1
|
Tong X, Huang T, Zhang M, Chen J, Zhang Z, Li J, Du H, Ling Z, Wu Z, Yang B, Xiao S, Ai H. Four genetic loci affecting swine lung lesions identified by whole-genome sequencing-based association studies. SCIENCE CHINA. LIFE SCIENCES 2021; 64:1571-1574. [PMID: 33521858 DOI: 10.1007/s11427-020-1826-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Xinkai Tong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mingpeng Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiaqi Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingquan Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huipeng Du
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhongzi Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
2
|
Mousel MR, White SN, Herndon MK, Herndon DR, Taylor JB, Becker GM, Murdoch BM. Genes involved in immune, gene translation and chromatin organization pathways associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep. PLoS One 2021; 16:e0247209. [PMID: 34252097 PMCID: PMC8274911 DOI: 10.1371/journal.pone.0247209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/26/2021] [Indexed: 12/20/2022] Open
Abstract
Mycoplasma ovipneumoniae contributes to polymicrobial pneumonia in domestic sheep. Elucidation of host genetic influences of M. ovipneumoniae nasal detection has the potential to reduce the incidence of polymicrobial pneumonia in sheep through implementation of selective breeding strategies. Nasal mucosal secretions were collected from 647 sheep from a large US sheep flock. Ewes of three breeds (Polypay n = 222, Rambouillet n = 321, and Suffolk n = 104) ranging in age from one to seven years, were sampled at three different times in the production cycle (February, April, and September/October) over four years (2015 to 2018). The presence and DNA copy number of M. ovipneumoniae was determined using a newly developed species-specific qPCR. Breed (P<0.001), age (P<0.024), sampling time (P<0.001), and year (P<0.001) of collection affected log10 transformed M. ovipneumoniae DNA copy number, where Rambouillet had the lowest (P<0.0001) compared with both Polypay and Suffolk demonstrating a possible genetic component to detection. Samples from yearlings, April, and 2018 had the highest (P<0.046) detected DNA copy number mean. Sheep genomic DNA was genotyped with the Illumina OvineHD BeadChip. Principal component analysis identified most of the variation in the dataset was associated with breed. Therefore, genome wide association analysis was conducted with a mixed model (EMMAX), with principal components 1 to 6 as fixed and a kinship matrix as random effects. Genome-wide significant (P<9x10-8) SNPs were identified on chromosomes 6 and 7 in the all-breed analysis. Individual breed analysis had genome-wide significant (P<9x10-8) SNPs on chromosomes 3, 4, 7, 9, 10, 15, 17, and 22. Annotated genes near these SNPs are part of immune (ANAPC7, CUL5, TMEM229B, PTPN13), gene translation (PIWIL4), and chromatin organization (KDM2B) pathways. Immune genes are expected to have increased expression when leukocytes encounter M. ovipneumoniae which would lead to chromatin reorganization. Work is underway to narrow the range of these associated regions to identify the underlying causal mutations.
Collapse
Affiliation(s)
- Michelle R. Mousel
- U.S. Department of Agriculture, Animal Disease Research Unit, Agricultural Research Service, Pullman, WA, United States of America
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA, United States of America
| | - Stephen N. White
- U.S. Department of Agriculture, Animal Disease Research Unit, Agricultural Research Service, Pullman, WA, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Maria K. Herndon
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States of America
| | - David R. Herndon
- U.S. Department of Agriculture, Animal Disease Research Unit, Agricultural Research Service, Pullman, WA, United States of America
| | - J. Bret Taylor
- U.S. Department of Agriculture, Range Sheep Production Efficiency Research, Agricultural Research Service, Dubois, ID, United States of America
| | - Gabrielle M. Becker
- Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, ID, United States of America
| | - Brenda M. Murdoch
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, ID, United States of America
| |
Collapse
|
3
|
Kaur G, Singh K, Maremanda KP, Li D, Chand HS, Rahman I. Differential plasma exosomal long non-coding RNAs expression profiles and their emerging role in E-cigarette users, cigarette, waterpipe, and dual smokers. PLoS One 2020; 15:e0243065. [PMID: 33290406 PMCID: PMC7723270 DOI: 10.1371/journal.pone.0243065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the varied set of transcripts that play a critical role in biological processes like gene regulation, transcription, post-transcriptional modification, and chromatin remodeling. Recent studies have reported the presence of lncRNAs in the exosomes that are involved in regulating cell-to-cell communication in lung pathologies including lung cancer, chronic obstructive pulmonary disease (COPD), asthma, and idiopathic pulmonary fibrosis (IPF). In this study, we compared the lncRNA profiles in the plasma-derived exosomes amongst non-smokers (NS), cigarette smokers (CS), E-cig users (E-cig), waterpipe smokers (WP) and dual smokers (CSWP) using GeneChip™ WT Pico kit for transcriptional profiling. We found alterations in a distinct set of lncRNAs among subjects exposed to E-cig vapor, cigarette smoke, waterpipe smoke and dual smoke with some overlaps. Gene enrichment analyses of the differentially expressed lncRNAs demonstrated enrichment in the lncRNAs involved in crucial biological processes including steroid metabolism, cell differentiation and proliferation. Thus, the characterized lncRNA profiles of the plasma-derived exosomes from smokers, vapers, waterpipe users, and dual smokers will help identify the biomarkers relevant to chronic lung diseases such as COPD, asthma or IPF.
Collapse
Affiliation(s)
- Gagandeep Kaur
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Kameshwar Singh
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Krishna P. Maremanda
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hitendra S. Chand
- Department of Immunology and Nanomedicine, Florida International University, Miami, FL, United States of America
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States of America
- * E-mail:
| |
Collapse
|