Swiss Institute for Experimental Cancer Research (M.D.)
Northwestern University (Postdoctoral fellow)
University of Chicago (Postdoctoral fellow)
My study is in genomics. The rapid progress of genome science in recent years has made revolutionary impact on biology and medicine. Analyzing life process at the genome level provides systems information to understand the biological basis of physiology and diseases. I have worked on multiple genomics topics as exemplified by the followings:
Gene expression reflects biological activities of the genome under physiological and pathological conditions. We studied transcriptome in the areas of annotating the transcribed regions in the genomes of human, Drosophila and rice, normal gene expression in early hematopoiesis including stem/progenitor cells, pre-B cells, pre-T cells, myeloid progenitors, NK progenitors, erythroid progenitors, abnormal gene expression in myeloid cells in acute myeloid leukemia, and fusion genes in normal-karyotype acute myeloid leukemia. We are performing genome-scale promoter mapping analysis to identify the altered gene expression regulation in multiple diseases.
Genomic study of familial breast cancer
Breast cancer is a leading cancer in women worldwide. Approximately 10% of breast cancers are clustered in family setting with multiple members affected (familial breast cancer), caused by the genetic predispositions inherited in the disease family. This is best demonstrated by the BRCA1 germline mutations (BRCA1+) in disease families that a woman who inherits a pathogenic BRCA1 pathogenic mutation has 70-80% chance of developing breast cancer by the age of 70. However, genetic predispositions have been identified in about 40% of the disease families. Since joining UNMC, my laboratory has been studying familial breast cancer, aiming to better understand genetic basis of the disease, and to provide new genetic markers for early prevention, diagnosis and personalized treatment of the disease. We are using next generation sequencing-based approaches to study the nature of genome instability in BRCA1+ families, and unknown genetic predisposition in the disease families without known predisposition (BRCAx). We are persuading the study through campus-wide, national-wide, and international-wide collaborations.
My study has been supported by grants from the National Human Genome Research Institute and National Cancer Institute of National Institute of Health, the Department of Defense, and multiple foundations.
- Wang SM, Fears SC, Zhang L, Chen JJ, Rowley JD. Screening poly dA/dT(-) cDNAs for gene identification. Proc. Natl. Acad. Sci. USA 97:4162-4167, 2000
- Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl. Acad. Sci. USA 99:12257-12262, 2002
- Lee S, Bao J, Zhou G, Shapiro J, Xu J, Shi RZ, Lu X, Clark T, Johnson D, Kim YC, Wing C, Tseng C, Sun M, Lin W, Wang J, Yang H, Wang J, Du W, Wu CI, Zhang X, Wang SM. Detecting novel low-abundant transcripts in Drosophila. RNA 11:939-946, 2005
- SAGE: Current Technologies and Applications. p1-375. Horizon Scientific Press, UK. Editor: Wang SM, 2005
- Lee S, Chen J, Zhou G, Shi RZ, Bouffard GG, Kocherginsky M, Ge X, Sun M, Jayathilaka N, Kim YC, Emmanuel N, Bohlander SK, Minden M, Kline J, Ozer O, Larson RA, LeBeau MM, Green ED, Trent J, Karrison T, Liu PP, Wang SM, Rowley JD. Gene Expression Profiles in Acute Myeloid Leukemia with Common Translocations using SAGE, Proc. Natl. Acad. Sci. USA 103:1030-1035, 2006
- Wang SM. Understanding SAGE data. Trends in Genetics 23:42-50, 2007
- Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. The birth and death of microRNA genes in Drosophila. Nature Genetics 40:351-355, 2008.
- Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Research 18:751-762, 2008
- Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS ONE 3:e2803. 2008
- Kim YC, Wu Q, Chen J, Xuan Z, Jung YC, Zhang MQ, Rowley JD, Wang SM. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc. Natl. Acad. Sci. USA 106:8278-8283, 2009
- Wen H, Li Y, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Hou G, Rowley JD, Zhang MQ, Wang SM. New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One. 7:e51203., 2012
- COMPLEXO, Southey MC, Park DJ, Nguyen-Dumont T, Campbell I, Thompson E, Trainer AH, Chenevix-Trench G, Simard J, Dumont M, Soucy P, Thomassen M, Jønson L, Pedersen IS, Hansen TV, Nevanlinna H, Khan S, Sinilnikova O, Mazoyer S, Lesueur F, Damiola F, Schmutzler R, Meindl A, Hahnen E, Dufault MR, Chris Chan T, Kwong A, Barkardóttir R, Radice P, Peterlongo P, Devilee P, Hilbers F, Benitez J, Kvist A, Törngren T, Easton D, Hunter D, Lindstrom S, Kraft P, Zheng W, Gao YT, Long J, Ramus S, Feng BJ, Weitzel JN, Nathanson K, Offit K, Joseph V, Robson M, Schrader K, Wang SM, Kim YC, Lynch H, Snyder C, Tavtigian S, Neuhausen S, Couch FJ, Goldgar DE. COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration. Breast Cancer Res. 15(3):402, 2013
- Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, Wang SM. Can unknown predisposition in familial breast cancer be family-specific? The Breast Journal, 19:520-528, 2013
- Xiao FX, Kim YC, Snyder C, Wen H, Chen PX, Luo J, Becirovic D, Downs B, Cowan KH, Lynch H, Wang SM. Genome instability in blood cells of a BRCA1+ breast cancer family. BMC Cancer 14:342, 2014
- Wen H, Kim YC, Snyder C, Xiao F, Fleissner EA, Becirovic D, Luo J, Downs B, Sherman S, Cowan KH, Lynch HT, Wang SM. Family-specific, novel, deleterious germline variants provide a rich source to identify genetic predispositions for BRCAx familial breast cancer. BMC Cancer 14:470. 2014