Molecular Genetics Laboratory of Female Reproductive Cancer

Research Directions

Learn about our research:

Oncogenomics +

The Molecular Genetics Laboratory of Female Reproductive Cancer was established in 2004. We pioneered the elucidation of DNA copy number changes in ovarian cancer using Digital Karyotyping and have since identified several amplified oncogenes, including NOTCH3, CCNE1, RSF1, AKT2, PIK3CA, and the chr12p13 locus, as well as homozygously deleted tumor suppressor genes, including MKK4 and RB1 1-6. We later expanded the DNA copy number analysis to other types of gynecologic malignances, such as ovarian clear cell carcinoma, endometrioid carcinoma, and uterine serous carcinoma 7,8.

With the advancement of next generation sequencing, our team, in collaboration with Drs. Vogelstein and Velculescu at Hopkins, embarked on a project to analyze all coding exomes in gynecologic cancers. Thus far, we have completed whole-exome sequencing on ovarian clear cell carcinoma 9, ovarian low-grade serous carcinoma 10, and uterine serous carcinoma 11. Currently, we are applying genetic biomarkers identified in those studies to early detection and personalized treatment for women with gynecologic malignancies.

Notch 3 Amplification in Ovarian HG Carcinoma


  1. Wang TL, Maierhofer C, Speicher MR, et al. Digital karyotyping. Proc Natl Acad Sci USA. 2002;99(25):16156-16161.
  2. Wang TL, Rago C, Silliman N, et al. Prevalence of somatic alterations in the colorectal cancer cell genome. Proc Natl Acad Sci USA. Mar 5 2002;99(5):3076-3080.
  3. Wang TL, Diaz LA, Jr., Romans K, et al. Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc Natl Acad Sci USA. Mar 2 2004;101(9):3089-3094.
  4. Shih I-M, Sheu JJ, Santillan A, et al. Amplification of a chromatin remodeling gene, Rsf-1/HBXAP, in ovarian carcinoma. Proc Natl Acad Sci USA. Sep 27 2005;102(39):14004-14009.
  5. Nakayama K, Nakayama N, Davidson B, et al. Homozygous Deletion of MKK4 in Ovarian Serous Carcinoma. Cancer Biol Ther. Jun 2006;5(6):630-634.
  6. Nakayama K, Nakayama N, Davidson B, et al. A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival. Proc Natl Acad Sci USA. Dec 5 2006;103(49):18739-18744.
  7. Kuo K, Mao T, Feng Y, et al. DNA copy number profiles in affinity-purified ovarian clear cell carcinoma. Clin Cancer Res. 2010;16(7):1997-2008.
  8. Kuo KT, Guan B, Feng Y, et al. Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-Grade and high-grade carcinomas. Cancer Res. Apr 21 2009;69:4036-4042.
  9. Jones S, Wang TL, Shih Ie M, et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science. Oct 8 2010;330(6001):228-231.
  10. Jones S, Wang TL, Kurman RJ, et al. Low-grade serous carcinomas of the ovary contain very few point mutations. J Pathol. Feb 2012;226(3):413-420.
  11. Kuhn E, Wu RC, Guan B, et al. Identification of Molecular Pathway Aberrations in Uterine Serous Carcinoma by Genome-wide Analyses. J Natl Cancer Inst. Oct 3 2012;104(19):1503-1513.

Epigenetics of Cancer +

In eukaryotes, genomic DNA is associated with specific nuclear proteins, histones, and organized into defined structures called chromatin. Chromatin then further condenses into chromosomes. In addition to the histones involved in packaging DNA, chromosomes are also associated with many non-histone proteins required for gene expression, DNA replication, and DNA damage repair.

A class of these non-histone nuclear proteins with ATP-dependent chromatin remodeling function has been recently identified as frequently mutated genes in human cancers. Gynecologic malignancies associated with endometriosis, including clear cell carcinoma and endometrioid carcinoma, were shown by our group and others to harbor frequent inactivating mutations in ARID1A, a member of the SWI/SNF chromatin remodeling protein 1,2. Another class of non-histone nuclear proteins that consists of enzymes that catalyze covalent modification of histone N-terminal tails was also found to be mutated in a subset of cancers. Genetic alterations of these epigenetic modifiers can re-program the epigenome of cancer cells to promote tumorigenesis.

To understand the role of epigenomic regulation and alterations in cancer initiation and progression, we have employed a system biology approach by employing multiple genome-wide next generation sequencing (NGS) methods, including ChIP-seq, Faire-seq, ATAC-seq, and RNA-seq, to comprehensively elucidate the evolution of the chromatin landscape and transcriptome regulated by chromatin modifiers during tumor initiation and progression.

We are also exploring the functional roles of the NOTCH3 and PBX1 signaling pathways in ovarian cancer using similar approaches to understand the transcriptional networks regulated by these two signaling pathways 3,4.

Chromatin modifier ChlP binding peaks

Binding signals of PBX1(blue) and NOTCH3 (red) on selected target genes


  1. Jones S, Wang TL, Shih Ie M, et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science. Oct 8 2010;330(6001):228-231.
  2. Wiegand KC, Shah SP, Al-Agha OM, et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. New Eng J Med. Oct 14 2010;363(16):1532-1543.
  3. Thiaville MM, Stoeck A, Chen L, et al. Identification of PBX1 target genes in cancer cells by global mapping of PBX1 binding sites. PLoS One. 2012;7(5):e36054.
  4. Chen X, Jung JG, Shajahan-Haq AN, et al. ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res. Apr 20 2016;44(7):e65.

GYN Tumor Bank +

The GYN tumor tissue bank at Hopkins was established in 1998 by Dr. Fredrick J. Montz and Dr. Robert J. Kurman. It was subsequently maintained and expanded by Dr. Richard Roden and Dr. Ie-Ming Shih. Since 2014, the bank has been directed by Dr. Tian-Li Wang and Dr. Amanda Fader, as well as a team of dedicated staff members. The goals of tissue banking entail comprehensive and research-specific banking tasks in order to meet the growing research needs in the post-genomic era. The bank also has expanded to the Johns Hopkins Sibley Memorial Hospital in Washington D.C.

During the past decade, the GYN tissue bank has supported many research projects, secured numerous funding opportunities from private and government sectors, and the research activities has led to more than 60 publications in leading journals. Current research areas supported by the GYN tissue bank includes early detection of GYN tumors, led by Dr. Bert Vogelstein and Dr. Jeff Wang, molecular genomic characterization of GYN tumors, led by Dr. Victor Velculescu, functional characterization of ovarian cancer immune-environment, led by Dr. Drew Pardoll, and molecular pathology study of GYN neoplasms, led by Dr. Ie-Ming Shih.

In the past decade, the pathology team has collaborated with Dr. Denis Wirtz in the Department of Chemical Engineering on imaging analysis for studying tumor cell migration and invasion as well as for differential diagnosis.

Mechanisms of Chemoresistance +

One of the major obstacles to improving the dismal survival rate in patients with ovarian cancer is to overcome the development of chemoresistance to platinum-based therapy. Only a small fraction of women with ovarian cancer achieve long-term remission, as up to 75% women with ovarian cancers suffer from either intrinsic or acquired resistance to chemotherapy. Therefore, understanding the molecular mechanisms underpinning chemoresistance represents an unmet medical need.

Applying global genomic and proteomic approaches, we have identified several signaling pathways which are important in embryonic development are re-activated in chemoresistant tumors. Some of these pathways, such as the NOTCH 1-3 and SYK 4 pathways, also play roles in maintaining viable stem cell pools and in tissue regeneration in adults. Therefore, we hypothesize that the tissue damage induced by chemotherapy may trigger reactivation of signaling pathway(s) that function to generate a tissue environmental niche for cancer cell stem repopulation. Targeting these pathways can, in theory, restrict repopulation of cancer stem cells and prevent tumor recurrence. Clinical-grade small molecule inhibitors have been developed for both the NOTCH and SYK pathways. It is critical to test the efficacy of these drugs singly or in combination with chemotherapeutic agents in women who develop recurrent ovarian cancers.

To elucidate mechanistic details, we have investigated epigenetic regulation by NOTCH. More details can be found in the "Epigenomics in Cancer" section and in our recent publications.

NOTCH and Cancer Stem Cell


  1. Park JT, Chen X, Trope CG, Davidson B, Shih Ie M, Wang TL. Notch3 overexpression is related to the recurrence of ovarian cancer and confers resistance to Carboplatin. Am J Pathol. Sep 2010;177(3):1087-1094.
  2. Park JT, Li M, Nakayama N, et al. Notch-3 gene amplification in ovarian cancer. Cancer Res. 2006;66:6312-6318.
  3. Park JT, Shih Ie M, Wang TL. Identification of pbx1, a potential oncogene, as a notch3 target gene in ovarian cancer. Cancer Res. Nov 1 2008;68(21):8852-8860.
  4. Yu Y, Gaillard S, Phillip JM, et al. Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules. Cancer Cell. Jul 13 2015;28(1):82-96.