Kishor bhakat, PhD
Associate Professor, Department of Genetics, Cell Biology & Anatomy | University of Nebraska Medical Center
Education:
MS 1992 University of Calcutta, India
Ph.D. 1999 Indian Institute of Chemical Biology
Postdoc. 2001 University of Texas Medical Branch, USA
Academic Appointments:
Co-Course Director, IPBS 802 Molecular Cell Biology
Co-Course Director, MGCB 903 Journal Club
Co-Course director MGCB 912 Modern Approaches in Cell Biology and Molecular Genetics
Research Grant
July 2023 – June 2025
Targeting G-quadruplex structure and FACT complex to sensitize medulloblastoma to radiation and chemotherapy.
$150,000
Update from Dr. Bhakat | March 2024 | Treatment of Medulloblastoma (MB), a highly aggressive pediatric brain tumor, rely on maximal surgical resection followed by ionizing radiation and high doses of combination of chemotherapies. Tumor recurrence and therapy-related neurological sequels remain the major clinical challenges for MB treatment. Our goals in this project are to identify and characterize the factors that promote IR/chemo-resistance and develop new therapeutic agents to prevent tumor recurrence and improve the quality of life of MB patients. Based on published study (Song et al., Cancer Lett. 2021) and other preliminary results two aims were proposed. Aim1: Delineate the mechanistic link of G4 with APE1-mediated faster and preferential repair of damage in the transcribed gene regions. Aim2: Determine the efficacy of CTX decorated NPs loaded with CBL0137 and TMPyP4 in preventing recurrence of therapy–adapted residual tumor in a spontaneous SHH-driven MB mouse model. We showed earlier that pre-treatment of MB cells with CBL0137 for 1 hour followed by radiation or cisplatin treatment reduced cell viability of both SHH ONS-76 and group3 HDMB03 MB cells in a dose-dependent manner. Our current study shows that while treatment with TMPyP4 (100 µM) alone has a moderate effect on ONS-76 cell killing, it significantly augmented the sensitivity of cells to radiation. As proposed in Aim2, we have characterized MPyP4 by using Mass spectroscopy. In collaboration with Dr. Chonnker, we examined TMPyP4 biodistribution in nude mice. We have developed a sensitive and rapid LC-MS/MS method for analyzing TMPyP4 PK in vitro and in mouse plasma and tissues. We have performed a pilot PK analysis of TMPyP4 in BALB/c mice. Serial blood samples were obtained at 0.25, 0.5, 1, 2, 4, 8, and 24 hours following a single intraperitoneal (IP) dose of TMPyP4 (30 mg/kg) in mice (n=4). Plasma and tissue samples were analyzed for TMPyP4 concentrations. Following the IP administration, a peak plasma concentration (Cmax) of TMPyP4 with 12124.2 ng/ mL was achieved, with an AUC0-∞ of 17013.6 hrxng/mL. TMPyP4 was detectable up to 24 hrs, with an elimination t1/2 of 4.4 hrs. To assess the distribution of TMPyP4 into tissues, mice were sacrificed at 2 and 24 hours after the administration of the drug. Measurable concentrations of TMPyP4 were detected in the brains of all mice. The brain concentration of TMPyP4 494 and 260 ng/g was achieved at 2 and 24 hr, respectively. Slow clearance and >50% retained after 24, indicating that this novel TMPyP4 has promising potential to cross the BBB and target brain. Higher concentrations of TMPyP4 in the liver and lungs tissues suggest that further toxicological studies are warranted to investigate the relationship between drug concentration and effect, both therapeutic and toxic, after repeated dosing.
Research Details
Tumor recurrence and metastasis remain the major clinical challenges for cancer treatment. Ionizing radiation (IR) and chemotherapies have been the first line of care for treatment of many types of cancers including brain and pancreatic cancer. These conventional cytotoxic therapies cause DNA damage and induce cell death. Although this standard of care has significantly improved the overall survival rates, high doses of chemo and IR are associated with long-term toxicities in surviving patients. Moreover, postsurgical residual tumor in some groups of patients rapidly develop therapy-resistant which often leads to tumor recurrence and distal metastasis. The major goals of our lab are to understand the molecular mechanisms that alter the damage repair pathways and gene expression in tumor cells to promote therapy resistance and tumor recurrence and develop second line of interventions to prevent tumor recurrence and metastasis and improve the quality of life of patients.
We have recently discovered a novel mechanistic connection between elevated levels of a DNA repair protein APE1, a histone chaperone FACT complex and G-quadruplex (G4), a non-canonical (non-B form) four-stranded DNA secondary structure in promoting therapy-induced damage repair and gene expression. Our research goals are to elucidate how these factors work together to promote resistance to radiation and chemo and develop targeted multifunctional nanoparticles (NP) loaded with chemo or radiosensitizers to target therapy resistance tumor cells and prevent tumor recurrence and metastasis in a preclinical model.
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer (BC) among all the BC subtypes due to its exceptionally high metastasis rate. TNBC patients with metastasis have a short overall survival as the endocrine therapy and chemotherapy are inefficient in TNBC treatment. Studies have revealed that G4 DNA is highly enriched in TNBC signature genes’ promoters, and our lab was the first one to uncover that DNA repair protein APE1 binds to G4 and regulates its stability in cells. We are interested in elucidating the interaction between APE1 and G4 in TNBC and their roles in regulating TNBC metastasis and targeting APE1-G4 interaction as a potential therapeutic approach to inhibit TNBC metastasis.
Our collaborative multidisciplinary approaches use cutting edge genetic and molecular tools and drug delivery systems to understand therapy resistance and metastasis. We are looking for talented students and postdocs. who get the opportunity to develop innovative ideas in individualized project.
Publications:
- Pramanik S, Chen Y, Song H, Khutsishvili I, Marky LA, Ray S, Natarajan A, Singh PK, Bhakat KK. The Human AP-endonuclease 1 (APE1) is a DNA G-quadruplex Structure Binding Protein and Regulates KRAS Expression in Pancreatic Ductal Adenocarcinoma Cells. Nucleic Acids Res. (2022),50:3394-3412. PMCID: PMC8990529 DOI: 1093/nar/gkac172
- Song, H., Xi, , Chen, Y., Pramanik, S., Zeng, J , Roychoudhury , S., Harris , H., Akbar , A., Elhag , S., Coulter , D., Ray , S., Bhakat, KK.. Histone chaperone FACT complex inhibitor CBL0137 interferes with DNA damage repair and enhances sensitivity of medulloblastoma to chemotherapy and radiation. Cancer Lett. (2021), 520:201-212. PMCID: PMC8440470 DOI: 10.1016/j.canlet.2021.07.020
- Pramanik S, Roychoudhury S and Bhakat KK. Oxidized DNA base damage repair and transcription: a new mechanism for regulation of gene expression in cancer. Handbook of Oxidative stress and Cancer, Springer Nature (2022).
- Bhakat KK. and Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair, (2022), 109: doi: 10.1016/j.dnarep.2021.103246.
- Roychoudhury S, Pramanik S, Harris H, Tarpley M, Sarkar A, Spagnol G, Sorgen P, Chowdhury D, Band V, Klinkebiel D, Bhakat KK. Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome. Proceedings of National Academy of Sciences, USA (2020), 117: (21) 11409-11420. PMCID: PMC7260947 DOI: 1073/pnas.1912355117
- Ray S, Chaturvedi NK, Bhakat KK., Rizzino A, Mahapatra S. Subgroup-Specific Diagnostic, Prognostic, and Predictive Markers Influencing Pediatric Medulloblastoma Treatment. Diagnostics (Basel), (2021), 12 (1) 61. doi: 10.3390/diagnostics12010061.
- Song H, Zeng J, Roychoudhury S, Biswas P, Mohapatra B, Ray S, Dowlatshahi K, Wang J, Band V, Talmon G, Bhakat KK. Targeting Histone Chaperone FACT Complex Overcomes 5-Fluorouracil Resistance in Colon Cancer. Mol Cancer Ther. (2020) 19:258-269.
- Roychoudhury S, Nath S, Song H, Hegde ML, Bellot LJ, Mantha AK, Sengupta S, Ray S, Natarajan A, Bhakat KK. Human Apurinic/Apyrimidinic Endonuclease (APE1) Is Acetylated at DNA Damage Sites in Chromatin, and Acetylation Modulates Its DNA Repair Activity. Mol Cell Biol. (2017) 37(6). PMCID: PMC5335514 DOI: 1128/MCB.00401-16
- Nath S, Roychoudhury S, Kling MJ, Song H, Biswas P, Shukla A, Band H, Joshi S, Bhakat KK. The extracellular role of DNA damage repair protein APE1 in regulation of IL-6 expression..Cell Signal. (2017) Nov;39:18-31. PMID:28751279
- Sengupta S, Mantha AK, Song H, Roychoudhury S, Nath S, Ray S, Bhakat KK. Elevated level of acetylation of APE1 in tumor cells modulates DNA damage repair. 2016;7(46):75197-209.
Read from original source here.