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Tshilate TS, Ishengoma E, Rhode C. Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae). Anim Genet 2024. [PMID: 38945682 DOI: 10.1111/age.13462] [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: 10/02/2023] [Revised: 03/23/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024]
Abstract
Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.
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Affiliation(s)
| | - Edson Ishengoma
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Mkwawa University College of Education, University of Dar es Salaam, Iringa, Tanzania
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Matieland, South Africa
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2
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Luo Z, Zeng H, Yang K, Wang Y. FOXQ1 inhibits the progression of osteoarthritis by regulating pyroptosis. Aging (Albany NY) 2024; 16:5077-5090. [PMID: 38503493 PMCID: PMC11006491 DOI: 10.18632/aging.205600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/17/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Osteoarthritis (OA) is the most common age-related joint disease, and the NLRP3-induced pyroptosis has been demonstrated in its progression. The upstream molecules or specific mechanisms controlling NLRP3 and pyroptosis in OA remain unclear. METHODS Transcriptome sequencing was performed in the OA mice model, and the expression levels of differentially expressed genes were assessed by qRT-PCR. The cell model was constructed by IL-1β-induced ATDC5 cells. The cell proliferation was examined using CCK-8 assay, and apoptosis was tested using flow cytometry. Western blot was used in protein inspection, and ELISA was used in inflammatory response evaluation. RESULTS Compared with the control group, there were 229 up-regulated and 32 down-regulated genes in model group. We detected that FOXQ1 was down-regulated in the OA mice model, improved proliferation, and restrained apoptosis of chondrocytes. Over-expression of FOXQ1 could inhibit pyroptosis-related proteins and inflammatory cytokines, containing NLRP3, Caspase-1, GSDMD, IL-6, IL-18, and TNF-α, and in contrast, FOXQ1 silencing exerted the opposite trend. CONCLUSIONS FOXQ1 may inhibit OA progression via down-regulating NLRP3-induced pyroptosis in the present study.
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Affiliation(s)
- Zhihuan Luo
- Department of Sports Medicine, Ganzhou People’s Hospital, Ganzhou 341000, Jiangxi Province, China
| | - Hui Zeng
- Department of Sports Medicine, Ganzhou People’s Hospital, Ganzhou 341000, Jiangxi Province, China
| | - Kanghua Yang
- Department of Sports Medicine, Ganzhou People’s Hospital, Ganzhou 341000, Jiangxi Province, China
| | - Yihai Wang
- Department of Sports Medicine, Ganzhou People’s Hospital, Ganzhou 341000, Jiangxi Province, China
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3
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Taniguchi J, Masuda T, Iwatani Y, Yamamoto K, Sakai N, Okada Y, Watanabe M. Rigorous evaluation of genetic and epigenetic effects on clinical laboratory measurements using Japanese monozygotic twins. Clin Genet 2024; 105:159-172. [PMID: 37899590 DOI: 10.1111/cge.14443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/10/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
The investigation of environmental effects on clinical measurements using individual samples is challenging because their genetic and environmental factors are different. However, using monozygotic twins (MZ) makes it possible to investigate the influence of environmental factors as they have the same genetic factors within pairs because the difference in the clinical traits within the MZ mostly reflect the influence of environmental factors. We hypothesized that the within-pair differences in the traits that are strongly affected by genetic factors become larger after genetic risk score (GRS) correction. Using 278 Japanese MZ pairs, we compared the change in within-pair differences in each of the 45 normalized clinical measurements before and after GRS correction, and we also attempted to correct for the effects of genetic factors to identify Cytosine-phosphodiester-Guanine (CpG) sites in DNA sequences with epigenetic effects that are regulated by genetic factors. Five traits were classified into the high heritability group, which was strongly affected by genetic factors. CpG sites could be classified into three groups: regulated only by environmental factors, regulated by environmental factors masked by genetic factors, and regulated only by genetic factors. Our method has the potential to identify trait-related methylation sites that have not yet been discovered.
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Affiliation(s)
- Jumpei Taniguchi
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshinori Iwatani
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Norio Sakai
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
- Child Healthcare and Genetic Science Laboratory, Division of Health Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Twin Research, Osaka University Graduate School of Medicine, Suita, Japan
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4
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Liang H, Liu G, Zeng W, Fan Q, Nie Z, Hu H, Zhang R, Xie S. MEGF6 prevents sepsis-induced acute lung injury in mice. Int Immunopharmacol 2023; 123:110727. [PMID: 37597402 DOI: 10.1016/j.intimp.2023.110727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
OBJECTIVE Acute lung injury (ALI) is featured as excessive inflammatory response and oxidative damage, and results in high death rate of septic patients. This research intends to determine the function of multiple EGF like domains 6 (MEGF6) in sepsis-induced ALI. METHODS Mice were intratracheally treated with adenovirus to knock down or overexpress MEGF6 in lung tissues, and then were subjected to cecum ligation and puncture (CLP) operation to induce ALI. Primary peritoneal macrophages were isolated, and were knocked down or overexpressed with MEGF6, and then, were stimulated with lipopolysaccharide (LPS) to confirm its role in vitro. RESULTS Serum and lung MEGF6 levels were significantly elevated in septic mice. MEGF6 knockdown exacerbated, while MEGF6 overexpression prevented inflammation, oxidative damage and ALI in CLP mice. Meanwhile, LPS-elicited inflammatory response and oxidative damage in primary macrophages were reduced by MEGF6 overexpression, but were further aggravated by MEGF6 knockdown. Mechanistic studies revealed that MEGF6 reduced cluster of differentiation 38 (CD38) expression and subsequently elevated intracellular nicotinamide adenine dinucleotide levels, thereby activating sirtuin 1 (SIRT1) without affecting the protein expression. SIRT1 suppression or CD38 overexpression with either genetic or pharmacologic methods remarkably blunted the lung protective effects of MEGF6 in CLP mice. CONCLUSION MEGF6 prevents CLP-induced ALI through CD38/SIRT1 pathway, and it might be a valuable therapeutic candidate for the management of sepsis-induced ALI.
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Affiliation(s)
- Hui Liang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Gaoli Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Wenhui Zeng
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Qinglu Fan
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Zhihao Nie
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Haifeng Hu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Renquan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China.
| | - Songping Xie
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China.
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Paz-González R, Lourido L, Calamia V, Fernández-Puente P, Quaranta P, Picchi F, Blanco FJ, Ruiz-Romero C. An Atlas of the Knee Joint Proteins and Their Role in Osteoarthritis Defined by Literature Mining. Mol Cell Proteomics 2023; 22:100606. [PMID: 37356495 PMCID: PMC10393810 DOI: 10.1016/j.mcpro.2023.100606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/14/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023] Open
Abstract
Osteoarthritis (OA) is the most prevalent rheumatic pathology. However, OA is not simply a process of wear and tear affecting articular cartilage but rather a disease of the entire joint. One of the most common locations of OA is the knee. Knee tissues have been studied using molecular strategies, generating a large amount of complex data. As one of the goals of the Rheumatic and Autoimmune Diseases initiative of the Human Proteome Project, we applied a text-mining strategy to publicly available literature to collect relevant information and generate a systematically organized overview of the proteins most closely related to the different knee components. To this end, the PubPular literature-mining software was employed to identify protein-topic relationships and extract the most frequently cited proteins associated with the different knee joint components and OA. The text-mining approach searched over eight million articles in PubMed up to November 2022. Proteins associated with the six most representative knee components (articular cartilage, subchondral bone, synovial membrane, synovial fluid, meniscus, and cruciate ligament) were retrieved and ranked by their relevance to the tissue and OA. Gene ontology analyses showed the biological functions of these proteins. This study provided a systematic and prioritized description of knee-component proteins most frequently cited as associated with OA. The study also explored the relationship of these proteins to OA and identified the processes most relevant to proper knee function and OA pathophysiology.
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Affiliation(s)
- Rocío Paz-González
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Lucía Lourido
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Valentina Calamia
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Patricia Fernández-Puente
- Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Grupo de Investigación de Reumatología y Salud (GIR-S), Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Patricia Quaranta
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Florencia Picchi
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain
| | - Francisco J Blanco
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Grupo de Investigación de Reumatología y Salud (GIR-S), Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain.
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - Unidad de Proteómica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Sergas, Complexo Hospitalario Universitario de A Coruña (CHUAC), A Coruña, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
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6
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Schweizer RM, Ivy CM, Natarajan C, Scott GR, Storz JF, Cheviron ZA. Gene regulatory changes underlie developmental plasticity in respiration and aerobic performance in highland deer mice. Mol Ecol 2023; 32:3483-3496. [PMID: 37073620 PMCID: PMC10330314 DOI: 10.1111/mec.16953] [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: 09/26/2022] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
Phenotypic plasticity can play an important role in the ability of animals to tolerate environmental stress, but the nature and magnitude of plastic responses are often specific to the developmental timing of exposure. Here, we examine changes in gene expression in the diaphragm of highland deer mice (Peromyscus maniculatus) in response to hypoxia exposure at different stages of development. In highland deer mice, developmental plasticity in diaphragm function may mediate changes in several respiratory traits that influence aerobic metabolism and performance under hypoxia. We generated RNAseq data from diaphragm tissue of adult deer mice exposed to (1) life-long hypoxia (before conception to adulthood), (2) post-natal hypoxia (birth to adulthood), (3) adult hypoxia (6-8 weeks only during adulthood) or (4) normoxia. We found five suites of co-regulated genes that are differentially expressed in response to hypoxia, but the patterns of differential expression depend on the developmental timing of exposure. We also identified four transcriptional modules that are associated with important respiratory traits. Many of the genes in these transcriptional modules bear signatures of altitude-related selection, providing an indirect line of evidence that observed changes in gene expression may be adaptive in hypoxic environments. Our results demonstrate the importance of developmental stage in determining the phenotypic response to environmental stressors.
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Affiliation(s)
- Rena M. Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Catherine M. Ivy
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | | | - Graham R. Scott
- Department of Biology, McMaster University, Hamilton, ON, Canada, L8S 4K1
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Zachary A. Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Cannon-Albright LA, Stevens J, Facelli JC, Teerlink CC, Allen-Brady K, Agarwal N. High-Risk Pedigree Study Identifies LRBA (rs62346982) as a Likely Predisposition Variant for Prostate Cancer. Cancers (Basel) 2023; 15:cancers15072085. [PMID: 37046747 PMCID: PMC10092952 DOI: 10.3390/cancers15072085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each died from prostate cancer and who were members of high-risk prostate cancer pedigrees in order to identify rare variants shared by the cousins as candidate predisposition variants. Candidate variants were tested for association with prostate cancer risk in UK Biobank data. Candidate variants were also assayed in 1195 additional sampled Utah prostate cancer cases. We used 3D protein structure prediction methods to analyze structural changes and provide insights into mechanisms of pathogenicity. Almost 4000 rare (<0.005) variants were identified as shared in the 51 affected cousin pairs. One candidate variant was also significantly associated with prostate cancer risk among the 840 variants with data in UK Biobank, in the gene LRBA (p = 3.2 × 10−5; OR = 2.09). The rare risk variant in LRBA was observed to segregate in five pedigrees. The overall predicted structures of the mutant protein do not show any significant overall changes upon mutation, but the mutated structure loses a helical structure for the two residues after the mutation. This unique analysis of closely related individuals with lethal prostate cancer, who were members of high-risk prostate cancer pedigrees, has identified a strong set of candidate predisposition variants which should be pursued in independent studies. Validation data for a subset of the candidates identified are presented, with strong evidence for a rare variant in LRBA.
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Xiao J, Shang W, Zhao Z, Jiang J, Chen J, Cai H, He J, Cai Z, Zhao Z. Pharmacodynamic Material Basis and Potential Mechanism Study of Spatholobi Caulis in Reversing Osteoporosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:3071147. [PMID: 37089711 PMCID: PMC10121353 DOI: 10.1155/2023/3071147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/03/2022] [Indexed: 04/25/2023]
Abstract
Objective To elucidate the mechanism of Spatholobi Caulis (SC) in treating osteoporosis (OP) integrated zebrafish model and bioinformatics. Methods Skeleton staining coupled with image quantification was performed to evaluate the effects of SC on skeleton mineralization area (SSA) and total optical density (TOD). Zebrafish locomotor activity was monitored using the EthoVision XT. Bioactive compounds of SC and their corresponding protein targets were acquired from Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Potential therapeutic targets for OP were summarized through retrieving 5 databases, and then, the overlapping genes between SC and OP were acquired. The core genes were selected by CytoHubba. Subsequently, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) functional analysis of the intersection target genes were carried out by R software. Finally, the molecular docking simulation was manipulated between the ingredients and the hub genes. Results Compared with the model group, SC significantly increased the SSA and TOD at 10 mg/mL and improved the locomotor activity in a dose-dependent manner (p < 0.001). 33 components of SC were associated with 72 OP-related genes including 10 core genes (MAPK1, VEGFA, MMP9, AKT1, AR, IL6, CALM3, TP53, EGFR, and CAT). Advanced Glycation End Product (AGE) Receptor for AGE (RAGE) signaling pathway was screened out as the principal pathway of SC in anti-OP. The bioactive components (Aloe-emodin, Emodin, Formononetin, Licochalcone A, Luteolin, and Lopac-I-3766) have excellent affinity to core genes (MAPK1, VEGFA, MMP9, AKT1, and IL6). Conclusion SC had the hierarchical network characteristics of "multicomponents/multitargets/multifunctions/multipathways" in reversing OP, but AGE-RAGE signaling pathway may be the main regulatory mechanism.
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Affiliation(s)
- Jianpeng Xiao
- Department of TCM, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Wei Shang
- Department of TCM, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Zhiming Zhao
- Department of TCM, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jun Jiang
- Department of TCM, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Jianping Chen
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China
| | - Hui Cai
- Department of TCM, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jinjin He
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Zhihui Cai
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Zihan Zhao
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
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Rong K, Lang Y, Zhou Y, Ni L, Wang L, Wang L, Zhang Y, Wen F, Wang Z, Chen P. Risk Genetic Variants ( IL-10) for Osteoporosis in Han Population from Northwest China. J Inflamm Res 2023; 16:1091-1102. [PMID: 36941985 PMCID: PMC10024466 DOI: 10.2147/jir.s396914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/04/2023] [Indexed: 03/14/2023] Open
Abstract
Background Osteoporosis (OP) is a common metabolic bone disease characterized by loss of bone mass. IL-10 is considered to be a powerful immune and inflammatory suppressor. This study aimed to assess association between genetic loci in IL-10 and susceptibility to OP. Methods Association analysis between IL-10 genetic loci and OP risk through SNPStats online software. FPRP analysis (false-positive report probability) verified whether the positive results were noteworthy findings. Linkage disequilibrium (LD) and haplotype analysis were completed by Haploview 4.2 and SNPStats. Multi-factor dimensionality reduction (MDR) was used to assess interaction of SNP-SNP in susceptibility to OP. Results Allele "G" of IL-10-rs1554286 (OR = 1.21, p = 0.013), allele "C" of IL-10-rs1518111 (OR = 1.22, p = 0.011), allele "C" of IL-10-rs3024490 (OR = 1.20, p = 0.018), and allele "G" of IL-10-rs1800871 (OR = 1.21, p = 0.015) were risk factors for OP. In females, smoking, drinking, or aging ≤60 years old participants, the above genetic loci are also significantly associated with the increased risk of OP. FPRP analysis showed that all positive results are noteworthy findings. There are significant differences in serum levels of uric acid, mean hemoglobin concentration, or mean hemoglobin among different genotypes of IL-10 gene loci. MDR showed that four loci model composed rs1554286, rs1518111, rs3021094, and rs1800871 is the best model for predicting OP risk. Conclusion IL-10-rs1554286, -rs1518111, -rs3021094, and -rs1800871 are risk factors for susceptibility to OP.
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Affiliation(s)
- Kai Rong
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Yi Lang
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Yubo Zhou
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Liangtao Ni
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Lei Wang
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Long Wang
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Yaowu Zhang
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Fengli Wen
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Zhan Wang
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
| | - Pingbo Chen
- Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Wulumuqi, Xinjiang, People’s Republic of China
- Correspondence: Pingbo Chen, Department of Traumatology, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, No. 116, Huanghe Street, Wulumuqi, Xinjiang, People’s Republic of China, Tel/Fax +86-13899907800, Email
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10
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Puente N, Vega AI, Hernandez JL, Fernandez-Luna JL, Riancho JA. An LRP6 mutation (Arg360His) associated with low bone mineral density but not cardiovascular events in a Caucasian family. Osteoporos Int 2022; 33:2445-2448. [PMID: 35840698 PMCID: PMC9568478 DOI: 10.1007/s00198-022-06494-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
Abstract
UNLABELLED We present a family with a rare mutation of the LRP6 gene and for the first time provide evidence for its association with low bone mineral density. INTRODUCTION The Wnt pathway plays a critical role in bone homeostasis. Pathogenic variants of the Wnt co-receptor LRP6 have been associated with abnormal skeletal phenotypes or increased risk of cardiovascular events. PATIENT AND METHODS Here we report an index premenopausal patient and her family carrying a rare missense LRP6 pathogenic variant (rs141212743; 0.0002 frequency among Europeans). This variant has been previously associated with metabolic syndrome and atherosclerosis, in the presence of normal bone mineral density. However, the LRP6 variant was associated with low bone mineral density in this family, without evidence for association with serum lipid levels or cardiovascular events. CONCLUSION Thus, this novel association shows that LRP6 pathogenic variants may be involved in some cases of early-onset osteoporosis, but the predominant effect, either skeletal or cardiovascular, may vary depending on the genetic background or other acquired factors.
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Affiliation(s)
- Nuria Puente
- Servicio de Medicina Interna, Hospital UM Valdecilla, Universidad de Cantabria, IDIVAL, Avda Valdecilla sn, 39008, Santander, Spain
| | - Ana I Vega
- Servicio de Genética, Hospital UM Valdecilla, IDIVAL, Santander, Spain
| | - José L Hernandez
- Servicio de Medicina Interna, Hospital UM Valdecilla, Universidad de Cantabria, IDIVAL, Avda Valdecilla sn, 39008, Santander, Spain
| | | | - Jose A Riancho
- Servicio de Medicina Interna, Hospital UM Valdecilla, Universidad de Cantabria, IDIVAL, Avda Valdecilla sn, 39008, Santander, Spain.
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Garg B, Tomar N, Biswas A, Mehta N, Malhotra R. Understanding Musculoskeletal Disorders Through Next-Generation Sequencing. JBJS Rev 2022; 10:01874474-202204000-00001. [PMID: 35383688 DOI: 10.2106/jbjs.rvw.21.00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
» An insight into musculoskeletal disorders through advancements in next-generation sequencing (NGS) promises to maximize benefits and improve outcomes through improved genetic diagnosis. » The primary use of whole exome sequencing (WES) for musculoskeletal disorders is to identify functionally relevant variants. » The current evidence has shown the superiority of NGS over conventional genotyping for identifying novel and rare genetic variants in patients with musculoskeletal disorders, due to its high throughput and low cost. » Genes identified in patients with scoliosis, osteoporosis, osteoarthritis, and osteogenesis imperfecta using NGS technologies are listed for further reference.
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Affiliation(s)
- Bhavuk Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
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12
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Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models. Genes (Basel) 2022; 13:genes13020279. [PMID: 35205324 PMCID: PMC8872034 DOI: 10.3390/genes13020279] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
The advancement of human genomics has revolutionized our understanding of the genetic architecture of many skeletal diseases, including osteoporosis. However, interpreting results from human association studies remains a challenge, since index variants often reside in non-coding regions of the genome and do not possess an obvious regulatory function. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary, such as the one offered by animal models. These models enable us to identify causal mechanisms, clarify the underlying biology, and apply interventions. Over the past several decades, small teleost fishes, mostly zebrafish and medaka, have emerged as powerful systems for modeling the genetics of human diseases. Due to their amenability to genetic intervention and the highly conserved genetic and physiological features, fish have become indispensable for skeletal genomic studies. The goal of this review is to summarize the evidence supporting the utility of Zebrafish (Danio rerio) for accelerating our understanding of human skeletal genomics and outlining the remaining gaps in knowledge. We provide an overview of zebrafish skeletal morphophysiology and gene homology, shedding light on the advantages of human skeletal genomic exploration and validation. Knowledge of the biology underlying osteoporosis through animal models will lead to the translation into new, better and more effective therapeutic approaches.
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Evidence for an Inherited Contribution to Sepsis Susceptibility Among a Cohort of U.S. Veterans. Crit Care Explor 2022; 4:e0603. [PMID: 35036923 PMCID: PMC8754185 DOI: 10.1097/cce.0000000000000603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Analyze a unique clinical and genealogical resource for evidence of familial clustering of sepsis to test for an inherited contribution to sepsis predisposition.
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Teerlink CC, Stevens J, Hernandez R, Facelli JC, Cannon-Albright LA. An intronic variant in the CELF4 gene is associated with risk for colorectal cancer. Cancer Epidemiol 2021; 72:101941. [PMID: 33930674 PMCID: PMC8158787 DOI: 10.1016/j.canep.2021.101941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/17/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Germline predisposition variants associated with colorectal cancer (CRC) have been identified but all are not yet identified. We sought to identify the responsible predisposition germline variant in an extended high-risk CRC pedigree that exhibited evidence of linkage to the 18q12.2 region (TLOD = +2.81). METHODS DNA from two distantly related carriers of the hypothesized predisposition haplotype on 18q12.2 was sequenced to identify candidate variants. The candidate rare variants shared by the related sequenced subjects were screened in 3,094 CRC cases and 5x population-matched controls from UKBiobank to test for association. Further segregation of the variant was tested via Taqman assay in other sampled individuals in the pedigree. RESULTS Analysis of whole genome sequence data for the two related hypothesized predisposition haplotype carriers, restricted to the shared haplotype boundaries, identified multiple (n = 6) rare candidate non-coding variants that were tested for association with CRC risk in UKBiobank. A rare intronic variant ofCELF4 gene, rs568643870, was significantly associated with CRC (p = 0.004, OR = 5.0), and segregated with CRC in other members of the linked pedigree. CONCLUSION Evidence of segregation in a high-risk pedigree, case-control association in an external dataset, and identification of additional CRC-affected carriers in the linked pedigree support a role for a rareCELF4 intronic variant in CRC risk.
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Affiliation(s)
- Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Jeff Stevens
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Rolando Hernandez
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
| | - Julio C Facelli
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; Center for Clinical and Translational Science, University of Utah School of Medicine, Salt Lake City, UT 84108, USA.
| | - Lisa A Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT 84148, USA; Huntsman Cancer Institute, Salt Lake City, UT 84112, USA.
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15
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A Rare Variant in ERF (rs144812092) Predisposes to Prostate and Bladder Cancers in an Extended Pedigree. Cancers (Basel) 2021; 13:cancers13102399. [PMID: 34063511 PMCID: PMC8156789 DOI: 10.3390/cancers13102399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Here we applied a powerful predisposition candidate gene identification strategy to identify rare variants shared by two related bladder cancer cases who were members of pedigrees exhibiting a significant excess of bladder cancers. We sequenced the exomes of pairs of related bladder cancer cases belonging to high-risk bladder cancer pedigrees to identify rare, shared variants shared as candidates for predisposition. A rare, shared variant in ERF was also found to show significant association with bladder cancer risk in an independent population, was present in other prostate cancer-affected members in the pedigree, and showed evidence for altering the function of the associated protein. This evidence supports ERF (ETS2 Repressor Factor) as a bladder and prostate cancer predisposition gene. Abstract Pairs of related bladder cancer cases who belong to pedigrees with an excess of bladder cancer were sequenced to identify rare, shared variants as candidate predisposition variants. Candidate variants were tested for association with bladder cancer risk. A validated variant was assayed for segregation to other related cancer cases, and the predicted protein structure of this variant was analyzed. This study of affected bladder cancer relative pairs from high-risk pedigrees identified 152 bladder cancer predisposition candidate variants. One variant in ERF (ETS Repressing Factor) was significantly associated with bladder cancer risk in an independent population, was observed to segregate with bladder and prostate cancer in relatives, and showed evidence for altering the function of the associated protein. This finding of a rare variant in ERF that is strongly associated with bladder and prostate cancer risk in an extended pedigree both validates ERF as a cancer predisposition gene and shows the continuing value of analyzing affected members of high-risk pedigrees to identify and validate rare cancer predisposition variants.
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