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Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024:e2300210. [PMID: 38715516 DOI: 10.1002/bies.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type differences. This review discusses the role of gene regulatory networks in enhancing understanding of transcriptional regulation and covers construction methods ranging from expression-based approaches to supervised machine learning. Additionally, key experimental methods, including MPRAs and CRISPR-Cas9-based screening, which have significantly contributed to understanding TF binding preferences and cis-regulatory element functions, are explored. Lastly, the potential of machine learning and artificial intelligence to unravel cis-regulatory logic is analyzed. These computational advances have far-reaching implications for precision medicine, therapeutic target discovery, and the study of genetic variations in health and disease.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ioannis Mouratidis
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nikol Chantzi
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Yasin Uzun
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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2
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Stenke E, Dunne C, Bryce-Smyth A, Hurley M, Pode-Shakked B, Anikster Y, Tan T, Kowalka A, Bech P, Bourke B. Reversal of Intestinal Failure With Teduglutide in PERCC1-Associated Enteropathy: A Case Report. Ann Intern Med 2024. [PMID: 38710080 DOI: 10.7326/m24-0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Affiliation(s)
- Emily Stenke
- National Centre for Paediatric Gastroenterology, Hepatology and Nutrition, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Cara Dunne
- National Centre for Paediatric Gastroenterology, Hepatology and Nutrition, Children's Health Ireland at Crumlin, Dublin; and Department of Gastroenterology, St James' Hospital, Dublin, Ireland
| | - Anthea Bryce-Smyth
- National Centre for Paediatric Gastroenterology, Hepatology and Nutrition, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Michelle Hurley
- National Centre for Paediatric Gastroenterology, Hepatology and Nutrition, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Ben Pode-Shakked
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; and School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yair Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; and School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tricia Tan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom
| | - Anna Kowalka
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom
| | - Paul Bech
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom
| | - Billy Bourke
- National Centre for Paediatric Gastroenterology, Hepatology and Nutrition, Children's Health Ireland at Crumlin, Dublin; National Children's Research Centre, Dublin; and School of Medicine, University College Dublin, Dublin, Ireland
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Fleck K, Luria V, Garag N, Karger A, Hunter T, Marten D, Phu W, Nam KM, Sestan N, O’Donnell-Luria AH, Erceg J. Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585403. [PMID: 38559085 PMCID: PMC10980080 DOI: 10.1101/2024.03.17.585403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome organization is intricately tied to regulating genes and associated cell fate decisions. In this study, we examine the positioning and functional significance of human genes, grouped by their evolutionary age, within the 3D organization of the genome. We reveal that genes of different evolutionary origin have distinct positioning relationships with both domains and loop anchors, and remarkably consistent relationships with boundaries across cell types. While the functional associations of each group of genes are primarily cell type-specific, such associations of conserved genes maintain greater stability across 3D genomic features and disease than recently evolved genes. Furthermore, the expression of these genes across various tissues follows an evolutionary progression, such that RNA levels increase from young genes to ancient genes. Thus, the distinct relationships of gene evolutionary age, function, and positioning within 3D genomic features contribute to tissue-specific gene regulation in development and disease.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Nitanta Garag
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115
| | - Trevor Hunter
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Daniel Marten
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - William Phu
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Kee-Myoung Nam
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
| | - Anne H. O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030
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4
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Marek-Yagel D, Stenke E, Pode-Shakked B, Dunne C, Crushell E, Bryce-Smith A, McDermott M, O'Sullivan MJ, Veber A, Krishnamurthy M, Wells JM, Anikster Y, Bourke B. Nonsense mutation in the novel PERCC1 gene as a genetic cause of congenital diarrhea and enteropathy. Hum Genet 2023; 142:691-696. [PMID: 36076104 PMCID: PMC10182134 DOI: 10.1007/s00439-022-02486-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/29/2022] [Indexed: 11/04/2022]
Abstract
Congenital diarrheas and enteropathies (CODEs) constitute a heterogeneous group of individually rare disorders manifesting with infantile-onset chronic diarrhea. Genomic deletions in chromosome 16, encompassing a sequence termed the 'intestine-critical region (ICR)', were recently identified as the cause of an autosomal recessive congenital enteropathy. The regulatory sequence within the ICR is flanked by an unannotated open reading frame termed PERCC1, which plays a role in enteroendocrine cell (EEC) function. We investigated two unrelated children with idiopathic congenital diarrhea requiring home parenteral nutrition attending the Irish Intestinal Failure Program. Currently 12 and 19-years old, these Irish male patients presented with watery diarrhea and hypernatremic dehydration in infancy. Probands were phenotyped by comprehensive clinical investigations, including endoscopic biopsies and serum gastrin level measurements. Following negative exome sequencing, PCR and Sanger sequencing of the entire coding region and intron boundaries of PERCC1 were performed for each proband and their parents. In both patients, serum gastrin levels were low and failed to increase following a meal challenge. While no deletions involving the ICR were detected, targeted sequencing of the PERCC1 gene revealed a shared homozygous c.390C > G stop gain variant. We report clinical and molecular findings in two unrelated patients harboring a shared homozygous variant in PERCC1, comprising the first description of a point mutation in this gene in association with CODE. That both parenteral nutrition dependent children with unexplained diarrhea at our institution harbored a PERCC1 mutation underscores the importance of its inclusion in exome sequencing interpretation.
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Affiliation(s)
- Dina Marek-Yagel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
- Clalit Research Institute, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Emily Stenke
- National Centre for Paediatric Gastroenterology, National Children's Research Center, Children's Health Ireland-Crumlin, Dublin, Ireland
| | - Ben Pode-Shakked
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Cara Dunne
- National Centre for Paediatric Gastroenterology, National Children's Research Center, Children's Health Ireland-Crumlin, Dublin, Ireland
- Department of Gastroenterology, St James' Hospital, Dublin, Ireland
| | - Ellen Crushell
- National Centre for Inherited Metabolic Disorders, Children's Health Ireland-Temple Street, Dublin, Ireland
| | - Anthea Bryce-Smith
- National Centre for Paediatric Gastroenterology, National Children's Research Center, Children's Health Ireland-Crumlin, Dublin, Ireland
| | - Michael McDermott
- Department of Histopathology, Children's Health Ireland-Crumlin, Dublin, Ireland
| | - Maureen J O'Sullivan
- Department of Histopathology, Children's Health Ireland-Crumlin, Dublin, Ireland
| | - Alvit Veber
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Mansa Krishnamurthy
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA
| | - Yair Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Billy Bourke
- National Centre for Paediatric Gastroenterology, National Children's Research Center, Children's Health Ireland-Crumlin, Dublin, Ireland.
- School of Medicine, University College Dublin, Dublin, Ireland.
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Kurolap A, Baris Feldman H. Special issue: the genetics of early onset inflammatory bowel disease (IBD) and diarrheal disorders. Hum Genet 2023; 142:595-597. [PMID: 37106128 DOI: 10.1007/s00439-023-02566-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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6
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The genetics of monogenic intestinal epithelial disorders. Hum Genet 2022; 142:613-654. [PMID: 36422736 PMCID: PMC10182130 DOI: 10.1007/s00439-022-02501-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022]
Abstract
Monogenic intestinal epithelial disorders, also known as congenital diarrheas and enteropathies (CoDEs), are a group of rare diseases that result from mutations in genes that primarily affect intestinal epithelial cell function. Patients with CoDE disorders generally present with infantile-onset diarrhea and poor growth, and often require intensive fluid and nutritional management. CoDE disorders can be classified into several categories that relate to broad areas of epithelial function, structure, and development. The advent of accessible and low-cost genetic sequencing has accelerated discovery in the field with over 45 different genes now associated with CoDE disorders. Despite this increasing knowledge in the causal genetics of disease, the underlying cellular pathophysiology remains incompletely understood for many disorders. Consequently, clinical management options for CoDE disorders are currently limited and there is an urgent need for new and disorder-specific therapies. In this review, we provide a general overview of CoDE disorders, including a historical perspective of the field and relationship to other monogenic disorders of the intestine. We describe the genetics, clinical presentation, and known pathophysiology for specific disorders. Lastly, we describe the major challenges relating to CoDE disorders, briefly outline key areas that need further study, and provide a perspective on the future genetic and therapeutic landscape.
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7
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Mohajeri K, Yadav R, D'haene E, Boone PM, Erdin S, Gao D, Moyses-Oliveira M, Bhavsar R, Currall BB, O'Keefe K, Burt ND, Lowther C, Lucente D, Salani M, Larson M, Redin C, Dudchenko O, Aiden EL, Menten B, Tai DJC, Gusella JF, Vergult S, Talkowski ME. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models. Am J Hum Genet 2022; 109:2049-2067. [PMID: 36283406 PMCID: PMC9674968 DOI: 10.1016/j.ajhg.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 01/26/2023] Open
Abstract
Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
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Affiliation(s)
- Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas D Burt
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathew Larson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Claire Redin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
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Cao J, Yuan L. Identification of key genes for hypertrophic cardiomyopathy using integrated network analysis of differential lncRNA and gene expression. Front Cardiovasc Med 2022; 9:946229. [PMID: 35990977 PMCID: PMC9386162 DOI: 10.3389/fcvm.2022.946229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Hypertrophic cardiomyopathy (HCM) is a complex heterogeneous heart disease. Recent reports found that long non-coding RNAs (lncRNAs) play an important role in the progression of cardiovascular diseases. The present study aimed to identify the novel lncRNAs and messenger RNAs (mRNAs) and determine the key pathways involved in HCM. Methods The lncRNA and mRNA sequencing datasets of GSE68316 and GSE130036 were downloaded from the Gene Expression Omnibus (GEO) database. An integrated co-expression network analysis was conducted to identify differentially expressed lncRNAs and differentially expressed mRNAs in patients with HCM. Then, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were explored to identify the biological functions and signaling pathways of the co-expression network. Protein–protein interaction (PPI) and hub gene networks were constructed by using Cytoscape software. Plasma samples of patients with HCM and the GSE89714 dataset were used to validate the bioinformatics results. Results A total of 1,426 differentially expressed long non-coding RNAs (lncRNAs) and 1,715 differentially expressed mRNAs were obtained from GSE68316, of which 965 lncRNAs and 896 mRNAs were upregulated and 461 lncRNAs and 819 mRNAs were downregulated. A total of 469 differentially expressed lncRNAs and 2,407 differentially expressed mRNAs were screened from GSE130036, of which 183 lncRNAs and 1,283 mRNAs were upregulated and 286 lncRNAs and 1,124 mRNAs were downregulated. A co-expression network was constructed and contained 30 differentially expressed lncRNAs and 63 differentially expressed mRNAs, which were primarily involved in ‘G-protein beta/gamma-subunit complex binding,' ‘polyubiquitin modification-dependent protein binding,' ‘Apelin signaling pathway,' and ‘Wnt signaling pathway.' The 10 hub genes in the upregulated network [G Protein Subunit Alpha I2 (GNAI2), G Protein Subunit Alpha I1 (GNAI1), G Protein Subunit Alpha I3 (GNAI3), G Protein Subunit Gamma 2 (GNG2), G Protein Subunit Beta 1 (GNB1), G Protein Subunit Gamma 13 (GNG13), G Protein Subunit Gamma Transducin 1 (GNGT1), G Protein Subunit Gamma 12 (GNG12), AKT Serine/Threonine Kinase 1 (AKT1) and GNAS Complex Locus (GNAS)] and the 10 hub genes in the downregulated network [Nucleotide-Binding Oligomerization Domain Containing Protein 2 (NOD2), Receptor-Interacting Serine/Threonine Kinase 2 (RIPK2), Nucleotide-Binding Oligomerization Domain Containing Protein 1 (NOD1), Mitochondrial Antiviral Signaling Protein (MAVS), Autophagy Related 16-Like 1 (ATG16L1), Interferon Induced With Helicase C Domain 1 (IFIH1), Autophagy Related 5 (ATG5), TANK-Binding Kinase 1 (TBK1), Caspase Recruitment Domain Family Member 9 (CARD9), and von Willebrand factor (VWF)] were screened using cytoHubba. The expression of LA16c-312E8.2 and RP5-1160K1.3 in the plasma of patients with HCM was elevated, and the expression of the MIR22 host gene (MIR22HG) was decreased, which was consistent with our analysis, while the expression of LINC00324 and Small Nucleolar RNA Host Gene 12 (SNHG12) was not significantly different between the two groups. Verification analyses performed on GSE89714 showed the upregulated mRNAs of Chloride Voltage-Gated Channel 7 (CLCN7), N-Acetylglucosamine-1-Phosphate Transferase Subunit Gamma (GNPTG), Unk Like Zinc Finger (UNKL), Adenosine Monophosphate Deaminase 2 (AMPD2), GNAI3, WD Repeat Domain 81 (WDR81), and Serpin Family F Member 1 (SERPINF1) and downregulated mRNAs of TATA-Box Binding Protein Associated Factor 12 (TAF12) co-expressed with five crucial lncRNAs. Moreover, GNAI2, GNAI3, GNG12, and vWF were upregulated and GNAS was downregulated in the top 10 hub genes of upregulated and downregulated PPI networks. Conclusion These findings from integrative biological analysis of lncRNA-mRNA co-expression networks explored the key genes and pathways and provide new insights into the understanding of the mechanism and discovering new therapeutic targets for HCM. Three differentially expressed pivotal lncRNAs (LA16c-312E8.2, RP5-1160K1.3, and MIR22HG) in the co-expression network may serve as biomarkers and intervention targets for the diagnosis and treatment of HCM.
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Affiliation(s)
- Jing Cao
- Department of Cardiovascular Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Lei Yuan
- Department of Medical Affairs, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Lei Yuan
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Sanchez-Pulido L, Jia S, Hansen CG, Ponting CP. PERCC1, a new member of the Yap/TAZ/ FAM181 transcriptional co-regulator family. BIOINFORMATICS ADVANCES 2022; 2:vbac008. [PMID: 36699391 PMCID: PMC9710580 DOI: 10.1093/bioadv/vbac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 01/28/2023]
Abstract
Motivation Disrupted PERCC1 gene expression causes an intractable congenital diarrhoea in infants. However, this gene's molecular mechanism is unknown and no homologous proteins have been reported. Results Our detailed evolutionary analysis of PERCC1 sequence reveals it to be a previously unappreciated member of the YAP/TAZ/FAM181 family of homologous transcriptional regulators. Like YAP and TAZ, PERCC1 likely interacts with DNA via binding to TEA/ATTS domain transcription factors (TEADs) using its conserved interface-2 and -3 sequences. We compare the expression patterns of PERCC1 with those of YAP, TAZ, TEADs. Our report provides the identification and first in-depth bioinformatic analysis of a YAP/TAZ homologue, and a likely new regulator of the YAP/TAZ-TEAD transcriptional complex. Availability and implementation The data underlying this article are available in UniProt Database. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Siyang Jia
- Centre for Inflammation Research, Institute for Regeneration and Repair, Queen's Medical Research Institute, Edinburgh bioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Carsten Gram Hansen
- Centre for Inflammation Research, Institute for Regeneration and Repair, Queen's Medical Research Institute, Edinburgh bioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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10
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Goulet O, Pigneur B, Charbit-Henrion F. Congenital enteropathies involving defects in enterocyte structure or differentiation. Best Pract Res Clin Gastroenterol 2022; 56-57:101784. [PMID: 35331396 DOI: 10.1016/j.bpg.2021.101784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023]
Abstract
Congenital enteropathies (CE) are a group of rare inherited diseases with a typical onset early in life. They involve defects in enterocyte structure or differentiation. They can cause a severe condition of intestinal failure (IF). The diagnostic approach is based first on clinical presentation (consanguinity, prenatal expression, polyhydramnios, early neonatal onset, aspect of stools, persistence at bowel rest, associated extra-digestive manifestations….) and histo-pathological analyses. These rare intestinal diseases cause protracted diarrhea that might resolve, for a few, with a dietetic approach. However, protracted or permanent IF may require long term parenteral nutrition and, in limited cases, intestinal transplantation. With the progresses in both clinical nutrition and genetics, many of these CE are nowadays associated with recognized gene mutations. It improved our knowledge and the understanding in the patho-physiology of these diseases, thus, leading potentially to therapeutic perspectives. These review cover most of the early onset CE and excludes the immune related diarrhea.
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Affiliation(s)
- Olivier Goulet
- Division of Paediatric Gastroenterology Hepatology and Nutrition, University Paris-Centre, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France.
| | - Bénédicte Pigneur
- Division of Paediatric Gastroenterology Hepatology and Nutrition, University Paris-Centre, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France
| | - Fabienne Charbit-Henrion
- Department of Genetics, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France
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11
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Bubier JA, Chesler EJ, Weinstock GM. Host genetic control of gut microbiome composition. Mamm Genome 2021; 32:263-281. [PMID: 34159422 PMCID: PMC8295090 DOI: 10.1007/s00335-021-09884-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships.
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Affiliation(s)
- Jason A Bubier
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA
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12
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Shao Y, Bajikar SS, Tirumala HP, Gutierrez MC, Wythe JD, Zoghbi HY. Identification and characterization of conserved noncoding cis-regulatory elements that impact Mecp2 expression and neurological functions. Genes Dev 2021; 35:489-494. [PMID: 33737384 PMCID: PMC8015713 DOI: 10.1101/gad.345397.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/24/2021] [Indexed: 11/24/2022]
Abstract
In this study, Shao et al. investigated the transcriptional regulation of MeCP2, and identified six putative noncoding regulatory elements of Mecp2, two of which are conserved in humans. Their findings provide insight into transcriptional regulation of Mecp2/MECP2 and highlight genomic sites that could serve as diagnostic and therapeutic targets in Rett syndrome (RTT) and MECP2 duplication syndrome (MDS). While changes in MeCP2 dosage cause Rett syndrome (RTT) and MECP2 duplication syndrome (MDS), its transcriptional regulation is poorly understood. Here, we identified six putative noncoding regulatory elements of Mecp2, two of which are conserved in humans. Upon deletion in mice and human iPSC-derived neurons, these elements altered RNA and protein levels in opposite directions and resulted in a subset of RTT- and MDS-like behavioral deficits in mice. Our discovery provides insight into transcriptional regulation of Mecp2/MECP2 and highlights genomic sites that could serve as diagnostic and therapeutic targets in RTT or MDS.
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Affiliation(s)
- Yingyao Shao
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sameer S Bajikar
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harini P Tirumala
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manuel Cantu Gutierrez
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joshua D Wythe
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
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13
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Hung YH, Huang S, Dame MK, Yu Q, Yu QC, Zeng YA, Camp JG, Spence JR, Sethupathy P. Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Nucleic Acids Res 2021; 49:726-744. [PMID: 33406262 PMCID: PMC7826262 DOI: 10.1093/nar/gkaa1204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The establishment of the small intestinal (SI) lineage during human embryogenesis ensures functional integrity of the intestine after birth. The chromatin dynamics that drive SI lineage formation and regional patterning in humans are essentially unknown. To fill this knowledge void, we apply a cutting-edge genomic technology to a state-of-the-art human model of early SI development. Specifically, we leverage chromatin run-on sequencing (ChRO-seq) to define the landscape of active promoters, enhancers and gene bodies across distinct stages of directed differentiation of human pluripotent stem cells into SI spheroids with regional specification. Through comprehensive ChRO-seq analysis we identify candidate stage-specific chromatin activity states, novel markers and enhancer hotspots during the directed differentiation. Moreover, we propose a detailed transcriptional network associated with SI lineage formation or regional patterning. Our ChRO-seq analyses uncover a previously undescribed pattern of enhancer activity and transcription at HOX gene loci underlying SI regional patterning. We also validated this unique HOX dynamics by the analysis of single cell RNA-seq data from human fetal SI. Overall, the results lead to a new proposed working model for the regulatory underpinnings of human SI development, thereby adding a novel dimension to the literature that has relied almost exclusively on non-human models.
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Affiliation(s)
- Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland
| | - Qing C Yu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yi A Zeng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basal, Basel 4056, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4001, Switzerland
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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14
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Zhang C, Xiao X, Li T, Li M. Translational genomics and beyond in bipolar disorder. Mol Psychiatry 2021; 26:186-202. [PMID: 32424235 DOI: 10.1038/s41380-020-0782-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWAS) have revealed multiple genomic loci conferring risk of bipolar disorder (BD), providing hints for its underlying pathobiology. However, there are still remaining questions to answer. For example, discordance exists between BD heritability estimated with earlier epidemiological evidence and that calculated based on common GWAS variations. Where is the "missing heritability"? How can we explain the biology of the disease based on genetic findings? In this review, we summarize the accomplishments and limitations of current BD GWAS, and discuss potential reasons for the "missing heritability." In addition, progresses of research for the biological mechanisms underlying BD genetic risk using brain tissues, reprogrammed cells, and model animals are reviewed. While our knowledge of BD genetic basis is significantly promoted by these efforts, the complexities of gene regulation in the genome, the spatial-temporal heterogeneity during brain development, and the limitations of different experimental models should always be considered. Notably, several genes have been widely studied given their relatively well-characterized involvement in BD (e.g., CACAN1C and ANK3), and findings of these genes are summarized to both outline possible biological mechanisms of BD and describe examples of translating GWAS discoveries into the pathophysiology.
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Affiliation(s)
- Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Tao Li
- Mental Health Center and Psychiatric Laboratory, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China. .,West China Brain Research Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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15
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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16
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Vonica A, Bhat N, Phan K, Guo J, Iancu L, Weber JA, Karger A, Cain JW, Wang ECE, DeStefano GM, O'Donnell-Luria AH, Christiano AM, Riley B, Butler SJ, Luria V. Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin. Dev Biol 2020; 464:71-87. [PMID: 32320685 PMCID: PMC7307705 DOI: 10.1016/j.ydbio.2020.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 02/02/2023]
Abstract
Animal development and homeostasis depend on precise temporal and spatial intercellular signaling. Components shared between signaling pathways, generally thought to decrease specificity, paradoxically can also provide a solution to pathway coordination. Here we show that the Bone Morphogenetic Protein (BMP) and Wnt signaling pathways share Apcdd1 as a common inhibitor and that Apcdd1 is a taxon-restricted gene with novel domains and signaling functions. Previously, we showed that Apcdd1 inhibits Wnt signaling (Shimomura et al., 2010), here we find that Apcdd1 potently inhibits BMP signaling in body axis formation and neural differentiation in chicken, frog, zebrafish. Furthermore, we find that Apcdd1 has an evolutionarily novel protein domain. Our results from experiments and modeling suggest that Apcdd1 may coordinate the outputs of two signaling pathways that are central to animal development and human disease.
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Affiliation(s)
- Alin Vonica
- Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA; Department of Biology, The Nazareth College, Rochester, NY, 14618, USA
| | - Neha Bhat
- Department of Biology, Texas A&M University, College Station, TX, 7783-3258, USA; Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Keith Phan
- Department of Neurobiology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Jinbai Guo
- Department of Biology, Texas A&M University, College Station, TX, 7783-3258, USA
| | - Lăcrimioara Iancu
- Institut für Algebra und Zahlentheorie, Universität Stuttgart, D-70569, Stuttgart, Germany; Institute of Mathematics, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK
| | - Jessica A Weber
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, 02115, USA
| | - John W Cain
- Department of Mathematics, Harvard University, Cambridge, MA, 02138, USA
| | - Etienne C E Wang
- Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Gina M DeStefano
- Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Angela M Christiano
- Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Bruce Riley
- Department of Biology, Texas A&M University, College Station, TX, 7783-3258, USA.
| | - Samantha J Butler
- Department of Neurobiology, University of California, Los Angeles, CA, 90095-7239, USA.
| | - Victor Luria
- Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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17
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Maddirevula S, Kuwahara H, Ewida N, Shamseldin HE, Patel N, Alzahrani F, AlSheddi T, AlObeid E, Alenazi M, Alsaif HS, Alqahtani M, AlAli M, Al Ali H, Helaby R, Ibrahim N, Abdulwahab F, Hashem M, Hanna N, Monies D, Derar N, Alsagheir A, Alhashem A, Alsaleem B, Alhebbi H, Wali S, Umarov R, Gao X, Alkuraya FS. Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics. Genome Biol 2020; 21:145. [PMID: 32552793 PMCID: PMC7298854 DOI: 10.1186/s13059-020-02053-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Background At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fraction is unclear. Whole transcriptome sequencing is a promising supplement to WES, although empirical data on the contribution of RNA analysis to the diagnosis of Mendelian diseases on a large scale are scarce. Results Here, we describe our experience with transcript-deleterious variants (TDVs) based on a cohort of 5647 families with suspected Mendelian diseases. We first interrogate all families for which the respective Mendelian phenotype could be mapped to a single locus to obtain an unbiased estimate of the contribution of TDVs at 18.9%. We examine the entire cohort and find that TDVs account for 15% of all “solved” cases. We compare the results of RT-PCR to in silico prediction. Definitive results from RT-PCR are obtained from blood-derived RNA for the overwhelming majority of variants (84.1%), and only a small minority (2.6%) fail analysis on all available RNA sources (blood-, skin fibroblast-, and urine renal epithelial cells-derived), which has important implications for the clinical application of RNA-seq. We also show that RNA analysis can establish the diagnosis in 13.5% of 155 patients who had received “negative” clinical WES reports. Finally, our data suggest a role for TDVs in modulating penetrance even in otherwise highly penetrant Mendelian disorders. Conclusions Our results provide much needed empirical data for the impending implementation of diagnostic RNA-seq in conjunction with genome sequencing.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa AlSheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman AlObeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mona Alenazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Alqahtani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha AlAli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hatoon Al Ali
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nadine Hanna
- Département de génétique, AP-HP, Hôpital Bichat, Université de Paris, LVTS INSERM U1148, Paris, France
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Derar
- Deparmtent of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Afaf Alsagheir
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Badr Alsaleem
- Division of Pediatric Gastroenterology, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamoud Alhebbi
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Sami Wali
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ramzan Umarov
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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18
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Xu D, Gokcumen O, Khurana E. Loss-of-function tolerance of enhancers in the human genome. PLoS Genet 2020; 16:e1008663. [PMID: 32243438 PMCID: PMC7159235 DOI: 10.1371/journal.pgen.1008663] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/15/2020] [Accepted: 02/12/2020] [Indexed: 12/21/2022] Open
Abstract
Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that individual human genomes possess at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers tend to be more tissue-specific and regulate fewer and more dispensable genes relative to other enhancers. They are enriched in immune-related cells while enhancers with low LoF-tolerance are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoF-tolerance of all enhancers, which achieved an area under the receiver operating characteristics curve (AUROC) of 98%. We predict 3,519 more enhancers would be likely tolerant to LoF and 129 enhancers that would have low LoF-tolerance. Our predictions are supported by a known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies. Enhancers are elements where transcription factors bind and regulate the expression of protein-coding genes. Although multiple previous studies have focused on which genes can tolerate loss-of-function (LoF), none has systematically evaluated the tolerance of all enhancers in the human genome to LoF. Individual studies have shown a broad range of phenotypic effects of enhancer LoF. The phenotypic effects of enhancer LoF likely fall into a spectrum where deletion of LoF-tolerant enhancers would not elicit substantial phenotypic impact, while some enhancers are likely to cause fitness defects when deleted. Here we report a systematic computational approach that uses machine learning and properties of enhancers in a unified human regulatory network with tissue-specific annotations to predict the LoF-tolerance of all enhancers identified in the human genome. The LoF-tolerance scores of enhancers provided in this study can significantly facilitate the interpretation and prioritization of non-coding sequence variants for disease and functional studies.
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Affiliation(s)
- Duo Xu
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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Abstract
Congenital diarrheal disorders are heterogeneous conditions characterized by diarrhea with onset in the first years of life. They range from simple temporary conditions, such as cow's milk protein intolerance to irreversible complications, such as microvillous inclusion disease with significant morbidity and mortality. Advances in genomic medicine have improved our understanding of these disorders, leading to an ever-increasing list of identified causative genes. The diagnostic approach to these conditions consists of establishing the presence of diarrhea by detailed review of the history, followed by characterizing the composition of the diarrhea, the response to fasting, and with further specialized testing.
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Affiliation(s)
- Abdul Aziz Elkadri
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA.
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Hekselman I, Yeger-Lotem E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat Rev Genet 2020; 21:137-150. [DOI: 10.1038/s41576-019-0200-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
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