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Cha J, Choi S. Gene-Smoking Interaction Analysis for the Identification of Novel Asthma-Associated Genetic Factors. Int J Mol Sci 2023; 24:12266. [PMID: 37569643 PMCID: PMC10419280 DOI: 10.3390/ijms241512266] [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: 07/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Asthma is a complex heterogeneous disease caused by gene-environment interactions. Although numerous genome-wide association studies have been conducted, these interactions have not been systemically investigated. We sought to identify genetic factors associated with the asthma phenotype in 66,857 subjects from the Health Examination Study, Cardiovascular Disease Association Study, and Korea Association Resource Study cohorts. We investigated asthma-associated gene-environment (smoking status) interactions at the level of single nucleotide polymorphisms, genes, and gene sets. We identified two potentially novel (SETDB1 and ZNF8) and five previously reported (DM4C, DOCK8, MMP20, MYL7, and ADCY9) genes associated with increased asthma risk. Numerous gene ontology processes, including regulation of T cell differentiation in the thymus (GO:0033081), were significantly enriched for asthma risk. Functional annotation analysis confirmed the causal relationship between five genes (two potentially novel and three previously reported genes) and asthma through genome-wide functional prediction scores (combined annotation-dependent depletion, deleterious annotation of genetic variants using neural networks, and RegulomeDB). Our findings elucidate the genetic architecture of asthma and improve the understanding of its biological mechanisms. However, further studies are necessary for developing preventive treatments based on environmental factors and understanding the immune system mechanisms that contribute to the etiology of asthma.
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Affiliation(s)
- Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
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Schedel M, Leach SM, Strand MJ, Danhorn T, MacBeth M, Faino AV, Lynch AM, Winn VD, Munoz LL, Forsberg SM, Schwartz DA, Gelfand EW, Hauk PJ. Molecular networks in atopic mothers impact the risk of infant atopy. Allergy 2023; 78:244-257. [PMID: 35993851 DOI: 10.1111/all.15490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The prevalence of atopic diseases has increased with atopic dermatitis (AD) as the earliest manifestation. We assessed if molecular risk factors in atopic mothers influence their infants' susceptibility to an atopic disease. METHODS Pregnant women and their infants with (n = 174, high-risk) or without (n = 126, low-risk) parental atopy were enrolled in a prospective birth cohort. Global differentially methylated regions (DMRs) were determined in atopic (n = 92) and non-atopic (n = 82) mothers. Principal component analysis was used to predict atopy risk in children dependent on maternal atopy. Genome-wide transcriptomic analyses were performed in paired atopic (n = 20) and non-atopic (n = 15) mothers and cord blood. Integrative genomic analyses were conducted to define methylation-gene expression relationships. RESULTS Atopic dermatitis was more prevalent in high-risk compared to low-risk children by age 2. Differential methylation analyses identified 165 DMRs distinguishing atopic from non-atopic mothers. Inclusion of DMRs in addition to maternal atopy significantly increased the odds ratio to develop AD in children from 2.56 to 4.26. In atopic compared to non-atopic mothers, 139 differentially expressed genes (DEGs) were identified significantly enriched of genes within the interferon signaling pathway. Expression quantitative trait methylation analyses dependent on maternal atopy identified 29 DEGs controlled by 136 trans-acting methylation marks, some located near transcription factors. Differential expression for the same nine genes, including MX1 and IFI6 within the interferon pathway, was identified in atopic and non-atopic mothers and high-risk and low-risk children. CONCLUSION These data suggest that in utero epigenetic and transcriptomic mechanisms predominantly involving the interferon pathway may impact and predict the development of infant atopy.
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Affiliation(s)
- Michaela Schedel
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Pulmonary Medicine, University Medicine Essen-Ruhrlandklinik, Essen, Germany.,Department of Pulmonary Medicine, University Medicine Essen, University Hospital, Essen, Germany
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, Denver, Colorado, USA.,Center for Genes, Environment & Health, National Jewish Health, Denver, Colorado, USA
| | - Matthew J Strand
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA.,Department of Pharmacology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Morgan MacBeth
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Anna V Faino
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA.,Biostatistics, Epidemiology and Research Core, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Anne M Lynch
- Department of Ophthalmology, School of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Obstetrics and Gynecology, Stanford University, Stanford, California, USA
| | - Lindsay L Munoz
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Obstetrics and Gynecology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Shannon M Forsberg
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Department of Thoracic Oncology, University of Colorado Cancer Center, University of Colorado, Aurora, Colorado, USA
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Erwin W Gelfand
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Pia J Hauk
- Divisions of Allergy and Immunology and Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA.,Section Allergy/Immunology, Children's Hospital Colorado, University of Colorado, Aurora, Colorado, USA
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Xin J, Chai Z, Zhang C, Zhang Q, Zhu Y, Cao H, Yangji C, Chen X, Jiang H, Zhong J, Ji Q. Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production. BMC Genomics 2020; 21:731. [PMID: 33081725 PMCID: PMC7576800 DOI: 10.1186/s12864-020-07151-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Domestic yaks play an indispensable role in sustaining the livelihood of Tibetans and other ethnic groups on the Qinghai-Tibetan Plateau (QTP), by providing milk and meat. They have evolved numerous physiological adaptations to high-altitude environment, including strong blood oxygen transportation capabilities and high metabolism. The roles of DNA methylation and gene expression in milk production and high-altitudes adaptation need further exploration. Results We performed genome-wide DNA methylome and transcriptome analyses of breast, lung, and biceps brachii muscle tissues from yaks of different ages. We identified 432,350 differentially methylated regions (DMRs) across the age groups within each tissue. The post-mature breast tissue had considerably more differentially methylated regions (155,957) than that from the three younger age groups. Hypomethylated genes with high expression levels might regulate milk production by influencing protein processing in the endoplasmic reticulum. According to weighted gene correlation network analysis, the “hub” gene ZGPAT was highly expressed in the post-mature breast tissue, indicating that it potentially regulates the transcription of 280 genes that influence protein synthesis, processing, and secretion. The tissue network analysis indicated that high expression of HIF1A regulates energy metabolism in the lung. Conclusions This study provides a basis for understanding the epigenetic mechanisms underlying milk production in yaks, and the results offer insight to breeding programs aimed at improving milk production. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07151-3.
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Affiliation(s)
- Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Cidan Yangji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Xiaoying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet, China. .,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China.
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Sitagliptin Mitigates Total Body Irradiation-Induced Hematopoietic Injury in Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8308616. [PMID: 32774687 PMCID: PMC7397422 DOI: 10.1155/2020/8308616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/07/2020] [Accepted: 06/02/2020] [Indexed: 01/21/2023]
Abstract
Sitagliptin, an inhibitor of the dipeptidyl peptidase IV (DPP4), has been implicated in the regulation of type 2 diabetes. However, the role and mechanism of sitagliptin administration in total body irradiation (TBI)- induced hematopoietic cells injury are unclear. In this study, we demonstrated that sitagliptin had therapeutic effects on hematopoietic damage, which protected mice from 7.5 Gy TBI-induced death, increased the numbers and colony formation ability of hematopoietic cells. These therapeutic effects might be attributed to the inhibition of NOX4-mediated oxidative stress in hematopoietic cells, and the alleviation of inflammation was also helpful. Therefore, sitagliptin has potential as an effective radiotherapeutic agent for ameliorating TBI-induced hematopoietic injury.
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