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Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J, Wang K. Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia. SCIENCE ADVANCES 2019; 5:eaau4139. [PMID: 31535015 PMCID: PMC6739105 DOI: 10.1126/sciadv.aau4139] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Applying tissue-specific deconvolution of transcriptional networks to identify their master regulators (MRs) in neuropsychiatric disorders has been largely unexplored. Here, using two schizophrenia (SCZ) case-control RNA-seq datasets, one on postmortem dorsolateral prefrontal cortex (DLPFC) and another on cultured olfactory neuroepithelium, we deconvolved the transcriptional networks and identified TCF4 as a top candidate MR that may be dysregulated in SCZ. We validated TCF4 as a MR through enrichment analysis of TCF4-binding sites in induced pluripotent stem cell (hiPSC)-derived neurons and in neuroblastoma cells. We further validated the predicted TCF4 targets by knocking down TCF4 in hiPSC-derived neural progenitor cells (NPCs) and glutamatergic neurons (Glut_Ns). The perturbed TCF4 gene network in NPCs was more enriched for pathways involved in neuronal activity and SCZ-associated risk genes, compared to Glut_Ns. Our results suggest that TCF4 may serve as a MR of a gene network dysregulated in SCZ at early stages of neurodevelopment.
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Affiliation(s)
- Abolfazl Doostparast Torshizi
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chris Armoskus
- College of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
- Zilkhe Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201, USA
| | - Marc P. Forrest
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Siwei Zhang
- Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL 60015, USA
| | - Tade Souaiaia
- College of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
- Zilkhe Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Oleg V. Evgrafov
- College of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
- Zilkhe Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - James A. Knowles
- College of Medicine, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
- Zilkhe Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL 60015, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Zilkhe Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA
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Chen H, Ji L, Liu X, Zhong J. Correlation between the rs7101 and rs1063169 polymorphisms in the FOS noncoding region and susceptibility to and prognosis of colorectal cancer. Medicine (Baltimore) 2019; 98:e16131. [PMID: 31261535 PMCID: PMC6617440 DOI: 10.1097/md.0000000000016131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The FOS gene is located on human chromosome 14q21-31 and encodes the nuclear oncoprotein c-Fos. This study analyzed the correlation between the FOS noncoding region rs7101 and rs1063169 polymorphisms and colorectal cancer susceptibility and prognosis. METHODS We analyzed the FOS genotypes in 432 colorectal cancer patients and 315 healthy subjects by PCR/Sanger sequencing. Survival was analyzed by Kaplan-Meier and Cox regression analysis. Western blot was used to detect the expression of c-Fos protein in cancer tissues and adjacent tissues in colorectal cancer patients with different genotypes. RESULTS The presence of a T allele at rs7101 and a T allele at rs1063169 in FOS carried a higher risk of colorectal cancer [adjusted odds ratio (OR) = 1.237, 95% confidence interval (95% CI) = 1.131-1.346, P ≤ .001 and adjusted OR = 1.218, 95% CI = 1.111-1.327, P ≤ .001, respectively]. c-Fos protein levels were significantly higher in variant cancer tissues than in normal mucosa tissues (P < .05), and c-Fos proteins levels were also higher in homozygous variant cancer tissues than in heterozygous variant cancer tissues. The 3-year survival rate of patients with wild-type FOS was higher than that of patients with variant FOS (P < .05). CONCLUSION The rs7101 and rs1063169 polymorphisms in the noncoding region of FOS are associated with the risk of developing colorectal cancer and the progression of colorectal cancer, which may be because the mutation enhances the expression of c-Fos protein to promote the incidence and development of colorectal cancer.
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Affiliation(s)
- Hongshu Chen
- Yidu Central Hospital of Weifang, Qingzhou, Shandong Province
| | - Lijuan Ji
- Yidu Central Hospital of Weifang, Qingzhou, Shandong Province
| | - Xiuzhen Liu
- Yidu Central Hospital of Weifang, Qingzhou, Shandong Province
| | - Jihong Zhong
- Department of Digestion, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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