retain a patient's own genome and examine patient-specific disease mechanisms, paving the way for precision medicine. Combined with the rapid development of pharmacogenomic analysis, the ability of induced pluripotent stem cell-derivatives to recapitulate patient-specific drug responses provides a powerful platform to identify subsets of patients who are particularly vulnerable to drug-induced cardiotoxicity. In this review, we will discuss the current use of patient-specific induced pluripotent stem cells in identifying populations who are at risk to drug-induced cardiotoxicity and their potential applications in future precision medicine practice. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Chi Keung Lam
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA
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40
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Thomas D, Shenoy S, Sayed N. Building Multi-Dimensional Induced Pluripotent Stem Cells-Based Model Platforms to Assess Cardiotoxicity in Cancer Therapies. Front Pharmacol 2021; 12:607364. [PMID: 33679396 PMCID: PMC7930625 DOI: 10.3389/fphar.2021.607364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) complications have contributed significantly toward poor survival of cancer patients worldwide. These complications that result in myocardial and vascular damage lead to long-term multisystemic disorders. In some patient cohorts, the progression from acute to symptomatic CVD state may be accelerated due to exacerbation of underlying comorbidities such as obesity, diabetes and hypertension. In such situations, cardio-oncologists are often left with a clinical predicament in finding the optimal therapeutic balance to minimize cardiovascular risks and maximize the benefits in treating cancer. Hence, prognostically there is an urgent need for cost-effective, rapid, sensitive and patient-specific screening platform to allow risk-adapted decision making to prevent cancer therapy related cardiotoxicity. In recent years, momentous progress has been made toward the successful derivation of human cardiovascular cells from induced pluripotent stem cells (iPSCs). This technology has not only provided deeper mechanistic insights into basic cardiovascular biology but has also seamlessly integrated within the drug screening and discovery programs for early efficacy and safety evaluation. In this review, we discuss how iPSC-derived cardiovascular cells have been utilized for testing oncotherapeutics to pre-determine patient predisposition to cardiovascular toxicity. Lastly, we highlight the convergence of tissue engineering technologies and precision medicine that can enable patient-specific cardiotoxicity prognosis and treatment on a multi-organ level.
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Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States
| | - Sushma Shenoy
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States.,Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
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41
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Ward MC, Banovich NE, Sarkar A, Stephens M, Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. eLife 2021; 10:57345. [PMID: 33554857 PMCID: PMC7906610 DOI: 10.7554/elife.57345] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
One life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established an in vitro model of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia, and short- or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with a cis expression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.
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Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, United States
| | - Nicholas E Banovich
- Department of Human Genetics, University of Chicago, Chicago, United States.,Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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42
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Umans BD, Battle A, Gilad Y. Where Are the Disease-Associated eQTLs? Trends Genet 2021; 37:109-124. [PMID: 32912663 PMCID: PMC8162831 DOI: 10.1016/j.tig.2020.08.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem, mostly from adults. In this review we evaluate recent findings and suggest an alternative strategy, drawing on the dynamic and highly context-specific nature of gene regulation. We discuss new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states.
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Affiliation(s)
- Benjamin D Umans
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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43
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Karabekmez ME, Taymaz-Nikerel H, Eraslan S, Kirdar B. Time-dependent re-organization of biological processes by the analysis of the dynamic transcriptional response of yeast cells to doxorubicin. Mol Omics 2021; 17:572-582. [PMID: 34095940 DOI: 10.1039/d1mo00046b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Doxorubicin is an efficient chemotherapeutic reagent in the treatment of a variety of cancers. However, its underlying molecular mechanism is not fully understood and several severe side effects limit its application. In this study, the dynamic transcriptomic response of Saccharomyces cerevisiae cells to a doxorubicin pulse in a chemostat system was investigated to reveal the underlying molecular mechanism of this drug. The clustering of differentially and significantly expressed genes (DEGs) indicated that the response of yeast cells to doxorubicin is time dependent and may be classified as short-term, mid-term and long-term responses. The cells have started to reorganize their response after the first minute following the injection of the pulse. A modified version of Weighted Gene Co-expression Network Analysis (WGCNA) was used to cluster the positively correlated co-expression profiles, and functional enrichment analysis of these clusters was carried out. DNA replication and DNA repair processes were significantly affected and induced 60 minutes after exposure to doxorubicin. The response to oxidative stress was not identified as a significant term. A transcriptional re-organization of the metabolic pathways seems to be an early event and persists afterwards. The present study reveals for the first time that the RNA surveillance pathway, which is a post-transcriptional regulatory pathway, may be implicated in the short-term reaction of yeast cells to doxorubicin. Integration with regulome revealed the dynamic re-organization of the transcriptomic landscape. Fhl1p, Mbp1p, and Mcm1p were identified as primary regulatory factors responsible for tuning the differentially expressed genes.
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Affiliation(s)
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Eyup, Istanbul, Turkey
| | - Serpil Eraslan
- Koç University Hospital, Diagnosis Centre for Genetic Disorders, Topkapı, Istanbul, Turkey
| | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
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44
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Bhatia S. Genetics of Anthracycline Cardiomyopathy in Cancer Survivors: JACC: CardioOncology State-of-the-Art Review. JACC: CARDIOONCOLOGY 2020; 2:539-552. [PMID: 33364618 PMCID: PMC7757557 DOI: 10.1016/j.jaccao.2020.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Anthracyclines are an integral part of chemotherapy regimens used to treat a variety of childhood-onset and adult-onset cancers. However, the development of cardiac dysfunction and heart failure often compromises the clinical utility of anthracyclines. The risk of cardiac dysfunction increases with anthracycline dose. This anthracycline-cardiac dysfunction association is modified by several demographic and clinical factors, such as age at anthracycline exposure (<4 years and ≥65 years); female sex; chest radiation; presence of cardiovascular risk factors (diabetes, hypertension); and concurrent use of cyclophosphamide, paclitaxel, and trastuzumab. However, the clinical variables alone yield modest predictive power in detecting cardiac dysfunction. Recently, attention has focused on the molecular basis of anthracycline-related cardiac dysfunction, providing an initial understanding of the mechanism of anthracycline-related cardiomyopathy. This review describes the current state of knowledge with respect to the pathogenesis of anthracycline-related cardiomyopathy and identifies the critical next steps to mitigate this problem. Anthracycline chemotherapy results in an increased risk of cardiac dysfunction. Most recent studies have suggested that there is a genetic basis for anthracycline-related cardiac dysfunction. Integration of genetics with the clinical characteristics may be used to enhance the ability to predict the risk for anthracycline-related cardiomyopathy.
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Affiliation(s)
- Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, USA
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45
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Pang L, Liu Z, Wei F, Cai C, Yang X. Improving cardiotoxicity prediction in cancer treatment: integration of conventional circulating biomarkers and novel exploratory tools. Arch Toxicol 2020; 95:791-805. [PMID: 33219404 DOI: 10.1007/s00204-020-02952-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/05/2020] [Indexed: 12/31/2022]
Abstract
Early detection strategies and improvements in cancer treatment have dramatically reduced the cancer mortality rate in the United States (US). However, cardiovascular (CV) side effects of cancer therapy are frequent among the 17 million cancer survivors in the US today, and cardiovascular disease (CVD) has become the second leading cause of morbidity and mortality among cancer survivors. Circulating biomarkers are ideal for detecting and monitoring CV side effects of cancer therapy. Here, we summarize the current state of clinical studies on conventional serum and plasma CVD biomarkers to detect and prevent cardiac injury during cancer treatment. We also review how novel exploratory tools such as genetic testing, human stem cell-derived cardiomyocytes, Omics technologies, and artificial intelligence can elucidate underlying molecular and genetic mechanisms of CV injury and to improve predicting cancer therapy-related cardiotoxicity (CTRC). Current regulatory requirements for biomarker qualifications are also addressed. We present generally applicable lessons learned from published studies, particularly on how to improve reproducibility. The combination of conventional circulating biomarkers and novel exploratory tools will pave the way for precision medicine and improve the clinical practice of prediction, detection, and management of CTRC.
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Affiliation(s)
- Li Pang
- Division of Systems Biology, National Center for Toxicological Research, US. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
| | - Zhichao Liu
- Division of Bioinformation and Biostatistics, National Center for Toxicological Research, US. Food and Drug Administration, Jefferson, AR, USA
| | - Feng Wei
- Department of Structural Heart Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Chengzhong Cai
- Division of Systems Biology, National Center for Toxicological Research, US. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Xi Yang
- Division of Pharmacology & Toxicology, Office of Cardiology, Hematology, Endocrinology, & Nephrology, Office of New Drug, Center for Drug Evaluation and Research, US. Food and Drug Administration, Silver Spring, MD, USA
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46
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Abstract
Oncocardiology is an emerging field in cardiovascular healthcare. Besides establishing surveillance and follow-up strategies for cancer patients, it will be essential to set up specialized oncocardiology services. However, there is a lack of clinical studies to give evidence-based recommendations regarding cardiological diagnostic and therapeutic approaches for cancer patients. An oncocardiology service is a patient-centered structure that aims to integrate research and interdisciplinary patient care to bridge this gap. We discuss the current challenges in developing an oncocardiology service and review the literature on this topic. We further provide an overview of the essential diagnostic tools and upcoming ethical issues to be considered in the management of oncology patients.
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47
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Fair BJ, Blake LE, Sarkar A, Pavlovic BJ, Cuevas C, Gilad Y. Gene expression variability in human and chimpanzee populations share common determinants. eLife 2020; 9:59929. [PMID: 33084571 PMCID: PMC7644215 DOI: 10.7554/elife.59929] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.
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Affiliation(s)
| | - Lauren E Blake
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, United States
| | - Claudia Cuevas
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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48
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Hockings JK, Castrillon JA, Cheng F. Pharmacogenomics meets precision cardio-oncology: is there synergistic potential? Hum Mol Genet 2020; 29:R177-R185. [PMID: 32601683 PMCID: PMC7574955 DOI: 10.1093/hmg/ddaa134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 11/12/2022] Open
Abstract
An individual's inherited genetic makeup and acquired genomic variants may account for a significant portion of observable variability in therapy efficacy and toxicity. Pharmacogenomics (PGx) is the concept that treatments can be modified to account for these differences to increase chances of therapeutic efficacy while minimizing risk of adverse effects. This is particularly applicable to oncology in which treatment may be multimodal. Each tumor type has a unique genomic signature that lends to inclusion of targeted therapy but may be associated with cumulative toxicity, such as cardiotoxicity, and can impact quality of life. A greater understanding of therapeutic agents impacted by PGx and subsequent implementation has the potential to improve outcomes and reduce risk of drug-induced adverse effects.
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Affiliation(s)
- Jennifer K Hockings
- Department of Pharmacy, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jessica A Castrillon
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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49
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Fonoudi H, Burridge PW. Cellular model systems to study cardiovascular injury from chemotherapy. J Thromb Thrombolysis 2020; 51:890-896. [PMID: 33051807 PMCID: PMC10150647 DOI: 10.1007/s11239-020-02299-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
In spite of all the efforts for generating efficient pharmacological treatment options for cancer patients, the unwanted side effect of these substances on the cardiovascular system is becoming a major issue for cancer survivors. The fast pacing oncology field necessitate the quest for more accurate and reliable preclinical screenings. hiPSCs derived cardiomyocytes, endothelial and vascular smooth muscle cells provide unlimited source of physiologically relevant cells that could be used in the screening platforms. Cells derived from hiPSCs can measure drug induced alterations to different aspect of the heart including electrophysiology, contractility and structure. In this review, we will give an overview of the different in vivo and in vitro preclinical drug safety screenings. In following sections, we will focus on hiPSCs derived cardiomyocytes, endothelial and vascular smooth muscle cells and present the current knowledge of the application of these cells in unicellular cardiotoxicity assays. In the final part, we will focus on cardiac organoids as multi cell type platform and their role in cardiotoxicity screening of the chemotherapeutic drugs.
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Affiliation(s)
- Hananeh Fonoudi
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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50
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Pang L. Toxicity testing in the era of induced pluripotent stem cells: A perspective regarding the use of patient-specific induced pluripotent stem cell–derived cardiomyocytes for cardiac safety evaluation. CURRENT OPINION IN TOXICOLOGY 2020. [DOI: 10.1016/j.cotox.2020.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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