Faculty Profile

Dr. Ganjam V. Kalpana, Ph.D.

Ganjam V. Kalpana, Ph.D.

Professor, Department of Genetics

Professor, Department of Microbiology & Immunology

Mark Trauner Faculty Scholar in Neuro-oncology

Areas of Research: To understand the role of INI1/hSNF5/SMARCB1, a component of the SWI/SNF complex and a tumor suppressor, in HIV-1 replication and human Cancers using cell culture and mouse models, and to develop novel therapeutic strategies.

Professional Interests

Molecular Genetic Analysis of Tumor Suppressor INI1/hSNF5 in HIV-1 Replication and Cancer 

INI1/hSNF5 is a component of the chromatin remodeling SWI/SNF complex. It is an interacting partner for HIV-1 integrase (IN) and also a tumor suppressor biallelically mutated in rhabdoid tumors, a rare but highly aggressive pediatric malignancy. The two major areas of focus in the laboratory are: (i) understanding the role of INI1 in HIV-1 replication and exploring its potential as a drug target for intervention of AIDS; and (ii) understanding the mechanism of tumor suppression by INI1/hSNF5 and developing novel and effective therapeutic strategies for rhabdoid tumors.

INI1 in HIV-1 replication: We have found that INI1/hSNF5 directly binds and recruits components of Sin3a-histone deacetylase (HDAC) complex into the HIV-1 virions and this HDAC1 complex appears to be required for viral infectivity. By using genetic systems we are currently isolating and characterizing IN and INI1 mutants defective for binding to HDAC1 complex and testing their effect on HIV-1 replication. We also found that INI1 induces interferon signaling by transcriptionally regulating interferon signal induced genes (ISGs). We are determining the mechanism of interferon signal induction by INI1 during HIV-1 replication and its significance in exhibiting antiviral function. These studies are likely to open up a new paradigm for role of INI1 in HIV-1 replication and may provide novel strategies to inhibit viral replication.

Mechanism of Tumor suppression by INI1/hSNF5: By using a series of genetic systems developed in our laboratory and by isolating cancer-associated mutations of INI1, and a wealth of protein-protein interaction defective mutants of INI1, we are dissecting the exact mechanism of INI1-medaited G0/G1 cell cycle arrest, mitotic arrest, and senescence and tumor suppression. Furthermore, characterizing the INI1-associated HDAC1 complex has revealed an unanticipated role of INI1 in interferon signaling and tumor suppression.

Development of targeted therapies for rhabdoid tumors based on INI1 function: One of the goals of our laboratory is to develop molecularly targeted therapies based on the understanding of genesis of rhabdoid tumors. Majority of rhabdoid tumors have biallelic inactivation of INI1 gene. Our previous studies demonstrated that Cyclin D1 is a direct downstream target of INI1 mediated repression and that rhabdoid tumors are exquisitely dependent on Cyclin D1 for genesis and survival. Our preclinical studies have provided proof of principle for our hypothesis that targeting Cyclin/cdk axis is an effective means of inhibiting rhabdoid tumors in vitro and in vivo. The current goal is to develop novel strategies to facilitate clinical translation of laboratory findings to establish an effective therapy for these tumors. For this purpose, we are using non-invasive imaging technology such as microPET to monitor the effectiveness of novel therapeutic strategies in primary mouse tumor models, developing novel drugs to target these tumors and investigating the interaction between Cyclin D1, the cdk pathway and Ini1 in mouse models. 

Selected Publications

Yung, E., Sorin, M., Pal, A., Craig, E., Morozov, A., Delattre, O. Kappes J., Ott, D. and Kalpana, G.V. (2001) Inhibition of HIV-1 particle production by a dominant negative mutant of INI1/hSNF5. Nature Med. 7, 920-926.

Craig, E., Zhang, Z., Davies, K., and Kalpana, G.V. (2002) A masked NES in INI1/hSNF5 mediates hCRM1-dependant Nuclear Export: Implications for tumorigenesis. EMBO J. 21, 31-42. 

Yung, E., Sorin, M. Wang, E., Perumal, S., and Kalpana, G.V. (2004) Specificity of interaction of INI1/hSNF5 with retroviral integrases and its functional significance. J. Virol., 78, 2222-2231.


Tsikitis, M., Zhang, Z., Zagzag, D. and Kalpana, G.V. (2005) Genetic ablation of CyclinD1 abrogates the genesis of rhabdoid tumors that arise due to Ini1 loss. Proc. Natl. Acad. Sci. USA, 102, 12129-34.

Alarcon-Vargas, D., Zhang, Z., Agarwal, B., Challagulla, K., Mani, S.* and Kalpana, G.V.* (2006)  Targeting Cyclin D1, a downstream effector of INI1/hSNF5, in Rhabdoid tumors. Oncogene 25, 722�734.

Sorin, M. and Kalpana, G. V. (2006) Dynamics of host-virus interplay during HIV-1 replication. Curr HIV Res. 4, 117-30). 

Masha Sorin1, Eric Yung1, Xuhong Wu1 and Ganjam Kalpana (2006) Replication of HIV-1 in cell lines defective for INI1/hSNF5 Retrovirology, 3:56.

Morozov, A.  Lee, S-J, Zhnag, ZK, Cimica, V., Zagzag, D. Kalpana, G. V. (2007) Induction of interferon signaling and mitotic spindle check-point by INI1/hSNF5:  Identification of potential therapeutic targets for rhabdoid tumors. Clin Cancer Res.13:4721-30. 

Smith ME, Cimica V, Chinni S, Challagulla K, Mani S, Kalpana GV. (2008) Rhabdoid tumor growth is inhibited by flavopiridol. Clin Cancer Res. 14(2):523-32.

 Das BC, Smith ME, Kalpana GV.(2008) Design, synthesis of novel peptidomimetic derivatives of 4-HPR for rhabdoid tumors. Bioorg Med Chem Lett. 18(14):4177-80. Epub 2008 May 29.

 Das S, Cano J, Kalpana GV.(2009) Multimerization and DNA Binding Properties of INI1/hSNF5 and Its Functional Significance. J Biol Chem. 284(30):19903-14. Epub 2009 Apr 27.

Das S, Kalpana GV. (2009) Reverse two-hybrid screening to analyze protein-protein interaction of HIV-1 viral and cellular proteins. Methods Mol Biol. 485:271-93.


Sorin M, Cano J, Das S, Mathew S, Wu X, Davies KP, Shi X, Cheng SW, Ott D, Kalpana GV. (2009) Recruitment of a SAP18-HDAC1 complex into HIV-1 virions and its requirement for viral replication. PLoS Pathog. 5(6).

 Kalpana, G. V. and M. Smith (2009) �Development of targeted therapies for rhabdoid tumors based on the functions of INI1/hSNF5 tumor suppressor� (invited chapter for the monograph on Molecularly targeted Therapies for pediatric tumors Edited by Bob Arceci and Peter Houghton, in press).

Cimica V, Smith ME, Zhang Z, Mathur D, Mani S, Kalpana GV. (2010) Potent inhibition of rhabdoid tumor cells by combination of flavopiridol and 4OH-tamoxifen. BMC Cancer. 10:634. PMID: 21092078

Smith ME, Cimica V, Chinni S, Jana S, Koba W, Yang Z, Fine E, Zagzag D, Montagna C, Kalpana GV. (2011). Therapeutically targeting Cyclin D1 in primary tumors arising from loss of Ini1. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):319-24. Epub 2010 Dec 20. PMID: 21173237

 Cano, J. and Kalpana, G. V. (2011) Inhibition of early stages of HIV-1 assembly by INI1/hSNF5 transdominant negative mutant S6. J Virol.  85(5):2254-65. Epub 2010 Dec 15.  PMID: 21159874

Lee, S-J., Cimica, V., Zagzag, D., and Kalpana, G. V. Aurora A Is a Repressed Effector Target of the Chromatin Remodeling Protein INI1/hSNF5 Required for Rhabdoid Tumor Cell Survival. Cancer Res. 71(9):3225-35. Epub 2011 Apr 26. PMID: 21521802

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Research Information