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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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2
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Nappi F. In-Depth Genomic Analysis: The New Challenge in Congenital Heart Disease. Int J Mol Sci 2024; 25:1734. [PMID: 38339013 PMCID: PMC10855915 DOI: 10.3390/ijms25031734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
The use of next-generation sequencing has provided new insights into the causes and mechanisms of congenital heart disease (CHD). Examinations of the whole exome sequence have detected detrimental gene variations modifying single or contiguous nucleotides, which are characterised as pathogenic based on statistical assessments of families and correlations with congenital heart disease, elevated expression during heart development, and reductions in harmful protein-coding mutations in the general population. Patients with CHD and extracardiac abnormalities are enriched for gene classes meeting these criteria, supporting a common set of pathways in the organogenesis of CHDs. Single-cell transcriptomics data have revealed the expression of genes associated with CHD in specific cell types, and emerging evidence suggests that genetic mutations disrupt multicellular genes essential for cardiogenesis. Metrics and units are being tracked in whole-genome sequencing studies.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord, 93200 Saint-Denis, France
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Liu S, Liu X, Lin X, Chen H. Zinc Finger Proteins in the War on Gastric Cancer: Molecular Mechanism and Clinical Potential. Cells 2023; 12:cells12091314. [PMID: 37174714 PMCID: PMC10177130 DOI: 10.3390/cells12091314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
According to the 2020 global cancer data released by the World Cancer Research Fund (WCRF) International, gastric cancer (GC) is the fifth most common cancer worldwide, with yearly increasing incidence and the second-highest fatality rate in malignancies. Despite the contemporary ambiguous molecular mechanisms in GC pathogenesis, numerous in-depth studies have demonstrated that zinc finger proteins (ZFPs) are essential for the development and progression of GC. ZFPs are a class of transcription factors with finger-like domains that bind to Zn2+ extensively and participate in gene replication, cell differentiation and tumor development. In this review, we briefly outline the roles, molecular mechanisms and the latest advances in ZFPs in GC, including eight principal aspects, such as cell proliferation, epithelial-mesenchymal transition (EMT), invasion and metastasis, inflammation and immune infiltration, apoptosis, cell cycle, DNA methylation, cancer stem cells (CSCs) and drug resistance. Intriguingly, the myeloid zinc finger 1 (MZF1) possesses reversely dual roles in GC by promoting tumor proliferation or impeding cancer progression via apoptosis. Therefore, a thorough understanding of the molecular mechanism of ZFPs on GC progression will pave the solid way for screening the potentially effective diagnostic indicators, prognostic biomarkers and therapeutic targets of GC.
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Affiliation(s)
- Shujie Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xingzhu Liu
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Xin Lin
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
- Medical Department, Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College, Nanchang University, Nanchang 330006, China
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Splenic Torsion in Heterotaxy Syndrome with Left Isomerism: A Case Report and Literature Review. Diagnostics (Basel) 2022; 12:diagnostics12122920. [PMID: 36552927 PMCID: PMC9776906 DOI: 10.3390/diagnostics12122920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Splenic torsion is an unusual condition that results in congenital abnormality, especially in the visceral abnormal arrangement. We report the case of an 8.5-year-old boy with features in the right upper quadrant. Radiological investigations revealed heterotaxy syndrome with polysplenia and a hypodense tumor in the right upper quadrant adjacent to several spleens. We initially treated it as an intra-abdominal tumor. Laparoscopy was performed to check the tumor condition and revealed a congestive tumor located in the abdomen of the right upper quadrant below the central liver, which was suspected to be a torsion spleen without attaching ligaments. Laparoscopic splenectomy was successfully carried out without complications. The pathological report shows splenic tissue with hemorrhagic infarction. Physicians should be vigilant of the differential diagnosis of the acute abdomen in adolescents.
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Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. Human-gained heart enhancers are associated with species-specific cardiac attributes. NATURE CARDIOVASCULAR RESEARCH 2022; 1:830-843. [PMID: 36817700 PMCID: PMC9937543 DOI: 10.1038/s44161-022-00124-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.
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Affiliation(s)
- Eugin Destici
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fugui Zhu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaina Tran
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elie N. Farah
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Xiameng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivier B. Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Jonathan D. Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hong Sook Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Hu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neil C. Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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Soofi M, Alpert MA, Barbadora J, Mukerji B, Mukerji V. Human Laterality Disorders: Pathogenesis, Clinical Manifestations, Diagnosis, and Management. Am J Med Sci 2021; 362:233-242. [PMID: 34052215 DOI: 10.1016/j.amjms.2021.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/18/2021] [Accepted: 05/24/2021] [Indexed: 12/22/2022]
Abstract
Human laterality disorders comprise a group of diseases characterized by abnormal location (situs) and orientation of thoraco-abdominal organs and vessels across the left-right axis. Situs inversus totalis is mirror image reversal of thoraco-abdominal organs/great vessels. Situs ambiguus, better known as heterotaxy, is abnormal arrangement of thoraco-abdominal organs across the left-right axis excluding situs inversus totalis. Heterotaxy, also referred to as atrial or atrial appendage isomerism, is characterized by abnormal location of left-sided or right-sided organs with loss of asymmetry of normally paired asymmetric organs. It is associated with a variety of anomalies involving the heart, great vessels, lungs and intra-abdominal organs. Right and left atrial isomerism are associated with multiple complex congenital cardiac and vascular anomalies, many of which are lethal when untreated. Isomerism may also affect the lungs, spleen, liver, gall bladder, and intestines. Innovative surgical therapy of heterotaxy/isomerism has reduced early mortality and markedly improved long-term prognosis.
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Affiliation(s)
- Muhammad Soofi
- Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Martin A Alpert
- University of Missouri School of Medicine, Columbia, MO, USA.
| | | | - Basanti Mukerji
- Boonshoft School of Medicine, Wright State University, Dayton, OH, USA; Dayton VA Medical Center, Dayton, OH, USA
| | - Vaskar Mukerji
- Boonshoft School of Medicine, Wright State University, Dayton, OH, USA; Dayton VA Medical Center, Dayton, OH, USA; Kettering Medical Center, Kettering, OH, USA
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Pierpont ME, Brueckner M, Chung WK, Garg V, Lacro RV, McGuire AL, Mital S, Priest JR, Pu WT, Roberts A, Ware SM, Gelb BD, Russell MW. Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association. Circulation 2019; 138:e653-e711. [PMID: 30571578 DOI: 10.1161/cir.0000000000000606] [Citation(s) in RCA: 317] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review provides an updated summary of the state of our knowledge of the genetic contributions to the pathogenesis of congenital heart disease. Since 2007, when the initial American Heart Association scientific statement on the genetic basis of congenital heart disease was published, new genomic techniques have become widely available that have dramatically changed our understanding of the causes of congenital heart disease and, clinically, have allowed more accurate definition of the pathogeneses of congenital heart disease in patients of all ages and even prenatally. Information is presented on new molecular testing techniques and their application to congenital heart disease, both isolated and associated with other congenital anomalies or syndromes. Recent advances in the understanding of copy number variants, syndromes, RASopathies, and heterotaxy/ciliopathies are provided. Insights into new research with congenital heart disease models, including genetically manipulated animals such as mice, chicks, and zebrafish, as well as human induced pluripotent stem cell-based approaches are provided to allow an understanding of how future research breakthroughs for congenital heart disease are likely to happen. It is anticipated that this review will provide a large range of health care-related personnel, including pediatric cardiologists, pediatricians, adult cardiologists, thoracic surgeons, obstetricians, geneticists, genetic counselors, and other related clinicians, timely information on the genetic aspects of congenital heart disease. The objective is to provide a comprehensive basis for interdisciplinary care for those with congenital heart disease.
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8
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Role of Zic Family Proteins in Transcriptional Regulation and Chromatin Remodeling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:353-380. [DOI: 10.1007/978-981-10-7311-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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9
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Bellchambers HM, Ware SM. ZIC3 in Heterotaxy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:301-327. [PMID: 29442328 DOI: 10.1007/978-981-10-7311-3_15] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutation of ZIC3 causes X-linked heterotaxy, a syndrome in which the laterality of internal organs is disrupted. Analysis of model organisms and gene expression during early development suggests ZIC3-related heterotaxy occurs due to defects at the earliest stage of left-right axis formation. Although there are data to support abnormalities of the node and cilia as underlying causes, it is unclear at the molecular level why loss of ZIC3 function causes such these defects. ZIC3 has putative roles in a number of developmental signalling pathways that have distinct roles in establishing the left-right axis. This complicates the understanding of the mechanistic basis of Zic3 in early development and left-right patterning. Here we summarise our current understanding of ZIC3 function and describe the potential role ZIC3 plays in important signalling pathways and their links to heterotaxy.
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Affiliation(s)
- Helen M Bellchambers
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA. .,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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10
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Catana A, Apostu AP. The determination factors of left-right asymmetry disorders- a short review. ACTA ACUST UNITED AC 2017; 90:139-146. [PMID: 28559696 PMCID: PMC5433564 DOI: 10.15386/cjmed-701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/02/2016] [Accepted: 11/23/2016] [Indexed: 12/17/2022]
Abstract
Laterality defects in humans, situs inversus and heterotaxy, are rare disorders, with an incidence of 1:8000 to 1:10 000 in the general population, and a multifactorial etiology. It has been proved that 1.44/10 000 of all cardiac problems are associated with malformations of left-right asymmetry and heterotaxy accounts for 3% of all congenital heart defects. It is considered that defects of situs appear due to genetic and environmental factors. Also, there is evidence that the ciliopathies (defects of structure or function) are involved in development abnormalities. Over 100 genes have been reported to be involved in left-right patterning in model organisms, but only a few are likely to candidate for left-right asymmetry defects in humans. Left-right asymmetry disorders are genetically heterogeneous and have variable manifestations (from asymptomatic to serious clinical problems). The discovery of the right mechanism of left-right development will help explain the clinical complexity and may contribute to a therapy of these disorders.
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Affiliation(s)
- Andreea Catana
- Genetics Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adina Patricia Apostu
- Genetics Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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11
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Paulussen ADC, Steyls A, Vanoevelen J, van Tienen FHJ, Krapels IPC, Claes GRF, Chocron S, Velter C, Tan-Sindhunata GM, Lundin C, Valenzuela I, Nagy B, Bache I, Maroun LL, Avela K, Brunner HG, Smeets HJM, Bakkers J, van den Wijngaard A. Rare novel variants in the ZIC3 gene cause X-linked heterotaxy. Eur J Hum Genet 2016; 24:1783-1791. [PMID: 27406248 PMCID: PMC5117940 DOI: 10.1038/ejhg.2016.91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/25/2016] [Accepted: 05/20/2016] [Indexed: 02/08/2023] Open
Abstract
Variants in the ZIC3 gene are rare, but have demonstrated their profound clinical significance in X-linked heterotaxy, affecting in particular male patients with abnormal arrangement of thoracic and visceral organs. Several reports have shown relevance of ZIC3 gene variants in both familial and sporadic cases and with a predominance of mutations detected in zinc-finger domains. No studies so far have assessed the functional consequences of ZIC3 variants in an in vivo model organism. A study population of 348 patients collected over more than 10 years with a large variety of congenital heart disease including heterotaxy was screened for variants in the ZIC3 gene. Functional effects of three variants were assessed both in vitro and in vivo in the zebrafish. We identified six novel pathogenic variants (1,7%), all in either male patients with heterotaxy (n=5) or a female patient with multiple male deaths due to heterotaxy in the family (n=1). All variants were located within the zinc-finger domains or leading to a truncation before these domains. Truncating variants showed abnormal trafficking of mutated ZIC3 proteins, whereas the missense variant showed normal trafficking. Overexpression of wild-type and mutated ZIC protein in zebrafish showed full non-functionality of the two frame-shift variants and partial activity of the missense variant compared with wild-type, further underscoring the pathogenic character of these variants. Concluding, we greatly expanded the number of causative variants in ZIC3 and delineated the functional effects of three variants using in vitro and in vivo model systems.
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Affiliation(s)
- Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jo Vanoevelen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Florence HJ van Tienen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Godelieve RF Claes
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Chocron
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gita M Tan-Sindhunata
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Catarina Lundin
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Irene Valenzuela
- Department of Clinical Genetics and Cytogenetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Balint Nagy
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Leth Maroun
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hubert J M Smeets
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Bakkers
- Cardiac Development and Genetics, Hubrecht Institute-KNAW and University Medical Centre Utrecht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
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12
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Hilger AC, Halbritter J, Pennimpede T, van der Ven A, Sarma G, Braun DA, Porath JD, Kohl S, Hwang DY, Dworschak GC, Hermann BG, Pavlova A, El-Maarri O, Nöthen MM, Ludwig M, Reutter H, Hildebrandt F. Targeted Resequencing of 29 Candidate Genes and Mouse Expression Studies Implicate ZIC3 and FOXF1 in Human VATER/VACTERL Association. Hum Mutat 2015; 36:1150-4. [PMID: 26294094 DOI: 10.1002/humu.22859] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/06/2015] [Indexed: 01/14/2023]
Abstract
The VATER/VACTERL association describes the combination of congenital anomalies including vertebral defects, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal malformations, and limb defects. As mutations in ciliary genes were observed in diseases related to VATER/VACTERL, we performed targeted resequencing of 25 ciliary candidate genes as well as disease-associated genes (FOXF1, HOXD13, PTEN, ZIC3) in 123 patients with VATER/VACTERL or VATER/VACTERL-like phenotype. We detected no biallelic mutation in any of the 25 ciliary candidate genes; however, identified an identical, probably disease-causing ZIC3 missense mutation (p.Gly17Cys) in four patients and a FOXF1 de novo mutation (p.Gly220Cys) in a further patient. In situ hybridization analyses in mouse embryos between E9.5 and E14.5 revealed Zic3 expression in limb and prevertebral structures, and Foxf1 expression in esophageal, tracheal, vertebral, anal, and genital tubercle tissues, hence VATER/VACTERL organ systems. These data provide strong evidence that mutations in ZIC3 or FOXF1 contribute to VATER/VACTERL.
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Affiliation(s)
- Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Halbritter
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Internal Medicine, Division of Nephrology, University Clinic Leipzig, Leipzig, Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.,Division of Cancer Biology and Genetics, Queen's University, Kingston, Ontario, Canada
| | - Amelie van der Ven
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Georgia Sarma
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan D Porath
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stefan Kohl
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gabriel C Dworschak
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bernhard G Hermann
- Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Osman El-Maarri
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
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13
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Lopez KN, Marengo LK, Canfield MA, Belmont JW, Dickerson HA. Racial disparities in heterotaxy syndrome. ACTA ACUST UNITED AC 2015; 103:941-50. [PMID: 26333177 DOI: 10.1002/bdra.23416] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Heterotaxy syndrome (HTX) is a constellation of defects including abnormal organ lateralization and often including congenital heart defects. HTX has widely divergent population-based estimates of prevalence, racial and ethnic predominance, and mortality in current literature. METHODS The objective of this study was to use a population-based registry to investigate potential racial and ethnic disparities in HTX. Using the Texas Birth Defects Registry, we described clinical features and mortality of HTX among infants delivered from 1999 to 2006. We calculated birth prevalence and crude prevalence (cPR) ratios for infant sex, maternal diabetes, and sociodemographic factors. RESULTS A total of 353 HTX cases were identified from 2,993,604 births (prevalence ratio = 1.18 per 10,000 live births. HTX prevalence was approximately 70% higher among infants of Hispanic and non-Hispanic black mothers and 28% higher among female infants (cPR = 1.28; 95% confidence interval,1.04-1.59). There was a twofold higher female preponderance for infants of mothers who were non-Hispanic white or black. Mothers with diabetes were three times more likely to have a child with HTX compared with nondiabetics (cPR = 3.13; 95% confidence interval, 2.12-4.45). Among nondiabetics, HTX cases were 86% more likely to have a Hispanic mother and 72% a non-Hispanic black mother. First-year mortality for live born children with HTX was 30.9%. CONCLUSION This study represents one of the largest population-based studies of HTX to date, with a novel finding of higher rates of HTX among Hispanic infants of mostly Mexican origin, as well as among female infants of only non-Hispanic white and black mothers. These findings warrant further investigation.
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Affiliation(s)
| | - Lisa K Marengo
- Birth Defects Epidemiology and Surveillance Section, Texas Department of State Health Services, Austin, Texas
| | - Mark A Canfield
- Birth Defects Epidemiology and Surveillance Section, Texas Department of State Health Services, Austin, Texas
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14
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Cowan J, Tariq M, Ware SM. Genetic and functional analyses of ZIC3 variants in congenital heart disease. Hum Mutat 2014; 35:66-75. [PMID: 24123890 DOI: 10.1002/humu.22457] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/06/2013] [Accepted: 09/23/2013] [Indexed: 12/13/2022]
Abstract
Mutations in zinc-finger in cerebellum 3 (ZIC3) result in heterotaxy or isolated congenital heart disease (CHD). The majority of reported mutations cluster in zinc-finger domains. We previously demonstrated that many of these lead to aberrant ZIC3 subcellular trafficking. A relative paucity of N- and C-terminal mutations has, however, prevented similar analyses in these regions. Notably, an N-terminal polyalanine expansion was recently identified in a patient with VACTERL, suggesting a potentially distinct function for this domain. Here we report ZIC3 sequencing results from 440 unrelated patients with heterotaxy and CHD, the largest cohort yet examined. Variants were identified in 5.2% of sporadic male cases. This rate exceeds previous estimates of 1% and has important clinical implications for genetic testing and risk-based counseling. Eight of 11 were novel, including 5 N-terminal variants. Subsequent functional analyses included four additional reported but untested variants. Aberrant cytoplasmic localization and decreased luciferase transactivation were observed for all zinc-finger variants, but not for downstream or in-frame upstream variants, including both analyzed polyalanine expansions. Collectively, these results expand the ZIC3 mutational spectrum, support a higher than expected prevalence in sporadic cases, and suggest alternative functions for terminal mutations, highlighting a need for further study of these domains.
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15
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Haaning AM, Quinn ME, Ware SM. Heterotaxy-spectrum heart defects in Zic3 hypomorphic mice. Pediatr Res 2013; 74:494-502. [PMID: 23999067 PMCID: PMC4176930 DOI: 10.1038/pr.2013.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/08/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND Mutations in Zinc Finger Protein of the Cerebellum 3 (ZIC3) cause X-linked heterotaxy and isolated cardiovascular malformations. Recent data suggest a potential cell-autonomous role for Zic3 in myocardium via regulation of Nppa and Tbx5. We sought to develop a hypomorphic Zic3 mouse to model human heterotaxy and investigate developmental mechanisms underlying variability in cardiac phenotypes. METHODS Zic3 hypomorphic mice were created by targeted insertion of a neomycin cassette and investigated by gross, histologic, and molecular methods. RESULTS Low-level Zic3 expression is sufficient for partial rescue of viability as compared with Zic3 null mice. Concordance of early left-right molecular marker abnormalities and later anatomic abnormalities suggests that the primary effect of Zic3 in heart development occurs during left-right patterning. Cardiac-specific gene expression of Nppa (atrial natriuretic factor) and Tbx5 marked the proper morphological locations in the heart regardless of looping abnormalities. CONCLUSION Zic3 hypomorphic mice are useful models to investigate the variable cardiac defects resulting from a single genetic defect. Low-level Zic3 expression rescues the left pulmonary isomerism identified in Zic3 null embryos. Our data do not support a direct role for Zic3 in the myocardium via regulation of Nppa and Tbx5 and suggest that the primary effect of Zic3 on cardiac development occurs during left-right patterning.
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Affiliation(s)
- Allison M. Haaning
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
| | - Malgorzata E. Quinn
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
| | - Stephanie M. Ware
- Cincinnati Children’s Hospital Medical Center, Division of Molecular Cardiovascular Biology, Cincinnati, OH
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16
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Houtmeyers R, Souopgui J, Tejpar S, Arkell R. The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis. Cell Mol Life Sci 2013; 70:3791-811. [PMID: 23443491 PMCID: PMC11113920 DOI: 10.1007/s00018-013-1285-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 01/16/2013] [Accepted: 01/28/2013] [Indexed: 12/18/2022]
Abstract
The zinc finger of the cerebellum gene (ZIC) discovered in Drosophila melanogaster (odd-paired) has five homologs in Xenopus, chicken, mice, and humans, and seven in zebrafish. This pattern of gene copy expansion is accompanied by a divergence in gene and protein structure, suggesting that Zic family members share some, but not all, functions. ZIC genes are implicated in neuroectodermal development and neural crest cell induction. All share conserved regions encoding zinc finger domains, however their heterogeneity and specification remain unexplained. In this review, the evolution, structure, and expression patterns of the ZIC homologs are described; specific functions attributable to individual family members are supported. A review of data from functional studies in Xenopus and murine models suggest that ZIC genes encode multifunctional proteins operating in a context-specific manner to drive critical events during embryogenesis. The identification of ZIC mutations in congenital syndromes highlights the relevance of these genes in human development.
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Affiliation(s)
- Rob Houtmeyers
- Department of Oncology, Katholieke Universiteit Leuven, O&N1, 3000, Leuven, Belgium,
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17
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Ware SM, Jefferies JL. New Genetic Insights into Congenital Heart Disease. JOURNAL OF CLINICAL & EXPERIMENTAL CARDIOLOGY 2012; S8:003. [PMID: 22822471 PMCID: PMC3401115 DOI: 10.4172/2155-9880.s8-003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There has been remarkable progress in understanding the genetic basis of cardiovascular malformations. Chromosome microarray analysis has provided a new tool to understand the genetic basis of syndromic cardiovascular malformations resulting from microdeletion or microduplication of genetic material, allowing the delineation of new syndromes. Improvements in sequencing technology have led to increasingly comprehensive testing for aortopathy, cardiomyopathy, single gene syndromic disorders, and Mendelian-inherited congenital heart disease. Understanding the genetic etiology for these disorders has improved their clinical recognition and management and led to new guidelines for treatment and family-based diagnosis and surveillance. These new discoveries have also expanded our understanding of the contribution of genetic variation, susceptibility alleles, and epigenetics to isolated congenital heart disease. This review summarizes the current understanding of the genetic basis of syndromic and non-syndromic congenital heart disease and highlights new diagnostic and management recommendations.
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Affiliation(s)
- Stephanie M. Ware
- The Heart Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, MLC 7020, Cincinnati, OH 45229-3039, USA
| | - John Lynn Jefferies
- The Heart Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, MLC 7020, Cincinnati, OH 45229-3039, USA
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18
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Abstract
Congenital heart disease is a major cause of morbidity and mortality throughout life. Mutations in numerous transcription factors have been identified in patients and families with some of the most common forms of cardiac malformations and arrhythmias. This review discusses transcription factor pathways known to be important for normal heart development and how abnormalities in these pathways have been linked to morphological and functional forms of congenital heart defects. A comprehensive, current list of known transcription factor mutations associated with congenital heart disease is provided, but the review focuses primarily on three key transcription factors, Nkx2-5, GATA4, and Tbx5, and their known biochemical and genetic partners. By understanding the interaction partners, transcriptional targets, and upstream activators of these core cardiac transcription factors, additional information about normal heart formation and further insight into genes and pathways affected in congenital heart disease should result.
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Affiliation(s)
- David J McCulley
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
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