• The Huang Lab

    University of Minnesota Twin Cities

  • Welcome!

    Principal Investigator

    R. Stephanie Huang, Ph.D.

    About Dr. Huang

    Associate Professor

    R. Stephanie Huang received her M.S. and Ph.D from Purdue University specializing in Clinical Pharmacology. After her training, Dr. Huang performed her postdoctoral research at the University of Chicago and joined the faculty at the University of Chicago as an assistant professor. In 2017, she became an associate professor at the University of Minnesota Twin Cities.

     

    Dr. Huang has won multiple awards such as the American Federation for Medical Research (AFMR) Scholar award, the Central Society of Clinical and Translational Research CSCTR Outstanding Young Investigator Award, American Association of Cancer Research (AACR) Merck Scholar-in-Training Award, and the American Society for Clinical Pharmacology and Therapeutics (ASCPT) Presidential Trainee Award.

     

     

  • What We Research.

    Translational Pharmacogenomics and Cancer Biology

    Novel drug sensitivity model development

    We are currently working on developing drug sensitivity prediction models for various types of cancers and medications. We seek to identify genetic variants (in the form of SNPs or CNVs), microRNA and/or gene expression that are associated with drug sensitivity both in vitro and in vivo.  We are also exploring the opportunity in using blood samples derived from patients as a drug sensitivity screening model.

    Mechanistic investigations in Cancer genomics

    We employ multiple bioinformatic tools to identify potential pharmacogenomic biomarkers in publicly existing high-throughput datasets. These novel biomarkers were then experimentally evaluated in various cancer and normal cell lines as well as in clinical samples.

    Integrative Research

    Through ongoing clinical trials, our lab collects patient samples over time to generate longitudinal "omics" data after drug treatment. We integrate multiple levels of "omics" data (including but not limited to DNA/mRNA/non-coding RNA/protein) along with clinical treatment information over time to develop better omic prediction model for drug response.

    Drug Repurposing

    Our lab has developed a genome-wide gene expression based drug sensitivity prediction method, which utilizes the expression of every gene in the genome to determine drug sensitivity.  We are currently applying this novel method in repurposing drugs in various cancer types. 

  • Lab Announcements

    what's new with the lab?

    Congratulations to Aritro!

    The Huang Lab would like to congratulate Aritro for acting as the Chair of the UChicago 2016 Post-Doc Research and Career Development Symposium. We are very proud of him, and the event was a blast!

    Welcome Shuqin Zhou

    The Huang Lab would like to welcome Shuqin Zhou, a visiting scholar who will be staying with us over the year. We hope you have a great time!

    Announcing Alex Ling

    We would like to welcome Alex Ling, a new graduate student to the Huang Lab! We hope you have a wonderful experience.

    Announcing Robert Gruener

    Welcome Robert Gruener, our new graduate student, to the Huang lab! We look forward to working with you!

    Our Archive.

    Looking for something? View previous lab announcements here.

  • Meet the Members

    We've got a top notch team!

    Paul Geeleher

    Post-Doctorate Researcher

    I am from Ireland and work currently as a postdoctoral researcher specializing in bioinformatics. I received my M.Sc. (by research) and Ph.D in bioinformatics from the Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland (NUI), Galway. My research focuses on applying high-throughput genomics, such as next-generation sequencing and microarrays, to solve biological problems with a particular emphasis on cancer. This work primarily involves leveraging “omics” level datasets (e.g. genome-wide gene expression profiles, whole-genome sequence data) to predict patient response to chemotherapeutic agents.

    Aritro Nath

    Post-Doctorate Researcher

    I graduated from Michigan State University in 2015 with a PhD in genetics, after completing my undergraduate education in biomedical genetics from VIT University in India. My primary research objective in the lab is to establish a tyrosine kinase inhibitor response prediction model in chronic myeloid leukemia (CML) patients utilizing clinical information in conjunction with multi-level longitudinal omic data (including microarray/RNAseq expression, whole-genome sequencing, and protein profiling data). Additionally, I am developing a combinatorial drug-response prediction algorithm that can identify potential synergistic drug-pairs utilizing baseline genetic profile (including expression, CNV, mutation and methylation data) of multiple cancer cell lines. 

    Chester Kao

    Medical Student

    I hail from the mitten state of Michigan, and I graduated from the University of Michigan in Cellular and Molecular Biology with a Master’s degree in Biomedical Engineering. I joined the lab in 2015 as a medical student in the Pritzker Summer Research Program working on a pilot study focused on the analysis of longitudinal omics data of chronic myeloid leukemia (CML) patients. I am currently focused on using a bioinformatics approach to select for and validate gene networks of interest responsive to imatinib treatment in CML.

     

    Robert Gruener

    Graduate Student

    I received my undergraduate degree in Biochemistry from the University of Wisconsin-Madison, and am currently a graduate student in the Committee on Cancer Biology here at the University of Chicago. My research involves using drug screening and genomic data to predict drugs that may be effective in treating cancers that have limited treatment options, particularly triple negative breast cancer. After generating these predictions, the compounds will then be tested for efficacy in appropriate cell line and mouse models.

    Alex Ling

    Graduate Student

    I come from the prairielands of Minnesota where I got an AA and an AS from the local community college before doing my BS in Biochemistry at Northern Michigan University. I took two years off to farm with my Dad before joining the Ph.D. program in Cancer Biology, where I now work with Kenan Onel and Stephanie Huang to determine the genetic basis for treatment resistance in osteosarcoma. I’m currently generating and analyzing a large set of whole genome and RNA sequencing data from pre- and post-treatment osteosarcomas as well as studying the contribution of rare germline mutations to cancer risk in general.

    Shuqin Zhou

    Visiting Scholar

    I hail from Shanghai of China, and I graduated from the Nanjing Medical University with a Master’s degree in Nephrology. I joined the lab in 2016 as a visiting scholar working on a pilot study focused on the analysis of longitudinal omics data of chronic myeloid leukemia (CML) patients. I am currently focused on using a bioinformatics approach to select for and validate gene networks of interest responsive to imatinib treatment in CML.

    Jeremy Chang

    Undergraduate Student

    I come from Arcadia, California (near Los Angeles) and am a current second-year student at the College majoring in the biological sciences. I spent the summer of 2015 as a BSCD Summer Fellow researching the functional role of the microRNA called miR-532-5p in ovarian cancer. I am currently working with Fan Wang and Dr. Huang on finding microRNAs with prognostic value in breast cancer patients.

  • Download pRRophetic 

    An R package for prediction of clinical chemotherapeutic response from only tumor gene expression levels.

  • Publications 

    Additional publications may be found Here on PUBMED.

    2016

    Wang F, Chang JT, Kao CJ, Huang RS. High expression of miR-532-5p, a tumor suppressor, leads to better prognosis in ovarian cancer both in vivo and in vitro. Mol Cancer Ther. 2015.15:0943. doi: 10.1158/1535-7163.

     

    Gladys Morrison, Divya Lenkala, Bonnie LaCroix, Dana Ziliak ,Ingrid A. Mayer, Phuong Khanh Morrow, Andres Forero, Catherine Van Poznak, Hope S Rugo, Rita Nanda, Peter H. O’Donnell, and Huang RS. Utility of patient-derived lymphoblastoid cell lines as an ex vivocapecitabine sensitivity prediction model for breast cancer patients. Oncotarget. 2016. 7(25):38359-38366. PMID: 27224917.

     

    Michael A. Grassi, Vidhya Rao, Siquan Chen, Dingcai Cao, Xiaoyu Gao, Patricia A. Cleary, Huang RS, Jalees Rehman, Timothy S. Kern, Yoav Gilad, Nancy J. Cox. Lymphoblastoid cell lines as a tool to study inter-individual differences in the response to glucose. Accepted by PLoS One, 2016.

     

    Geeleher P, Cox NJ and Huang RS. Improvement of biomarker discovery by accounting for variability in general levels of drug sensitivity in pre-clinical models. Genome Biology. 2016. 17(1):190.

     

    Geeleher P, Gamazon ER, Seoighe C, Cox NJ and Huang RS. Consistency in large pharmacogenomic studies. Nature. 2016. 540 (7631):E1-E2.

     

    Chang JT, Wang F, Chapin W, Huang RS. Identification of microRNAs as breast cancer prognosis markers through the Cancer Genome Atlas. PLoS One. 2016. 11(12):e0168284. PMID: 27959953.

    2015

    Chapin WJ, Lenkala D, Mai Y, Mao Y, White SR, and Huang RS. Peripheral blood IRF1 expression as a marker for glucocorticoid sensitivity. Pharmacogenetics and Genomics, 2015. 25(3): 126-133. PMID: 25564375. PMCID: PMC4315702.


    Lenkala D, Gamazon ER, LaCroix B, Im HK, and Huang RS. MicroRNA biogenesis and cellular proliferation. Translational Research. 2015. Epub ahead of print. PMID: 25724890.


    Geeleher P, Andrey Loboda, Divya Lenkala, Fan Wang, Bonnie LaCroix, Sanja Karovic, Jacqueline Wang, Michael Nebozhyn, Michael Chisamore, James Hardwick, Michael L. Maitland and Huang RS. Predicting Response to Histone Deacetylase Inhibitors Using High-Throughput Genomics. JNCI J Natl Cancer Inst 2015; 107 (11): djv247. doi: 10.1093/jnci/djv247

     

    Delaney Christopher, Samuel Frank, and Huang RS. Pharmacogenomics of EGFR-Targeted Therapies in Non-Small Cell Lung Cancer (NSCLC): EGFR and Beyond. Chinese Journal of Cancer. 2015. 34(1): 7. PMID: 25962919.

     

    Chang JT, Lee YM, and Huang RS. The impact of the Cancer Genome Atlas on lung cancer. Translational Research 2015. 166(6):568-85. doi: 10.1016/j.trsl.2015.08.001.

     

    2014

    Grassi M., Rao V, Winkler KP, Zhang W, Bogaard JD, Chen SC, LaCroix B, Lenkala D, Rehman J, Malik AB, Cox NJ, and Huang RS. Genetic Variation is the Major Determinant of Individual Differences in Leukocyte Endothelial Adhesion. PLoS One, 2014. 9(2): e87883. PMID: 24520339. PMCID: PMC3919726.

     

    Geeleher P, Cox NJ, and Huang RS. Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biology, 2014. 15(3):R47. PMID: 24580837. PMCID: PMC4054092.

     

    Note: Code can be downloaded here.

     

    Lenkala D, LaCroix B, Gamazon ER, Im HK, and Huang RS. The impact of microRNA expression on cellular proliferation. Human Genetics. 2014. 133(7): 931-938. PMID: 24609542.

     

    Weng LM, Ziliak D, LaCroix B, Geeleher P, and Huang RS. Integrative “omic” analysis for tamoxifen sensitivity through cell based models. PLoS One. 2014. 9(4): e93420. PMID: 24699530. PMCID: PMC3974759.

     

    Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy V, Dolan ME, Huang RS, Cox NJ and Im HK. Poly-Omic Prediction of Complex Traits: OmicKriging. Genetics Epidemiology. 2014. 38(5): 402-415. PMID: 24799323. PMCID: PMC4072756.

     

    LaCroix B, Gamazon ER, Lenkala D, Im HK, Geeleher P, Ziliak D, Cox NJ and Huang RS. Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity. BMC Genomics. 2014. 15(1):292. PMID: 24739237. PMCID:PMC3996490.

     

    Wu KH, Gamazon ER, Im HK, Geeleher Paul, White S, Solway J, Clemmer G, Weiss ST, Tantisira K, Ratain MJ and Huang RS. Genome-wide interrogation of longitudinal FEV1 in children with asthma. Am J Respiratory and Critical Care Medicine. 2014. 190(6): 619-627. PMID: 25221879. PMCID: PMC4214107.

     

    Geeleher P, Cox NJ, and Huang RS. pRRophetic: An R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One, 2014. 9(9):e107468. PMID: 25229481. PMCID: PMC4167990.

     

    Note: Source code can be downloaded here. 

     

    Bhutra S, LaCroix B, Lenkala D, Ye M, and Huang RS. Identifying and validating a combined mRNA and microRNA signature in response to imatinib treatment in a chronic myeloid leukemia cell line. PLoS One, 2014. 9(12):e115003. PMID: 25506832.

     

    Kehua Wu, R. Stephanie Huang, Larry House and William CS Cho. Next generation sequencing for lung cancer. Chinese translated version. Zhongguo Gei Ai Za Zhi. 2014. 17(1):C1-C12. PMID: 24398316.

     

    Rose Maimon, Kostyanovskaya Elina, and Huang RS. Pharmacogenomics of Cisplatin Sensitivity in Non-Small Cell Lung Cancer. Genomics, Proteomics & Bioinformatics. 2014. 12(5): 198-209. PMID: 25449594. PMC 4411417.

    2013

    Paul Geeleher, R. Stephanie Huang, Eric R. Gamazon, Aaron Golden and Cathal Seoighe. The regulatory effect of miRNAs is a heritable genetic trait in humans. BMC Genomics, 2013; 13:383. PMID: 23272639. PMCID: PMC3532363.

     

    Jiangfang Lian, Yi Huang, R. Stephanie Huang, Limin Xu, Yanping Le, Xi Yang, Weifeng Xu, Xiaoyan Huang, Meng Ye, Jianqing Zhou and Shiwei Duan. Meta-analyses of four eosinophil related gene variants in coronary heart disease. J Thromb Thrombolysis. 2013; 36(4): 394-401. PMID: 23328882.

     

    LN Zhang, PP Liu, Jianqing Zhou, R. Stephanie Huang, F Yuan, LJ Fei, Yi Huang, L Xu, LM Hao, XJ Qiu, Yanping Le, Xi Yang, Weifeng Xu, Xiaoyan Huang, Meng Ye, Jiangfang Lian, Shiwei Duan. Positive correlation between variants of lipid metabolism-related genes and coronary heart disease. Mol Med Rep. 2013; 8(1):260-266. PMID: 23653095. PMC3724684.

     

    Liming Weng, Dana Ziliak, Hae Kyung Im, Eric R. Gamazon, Santosh Philips, Anne T. Nguyen, Zeruesenay Desta, Todd C. Skaar, David A. Flockhart, and R. Stephanie Huang. Genome-wide discovery of genetic variants affecting tamoxifen sensitivity and their clinical and functional validation. Annals of Oncology. 2013; 24(7): 1867-1873. PMID: 23508821. PMCID:PMC3690911.


    Eric Gamazon, R. Stephanie Huang, M. Eileen Dolan, Nancy Cox and Hae Kyung Im. Integrative Genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Front Genet. 2013; 3:202. PMID: 23755062. PMCID: PMC3668276.

     

    Eric Gamazon, Federico Innocenti, Rongrong Wei, Libo Wang, Min Zhang, Snezana Mirkov, Jacqueline Ramirez, R. Stephanie Huang, Nancy Cox, Mark Ratain and Wanqing Liu. A genome-wide integrative study of microRNAs in human liver. BMC Genomics. 2013; 14(1):395. PMID: 23758991. PMC3710218.

    Jianqing Zhou, Limin Xu, R. Stephanie Huang, Yi Huang, Yanping Le, Danjie Jiang, Yang Xi, Weifeng Xu, Xiaoyan Huang, Changzheng Dong, M. Ye, Jiangfang Lian, Shiwei Duan. Apolipoprotein A5 gene variants and the risk of coronary heart disease: A casecontrol study and metaanalysis. Mol Med Rep, 2013. 8(4): 1175-82. PMID: 23970179.

     

    Xiuqin Ni, Wei Zhang and R. Stephanie Huang. Pharmacogenomics discovery and implementation in genome-wide association studies era. WIREs Systems Biology and Medicine, 2013; 5(1):1-9. PMID: 23188748.


    Liming Weng, Li Zhang, Yan Peng and R. Stephanie Huang. Pharmacogenetics and pharmacogenomics: a bridge to individualized cancer therapy. Pharmacogenomics, 2013; 14(3):315-324. PMID: 23394393.


    Shuangli Mi, Jian Zhang, Wei Zhang and R. Stephanie Huang. Circulating microRNAs as biomarkers for inflammatory diseases. MicroRNA, 2013; 2(1): 64-72.

     

    Kehua Wu, R. Stephanie Huang, Larry House and William CS Cho. Next generation sequencing for lung cancer. Future Oncology, 2013; 9(9): 1323-1336. PMID: 23980680.


    Jean Lee and R. Stephanie Huang. Cancer Epigenetics: Mechanisms and Crosstalk of a HDAC inhibitor, Vorinostat. Chemotherapy, 2013; 2:111. http://dx.doi.org/10.4172/2167-7700.1000111.


    Eric R. Gamazon, R. Stephanie Huang, Nancy J. Cox. SCAN: a systems biology approach to pharmacogenomic discovery. Methods Mol Biol. 2013; 1015:213-224. PMID: 23824859.

     

     

    Publications from previous years may be found on PubMed.

     

     

  • Past Lab Members

    Thank you for your hard work!

    Technicians

    Dana Ziliak (Goodman) - Clinical Project Manager at Cook Medical

    Bonnie LaCroix - Duke Research Analyst at Duke University

    Divya Lenkala

    Fan Wang

    Post-Doctorates

    Liming Weng - University of Florida

    Gladys Morrison

    Medical Students

    Steven Bhutra

    William Chapin

    Alice Lee

    Rotating Graduate Students

    Larischa de wet

    Jessica Fessler

    College Students

    Ann Ryu - UCSF

    Yarden Fraiman - John Hopkins

    Stephanie Joseph - Project assistant at Urban GIS

    Kurtis Anthony                   

    Jean Lee - University of Chicago

    High School Students

    Viren Makhijani - UCLA

  • Contact the Lab.

    We look forward to hearing from you!