Faculty Summaries
Xiaowei Chen, PhD
Xiaowei Chen, PhD
Assistant Professor
Office Phone: 215-214-4288
Fax: 215-728-2741
Office: W363
Differential allele-specific expression (DASE) and intra-individual tumor heterogeneity

The heterogeneity among pre-invasive lesions within the same patient, also diagnosed with invasive carcinoma, has not been well evaluated, leaving clinical and research implications of this intra-individual heterogeneity of pre-invasive lesions yet to be explored. Using ductal carcinoma in situ (DCIS) as the model, we have clearly demonstrated that intra-individual heterogeneity in pre-invasive lesions is very common in patients with concurrent diagnoses of invasive carcinoma. Importantly, by comparing the expression of promising DCIS risk biomarkers among different DCIS subgroups, our results suggest the existence of an “indolent” DCIS subgroup as well as an “invasion-prone” DCIS subgroup. Molecular characterization of pre-invasive lesions with different “aggressiveness” by genome-wide approach [e.g., global DASE analysis] could provide a novel strategy to pinpoint “driver” genes for tumor progression. Our long-term research goal is to identify differences among normal, pre-malignant and cancerous breast tissue, determine their consequences, and use this information to improve patient care.

Description of research projects
Selected Publications

Fox Chase Programs

  1. Pape-Zambito, D., Jiang, Z., Wu, H., Devarajan, K., Slater, C.M., Cai, K.Q., Patchefsky, A., Daly, M.B., and Chen, X. (2014). Identifying a highly-aggressive DCIS subgroup by studying intra-individual DCIS heterogeneity among invasive breast cancer patients. PLoS One 9, e100488. Pubmed
  2. Paliwal, A., Temkin, A.M., Kerkel, K., Yale, A., Yotova, I., Drost, N., Lax, S., Nhan-Chang, C.L., Powell, C., Borczuk, A., Aviv, A., Wapner, R., Chen, X., Nagy, P.L., Schork, N., Do, C., Torkamani, A., and Tycko, B. (2013). Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. PLoS Genet 9, e1003622. Pubmed
  3. Jiang, Z, Zhou, Y, Devarajan, K, Slater, CM, Daly, MB, Chen, X. Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis. Front Genet. 3: 299. 2012. Pubmed
  4. Gao C, Devarajan K, Zhou Y, Slater CM, Daly MB, Chen X. Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome. BMC genomics 2012; 13: 570. PubMed
  5. Chen X, Weaver J, Bove BA, Vanderveer LA, Weil SC, Miron A, Daly MB, Godwin AK. Allelic Imbalance in BRCA1 and BRCA2 Gene Expression Is Associated with an Increased Breast Cancer Risk. Hum Mol Genet. 2008;17:1336-48. PubMed
  6. Chen X, Truong TT, Weaver J, Bove BA, Cattie K, Armstrong BA, Daly MB, Godwin AK. Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Human Mutation. 2006;27:427-35. PubMed
  7. Chen X, Arciero CA, Wang C, Broccoli D, Godwin AK. BRCC36 is essential for IR-induced BRCA1 phosphorylation and nuclear foci formation. Cancer Res. 2006;66:5039-46. PubMed
All publications