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Han L, Cheng B, Wei W, Liu L, Cheng S, Liu H, Jia Y, Wen Y, Zhang F. Whole-Transcriptome Sequencing of Knee Joint Cartilage from Kashin-Beck Disease and Osteoarthritis Patients. Int J Mol Sci 2024; 25:4348. [PMID: 38673933 PMCID: PMC11049856 DOI: 10.3390/ijms25084348] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study was to provide a comprehensive understanding of similarities and differences in mRNAs, lncRNAs, and circRNAs within cartilage for Kashin-Beck disease (KBD) compared to osteoarthritis (OA). We conducted a comparison of the expression profiles of mRNAs, lncRNAs, and circRNAs via whole-transcriptome sequencing in eight KBD and ten OA individuals. To facilitate functional annotation-enriched analysis for differentially expressed (DE) genes, DE lncRNAs, and DE circRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and KEGG. Additionally, using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we validated the expression levels of four cartilage-related genes in chondrocytes. We identified a total of 43 DE mRNAs, 1451 DE lncRNAs, and 305 DE circRNAs in KBD cartilage tissue compared to OA (q value < 0.05; |log2FC| > 1). We also performed competing endogenous RNA network analysis, which identified a total of 65 lncRNA-mRNA interactions and 4714 miRNA-circRNA interactions. In particular, we observed that circRNA12218 had binding sites for three miRNAs targeting ACAN, while circRNA12487 had binding sites for seven miRNAs targeting COL2A1. Our results add a novel set of genes and non-coding RNAs that could potentially serve as candidate diagnostic biomarkers or therapeutic targets for KBD patients.
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Affiliation(s)
- Lixin Han
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Bolun Cheng
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Wenming Wei
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Li Liu
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Shiqiang Cheng
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Huan Liu
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Yumeng Jia
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Yan Wen
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
| | - Feng Zhang
- Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (L.H.); (B.C.); (W.W.); (L.L.); (S.C.); (H.L.); (Y.J.); (Y.W.)
- Key Laboratory of Trace Elements and Endemic Diseases (Xi’an Jiaotong University), National Health and Family Planning Commission, Xi’an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an 710061, China
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Xu W, Goreczny GJ, Forsythe I, Brennan G, Stowell T, Brock K, Capella B, Turner CE. Hic-5 regulates extracellular matrix-associated gene expression and cytokine secretion in cancer associated fibroblasts. Exp Cell Res 2024; 435:113930. [PMID: 38237846 PMCID: PMC10923124 DOI: 10.1016/j.yexcr.2024.113930] [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: 09/21/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
The focal adhesion protein, Hic-5 plays a key role in promoting extracellular matrix deposition and remodeling by cancer associated fibroblasts within the tumor stroma to promote breast tumor cell invasion. However, whether stromal matrix gene expression is regulated by Hic-5 is still unknown. Utilizing a constitutive Hic-5 knockout, Mouse Mammary Tumor Virus-Polyoma Middle T-Antigen spontaneous breast tumor mouse model, bulk RNAseq analysis was performed on cancer associated fibroblasts isolated from Hic-5 knockout mammary tumors. Functional network analysis highlighted a key role for Hic-5 in extracellular matrix organization, with both structural matrix genes, as well as matrix remodeling genes being differentially expressed in relation to Hic-5 expression. The subcellular distribution of the MRTF-A transcription factor and expression of a subset of MRTF-A responsive genes was also impacted by Hic-5 expression. Additionally, cytokine array analysis of conditioned media from the Hic-5 and Hic-5 knockout cancer associated fibroblasts revealed that Hic-5 is important for the secretion of several key factors that are associated with matrix remodeling, angiogenesis and immune evasion. Together, these data provide further evidence of a central role for Hic-5 expression in cancer associated fibroblasts in regulating the composition and organization of the tumor stroma microenvironment to promote breast tumor progression.
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Affiliation(s)
- Weiyi Xu
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gregory J Goreczny
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA; Jnana Therapeutics, Boston, MA, USA
| | - Ian Forsythe
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA; Zymo Research Corp, Huntington Beach, CA, USA
| | - Grant Brennan
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Theresa Stowell
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Katia Brock
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Benjamin Capella
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Christopher E Turner
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY, USA.
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He N, Hong A, Zhao K, Zhang Z, Wang S, Jia Y. Association of SOX6 gene polymorphisms with Kashin-Beck disease risk in the Chinese Han population. Open Med (Wars) 2024; 19:20230883. [PMID: 38205152 PMCID: PMC10775412 DOI: 10.1515/med-2023-0883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Kashin-Beck disease (KBD) is an endemic osteochondropathy. A specific gene called SRY-box transcription factor 6 (SOX6) is important for forming cartilage. This study aims to explore the potential correlation between SOX6 single nucleotide polymorphisms (SNPs) and KBD risk for the first time. In the case-control study, 735 unrelated Chinese Han individuals were enrolled. The four mutation sites of the SOX6 gene (rs4539287 G/A, rs3203295 C/A, rs7928675 C/A, and rs10832681 A/G) were screened and genotyped on the Agena MassARRAY platform. The correlation between SOX6 SNPs and KBD risk was explored based on logistic regression analysis. The interaction between SNP and SNP was analyzed based on the multi-factor dimensionality reduction (MDR) method. Overall analysis revealed a remarkable correlation between rs7928675 and rs10832681 and the reduction of KBD risk (p < 0.05). Subgroup analyses further indicated that these two SNPs have a significant protective effect on KBD risk among participants aged ≤65 years, males, and non-smokers (p < 0.05). MDR displayed a marked interaction between rs3203295 and rs10832681. Our study revealed that SOX6 rs7928675 and rs10832681 are markedly correlated with a reduced risk of KBD in the Chinese Han population, providing a new direction for the prevention, diagnosis, and treatment of KBD.
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Affiliation(s)
- Na He
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
| | - Aiwen Hong
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
| | - Kun Zhao
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
| | - Zhefan Zhang
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
| | - Shengli Wang
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
| | - Yaofei Jia
- People’s Hospital of Changwu County, Zhaoren Street, Xianyang, Shaanxi 713600, China
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Wu J, Wu T, Xie X, Niu Q, Zhao Z, Zhu B, Chen Y, Zhang L, Gao X, Niu X, Gao H, Li J, Xu L. Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle. Foods 2023; 12:3986. [PMID: 37959106 PMCID: PMC10647706 DOI: 10.3390/foods12213986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.
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Affiliation(s)
- Jiayuan Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Tianyi Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xueyuan Xie
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Qunhao Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Zhida Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Bo Zhu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Yan Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xiaoyan Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
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Mezzi N, Messaoud O, Mkaouar R, Zitouna N, Romdhane S, Abdessalem G, Charfeddine C, Maazoul F, Ouerteni I, Hamdi Y, Zaouak A, Mrad R, Abdelhak S, Romdhane L. Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved. Genes (Basel) 2021; 12:1820. [PMID: 34828426 PMCID: PMC8617973 DOI: 10.3390/genes12111820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases. Collected data were classified according to the CIM-10 classification and the transmission mode. The spectrum of these diseases is estimated to be 589 entities. This suggests remarkable progress through the development of biomedical health research activities and building capacities. Sixty percent of the reported disorders are autosomal recessive, which could be explained by the high prevalence of endogamous mating. Congenital malformations (29.54%) are the major disease group, followed by metabolic diseases (22%). Sixty percent of the genetic diseases have a known molecular etiology. We also reported additional cases of comorbidity that seem to be a common phenomenon in our population. We also noticed that epidemiological data are scarce. Newborn and carrier screening was only limited to pilot projects for a few genetic diseases. Collected data are being integrated into a database under construction that will be a valuable decision-making tool. This study provides the current situation of genetic diseases in Tunisia and highlights their particularities. Early detection of the disease is important to initiate critical intervention and to reduce morbidity and mortality.
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Affiliation(s)
- Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Nadia Zitouna
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Safa Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana 2080, Tunisia
| | - Faouzi Maazoul
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Ines Ouerteni
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Research Unit Genodermatosis and Cancer LR12SP03, Habib Thameur Hospital, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
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Cheng B, Liang C, Yang X, Li P, Liu L, Cheng S, Jia Y, Zhang L, Ma M, Qi X, Yao Y, Chu X, Ye J, Lu C, Guo X, Wen Y, Zhang F. Genetic association scan of 32 osteoarthritis susceptibility genes identified TP63 associated with an endemic osteoarthritis, Kashin-Beck disease. Bone 2021; 150:115997. [PMID: 33964467 DOI: 10.1016/j.bone.2021.115997] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/20/2021] [Accepted: 04/15/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Kashin-Beck disease (KBD) is an endemic chronic osteochondropathy. The clinical manifestations and radiographic features of adult KBD were similar to those of osteoarthritis (OA). METHODS We first performed a genetic association scan of 32 OA susceptibility genes with KBD in 898 Han Chinese subjects. The MassARRAY genotyping system (Agena) was used for SNP genotyping. PLINK 1.9 was used for quality control and association testing. Using articular cartilage specimens from 7 adult KBD patients and 4 control subjects, lentivirus-mediated RNA interference (RNAi), qRT-PCR, Western blot and immunohistochemistry were employed to explore the functional relevance of TP63 to KBD chondrocyte. RESULTS SNP genotyping and association analysis identified TP63 (rs12107036, P = 0.005, OR = 0.71) and OARD1 (rs11280, P = 0.004, OR = 1.51) were significantly associated with KBD. It was also found that TP63 was significantly up-regulated in KBD articular cartilage in both mRNA and protein level compared with the controls (P < 0.05). TP63 suppression by lentivirus-mediated RNAi notably decreased the abundance of Caspase3 and SOX9 in chondrocytes. Most importantly, compared with the scrambled sequence (shControl) group, the protein level of ACAN was increased in the shTP63 group. The mRNA expression of chondrocyte marker genes (COL2A1 and ACAN) was not significantly changed after TP63 knockdown relative to shControl group. CONCLUSION Our study identifies TP63 as a novel susceptibility gene for KBD, and demonstrates that the inhibition of TP63 suppresses chondrocyte apoptosis and partly facilitates chondrogenesis. The combination of SNP genotyping and molecular biology techniques provides a useful tool for understanding the biological mechanism and differential diagnosis studies of KBD and OA.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Chao Lu
- Department of Joint Surgery, Xi'an Honghui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China.
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China.
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Romdhane L, Mezzi N, Dallali H, Messaoud O, Shan J, Fakhro KA, Kefi R, Chouchane L, Abdelhak S. A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa. NPJ Genom Med 2021; 6:3. [PMID: 33420067 PMCID: PMC7794582 DOI: 10.1038/s41525-020-00166-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022] Open
Abstract
Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.
- Department of Biology, Faculty of Science of Bizerte, Jarzouna, Tunisia.
| | - Nessrine Mezzi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rym Kefi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
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Lei J, Yan S, Zhou Y, Wang L, Zhang J, Guo X, Lammi MJ, Han J, Qu C. Abnormal expression of chondroitin sulfate sulfotransferases in the articular cartilage of pediatric patients with Kashin-Beck disease. Histochem Cell Biol 2020; 153:153-164. [PMID: 31845005 DOI: 10.1007/s00418-019-01833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
The objective of this study is to investigate the expression of enzymes involved in the sulfation of articular cartilage from proximal metacarpophalangeal (PMC) joint cartilage and distal metacarpophalangeal (DMC) joint cartilage in children with Kashin-Beck disease (KBD). The finger cartilage samples of PMC and DMC were collected from KBD and normal children aged 5-14 years old. Hematoxylin and eosin staining as well as immunohistochemical staining were used to observe the morphology and quantitate the expression of carbohydrate sulfotransferase 3 (CHST-3), carbohydrate sulfotransferase 12 (CHST-12), carbohydrate sulfotransferase 13 (CHST-13), uronyl 2-O-sulfotransferase (UST), and aggrecan. In the results, the numbers of chondrocyte decreased in all three zones of PMC and DMC in the KBD group. Less positive staining cells for CHST-3, CHST-12, CHST-13, UST, and aggrecan were observed in almost all three zones of PMC and DMC in KBD. The positive staining cell rates of CHST-12 were higher in superficial and middle zones of PMC and DMC in KBD, and a significantly higher rate of CHST-13 was observed only in superficial zone of PMC in KBD. In conclusion, the abnormal expression of chondroitin sulfate sulfotransferases in chondrocytes of KBD children may provide an explanation for the cartilage damage, and provide therapeutic targets for the treatment.
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Affiliation(s)
- Jian Lei
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
| | - Siqi Yan
- Shenzhen Institute, Xi'an Jiaotong University, Shenzhen, 518057, P. R. China
- Department of Ophthalmology, The First Affiliated Hospital, Health Science Center of Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yuan Zhou
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
| | - Liyun Wang
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
- Shenzhen Institute, Xi'an Jiaotong University, Shenzhen, 518057, P. R. China
| | - Jinghua Zhang
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
| | - Xiong Guo
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
| | - Mikko J Lammi
- School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, P. R. China
- Department of Integrative Medical Biology, Umeå University, 90187, Umeå, Sweden
| | - Jing Han
- Shenzhen Institute, Xi'an Jiaotong University, Shenzhen, 518057, P. R. China.
| | - Chengjuan Qu
- Department of Integrative Medical Biology, Umeå University, 90187, Umeå, Sweden
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Zhang S, Pan X, Zeng T, Guo W, Gan Z, Zhang YH, Chen L, Zhang Y, Huang T, Cai YD. Copy Number Variation Pattern for Discriminating MACROD2 States of Colorectal Cancer Subtypes. Front Bioeng Biotechnol 2019; 7:407. [PMID: 31921812 PMCID: PMC6930883 DOI: 10.3389/fbioe.2019.00407] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Copy number variation (CNV) is a common structural variation pattern of DNA, and it features a higher mutation rate than single-nucleotide polymorphisms (SNPs) and affects a larger fragment of genomes. CNV is related with the genesis of complex diseases and can thus be used as a strategy to identify novel cancer-predisposing markers or mechanisms. In particular, the frequent deletions of mono-ADP-ribosylhydrolase 2 (MACROD2) locus in human colorectal cancer (CRC) alters DNA repair and the sensitivity to DNA damage and results in chromosomal instability. The relationship between CNV and cancer has not been explained. In this study, on the basis of the genome variation profiling by the SNP array from 651 CRC primary tumors, we computationally analyzed the CNV data to select crucial SNP sites with the most relevance to three different states of MACROD2 (heterozygous deletion, homozygous deletion, and normal state), suggesting that these CNVs may play functional roles in CRC tumorigenesis. Our study can shed new insights into the genesis of cancer based on CNV, providing reference for clinical diagnosis, and treatment prognosis of CRC.
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Affiliation(s)
- ShiQi Zhang
- School of Life Sciences, Shanghai University, Shanghai, China.,Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Institute of Image Processing and Pattern Recognition, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Guo
- Institute of Health Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Zijun Gan
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China.,Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai, China
| | - YunHua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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10
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He X, Bai M, Liu M, Wang L, He Y, Rong H, Yuan D, Jin T. Genetic variants in the ITPR2 gene are associated with Kashin-Beck Disease in Tibetan. Mol Genet Genomic Med 2019; 7:e00715. [PMID: 31066235 PMCID: PMC6625103 DOI: 10.1002/mgg3.715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/22/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Background Kashin‐Beck Disease (KBD) is a chronic, endemic osteoarthropathy. Inositol 1,4,5‐triphosphate receptor type 2 (ITPR2) gene is involved in chondrocytes. We speculated that single‐nucleotide polymorphisms (SNPs) in ITPR2 gene may have an association with KBD in Tibetan. Methods To prove this hypothesis, a total of eight SNPs (rs1049376, rs11048526, rs11048556, rs11048585, rs16931011, rs10842759, rs2230372, and rs7134213) were selected, and genotyped in 316 KBD patients and 320 controls. The association between ITPR2 variants and KBD risk was assessed by logistic regression analysis. Results The study identified significant association (p = 0.019) between KBD and a novel locus, ITPR2 SNP rs11048526 (OR = 1.49, 95% CI = 1.07–2.08). The variant A/G genotype frequency in rs11048526 had a significantly increased risk of KBD in co‐dominant model (OR = 3.70, 95% CI = 1.26–10.89, p = 0.018), dominant model (OR = 3.56, 95% CI = 1.22–10.40, p = 0.020), log‐additive model (OR = 3.00, 95% CI = 1.12–8.00, p = 0.029) after adjusted for age and gender. Conclusion The results indicate a potential association between ITPR2 and KBD risk in Tibetan. Further work is required to confirm these results and explore the mechanisms of these effects.
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Affiliation(s)
- Xue He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Mei Bai
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Ming Liu
- Department of gynaecology and obstetricsThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
- Department of gynaecology and obstetricsThe Ngari Prefecture People's HospitalNgari PrefectureChina
| | - Li Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Yongjun He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Hao Rong
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Dongya Yuan
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
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11
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Zhang R, Guo H, Yang X, Zhang D, Li B, Li Z, Xiong Y. Pathway-based network analyses and candidate genes associated with Kashin-Beck disease. Medicine (Baltimore) 2019; 98:e15498. [PMID: 31045836 PMCID: PMC6504273 DOI: 10.1097/md.0000000000015498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To perform a comprehensive analysis focusing on the biological functions and interactions of Kashin-Beck disease (KBD)-related genes to provide information towards understanding the pathogenesis of KBD.A retrospective, integrated bioinformatics analysis was designed and conducted. First, by reviewing the literature deposited in PubMed, we identified 922 genes genetically associated with KBD. Then, biological function and network analyses were conducted with Cytoscape software. Moreover, KBD specific molecular network analysis was conducted by Cytocluster using the Molecular Complex Detection Algorithm (MCODE).The biological function enrichment analysis suggested that collagen catabolic process, protein activation cascade, cellular response to growth factor stimulus, skeletal system development, and extrinsic apoptosis played important roles in KBD development. The apoptosis pathway, NF-kappa B signaling pathway, and the glutathione metabolism pathway were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway network, suggesting that these pathways may play key roles in KBD occurrence and development. MCODE clusters showed that in top 3 clusters, 54 of KBD-related genes were included in the network and 110 candidate genes were discovered might be potentially related to KBD.The 110 candidate genes discovered in the current study may be related to the development of KBD. The expression changes of apoptosis and oxidative stress-related genes might serve as biomarkers for early diagnosis and treatment of KBD.
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Affiliation(s)
- Rongqiang Zhang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
- Shaanxi University of Chinese Medicine, Xianyang, China
| | - Hao Guo
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
| | - Xiaoli Yang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
| | - Dandan Zhang
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
| | - Baorong Li
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
| | - Zhaofang Li
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
| | - Yongmin Xiong
- School of Public Health, Xi’an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi’an
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12
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Wu LF, Zhu DC, Tang CH, Ge B, Shi J, Wang BH, Lu YH, He P, Wang WY, Lu SQ, Zhong J, Zhou X, Zhu K, Ji W, Gao HQ, Gu HB, Mo XB, Lu X, Zhang L, Zhang YH, Deng FY, Lei SF. Association of Plasma Irisin with Bone Mineral Density in a Large Chinese Population Using an Extreme Sampling Design. Calcif Tissue Int 2018; 103:246-251. [PMID: 29582132 DOI: 10.1007/s00223-018-0415-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 03/20/2018] [Indexed: 12/16/2022]
Abstract
Irisin, a myokine produced by skeletal muscle in response to physical exercise, promotes trans-differentiation of white adipose tissue into brown adipose tissue. Recent evidences suggested that irisin also plays an important role in the control of bone metabolism. This study aimed to ascertain the relationship between plasma irisin and bone mineral density (BMD) in Chinese population by adoption of an extreme sampling method. Based on a large and screened Chinese elderly population (N = 6308), two subgroups with extremely high and low hip BMD were selected for discovery (N = 80, high vs. low BMD = 44:36) and validation (N = 60, high vs. low BMD = 30:30), respectively. Plasma irisin, P1NP, and β-CTx were measured using commercially available ELISA kits. Other metabolic parameters (e.g., blood glucose, total cholesterol and triglycerides) were collected. Student's t test and Spearman correlation analyses were conducted in SPSS. Significant difference was discovered for plasma irisin between females and age-matched males (N = 80, male vs. female = 42:38, P = 0.002). The plasma irisin levels were significantly higher in high BMD subjects than in low BMD subjects, which was observed in both discovery (P = 0.012) and validation samples (P = 0.022). However, such observation was limited to males only. Further correlation analyses in males showed that plasma irisin was correlated with BMD (r = 0.362, P = 0.025) and triglyceride (r = - 0.354, P = 0.032). Plasma irisin levels were associated with hip BMD in Chinese elderly men. This study represented the first effort of investigating the relationship of plasma irisin and BMD in elderly population. The positive correlation between plasma irisin and BMD hints intrinsic communication between muscle and bone.
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Affiliation(s)
- Long-Fei Wu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Dong-Cheng Zhu
- Department of Orthopedics, Sihong People's Hospital, Suqian, 223900, Jiangsu, People's Republic of China
| | - Chang-Hua Tang
- Department of Orthopedics, Sihong People's Hospital, Suqian, 223900, Jiangsu, People's Republic of China
| | - Bing Ge
- Department of Orthopedics, Sihong People's Hospital, Suqian, 223900, Jiangsu, People's Republic of China
| | - Ju Shi
- Department of Orthopedics, Sihong People's Hospital, Suqian, 223900, Jiangsu, People's Republic of China
| | - Bing-Hua Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Yi-Hua Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Wen-Yu Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Si-Qi Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Jiao Zhong
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xu Zhou
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Kan Zhu
- Loujiang Community Health Service Center, Suzhou Gusu District, Suzhou, Jiangsu, People's Republic of China
| | - Wen Ji
- Disease Prevention and Control Center of Suzhou high Tech Zone, Suzhou, Jiangsu, People's Republic of China
| | - Hong-Qin Gao
- Shishan Community Health Service Center, Suzhou High Tech Zone, Suzhou, Jiangsu, People's Republic of China
| | - Hong-Bo Gu
- Shishan Community Health Service Center, Suzhou High Tech Zone, Suzhou, Jiangsu, People's Republic of China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
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Xu C, Fang J, Shen H, Wang YP, Deng HW. EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits. Bioinformatics 2018; 34:1996-2003. [PMID: 29385408 PMCID: PMC6454442 DOI: 10.1093/bioinformatics/bty042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 01/19/2023] Open
Abstract
Motivation Extreme phenotype sampling (EPS) is a broadly-used design to identify candidate genetic factors contributing to the variation of quantitative traits. By enriching the signals in extreme phenotypic samples, EPS can boost the association power compared to random sampling. Most existing statistical methods for EPS examine the genetic factors individually, despite many quantitative traits have multiple genetic factors underlying their variation. It is desirable to model the joint effects of genetic factors, which may increase the power and identify novel quantitative trait loci under EPS. The joint analysis of genetic data in high-dimensional situations requires specialized techniques, e.g. the least absolute shrinkage and selection operator (LASSO). Although there are extensive research and application related to LASSO, the statistical inference and testing for the sparse model under EPS remain unknown. Results We propose a novel sparse model (EPS-LASSO) with hypothesis test for high-dimensional regression under EPS based on a decorrelated score function. The comprehensive simulation shows EPS-LASSO outperforms existing methods with stable type I error and FDR control. EPS-LASSO can provide a consistent power for both low- and high-dimensional situations compared with the other methods dealing with high-dimensional situations. The power of EPS-LASSO is close to other low-dimensional methods when the causal effect sizes are small and is superior when the effects are large. Applying EPS-LASSO to a transcriptome-wide gene expression study for obesity reveals 10 significant body mass index associated genes. Our results indicate that EPS-LASSO is an effective method for EPS data analysis, which can account for correlated predictors. Availability and implementation The source code is available at https://github.com/xu1912/EPSLASSO. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chao Xu
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Jian Fang
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, USA
| | - Hui Shen
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
| | - Yu-Ping Wang
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, USA
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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Wen Y, Li P, Hao J, Duan C, Han J, He A, Du Y, Liu L, Liang X, Zhang F, Guo X. Integrating genome-wide DNA methylation and mRNA expression profiles identified different molecular features between Kashin-Beck disease and primary osteoarthritis. Arthritis Res Ther 2018. [PMID: 29514696 PMCID: PMC5842623 DOI: 10.1186/s13075-018-1531-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Kashin-Beck disease (KBD) is an endemic osteochondropathy of unknown etiology. Osteoarthritis (OA) is a form of degenerative joint disease sharing similar clinical manifestations and pathological changes to articular cartilage with KBD. Methods A genome-wide DNA methylation profile of articular cartilage from five KBD patients and five OA patients was first performed using the Illumina Infinium HumanMethylation450 BeadChip. Together with a previous gene expression profiling dataset comparing KBD cartilage with OA cartilage, an integrative pathway enrichment analysis of the genome-wide DNA methylation and the mRNA expression profiles conducted in articular cartilage was performed by InCroMAP software. Results We identified 241 common genes altered in both the DNA methylation profile and the mRNA expression profile of articular cartilage of KBD versus OA, including CHST13 (NM_152889, fold-change = 0.5979, Pmethy = 0.0430), TGFBR1 (NM_004612, fold-change = 2.077, Pmethy = 0.0430), TGFBR2 (NM_001024847, fold-change = 1.543, Pmethy = 0.037), TGFBR3 (NM_001276, fold-change = 0.4515, Pmethy = 6.04 × 10−4), and ADAM12 (NM_021641, fold-change = 1.9768, Pmethy = 0.0178). Integrative pathway enrichment analysis identified 19 significant KEGG pathways, including mTOR signaling (P = 0.0301), glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate (P = 0.0391), glycosaminoglycan biosynthesis-keratan sulfate (P = 0.0278), and PI3K-Akt signaling (P = 0.0243). Conclusion This study identified different molecular features between Kashin-Beck disease and primary osteoarthritis and provided novel clues for clarifying the pathogenetic differences between KBD and OA. Electronic supplementary material The online version of this article (10.1186/s13075-018-1531-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Jingcan Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.,The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Chen Duan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Jing Han
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Awen He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yanan Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Xiao Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University, Health Science Center, No.76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.
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15
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Radder JE, Gregory AD, Leme AS, Cho MH, Chu Y, Kelly NJ, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Beaty TH, Crapo JD, Silverman EK, Zhang Y, Berndt A, Shapiro SD. Variable Susceptibility to Cigarette Smoke-Induced Emphysema in 34 Inbred Strains of Mice Implicates Abi3bp in Emphysema Susceptibility. Am J Respir Cell Mol Biol 2017; 57:367-375. [PMID: 28441029 DOI: 10.1165/rcmb.2016-0220oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge about the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. To that end, we sought to measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD. Alveolar chord length (CL) in 34 inbred strains of mice was measured after 6 months of exposure to cigarette smoke. After testing for association, we connected a murine candidate locus to a published meta-analysis of moderate-to-severe COPD. We identified deleterious mutations in a candidate gene in silico and measured gene expression in extreme strains. A/J was the most susceptible strain in our survey (Δ CL 7.0 ± 2.2 μm) and CBA/J was the least susceptible (Δ CL -0.3 ± 1.2 μm). By integrating mouse and human genome-wide scans, we identified the candidate gene Abi3bp. CBA/J mice harbor predicted deleterious variants in Abi3bp, and expression of the gene differs significantly between CBA/J and A/J mice. This is the first report of susceptibility to cigarette smoke-induced emphysema in 34 inbred strains of mice, and Abi3bp is identified as a potential contributor to this phenotype.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adriana S Leme
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael H Cho
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yanxia Chu
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Per Bakke
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Augusto A Litonjua
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 5 School of Public Health and.,6 School of Medicine, Boston University, Boston, Massachusetts.,7 Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Terri H Beaty
- 8 Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | - James D Crapo
- 9 Department of Radiology, National Jewish Health, Denver, Colorado
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Annerose Berndt
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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16
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Genome-wide association study identifies COL2A1 locus involved in the hand development failure of Kashin-Beck disease. Sci Rep 2017; 7:40020. [PMID: 28059113 PMCID: PMC5216336 DOI: 10.1038/srep40020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 12/01/2016] [Indexed: 11/09/2022] Open
Abstract
Kashin-Beck disease (KBD) is a chronic osteochondropathy. The pathogenesis of growth and development failure of hand of KBD remains elusive now. In this study, we conducted a two-stage genome-wide association study (GWAS) of palmar length-width ratio (LWR) of KBD, totally including 493 study subjects. Affymetrix Genome Wide Human SNP Array 6.0 was applied for genome-wide SNP genotyping of 90 KBD patients. Association analysis was conducted by PLINK. Imputation analysis was performed by IMPUTE against the reference panel of the 1000 genome project. Two SNPs were selected for replication in an independent validation sample of 403 KBD patients. In the discovery GWAS, significant association was observed between palmar LWR and rs2071358 of COL2A1 gene (P value = 4.68 × 10−8). In addition, GWAS detected suggestive association signal at rs4760608 of COL2A1 gene (P value = 1.76 × 10−4). Imputation analysis of COL2A1 further identified 2 SNPs with association evidence for palmar LWR. Replication study observed significant association signals at both rs2071358 (P value = 0.017) and rs4760608 (P value = 0.002) of COL2A1 gene. Based on previous and our study results, we suggest that COL2A1 was a likely susceptibility gene involved in the hand development failure of KBD.
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17
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Yang H, Chen W, Shi J, Huang D, Li J, Hu B, Zhang M, Wang Z, Fei J. Knockout of Abi3bp in mice does not affect their olfactory function, mental state and NNK-induced lung tumorigenesis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:820-6. [PMID: 27521794 DOI: 10.1093/abbs/gmw071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023] Open
Abstract
Abi3bp was originally discovered as Abi3-Src homology 3 (SH3) binding protein and has been proved to have a broad expression profile in adult tissues. Although previous studies have indicated that Abi3bp may be associated with cancer suppression, cell senescence, dendritic refinement and mental disorder, most conclusions achieved were based on in vitro model or genome-wide association study. In this work, we constructed an Abi3bp-deficient mouse model and observed phenotypic changes. The generated Abi3bp-knockout mice are viable and fertile, develop normally and exhibit no significant differences in anxiety or depression-like behaviors, olfactory function and tumor incidence. These data suggest that the function of Abi3bp in in vitro models does not translate to a similar role in the intact animal. Its depletion may be compensated by other genes, which needs to be addressed in future studies.
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Affiliation(s)
- Hua Yang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Weidong Chen
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jiahao Shi
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Dandan Huang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jun Li
- Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Binyang Hu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengjie Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Zhugang Wang
- Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Jian Fei
- School of Life Science and Technology, Tongji University, Shanghai 200092, China Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
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18
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A bivariate genome-wide association study identifies ADAM12 as a novel susceptibility gene for Kashin-Beck disease. Sci Rep 2016; 6:31792. [PMID: 27545300 PMCID: PMC4992896 DOI: 10.1038/srep31792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/26/2016] [Indexed: 11/28/2022] Open
Abstract
Kashin-Beck disease (KBD) is a chronic osteoarthropathy, which manifests as joint deformities and growth retardation. Only a few genetic studies of growth retardation associated with the KBD have been carried out by now. In this study, we conducted a two-stage bivariate genome-wide association study (BGWAS) of the KBD using joint deformities and body height as study phenotypes, totally involving 2,417 study subjects. Articular cartilage specimens from 8 subjects were collected for immunohistochemistry. In the BGWAS, ADAM12 gene achieved the most significant association (rs1278300 p-value = 9.25 × 10−9) with the KBD. Replication study observed significant association signal at rs1278300 (p-value = 0.007) and rs1710287 (p-value = 0.002) of ADAM12 after Bonferroni correction. Immunohistochemistry revealed significantly decreased expression level of ADAM12 protein in the KBD articular cartilage (average positive chondrocyte rate = 47.59 ± 7.79%) compared to healthy articular cartilage (average positive chondrocyte rate = 64.73 ± 5.05%). Our results suggest that ADAM12 gene is a novel susceptibility gene underlying both joint destruction and growth retardation of the KBD.
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19
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Kader A, Liu X, Dong K, Song S, Pan J, Yang M, Chen X, He X, Jiang L, Ma Y. Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array. Anim Genet 2016; 47:560-9. [PMID: 27440410 DOI: 10.1111/age.12451] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 02/06/2023]
Abstract
Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.
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Affiliation(s)
- Adiljan Kader
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,Xinjiang Academy of Animal Science, Urumqi, Xinjiang, 83000, China
| | - Xuexue Liu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Kunzhe Dong
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Shen Song
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.,Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100094, China
| | - Jianfei Pan
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Min Yang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Xiaofei Chen
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Xiaohong He
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), No 2 Yuanmingyuan West Rd., Haidian, Beijing, 100193, China.
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20
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Field synopsis and meta-analyses of genetic epidemiological evidence for Kashin–Beck disease, an endemic osteoarthropathy in China. Mol Genet Genomics 2016; 291:1823-33. [DOI: 10.1007/s00438-016-1222-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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21
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Rohart F, Mason EA, Matigian N, Mosbergen R, Korn O, Chen T, Butcher S, Patel J, Atkinson K, Khosrotehrani K, Fisk NM, Lê Cao KA, Wells CA. A molecular classification of human mesenchymal stromal cells. PeerJ 2016; 4:e1845. [PMID: 27042394 PMCID: PMC4811172 DOI: 10.7717/peerj.1845] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stromal cells (MSC) are widely used for the study of mesenchymal tissue repair, and increasingly adopted for cell therapy, despite the lack of consensus on the identity of these cells. In part this is due to the lack of specificity of MSC markers. Distinguishing MSC from other stromal cells such as fibroblasts is particularly difficult using standard analysis of surface proteins, and there is an urgent need for improved classification approaches. Transcriptome profiling is commonly used to describe and compare different cell types; however, efforts to identify specific markers of rare cellular subsets may be confounded by the small sample sizes of most studies. Consequently, it is difficult to derive reproducible, and therefore useful markers. We addressed the question of MSC classification with a large integrative analysis of many public MSC datasets. We derived a sparse classifier (The Rohart MSC test) that accurately distinguished MSC from non-MSC samples with >97% accuracy on an internal training set of 635 samples from 41 studies derived on 10 different microarray platforms. The classifier was validated on an external test set of 1,291 samples from 65 studies derived on 15 different platforms, with >95% accuracy. The genes that contribute to the MSC classifier formed a protein-interaction network that included known MSC markers. Further evidence of the relevance of this new MSC panel came from the high number of Mendelian disorders associated with mutations in more than 65% of the network. These result in mesenchymal defects, particularly impacting on skeletal growth and function. The Rohart MSC test is a simple in silico test that accurately discriminates MSC from fibroblasts, other adult stem/progenitor cell types or differentiated stromal cells. It has been implemented in the www.stemformatics.org resource, to assist researchers wishing to benchmark their own MSC datasets or data from the public domain. The code is available from the CRAN repository and all data used to generate the MSC test is available to download via the Gene Expression Omnibus or the Stemformatics resource.
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Affiliation(s)
- Florian Rohart
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Elizabeth A. Mason
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Matigian
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Rowland Mosbergen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
| | - Tyrone Chen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Suzanne Butcher
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Jatin Patel
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Kerry Atkinson
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Kiarash Khosrotehrani
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Prenatal Care, Royal Brisbane & Women’s Hospital, Brisbane, Queensland, Australia
| | - Nicholas M. Fisk
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Prenatal Care, Royal Brisbane & Women’s Hospital, Brisbane, Queensland, Australia
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Christine A. Wells
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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22
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Song YJ, Li G, He JH, Guo Y, Yang L. Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes. PLoS One 2015; 10:e0137551. [PMID: 26359667 PMCID: PMC4567271 DOI: 10.1371/journal.pone.0137551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/19/2015] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) act as epigenetic markers and regulate the expression of their target genes, including those characterized as regulators in autoimmune diseases. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases. The potential roles of miRNA-regulated genes in RA pathogenesis have greatly aroused the interest of clinicians and researchers in recent years. In the current study, RA-related miRNAs records were obtained from PubMed through conditional literature retrieval. After analyzing the selected records, miRNA targeted genes were predicted. We identified 14 RA-associated miRNAs, and their sub-analysis in 5 microarray or RNA sequencing (RNA-seq) datasets was performed. The microarray and RNA-seq data of RA were also downloaded from NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), analyzed, and annotated. Using a bioinformatics approach, we identified a series of differentially expressed genes (DEGs) by comparing studies on RA and the controls. The RA-related gene expression profile was thus obtained and the expression of miRNA-regulated genes was analyzed. After functional annotation analysis, we found GO molecular function (MF) terms significantly enriched in calcium ion binding (GO: 0005509). Moreover, some novel dysregulated target genes were identified in RA through integrated analysis of miRNA/mRNA expression. The result revealed that the expression of a number of genes, including ROR2, ABI3BP, SMOC2, etc., was not only affected by dysregulated miRNAs, but also altered in RA. Our findings indicate that there is a close association between negatively correlated mRNA/miRNA pairs and RA. These findings may be applied to identify genetic markers for RA diagnosis and treatment in the future.
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Affiliation(s)
- Yi-Jiang Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Guiling Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jian-Hua He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Yao Guo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
- * E-mail:
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23
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Zhang F, Dai L, Lin W, Wang W, Liu X, Zhang J, Yang T, Liu X, Shen H, Chen X, Tan L, Tian Q, Deng HW, Xu X, Guo X. Exome sequencing identified FGF12 as a novel candidate gene for Kashin-Beck disease. Funct Integr Genomics 2015; 16:13-7. [PMID: 26290467 DOI: 10.1007/s10142-015-0462-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/30/2015] [Accepted: 08/02/2015] [Indexed: 11/28/2022]
Abstract
The objective of this study was to identify novel causal genes involved in the pathogenesis of Kashin-Beck disease (KBD). A representative grade III KBD sib pair with serious skeletal growth and development failure was subjected to exome sequencing using the Illumina Hiseq2000 platform. The detected gene mutations were then filtered against the data of 1000 Genome Project, dbSNP database, and BGI inhouse database, and replicated by a genome-wide association study (GWAS) of KBD. Ninety grade II or III KBD patients with extreme KBD phenotypes and 1627 healthy controls were enrolled in the GWAS. Affymetrix Genome-Wide Human SNP Array 6.0 was applied for genotyping. PLINK software was used for association analysis. We identified a novel 106T>C at the 3'UTR of the FGF12 gene, which has not been reported by now. Sequence alignment observed high conversation at the mutated 3'UTR+106T>C locus across various vertebrates. In the GWAS of KBD, we detected nine SNPs of the FGF12 gene showing association evidence (P value < 0.05) with KBD. The most significant association signal was observed at rs1847340 (P value = 1.90 × 10(-5)). This study suggests that FGF12 was a susceptibility gene of KBD. Our results provide novel clues for revealing the pathogenesis of KBD and the biological function of FGF12.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | | | - Weimin Lin
- Department of Nephrology and Traditional Chinese Medicine, The People's Liberating Army 451 Hospital, Xi'an, People's Republic of China
| | - Wenyu Wang
- Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | | | | | - Tielin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Xiaogang Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Hui Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Xiangding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Lijun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Du XA, Wang HM, Dai XX, Kou Y, Wu RP, Chen Q, Cao JL, Mo XY, Xiong YM. Role of selenoprotein S (SEPS1) -105G>A polymorphisms and PI3K/Akt signaling pathway in Kashin-Beck disease. Osteoarthritis Cartilage 2015; 23:210-6. [PMID: 25433273 DOI: 10.1016/j.joca.2014.11.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To investigate the relationship between SEPS1 polymorphism and phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway in Kashin-Beck disease (KBD) and further explore the pathogenesis of KBD. METHODS Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to detect SEPS1 -105G>A polymorphism in 232 cases and 331 controls. The protein expressions of PI3K/Akt signaling molecules in whole blood and chondrocytes were detected by Western blot. RESULTS The frequencies of SEPS1 -105G>A genotype AA (21.1% vs 3.0%) and minor allele A (34.1% vs 16.0%) in KBD are significantly higher than those in controls (OR: 8.020, 95% confidence interval (95% CI) 6.341-10.290, P < 0.0001; OR: 2.470, 95% CI 2.001-4.463, P < 0.0001, respectively). SEPS1 AA genotype was an independent risk factor for KBD (adjusted OR: 9.345, 95% CI 4.254-20.529; P < 0.0001). The expression of Gβγ, PI3Kp110, pAkt and pGSK3β in KBD group were higher than that in control group (all P < 0.05). Gβγ, pAkt and pGSK3β protein expression of AA and GA increased than GG (all P < 0.05). Cell apoptosis was increasing and molecule expression of PI3K/Akt signaling pathway were up-regulated in the tert-Butyl hydroperoxide (tBHP)-injured group, the cell apoptosis and expression levels of PI3K/Akt in Na2SeO3 group were decreased. CONCLUSIONS The SEPS1 -105G>A is associated with an increased risk of KBD and influences the expression of PI3K/Akt signaling pathway in KBD patients. Apoptosis induced by tBHP in chondrocyte might be mediated via up-regulation of PI3K/Akt, Na2SeO3 has an effect of anti-apoptosis by down-regulating of PI3K/Akt signaling pathway.
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Affiliation(s)
- X A Du
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - H M Wang
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - X X Dai
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - Y Kou
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - R P Wu
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - Q Chen
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - J L Cao
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China
| | - X Y Mo
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, PR China
| | - Y M Xiong
- Institute of Endemic Diseases, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, PR China.
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25
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Rose-Martel M, Smiley S, Hincke MT. Novel identification of matrix proteins involved in calcitic biomineralization. J Proteomics 2015; 116:81-96. [DOI: 10.1016/j.jprot.2015.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/01/2015] [Accepted: 01/03/2015] [Indexed: 02/06/2023]
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Guo X, Ma WJ, Zhang F, Ren FL, Qu CJ, Lammi MJ. Recent advances in the research of an endemic osteochondropathy in China: Kashin-Beck disease. Osteoarthritis Cartilage 2014; 22:1774-83. [PMID: 25106677 DOI: 10.1016/j.joca.2014.07.023] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/12/2014] [Accepted: 07/29/2014] [Indexed: 02/02/2023]
Abstract
Kashin-Beck disease (KBD) is an endemic chronic osteochondral disease, which has a high prevalence and morbidity in the Eastern Siberia of Russia, and in the broad diagonal, northern-east to southern-west belt in China and North Korea. In 1990's, it was estimated that in China 1-3 million people had some degree of symptoms of the disease, although even higher estimates have been presented. In China, the extensive prevalence peaked in the late 1950's, but since then, in contrast to the global trend of the osteoarthritis (OA), the number of cases has been dramatically falling. Up to 2013, there are 0.64 millions patients with the KBD and 1.16 millions at risk in 377 counties of 13 provinces or autonomous regions. This is obviously thanks to the preventive efforts carried out, which include providing millions of people with dietary supplements and clean water, as well as relocation of whole villages in China. However, relatively little is known about the molecular mechanisms behind the cartilage damage, the genetic and the environmental risk factors, and the rationale of the preventive effects. During the last decade, new data on a cellular and molecular level has begun to accumulate, which hopefully will uncover the grounds of the disease.
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Affiliation(s)
- X Guo
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases in the Education Ministry and Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China.
| | - W-J Ma
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases in the Education Ministry and Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China
| | - F Zhang
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases in the Education Ministry and Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China
| | - F-L Ren
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Environment and Genes Related to Diseases in the Education Ministry and Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China
| | - C-J Qu
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - M J Lammi
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland.
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