Karpf Laboratory

Research Interests:

DNA hypomethylation in epithelial ovarian cancer (EOC)
We have recently defined a DNA hypomethylation phenotype in EOC.  This phenotype consists of coordinate hypomethylation of global genomic DNA as well as of repetitive DNA elements (LINE-1, Alu, microsatellites) and a family of genes known as cancer testis or cancer germline (CG) antigens.  Importantly, DNA hypomethylation is linked to tumor progression and poor survival in EOC.  These data support the relevance of DNA hypomethylation to EOC biology and encourage further exploration of the causes and consequences of this phenotype.  To this end, we are using whole genome mRNA and miRNA expression analyses and exome sequencing to define the molecular profile of EOC tumors that display global DNA hypomethylation. We find that ~70% of differentially expressed mRNAs are activated in hypomethylated tumors, and that hypomethylated tumors show a distinct mRNA expression profile (Figure 1).  These data are providing new insight into the genes targeted by this process as well as a number of testable hypotheses to account for the induction of DNA hypomethylation in these lesions.  Related studies in our lab are focused on understanding the relationship between DNA hypomethylation and genomic instability in EOC.  In this context, recent Cancer Genome Anatomy Project (TCGA) data indicate that, for EOC in particular, genomic instability is a defining and clinically relevant characteristic of this malignancy.
mRNA expression profile of globally hypomethylated EOC
Cancer germline (CG) antigen gene regulation
CG antigens are a family of over 150 genes defined by their specific expression in germ cells and cancer, and by the inherent immunogenicity of many family members.  CG gene expression in normal cells and cancer is closely linked to promoter methylation status. In particular, CG gene activation in cancer is associated with promoter DNA hypomethylation and also with global DNA hypomethylation, as mentioned above.  A long term goal of the research in our lab is to more completely define the mechanisms leading to activation of CG genes in cancer (Figure 2). The mechanisms under current study include: DNA methylation, histone modifications, nucleosome positioning, and the interaction of epigenetic factors with transcription factor driven oncogenic signaling mechanisms.
Caner germline (CG) antigen gene regulation in human cancer
CG antigen gene function in vivo
An additional area of interest in our laboratory focuses on the oncogenic function of a CG antigen gene known as BORIS or CTCFL.  BORIS is an autosomal CG antigen gene located at chromosome 20q13, a common region of amplification in cancer.  We have shown that BORIS is activated in EOC by a mechanism involving promoter DNA hypomethylation, and that BORIS expression correlates with tumor progression and poor prognosis in this malignancy.  As a paralog of the chromatin insulator CTCF, BORIS has a putative function in global epigenomic remodeling in cancer cells in which it is expressed.  BORIS has also been proposed as a master regulator of other CG genes. To assess the potential role of BORIS in EOC, in collaborative studies with Dr. Michael Higgins, we are determining the impact of BORIS expression on EOC development in mice, alone and in combination with p53 and/or Rb knockout.  In related studies, we will profile the epigenomic and genomic landscape of EOC tumors driven by BORIS expression.  The resulting data will provide important new insight into BORIS’s function in EOC, and more generally the oncogenic role of CG antigen gene expression in cancer.

Translational EOC studies
EOC is comprised of a variety of different disease subtypes including high-grade serous (HG-SOC), endometrioid, mucinous, and clear cell tumors. Each of these subtypes has a distinct cell of origin and underlying molecular phenotype, thus they may be considered separate diseases sharing a common anatomical location (Figure 3).  Of EOC subtypes, HG-SOC makes up the majority of EOC (and all ovarian cancer) cases and is characterized by frequent late stage diagnosis and high rates of disease recurrence following front line therapy.  Together, these characteristics lead to poor overall and progression free survival for afflicted patients.  Our research, which is focused on DNA methylation changes in HG-SOC, has high relevance for the development of improved diagnostic and prognostic markers for this disease, as well as for novel therapeutic strategies.  As one example, in collaboration with Dr. Kunle Odunsi, we are developing new therapeutic approaches to augment the efficacy of CG antigen targeted cancer vaccines by the use of epigenetic modulators (Figure 4).  We have recently completed a Phase I clinical trial for recurrent EOC that combined the DNA methyltransferase inhibitor decitabine with a vaccine targeted against the CG antigen NY-ESO-1, which we have shown is robustly upregulated by decitabine treatment.  This approach was safe and promoted antigen-specific humoral and cellular immunity, and showed clinical benefit in a number of patients.  Our future work will refine this approach and extend it to other appropriate patient populations.
Epithelial ovarian cancer subtypes
Epigenetic therapy augmentation of CG antigen immunotherapy

Selected References
James, S. R., P. A. Link, and A. R. Karpf. (2006). Epigenetic regulation of X-linked cancer/germ-line antigen genes by DNMT1 and DNMT3b. Oncogene, 25, 6975-6985.

Karpf, A. R. (2006). A potential role for epigenetic modulatory drugs in the enhancement of cancer/germ-line antigen vaccine efficacy. Epigenetics, 1, 116-120. PMCID: PMC1963490.

Woloszynska-Read, A, James, S. R., Link, P. A., Yu, J., Odunsi, K., and A. R. Karpf(2007). DNA methylation-dependent regulation of BORIS/CTCFL expression in ovarian cancer. Cancer Immunity, 7, 21.

Woloszynska-Read, A, Mhawech-Fauceglia, P., Yu, J., Odunsi, K., and A. R. Karpf. (2008). Intertumor and intratumor NY-ESO-1 expression heterogeneity is associated with promoter-specific and global DNA methylation status in ovarian cancer. Clinical Cancer Research, 14, 3283-3290. PMCID: PMC2835568.

Karpf, A. R., Bai, S., James, S. R., Mohler, J. L., and E. M. Wilson. (2009). Increased expression of androgen receptor coregulator MAGE-11 in prostate cancer by DNA hypomethylation and cyclic AMP. Molecular Cancer Research, 7, 523-535. PMCID: PMC2670465.

Akers, S., Odunsi, K., and A. R. Karpf. (2010). Regulation of cancer germline antigen gene expression: implications for cancer immunotherapy. Future Oncology, 6, 717-732. PMCID: PMC2896020.

Woloszynska-Read, A., James, S. R., Song, C., Jin, B., Odunsi, K., and A. R. Karpf. (2010). BORIS/CTCFL expression is insufficient for cancer-germline antigen gene expression and DNA hypomethylation in ovarian cell lines. Cancer Immunity, 10, 6. PMCID: PMC2916237.

Woloszynska-Read, A., Zhang, W., Yu, J., Link, P. A., Mhawech-Fauceglia, P., Collamat, G., Akers, S. N., Ostler, K., Godley, L. A., Odunsi, K., and  A. R. Karpf.  (2011). Coordinated cancer germline antigen promoter and global DNA hypomethylation in ovarian cancer: association with BORIS/CTCF mRNA expression ratio and advanced stage. Clinical Cancer Research, 17, 2170-2180. PMCID: PMC21296871.

Decitabine, Vaccine Therapy, and Doxorubicin Hydrochloride Liposome in Treating Patients with Recurrent Ovarian Epithelial Cancer, Fallopian Tube Cancer, or Primary Peritoneal Cancer. Roswell Park Cancer Institute. Kunle Odunsi, PI. ClinicalTrial.gov identifier: NCT00887796.  

Epigenetic Alterations in Oncogenesis, in the series: Advances in Experimental Medicine and Biology. (2012). A. R. Karpf (Editor). Springer; New York. In Press.

Full Publication List
See: http://www.ncbi.nlm.nih.gov/pubmed?term=Karpf%20AR%5BAuthor%5D

Funding Support
National Cancer Institute
Department of Defense Ovarian Cancer Research Program
Ovarian Cancer Research Fund
Eppley Institute for Cancer Research

Lab Personnel
Adam R. Karpf, Principal Investigator
Ashok Sharma, Post Doctoral Fellow
Wa Zhang, Ph.D. Student
Carter Barger, Ph.D. Student

Key Collaborators
Kunle Odunsi, M.D., Ph.D.
Professor and Chair
Departments of Gynecological Oncology and Immunology
Roswell Park Cancer Institute
Area of collaboration: EOC biology, cancer germline antigen vaccines

Michael Higgins, Ph.D.
Associate Professor
Department of Molecular and Cellular Biology
Roswell Park Cancer Institute
Area of collaboration: Mouse models of cancer, cancer epigenetics

David Klinkebiel, Ph.D.
Assistant Professor, Department of Biochemistry and Cell Biology
Director, Epigenomics Core Facility
University of Nebraska Medical Center
Area of collaboration: Epigenomics

Position Inquiries
Highly motivated and interested fellows and students are encouraged to inquire regarding the availability of research positions. 

Contact Information
Adam R. Karpf, Ph.D.
Associate Professor
Eppley Institute for Research in Cancer
UNMC Eppley Cancer Center
University of Nebraska Medical Center
DRC II, Room 4030
985950 Nebraska Medical Center
Omaha, NE 68198-5950
Phone: 402-559-6115
Fax: 402-559-4651
E-mail: adam.karpf@unmc.edu