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A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass

Science China(Life Sciences) 2010年第9期53卷 1065-1072页

作者： shawn levy Vanderbilt Microarray Shared Resource Vanderbilt University

Osteoporosis is a highly heritable common bone disease leading to fractures that severely impair the life quality of *** fractures caused by osteoporosis are largely due to the scarcity of wrist bone *** we report the results of a genome-wide association study (GWAS) of wrist bone mineral density (BMD).We examined ～500000 SNP markers in 1000 unrelated homogeneous Caucasian subjects and found a novel allelic association with wrist BMD at rs11023787 in the SOX6 (SRY (sex determining region Y)-box 6) gene (P=9.00×10-5).Subjects carrying the C allele of rs11023787 in SOX6 had significantly higher mean wrist BMD values than those with the T allele (0.485:0.462 g cm-2 for C allele vs.T allele carriers).For validation,we performed SOX6 association for BMD in an independent Chinese sample and found that SNP rs11023787 was significantly associated with wrist BMD in the Chinese sample (P=6.41×10-3).Meta-analyses of the GWAS scan and the replication studies yielded P-values of 5.20×10-6 for *** of this study,together with the functional relevance of SOX6 in cartilage formation,support the SOX6 gene as an important gene for BMD variation.

关键词： osteoporosis GWAS SOX6 SNPs wrist BMD

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Genome and clonal hematopoiesis stability contrasts with immune,cfDNA,mitochondrial,and telomere length changes during short duration spaceflight

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Precision Clinical Medicine 2024年第1期7卷 1-13页

作者： J.Sebastian Garcia-Medina Karolina Sienkiewicz S.Anand Narayanan Eliah G.Overbey Kirill Grigorev Krista A.Ryon Marissa Burke Jacqueline Proszynski Braden Tierney Caleb M.Schmidt Nuria Mencia-Trinchant Remi Klotz Veronica Ortiz Jonathan Foox Christopher Chin Deena Najjar Irina Matei Irenaeus Chan Carlos Cruchaga Ashley Kleinman JangKeun Kim Alexander Lucaci Conor Loy Omary Mzava Iwijn De Vlaminck Anvita Singaraju Lynn E.Taylor Julian C.Schmidt Michael A.Schmidt Kelly Blease Juan Moreno Andrew Boddicker Junhua Zhao Bryan Lajoie Andrew Altomare Semyon Kruglyak shawn levy Min Yu Duane C.Hassane Susan M.Bailey Kelly Bolton Jaime Mateus Christopher E.Mason Department of Physiology and Biophysics Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell MedicineNew YorkNY 10021USA Department of Immunology Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA Department of Stem Cell Biology and Regenerative Medicine Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA Space Exploration Technologies Corporation HawthomeCA 90250USA Sovaris Aerospace BoulderCO 80302USA Advanced Pattern Analysis&Human Performance Group BoulderCO 80302USA Children's Cancer and Blood Foundation Laboratories Departments of Pediatrics and Cell and Developmental BiologyDrukier Institute for Children's HealthMeyer Cancer CenterWeill Cornell MedicineNew YorkNY 10021USA Meyer Cancer Center Weill Cornell MedicineNew YorkNY 10065USA Department of Nutrition and Integrative Physiology Florida State UniversityTallahasseeFL 32306USA Department of Systems Engineering Colorado State UniversityFort CollinsCO 80523USA Element Biosciences San DiegoCA 10055USA Department of Environmental and Radiological Health Sciences Colorado State UniversityFort CollinsCO 80523USA Cell and Molecular Biology Program Colorado State UniversityFort CollinsCO 80523USA BioAstra Inc New YorkNYUSA Washington University St Louis Oncology Division St.LouisMO 63100USA Meinig School of Biomedical Engineering Cornell UniversityIthacaNY 14853USA The Feil Family Brain and Mind Research Institute Weill Cornell MedicineNY 10021USA WorldQuant Initiative for Quantitative Prediction Weill Cornell MedicineNew YorkNY 10021USA

Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic *** advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation *** To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA *** length was measured by quantitative PCR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational *** Telomere elongation occurred during spaceflight and shortened after return to ***-free DNA analysis revealed increased immune cell signatures *** significant clonal hematopoiesis of indeterminate potential(CHIP)or whole-genome instability was *** long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months *** Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to *** sequencing data will serve as a reference point for studying the early development of CHIP in astronauts,an understudied phenomenon as previous studies have focused on career *** study will serve as a reference point for future commercial and non-commercial spaceflight,low Earth orbit(LEO)missions,and deep-space exploration.

关键词： genomes clonal hematopoiesis stability immune mitochondria ribosomes spaceflight

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全基因组关联分析显示SOX6为影响腕部骨密度的候选基因

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中国科学：生命科学 2010年第8期40卷 685-693页

作者：谭丽君刘荣雷署丰潘蓉杨铁林阎函培育芳杨芳张峰潘峰张银萍 levy shawn 邓红文湖南师范大学生命科学学院分子与统计遗传学研究室长沙410081 Departments of Orthopedic Surgery and Basic Medical Sciences University of Missouri-Kansas CityKansas CityMO 64108USA 西安交通大学生命科学与技术学院分子遗传所西安710049 北京交通大学生命科学与生物工程研究院北京100044 Vanderbilt Microarray Shared Resource Vanderbilt UniversityNashvilleTN 37232USA

骨质疏松症是一种高度遗传且极易导致骨折的骨骼疾病,它严重损害患者的生活质量.因骨质疏松而导致的手腕骨折,很大程度是由于手腕部位的骨量低.本研究在1000个不相关的白人中采用Affymetix 500K芯片扫描了500000个SNPs,运用全基因组关... 详细信息

骨质疏松症是一种高度遗传且极易导致骨折的骨骼疾病,它严重损害患者的生活质量.因骨质疏松而导致的手腕骨折,很大程度是由于手腕部位的骨量低.本研究在1000个不相关的白人中采用Affymetix 500K芯片扫描了500000个SNPs,运用全基因组关联分析(GWAS),发现SOX6为影响手腕骨密度的一个新的基因,SOX6基因中rs11023787与手腕部骨密度关联,P值为9.00×***6基因中,rs11023787 C等位基因携带者的手腕骨密度显著高于T等位基因携带者(C等位基因vs.T等位基因携带者:0.485g/cm2vs.0.462g/cm2).为进一步验证该结果,在中国人群中检测了SOX6基因与骨密度的关联并发现,rs11023787与手腕骨密度显著关联(P=6.41×10-3).对GWAS与验证结果进行荟萃分析,得到联合P值为5.20×10-6,SOX6基因参与软骨形成过程.本结果提示,SOX6基因是影响骨密度变异的重要基因.

关键词：骨质疏松症全基因组关联分析 SOX6 单核苷酸多态性手腕骨密度

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ANKRD7 and CYTL1 are novel risk genes for alcohol drinking behavior

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Chinese Medical Journal 2012年第6期125卷 1127-1134页

作者： CHEN Xiang-ding XIONG Dong-hai YANG Tie-lin PEI Yu-fang GUO Yan-fang LI Jian YANG Fang PAN Feng TAN Li-jun YAN Han LIU Xiao-gang LEI Shu-feng LI Xi NING Ling-ling ZHU Xue-zhen shawn levy Henry R. Kranzler Lindsay A. Farrer Joel Gelernter Robert R. Recker DENG Hong-wen Laboratory of Molecular and Statistical Genetics Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education College of Life Sciences Hunan Institute of Biology Hunan Normal University Changsha Hunan 410081 China Departments of Orthopedic Surgery and Basic Medical Sciences University of Missouri-Kansas City Kansas City MO 64108 USA Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics School of Life Science and Technology Xi＇an Jiaotong University Xi＇an Shannxi 710049 China Department of Biomedical Informatics Vanderbilt University Medical Center Nashville TN 37232 USA University of Connecticut Health Center Farmington CT 06030 USA Boston University School of Medicine Boston MA 02118 USA Department of Psychiatry Yale University School of Medicine West Haven CT 06516 USA Osteoporosis research Center Creighton University Omaha NE 68131 USA Systematic Biomedicine Research Center University of Shanghai for Science and Technology Shanghai 200093 China

Background Alcohol dependence （AD） is a complex disorder characterized by impaired control over drinking. It is determined by both genetic and environmental factors. The recent approach of genome-wide association study （GWAS） is a powerful tool for identifying complex disease-associated susceptibility alleles, however, a few GWASs have been conducted for AD, and their results are largely inconsistent. The present study aimed to screen the loci associated with alcohol-related phenotypes using GWAS technology. Methods A genome-wide association study with the behavior of regular alcohol drinking and alcohol consumption was performed to identify susceptibility genes associated with AD, using the Affymetrix 500K SNP array in an initial sample consisting of 904 unrelated Caucasian subjects. Then, the initial results in GWAS were replicated in three independent samples： 1972 Caucasians in 593 nuclear families, 761 unrelated Caucasian subjects, and 2955 unrelated Chinese Hans. Results Several genes were associated with the alcohol-related phenotypes at the genome-wide significance level, with the ankyrin repeat domain 7 gene （ANKRDT） showing the strongest statistical evidence for regular alcohol drinking and suggestive statistical evidence for alcohol consumption. In addition, certain haplotypes within the ANKRD7 and cytokine-likel （CYTL 1） genes were significantly associated with regular drinking behavior, such as one ANKRD7 block composed of the SNPs rs6466686-rs4295599-rs12531066 （P = 6.51×10^-8）. The association of alcohol consumption was successfully replicated with rs4295599 in ANKRD7 gene in independent Caucasian nuclear families and independent unrelated Chinese Hans, and with rs16836497 in CYTL1 gene in independent unrelated Caucasians. Meta-analyses based on both the GWAS and replication samples further supported the observed significant associations between the ANKRDTor CYTL1 gene and alcohol consumption. Conclusion The evidence suggests that ANKRD7 and CYTL 1 ge

关键词： alcohol dependence ANKRD7 CYTL1 genome-wide association study

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白介素-33至白介素-13信号级联调节小鼠胃组织上皮化生

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英国医学杂志中文版 2018年第7期21卷 418-418页

作者： Christine P Petersen Anne R Meyer Carlo De Salvo Eunyoung Choi Cameron Schlegel Alec Petersen Amy C Engevik Nripesh Prasad shawn E levy R Stokes Peebles Theresa T Pizarro James R Goldenring 李佳宁(译) 吴东(校) 不详北京协和医院消化科

目的选择性活化巨噬细胞（Alternativelyactivated macrophages, M2）与胃部解痉多肽表达性化生（spasmolytic polypeptide-expressingmetaplasia, SPEM）过程相关。然而，诱导SPEM的确切机制及关键介质尚不明确。研究设计为确定这一... 详细信息

目的选择性活化巨噬细胞（Alternativelyactivated macrophages, M2）与胃部解痉多肽表达性化生（spasmolytic polypeptide-expressingmetaplasia, SPEM）过程相关。然而，诱导SPEM的确切机制及关键介质尚不明确。研究设计为确定这一过程中的关键基因，分离胃部SPEM小鼠（DMP-777处理）及高级胃部SPEM小鼠（L635处理）胃体的巨噬细胞进行RNA测序。评估白介素．33、白介素-33受体（ST2）及白介素-13基因敲除小鼠，经L635处理急性壁细胞缺失后对上皮细胞化生过程的影响。结果胃部上皮化生相关性巨噬细胞中可鉴定出M2极化亚群。高级胃部SPEM小鼠巨噬细胞中自介素-33的表达显著上调。L635可在野生型小鼠胃组织中诱导上皮化生，但在白介素-33及白介素．33受体敲除鼠中未观察到这一现象。尽管在诱导上皮化生过程中不需白介素．5及白介素-9，白介素-13基因敲除小鼠无法在L635诱导下发生上皮化生。对白介素-33受体基因敲除小鼠应用白介素-13，可重新诱导急性壁细胞缺失后的上皮化生。结论壁细胞缺失后上皮化生及巨噬细胞极化过程通过白介素．33及白介素-13的细胞信号网络协调进行，将损伤应答过程中固有黏膜机制及M2浸润联系起来。

关键词： IL-13 组织变形调整老鼠串联信号胃

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