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Dugger SA, Dhindsa RS, Sampaio GDA, Ressler AK, Rafikian EE, Petri S, Letts VA, Teoh J, Ye J, Colombo S, Peng Y, Yang M, Boland MJ, Frankel WN, Goldstein DB. Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency. PLoS Genet 2023; 19:e1010952. [PMID: 37782669 PMCID: PMC10569524 DOI: 10.1371/journal.pgen.1010952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/12/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Heterozygous de novo loss-of-function mutations in the gene expression regulator HNRNPU cause an early-onset developmental and epileptic encephalopathy. To gain insight into pathological mechanisms and lay the potential groundwork for developing targeted therapies, we characterized the neurophysiologic and cell-type-specific transcriptomic consequences of a mouse model of HNRNPU haploinsufficiency. Heterozygous mutants demonstrated global developmental delay, impaired ultrasonic vocalizations, cognitive dysfunction and increased seizure susceptibility, thus modeling aspects of the human disease. Single-cell RNA-sequencing of hippocampal and neocortical cells revealed widespread, yet modest, dysregulation of gene expression across mutant neuronal subtypes. We observed an increased burden of differentially-expressed genes in mutant excitatory neurons of the subiculum-a region of the hippocampus implicated in temporal lobe epilepsy. Evaluation of transcriptomic signature reversal as a therapeutic strategy highlights the potential importance of generating cell-type-specific signatures. Overall, this work provides insight into HNRNPU-mediated disease mechanisms and provides a framework for using single-cell RNA-sequencing to study transcriptional regulators implicated in disease.
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Affiliation(s)
- Sarah A. Dugger
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ryan S. Dhindsa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute of Texas Children’s Hospital, Houston, Texas, United States of America
| | - Gabriela De Almeida Sampaio
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrew K. Ressler
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Elizabeth E. Rafikian
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sabrina Petri
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Verity A. Letts
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - JiaJie Teoh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Junqiang Ye
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, United States of America
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York, United States of America
| | - Sophie Colombo
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Yueqing Peng
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mu Yang
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Michael J. Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Wayne N. Frankel
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
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Pérez-Villa A, Echeverría-Garcés G, Ramos-Medina MJ, Prathap L, Martínez-López M, Ramírez-Sánchez D, García-Cárdenas JM, Armendáriz-Castillo I, Guerrero S, Paz C, López-Cortés A. Integrated multi-omics analysis reveals the molecular interplay between circadian clocks and cancer pathogenesis. Sci Rep 2023; 13:14198. [PMID: 37648722 PMCID: PMC10469199 DOI: 10.1038/s41598-023-39401-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Circadian rhythms (CRs) are fundamental biological processes that significantly impact human well-being. Disruption of these rhythms can trigger insufficient neurocognitive development, insomnia, mental disorders, cardiovascular diseases, metabolic dysfunctions, and cancer. The field of chronobiology has increased our understanding of how rhythm disturbances contribute to cancer pathogenesis, and how circadian timing influences the efficacy of cancer treatments. As the circadian clock steadily gains recognition as an emerging factor in tumorigenesis, a thorough and comprehensive multi-omics analysis of CR genes/proteins has never been performed. To shed light on this, we performed, for the first time, an integrated data analysis encompassing genomic/transcriptomic alterations across 32 cancer types (n = 10,918 tumors) taken from the PanCancer Atlas, unfavorable prognostic protein analysis, protein-protein interactomics, and shortest distance score pathways to cancer hallmark phenotypes. This data mining strategy allowed us to unravel 31 essential CR-related proteins involved in the signaling crossroad between circadian rhythms and cancer. In the context of drugging the clock, we identified pharmacogenomic clinical annotations and drugs currently in late phase clinical trials that could be considered as potential cancer therapeutic strategies. These findings highlight the diverse roles of CR-related genes/proteins in the realm of cancer research and therapy.
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Affiliation(s)
- Andy Pérez-Villa
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lavanya Prathap
- Department of Anatomy, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Mayra Martínez-López
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Jennyfer M García-Cárdenas
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - Isaac Armendáriz-Castillo
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Santiago Guerrero
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Clara Paz
- Grupo de Investigación Bienestar, Salud y Sociedad, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.
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Marenda M, Lazarova E, Gilbert N. The role of SAF-A/hnRNP U in regulating chromatin structure. Curr Opin Genet Dev 2021; 72:38-44. [PMID: 34823151 DOI: 10.1016/j.gde.2021.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023]
Abstract
Scaffold attachment factor A (SAF-A) or hnRNP U is a nuclear RNA-binding protein with a well-documented role in processing newly transcribed RNA. Recent studies also indicate that SAF-A can oligomerise in an ATP-dependent manner and interact with RNA to form a dynamic nuclear mesh. This mesh is thought to regulate nuclear and chromatin architecture, yet a mechanistic understanding is lacking. Here, we review developments in the field to understand how the SAF-A/RNA mesh affects chromatin organisation in interphase and mitosis. As SAF-A has an intrinsically disordered domain we discuss how the chromatin mesh is related to nuclear phase-separated condensates, which in other situations have been shown to regulate transcription and cell functions. Finally, we infer possible links between diseases emerging from SAF-A mutations and its role in chromatin organisation and regulation.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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