1
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Oliveros W, Delfosse K, Lato DF, Kiriakopulos K, Mokhtaridoost M, Said A, McMurray BJ, Browning JW, Mattioli K, Meng G, Ellis J, Mital S, Melé M, Maass PG. Systematic characterization of regulatory variants of blood pressure genes. Cell Genom 2023; 3:100330. [PMID: 37492106 PMCID: PMC10363820 DOI: 10.1016/j.xgen.2023.100330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 04/28/2023] [Indexed: 07/27/2023]
Abstract
High blood pressure (BP) is the major risk factor for cardiovascular disease. Genome-wide association studies have identified genetic variants for BP, but functional insights into causality and related molecular mechanisms lag behind. We functionally characterize 4,608 genetic variants in linkage with 135 BP loci in vascular smooth muscle cells and cardiomyocytes by massively parallel reporter assays. High densities of regulatory variants at BP loci (i.e., ULK4, MAP4, CFDP1, PDE5A) indicate that multiple variants drive genetic association. Regulatory variants are enriched in repeats, alter cardiovascular-related transcription factor motifs, and spatially converge with genes controlling specific cardiovascular pathways. Using heuristic scoring, we define likely causal variants, and CRISPR prime editing finally determines causal variants for KCNK9, SFXN2, and PCGF6, which are candidates for developing high BP. Our systems-level approach provides a catalog of functionally relevant variants and their genomic architecture in two trait-relevant cell lines for a better understanding of BP gene regulation.
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Affiliation(s)
- Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain
| | - Kate Delfosse
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Daniella F. Lato
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Katerina Kiriakopulos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Milad Mokhtaridoost
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Abdelrahman Said
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brandon J. McMurray
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jared W.L. Browning
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James Ellis
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON M5G 1X8, Canada
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034 Barcelona, Catalonia, Spain
| | - Philipp G. Maass
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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2
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Serra-Camprubí Q, Verdaguer H, Oliveros W, Lupión-Garcia N, Llop-Guevara A, Molina C, Vila-Casadesús M, Turpin A, Neuzillet C, Frigola J, Querol J, Yáñez-Bartolomé M, Castet F, Fabregat-Franco C, Escudero-Iriarte C, Escorihuela M, Arenas EJ, Bernadó-Morales C, Haro N, Giles FJ, Pozo ÓJ, Miquel JM, Nuciforo PG, Vivancos A, Melé M, Serra V, Arribas J, Tabernero J, Peiró S, Macarulla T, Tian TV. Human Metastatic Cholangiocarcinoma Patient-Derived Xenografts and Tumoroids for Preclinical Drug Evaluation. Clin Cancer Res 2023; 29:432-445. [PMID: 36374558 PMCID: PMC9873249 DOI: 10.1158/1078-0432.ccr-22-2551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/16/2022] [Revised: 10/14/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Cholangiocarcinoma (CCA) is usually diagnosed at advanced stages, with limited therapeutic options. Preclinical models focused on unresectable metastatic CCA are necessary to develop rational treatments. Pathogenic mutations in IDH1/2, ARID1A/B, BAP1, and BRCA1/2 have been identified in 30%-50% of patients with CCA. Several types of tumor cells harboring these mutations exhibit homologous recombination deficiency (HRD) phenotype with enhanced sensitivity to PARP inhibitors (PARPi). However, PARPi treatment has not yet been tested for effectiveness in patient-derived models of advanced CCA. EXPERIMENTAL DESIGN We have established a collection of patient-derived xenografts from patients with unresectable metastatic CCA (CCA_PDX). The CCA_PDXs were characterized at both histopathologic and genomic levels. We optimized a protocol to generate CCA tumoroids from CCA_PDXs. We tested the effects of PARPis in both CCA tumoroids and CCA_PDXs. Finally, we used the RAD51 assay to evaluate the HRD status of CCA tissues. RESULTS This collection of CCA_PDXs recapitulates the histopathologic and molecular features of their original tumors. PARPi treatments inhibited the growth of CCA tumoroids and CCA_PDXs with pathogenic mutations of BRCA2, but not those with mutations of IDH1, ARID1A, or BAP1. In line with these findings, only CCA_PDX and CCA patient biopsy samples with mutations of BRCA2 showed RAD51 scores compatible with HRD. CONCLUSIONS Our results suggest that patients with advanced CCA with pathogenic mutations of BRCA2, but not those with mutations of IDH1, ARID1A, or BAP1, are likely to benefit from PARPi therapy. This collection of CCA_PDXs provides new opportunities for evaluating drug response and prioritizing clinical trials.
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Affiliation(s)
- Queralt Serra-Camprubí
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Helena Verdaguer
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Núria Lupión-Garcia
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alba Llop-Guevara
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Molina
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Maria Vila-Casadesús
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Anthony Turpin
- Université de Lille, CNRS INSERM UMR9020-U1277, CANTHER Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France.,Medical Oncology Department, CHRU Lille, Lille, France
| | - Cindy Neuzillet
- Gastrointestinal Oncology, Medical Oncology Department, Curie Institute, Versailles St-Quentin-Paris Saclay University, Saint-Cloud, France
| | - Joan Frigola
- Clinical Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jessica Querol
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mariana Yáñez-Bartolomé
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Florian Castet
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carles Fabregat-Franco
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carmen Escudero-Iriarte
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Escorihuela
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enrique J. Arenas
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Bernadó-Morales
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Noemí Haro
- Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Óscar J. Pozo
- Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Josep M. Miquel
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Paolo G. Nuciforo
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Violeta Serra
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Joaquín Arribas
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Monforte de Lemos, Madrid, Spain.,Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Josep Tabernero
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sandra Peiró
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
| | - Teresa Macarulla
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Gastrointestinal and Endocrine Tumor Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
| | - Tian V. Tian
- Preclinical and Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Corresponding Authors: Tian V. Tian, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain. Phone: (34)932543450, ext. 8656; E-mail: ; Teresa Macarulla, ; and Sandra Peiró,
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3
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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. Cell Genom 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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4
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Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Yue MCS, Sung WWL, Thiruvahindrapuram B, Lougheed J, Oechslin E, Mondal T, Bergin L, Smythe J, Jayappa S, Rao VJ, Shenthar J, Dhandapany PS, Semsarian C, Weintraub RG, Bagnall RD, Ingles J, Melé M, Maass PG, Ellis J, Scherer SW, Mital S. Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genom Med 2022; 7:18. [PMID: 35288587 PMCID: PMC8921194 DOI: 10.1038/s41525-022-00288-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.
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Affiliation(s)
- Robert Lesurf
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Abdelrahman Said
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Oyediran Akinrinade
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- St. George's University School of Medicine, Grenada, Grenada
| | | | - Kathleen Delfosse
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ting Liu
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roderick Yao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabrielle Persad
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Fintan McKenna
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ramil R Noche
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Zebrafish Genetics and Disease Models Core, The Hospital for Sick Children, Toronto, ON, Canada
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shreya Shah
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anastasia Miron
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qian Yang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Erwin Oechslin
- Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Tapas Mondal
- Department of Pediatrics, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Lynn Bergin
- Division of Cardiology, London Health Sciences Centre, London, ON, Canada
| | - John Smythe
- Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Robert G Weintraub
- Cardiology Department, Royal Children's Hospital, Melbourne, Australia
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard D Bagnall
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Philipp G Maass
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada.
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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5
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Said A, Lesurf R, Delfosse K, Oliveros W, Mattiolo K, Meng G, Mele M, Maass P, Ellis J, Scherer S, Mital S. FUNCTIONAL VALIDATION OF NON-CODING REGULATORY VARIANTS ASSOCIATED WITH CHILDHOOD CARDIOMYOPATHY. Can J Cardiol 2021. [DOI: 10.1016/j.cjca.2021.07.140] [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: 10/20/2022] Open
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6
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Mattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Melé M. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol 2020; 21:210. [PMID: 32819422 PMCID: PMC7439725 DOI: 10.1186/s13059-020-02110-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure cis and trans effects between human and mouse. RESULTS Our approach reveals that cis effects are widespread across transcribed regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that trans effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that cis-trans compensation is common within promoters, we do not see evidence of widespread cis-trans compensation at enhancers. Cis-trans compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers. CONCLUSIONS Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.
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Affiliation(s)
- Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel Andergassen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Philipp G Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - John L Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO, 80301, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain.
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7
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Cosín M, Tian T, Oliveros W, Kharenko OA, van der Horst EH, Patel RG, Calosing C, Campeau E, Jahagirdar R, Lakhotia S, Melé M, Palafox M, Arribas J, Oliveira M, Saura C, Serra V, Peiro S. Abstract 1282: Overcoming resistance to inhibitors of CDK4/6 and BET in estrogen receptor-positive breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Three inhibitors of CDK4/6 kinases have been recently approved for use in combination with endocrine therapy. These inhibitors considerably increase the progression-free survival of patients with advanced Estrogen receptor (ER)-positive breast cancer in first-line treatment. As the resistance to CDK4/6 inhibitors is currently a major problem faced in pre-clinical and clinical drug development, the identification of novel treatment combinations and predictive markers is of high importance. BET proteins, specifically BRD2/4, have important roles in cell cycle regulation and proliferation. Thus, BET inhibitors (BETi)have the potential to overcome some pathways of resistance, especially for those mediated by upregulation of specific transcription factors.
We have investigated the response to BET inhibition in patient-derived xenographs (PDXs) from patients with advanced ER+ breast cancer ex vivo and in vivo. Specifically, 14 breast cancer PDXs (10 ER+/HER2- and 4 ER+/HER2+) that were resistant to CDK4/6i in vivo were treated with ZEN-3694, a selective BET inhibitor currently in clinical development. Nine of the PDXs were sensitive to BET inhibition in monotherapy (65%). The non-responder PDXs showed an improved response when they were treated with ZEN-3694 in combination with fulvestrant (a selective ER degrader) or with a CDK4/6 inhibitor (ribociclib or abemaciclib). RNA-seq and computational analyses comparing responder versus non-responder PDXs revealed 493 differential expressed genes for responders, and 252 for non-responders. From those, 142 genes were differentially expressed in both conditions (untreated and treated). Furthermore, phosphorylation of BRD4 was observed in the ZEN-3694 non-responder PDX group, a mechanism of resistance previously observed in triple-negative breast cancer cell lines. This phosphorylation was abrogated by adding a CDK4/6 inhibitor. In the PDXs, resistance to single agent CDK4/6 and BET inhibitors might be overcome using a combination of both inhibitors. Finally, the molecular mechanism involved in phosphorylation of BRD4 was characterized in a MCF-7 cell line resistant to CDK4/6 inhibitors. Our results show that CDK2 could be one of the kinases involved in the phosphorylation of BRD4.
Conclusion: BET inhibition has an impact in advanced ER+ breast cancer cells, either used alone or in combination with endocrine therapy and CDK4/6 inhibitors. Detection of phosphorylated BRD4 (as a mechanism of resistance to BETi) has high potential for use as a biomarker for selecting patients who could benefit from a combined treatment of BET and CDK4/6 inhibitors.
Citation Format: Marc Cosín, Tian Tian, Winona Oliveros, Olesya A. Kharenko, Edward H. van der Horst, Reena G. Patel, Cyrus Calosing, Eric Campeau, Ravi Jahagirdar, Sanjay Lakhotia, Marta Melé, Marta Palafox, Joaquín Arribas, Mafalda Oliveira, Cristina Saura, Violeta Serra, Sandra Peiro. Overcoming resistance to inhibitors of CDK4/6 and BET in estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1282.
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Affiliation(s)
- Marc Cosín
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Tian Tian
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | | | | | | | - Reena G. Patel
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Cyrus Calosing
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Eric Campeau
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | | | | | - Marta Melé
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Marta Palafox
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | | | | | - Cristina Saura
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Violeta Serra
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
| | - Sandra Peiro
- Vall d'Hebron Oncology Institute (VHIO), Barcelona, Spain
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