Assistant Professor of Oncological Sciences
Cancer Genomics, 3D Genomics, Genome/Epigenome Editing
The Zhang Lab applies 3D genomics approaches to investigate the interplay between cancer genome and epigenome. We are interested in how genetic alterations cause epigenetic and transcriptional dysregulation favoring tumorigenesis, with a long-term goal of discovering novel therapeutic targets. Our group utilizes genome/epigenome analysis and high-throughput screening to generate hypotheses that we test using cutting-edge CRISPR technologies.
Our research uniquely spans the interface between computational and experimental biology. The research directions include the following:
- Identify and characterize recurrent noncoding genomic/epigenomic alterations in cancer
- Investigate the function of oncogenic transcription factors in cancer, particularly in 3D genome context.
References (Selected Publications)
- Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD#, Zhang X# (2021) A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nature Communications12, 7139.
- Liu Y, Guo B, Aguilera-Jimenez E, Chu VS, Zhou J, Wu Z, Francis JM, Yang X, Choi PS, Bailey SD#, Zhang X# (2020). Chromatin Looping Shapes KLF5-dependent Transcriptional Programs in Human Epithelial Cancers. Cancer Research80, 5464-5477.
- Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M#, Zhang X# (2020). Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma.Molecular Cancer Research18, 574-584 PMID: 31862696. PMCID: PMC7219472.
- Zhang X, Meyerson M (2020). Illuminating the noncoding genome in cancer.Nature Cancer 1, 864-872.
- Zhang X, Choi PS, Francis JM, Gao G, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger A, Giannakis M, Hahn WC, Cherniack AD, Meyerson M. (2018). Somatic super-enhancer duplications and hotspot mutations lead to oncogenic activation of the KLF5 transcription factor. Cancer Discovery 8, 108-125
- Zhang X*, Choi PS*, Francis JM*, Imielinski M, Watanabe H, Cherniack AD, Meyerson M. (2016). Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers. Nature Genetics 48, 176-182