Molecular Oncology & Biomarkers


Dr. Shi studies epigenomics, and development of high-throughput technologies for dissecting the complex epigenetic regulation in normal and tumor cells. Epigenetics is heritable chromatin organization and gene expression not encoded by DNA sequence. While epigenetics refers to the study of single genes or sets of genes, epigenomics is the global analyses of epigenetic changes across the genome.

Research projects in my laboratory are aimed to understand how epigenetic processes become misregulated in cancer and contribute to the disease phenotype. Next-generation sequencing-based approaches, including RNA-seq, genome-wide bisulfite sequencing, and ChIP-seq, are used to generate genome-scale epigenetic profiles of various cancer subtypes. Statistical and bioinformatics tools are used to develop biological models of epigenetic regulation of gene expression in tumor cells. Current specific areas are outlined below:

Epigenomics of chronic lymphocytic leukemia

One of the major focuses of our research is chronic lymphocytic leukemia (CLL), which is the most common form of adult leukemias in the United States. We are interested in understanding the molecular heterogeneity of CLL and identifying prognostic biomarkers as well as novel therapeutic targets in CLL. Using genome-wide DNA methylation profiling, we have has shown that two molecular subtypes of CLL (IGHV mutated vs unmutated CLL) has distinct DNA methylation profiles that seem to represent epigenetic imprints from normal B-cell subpopulations. Through integrated DNA methylation and gene expression analysis, specific genes have been identified that distinguish new clinico-biological subtypes of CLL. Particularly, DNA hypomethylation was observed in a significant number of genes involved in lymphocyte activation such as PDCD1, NFAT2, CD5, and LCK, which may have functional and clinical implications in leukemiagenesis. We found that a significant number of the hypomethylated genes in CLL are associated with the so-called super enhancers and marked with significant enrichment of histone H3K27 acetylation. On-going studies are designed not only to further understand the function of these hypomethylated genes, but also to target the super enhancer-driven oncogene transcription using small molecule inhibitors. A key feature of the clinical course of CLL is that patients with CLL also present with humoral immune deficiency that worsens with disease progression. We are investigating the molecular mechanisms of T-cell dysfunction in CLL using epigenomic approaches.

Epigenetic regulation of IDO expression in triple negative breast cancer

Triple-negative breast cancer (TNBC) is most clinically challenging among all breast cancer subtypes due to its aggressive clinical behavior, the lack of treatment options and its heterogeneous response to chemotherapy. Recent studies have also shown that TNBC is characterized by frequent lymphocyte-infiltration and elevated expression of immune responsive genes, suggesting that TNBC patients may benefit from immunotherapy. Indoleamine 2,3-dioxygenase (IDO), a single chain oxido-reductase that serves as a catalyst for the degradation of tryptophan into kynurenine, has emerged as a key player in T-cell suppression and in the induction of immune tolerance to tumors. We discovered that promoter hypomethylation and up-regulation of IDO1, which encodes IDO enzyme, is a unique molecular feature of TNBC or basal-like breast cancer as compared to other subtypes of breast cancer. Our in vitro studies demonstrated that IDO1 promoter methylation controls its expression in response to the interferon γ treatment in breast cancer cells. This novel finding leads us to hypothesize that IDO1 promoter methylation may be developed into a biomarker for predicting TNBC prognosis and the response to IDO inhibitor-based immunotherapy. Currently we are determining the prognostic value of IDO1 promoter methylation in TNBC patients and dissecting the mechanisms of epigenetic regulation of IDO1 expression in breast cancer cells. In addition, we have identified several small molecules that inhibit interferon γ-induced IDO1 expression at the transcription level. We are investigating the molecular mechanisms of these drugs and evaluating their ability to block IDO1 expression in breast cancer cells.

Lee EJ, Pei L, Srivastava G, Trupti J, Kushwaha G, Choi JH, Wang X, Colbourne J, Zhang L, Schroth GP, Xu D, Zhang K, Shi H. (2011) Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Research. 19:e127.

Pei L, Choi JH, Liu J, Lee EJ, McCarthy B, Wilson JM, Speir E, Awan F, Tae H, Arthur G, Schnabel JL, Taylor KH, Wang X, Xu D, Ding HF, Munn DH, Caldwell C, Shi H. (2012) Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics. 7:567-578. 

Lee EJ, Luo J, Wilson JM, Shi H. (2012) Analyzing the cancer methylome through targeted bisulfite sequencing. Cancer Letters.S0304-3835(12)00645-3.

Luo D, Wilson JM, Harvel N, Liu J, Pei L, Huang S, Hawthorn L, Shi H. (2013) A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells. J Transl Med.11:57.

Sharma MD, Huang L, Choi JH, Lee EJ, Wilson JM, Lemos H, Pan F, Blazar BR, Pardoll DM, Mellor AL, Shi H, Munn DH. (2013) An inherently bi-functional subset of Foxp3+ Treg/T-helper cells is controlled by the transcription factor Eos. Immunity.38:998-1012.

Liu Z, Zhang J, Gao Y, Pei L, Sun Y, Zhou J, Gu L, Zheng X, Zhang L, Zhu B, Hattori N, Ji J, Yuasa Y, Kim W, Ushijima T, Shi H*, Deng D*. (2014) Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis. Clin Cancer Res. 20:4598-612. (*: Co-corresponding author) 

Lee EJ, Rath P, Liu J, Ryu D, Free A, Pei L, Feng Q, Litofsky NS, Miller, DC, Anthony DC, Sharma S, Kirk MD, Laterra JJ, Ryu D, Choi J, Shi H. (2015) Identification of Global DNA Methylation Signatures in Glioblastoma-derived Cancer Stem Cells. J Genet Genomics.42:355-71.

Shull A, Noonepalle SK, Lee EJ, Choi J, Shi H. (2015) Sequencing the Cancer Methylome. Methods Mol Biol. 1238:627-51. 

ShullAY, NoonepalleS, PeiL, AwanFT, Mills GB, Ding Z, Shi H. (2015) RPPA-based protein profiling reveals eIF4G overexpression and 4E-BP1 serine 65 hyperphosphorylation as molecular events that correspond with a pro-survial phenotype in chronic lymphocytic leukemia. Oncotarget, 6:14632-45.

Kushwaha G, Dozmorov M, Wren JD, Qiu J, Shi H*, Xu D*. (2016) Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. Hum Genomics. 10 Suppl 2:18. (*: Co-corresponding author) 

Wu J, Xu X, Lee EJ, Shull AY, Pei L, Awan F, Wang X, Choi JH, Deng L, Xin HB, Zhong W, Liang J, Miao Y, Wu Y, Fan L, Li J, Xu W, Shi H. (2016) Phenotypic alteration of CD8+ T cells in chronic lymphocytic leukemia is associated with epigenetic reprogramming. Oncotarget. 7:40558-70.

Noonepalle SK, Gu F, Lee EJ, Choi JH, Han Q, Kim JJ, Ouzounova M, Shull AY, Pei L, Hsu PY, Kolhe R, Shi F, Choi J, Chiou K, Huang THM, Korkaya H, Deng L, Xin HB, Huang S, Thangaraju M, Sreekumar A, Ambs S, Tang SC, Munn DH, Shi H. (2017) Promoter methylation modulates indoleamine 2, 3-dioxygenase 1 induction by activated T cells in human breast cancers. Cancer Immunol Res. 5: 330-344.