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Adams JW, Vinokur A, de Souza JS, Austria C, Guerra BS, Herai RH, Wahlin KJ, Muotri AR. Loss of GTF2I promotes neuronal apoptosis and synaptic reduction in human cellular models of neurodevelopment. Cell Rep 2024; 43:113867. [PMID: 38416640 PMCID: PMC11002531 DOI: 10.1016/j.celrep.2024.113867] [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: 09/05/2023] [Revised: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/01/2024] Open
Abstract
Individuals with Williams syndrome (WS), a neurodevelopmental disorder caused by hemizygous loss of 26-28 genes at 7q11.23, characteristically portray a hypersocial phenotype. Copy-number variations and mutations in one of these genes, GTF2I, are associated with altered sociality and are proposed to underlie hypersociality in WS. However, the contribution of GTF2I to human neurodevelopment remains poorly understood. Here, human cellular models of neurodevelopment, including neural progenitors, neurons, and three-dimensional cortical organoids, are differentiated from CRISPR-Cas9-edited GTF2I-knockout (GTF2I-KO) pluripotent stem cells to investigate the role of GTF2I in human neurodevelopment. GTF2I-KO progenitors exhibit increased proliferation and cell-cycle alterations. Cortical organoids and neurons demonstrate increased cell death and synaptic dysregulation, including synaptic structural dysfunction and decreased electrophysiological activity on a multielectrode array. Our findings suggest that changes in synaptic circuit integrity may be a prominent mediator of the link between alterations in GTF2I and variation in the phenotypic expression of human sociality.
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Affiliation(s)
- Jason W Adams
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA; Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, CA 92093, USA
| | - Annabelle Vinokur
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Janaína S de Souza
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Charles Austria
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Bruno S Guerra
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Experimental Multiuser Laboratory, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Roberto H Herai
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Experimental Multiuser Laboratory, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Karl J Wahlin
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital, Department of Cellular & Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA; Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, CA 92093, USA.
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Liu J, Jia J, Wang S, Zhang J, Xian S, Zheng Z, Deng L, Feng Y, Zhang Y, Zhang J. Prognostic Ability of Enhancer RNAs in Metastasis of Non-Small Cell Lung Cancer. Molecules 2022; 27:molecules27134108. [PMID: 35807355 PMCID: PMC9268450 DOI: 10.3390/molecules27134108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023] Open
Abstract
(1) Background: Non-small cell lung cancer (NSCLC) is the most common lung cancer. Enhancer RNA (eRNA) has potential utility in the diagnosis, prognosis and treatment of cancer, but the role of eRNAs in NSCLC metastasis is not clear; (2) Methods: Differentially expressed transcription factors (DETFs), enhancer RNAs (DEEs), and target genes (DETGs) between primary NSCLC and metastatic NSCLC were identified. Prognostic DEEs (PDEEs) were screened by Cox regression analyses and a predicting model for metastatic NSCLC was constructed. We identified DEE interactions with DETFs, DETGs, reverse phase protein arrays (RPPA) protein chips, immunocytes, and pathways to construct a regulation network using Pearson correlation. Finally, the mechanisms and clinical significance were explained using multi-dimensional validation unambiguously; (3) Results: A total of 255 DEEs were identified, and 24 PDEEs were selected into the multivariate Cox regression model (AUC = 0.699). Additionally, the NSCLC metastasis-specific regulation network was constructed, and six key PDEEs were defined (ANXA8L1, CASTOR2, CYP4B1, GTF2H2C, PSMF1 and TNS4); (4) Conclusions: This study focused on the exploration of the prognostic value of eRNAs in the metastasis of NSCLC. Finally, six eRNAs were identified as potential markers for the prediction of metastasis of NSCLC.
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Affiliation(s)
- Jun Liu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Jingyi Jia
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Shanghai Clinical Research Center for Infectious Diseases (Tuberculosis), Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Siqiao Wang
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Junfang Zhang
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Shuyuan Xian
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Zixuan Zheng
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Lin Deng
- Normal College, Qingdao University, Qingdao 266071, China;
| | - Yonghong Feng
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Shanghai Clinical Research Center for Infectious Diseases (Tuberculosis), Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
| | - Yuan Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
| | - Jie Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
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Kopp ND, Nygaard KR, Liu Y, McCullough KB, Maloney SE, Gabel HW, Dougherty JD. Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA binding and long-term behavioral consequences. Hum Mol Genet 2021; 29:1498-1519. [PMID: 32313931 DOI: 10.1093/hmg/ddaa070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/19/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Gtf2ird1 and Gtf2i are two transcription factors (TFs) among the 28 genes deleted in Williams syndrome, and prior mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain and test for additive effects of their mutation on transcription and behavior. GTF2IRD1 binding targets were enriched for transcriptional and chromatin regulators and mediators of ubiquitination. GTF2I targets were enriched for signal transduction proteins, including regulators of phosphorylation and WNT. Both TFs are highly enriched at promoters, strongly overlap CTCF binding and topological associating domain boundaries and moderately overlap each other, suggesting epistatic effects. Shared TF targets are enriched for reactive oxygen species-responsive genes, synaptic proteins and transcription regulators such as chromatin modifiers, including a significant number of highly constrained genes and known ASD genes. We next used single and double mutants to test whether mutating both TFs will modify transcriptional and behavioral phenotypes of single Gtf2ird1 mutants, though with the caveat that our Gtf2ird1 mutants, like others previously reported, do produce low levels of a truncated protein product. Despite little difference in DNA binding and transcriptome-wide expression, homozygous Gtf2ird1 mutation caused balance, marble burying and conditioned fear phenotypes. However, mutating Gtf2i in addition to Gtf2ird1 did not further modify transcriptomic or most behavioral phenotypes, suggesting Gtf2ird1 mutation alone was sufficient for the observed phenotypes.
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Affiliation(s)
- Nathan D Kopp
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kayla R Nygaard
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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Candia J, Bayarsaikhan E, Tandon M, Budhu A, Forgues M, Tovuu LO, Tudev U, Lack J, Chao A, Chinburen J, Wang XW. The genomic landscape of Mongolian hepatocellular carcinoma. Nat Commun 2020; 11:4383. [PMID: 32873799 PMCID: PMC7462863 DOI: 10.1038/s41467-020-18186-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Mongolia has the highest incidence of hepatocellular carcinoma (HCC) in the world, but its causative factors and underlying tumor biology remain unknown. Here, we describe molecular characteristics of HCC from 76 Mongolian patients by whole-exome and transcriptome sequencing. We present a comprehensive analysis of mutational signatures, driver genes, and molecular subtypes of Mongolian HCC compared to 373 HCC patients of different races and ethnicities and diverse etiologies. Mongolian HCC consists of prognostic molecular subtypes similar to those found in patients from other areas of Asia, Europe, and North America, as well as other unique subtypes, suggesting the presence of distinct etiologies linked to Mongolian patients. In addition to common driver mutations (TP53, CTNNB1) frequently found in pan-cancer analysis, Mongolian HCC exhibits unique drivers (most notably GTF2IRD2B, PNRC2, and SPTA1), the latter of which is associated with hepatitis D viral infection. These results suggest the existence of new molecular mechanisms at play in Mongolian hepatocarcinogenesis.
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Affiliation(s)
- Julián Candia
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lkhagva-Ochir Tovuu
- General Laboratory Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Undarmaa Tudev
- Cancer Registry and Screening Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Justin Lack
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ann Chao
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Jigjidsuren Chinburen
- Hepato-Pancreatic-Biliary Surgical Department, National Cancer Center, Ulaanbaatar, Mongolia
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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López-Tobón A, Trattaro S, Testa G. The sociability spectrum: evidence from reciprocal genetic copy number variations. Mol Autism 2020; 11:50. [PMID: 32546261 PMCID: PMC7298749 DOI: 10.1186/s13229-020-00347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/11/2020] [Indexed: 02/14/2023] Open
Abstract
Sociability entails some of the most complex behaviors processed by the central nervous system. It includes the detection, integration, and interpretation of social cues and elaboration of context-specific responses that are quintessentially species-specific. There is an ever-growing accumulation of molecular associations to autism spectrum disorders (ASD), from causative genes to endophenotypes across multiple functional layers; these however, have rarely been put in context with the opposite manifestation featured in hypersociability syndromes. Genetic copy number variations (CNVs) allow to investigate the relationships between gene dosage and its corresponding phenotypes. In particular, CNVs of the 7q11.23 locus, which manifest diametrically opposite social behaviors, offer a privileged window to look into the molecular substrates underlying the developmental trajectories of the social brain. As by definition sociability is studied in humans postnatally, the developmental fluctuations causing social impairments have thus far remained a black box. Here, we review key evidence of molecular players involved at both ends of the sociability spectrum, focusing on genetic and functional associations of neuroendocrine regulators and synaptic transmission pathways. We then proceed to propose the existence of a molecular axis centered around the paradigmatic dosage imbalances at the 7q11.23 locus, regulating networks responsible for the development of social behavior in humans and highlight the key role that neurodevelopmental models from reprogrammed pluripotent cells will play for its understanding.
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Affiliation(s)
- Alejandro López-Tobón
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Sebastiano Trattaro
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
- Human Technopole, Via Cristina Belgioioso 171, Milan, Italy.
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Carmona-Mora P, Widagdo J, Tomasetig F, Canales CP, Cha Y, Lee W, Alshawaf A, Dottori M, Whan RM, Hardeman EC, Palmer SJ. The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation. Hum Genet 2015; 134:1099-115. [PMID: 26275350 DOI: 10.1007/s00439-015-1591-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/04/2015] [Indexed: 12/11/2022]
Abstract
GTF2IRD1 is one of the three members of the GTF2I gene family, clustered on chromosome 7 within a 1.8 Mb region that is prone to duplications and deletions in humans. Hemizygous deletions cause Williams-Beuren syndrome (WBS) and duplications cause WBS duplication syndrome. These copy number variations disturb a variety of developmental systems and neurological functions. Human mapping data and analyses of knockout mice show that GTF2IRD1 and GTF2I underpin the craniofacial abnormalities, mental retardation, visuospatial deficits and hypersociability of WBS. However, the cellular role of the GTF2IRD1 protein is poorly understood due to its very low abundance and a paucity of reagents. Here, for the first time, we show that endogenous GTF2IRD1 has a punctate pattern in the nuclei of cultured human cell lines and neurons. To probe the functional relationships of GTF2IRD1 in an unbiased manner, yeast two-hybrid libraries were screened, isolating 38 novel interaction partners, which were validated in mammalian cell lines. These relationships illustrate GTF2IRD1 function, as the isolated partners are mostly involved in chromatin modification and transcriptional regulation, whilst others indicate an unexpected role in connection with the primary cilium. Mapping of the sites of protein interaction also indicates key features regarding the evolution of the GTF2IRD1 protein. These data provide a visual and molecular basis for GTF2IRD1 nuclear function that will lead to an understanding of its role in brain, behaviour and human disease.
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Affiliation(s)
- Paulina Carmona-Mora
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Jocelyn Widagdo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Florence Tomasetig
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Cesar P Canales
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Yeojoon Cha
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Wei Lee
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Abdullah Alshawaf
- Centre for Neural Engineering, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mirella Dottori
- Centre for Neural Engineering, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Renee M Whan
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Stephen J Palmer
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia.
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Sassa T. The Role of Human-Specific Gene Duplications During Brain Development and Evolution. J Neurogenet 2013; 27:86-96. [DOI: 10.3109/01677063.2013.789512] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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