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Zhang J, Yang L, Sun Y, Zhang L, Wang Y, Liu M, Li X, Liang Y, Zhao H, Liu Z, Qiu Z, Zhang T, Xie J. Up-regulation of miR-10a-5p expression inhibits the proliferation and differentiation of neural stem cells by targeting Chl1. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38841745 DOI: 10.3724/abbs.2024078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Neural tube defects (NTDs) are characterized by the failure of neural tube closure during embryogenesis and are considered the most common and severe central nervous system anomalies during early development. Recent microRNA (miRNA) expression profiling studies have revealed that the dysregulation of several miRNAs plays an important role in retinoic acid (RA)-induced NTDs. However, the molecular functions of these miRNAs in NTDs remain largely unidentified. Here, we show that miR-10a-5p is significantly upregulated in RA-induced NTDs and results in reduced cell growth due to cell cycle arrest and dysregulation of cell differentiation. Moreover, the cell adhesion molecule L1-like ( Chl1) is identified as a direct target of miR-10a-5p in neural stem cells (NSCs) in vitro, and its expression is reduced in RA-induced NTDs. siRNA-mediated knockdown of intracellular Chl1 affects cell proliferation and differentiation similar to those of miR-10a-5p overexpression, which further leads to the inhibition of the expressions of downstream ERK1/2 MAPK signaling pathway proteins. These cellular responses are abrogated by either increased expression of the direct target of miR-10a-5p ( Chl1) or an ERK agonist such as honokiol. Overall, our study demonstrates that miR-10a-5p plays a major role in the process of NSC growth and differentiation by directly targeting Chl1, which in turn induces the downregulation of the ERK1/2 cascade, suggesting that miR-10a-5p and Chl1 are critical for NTD formation in the development of embryos.
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Affiliation(s)
- Juan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuqing Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yufei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Ming Liu
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xiujuan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuxiang Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Hong Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
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Ray D, Venkataraghavan S, Zhang W, Leslie EJ, Hetmanski JB, Weinberg SM, Murray JC, Marazita ML, Ruczinski I, Taub MA, Beaty TH. Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios. PLoS Genet 2021; 17:e1009584. [PMID: 34242216 PMCID: PMC8270211 DOI: 10.1371/journal.pgen.1009584] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Based on epidemiologic and embryologic patterns, nonsyndromic orofacial clefts- the most common craniofacial birth defects in humans- are commonly categorized into cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which are traditionally considered to be etiologically distinct. However, some evidence of shared genetic risk in IRF6, GRHL3 and ARHGAP29 regions exists; only FOXE1 has been recognized as significantly associated with both CL/P and CP in genome-wide association studies (GWAS). We used a new statistical approach, PLACO (pleiotropic analysis under composite null), on a combined multi-ethnic GWAS of 2,771 CL/P and 611 CP case-parent trios. At the genome-wide significance threshold of 5 × 10-8, PLACO identified 1 locus in 1q32.2 (IRF6) that appears to increase risk for one OFC subgroup but decrease risk for the other. At a suggestive significance threshold of 10-6, we found 5 more loci with compelling candidate genes having opposite effects on CL/P and CP: 1p36.13 (PAX7), 3q29 (DLG1), 4p13 (LIMCH1), 4q21.1 (SHROOM3) and 17q22 (NOG). Additionally, we replicated the recognized shared locus 9q22.33 (FOXE1), and identified 2 loci in 19p13.12 (RAB8A) and 20q12 (MAFB) that appear to influence risk of both CL/P and CP in the same direction. We found locus-specific effects may vary by racial/ethnic group at these regions of genetic overlap, and failed to find evidence of sex-specific differences. We confirmed shared etiology of the two OFC subtypes comprising CL/P, and additionally found suggestive evidence of differences in their pathogenesis at 2 loci of genetic overlap. Our novel findings include 6 new loci of genetic overlap between CL/P and CP; 3 new loci between pairwise OFC subtypes; and 4 loci not previously implicated in OFCs. Our in-silico validation showed PLACO is robust to subtype-specific effects, and can achieve massive power gains over existing approaches for identifying genetic overlap between disease subtypes. In summary, we found suggestive evidence for new genetic regions and confirmed some recognized OFC genes either exerting shared risk or with opposite effects on risk to OFC subtypes.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
| | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wanying Zhang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Seth M. Weinberg
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
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Jia X, Zhao Q, Zhang Y, Dong Y, Lei L, Williamson RA, Lei Y, Tan X, Zhang D, Hu J. Identification of a Five-CpG Signature with Diagnostic Value in Thyroid Cancer. J Comput Biol 2019; 26:1409-1417. [PMID: 31290678 DOI: 10.1089/cmb.2019.0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Thyroid cancer (TC) ranks as the most common endocrine malignancy, and its incidence and mortality rates continue to rise annually. Increasing evidence have shown that DNA methylation, a kind of stable epigenetic modification, is associated with carcinogenesis, suggesting its potential as biomarkers for the early detection of tumors. With the aim of exploring likely DNA methylation biomarkers for TC diagnosis, we conducted a synthetic analysis of DNA methylation profiles based on 789 samples from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. In the discovery phase, we identified five CpG probes (cg11228682, cg01291854, cg06778183, cg01668008, and cg01702055) on the condition of DNA methylation data from GSE86961 (n = 82) and constructed a five-CpG signature-based diagnostic model for TC. In addition, we validated the diagnostic score formula in two independent training cohorts, GSE97466 (n = 141) and TCGA (n = 566), as well as the previous developing cohort GSE86961. Receiver operating characteristic analysis revealed that the five-CpG signature had a good diagnostic performance to distinguish TC samples from benign samples. In conclusion, our findings suggest that the five-CpG signature could provide a novel biomarker with useful applications in TC diagnosis.
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Affiliation(s)
- Xi Jia
- Department of Nuclear Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qian Zhao
- Department of Otolaryngology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yuanyuan Zhang
- Department of Pediatrics, and The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yiping Dong
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Li Lei
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Ramone A Williamson
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yutiantian Lei
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xinyue Tan
- Department of Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dan Zhang
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jinsong Hu
- Department of Cell Biology and Genetics, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, China
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Zhang H, Guo Y, Gu H, Wei X, Ma W, Liu D, Yu K, Luo W, Ma L, Liu Y, Xue J, Huang J, Wang Y, Jia S, Dong N, Wang H, Yuan Z. TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis. Clin Epigenetics 2019; 11:17. [PMID: 30709423 PMCID: PMC6359777 DOI: 10.1186/s13148-018-0603-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 12/20/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are complex abnormalities associated with gene-environment interactions. The underlying cause has not been determined. METHODS Spinal cord tissues from cases with NTDs and healthy controls were collected. Methylation patterns between cases and normal individuals were compared using 450K Infinium Methylation BeadChip Illumina. DNA methylation analysis by pyrosequencing (PyroMark Q96) and mRNA and protein expression were analyzed using real-time quantitative PCR and Western blotting, respectively. Next-generation and Sanger sequencing were used to determine genetic variants in the target genes. RESULTS Spinal cord tissues from cases with NTDs had more hypomethylated than hypermethylated genes. Further evaluation showed that the exon 1 region of TRIM4 was hypomethylated, and TRIM4 mRNA and protein levels were significantly increased in NTDs compared to controls. A rare missense variant (rs76665876) in TRIM4 was found in 3 of the 14 NTD cases but was not related to TRIM4 expression. TRIM4 mRNA levels were significantly increased in cases with hypomethylation and without the rs76665876 variant. CONCLUSION These findings suggest that spinal cord tissues in cases with NTDs had a different genome-wide methylation pattern compared to controls. Abnormal methylation patterns in TRIM4 in immunity pathways might be involved in NTD pathogenesis. Genetic variants in TRIM4 genes only slightly contribute to the etiology of human NTDs.
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Affiliation(s)
- Henan Zhang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yi Guo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Kun Yu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Ling Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yusi Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Jia Xue
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Jieting Huang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yanfu Wang
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Naixuan Dong
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, Key Lab of Reproduction Regulation of NPFPC in SIPPR, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China.
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018; 16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
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Affiliation(s)
- Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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