1
|
Zhao J, Mu Y, Gong P, Liu B, Zhang F, Zhu L, Shi C, Lv X, Luo J. Whole-genome resequencing of native and imported dairy goat identifies genes associated with productivity and immunity. Front Vet Sci 2024; 11:1409282. [PMID: 39040818 PMCID: PMC11260678 DOI: 10.3389/fvets.2024.1409282] [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: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 07/24/2024] Open
Abstract
Understanding the differences in genetic variation between local Chinese dairy goat breeds and imported breeds can help germplasm innovation and molecular breeding. However, the research is limited in this area. In this study, whole-genome resequencing data from 134 individuals of both local and imported dairy goat breeds were analyzed, and their differences in genomic genetic variation, genetic diversity, and population structure were subsequently identified. We also screened candidate genes associated with important traits of dairy goats such as milk production (STK3, GHR, PRELID3B), reproduction (ATP5E), growth and development (CTSZ, GHR), and immune function (CTSZ, NELFCD). Furthermore, we examined allele frequency distributions for the genes of interest and found significant differences between the two populations. This study provides valuable resources for the study of genetic diversity in dairy goats and lays the foundation for the selective breeding of dairy goats in the future.
Collapse
Affiliation(s)
- Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yuanpan Mu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xuefeng Lv
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| |
Collapse
|
2
|
Liu X, Yuan R, Peng J, Xu A, Nie X, Tang R, Li G. SLMO2 is a potential prognostic and immunological biomarker in human pan-cancer. Sci Rep 2024; 14:1070. [PMID: 38212657 PMCID: PMC10784594 DOI: 10.1038/s41598-024-51720-5] [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: 06/06/2023] [Accepted: 01/09/2024] [Indexed: 01/13/2024] Open
Abstract
SLMO2 is a lipid transporter that transports phosphatidylserine to the interior of mitochondria, also known as PRELID3B, which plays an important role in lipid metabolism. It has also been reported to be involved in the growth process of breast and lung tumors. However, its functions and underlying mechanisms in cancer progress remain elusive, and the potential as pan-cancer biomarker and therapeutic target remains unexplored. Using the TCGA project and GEO database, we performed pan-cancer analysis of SLMO2, which including the expression pattern, prognostic value, mutation landscape, methylation modification, protein-protein interaction network and the relationship between SLMO2 expression and immune infiltration. KEGG enrichment analysis was also performed to predict function and relevant cellular pathways of SLMO2. In addition, proliferation and migration assays were performed to detect the proliferation and metastasis capacity of breast cancer and lung cancer cells. In our study, we found that SLMO2 was overexpressed in pan-cancer and the elevated expression of SLMO2 was correlated with poorer prognosis. SLMO2 mutations were distributed in a variety of tumors and correlated with prognosis. Promoter methylation analysis showed that SLMO2 methylation levels were lower in most tumors compared with normal tissues, while a few tumors showed increased methylation levels of SLMO2. SLMO2 expression was also positively correlated with immune infiltration of MDSCs. Further pathway enrichment analysis indicated that SLMO2 was involved in regulating of cytoplasmic transport and other oncogenic processes. In vitro experiments have shown that SLMO2 promotes the proliferation and migration of breast cancer and lung cancer cells. In conclusion, our findings suggested that SLMO2 was a potential prognostic and immunological marker in pan-cancer. This study suggested a potential strategy for targeting SLMO2 to treat tumors, including manipulating tumor growth or the tumor microenvironment, especially the infiltration of MDSC.
Collapse
Affiliation(s)
- Xiong Liu
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China.
- School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Renming Yuan
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Jie Peng
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Ailei Xu
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Xiaoxia Nie
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China
| | - Ruiti Tang
- Clinical Laboratory, Hunan Aerospace Hospital, 189 Fenglin 3rd Road, Yuelu District, Changsha, 410205, Hunan, China.
| | - Guangqiang Li
- Biomedical Translational Research Institute, The First Affiliated Hospital, Jinan University, 601 W. Huangpu Ave., Guangzhou, 510632, Guangdong, China.
| |
Collapse
|
3
|
Hitomi Y, Nakamura M. The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update. Genes (Basel) 2023; 14:405. [PMID: 36833332 PMCID: PMC9957238 DOI: 10.3390/genes14020405] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways.
Collapse
Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, 2-1001-1 Kubara, Omura 856-8562, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
| |
Collapse
|
4
|
Regional heritability mapping identifies several novel loci (STAT4, ULK4, and KCNH5) for primary biliary cholangitis in the Japanese population. Eur J Hum Genet 2021; 29:1282-1291. [PMID: 33833419 PMCID: PMC8385030 DOI: 10.1038/s41431-021-00854-5] [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: 12/19/2019] [Revised: 01/22/2021] [Accepted: 02/23/2021] [Indexed: 02/02/2023] Open
Abstract
While the advent of GWAS more than a decade ago has ushered in remarkable advances in our understanding of complex traits, the limitations of single-SNP analysis have also led to the development of several other approaches. Simulation studies have shown that the regional heritability mapping (RHM) method, which makes use of multiple adjacent SNPs jointly to estimate the genetic effect of a given region of the genome, generally has higher detection power than single-SNP GWAS. However, thus far its use has been mostly limited to agricultural settings, and its potential for the discovery of new genes in human diseases is yet to be fully exploited. In this study, by applying the RHM method to primary biliary cholangitis (PBC) in the Japanese population, we identified three novel loci (STAT4, ULK4, and KCNH5) at the genome-wide significance level, two of which (ULK4 and KCNH5) have not been found associated with PBC in any population previously. Notably, these genes could not be detected by using conventional single-SNP GWAS, highlighting the potential of the RHM method for the detection of new susceptibility loci in human diseases. These findings thereby provide strong empirical evidence that RHM is an effective and practical complementary approach to GWAS in this context. Also, liver tissue mRNA microarray analysis revealed higher gene expression levels in ULK4 in PBC patients (P < 0.01). Lastly, we estimated the common SNP heritability of PBC in the Japanese population (0.210 ± 0.026).
Collapse
|
5
|
Stone RC, Chen V, Burgess J, Pannu S, Tomic-Canic M. Genomics of Human Fibrotic Diseases: Disordered Wound Healing Response. Int J Mol Sci 2020; 21:ijms21228590. [PMID: 33202590 PMCID: PMC7698326 DOI: 10.3390/ijms21228590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Fibrotic disease, which is implicated in almost half of all deaths worldwide, is the result of an uncontrolled wound healing response to injury in which tissue is replaced by deposition of excess extracellular matrix, leading to fibrosis and loss of organ function. A plethora of genome-wide association studies, microarrays, exome sequencing studies, DNA methylation arrays, next-generation sequencing, and profiling of noncoding RNAs have been performed in patient-derived fibrotic tissue, with the shared goal of utilizing genomics to identify the transcriptional networks and biological pathways underlying the development of fibrotic diseases. In this review, we discuss fibrosing disorders of the skin, liver, kidney, lung, and heart, systematically (1) characterizing the initial acute injury that drives unresolved inflammation, (2) identifying genomic studies that have defined the pathologic gene changes leading to excess matrix deposition and fibrogenesis, and (3) summarizing therapies targeting pro-fibrotic genes and networks identified in the genomic studies. Ultimately, successful bench-to-bedside translation of observations from genomic studies will result in the development of novel anti-fibrotic therapeutics that improve functional quality of life for patients and decrease mortality from fibrotic diseases.
Collapse
Affiliation(s)
- Rivka C. Stone
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Correspondence: (R.C.S.); (M.T.-C.)
| | - Vivien Chen
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
| | - Jamie Burgess
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Medical Scientist Training Program in Biomedical Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sukhmani Pannu
- Department of Dermatology, Tufts Medical Center, Boston, MA 02116, USA;
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- John P. Hussman Institute for Human Genomics, University of Miami-Miller School of Medicine, Miami, FL 33136, USA
- Correspondence: (R.C.S.); (M.T.-C.)
| |
Collapse
|
6
|
Olvany JM, Sausville LN, White MJ, Tacconelli A, Tavera G, Sobota RS, Ciccacci C, Bohlbro AS, Wejse C, Williams SM, Sirugo G. CLEC4E (Mincle) genetic variation associates with pulmonary tuberculosis in Guinea-Bissau (West Africa). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104560. [PMID: 32971250 PMCID: PMC7962542 DOI: 10.1016/j.meegid.2020.104560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent. According to the WHO, 85% of cases in 2018 were pulmonary tuberculosis (PTB), making it the most prevalent form of the disease. Although the bacillus responsible for disease, Mycobacterium tuberculosis (MTB), is estimated to infect 1.7 billion people worldwide, only a small portion of those infected (5-10%) will transition into active TB. Because such a small fraction of infected people develop active disease, we hypothesized that underlying host genetic variation associates with developing active pulmonary disease. Variation in CLEC4E has been of interest in previous association studies showing either no effect or protection from PTB. For our study we assessed 60 SNPs in 11 immune genes, including CLEC4E, using a case-control study from Guinea-Bissau. The 289 cases and 322 controls differed in age, sex, and ethnicity all of which were included in adjusted models. Initial association analysis with unadjusted logistic regression revealed putative association with seven SNPs (p < 0.05). All SNPs were then assessed in an adjusted model. Of the six SNPs that remained significant, three of them were assigned to the CLEC4E gene (rs12302046, rs10841847, and rs11046143). Of these, only rs10841847 passed FDR adjustment for multiple testing. Adjusted regression analyses showed that the minor allele at rs10841847 associated with higher risk of developing PTB (OR = 1.55, CI = 1.22-1.96, p-value = 0.00036). Based on these initial association tests, CLEC4E seemed to be the predictor of interest for PTB risk in this population. Haplotype analysis (2-SNP and 3-SNP windows) showed that minor alleles in segments including rs10841847 were the only ones to pass the threshold of global significance, compared to other haplotypes (p-value < 0.05). Linkage disequilibrium patterns showed that rs12302046 is in high LD with rs10841847 (r2 = 0.67), and all other SNPs lost significance when adjusted for rs10841847 effects. These findings indicate that rs10841847 in CLEC4E is the single best predictor of pulmonary tuberculosis risk in our study population. These results provide evidence for the hypothesis that genetic variation of CLEC4E influences risk to TB in Guinea-Bissau.
Collapse
Affiliation(s)
- Jasmine M Olvany
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lindsay N Sausville
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Gloria Tavera
- Department of Clinical Translational Science Collaborative, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rafal S Sobota
- Northwestern Memorial Hospital, Northwestern University, Chicago, IL 60611, USA
| | - Cinzia Ciccacci
- UniCamillus, Saint Camillus International University of Health Sciences, 00131, Rome, Italy; Department of Biomedicine and Prevention, Genetics Section, University of Rome Tor Vergata, Rome, Italy
| | - Anders S Bohlbro
- Department of Clinical Medicine, Aarhus University Hospital, Skejby, Denmark
| | - Christian Wejse
- Bandim Health Project, Danish Epidemiology Science Centre and Statens Serum Institute, Bissau, Guinea-Bissau; Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark; Center for Global Health, School of Public Health, Aarhus University, Skejby, Denmark
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
7
|
Aiba Y, Harada K, Ito M, Suematsu T, Aishima S, Hitomi Y, Nishida N, Kawashima M, Takatsuki M, Eguchi S, Shimoda S, Nakamura H, Komori A, Abiru S, Nagaoka S, Migita K, Yatsuhashi H, Tokunaga K, Nakamura M. Increased expression and altered localization of cathepsin Z are associated with progression to jaundice stage in primary biliary cholangitis. Sci Rep 2018; 8:11808. [PMID: 30087368 PMCID: PMC6081405 DOI: 10.1038/s41598-018-30146-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Our recent genome-wide association study found that the NELFCD/CTSZ locus was significantly associated with progression of primary biliary cholangitis (PBC) to jaundice stage in the Japanese population. In this study, we investigated the role of cathepsin Z in the etiology and pathology of PBC. Serum cathepsin Z levels were measured using enzyme-linked immunosorbent assay. The expression and localization of cathepsin Z in liver specimens were analyzed by western blotting and immunohistochemistry. In PBC patients, serum cathepsin Z levels were significantly increased with disease progression. In addition, its levels were positively correlated with alanine transaminase, aspartate transaminase and total bilirubin, and were negatively correlated with platelet count and albumin. Cathepsin Z expression was markedly increased in hepatocytes at later stages of PBC, and its localization was altered from the peri-bile canaliculus to the cytoplasm, where a fraction was no longer colocalized with endosomal/lysosomal vesicles. Similar altered expression of cathepsin Z was observed in end-stage of other cholestatic liver diseases including sepsis, obstructive jaundice, and Alagille syndrome. Our results indicate that altered expression and localization of cathepsin Z in hepatocytes are characteristic features of PBC and other cholestatic liver diseases, and are implicated in the progression of PBC.
Collapse
Affiliation(s)
- Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Kenichi Harada
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Masahiro Ito
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Takashi Suematsu
- Central Electron Microscope Laboratory, Nagasaki University School of Medicine, Nagasaki, Nagasaki, Japan
| | - Shinichi Aishima
- Departments of Pathology & Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | | | - Mitsuhisa Takatsuki
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Susumu Eguchi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Hitomi Nakamura
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Atsumasa Komori
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Seigo Abiru
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Shinya Nagaoka
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Kiyoshi Migita
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan. .,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan. .,Headquarters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Omura, Japan.
| |
Collapse
|