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Shen J, Shentu J, Zhong C, Huang Q, Duan S. RNA splicing factor RBFOX2 is a key factor in the progression of cancer and cardiomyopathy. Clin Transl Med 2024; 14:e1788. [PMID: 39243148 PMCID: PMC11380049 DOI: 10.1002/ctm2.1788] [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: 04/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Alternative splicing of pre-mRNA is a fundamental regulatory process in multicellular eukaryotes, significantly contributing to the diversification of the human proteome. RNA-binding fox-1 homologue 2 (RBFOX2), a member of the evolutionarily conserved RBFOX family, has emerged as a critical splicing regulator, playing a pivotal role in the alternative splicing of pre-mRNA. This review provides a comprehensive analysis of RBFOX2, elucidating its splicing activity through direct and indirect binding mechanisms. RBFOX2 exerts substantial influence over the alternative splicing of numerous transcripts, thereby shaping essential cellular processes such as differentiation and development. MAIN BODY OF THE ABSTRACT Dysregulation of RBFOX2-mediated alternative splicing has been closely linked to a spectrum of cardiovascular diseases and malignant tumours, underscoring its potential as a therapeutic target. Despite significant progress, current research faces notable challenges. The complete structural characterisation of RBFOX2 remains elusive, limiting in-depth exploration beyond its RNA-recognition motif. Furthermore, the scarcity of studies focusing on RBFOX2-targeting drugs poses a hindrance to translating research findings into clinical applications. CONCLUSION This review critically assesses the existing body of knowledge on RBFOX2, highlighting research gaps and limitations. By delineating these areas, this analysis not only serves as a foundational reference for future studies but also provides strategic insights for bridging these gaps. Addressing these challenges will be instrumental in unlocking the full therapeutic potential of RBFOX2, paving the way for innovative and effective treatments in various diseases.
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Affiliation(s)
- Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jianqiao Shentu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Chenming Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, China
| | - Qiankai Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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2
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McKean DM, Zhang Q, Narayan P, Morton SU, Strohmenger V, Tang VT, McAllister S, Sharma A, Quiat D, Reichart D, DeLaughter DM, Wakimoto H, Gorham JM, Brown K, McDonough B, Willcox JA, Jang MY, DePalma SR, Ward T, Kim R, Cleveland JD, Seidman J, Seidman CE. Increased endothelial sclerostin caused by elevated DSCAM mediates multiple trisomy 21 phenotypes. J Clin Invest 2024; 134:e167811. [PMID: 38828726 PMCID: PMC11142749 DOI: 10.1172/jci167811] [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: 12/06/2022] [Accepted: 04/11/2024] [Indexed: 06/05/2024] Open
Abstract
Trisomy 21 (T21), a recurrent aneuploidy occurring in 1:800 births, predisposes to congenital heart disease (CHD) and multiple extracardiac phenotypes. Despite a definitive genetic etiology, the mechanisms by which T21 perturbs development and homeostasis remain poorly understood. We compared the transcriptome of CHD tissues from 49 patients with T21 and 226 with euploid CHD (eCHD). We resolved cell lineages that misexpressed T21 transcripts by cardiac single-nucleus RNA sequencing and RNA in situ hybridization. Compared with eCHD samples, T21 samples had increased chr21 gene expression; 11-fold-greater levels (P = 1.2 × 10-8) of SOST (chr17), encoding the Wnt inhibitor sclerostin; and 1.4-fold-higher levels (P = 8.7 × 10-8) of the SOST transcriptional activator ZNF467 (chr7). Euploid and T21 cardiac endothelial cells coexpressed SOST and ZNF467; however, T21 endothelial cells expressed 6.9-fold more SOST than euploid endothelial cells (P = 2.7 × 10-27). Wnt pathway genes were downregulated in T21 endothelial cells. Expression of DSCAM, residing within the chr21 CHD critical region, correlated with SOST (P = 1.9 × 10-5) and ZNF467 (P = 2.9 × 10-4). Deletion of DSCAM from T21 endothelial cells derived from human induced pluripotent stem cells diminished sclerostin secretion. As Wnt signaling is critical for atrioventricular canal formation, bone health, and pulmonary vascular homeostasis, we concluded that T21-mediated increased sclerostin levels would inappropriately inhibit Wnt activities and promote Down syndrome phenotypes. These findings imply therapeutic potential for anti-sclerostin antibodies in T21.
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Affiliation(s)
- David M. McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Priyanka Narayan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Walter Brendle Centre of Experimental Medicine, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Vi T. Tang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sophie McAllister
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ananya Sharma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Barbara McDonough
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jon A. Willcox
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven R. DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Richard Kim
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - John D. Cleveland
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - J.G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
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3
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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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4
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Lu YW, Liang Z, Guo H, Fernandes T, Espinoza-Lewis RA, Wang T, Li K, Li X, Singh GB, Wang Y, Cowan D, Mably JD, Philpott CC, Chen H, Wang DZ. PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.540420. [PMID: 37293078 PMCID: PMC10245752 DOI: 10.1101/2023.05.18.540420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alanyl-transfer RNA synthetase 2 (AARS2) is a nuclear encoded mitochondrial tRNA synthetase that is responsible for charging of tRNA-Ala with alanine during mitochondrial translation. Homozygous or compound heterozygous mutations in the Aars2 gene, including those affecting its splicing, are linked to infantile cardiomyopathy in humans. However, how Aars2 regulates heart development, and the underlying molecular mechanism of heart disease remains unknown. Here, we found that poly(rC) binding protein 1 (PCBP1) interacts with the Aars2 transcript to mediate its alternative splicing and is critical for the expression and function of Aars2. Cardiomyocyte-specific deletion of Pcbp1 in mice resulted in defects in heart development that are reminiscent of human congenital cardiac defects, including noncompaction cardiomyopathy and a disruption of the cardiomyocyte maturation trajectory. Loss of Pcbp1 led to an aberrant alternative splicing and a premature termination of Aars2 in cardiomyocytes. Additionally, Aars2 mutant mice with exon-16 skipping recapitulated heart developmental defects observed in Pcbp1 mutant mice. Mechanistically, we found dysregulated gene and protein expression of the oxidative phosphorylation pathway in both Pcbp1 and Aars2 mutant hearts; these date provide further evidence that the infantile hypertrophic cardiomyopathy associated with the disorder oxidative phosphorylation defect type 8 (COXPD8) is mediated by Aars2. Our study therefore identifies Pcbp1 and Aars2 as critical regulators of heart development and provides important molecular insights into the role of disruptions in metabolism on congenital heart defects.
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Øyen N, Boyd HA, Carstensen L, Søndergaard L, Wohlfahrt J, Melbye M. Risk of Congenital Heart Defects in Offspring of Affected Mothers and Fathers. Circ Genom Precis Med 2022; 15:e003533. [PMID: 35608601 PMCID: PMC9384828 DOI: 10.1161/circgen.121.003533] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
Smaller studies have reported a higher offspring risk of congenital heart defects (CHDs) for mothers with CHDs than for fathers with CHDs. In a large population-based study, we investigated whether offspring risk of CHD differed for mothers and fathers with CHDs.
Methods:
All people born in Denmark, 1977 to 2011, with at least 1 registered parent, were included in our cohort (n=2 341 061). Parent-child recurrence of CHDs was evaluated using risk ratios (RRs) comparing risks of CHDs in individuals with and without a parent with a CHD, estimated using log-linear binomial regression.
Results:
The RRs for any CHD in offspring were 5.39 (95% CI, 4.88–5.96) for mothers and 3.04 (95% CI, 2.59–3.57) for fathers affected with any CHD; the ratio of RRs for mothers versus fathers was 1.82 (
P
<0.0001). Recurrence RRs for the same cardiac phenotype in parent and offspring were significantly stronger for mothers than for fathers for conotruncal defects (ratio of RRs, 4.98), left ventricular outlet tract obstruction (ratio of RRs, 4.98), and ventricular septal defects (ratio of RRs, 2.51) but not for atrioventricular septal defects (ratio of RRs, 1.06). Birth rates among people with CHDs, relative to the general population, were 18% higher for women than for men, regardless of parental cardiac phenotype.
Conclusions:
Recurrence risks of CHDs were significantly greater in the offspring of affected women than in the offspring of affected men. The excess maternal recurrence risks could not be explained by the slightly higher birth rates in women with CHDs.
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Affiliation(s)
- Nina Øyen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark (N.Ø., H.A.B., L.C., J.W.)
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Norway (N.Ø.)
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway (N.Ø.)
| | - Heather A. Boyd
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark (N.Ø., H.A.B., L.C., J.W.)
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark (N.Ø., H.A.B., L.C., J.W.)
| | - Lars Søndergaard
- Department of Cardiology (L.S.), University of Copenhagen, Denmark
| | - Jan Wohlfahrt
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark (N.Ø., H.A.B., L.C., J.W.)
| | - Mads Melbye
- Department of Clinical Medicine (M.M.), University of Copenhagen, Denmark
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo (M.M.)
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway (M.M.)
- Department of Genetics, Stanford University School of Medicine, Stanford, CA (M.M.)
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6
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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7
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Rbfox1 expression in amacrine cells is restricted to GABAergic and VGlut3 glycinergic cells. Biosci Rep 2022; 42:231460. [PMID: 35730583 PMCID: PMC9272594 DOI: 10.1042/bsr20220497] [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: 03/07/2022] [Revised: 05/20/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Rbfox1 is a multifunctional RNA binding protein that regulates alternative splicing, transcription, mRNA stability and translation. Rbfox1 is an important regulator of gene networks involved in neurogenesis and neuronal function. Disruption of Rbfox function has been associated with several neurodevelopmental and neuropsychiatric disorders. We have shown earlier that Rbfox1 is expressed in retinal ganglion and amacrine cells (ACs) and that its downregulation in adult mouse retinas leads to deficiency of depth perception. In this study, we used several markers of ACs, including GABA, choline acetyltransferase (ChAT), neuropeptide Y (NPY), glycine transporter (GlyT1) and vesicular glutamate transporter 3 (VGlut3) to identify types of ACs that express Rbfox1. Expression of Rbfox1 was observed predominantly in GABAergic ACs located in the INL and GCL. All GABAergic/cholinergic starburst ACs and virtually all NPY-positive GABAergic ACs were also Rbfox1-positive. Among glycinergic ACs, a sparse population of Rbfox1/VGlut3-positive cells was identified, indicating that Rbfox1 is expressed in a very small population of glycinergic ACs. These data contributes to our understanding about molecular differences between various types of amacrine cells and the cell-specific gene networks regulated by Rbfox1.
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8
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Harwood MP, Alves I, Edgington H, Agbessi M, Bruat V, Soave D, Lamaze FC, Favé MJ, Awadalla P. Recombination affects allele-specific expression of deleterious variants in human populations. SCIENCE ADVANCES 2022; 8:eabl3819. [PMID: 35559670 PMCID: PMC9106294 DOI: 10.1126/sciadv.abl3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
How the genetic composition of a population changes through stochastic processes, such as genetic drift, in combination with deterministic processes, such as selection, is critical to understanding how phenotypes vary in space and time. Here, we show how evolutionary forces affecting selection, including recombination and effective population size, drive genomic patterns of allele-specific expression (ASE). Integrating tissue-specific genotypic and transcriptomic data from 1500 individuals from two different cohorts, we demonstrate that ASE is less often observed in regions of low recombination, and loci in high or normal recombination regions are more efficient at using ASE to underexpress harmful mutations. By tracking genetic ancestry, we discriminate between ASE variability due to past demographic effects, including subsequent bottlenecks, versus local environment. We observe that ASE is not randomly distributed along the genome and that population parameters influencing the efficacy of natural selection alter ASE levels genome wide.
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Affiliation(s)
- Michelle P. Harwood
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Isabel Alves
- Université de Nantes, CHU Nantes, CNRS, INSERM, L’Institut du thorax, F-44000 Nantes, France
| | | | | | - Vanessa Bruat
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Mathematics, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Fabien C. Lamaze
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, QC, Canada
| | | | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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9
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Willcox JAL, Geiger JT, Morton SU, McKean D, Quiat D, Gorham JM, Tai AC, DePalma S, Bernstein D, Brueckner M, Chung WK, Giardini A, Goldmuntz E, Kaltman JR, Kim R, Newburger JW, Shen Y, Srivastava D, Tristani-Firouzi M, Gelb B, Porter GA, Seidman JG, Seidman CE. Neither cardiac mitochondrial DNA variation nor copy number contribute to congenital heart disease risk. Am J Hum Genet 2022; 109:961-966. [PMID: 35397206 PMCID: PMC9118105 DOI: 10.1016/j.ajhg.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
The well-established manifestation of mitochondrial mutations in functional cardiac disease (e.g., mitochondrial cardiomyopathy) prompted the hypothesis that mitochondrial DNA (mtDNA) sequence and/or copy number (mtDNAcn) variation contribute to cardiac defects in congenital heart disease (CHD). MtDNAcns were calculated and rare, non-synonymous mtDNA mutations were identified in 1,837 CHD-affected proband-parent trios, 116 CHD-affected singletons, and 114 paired cardiovascular tissue/blood samples. The variant allele fraction (VAF) of heteroplasmic variants in mitochondrial RNA from 257 CHD cardiovascular tissue samples was also calculated. On average, mtDNA from blood had 0.14 rare variants and 52.9 mtDNA copies per nuclear genome per proband. No variation with parental age at proband birth or CHD-affected proband age was seen. mtDNAcns in valve/vessel tissue (320 ± 70) were lower than in atrial tissue (1,080 ± 320, p = 6.8E-21), which were lower than in ventricle tissue (1,340 ± 280, p = 1.4E-4). The frequency of rare variants in CHD-affected individual DNA was indistinguishable from the frequency in an unaffected cohort, and proband mtDNAcns did not vary from those of CHD cohort parents. In both the CHD and the comparison cohorts, mtDNAcns were significantly correlated between mother-child, father-child, and mother-father. mtDNAcns among people with European (mean = 52.0), African (53.0), and Asian haplogroups (53.5) were calculated and were significantly different for European and Asian haplogroups (p = 2.6E-3). Variant heteroplasmic fraction (HF) in blood correlated well with paired cardiovascular tissue HF (r = 0.975) and RNA VAF (r = 0.953), which suggests blood HF is a reasonable proxy for HF in heart tissue. We conclude that mtDNA mutations and mtDNAcns are unlikely to contribute significantly to CHD risk.
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Affiliation(s)
- Jon A L Willcox
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua T Geiger
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Quiat
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Angela C Tai
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven DePalma
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Martina Brueckner
- Departments of Genetics and Pediatric Cardiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10019, USA
| | - Alessandro Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD 20892, USA
| | - Richard Kim
- Cardiothoracic Surgery, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10019, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Bruce Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiology, Brigham and Women's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard University, Boston, MA 02138, USA
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10
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Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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11
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Verma SK, Deshmukh V, Thatcher K, Belanger KK, Rhyner A, Meng S, Holcomb R, Bressan M, Martin J, Cooke J, Wythe J, Widen S, Lincoln J, Kuyumcu-Martinez M. RBFOX2 is required for establishing RNA regulatory networks essential for heart development. Nucleic Acids Res 2022; 50:2270-2286. [PMID: 35137168 PMCID: PMC8881802 DOI: 10.1093/nar/gkac055] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
Human genetic studies identified a strong association between loss of function mutations in RBFOX2 and hypoplastic left heart syndrome (HLHS). There are currently no Rbfox2 mouse models that recapitulate HLHS. Therefore, it is still unknown how RBFOX2 as an RNA binding protein contributes to heart development. To address this, we conditionally deleted Rbfox2 in embryonic mouse hearts and found profound defects in cardiac chamber and yolk sac vasculature formation. Importantly, our Rbfox2 conditional knockout mouse model recapitulated several molecular and phenotypic features of HLHS. To determine the molecular drivers of these cardiac defects, we performed RNA-sequencing in Rbfox2 mutant hearts and identified dysregulated alternative splicing (AS) networks that affect cell adhesion to extracellular matrix (ECM) mediated by Rho GTPases. We identified two Rho GTPase cycling genes as targets of RBFOX2. Modulating AS of these two genes using antisense oligos led to cell cycle and cell-ECM adhesion defects. Consistently, Rbfox2 mutant hearts displayed cell cycle defects and inability to undergo endocardial-mesenchymal transition, processes dependent on cell-ECM adhesion and that are seen in HLHS. Overall, our work not only revealed that loss of Rbfox2 leads to heart development defects resembling HLHS, but also identified RBFOX2-regulated AS networks that influence cell-ECM communication vital for heart development.
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Affiliation(s)
- Sunil K Verma
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vaibhav Deshmukh
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kaitlyn Thatcher
- Department of Pediatrics, Medical College of Wisconsin, Division of Pediatric Cardiology, The Herma Heart Institute, Children's WI, Milwaukee, WI 53226, USA
| | - KarryAnne K Belanger
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexander M Rhyner
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shu Meng
- Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX 77030, USA
| | - Richard Joshua Holcomb
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael Bressan
- Department of Cell Biology and Physiology, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
- Cardiomyocyte Renewal Lab;Texas Heart Institute, Houston, TX77030, USA
| | - John P Cooke
- Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX 77030, USA
| | - Joshua D Wythe
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
- Cardiomyocyte Renewal Lab;Texas Heart Institute, Houston, TX77030, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joy Lincoln
- Department of Pediatrics, Medical College of Wisconsin, Division of Pediatric Cardiology, The Herma Heart Institute, Children's WI, Milwaukee, WI 53226, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology and Anatomy, Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd. Galveston, TX 77555, USA
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12
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Morton SU, Quiat D, Seidman JG, Seidman CE. Genomic frontiers in congenital heart disease. Nat Rev Cardiol 2022; 19:26-42. [PMID: 34272501 PMCID: PMC9236191 DOI: 10.1038/s41569-021-00587-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The application of next-generation sequencing to study congenital heart disease (CHD) is increasingly providing new insights into the causes and mechanisms of this prevalent birth anomaly. Whole-exome sequencing analysis identifies damaging gene variants altering single or contiguous nucleotides that are assigned pathogenicity based on statistical analyses of families and cohorts with CHD, high expression in the developing heart and depletion of damaging protein-coding variants in the general population. Gene classes fulfilling these criteria are enriched in patients with CHD and extracardiac abnormalities, evidencing shared pathways in organogenesis. Developmental single-cell transcriptomic data demonstrate the expression of CHD-associated genes in particular cell lineages, and emerging insights indicate that genetic variants perturb multicellular interactions that are crucial for cardiogenesis. Whole-genome sequencing analyses extend these observations, identifying non-coding variants that influence the expression of genes associated with CHD and contribute to the estimated ~55% of unexplained cases of CHD. These approaches combined with the assessment of common and mosaic genetic variants have provided a more complete knowledge of the causes and mechanisms of CHD. Such advances provide knowledge to inform the clinical care of patients with CHD or other birth defects and deepen our understanding of the complexity of human development. In this Review, we highlight known and candidate CHD-associated human genes and discuss how the integration of advances in developmental biology research can provide new insights into the genetic contributions to CHD.
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Affiliation(s)
- Sarah U. Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard University, Boston, MA, USA.,
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13
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Xie Y, Li M, Dong W, Jiang W, Zhao H. M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits. PLoS Genet 2021; 17:e1009849. [PMID: 34735430 PMCID: PMC8568192 DOI: 10.1371/journal.pgen.1009849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have demonstrated that multiple early-onset diseases have shared risk genes, based on findings from de novo mutations (DNMs). Therefore, we may leverage information from one trait to improve statistical power to identify genes for another trait. However, there are few methods that can jointly analyze DNMs from multiple traits. In this study, we develop a framework called M-DATA (Multi-trait framework for De novo mutation Association Test with Annotations) to increase the statistical power of association analysis by integrating data from multiple correlated traits and their functional annotations. Using the number of DNMs from multiple diseases, we develop a method based on an Expectation-Maximization algorithm to both infer the degree of association between two diseases as well as to estimate the gene association probability for each disease. We apply our method to a case study of jointly analyzing data from congenital heart disease (CHD) and autism. Our method was able to identify 23 genes for CHD from joint analysis, including 12 novel genes, which is substantially more than single-trait analysis, leading to novel insights into CHD disease etiology.
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Affiliation(s)
- Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mo Li
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Wei Jiang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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14
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Yasuhara J, Garg V. Genetics of congenital heart disease: a narrative review of recent advances and clinical implications. Transl Pediatr 2021; 10:2366-2386. [PMID: 34733677 PMCID: PMC8506053 DOI: 10.21037/tp-21-297] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Congenital heart disease (CHD) is the most common human birth defect and remains a leading cause of mortality in childhood. Although advances in clinical management have improved the survival of children with CHD, adult survivors commonly experience cardiac and non-cardiac comorbidities, which affect quality of life and prognosis. Therefore, the elucidation of genetic etiologies of CHD not only has important clinical implications for genetic counseling of patients and families but may also impact clinical outcomes by identifying at-risk patients. Recent advancements in genetic technologies, including massively parallel sequencing, have allowed for the discovery of new genetic etiologies for CHD. Although variant prioritization and interpretation of pathogenicity remain challenges in the field of CHD genomics, advances in single-cell genomics and functional genomics using cellular and animal models of CHD have the potential to provide novel insights into the underlying mechanisms of CHD and its associated morbidities. In this review, we provide an updated summary of the established genetic contributors to CHD and discuss recent advances in our understanding of the genetic architecture of CHD along with current challenges with the interpretation of genetic variation. Furthermore, we highlight the clinical implications of genetic findings to predict and potentially improve clinical outcomes in patients with CHD.
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Affiliation(s)
- Jun Yasuhara
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
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15
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Wu B, Li N, Deng Z, Luo F, Duan Y. Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms. FRONTIERS IN PLANT SCIENCE 2021; 12:739108. [PMID: 34531892 PMCID: PMC8438139 DOI: 10.3389/fpls.2021.739108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/04/2021] [Indexed: 06/01/2023]
Abstract
The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny "mutants" (T). The results showed W, TL, and T varied in gene expression, allelic expression, and alternative splicing. Most genes/pathways with significantly altered expression in TL compared to W remained similarly altered in T. Pathway and gene ontology enrichment analysis revealed that the expression of multiple pathways, including photosynthesis and cell wall biosynthesis, was altered among the three genotypes. Remarkably, two polar auxin transporter genes, PIN7 and LAX3, were expressed at a significantly lower level in TL than in both W and T, implying alternation of polar auxin transport in TL may be responsible for the vigorous growth and thornless phenotype. Furthermore, 131 and 68 plant defense-related genes were significantly upregulated and downregulated, respectively, in TL and T compared with W. These genes may be involved in enhanced salicylic acid (SA) dependent defense and repression of defense inducing callose deposition and programmed cell death. Overall, these results indicated that the phenotype changes of the TL bud-sport were associated with tremendous transcriptome alterations, providing new clues and targets for breeding and gene editing for citrus improvement.
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Affiliation(s)
- Bo Wu
- School of Computing, Clemson University, Clemson, SC, United States
| | - Na Li
- United States Department of Agriculture-Agriculture Research Service-United States Horticultural Research Laboratory, Fort Pierce, FL, United States
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, United States
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Yongping Duan
- United States Department of Agriculture-Agriculture Research Service-United States Horticultural Research Laboratory, Fort Pierce, FL, United States
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16
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Cao J, Routh AL, Kuyumcu-Martinez MN. Nanopore sequencing reveals full-length Tropomyosin 1 isoforms and their regulation by RNA-binding proteins during rat heart development. J Cell Mol Med 2021; 25:8352-8362. [PMID: 34302435 PMCID: PMC8419188 DOI: 10.1111/jcmm.16795] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) contributes to the diversity of the proteome by producing multiple isoforms from a single gene. Although short‐read RNA‐sequencing methods have been the gold standard for determining AS patterns of genes, they have a difficulty in defining full‐length mRNA isoforms assembled using different exon combinations. Tropomyosin 1 (TPM1) is an actin‐binding protein required for cytoskeletal functions in non‐muscle cells and for contraction in muscle cells. Tpm1 undergoes AS regulation to generate muscle versus non‐muscle TPM1 protein isoforms with distinct physiological functions. It is unclear which full‐length Tpm1 isoforms are produced via AS and how they are regulated during heart development. To address these, we utilized nanopore long‐read cDNA sequencing without gene‐specific PCR amplification. In rat hearts, we identified full‐length Tpm1 isoforms composed of distinct exons with specific exon linkages. We showed that Tpm1 undergoes AS transitions during embryonic heart development such that muscle‐specific exons are connected generating predominantly muscle‐specific Tpm1 isoforms in adult hearts. We found that the RNA‐binding protein RBFOX2 controls AS of rat Tpm1 exon 6a, which is important for cooperative actin binding. Furthermore, RBFOX2 regulates Tpm1 AS of exon 6a antagonistically to the RNA‐binding protein PTBP1. In sum, we defined full‐length Tpm1 isoforms with different exon combinations that are tightly regulated during cardiac development and provided insights into the regulation of Tpm1 AS by RNA‐binding proteins. Our results demonstrate that nanopore sequencing is an excellent tool to determine full‐length AS variants of muscle‐enriched genes.
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Affiliation(s)
- Jun Cao
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA.,Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, Texas, USA
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17
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Abstract
Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.
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Affiliation(s)
- Siobhan Cleary
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
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18
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Gu L, Kwong JM, Caprioli J, Piri N. Loss of Rbfox1 Does Not Affect Survival of Retinal Ganglion Cells Injured by Optic Nerve Crush. Front Neurosci 2021; 15:687690. [PMID: 34108862 PMCID: PMC8180555 DOI: 10.3389/fnins.2021.687690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Rbfox1 is a multifunctional RNA binding protein that regulates alternative splicing, transcription, mRNA stability and translation. Its roles in neurogenesis and neuronal functions are well established. Recent studies also implicate Rbfox1 in the regulation of gene networks that support cell survival during stress. We have earlier characterized the expression of Rbfox1 in amacrine and retinal ganglion cells (RGCs) and showed that deletion of Rbfox1 in adult animals results in depth perception deficiency. The current study investigates the effect of Rbfox1 downregulation on survival of RGCs injured by optic nerve crush (ONC). Seven days after ONC, animals sustained severe degeneration of RGC axons in the optic nerve and significant loss of RGC somas. Semi-quantitative grading of optic nerve damage in control + ONC, control + tamoxifen + ONC, and Rbfox1 -/- + ONC groups ranged from 4.6 to 4.8 on a scale of 1 (normal; no degenerated axons were noted) to 5 (total degeneration; all axons showed degenerated organelles, axonal content, and myelin sheath), indicating a severe degeneration. Among these three ONC groups, no statistical significance was observed when any two groups were compared. The number of RGC somas were quantitatively analyzed in superior, inferior, nasal and temporal retinal quadrants at 0.5, 1, and 1.5 mm from the center of the optic disc. The average RGC densities (cells/mm2) were: control 6,438 ± 1,203; control + ONC 2,779 ± 573; control + tamoxifen 6,163 ± 861; control + tamoxifen + ONC 2,573 ± 555; Rbfox1 -/- 6,437 ± 893; and Rbfox1 -/- + ONC 2,537 ± 526. The RGC loss in control + ONC, control + tamoxifen + ONC and Rbfox1 -/- + ONC was 57% (P = 1.44954E-42), 58% (P = 1.37543E-57) and 61% (P = 5.552E-59) compared to RGC numbers in the relevant uninjured groups, respectively. No statistically significant difference was observed between any two groups of uninjured animals or between any two ONC groups. Our data indicate that Rbfox1-mediated pathways have no effect on survival of RGCs injured by ONC.
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Affiliation(s)
- Lei Gu
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jacky M Kwong
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Joseph Caprioli
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Natik Piri
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States.,Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
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19
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Cashman TJ, Trivedi CM. N-Acetyl Transferases: New Insights Into Human Congenital Cardiovascular Defects. Circ Res 2021; 128:1170-1172. [PMID: 33856919 DOI: 10.1161/circresaha.121.319049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Timothy J Cashman
- Division of Cardiovascular Medicine (T.J.C., C.M.T.), University of Massachusetts Medical School, Worcester.,Department of Medicine (T.J.C., C.M.T.), University of Massachusetts Medical School, Worcester
| | - Chinmay M Trivedi
- Division of Cardiovascular Medicine (T.J.C., C.M.T.), University of Massachusetts Medical School, Worcester.,Department of Medicine (T.J.C., C.M.T.), University of Massachusetts Medical School, Worcester.,Department of Molecular, Cell, and Cancer Biology (C.M.T.), University of Massachusetts Medical School, Worcester
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20
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Abstract
Congenital heart disease is the most common congenital defect observed in newborns. Within the spectrum of congenital heart disease are left‐sided obstructive lesions (LSOLs), which include hypoplastic left heart syndrome, aortic stenosis, bicuspid aortic valve, coarctation of the aorta, and interrupted aortic arch. These defects can arise in isolation or as a component of a defined syndrome; however, nonsyndromic defects are often observed in multiple family members and associated with high sibling recurrence risk. This clear evidence for a heritable basis has driven a lengthy search for disease‐causing variants that has uncovered both rare and common variants in genes that, when perturbed in cardiac development, can result in LSOLs. Despite advancements in genetic sequencing platforms and broadening use of exome sequencing, the currently accepted LSOL‐associated genes explain only 10% to 20% of patients. Further, the combinatorial effects of common and rare variants as a cause of LSOLs are emerging. In this review, we highlight the genes and variants associated with the different LSOLs and discuss the strengths and weaknesses of the present genetic associations. Furthermore, we discuss the research avenues needed to bridge the gaps in our current understanding of the genetic basis of nonsyndromic congenital heart disease.
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Affiliation(s)
- Lauren E Parker
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC
| | - Andrew P Landstrom
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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21
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Ma Z, Shen Z, Gong Y, Zhou J, Chen X, Lv Q, Wang M, Chen J, Yu M, Fu G, He H, Lai D. Weighted gene co-expression network analysis identified underlying hub genes and mechanisms in the occurrence and development of viral myocarditis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1348. [PMID: 33313093 PMCID: PMC7723587 DOI: 10.21037/atm-20-3337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Myocarditis is an inflammatory myocardial disease, which may lead to heart failure and sudden death. Despite extensive research into the pathogenesis of myocarditis, effective treatments for this condition remain elusive. This study aimed to explore the potential pathogenesis and hub genes for viral myocarditis. Methods A weighted gene co-expression network analysis (WGCNA) was performed based on the gene expression profiles derived from mouse models at different stages of viral myocarditis (GSE35182). Functional annotation was executed within the key modules. Potential hub genes were predicted based on the intramodular connectivity (IC). Finally, potential microRNAs that regulate gene expression were predicted by miRNet analysis. Results Three gene co-expression modules showed the strongest correlation with the acute or chronic disease stage. A significant positive correlation was detected between the acute disease stage and the turquoise module, the genes of which were mainly enriched in antiviral response and immune-inflammatory activation. Furthermore, a significant positive correlation and a negative correlation were identified between the chronic disease stage and the brown and yellow modules, respectively. These modules were mainly associated with the cytoskeleton, phosphorylation, cellular catabolic process, and autophagy. Subsequently, we predicted the underlying hub genes and microRNAs in the three modules. Conclusions This study revealed the main biological processes in different stages of viral myocarditis and predicted hub genes in both the acute and chronic disease stages. Our results may be helpful for developing new therapeutic targets for viral myocarditis in future research.
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Affiliation(s)
- Zetao Ma
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhida Shen
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingchao Gong
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoou Chen
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingbo Lv
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meihui Wang
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiawen Chen
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mei Yu
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guosheng Fu
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hong He
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dongwu Lai
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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22
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Molecular diagnostics for congenital heart disease: a narrative review of the current technologies and applications. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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23
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Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics 2020; 35:3906-3912. [PMID: 30903145 DOI: 10.1093/bioinformatics/btz202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 01/13/2019] [Accepted: 03/20/2019] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying outlier definitions were employed and no comprehensive open-source software was developed. RESULTS We developed Outlier-RV Enrichment (ORE) to identify biologically-meaningful non-coding RVs. We implemented ORE combining whole-genome sequencing and cardiac RNAseq from congenital heart defect patients from the Pediatric Cardiac Genomics Consortium and deceased adults from Genotype-Tissue Expression. Use of rank-based outliers maximized sensitivity while a most extreme outlier approach maximized specificity. Rarer variants had stronger associations, suggesting they are under negative selective pressure and providing a basis for investigating their contribution to Mendelian disorders. AVAILABILITY AND IMPLEMENTATION ORE, source code, and documentation are available at https://pypi.python.org/pypi/ore under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- F Richter
- Graduate School of Biomedical Sciences
| | - G E Hoffman
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - N Patel
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D McKean
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S U Morton
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S DePalma
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - J Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - A Kitaygorodksy
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - G A Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - A Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital and University College London, London, UK
| | - Y Shen
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - W K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - E E Schadt
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, A Mount Sinai Venture, Stamford, CT, USA
| | - B D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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24
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de Souza MM, Zerlotini A, Rocha MIP, Bruscadin JJ, Diniz WJDS, Cardoso TF, Cesar ASM, Afonso J, Andrade BGN, Mudadu MDA, Mokry FB, Tizioto PC, de Oliveira PSN, Niciura SCM, Coutinho LL, Regitano LCDA. Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. Sci Rep 2020; 10:10204. [PMID: 32576896 PMCID: PMC7311436 DOI: 10.1038/s41598-020-67089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.
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Affiliation(s)
- Marcela Maria de Souza
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, SP, Brazil
| | - Marina Ibelli Pereira Rocha
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jennifer Jessica Bruscadin
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Wellison Jarles da Silva Diniz
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Juliana Afonso
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Fabiana Barichello Mokry
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
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25
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Misra C, Bangru S, Lin F, Lam K, Koenig SN, Lubbers ER, Hedhli J, Murphy NP, Parker DJ, Dobrucki LW, Cooper TA, Tajkhorshid E, Mohler PJ, Kalsotra A. Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy. Dev Cell 2020; 52:748-763.e6. [PMID: 32109384 PMCID: PMC7098852 DOI: 10.1016/j.devcel.2020.01.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/25/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic genetic disorder caused by the CTG repeat expansion in the 3'-untranslated region of DMPK gene. Heart dysfunctions occur in ∼80% of DM1 patients and are the second leading cause of DM1-related deaths. Herein, we report that upregulation of a non-muscle splice isoform of RNA-binding protein RBFOX2 in DM1 heart tissue-due to altered splicing factor and microRNA activities-induces cardiac conduction defects in DM1 individuals. Mice engineered to express the non-muscle RBFOX240 isoform in heart via tetracycline-inducible transgenesis, or CRISPR/Cas9-mediated genome editing, reproduced DM1-related cardiac conduction delay and spontaneous episodes of arrhythmia. Further, by integrating RNA binding with cardiac transcriptome datasets from DM1 patients and mice expressing the non-muscle RBFOX2 isoform, we identified RBFOX240-driven splicing defects in voltage-gated sodium and potassium channels, which alter their electrophysiological properties. Thus, our results uncover a trans-dominant role for an aberrantly expressed RBFOX240 isoform in DM1 cardiac pathogenesis.
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Affiliation(s)
- Chaitali Misra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Feikai Lin
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Kin Lam
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Sara N Koenig
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Ellen R Lubbers
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Jamila Hedhli
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Nathaniel P Murphy
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Darren J Parker
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Lawrence W Dobrucki
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Centers for Macromolecular Modeling, Bioinformatics and Experimental Molecular Imaging at Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Peter J Mohler
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, College of Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
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26
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Deniz E, Jonas S, Khokha MK, Choma MA. Quantitative Phenotyping of Xenopus Embryonic Heart Pathophysiology Using Hemoglobin Contrast Subtraction Angiography to Screen Human Cardiomyopathies. Front Physiol 2019; 10:1197. [PMID: 31620018 PMCID: PMC6763566 DOI: 10.3389/fphys.2019.01197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/03/2019] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is a significant cause of mortality in infants and adults. Currently human genomic analysis has identified a number of candidate genes in these patients. These genes span diverse categories of gene function suggesting that despite the similarity in cardiac lesion, the underlying pathophysiology may be different. In fact, patients with similar CHDs can have drastically different outcomes, including a dramatic decrease in myocardial function. To test these human candidate genes for their impact on myocardial function, we need efficient animals models of disease. For this purpose, we paired Xenopus tropicalis with our microangiography technique, hemoglobin contrast subtraction angiography (HCSA). To demonstrate the gene-teratogen-physiology relationship, we modeled human cardiomyopathy in tadpoles. First we depleted the sarcomeric protein myosin heavy chain 6 (myh6) expression using morpholino oligos. Next, we exposed developing embryos to the teratogen ethanol and in both conditions showed varying degrees of cardiac dysfunction. Our results demonstrate that HCSA can distinguish biomechanical phenotypes in the context of gene dysfunction or teratogen. This approach can be used to screen numerous candidate CHD genes or suspected teratogens for their effect on cardiac function.
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Affiliation(s)
- Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT, United States
| | - Stephan Jonas
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Mustafa K Khokha
- Department of Pediatrics, Yale University, New Haven, CT, United States.,Department of Genetics, Yale University, New Haven, CT, United States
| | - Michael A Choma
- Department of Pediatrics, Yale University, New Haven, CT, United States.,Department of Diagnostic Radiology, Yale University, New Haven, CT, United States.,Department of Biomedical Engineering, Yale University, New Haven, CT, United States.,Department of Applied Physics, Yale University, New Haven, CT, United States
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27
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Mohammadi P, Castel SE, Cummings BB, Einson J, Sousa C, Hoffman P, Donkervoort S, Jiang Z, Mohassel P, Foley AR, Wheeler HE, Im HK, Bonnemann CG, MacArthur DG, Lappalainen T. Genetic regulatory variation in populations informs transcriptome analysis in rare disease. Science 2019; 366:351-356. [PMID: 31601707 PMCID: PMC6814274 DOI: 10.1126/science.aay0256] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022]
Abstract
Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential new diagnoses. Using our reference estimates from GTEx data, ANEVA-DOT can be incorporated in rare disease diagnostic pipelines to use RNA-sequencing data more effectively.
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Affiliation(s)
- Pejman Mohammadi
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephane E Castel
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Beryl B Cummings
- Analytical and Translation Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonah Einson
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Christina Sousa
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Hoffman
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Zhuoxun Jiang
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Heather E Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Carsten G Bonnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel G MacArthur
- Analytical and Translation Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
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28
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Harney DJ, Hutchison AT, Su Z, Hatchwell L, Heilbronn LK, Hocking S, James DE, Larance M. Small-protein Enrichment Assay Enables the Rapid, Unbiased Analysis of Over 100 Low Abundance Factors from Human Plasma. Mol Cell Proteomics 2019; 18:1899-1915. [PMID: 31308252 PMCID: PMC6731089 DOI: 10.1074/mcp.tir119.001562] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
Unbiased and sensitive quantification of low abundance small proteins in human plasma (e.g. hormones, immune factors, metabolic regulators) remains an unmet need. These small protein factors are typically analyzed individually and using antibodies that can lack specificity. Mass spectrometry (MS)-based proteomics has the potential to address these problems, however the analysis of plasma by MS is plagued by the extremely large dynamic range of this body fluid, with protein abundances spanning at least 13 orders of magnitude. Here we describe an enrichment assay (SPEA), that greatly simplifies the plasma dynamic range problem by enriching small-proteins of 2-10 kDa, enabling the rapid, specific and sensitive quantification of >100 small-protein factors in a single untargeted LC-MS/MS acquisition. Applying this method to perform deep-proteome profiling of human plasma we identify C5ORF46 as a previously uncharacterized human plasma protein. We further demonstrate the reproducibility of our workflow for low abundance protein analysis using a stable-isotope labeled protein standard of insulin spiked into human plasma. SPEA provides the ability to study numerous important hormones in a single rapid assay, which we applied to study the intermittent fasting response and observed several unexpected changes including decreased plasma abundance of the iron homeostasis regulator hepcidin.
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Affiliation(s)
- Dylan J Harney
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amy T Hutchison
- ¶Discipline of Medicine, University of Adelaide, Adelaide, Australia
| | - Zhiduan Su
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Luke Hatchwell
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Samantha Hocking
- §Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - David E James
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Mark Larance
- ‡Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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29
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Chen G, Ning B, Shi T. Single-Cell RNA-Seq Technologies and Related Computational Data Analysis. Front Genet 2019; 10:317. [PMID: 31024627 PMCID: PMC6460256 DOI: 10.3389/fgene.2019.00317] [Citation(s) in RCA: 502] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A number of scRNA-seq protocols have been developed, and these methods possess their unique features with distinct advantages and disadvantages. Due to technical limitations and biological factors, scRNA-seq data are noisier and more complex than bulk RNA-seq data. The high variability of scRNA-seq data raises computational challenges in data analysis. Although an increasing number of bioinformatics methods are proposed for analyzing and interpreting scRNA-seq data, novel algorithms are required to ensure the accuracy and reproducibility of results. In this review, we provide an overview of currently available single-cell isolation protocols and scRNA-seq technologies, and discuss the methods for diverse scRNA-seq data analyses including quality control, read mapping, gene expression quantification, batch effect correction, normalization, imputation, dimensionality reduction, feature selection, cell clustering, trajectory inference, differential expression calling, alternative splicing, allelic expression, and gene regulatory network reconstruction. Further, we outline the prospective development and applications of scRNA-seq technologies.
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Affiliation(s)
- Geng Chen
- Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Baitang Ning
- National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, AR, United States
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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30
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Yang RM, Tao J, Zhan M, Yuan H, Wang HH, Chen SJ, Chen Z, de Thé H, Zhou J, Guo Y, Zhu J. TAMM41 is required for heart valve differentiation via regulation of PINK-PARK2 dependent mitophagy. Cell Death Differ 2019; 26:2430-2446. [PMID: 30824836 PMCID: PMC6888875 DOI: 10.1038/s41418-019-0311-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 02/02/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022] Open
Abstract
TAMM41, located within the congenital heart diseases (CHD) sensitive region of 3p25 deletion syndrome, is a mitochondrial membrane maintenance protein critical for yeast survival, but its function in higher vertebrates remains unknown. Via in vivo zebrafish model, we found that tamm41 is highly expressed in the developing heart and deficiency of which led to heart valve abnormalities. Molecular mechanistic studies revealed that TAMM41 interacts and modulates the PINK1-PARK2 dependent mitophagy pathway, thereby implicating TAMM41 in heart valve development during zebrafish embryonic cardiogenesis. Furthermore, through screening of the congenital heart diseases (CHD) sensitive region of 3p25 deletion syndrome among 118 sporadic atrioventricular septal defect (AVSD) patients, we identified three cases carrying heterozygous pathogenic intronic variants of TAMM41. All three cases lacked normal full-length TAMM41 transcripts, most likely due to specific expression of the mutant allele. Collectively, our studies highlight essential roles for TAMM41-dependent mitophagy in development of the heart and provide novel insights into the etiology of AVSD.
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Affiliation(s)
- Rui Meng Yang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiong Tao
- Prenatal Diagnosis Center, Shanghai Jiao Tong University Affiliated First People's Hospital, 650 Xin song jiang Road, Shanghai, 201620, China
| | - Ming Zhan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Hao Yuan
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hai Hong Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Sai Juan Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hugues de Thé
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Guo
- Department of Cardiology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France.
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31
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Wu RS, Lam II, Clay H, Duong DN, Deo RC, Coughlin SR. A Rapid Method for Directed Gene Knockout for Screening in G0 Zebrafish. Dev Cell 2018; 46:112-125.e4. [PMID: 29974860 DOI: 10.1016/j.devcel.2018.06.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022]
Abstract
Zebrafish is a powerful model for forward genetics. Reverse genetic approaches are limited by the time required to generate stable mutant lines. We describe a system for gene knockout that consistently produces null phenotypes in G0 zebrafish. Yolk injection of sets of four CRISPR/Cas9 ribonucleoprotein complexes redundantly targeting a single gene recapitulated germline-transmitted knockout phenotypes in >90% of G0 embryos for each of 8 test genes. Early embryonic (6 hpf) and stable adult phenotypes were produced. Simultaneous multi-gene knockout was feasible but associated with toxicity in some cases. To facilitate use, we generated a lookup table of four-guide sets for 21,386 zebrafish genes and validated several. Using this resource, we targeted 50 cardiomyocyte transcriptional regulators and uncovered a role of zbtb16a in cardiac development. This system provides a platform for rapid screening of genes of interest in development, physiology, and disease models in zebrafish.
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Affiliation(s)
- Roland S Wu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ian I Lam
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hilary Clay
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel N Duong
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rahul C Deo
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shaun R Coughlin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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32
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Šeda O, Šedová L, Včelák J, Vaňková M, Liška F, Bendlová B. ZBTB16 and metabolic syndrome: a network perspective. Physiol Res 2018; 66:S357-S365. [PMID: 28948820 DOI: 10.33549/physiolres.933730] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Metabolic syndrome is a prevalent, complex condition. The search for genetic determinants of the syndrome is currently undergoing a paradigm enhancement by adding systems genetics approaches to association studies. We summarize the current evidence on relations between an emergent new candidate, zinc finger and BTB domain containing 16 (ZBTB16) transcription factor and the major components constituting the metabolic syndrome. Information stemming from studies on experimental models with altered Zbtb16 expression clearly shows its effect on adipogenesis, cardiac hypertrophy and fibrosis, lipid levels and insulin sensitivity. Based on current evidence, we provide a network view of relations between ZBTB16 and hallmarks of metabolic syndrome in order to elucidate the potential functional links involving the ZBTB16 node. Many of the identified genes interconnecting ZBTB16 with all or most metabolic syndrome components are linked to immune function, inflammation or oxidative stress. In summary, ZBTB16 represents a promising pleiotropic candidate node for metabolic syndrome.
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Affiliation(s)
- O Šeda
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic, Institute of Endocrinology, Prague, Czech Republic.
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33
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Hippo Signaling Plays an Essential Role in Cell State Transitions during Cardiac Fibroblast Development. Dev Cell 2018; 45:153-169.e6. [PMID: 29689192 DOI: 10.1016/j.devcel.2018.03.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 02/02/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022]
Abstract
During development, progenitors progress through transition states. The cardiac epicardium contains progenitors of essential non-cardiomyocytes. The Hippo pathway, a kinase cascade that inhibits the Yap transcriptional co-factor, controls organ size in developing hearts. Here, we investigated Hippo kinases Lats1 and Lats2 in epicardial diversification. Epicardial-specific deletion of Lats1/2 was embryonic lethal, and mutant embryos had defective coronary vasculature remodeling. Single-cell RNA sequencing revealed that Lats1/2 mutant cells failed to activate fibroblast differentiation but remained in an intermediate cell state with both epicardial and fibroblast characteristics. Lats1/2 mutant cells displayed an arrested developmental trajectory with persistence of epicardial markers and expanded expression of Yap targets Dhrs3, an inhibitor of retinoic acid synthesis, and Dpp4, a protease that modulates extracellular matrix (ECM) composition. Genetic and pharmacologic manipulation revealed that Yap inhibits fibroblast differentiation, prolonging a subepicardial-like cell state, and promotes expression of matricellular factors, such as Dpp4, that define ECM characteristics.
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34
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Sellier C, Cerro-Herreros E, Blatter M, Freyermuth F, Gaucherot A, Ruffenach F, Sarkar P, Puymirat J, Udd B, Day JW, Meola G, Bassez G, Fujimura H, Takahashi MP, Schoser B, Furling D, Artero R, Allain FHT, Llamusi B, Charlet-Berguerand N. rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences. Nat Commun 2018; 9:2009. [PMID: 29789616 PMCID: PMC5964235 DOI: 10.1038/s41467-018-04370-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/26/2018] [Indexed: 12/30/2022] Open
Abstract
Myotonic dystrophy type 1 and type 2 (DM1, DM2) are caused by expansions of CTG and CCTG repeats, respectively. RNAs containing expanded CUG or CCUG repeats interfere with the metabolism of other RNAs through titration of the Muscleblind-like (MBNL) RNA binding proteins. DM2 follows a more favorable clinical course than DM1, suggesting that specific modifiers may modulate DM severity. Here, we report that the rbFOX1 RNA binding protein binds to expanded CCUG RNA repeats, but not to expanded CUG RNA repeats. Interestingly, rbFOX1 competes with MBNL1 for binding to CCUG expanded repeats and overexpression of rbFOX1 partly releases MBNL1 from sequestration within CCUG RNA foci in DM2 muscle cells. Furthermore, expression of rbFOX1 corrects alternative splicing alterations and rescues muscle atrophy, climbing and flying defects caused by expression of expanded CCUG repeats in a Drosophila model of DM2.
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Affiliation(s)
- Chantal Sellier
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Estefanía Cerro-Herreros
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain
- INCLIVA Health Research Institute, 46010, Valencia, Spain
| | - Markus Blatter
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH) Zurich, 8092, Zurich, Switzerland
| | - Fernande Freyermuth
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Angeline Gaucherot
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Frank Ruffenach
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France
| | - Partha Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jack Puymirat
- Human Genetics Research Unit, Laval University, CHUQ, Ste-Foy, Quebec, QC G1V 4G2, Canada
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University Hospital, 33521, Tampere, Finland
- Department of Medical Genetics, Folkhälsan Institute of Genetics, Helsinki University, 00290, Helsinki, Finland
- Department of Neurology, Vasa Central Hospital, 65130, Vaasa, Finland
| | - John W Day
- Department of Neurology, Stanford University, San Francisco, CA, 94305, USA
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, University of Milan, 20097, Milan, Italy
- Neurology Unit, IRCCS Policlinico San Donato, San Donato Milanese, 20097, Milan, Italy
| | - Guillaume Bassez
- Sorbonne Université, Inserm, Association Institut de Myologie, Center of Research in Myology, 75013, Paris, France
| | - Harutoshi Fujimura
- Department of Neurology, Toneyama National Hospital, Toyonaka, 560-0045, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, Ludwig Maximilian University, 80539, Munich, Germany
| | - Denis Furling
- Sorbonne Université, Inserm, Association Institut de Myologie, Center of Research in Myology, 75013, Paris, France
| | - Ruben Artero
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain
- INCLIVA Health Research Institute, 46010, Valencia, Spain
| | - Frédéric H T Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH) Zurich, 8092, Zurich, Switzerland
| | - Beatriz Llamusi
- Translational Genomics Group, Interdisciplinary Research Structure for Biotechnology and Biomedicine BIOTECMED, University of Valencia, 46010, Valencia, Spain.
- INCLIVA Health Research Institute, 46010, Valencia, Spain.
| | - Nicolas Charlet-Berguerand
- IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, 67404, Illkirch, France.
- UMR7104, Centre National de la Recherche Scientifique, 67404, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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Sun C, Kontaridis MI. Physiology of Cardiac Development: From Genetics to Signaling to Therapeutic Strategies. CURRENT OPINION IN PHYSIOLOGY 2017. [PMID: 29532042 DOI: 10.1016/j.cophys.2017.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The heart is one of the first organs to form and function during embryonic development. It is comprised of multiple cell lineages, each integral for proper cardiac development, and include cardiomyocytes, endothelial cells, epicardial cells and neural crest cells. The molecular mechanisms regulating cardiac development and morphogenesis are dependent on signaling crosstalk between multiple lineages through paracrine interactions, cell-ECM interactions, and cell-cell interactions, which together, help facilitate survival, growth, proliferation, differentiation and migration of cardiac tissue. Aberrant regulation of any of these processes can induce developmental disorders and pathological phenotypes. Here, we will discuss each of these processes, the genetic factors that contribute to each step of cardiac development, as well as the current and future therapeutic targets and mechanisms of heart development and disease. Understanding the complex interactions that regulate cardiac development, proliferation and differentiation is not only vital to understanding the causes of congenital heart defects, but to also finding new therapeutics that can treat both pediatric and adult cardiac disease in the near future.
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Affiliation(s)
- Cheng Sun
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maria I Kontaridis
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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36
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Touma M, Reemtsen B, Halnon N, Alejos J, Finn JP, Nelson SF, Wang Y. A Path to Implement Precision Child Health Cardiovascular Medicine. Front Cardiovasc Med 2017; 4:36. [PMID: 28620608 PMCID: PMC5451507 DOI: 10.3389/fcvm.2017.00036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/04/2017] [Indexed: 12/17/2022] Open
Abstract
Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is multifactorial, involving genetic, epigenetic, and/or environmental contributors. Clear dissection of the underlying mechanism is a powerful step to establish individualized therapies. However, the majority of CHDs are yet to be clearly diagnosed for the underlying genetic and environmental factors, and even less with effective therapies. Although the survival rate for CHDs is steadily improving, there is still a significant unmet need for refining diagnostic precision and establishing targeted therapies to optimize life quality and to minimize future complications. In particular, proper identification of disease associated genetic variants in humans has been challenging, and this greatly impedes our ability to delineate gene–environment interactions that contribute to the pathogenesis of CHDs. Implementing a systematic multileveled approach can establish a continuum from phenotypic characterization in the clinic to molecular dissection using combined next-generation sequencing platforms and validation studies in suitable models at the bench. Key elements necessary to advance the field are: first, proper delineation of the phenotypic spectrum of CHDs; second, defining the molecular genotype/phenotype by combining whole-exome sequencing and transcriptome analysis; third, integration of phenotypic, genotypic, and molecular datasets to identify molecular network contributing to CHDs; fourth, generation of relevant disease models and multileveled experimental investigations. In order to achieve all these goals, access to high-quality biological specimens from well-defined patient cohorts is a crucial step. Therefore, establishing a CHD BioCore is an essential infrastructure and a critical step on the path toward precision child health cardiovascular medicine.
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Affiliation(s)
- Marlin Touma
- Department of Pediatrics, Children's Discovery and Innovation Institute, University of California at Los Angeles, Los Angeles, CA, United States.,Cardiovascular Research Laboratory, University of California at Los Angeles, Los Angeles, CA, United States
| | - Brian Reemtsen
- Department of Cardiothoracic Surgery, University of California at Los Angeles, Los Angeles, CA, United States
| | - Nancy Halnon
- Department of Pediatrics, University of California at Los Angeles, Los Angeles, CA, United States
| | - Juan Alejos
- Department of Pediatrics, University of California at Los Angeles, Los Angeles, CA, United States
| | - J Paul Finn
- Department of Radiology, Cardiovascular Imaging, University of California at Los Angeles, Los Angeles, CA, United States
| | - Stanley F Nelson
- Department of Human Genetics, University of California at Los Angeles, Los Angeles, CA, United States
| | - Yibin Wang
- Cardiovascular Research Laboratory, University of California at Los Angeles, Los Angeles, CA, United States.,Department of Anesthesiology, Physiology and Medicine, University of California at Los Angeles, Los Angeles, CA, United States
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37
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Zaidi S, Brueckner M. Genetics and Genomics of Congenital Heart Disease. Circ Res 2017; 120:923-940. [PMID: 28302740 DOI: 10.1161/circresaha.116.309140] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
Congenital heart disease is the most common birth defect, and because of major advances in medical and surgical management, there are now more adults living with congenital heart disease (CHD) than children. Until recently, the cause of the majority of CHD was unknown. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. This review will focus on the evidence for genetic causes underlying CHD and discuss data supporting both monogenic and complex genetic mechanisms underlying CHD. The discoveries from CHD genetic studies draw attention to biological pathways that simultaneously open the door to a better understanding of cardiac development and affect clinical care of patients with CHD. Finally, we address clinical genetic evaluation of patients and families affected by CHD.
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Affiliation(s)
- Samir Zaidi
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT
| | - Martina Brueckner
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT.
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38
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DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell 2016; 39:480-490. [PMID: 27840107 PMCID: PMC5198784 DOI: 10.1016/j.devcel.2016.10.001] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/30/2016] [Accepted: 09/30/2016] [Indexed: 12/29/2022]
Abstract
Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease.
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Affiliation(s)
| | - Alexander G. Bick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irfan S. Kathiriya
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco
| | - John T. Hinson
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - William Pu
- Department of Cardiology, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Benoit G. Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
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