1
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Demissei BG, Lv W, Wilcox NS, Sheline K, Smith AM, Sturgeon KM, McDermott-Roe C, Musunuru K, Lefebvre B, Domchek SM, Shah P, Ky B. BRCA1/2 Mutations and Cardiovascular Function in Breast Cancer Survivors. Front Cardiovasc Med 2022; 9:833171. [PMID: 35242827 PMCID: PMC8885808 DOI: 10.3389/fcvm.2022.833171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Objective Animal models suggest that BRCA1/2 mutations increase doxorubicin-induced cardiotoxicity risk but data in humans are limited. We aimed to determine whether germline BRCA1/2 mutations are associated with cardiac dysfunction in breast cancer survivors. Methods In a single-center cross-sectional study, stage I-III breast cancer survivors were enrolled according to three groups: (1) BRCA1/2 mutation carriers treated with doxorubicin; (2) BRCA1/2 mutation non-carriers treated with doxorubicin; and (3) BRCA1/2 mutation carriers treated with non-doxorubicin cancer therapy. In age-adjusted analysis, core-lab quantitated measures of echocardiography-derived cardiac function and cardiopulmonary exercise testing (CPET) were compared across the groups. A complementary in vitro study was performed to assess the impact of BRCA1 loss of function on human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) survival following doxorubicin exposure. Results Sixty-seven women with mean (standard deviation) age of 50 (11) years were included. Age-adjusted left ventricular ejection fraction (LVEF) was lower in participants receiving doxorubicin regardless of BRCA1/2 mutation status (p = 0.03). In doxorubicin-treated BRCA1/2 mutation carriers and non-carriers, LVEF was lower by 5.4% (95% CI; −9.3, −1.5) and 4.8% (95% CI; −9.1, −0.5), respectively compared to carriers without doxorubicin exposure. No significant differences in VO2max were observed across the three groups (poverall = 0.07). Doxorubicin caused a dose-dependent reduction in viability of iPSC-CMs in vitro without differences between BRCA1 mutant and wild type controls (p > 0.05). Conclusions BRCA1/2 mutation status was not associated with differences in measures of cardiovascular function or fitness. Our findings do not support a role for increased cardiotoxicity risk with BRCA1/2 mutations in women with breast cancer.
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Affiliation(s)
- Biniyam G Demissei
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - WenJian Lv
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Nicholas S Wilcox
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Karyn Sheline
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Amanda M Smith
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Kathleen M Sturgeon
- Department of Public Health Sciences, Pennsylvania State College of Medicine, Hershey, PA, United States
| | - Chris McDermott-Roe
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Kiran Musunuru
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Bénédicte Lefebvre
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Susan M Domchek
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Payal Shah
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Bonnie Ky
- Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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2
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McDermott-Roe C, Lv W, Maximova T, Wada S, Bukowy J, Marquez M, Lai S, Shehu A, Benjamin I, Geurts A, Musunuru K. Investigation of a dilated cardiomyopathy-associated variant in BAG3 using genome-edited iPSC-derived cardiomyocytes. JCI Insight 2019; 4:128799. [PMID: 31723063 DOI: 10.1172/jci.insight.128799] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in B cell lymphoma 2-associated athanogene 3 (BAG3) are recurrently associated with dilated cardiomyopathy (DCM) and muscular dystrophy. Using isogenic genome-edited human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we examined how a DCM-causing BAG3 mutation (R477H), as well as complete loss of BAG3 (KO), impacts myofibrillar organization and chaperone networks. Although unchanged at baseline, fiber length and alignment declined markedly in R477H and KO iPSC-CMs following proteasome inhibition. RNA sequencing revealed extensive baseline changes in chaperone- and stress response protein-encoding genes, and protein levels of key BAG3 binding partners were perturbed. Molecular dynamics simulations of the BAG3-HSC70 complex predicted a partial disengagement by the R477H mutation. In line with this, BAG3-R477H bound less HSC70 than BAG3-WT in coimmunoprecipitation assays. Finally, myofibrillar disarray triggered by proteasome inhibition in R477H cells was mitigated by overexpression of the stress response protein heat shock factor 1 (HSF1). These studies reveal the importance of BAG3 in coordinating protein quality control subsystem usage within the cardiomyocyte and suggest that augmenting HSF1 activity might be beneficial as a means to mitigate proteostatic stress in the context of BAG3-associated DCM.
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Affiliation(s)
- Chris McDermott-Roe
- Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wenjian Lv
- Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tania Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, USA
| | - Shogo Wada
- Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John Bukowy
- Cardiovascular Center & Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Maribel Marquez
- Cardiovascular Center & Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Shuping Lai
- Cardiovascular Center & Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, USA
| | - Ivor Benjamin
- Cardiovascular Center & Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Aron Geurts
- Cardiovascular Center & Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kiran Musunuru
- Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Hoshino A, Wang WJ, Wada S, McDermott-Roe C, Evans CS, Gosis B, Morley MP, Rathi KS, Li J, Li K, Yang S, McManus MJ, Bowman C, Potluri P, Levin M, Damrauer S, Wallace DC, Holzbaur ELF, Arany Z. The ADP/ATP translocase drives mitophagy independent of nucleotide exchange. Nature 2019; 575:375-379. [PMID: 31618756 PMCID: PMC6858570 DOI: 10.1038/s41586-019-1667-4] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/09/2019] [Indexed: 12/29/2022]
Abstract
Mitochondrial homeostasis depends on mitophagy, the programmed degradation of mitochondria. Only a few proteins are known to participate in mitophagy. Here we develop a multidimensional CRISPR-Cas9 genetic screen, using multiple mitophagy reporter systems and pro-mitophagy triggers, and identify numerous components of parkin-dependent mitophagy1. Unexpectedly, we find that the adenine nucleotide translocator (ANT) complex is required for mitophagy in several cell types. Whereas pharmacological inhibition of ANT-mediated ADP/ATP exchange promotes mitophagy, genetic ablation of ANT paradoxically suppresses mitophagy. Notably, ANT promotes mitophagy independently of its nucleotide translocase catalytic activity. Instead, the ANT complex is required for inhibition of the presequence translocase TIM23, which leads to stabilization of PINK1, in response to bioenergetic collapse. ANT modulates TIM23 indirectly via interaction with TIM44, which regulates peptide import through TIM232. Mice that lack ANT1 show blunted mitophagy and consequent profound accumulation of aberrant mitochondria. Disease-causing human mutations in ANT1 abrogate binding to TIM44 and TIM23 and inhibit mitophagy. Together, our findings show that ANT is an essential and fundamental mediator of mitophagy in health and disease.
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Affiliation(s)
- Atsushi Hoshino
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Wei-Jia Wang
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shogo Wada
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chris McDermott-Roe
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chantell S Evans
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bridget Gosis
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Morley
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Komal S Rathi
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jian Li
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina Li
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Yang
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meagan J McManus
- Department of Anesthesiology & Critical Care Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Caitlyn Bowman
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Levin
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott Damrauer
- Department of Surgery, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, and the Division of Human Genetics and Metabolism, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Arany
- Department of Medicine, Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Lv W, Qiao L, Petrenko N, Li W, Owens AT, McDermott-Roe C, Musunuru K. Functional Annotation of TNNT2 Variants of Uncertain Significance With Genome-Edited Cardiomyocytes. Circulation 2019; 138:2852-2854. [PMID: 30565988 DOI: 10.1161/circulationaha.118.035028] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Wenjian Lv
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Lyon Qiao
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Nataliya Petrenko
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Wenjun Li
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Anjali T Owens
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Chris McDermott-Roe
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
| | - Kiran Musunuru
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia
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5
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Haggerty CM, Damrauer SM, Levin MG, Birtwell D, Carey DJ, Golden AM, Hartzel DN, Hu Y, Judy R, Kelly MA, Kember RL, Lester Kirchner H, Leader JB, Liang L, McDermott-Roe C, Babu A, Morley M, Nealy Z, Person TN, Pulenthiran A, Small A, Smelser DT, Stahl RC, Sturm AC, Williams H, Baras A, Margulies KB, Cappola TP, Dewey FE, Verma A, Zhang X, Correa A, Hall ME, Wilson JG, Ritchie MD, Rader DJ, Murray MF, Fornwalt BK, Arany Z. Genomics-First Evaluation of Heart Disease Associated With Titin-Truncating Variants. Circulation 2019; 140:42-54. [PMID: 31216868 DOI: 10.1161/circulationaha.119.039573] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Truncating variants in the Titin gene (TTNtvs) are common in individuals with idiopathic dilated cardiomyopathy (DCM). However, a comprehensive genomics-first evaluation of the impact of TTNtvs in different clinical contexts, and the evaluation of modifiers such as genetic ancestry, has not been performed. METHODS We reviewed whole exome sequence data for >71 000 individuals (61 040 from the Geisinger MyCode Community Health Initiative (2007 to present) and 10 273 from the PennMedicine BioBank (2013 to present) to identify anyone with TTNtvs. We further selected individuals with TTNtvs in exons highly expressed in the heart (proportion spliced in [PSI] >0.9). Using linked electronic health records, we evaluated associations of TTNtvs with diagnoses and quantitative echocardiographic measures, including subanalyses for individuals with and without DCM diagnoses. We also reviewed data from the Jackson Heart Study to validate specific analyses for individuals of African ancestry. RESULTS Identified with a TTNtv in a highly expressed exon (hiPSI) were 1.2% individuals in PennMedicine BioBank and 0.6% at Geisinger. The presence of a hiPSI TTNtv was associated with increased odds of DCM in individuals of European ancestry (odds ratio [95% CI]: 18.7 [9.1-39.4] {PennMedicine BioBank} and 10.8 [7.0-16.0] {Geisinger}). hiPSI TTNtvs were not associated with DCM in individuals of African ancestry, despite a high DCM prevalence (odds ratio, 1.8 [0.2-13.7]; P=0.57). Among 244 individuals of European ancestry with DCM in PennMedicine BioBank, hiPSI TTNtv carriers had lower left ventricular ejection fraction (β=-12%, P=3×10-7), and increased left ventricular diameter (β=0.65 cm, P=9×10-3). In the Geisinger cohort, hiPSI TTNtv carriers without a cardiomyopathy diagnosis had more atrial fibrillation (odds ratio, 2.4 [1.6-3.6]) and heart failure (odds ratio, 3.8 [2.4-6.0]), and lower left ventricular ejection fraction (β=-3.4%, P=1×10-7). CONCLUSIONS Individuals of European ancestry with hiPSI TTNtv have an abnormal cardiac phenotype characterized by lower left ventricular ejection fraction, irrespective of the clinical manifestation of cardiomyopathy. Associations with arrhythmias, including atrial fibrillation, were observed even when controlling for cardiomyopathy diagnosis. In contrast, no association between hiPSI TTNtvs and DCM was discerned among individuals of African ancestry. Given these findings, clinical identification of hiPSI TTNtv carriers may alter clinical management strategies.
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Affiliation(s)
- Christopher M Haggerty
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Scott M Damrauer
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.).,Corporal Michael Crescenz VA Medical Center, Philadelphia, PA (S.M.D.)
| | - Michael G Levin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - David Birtwell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - David J Carey
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Alicia M Golden
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Dustin N Hartzel
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Yirui Hu
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Renae Judy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Melissa A Kelly
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Rachel L Kember
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - H Lester Kirchner
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Joseph B Leader
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Lusha Liang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Chris McDermott-Roe
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Apoorva Babu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Michael Morley
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Zachariah Nealy
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Thomas N Person
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Arichanah Pulenthiran
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Aeron Small
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Diane T Smelser
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Richard C Stahl
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Amy C Sturm
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Heather Williams
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY (A. Baras, F.E.D.)
| | - Kenneth B Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Thomas P Cappola
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | | | - Anurag Verma
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Xinyuang Zhang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Adolfo Correa
- Department of Medicine (A.C., M.E.H.), University of Mississippi Medical Center, Jackson
| | - Michael E Hall
- Department of Medicine (A.C., M.E.H.), University of Mississippi Medical Center, Jackson.,Department of Physiology and Biophysics (M.E.H., J.G.W.), University of Mississippi Medical Center, Jackson
| | - James G Wilson
- Department of Physiology and Biophysics (M.E.H., J.G.W.), University of Mississippi Medical Center, Jackson
| | - Marylyn D Ritchie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Daniel J Rader
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
| | - Michael F Murray
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Brandon K Fornwalt
- Geisinger, Danville, PA (C.M.H., D.J.C., A.M.G., D.N.H., Y.H., M.A.K., H.L.K., J.B.L., Z.N., T.N.P., A.P., D.T.S., R.C.S., A.C.S., M.F.M., B.K.F.)
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (S.M.D., M.G.L., D.B., R.J., R.L.K., L.L., C.M.-R., A. Babu, M.M., A.S., H.W., K.B.M., T.P.C., A.V., X.Z., M.D.R., D.J.R., Z.A.)
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6
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Lv W, Qiao L, Petrenko N, Li W, Owens AT, McDermott-Roe C, Musunuru K. Abstract 498: Functional Annotation of
TNNT2
Variants of Uncertain Significance With Induced Pluripotent Stem Cell-derived Cardiomyocytes. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The introduction of clinical sequencing is dramatically increasing the discovery of variants of uncertain significance (VUSs) in genes linked to inherited cardiomyopathies. We have established a platform for rapid and efficient insertion of
TNNT2
gene variants into an induced pluripotent stem cell (iPSC) line to generate an allelic series of isogenic clones for differentiation into cardiomyocytes (iPSC-CMs) for functional annotation of the variants. We first used CRISPR-Cas9 to introduce known pathogenic variants into iPSCs from a healthy person or to correct pathogenic variants in iPSCs from patients with severe cardiomyopathy. Whereas normal/corrected iPSC-CMs responded to isoproterenol treatment with a 50%-70% increase in spontaneous beating rate as assessed by patch-clamp studies, iPSC-CMs with pathogenic variants had minimal responses (close to 0%). Due to the inefficiency of CRISPR-Cas9 in introducing/correcting variants in iPSCs, we next used dual integrase cassette exchange (DICE) to allow for the introduction of a large number of variants in parallel into a pool of cells. In a single pilot use of the DICE platform, we isolated heterozygous clones with 14 unique variants, >10% of all
TNNT2
coding variants cataloged in ClinVar. We found that iPSC-CMs with any of 7 VUSs or likely pathogenic variants were impaired in their response to isoproterenol, in contrast to control DICE-treated iPSC-CMs. Finally, we sought to apply the DICE platform to a patient case in real time. A 65-year-old woman with severe hypertrophic cardiomyopathy underwent gene panel testing that identified a single VUS,
TNNT2
E251D. Between the first and second clinic visits (~10 weeks), we were able to use DICE to rapidly and efficiently generate iPSC-CMs with the E251D variant and determine they had normal responses to isoproterenol, suggesting that the variant is not pathogenic. Guided by this finding, we recommended that the patient’s children and grandchildren not undergo cascade genetic screening for the E251D variant. In conclusion, this work establishes the feasibility of rapid functional annotation of cardiomyopathy gene variants, which after further validation could be incorporated into clinical practice as a line of evidence to support variant classification.
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Affiliation(s)
| | | | | | - Wenjun Li
- Univ of Pennsylvania, Philadelphia, PA
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7
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Marquez M, McDermott-Roe C, Grzybowski M, Helbling D, Dimmock DP, Verbsky JW, Geurts AM. Abstract 378: Evaluation of Patient Specific
MTERF4
Variants in Gene Edited Human iPSC-derived Cardiomyocytes. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mitochondrial Transcription Termination Factor 4 (
MTERF4
) is a transcription factor involved in mitochondrial ribosomal biogenesis and was identified as a gene of interest via whole exome sequencing in a pediatric patient with hypertrophic cardiomyopathy (HCM) at Children’s Hospital of Wisconsin. The variants of interest identified in
MTERF4
have not been previously reported in the literature or associated with HCM. Here, we combined precision genome editing via CRISPR/Cas9 system with human iPSC-derived cardiomyocytes (hiPSC-derived CMs) to model the HCM patient-specific
MTERF4
variants. We hypothesize that
MTERF4
variants are contributing to cardiomyocyte impairment, leading to the development of the hypertrophic phenotype. To improve our efficiency of CRISPR/Cas9 precision genome editing in hiPSCs, we are using a co-targeting with selection method.
MTERF4
mutant clones and control hiPSCs (obtained from co-targeted but unmodified by CRISPR/Cas9) were identified by Sanger sequencing and assessed for pluripotency using immunostaining and gene expression.
MTERF4
clones and controls were subjected to our modified Palecek matrix-overlay method for CM differentiation and evaluated at 3-4 weeks for cell size, mitochondrial function, and gene expression. The hiPSC-derived CMs cell size analysis by average pixel area of the
MTERF4
mutant indicated that they are significantly (p=0.0012) larger compared to
MTERF4
control. The assessment of mitochondrial function demonstrated that the maximal mitochondrial respiration may be reduced in
MTERF4
mutant hiPSC-derived CMs compared to control (p=0.056). In known cardiovascular disease genes (NPPA, NPPB, GATA4, TNNT, MYL7, MYH7) associated with HCM, gene expression (qRT-PCR) were elevated. Preliminary data support our hypothesis through changes in CMs size, mitochondrial function, and transcriptional expression for one
MTERF4
mutant clone and control. This approach has generated an
in vitro
tool to evaluate aspects diseases such as cardiomyopathy that can be used for diagnostic screening and therapy. Repeating our initial studies, and adding mechanistic studies, with additional
MTERF4
mutant and control clones will further validate our hypothesis.
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Affiliation(s)
| | | | | | | | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
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8
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Prokop JW, Yeo NC, Ottmann C, Chhetri SB, Florus KL, Ross EJ, Sosonkina N, Link BA, Freedman BI, Coppola CJ, McDermott-Roe C, Leysen S, Milroy LG, Meijer FA, Geurts AM, Rauscher FJ, Ramaker R, Flister MJ, Jacob HJ, Mendenhall EM, Lazar J. Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD. J Am Soc Nephrol 2018; 29:1525-1535. [PMID: 29476007 DOI: 10.1681/asn.2017080856] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Background Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, SHROOM3 is an associated risk gene for CKD, yet causative mechanism(s) of SHROOM3 allele(s) are unknown.Methods We used our analytic pipeline that integrates genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiologic data to characterize coding and noncoding variants to study the human SHROOM3 risk locus for CKD.Results We identified a novel SHROOM3 transcriptional start site, which results in a shorter isoform lacking the PDZ domain and is regulated by a common noncoding sequence variant associated with CKD (rs17319721, allele frequency: 0.35). This variant disrupted allele binding to the transcription factor TCF7L2 in podocyte cell nuclear extracts and altered transcription levels of SHROOM3 in cultured cells, potentially through the loss of repressive looping between rs17319721 and the novel start site. Although common variant mechanisms are of high utility, sequencing is beginning to identify rare variants involved in disease; therefore, we used our biophysical tools to analyze an average of 112,849 individual human genome sequences for rare SHROOM3 missense variants, revealing 35 high-effect variants. The high-effect alleles include a coding variant (P1244L) previously associated with CKD (P=0.01, odds ratio=7.95; 95% CI, 1.53 to 41.46) that we find to be present in East Asian individuals at an allele frequency of 0.0027. We determined that P1244L attenuates the interaction of SHROOM3 with 14-3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD.Conclusions These data demonstrate multiple new SHROOM3-dependent genetic/molecular mechanisms that likely affect CKD.
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Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; .,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan
| | - Nan Cher Yeo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Kacie L Florus
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Emily J Ross
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee
| | | | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy and
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; and
| | - Candice J Coppola
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Chris McDermott-Roe
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Seppe Leysen
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Femke A Meijer
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Aron M Geurts
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Frank J Rauscher
- Gene Expression & Regulation Program, Wistar Institute, Philadelphia, Pennsylvania
| | - Ryne Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Michael J Flister
- Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Howard J Jacob
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
| | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama;
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9
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Rohacek AM, Bebee TW, Tilton RK, Radens CM, McDermott-Roe C, Peart N, Kaur M, Zaykaner M, Cieply B, Musunuru K, Barash Y, Germiller JA, Krantz ID, Carstens RP, Epstein DJ. ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development. Dev Cell 2017; 43:318-331.e5. [PMID: 29107558 DOI: 10.1016/j.devcel.2017.09.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 08/15/2017] [Accepted: 08/26/2017] [Indexed: 12/30/2022]
Abstract
Alternative splicing contributes to gene expression dynamics in many tissues, yet its role in auditory development remains unclear. We performed whole-exome sequencing in individuals with sensorineural hearing loss (SNHL) and identified pathogenic mutations in Epithelial Splicing-Regulatory Protein 1 (ESRP1). Patient-derived induced pluripotent stem cells showed alternative splicing defects that were restored upon repair of an ESRP1 mutant allele. To determine how ESRP1 mutations cause hearing loss, we evaluated Esrp1-/- mouse embryos and uncovered alterations in cochlear morphogenesis, auditory hair cell differentiation, and cell fate specification. Transcriptome analysis revealed impaired expression and splicing of genes with essential roles in cochlea development and auditory function. Aberrant splicing of Fgfr2 blocked stria vascularis formation due to erroneous ligand usage, which was corrected by reducing Fgf9 gene dosage. These findings implicate mutations in ESRP1 as a cause of SNHL and demonstrate the complex interplay between alternative splicing, inner ear development, and auditory function.
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Affiliation(s)
- Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Thomas W Bebee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard K Tilton
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Chris McDermott-Roe
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natoya Peart
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maninder Kaur
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael Zaykaner
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin Cieply
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - John A Germiller
- Division of Pediatric Otolaryngology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Russ P Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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10
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Mitzelfelt KA, McDermott-Roe C, Grzybowski MN, Marquez M, Kuo CT, Riedel M, Lai S, Choi MJ, Kolander KD, Helbling D, Dimmock DP, Battle MA, Jou CJ, Tristani-Firouzi M, Verbsky JW, Benjamin IJ, Geurts AM. Efficient Precision Genome Editing in iPSCs via Genetic Co-targeting with Selection. Stem Cell Reports 2017; 8:491-499. [PMID: 28238794 PMCID: PMC5355643 DOI: 10.1016/j.stemcr.2017.01.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/21/2017] [Accepted: 01/21/2017] [Indexed: 12/26/2022] Open
Abstract
Genome editing in induced pluripotent stem cells is currently hampered by the laborious and expensive nature of identifying homology-directed repair (HDR)-modified cells. We present an approach where isolation of cells bearing a selectable, HDR-mediated editing event at one locus enriches for HDR-mediated edits at additional loci. This strategy, called co-targeting with selection, improves the probability of isolating cells bearing HDR-mediated variants and accelerates the production of disease models. Increases the efficiency of genome editing in human iPSCs Enhances detectability of variants of interest derived by homology-directed repair Is a simple, scalable, and adaptable strategy for knocking in variants of interest
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Affiliation(s)
- Katie A Mitzelfelt
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Chris McDermott-Roe
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Michael N Grzybowski
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Maribel Marquez
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chieh-Ti Kuo
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Shuping Lai
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda J Choi
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kurt D Kolander
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Daniel Helbling
- Division of Genetics, Department of Pediatrics, Human Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - David P Dimmock
- Division of Genetics, Department of Pediatrics, Human Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chuanchau J Jou
- Nora Eccles Harrison CVRTI, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 83113, USA
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison CVRTI, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 83113, USA
| | - James W Verbsky
- Section of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ivor J Benjamin
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Aron M Geurts
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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11
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McDermott-Roe C, Leleu M, Rowe GC, Palygin O, Bukowy JD, Kuo J, Rech M, Hermans-Beijnsberger S, Schaefer S, Adami E, Creemers EE, Heinig M, Schroen B, Arany Z, Petretto E, Geurts AM. Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PLoS One 2017; 12:e0170458. [PMID: 28158196 PMCID: PMC5291451 DOI: 10.1371/journal.pone.0170458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/05/2017] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial dysfunction contributes to myriad monogenic and complex pathologies. To understand the underlying mechanisms, it is essential to define the full complement of proteins that modulate mitochondrial function. To identify such proteins, we performed a meta-analysis of publicly available gene expression data. Gene co-expression analysis of a large and heterogeneous compendium of microarray data nominated a sub-population of transcripts that whilst highly correlated with known mitochondrial protein-encoding transcripts (MPETs), are not themselves recognized as generating proteins either localized to the mitochondrion or pertinent to functions therein. To focus the analysis on a medically-important condition with a strong yet incompletely understood mitochondrial component, candidates were cross-referenced with an MPET-enriched module independently generated via genome-wide co-expression network analysis of a human heart failure gene expression dataset. The strongest uncharacterized candidate in the analysis was Leucine Rich Repeat Containing 2 (LRRC2). LRRC2 was found to be localized to the mitochondria in human cells and transcriptionally-regulated by the mitochondrial master regulator Pgc-1α. We report that Lrrc2 transcript abundance correlates with that of β-MHC, a canonical marker of cardiac hypertrophy in humans and experimentally demonstrated an elevation in Lrrc2 transcript in in vitro and in vivo rodent models of cardiac hypertrophy as well as in patients with dilated cardiomyopathy. RNAi-mediated Lrrc2 knockdown in a rat-derived cardiomyocyte cell line resulted in enhanced expression of canonical hypertrophic biomarkers as well as increased mitochondrial mass in the context of increased Pgc-1α expression. In conclusion, our meta-analysis represents a simple yet powerful springboard for the nomination of putative mitochondrially-pertinent proteins relevant to cardiac function and enabled the identification of LRRC2 as a novel mitochondrially-relevant protein and regulator of the hypertrophic response.
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Affiliation(s)
- Chris McDermott-Roe
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Glenn C. Rowe
- Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Oleg Palygin
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - John D. Bukowy
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Judy Kuo
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
| | - Monika Rech
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Steffie Hermans-Beijnsberger
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Sebastian Schaefer
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Esther E. Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Aron M. Geurts
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States of America
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12
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Prisco AR, Hoffmann BR, Kaczorowski CC, McDermott-Roe C, Stodola TJ, Exner EC, Greene AS. Tumor Necrosis Factor α Regulates Endothelial Progenitor Cell Migration via CADM1 and NF-kB. Stem Cells 2016; 34:1922-33. [PMID: 26867147 PMCID: PMC4931961 DOI: 10.1002/stem.2339] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/28/2016] [Indexed: 02/06/2023]
Abstract
Shortly after the discovery of endothelial progenitor cells (EPCs) in 1997, many clinical trials were conducted using EPCs as a cellular based therapy with the goal of restoring damaged organ function by inducing growth of new blood vessels (angiogenesis). Results were disappointing, largely because the cellular and molecular mechanisms of EPC-induced angiogenesis were not clearly understood. Following injection, EPCs must migrate to the target tissue and engraft prior to induction of angiogenesis. In this study EPC migration was investigated in response to tumor necrosis factor α (TNFα), a pro-inflammatory cytokine, to test the hypothesis that organ damage observed in ischemic diseases induces an inflammatory signal that is important for EPC homing. In this study, EPC migration and incorporation were modeled in vitro using a coculture assay where TNFα treated EPCs were tracked while migrating toward vessel-like structures. It was found that TNFα treatment of EPCs increased migration and incorporation into vessel-like structures. Using a combination of genomic and proteomic approaches, NF-kB mediated upregulation of CADM1 was identified as a mechanism of TNFα induced migration. Inhibition of NF-kB or CADM1 significantly decreased migration of EPCs in vitro suggesting a role for TNFα signaling in EPC homing during tissue repair. Stem Cells 2016;34:1922-1933.
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Affiliation(s)
- Anthony R. Prisco
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI
- Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI
| | - Brian R. Hoffmann
- Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI
- Medical College of Wisconsin, Department of Medicine, Division of Cardiology, Cardiovascular Center, Milwaukee, WI
| | - Catherine C. Kaczorowski
- University of Tennessee Health Science Center, Department of Anatomy and Neurobiology, Memphis, TN
| | - Chris McDermott-Roe
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI
- Medical College of Wisconsin, Human and Molecular Genetics Center, Milwaukee, WI
| | - Timothy J. Stodola
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI
- Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI
| | - Eric C. Exner
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI
- Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI
| | - Andrew S. Greene
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI
- Medical College of Wisconsin, Biotechnology and Bioengineering Center, Milwaukee, WI
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McDermott-Roe C, Ye J, Ahmed R, Sun XM, Serafín A, Ware J, Bottolo L, Muckett P, Cañas X, Zhang J, Rowe GC, Buchan R, Lu H, Braithwaite A, Mancini M, Hauton D, Martí R, García-Arumí E, Hubner N, Jacob H, Serikawa T, Zidek V, Papousek F, Kolar F, Cardona M, Ruiz-Meana M, García-Dorado D, Comella JX, Felkin LE, Barton PJR, Arany Z, Pravenec M, Petretto E, Sanchis D, Cook SA. Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function. Nature 2011; 478:114-8. [PMID: 21979051 PMCID: PMC3189541 DOI: 10.1038/nature10490] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 08/17/2011] [Indexed: 12/31/2022]
Abstract
Left ventricular mass (LVM) is a highly heritable trait and an independent risk factor for all-cause mortality. So far, genome-wide association studies have not identified the genetic factors that underlie LVM variation, and the regulatory mechanisms for blood-pressure-independent cardiac hypertrophy remain poorly understood. Unbiased systems genetics approaches in the rat now provide a powerful complementary tool to genome-wide association studies, and we applied integrative genomics to dissect a highly replicated, blood-pressure-independent LVM locus on rat chromosome 3p. Here we identified endonuclease G (Endog), which previously was implicated in apoptosis but not hypertrophy, as the gene at the locus, and we found a loss-of-function mutation in Endog that is associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly implicated ENDOG in fundamental mitochondrial processes that are unrelated to apoptosis. We showed direct regulation of ENDOG by ERR-α and PGC1α (which are master regulators of mitochondrial and cardiac function), interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, the Endog-deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated levels of reactive oxygen species, which were associated with enlarged and steatotic cardiomyocytes. Our study has further established the link between mitochondrial dysfunction, reactive oxygen species and heart disease and has uncovered a role for Endog in maladaptive cardiac hypertrophy.
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Affiliation(s)
- Chris McDermott-Roe
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
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Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, Sarwar R, Pravenec M, Hübner N, Aitman TJ, Cook SA, Richardson S. New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol 2010; 6:e1000737. [PMID: 20386736 PMCID: PMC2851562 DOI: 10.1371/journal.pcbi.1000737] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/03/2010] [Indexed: 01/29/2023] Open
Abstract
The majority of expression quantitative trait locus (eQTL) studies have been carried out in single tissues or cell types, using methods that ignore information shared across tissues. Although global analysis of RNA expression in multiple tissues is now feasible, few integrated statistical frameworks for joint analysis of gene expression across tissues combined with simultaneous analysis of multiple genetic variants have been developed to date. Here, we propose Sparse Bayesian Regression models for mapping eQTLs within individual tissues and simultaneously across tissues. Testing these on a set of 2,000 genes in four tissues, we demonstrate that our methods are more powerful than traditional approaches in revealing the true complexity of the eQTL landscape at the systems-level. Highlighting the power of our method, we identified a two-eQTL model (cis/trans) for the Hopx gene that was experimentally validated and was not detected by conventional approaches. We showed common genetic regulation of gene expression across four tissues for ∼27% of transcripts, providing >5 fold increase in eQTLs detection when compared with single tissue analyses at 5% FDR level. These findings provide a new opportunity to uncover complex genetic regulatory mechanisms controlling global gene expression while the generality of our modelling approach makes it adaptable to other model systems and humans, with broad application to analysis of multiple intermediate and whole-body phenotypes. Integrated analysis of genome-wide genetic polymorphisms and gene expression profiles from different tissues or cell types has been highly successful in identifying genes modulating complex phenotypes in animal models and humans. However, an important limitation of the current approaches consists in their sole application to individual tissues, thus ignoring information shared across different tissues. To uncover complex genetic regulatory mechanisms controlling gene expression at the whole organism's level, it is essential to develop appropriate analytical methods for the analysis of genome-wide genetic polymorphisms and gene expression profiles simultaneously in multiple tissues. This paper presents a novel, fully integrated Bayesian approach for mapping the genetic components of gene expression within and across multiple tissues. In addition to increased power and enhanced mapping resolution when compared with traditional approaches, our model directly provides information on potential systemic effects on transcriptional profiles and co-existing local (cis) and distant (trans) genetic control of gene expression. We also discuss the possibility to extend our approach for the analysis of different phenotypes, and other study designs, thus providing an integrated computational tool to explore the genetic control underlying transcriptional regulation at the systems-level, beyond the single tissue resolution.
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Affiliation(s)
- Enrico Petretto
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Leonardo Bottolo
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Sarah R. Langley
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Chris McDermott-Roe
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rizwan Sarwar
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences and Centre for Applied Genomics, Prague, Czech Republic
- Charles University in Prague, Institute of Biology and Medical Genetics of the First Faculty of Medicine and General Teaching Hospital, Prague, Czech Republic
| | - Norbert Hübner
- Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Timothy J. Aitman
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- Section of Molecular Genetics and Rheumatology, Division and Faculty of Medicine, Imperial College, London, United Kingdom
| | - Stuart A. Cook
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Sylvia Richardson
- Department of Epidemiology and Biostatistics, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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Roussoulieres A, Collot-Teixeira S, Morser K, Chalabreysse L, McDermott-Roe C, Cerutti C, Guzman A, Michel JB, Boissonnat P, Sebbag L, Thivolet-Bejui F, Bricca G, McGregor J. 138: T-Cadherin Expression in Cardiac Allograft Vasculopathy after Human Heart Transplantation. J Heart Lung Transplant 2009. [DOI: 10.1016/j.healun.2008.11.816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Rousoulieres A, Collot-Teixeira S, Chalabreysse L, Morser K, McDermott-Roe C, Yilmaz S, Leleu M, De Lorenzo F, Guzman A, Michel J, Sebbag L, Boissonnat P, Thivolet-Bejui F, McGregor J. USE OF MICROARRAYS AND IMMUNOHISTOCHEMISTRY TO INVESTIGATE ACCELERATED ATHEROSCLEROSIS IN HUMAN GRAFT CORONARY ARTERY DISEASE. ATHEROSCLEROSIS SUPP 2008. [DOI: 10.1016/s1567-5688(08)70623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Collot-Teixeira S, Martin J, McDermott-Roe C, Poston R, McGregor JL. CD36 and macrophages in atherosclerosis. Cardiovasc Res 2007; 75:468-77. [PMID: 17442283 DOI: 10.1016/j.cardiores.2007.03.010] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 03/02/2007] [Accepted: 03/09/2007] [Indexed: 11/22/2022] Open
Abstract
CD36 is a multi-ligand scavenger receptor present on the surface of a number of cells such as platelets, monocytes/macrophages, endothelial and smooth muscle cells. Monocyte/macrophage CD36 has been shown to play a critical role in the development of atherosclerotic lesions by its capacity to bind and endocytose oxidized low density lipoproteins (OxLDL), and it is implicated in the formation of foam cells. However, the significance of CD36 in atherosclerosis has recently been called into question by different studies, and therefore its exact role still needs to be clarified. The aim of this article is to carefully review the importance of CD36 as an essential component in the pathogenesis of atherosclerosis.
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Martin J, Collot-Teixeira S, McDermott-Roe C, Clogenson S, McGregor J. Th-P15:106 Advanced glycation end products (AGE), in contrast to OXLDL, do not stimulate macrophage gene expression VIA CD36. ATHEROSCLEROSIS SUPP 2006. [DOI: 10.1016/s1567-5688(06)82066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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