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1,386 results on '"Shen, Nan"'

9. Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry.

Author

Owen, Katherine A, Bell, Kristy A, Price, Andrew, Bachali, Prathyusha, Ainsworth, Hannah, Marion, Miranda C, Howard, Timothy D, Langefeld, Carl D, Shen, Nan, Yazdany, Jinoos, Dall'era, Maria, Grammer, Amrie C, and Lipsky, Peter E

Subjects
Humans, Lupus Erythematosus, Systemic, Genetic Predisposition to Disease, Case-Control Studies, Genotype, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Lupus, Clinical Research, Autoimmune Disease, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system
Abstract

Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of Asian-Ancestry (AsA) disproportionately experience more severe SLE compared to individuals of European-Ancestry (EA), including increased renal involvement and tissue damage. However, the mechanisms underlying elevated severity in the AsA population remain unclear. Here, we utilized available gene expression data and genotype data based on all non-HLA SNP associations in EA and AsA SLE patients detected using the Immunochip genotyping array. We identified 2778 ancestry-specific and 327 trans-ancestry SLE-risk polymorphisms. Genetic associations were examined using connectivity mapping and gene signatures based on predicted biological pathways and were used to interrogate gene expression datasets. SLE-associated pathways in AsA patients included elevated oxidative stress, altered metabolism and mitochondrial dysfunction, whereas SLE-associated pathways in EA patients included a robust interferon response (type I and II) related to enhanced cytosolic nucleic acid sensing and signaling. An independent dataset derived from summary genome-wide association data in an AsA cohort was interrogated and identified similar molecular pathways. Finally, gene expression data from AsA SLE patients corroborated the molecular pathways predicted by SNP associations. Identifying ancestry-related molecular pathways predicted by genetic SLE risk may help to disentangle the population differences in clinical severity that impact AsA and EA individuals with SLE.

Published
2023

25. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Author

Zhang, Jingcheng, Shen, Nan, Li, Chuang, Xiang, Xingjie, Liu, Gaolei, Gui, Ying, Patev, Sean, Hibbett, David S, Barry, Kerrie, Andreopoulos, William, Lipzen, Anna, Riley, Robert, He, Guifen, Yan, Mi, Grigoriev, Igor V, Kwan, Hoi Shan, Cheung, Man Kit, Bian, Yinbing, and Xiao, Yang

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Biotechnology, Human Genome, Agaricales, Genome, Genome-Wide Association Study, Metagenomics, Shiitake Mushrooms, Shiitake, Population genomics, Adaptation, Genetic divergence, GWAS, Phenotypic differentiation
Abstract

IntroductionMushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi.ObjectivesThis study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution.MethodsWe analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution.ResultsWe detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation.ConclusionAdaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

Published
2022

46. Anti-Toxoplasma gondii antibodies as a risk factor for the prevalence and severity of systemic lupus erythematosus

Author

Li, Zhongzhen, Lei, Zhiwei, Yang, Wanying, Jing, Chunxia, Sun, Xiaolin, Yang, Guang, Zhao, Xiaozhen, Zhang, Mingjiao, Xu, Miaomiao, Tang, Yuanjia, Wang, Qingwen, Zhao, Jing, Zhou, Zixing, Wen, Zihao, Chen, Xiaojing, Peng, Qinglin, Wang, Guochun, Zhang, Pingjing, Sun, Erwei, Shen, Nan, Xu, Weiguo, Li, Zhanguo, Yang, Hengwen, and Yin, Zhinan

Published
2024
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