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Li Z, Fang B, Dong P, Shan W. Selective sweep analysis of the adaptability of the Yarkand hare (Lepus yarkandensis) to hot arid environments using SLAF-seq. Anim Genet 2024; 55:681-686. [PMID: 38722026 DOI: 10.1111/age.13440] [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: 03/06/2023] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 07/04/2024]
Abstract
The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θπ ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.
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Affiliation(s)
- Zurui Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Bingwa Fang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Pengcheng Dong
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Hu F, Xiong L, Li Z, Li L, Wang L, Wang X, Zhou X, Zheng Y. Deciphering the shared mechanisms of Gegen Qinlian Decoction in treating type 2 diabetes and ulcerative colitis via bioinformatics and machine learning. Front Med (Lausanne) 2024; 11:1406149. [PMID: 38962743 PMCID: PMC11220276 DOI: 10.3389/fmed.2024.1406149] [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: 03/24/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Background Although previous clinical studies and animal experiments have demonstrated the efficacy of Gegen Qinlian Decoction (GQD) in treating Type 2 Diabetes Mellitus (T2DM) and Ulcerative Colitis (UC), the underlying mechanisms of its therapeutic effects remain elusive. Purpose This study aims to investigate the shared pathogenic mechanisms between T2DM and UC and elucidate the mechanisms through which GQD modulates these diseases using bioinformatics approaches. Methods Data for this study were sourced from the Gene Expression Omnibus (GEO) database. Targets of GQD were identified using PharmMapper and SwissTargetPrediction, while targets associated with T2DM and UC were compiled from the DrugBank, GeneCards, Therapeutic Target Database (TTD), DisGeNET databases, and differentially expressed genes (DEGs). Our analysis encompassed six approaches: weighted gene co-expression network analysis (WGCNA), immune infiltration analysis, single-cell sequencing analysis, machine learning, DEG analysis, and network pharmacology. Results Through GO and KEGG analysis of weighted gene co-expression network analysis (WGCNA) modular genes and DEGs intersection, we found that the co-morbidity between T2DM and UC is primarily associated with immune-inflammatory pathways, including IL-17, TNF, chemokine, and toll-like receptor signaling pathways. Immune infiltration analysis supported these findings. Three distinct machine learning studies identified IGFBP3 as a biomarker for GQD in treating T2DM, while BACE2, EPHB4, and EPHA2 emerged as biomarkers for GQD in UC treatment. Network pharmacology revealed that GQD treatment for T2DM and UC mainly targets immune-inflammatory pathways like Toll-like receptor, IL-17, TNF, MAPK, and PI3K-Akt signaling pathways. Conclusion This study provides insights into the shared pathogenesis of T2DM and UC and clarifies the regulatory mechanisms of GQD on these conditions. It also proposes novel targets and therapeutic strategies for individuals suffering from T2DM and UC.
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Affiliation(s)
| | | | | | | | | | | | - Xuemei Zhou
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yujiao Zheng
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
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Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC. Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566586. [PMID: 38014125 PMCID: PMC10680683 DOI: 10.1101/2023.11.10.566586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis- methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
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Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
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Candeias J, Zimmermann EJ, Bisig C, Gawlitta N, Oeder S, Gröger T, Zimmermann R, Schmidt-Weber CB, Buters J. The priming effect of diesel exhaust on native pollen exposure at the air-liquid interface. ENVIRONMENTAL RESEARCH 2022; 211:112968. [PMID: 35240115 DOI: 10.1016/j.envres.2022.112968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Pollen related allergic diseases have been increasing for decades. The reasons for this increase are unknown, but environmental pollution like diesel exhaust seem to play a role. While previous studies explored the effects of pollen extracts, we studied here for the first time priming effects of diesel exhaust on native pollen exposure using a novel experimental setup. METHODS Human bronchial epithelial BEAS-2B cells were exposed to native birch pollen (real life intact pollen, not pollen extracts) at the air-liquid interface (pollen-ALI). BEAS-2B cells were also pre-exposed in a diesel-ALI to diesel CAST for 2 h (a model for diesel exhaust) and then to pollen in the pollen-ALI 24 h later. Effects were analysed by genome wide transcriptome analysis after 2 h 25 min, 6 h 50 min and 24 h. Selected genes were confirmed by qRT-PCR. RESULTS Bronchial epithelial cells exposed to native pollen showed the highest transcriptomic changes after about 24 h. About 3157 genes were significantly up- or down-regulated for all time points combined. After pre-exposure to diesel exhaust the maximum reaction to pollen had shifted to about 2.5 h after exposure, plus the reaction to pollen was desensitised as only 560 genes were differentially regulated. Only 97 genes were affected synergistically. Of these, enrichment analysis showed that genes involved in immune and inflammatory response were involved. CONCLUSION Diesel exhaust seems to prime cells to react more rapidly to native pollen exposure, especially inflammation related genes, a factor known to facilitate the development of allergic sensitization. The marker genes here detected could guide studies in humans when investigating whether modern and outdoor diesel exhaust exposure is still detrimental for the development of allergic disease.
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Affiliation(s)
- Joana Candeias
- Center Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University Munich / Helmholtz Center Munich, Germany
| | - Elias J Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Christoph Bisig
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Nadine Gawlitta
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Thomas Gröger
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Center Munich, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr. Lorenzweg 2, D-18051, Rostock, Germany
| | - Carsten B Schmidt-Weber
- Center Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University Munich / Helmholtz Center Munich, Germany
| | - Jeroen Buters
- Center Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University Munich / Helmholtz Center Munich, Germany.
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Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer ( Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool 2020; 17:31. [PMID: 33072165 PMCID: PMC7565370 DOI: 10.1186/s12983-020-00379-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
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Affiliation(s)
- Buweihailiqiemu Ababaikeri
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China.,College of Xinjiang Uyghur Medicine, Hoten, 848000 Xinjiang China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China.,Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Yilamujiang Tohetahong
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Tayerjan Mamat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Adil Ahmat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Mahmut Halik
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
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Worth L, Michel S, Gaertner VD, Kabesch M, Schieck M. Asthma- and IgE-associated polymorphisms affect expression of T H 17 genes. Allergy 2018; 73:1342-1347. [PMID: 29380867 DOI: 10.1111/all.13422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- L. Worth
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
| | - S. Michel
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
| | - V. D. Gaertner
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
| | - M. Kabesch
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
| | - M. Schieck
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
- Department of Human Genetics Hannover Medical School Hannover Germany
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Rowe RK, Gill MA. Effects of Allergic Sensitization on Antiviral Immunity: Allergen, Virus, and Host Cell Mechanisms. Curr Allergy Asthma Rep 2017; 17:9. [PMID: 28233152 DOI: 10.1007/s11882-017-0677-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Multiple clinical and epidemiological studies demonstrate links between allergic sensitization and virus-induced atopic disease exacerbations. This review summarizes the recent findings regarding allergen, viral, and host cellular mechanisms relevant to these observations. RECENT FINDINGS Recent studies have focused on the molecular pathways and genetic influences involved in allergen-mediated inhibition of innate antiviral immune responses. Multiple tissue and cell types from atopic individuals across the atopy spectrum exhibit deficient interferon responses to a variety of virus infections. Impairment in barrier function, viral RNA and DNA recognition by intracellular sensing molecules, and dysregulation of signaling components are broadly affected by allergic sensitization. Finally, genetic predisposition by numerous nucleotide polymorphisms also impacts immune pathways and potentially contributes to virus-associated atopic disease pathogenesis. Allergen-virus interactions in the setting of atopy involve complex tissue and cellular mechanisms. Future studies defining the pathways underlying these interactions could uncover potential therapeutic targets. Available data suggest that therapies tailored to restore specific components of antiviral responses will likely lead to improved clinical outcomes in allergic disease.
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Affiliation(s)
- Regina K Rowe
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Michelle A Gill
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA. .,Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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