Bioinformatics for Better Medicine @ Su Lab

About

    We are a bioinformtics group focusing on the application of High throughput techniques, AI-related approaches and other new methods for studies in liver diseases and (re-)emerging infectious dieseases. Please visit the projects page for more information on the research being done in the Su group.


Murine4Covid
新冠肺炎(COVID-19)应急项目
Murine models of underlying diseases for COVID-19

(Latest update: 2020/08/21)

NSFC2021

国家自然科学基金申请(2021年度)
《I型马兜铃酸通过“花生四烯酸/CYLD/NF-κB”表观调控馈路
直接介导肝脏损伤的机制研究》
相关数据每月1日更新
(Latest update: 2020/09/01)

  • 项目摘要
            I型马兜铃酸(AAI)可导致肝脏疾病,当前研究多集中在DNA突变累积后的长期间接作用上,但RNA、蛋白层面的早期直接机制远未阐明。申请人最近发现:皮格犬口服AAI肝损伤的早期,直接出现花生四烯酸的5脂氧酶通路(AA-5LO)激活、脂质炎性产物CysLT增加、miR表达异常、去泛素酶CYLD下调、NF-κB和Lin28B等上调,并得到临床样本病理学验证。高通量测序生信筛选中,与AA-5LO、CYLD密切耦合的“lncRNA⋐miR⊣mRNA”可构成ceRNA馈路。本课题继续聚焦AAI肝损伤的早期直接进程,拟进一步明确AA-5LO、CYLD上下游机制,阐明背后ceRNA转录后调控,探明CYLD去泛素化NF-κB通路的翻译后修饰。生信大数据挖掘,收集临床样本,制备组织芯片,病理验证共享转化。相对于长期间接作用,揭示AAI肝损伤的早期直接生命现象本质,可望为更早、更特异诊治靶点的发现提供学术依据。

ZJNSF2019
浙江省自然科学基金(主持、已获批)
《GSNO调节糖尿病小鼠“肠道微生态—肝脏损伤”轴机制研究》

相关数据每月15日更新(请点击)
(Latest update: 2020/08/15)

China-Germany Cooperation Group
国家自然科学基金委员会
“中德科学中心”合作项目(参加、已获批)
《肠道微生态在终末期肝病:分子机制研究》

  •     尽管慢性肝病的病因多种多样,其后果无外乎三种:失代偿肝硬化、慢加急性肝衰竭和肝癌。这三类疾病构成的终末期肝病造成患者的高死亡率,以及包括中国和德国在内的巨大全球性社会经济负担。近年来,肠道微生态对终末期肝病的影响已引起学界重视,如已发现肠道微生态失调可导致自发性腹膜炎并引起肝衰竭,剖析并深刻理解其中的分子机制有希望为终末期肝病的治疗带来新的治疗方法。
        在中德科学中心的大力支持下,22位中德科学家于2018年9月5日至8日在杭州举办了主题为“肠道微生态和终末期肝病:肝肠对话”的双边学术论坛。该论坛深入探讨了这个热门领域的研究现状,并就双方的未来合作进行了实质性规划。至此,12名中德学者计划组织合作研究小组详细研究肠道微生态在慢性和终末期肝病的分子作用机制。这12名学者包括中方李兰娟院士,王保红、高海女、盛国平和苏锟楷博士,德方Andreas Teufel、Steven Dooley、Mattias Ebert教授和 Honglei Weng、Christoph Antoni、Janina Sollors、Philip Weidner博士。
        合作研究小组将重点探讨下列问题:(1)肠道微生态和非酒精性脂肪性肝病的作用机制;(2)肠道微生态和酒精性脂肪性肝病的分子机制。(3)肠道微生态和慢加急性肝衰竭:肠道微生态失调如何影响亚大块坏死后的肝再生。(4)肠道微生态和原发性肝癌:肠道微生态失调如何通过影响免疫应答并参与肝癌发生发展。

NKRDP2017
国家重点研发计划
“重要疫源微生物组学研究”(子课题主持、已获批)
《微生物组多组学生物信息学新算法研究与平台构建》



数据库内测中
(Latest update: 2020/08/18)
  • 本项目通过重要疫源动物、媒介生物及人的微生物多组学研究,阐明重要疫源微生物适应性、致病性以及耐药性变化规律。研究将揭示 20 余种家养及野生疫源动物体内特定微环境中微生物组特征、挖掘未知/新发病原、预测潜在病原体与新发或重大疫病的关联性;明确特定区域中媒介携带的微生物种群及其与宿主关系;阐明人体特定微环境中菌群结构变化与病原致病性与耐药性演变的相互关系及其对重症感染发生发展的影响;识别与重症病毒感染毒力因子和与宿主易受性相关的宿主蛋白,开发感染诊治的生物标志物;建立病毒-宿主蛋白互作网络,阐明疾病发生的分子机制;建立微生物分离富集新技术和比较定量蛋白组学方法;发展微生物组高通量测序数据的多组学分析的新算法和新方法;搭建微生物及宿主多组学的生物信息学数据大规模分析、共享以及整合的平台;建立重要疫源动物、媒介生物和人体微生物群落的致病、耐药相关基因和蛋白质的数据库。

Latest News

  • 2020/05/12:以单位外事秘书身份,陪同实验室主任李兰娟院士参加“中美新冠肺炎疫情防控视频交流会”,介绍中国的临床救治经验。本次交流会由美国科学院副院长Diane Griffin教授和美国医学科学院院长Harvey Fineberg教授联合致信中国科学院院长白春礼院士和中国国家疾病预防控制中心主任高福院士,希望围绕疫情防控联合召开中美专家视频会议,以帮助美国相关领域专家的临床救治、药物研发等工作。

  • 2020/04/29:旁听中国科学院、中国工程院的《公共卫生领域学科体系建设联合咨询项目-项目启会暨第一次咨询研讨会》,后续参与撰写以两院名义报送党中央、国务院的总报告和各专题研究报告。

  • 2020/04/27:在Infectious Microbes & Diseases期刊在线发表应急研究成果:《Transcriptomics Curation of SARS-CoV-2 Related Host Genes in Mice with COVID-19 Comorbidity: A Pilot Study》,为抗击COVID-19中糖尿病、心血管疾病、高血压和慢阻肺等各种合并症的交叉研究提供依据。

  • 2020/04/06:由浙江省毒理学会和所在单位推荐,进入“中国毒理学会优秀青年科技奖”的最终遴选。

  • 2020/04/02:受邀成为“中国毒理学会-表观遗传毒理专业委员会(筹)”委员,并积极参与专委会的建设工作。

  • 2020/03/25:以单位外事秘书身份,协助申报“国际联合实验室”,以SARS-CoV-2研究为契机,努力扩大我国在国际感染性疾病研究领域的话语权。

  • 2020/01/22:以视频形式,与中德“肠道微生态在终末期肝病:分子机制研究”合作研究小组的德方专家Andreas Terufel教授等就项目前期的准备、进展和后续进行研讨,努力克服COVID-19疫情的影响,保质保量地完成相关研究。

  • 2019/12/09:以单位外事秘书身份,协助接待越南河内医科大学NGUYEN DAT ANH教授等5人访问团,通过深入交流和讨论,商定后续合作研究中聚焦感染性疾病微生态防治等方向,践行国家“一带一路倡议”。

  • 2019/10/30:以单位外事秘书身份,协助接待泰国Siriraj医院Yupin Suputtamongkol教授等6人访问团,确定后续合作研究中聚焦重症肺炎的病原学监测,开发相应的快速检测试剂,践行国家“一带一路倡议”。


Upcoming Events


People and collaborators

  • SU Kunkai: Principal investigator
  • Christian Bréchot: Collaborator professor in liver diseases
  • YAO Jian: Research assistant in molecular and celluar biology
  • CAO Qingyi: Research assistant in bioinformtics
  • TAO Jingjing: Physicain in liver diseases
  • JIA Junjun: Surgeon in liver diseases
  • ZHAO Xinyi: PhD student
  • CHEN Jiali: PhD student

Publications

    1: Liu Q, Han H, Wang M, Yao Y, Wen L, Jiang K, Ma Y, Fan R, Chen J, Su K, Yang Z, Cui W, Yuan W, Jiang X, Li J, Payne TJ, Wang J, Li MD. Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population. Transl Psychiatry. 2018 Apr 18;8(1):83. doi: 10.1038/s41398-018-0130-x. PubMed PMID: 29666375; PubMed Central PMCID: PMC5904126.

    2: Ma Y, Wen L, Cui W, Yuan W, Yang Z, Jiang K, Jiang X, Huo M, Sun Z, Han H, Su K , Yang S, Payne TJ, Wang J, Li MD. Prevalence of Cigarette Smoking and Nicotine Dependence in Men and Women Residing in Two Provinces in China. Front Psychiatry. 2017 Dec 1;8:254. doi: 10.3389/fpsyt.2017.00254. eCollection 2017. PubMed PMID: 29249991; PubMed Central PMCID: PMC5716983.

    3: Jiang K, Yang Z, Cui W, Su K, Ma JZ, Payne TJ, Li MD. An exome-wide association study identifies new susceptibility loci for age of smoking initiation in African- and European-American populations. Nicotine Tob Res. 2017 Dec 5. doi: 10.1093/ntr/ntx262. [Epub ahead of print] PubMed PMID: 29216386.

    4: Yao J, Wu L, Meng X, Yang H, Ni S, Wang Q, Zhou J, Zhang Q, Su K, Shao L, Cao Q, Li M, Wu F, Li L. Profiling, clinicopathological correlation and functional validation of specific long non-coding RNAs for hepatocellular carcinoma. Mol Cancer. 2017 Oct 23;16(1):164. doi: 10.1186/s12943-017-0733-5. PubMed PMID: 29061191; PubMed Central PMCID: PMC5651594.

    5: Wen L, Han H, Liu Q, Su K, Yang Z, Cui W, Yuan W, Ma Y, Fan R, Chen J, Jiang K, Jiang X, Payne TJ, Wang J, Li MD. Significant association of the CHRNB3-CHRNA6 gene cluster with nicotine dependence in the Chinese Han population. Sci Rep. 2017 Aug 29;7(1):9745. doi: 10.1038/s41598-017-09492-8. PubMed PMID: 28851948; PubMed Central PMCID: PMC5575130.

    6: Jiang X, Su K, Tao J, Fan R, Xu Y, Han H, Li L, Li MD. Association of STAT4 polymorphisms with hepatitis B virus infection and clearance in Chinese Han population. Amino Acids. 2016 Nov;48(11):2589-2598. Epub 2016 Jul 21. PubMed PMID: 27444301.

    7: Li T, Jin K, Zhu DY, Li L, Mao ZR, Wu BW, Wang YF, Pan ZF, Li LJ, Xiang CS, Su KK *, Lou YJ. Premalignant alteration assessment in liver-like tissue derived from embryonic stem cells by aristolochic acid I exposure. Oncotarget. 2016 Nov 29;7(48):78872-78882. doi: 10.18632/oncotarget.12424. PubMed PMID: 27713163; PubMed Central PMCID: PMC5346684.

    8: Su K, Wang Q, Qi L, Hua D, Tao J, Mangan CJ, Lou Y, Li L. MicroRNA-674-5p/5-LO axis involved in autoimmune reaction of Concanavalin A-induced acute mouse liver injury. Toxicol Lett. 2016 Sep 6;258:101-107. doi: 10.1016/j.toxlet.2016.06.010. Epub 2016 Jun 14. PubMed PMID: 27313091.

    9: Guo J, Huang F, Liu J, Chen Y, Wang W, Cao B, Zou Z, Liu S, Pan J, Bao C, Zeng M, Xiao H, Gao H, Yang S, Zhao Y, Liu Q, Zhou H, Zhu J, Liu X, Liang W, Yang Y, Zheng S, Yang J, Diao H, Su K, Shao L, Cao H, Wu Y, Zhao M, Tan S, Li H, Xu X, Wang C, Zhang J, Wang L, Wang J, Xu J, Li D, Zhong N, Cao X, Gao GF, Li L, Jiang C. Corrigendum: The Serum Profile of Hypercytokinemia Factors Identified in H7N9-Infected Patients can Predict Fatal Outcomes. Sci Rep. 2016 Feb 23;6:21230. doi: 10.1038/srep21230. PubMed PMID: 26903038; PubMed Central PMCID: PMC4763171.

    10: Jin K, Su KK #, Li T, Zhu XQ, Wang Q, Ge RS, Pan ZF, Wu BW, Ge LJ, Zhang YH, Wang YF, Shen GF, Zhu DY, Xiang CS, Li LJ, Lou YJ. Hepatic Premalignant Alterations Triggered by Human Nephrotoxin Aristolochic Acid I in Canines. Cancer Prev Res (Phila). 2016 Apr;9(4):324-34. doi: 10.1158/1940-6207.CAPR-15-0339. Epub 2016 Feb 5. PubMed PMID: 26851235.

    11: Wang M, Ma Y, Yuan W, Su K, Li MD. Meta-Analysis of the COMT Val158Met Polymorphism in Major Depressive Disorder: Effect of Ethnicity. J Neuroimmune Pharmacol. 2016 Sep;11(3):434-45. doi: 10.1007/s11481-016-9651-3. Epub 2016 Jan 23. Review. PubMed PMID: 26803486.

    12: Tao J, Su K, Yu C, Liu X, Wu W, Xu W, Jiang B, Luo R, Yao J, Zhou J, Zhan Y, Ye C, Yuan W, Jiang X, Cui W, Li MD, Li L. Fine mapping analysis of HLA-DP/DQ gene clusters on chromosome 6 reveals multiple susceptibility loci for HBV infection. Amino Acids. 2015 Dec;47(12):2623-34. doi: 10.1007/s00726-015-2054-6. Epub 2015 Jul 22. PubMed PMID: 26197724.

    13: Guo J, Huang F, Liu J, Chen Y, Wang W, Cao B, Zou Z, Liu S, Pan J, Bao C, Zeng M, Xiao H, Gao H, Yang S, Zhao Y, Liu Q, Zhou H, Zhu J, Liu X, Liang W, Yang Y, Zheng S, Yang J, Diao H, Su K, Shao L, Cao H, Wu Y, Zhao M, Tan S, Li H, Xu X, Wang C, Zhang J, Wang L, Wang J, Xu J, Li D, Zhong N, Cao X, Gao GF, Li L, Jiang C. The Serum Profile of Hypercytokinemia Factors Identified in H7N9-Infected Patients can Predict Fatal Outcomes. Sci Rep. 2015 Jun 1;5:10942. doi: 10.1038/srep10942. Erratum in: Sci Rep. 2016;6:21230. PubMed PMID: 26028236; PubMed Central PMCID: PMC4450576.

    14: Gao HN, Yao HP, Liang WF, Wu XX, Wu HB, Wu NP, Yang SG, Zhang Q, Su KK, Guo J, Zheng SF, Zhu YX, Chen HL, Yuen KY, Li LJ. Viral genome and antiviral drug sensitivity analysis of two patients from a family cluster caused by the influenza A(H7N9) virus in Zhejiang, China, 2013. Int J Infect Dis. 2014 Dec;29:254-8. doi: 10.1016/j.ijid.2014.10.029. Epub 2014 Nov 13. PubMed PMID: 25462187.

    15: Liu X, Zhang Y, Xu X, Du W, Su K, Zhu C, Chen Y, Lei S, Zheng S, Jiang J, Yang S, Guo J, Shao L, Yang Q, Chen J, Li L. Evaluation of plasma exchange and continuous veno-venous hemofiltration for the treatment of severe avian influenza A (H7N9): a cohort study. Ther Apher Dial. 2015 Apr;19(2):178-84. doi: 10.1111/1744-9987.12240. Epub 2014 Nov 3. PubMed PMID: 25363618.

    16: Huang X, Su K, Zhou L, Shen G, Dong Q, Lou Y, Zheng S. Hypoxia preconditioning of mesenchymal stromal cells enhances PC3 cell lymphatic metastasis accompanied by VEGFR-3/CCR7 activation. J Cell Biochem. 2013 Dec;114(12):2834-41. doi: 10.1002/jcb.24629. PubMed PMID: 23939705.

    17: Zhu Z, Tong X, Zhu Z, Liang M, Cui W, Su K, Li MD, Zhu J. Development of GMDR-GPU for gene-gene interaction analysis and its application to WTCCC GWAS data for type 2 diabetes. PLoS One. 2013 Apr 23;8(4):e61943. doi: 10.1371/journal.pone.0061943. Print 2013. PubMed PMID: 23626757; PubMed Central PMCID: PMC3633958.

    18: Qin N, Ding W, Yao J, Su K, Wu L, Li L. Genome sequence of Staphylococcus capitis QN1, which causes infective endocarditis. J Bacteriol. 2012 Aug;194(16):4469-70. doi: 10.1128/JB.00827-12. PubMed PMID: 22843597; PubMed Central PMCID: PMC3416214.

    19: Kim S, Kim YC, Qi H, Su K, Morrison SL, Chow SA. Efficient identification of human immunodeficiency virus type 1 mutants resistant to a protease inhibitor by using a random mutant library. Antimicrob Agents Chemother. 2011 Nov;55(11):5090-8. doi: 10.1128/AAC.00687-11. Epub 2011 Aug 29. PubMed PMID: 21876045; PubMed Central PMCID: PMC3195011.

    20: Su K, Wang D, Ye J, Kim YC, Chow SA. Site-specific integration of retroviral DNA in human cells using fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc-finger protein E2C. Methods. 2009 Apr;47(4):269-76. doi: 10.1016/j.ymeth.2009.01.001. Epub 2009 Jan 30. Review. PubMed PMID: 19186211; PubMed Central PMCID: PMC2695809.

Teaching

  • Couse: Medical Statistics

  • Textbook: Medical Statistics (6th Edition, People’s medical Publishing House)

  • Level: Undergraduate (2nd year of the 5-year-course)

  • Type: Theory course (CAI)

  • Course website: http://geneureka.org/medstat.html

  • Period: 2 class hours.

  • Office hours: Mon. 2 - 4 pm


This site is maintained by Kunkai Su & Xin Huang

Contact: ksu(at)zju.edu.cn or xh(at)zju.edu.cn