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Dr. Saraswati Sukumar

(410) 614-4073 (f)
Saraswati Sukumar

Breast Cancer Genes


Barbara B. Rubenstein Professorship in Oncology
Professor of Pathology
Professor, Johns Hopkins School of Nursing
Visiting Professor, The Oncology Research Institute, National University of Singapore


M.S., Nagpur University, India Ph.D., Nagpur University, India


Fellow, Molecular Biology, National Cancer Institute, NIH, Bethesda, MD.

Research Summary

The research goal of the Sukumar laboratory is to obtain a molecular profile of breast cancer and to apply this knowledge to the early detection, diagnosis and therapy of breast cancer. Toward this end, SAGE, array, and proteomic analysis of breast carcinomas is being performed on noninvasive (ductal carcinoma in situ), invasive (invasive ductal carcinoma), and metastatic breast cancer (bone, ovarian, brain metastasis). The goal is to obtain mRNA and protein profiles of each cell type composing the lesion. This will help derive gene expression signatures typical for each stage of breast cancer for epithelial, stromal, and endothelial cells. By such careful analysis, candidate genes are identified, characterized and utilized for early detection and/or therapy of breast cancer.

Previous gene searches in breast cancer performed here identified a number of potential candidate tumor suppressors and oncogenes. These belonged to families of genes involved in a variety of functions in the cell. Transcription factors, such as HOXA5, WT1, RAR-beta and Twist; cell cycle regulators such as Cyclin D2 and 14.3.3 sigma; and tight junction proteins, such as Claudin-3, -4 and -7, were selected for further analysis. Biological analysis of these genes revealed molecular alterations that could lead to their aberrant function in breast cancer cells, results of which were published in the last three years. Hypermethylated promoter regions of a number of genes serve as tumor- specific markers for early detection of breast cancer. As described in a paper in Lancet in 2001, a marker panel consisting of Cyclin D2, RAR-beta and Twist was capable of detecting almost all breast cancers (96 percent) with a high level of specificity and sensitivity. This marker panel detected cancer in two high-risk women who were mammographically normal. This panel has now been improved by adding more markers, such as RASSF1A, HIN-1, ER-a and ER-b, and by developing a multiplex, quantitative methylation-specific PCR (Q-MSP). Q-MSP will allow accurate determination of the relative amount of methylation present in each gene, using less than nanogram amounts of DNA, in an objective manner. To test this premise, these markers are currently being applied to ductal cells obtained in two current trials aimed at validating the markers for early detection in high-risk women.

Soon, this panel will be tested as intermediate- response markers in a chemoprevention trial in collaboration with three other institutions in the United States. A combination of an objective test, such as MSP, with a subjective test, such as cytology, has the potential to provide an adjunct to mammography for early detection of breast cancer. This test is also being modified to detect tumor-specific DNA in serum from breast cancer patients.

The long-term goal is to provide a molecular blood test for early detection of breast cancer. Interrogating the hypothesis that breast cancer can be treated and prevented by delivery of agents via the intraductal route, both conventional and novel agents were tested. First, treatment of rats bearing carcinogen-induced tumors with Doxil results in complete regression of the tumors. Doxil administration via this route in a prevention setting, soon after carcinogen administration, also protected 90 percent of the treated glands. This mode of delivery can achieve therapeutic effects with less than one-third the systemic dose of the drug. This concept has also been tested in the HER2/neu mouse model for breast cancer. Here again, potent antitumor effects on established tumors were achieved by intraductal instillation of Doxil. Doxil also prevented the development of mammary tumors in this system. With the goal of eliminating the primary tumor and its metastasis, chemotherapy is being combined with immunotherapy (in collaboration with the Jaffee laboratory). Targeting genes that were found by our previous SAGE analysis searches to be overexpressed in breast cancer (the Claudins 3 and 4), we are testing therapies using Clostridium perfringens enterotoxin (CPE). CPE binds to the overexpressed tight junction proteins Claudin 3 and 4 on the tumor cells, resulting in tumor cell kill. No apparent cytotoxic effects are observed on normal epithelial cells. Additionally, the systemic toxic effects of CPE on the gastrointestinal tract are bypassed by utilizing the intraductal route of delivery. A combination of basic and preclinical research efforts in the laboratory aims at translating discoveries made at the bench to the clinic as rapidly as possible.

Journal Citations

Fackler, M.J.; Malone, K.; Zhang, Z.; Schilling, E.; Garrett-Mayer, E.; Swift-Scanlan, T.; Lange, J.; Nayar, R.; Davidson, N.E.; Khan, S.A.; Sukumar, S. Quantitative multiplex methylation-specific PCR analysis doubles detection of tumor cells in breast ductal fluid. Clin Cancer Res. 2006 Jun 1;12(11 Pt 1):3306-3310.
Hallur, G.; Jimeno, A.; Dalrymple, S.; Zhu, T.; Jung, M.K.; Hidalgo, M.; Isaacs, J.T.; Sukumar, S.; Hamel, E.; Khan, S.R. Benzoylphenylurea sulfur analogues with potent antitumor activity. J Med Chem. 2006 Apr 6;49(7):2357-2360.
Huang, Y.; Keen, J.C.; Pledgie, A.; Marton, L.J.; Zhu, T.; Sukumar, S.; Park, B.H.; Blair, B.; Brenner, K.; Casero, R.A., Jr.; Davidson, N.E. Polyamine analogues down-regulate estrogen receptor alpha expression in human breast cancer cells. J Biol Chem. 2006 Jul 14;281(28):19055-19063.
Lau, Q.C.; Raja, E.; Salto-Tellez, M.; Liu, Q.; Ito, K.; Inoue, M.; Putti, T.C.; Loh, M.; Ko, T.K.; Huang, C.; Bhalla, K.N.; Zhu, T.; Ito, Y.; Sukumar, S. RUNX3 is frequently inactivated by dual mechanisms of protein mislocalization and promoter hypermethylation in breast cancer. Cancer Res. 2006 Jul 1;66(13):6512-6520.
Lo, P.K.; Mehrotra, J.; D'Costa, A.; Fackler, M.J.; Garrett-Mayer, E.; Argani, P.; Sukumar, S. Epigenetic suppression of secreted frizzled related protein 1 (SFRP1) expression in human breast cancer. Cancer Biol Ther. 2006 Mar;5(3):281-286.
Lorincz, A.M.; Sukumar, S. Molecular links between obesity and breast cancer. Endocrine-related cancer. 2006 Jun;13(2):279-292.
Swift-Scanlan, T.; Blackford, A.; Argani, P.; Sukumar, S.; Fackler, M.J. Two-color quantitative multiplex methylation-specific PCR. Biotechniques. 2006 Feb;40(2):210-219.
Visvanathan, K.; Sukumar, S.; Davidson, N.E. Epigenetic biomarkers and breast cancer: cause for optimism. Clin Cancer Res. 2006 Nov 15;12(22):6591-6593.
Wu, G.; Guo, Z.; Chatterjee, A.; Huang, X.; Rubin, E.; Wu, F.; Mambo, E.; Chang, X.; Osada, M.; Sook Kim, M.; Moon, C.; Califano, J.A.; Ratovitski, E.A.; Gollin, S.M.; Sukumar, S.; Sidransky, D.; Trink, B. Overexpression of glycosylphosphatidylinositol (GPI) transamidase subunits phosphatidylinositol glycan class T and/or GPI anchor attachment 1 induces tumorigenesis and contributes to invasion in human breast cancer. Cancer Res. 2006 Oct 15;66(20):9829-9836.
Wu, X.; Chen, H.; Parker, B.; Rubin, E.; Zhu, T.; Lee, J.S.; Argani, P.; Sukumar, S. HOXB7, a Homeodomain Protein, Is Overexpressed in Breast Cancer and Confers Epithelial-Mesenchymal Transition. Cancer Res. 2006 Oct 1;66(19):9527-9534.
Chen, H.; Zhang, H.; Lee, J.; Liang, X.; Wu, X.; Zhu, T.; Lo, P.K.; Zhang, X.; Sukumar, S. HOXA5 acts directly downstream of retinoic acid receptor beta and contributes to retinoic acid-induced apoptosis and growth inhibition. Cancer Res. 2007 Sep 1;67(17):8007-8013.
Han, L.; Witmer, P.D.; Casey, E.; Valle, D.; Sukumar, S. DNA methylation regulates MicroRNA expression. Cancer Biol Ther. 2007 Aug;6(8):1284-1288.
Kominsky, S.L.; Tyler, B.; Sosnowski, J.; Brady, K.; Doucet, M.; Nell, D.; Smedley, J.G., 3rd; McClane, B.; Brem, H.; Sukumar, S. Clostridium perfringens enterotoxin as a novel-targeted therapeutic for brain metastasis. Cancer research. 2007 Sep 1;67(17):7977-7982.
Lee, J.S.; Lo, P.K.; Fackler, M.J.; Argani, P.; Zhang, Z.; Garrett-Mayer, E.; Sukumar, S. A Comparative Study of Korean with Caucasian Breast Cancer Reveals Frequency of Methylation in Multiple Genes Correlates with Breast Cancer in Young, ER, PR-negative Breast Cancer in Korean Women. Cancer Biol Ther. 2007 Apr 23;6:1114*1120.
Mohankumar, K.M.; Xu, X.Q.; Zhu, T.; Kannan, N.; Miller, L.D.; Liu, E.T.; Gluckman, P.D.; Sukumar, S.; Emerald, B.S.; Lobie, P.E. HOXA1-stimulated oncogenicity is mediated by selective upregulation of components of the p44/42 MAP kinase pathway in human mammary carcinoma cells. Oncogene. 2007 Jun 7;26(27):3998-4008.
Rubin, E.; Wu, X.; Zhu, T.; Cheung, J.C.; Chen, H.; Lorincz, A.; Pandita, R.K.; Sharma, G.G.; Ha, H.C.; Gasson, J.; Hanakahi, L.A.; Pandita, T.K.; Sukumar, S. A role for the HOXB7 homeodomain protein in DNA repair. Cancer Res. 2007 Feb 15;67(4):1527-1535.
Shipitsin, M.; Campbell, L.L.; Argani, P.; Weremowicz, S.; Bloushtain-Qimron, N.; Yao, J.; Nikolskaya, T.; Serebryiskaya, T.; Beroukhim, R.; Hu, M.; Halushka, M.K.; Sukumar, S.; Parker, L.M.; Anderson, K.S.; Harris, L.N.; Garber, J.E.; Richardson, A.L.; Schnitt, S.J.; Nikolsky, Y.; Gelman, R.S.; Polyak, K. Molecular definition of breast tumor heterogeneity. Cancer Cell. 2007 Mar;11(3):259-273.
Wood, L.D.; Parsons, D.W.; Jones, S.; Lin, J.; Sjoblom, T.; Leary, R.J.; Shen, D.; Boca, S.M.; Barber, T.; Ptak, J.; Silliman, N.; Szabo, S.; Dezso, Z.; Ustyanksky, V.; Nikolskaya, T.; Nikolsky, Y.; Karchin, R.; Wilson, P.A.; Kaminker, J.S.; Zhang, Z.; Croshaw, R.; Willis, J.; Dawson, D.; Shipitsin, M.; Willson, J.K.; Sukumar, S.; Polyak, K.; Park, B.H.; Pethiyagoda, C.L.; Pant, P.V.; Ballinger, D.G.; Sparks, A.B.; Hartigan, J.; Smith, D.R.; Suh, E.; Papadopoulos, N.; Buckhaults, P.; Markowitz, S.D.; Parmigiani, G.; Kinzler, K.W.; Velculescu, V.E.; Vogelstein, B. The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16;318(5853):1108-1113.
Wu, X.; Sukumar, S. ETS genes in breast cancer: a step in the right direction. Cancer Biol Ther. 2007 Jan;6(1):83-84.
Cao, D.; Polyak, K.; Halushka, M.K.; Nassar, H.; Kouprina, N.; Iacobuzio-Donahue, C.; Wu, X.; Sukumar, S.; Hicks, J.; De Marzo, A.; Argani, P. Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9. Breast Cancer Res. 2008;10(5):R91.
Chen, H.; Lee, J.S.; Liang, X.; Zhang, H.; Zhu, T.; Zhang, Z.; Taylor, M.E.; Zahnow, C.; Feigenbaum, L.; Rein, A.; Sukumar, S. Hoxb7 inhibits transgenic HER-2/neu-induced mouse mammary tumor onset but promotes progression and lung metastasis. Cancer Res. 2008 May 15;68(10):3637-3644.
Lee, J.S.; Fackler, M.J.; Teo, W.W.; Lee, J.H.; Choi, C.; Park, M.H.; Yoon, J.H.; Zhang, Z.; Argani, P.; Sukumar, S. Quantitative promoter hypermethylation profiles of ductal carcinoma in situ in North American and Korean women: Potential applications for diagnosis. Cancer Biol Ther. 2008 Sep;7(9):1398-1406.
Lo, P.K.; Sukumar, S. Epigenomics and breast cancer. Pharmacogenomics. 2008 Dec;9(12):1879-1902.
Marlow, R.; Strickland, P.; Lee, J.S.; Wu, X.; Pebenito, M.; Binnewies, M.; Le, E.K.; Moran, A.; Macias, H.; Cardiff, R.D.; Sukumar, S.; Hinck, L. SLITs suppress tumor growth in vivo by silencing Sdf1/Cxcr4 within breast epithelium. Cancer Res. 2008 Oct 1;68(19):7819-7827.
Suijkerbuijk, K.P.; Fackler, M.J.; Sukumar, S.; van Gils, C.H.; van Laar, T.; van der Wall, E.; Vooijs, M.; van Diest, P.J. Methylation is less abundant in BRCA1-associated compared with sporadic breast cancer. Ann Oncol. 2008 Nov;19(11):1870-1874.
Winnard, P.T., Jr.; Sukumar, S. A PET rat model for assessing the effectiveness of new chemotherapies. Cancer Biol Ther. 2008 Apr;7(4):538-539.
Wu, J.M.; Fackler, M.J.; Halushka, M.K.; Molavi, D.W.; Taylor, M.E.; Teo, W.W.; Griffin, C.; Fetting, J.; Davidson, N.E.; De Marzo, A.M.; Hicks, J.L.; Chitale, D.; Ladanyi, M.; Sukumar, S.; Argani, P. Heterogeneity of breast cancer metastases: comparison of therapeutic target expression and promoter methylation between primary tumors and their multifocal metastases. Clin Cancer Res. 2008 Apr 1;14(7):1938-1946.
Cimino, A.; Halushka, M.; Illei, P.; Wu, X.; Sukumar, S.; Argani, P. Epithelial cell adhesion molecule (EpCAM) is overexpressed in breast cancer metastases. Breast Cancer Res Treat. 2009 Dec 11.
Fackler, M.J.; Rivers, A.; Teo, W.W.; Mangat, A.; Taylor, E.; Zhang, Z.; Goodman, S.; Argani, P.; Nayar, R.; Susnik, B.; Sukumar, S.; Khan, S.A. Hypermethylated genes as biomarkers of cancer in women with pathologic nipple discharge. Clin Cancer Res. 2009 Jun 1;15(11):3802-3811.
Lo, P.K.; Watanabe, H.; Cheng, P.C.; Teo, W.W.; Liang, X.; Argani, P.; Lee, J.S.; Sukumar, S. MethySYBR, a novel quantitative PCR assay for the dual analysis of DNA methylation and CpG methylation density. J Mol Diagn. 2009 Sep;11(5):400-414.
Mankoo, P.K.; Sukumar, S.; Karchin, R. PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins. 2009 May 1;75(2):499-508.
Sukumar, S.; Spencer, F.; Fenerty, C.; Harper, R.; Henson, D. The influence of socioeconomic and clinical factors upon the presenting visual field status of patients with glaucoma. Eye (Lond). 2009 May;23(5):1038-1044.
Chen, H.; Pimienta, G.; Gu, Y.; Sun, X.; Hu, J.; Kim, M.S.; Chaerkady, R.; Gucek, M.; Cole, R.N.; Sukumar, S.; Pandey, A. Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 2010 Nov;10(21):3800-3810.
Cimino, A.; Halushka, M.; Illei, P.; Wu, X.; Sukumar, S.; Argani, P. Epithelial cell adhesion molecule (EpCAM) is overexpressed in breast cancer metastases. Breast Cancer Res Treat. 2010 Oct;123(3):701-708.
Feng, M.; Grice, D.M.; Faddy, H.M.; Nguyen, N.; Leitch, S.; Wang, Y.; Muend, S.; Kenny, P.A.; Sukumar, S.; Roberts-Thomson, S.J.; Monteith, G.R.; Rao, R. Store-independent activation of Orai1 by SPCA2 in mammary tumors. Cell. 2010 Oct 1;143(1):84-98.
Gupta, R.A.; Shah, N.; Wang, K.C.; Kim, J.; Horlings, H.M.; Wong, D.J.; Tsai, M.C.; Hung, T.; Argani, P.; Rinn, J.L.; Wang, Y.; Brzoska, P.; Kong, B.; Li, R.; West, R.B.; van de Vijver, M.J.; Sukumar, S.; Chang, H.Y. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010 Apr 15;464(7291):1071-1076.
Jacobs, L.; Sukumar, S.; Stearns, V. Intraductal therapy for the prevention of breast cancer. Curr Opin Investig Drugs. 2010 Jun;11(6):646-652.
Jin, K.; Sukumar, S. BRCA1: linking HOX to breast cancer suppression. Breast Cancer Res. 2010;12(4):306.
Kim, J.H.; Shin, M.H.; Kweon, S.S.; Park, M.H.; Yoon, J.H.; Lee, J.S.; Choi, C.; Fackler, M.J.; Sukumar, S. Evaluation of promoter hypermethylation detection in serum as a diagnostic tool for breast carcinoma in Korean women. Gynecol Oncol. 2010 Aug 1;118(2):176-181.
Lo, P.K.; Lee, J.S.; Liang, X.; Han, L.; Mori, T.; Fackler, M.J.; Sadik, H.; Argani, P.; Pandita, T.K.; Sukumar, S. Epigenetic inactivation of the potential tumor suppressor gene FOXF1 in breast cancer. Cancer Res. 2010 Jul 15;70(14):6047-6058.
Maruyama, R.; Shipitsin, M.; Choudhury, S.; Wu, Z.; Protopopov, A.; Yao, J.; Lo, P.K.; Bessarabova, M.; Ishkin, A.; Nikolsky, Y.; Liu, X.S.; Sukumar, S.; Polyak, K. Breast Cancer Special Feature: Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A. 2010 Nov 22.
Ward, C.S.; Venkatesh, H.S.; Chaumeil, M.M.; Brandes, A.H.; Vancriekinge, M.; Dafni, H.; Sukumar, S.; Nelson, S.J.; Vigneron, D.B.; Kurhanewicz, J.; James, C.D.; Haas-Kogan, D.A.; Ronen, S.M. Noninvasive detection of target modulation following phosphatidylinositol 3-kinase inhibition using hyperpolarized 13C magnetic resonance spectroscopy. Cancer Res. 2010 Feb 15;70(4):1296-1305.
Wu, Z.J.; Meyer, C.A.; Choudhury, S.; Shipitsin, M.; Maruyama, R.; Bessarabova, M.; Nikolskaya, T.; Sukumar, S.; Schwartzman, A.; Liu, J.S.; Polyak, K.; Liu, X.S. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec;20(12):1730-1739.


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