Division of Molecular Genetics and Cancer
Research activities in this division are focused on seeking answers for treatment and management of complex human diseases such as cancer and rare bone marrow failure syndromes and hematological disorders. The division is equipped with state-of-art research instruments and highly competent faculty with vast experience in the fields of genetics and cancer. Some of the thrust areas include genomics and epigenetics of rare genetic diseases and cancers, role of small RNAs and noncoding RNAs in cell signaling pathways, role of ribosomes in human diseases, nucleolar proteins and their role in tumorigenesis, and stem cell deregulation in cancer. The division also focuses on discovery and development of small molecule anti-cancer drugs through the whole animal small molecule screening or high throughput screening of chemicals using the zebrafish model system. Recently, zebrafish has emerged as a powerful cancer model system because they develop tumors that are histologically similar to human tumors and many human cancer genes are conserved structurally and functionally in zebrafish. In addition, this fish is amenable to pharmacological testing which makes them useful for screening anti-cancer agents. Apart from fish models, the division also houses mice models, which provide exceptional insights into the biology and genetics of human cancer. They are easy to handle and have disease manifestations consistent to humans. In addition to the research activities, the division is dedicated to educate and train the next generation of cancer investigators and human geneticists. The division has been established with a vision of bringing research scientists and clinicians together in order to effectively translate research findings into new ways to detect and treat cancer and genetic disorders.
Prof. (Dr.) ANIRBAN CHAKRABORTY
- DesignationDirector, Dean-Faculty of Biological Sciences
- Email anirban@nitte.edu.in
- Contact No..
- Joining date 01-08-2014
My specific area of research is to understand the role of ribosomes in bone marrow failure syndromes and cancer. Other areas of research include developing non-invasive and alternative DNA-based molecular tools for detection of specific mutations in cancer, developing transgenic zebrafish as cancer models and screening of natural antic-cancer compounds in zebrafish using HTS technology.
- Master of Science (Microbiology), University of Agricultural Sciences, Bangalore, 1999
- Doctor of Philosophy (Molecular Biology), United Graduate School of Agricultural Sciences, Kagoshima University, Japan, 2006
- Director, Centre for Science Education and Research (Oct 2020 - To date)
- Deputy Director, Centre for Science Education and Research (Oct 2017 – Sep 2020)
- Professor, Centre for Science Education and Research (Jan 2017- to date)
- Associate Professor, Centre for Science Education and Research (Aug 2014- Dec 2016)
- Senior Research Associate, Laboratoire de Biologie Moleculaire Eucaryote (LBME), UMR CNRS 5099, Toulouse, France (June 2012- June 2014)
- Postdoctoral Fellow, Frontier Science Research Center, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan (May 2006- March 2012)
- Molecular mechanisms of cancer and inherited bone marrow failure disorders
- Role of ribosomes in cancer
- Nucleolar proteins and their role in tumorigenesis
- Small molecule screening in zebrafish
- Best Researcher of Nitte (Deemed to be University) and Best Researcher of NUCSER by the Nitte (Deemed to be University), 2018
- Early Career Research Award by Dept. of Science and Technology, Science and Engineering Board (DST-SERB), Govt. of India, 2016
- Japan-Asia Youth Exchange program in Science (SAKURA exchange program in science) coordinator, 2015
- The Strategic Priority Research Award by the University of Miyazaki, Faculty of Medicine, Japan, 2011
- Post-doctoral Fellowship for Foreign Researchers by the Japanese Society for Promotion of Science (JSPS), 2006-2008
- Dr. V.G. Jhingran Award for the Best Overseas Indian PhD Thesis Award for the year 2006 by Professional Fisheries Graduates Forum, Mumbai, India
- Monbukagakusho (MEXT) fellowship for PhD by the Government of Japan, 2002-2006
- Senior Research Fellowship by Indian Council of Agricultural Research, India, 2002-2003
- National Eligibility Test (NET) Certificate by ASRB, New Delhi, 1999
- Certificate of Merit by University of Agricultural Sciences, Bangalore for first rank in Masters Degree, 1999
- University Merit Scholarship by University of Agricultural Sciences, Bangalore, during undergraduate studies 1996- 1997
- Member, IQAC, NUCSER
- Member Secretary, Board of Studies, NUCSER
- Member Secretary, Research Advisory Committee, NUCSER
- Member Secretary, Institute Ethics Committee, NUCSER
- Member Secretary, Anti-Ragging Committee, NUCSER
- Member Secretary, Institutional Committee Against Substance Abuse, NUCSER
- Member Secretary, Students Grievance Cell, NUCSER
- In charge, Institutional Public Relations Committee, NUCSER
- Life member, Indian Society of Developmental Biology
- Life member, Molecular Pathology Association of India
- Life member, The Society of Biological Chemists, India
- Life member, Indian Association for Cancer Research
- Life member, Association of Microbiologists of India
Undergraduate-
Cancer Biology; Radiation Biology; Toxicology
Postgraduate-
Medical Genetics; Biology and Genetics of Cancer
Currently enrolled PhD students: 06
Guided PhD students: 01
Guided PG Students: 10
Journal Publications-
- Henras A., Plisson-Chastang C., O'Donohue M-F, Anirban Chakraborty, Gleizes P-E. 2014. An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdisciplinary Reviews: RNA, 6: 225-242
- Anirban Chakraborty, Tamayo Uechi, Yukari Nakajima, Hanna T. Gazda, Marie-Françoise O'Donohue, Pierre-Emmanuel Gleizes, and Naoya Kenmochi. Cross talk between TP53 and c-Myc in the pathophysiology of Diamond-Blackfan anemia: Evidence from RPL11-deficient in vivo and in vitro models. Biochemical and Biophysical Research Communications 495: 1839-1845.
- Alexis H Bennett, Marie Francoise O'Donohue, Stacey R Gundry, Aye T Chan, Jeffery Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I Zon, Pierre-Emmanuel Gleizes, Alan H Beggs, and Vandana Gupta. 2018. RNA helicase, DDX27 regulates skeletal muscle growth and regeneration by modulation of translational processes. PLoS Genetics 14(3): e1007226
- Shiwangi Dwivedi, Raghav Sharma, Prasanna Kumar Shetty, Anirban Chakraborty. 2018. Association of INS VNTR polymorphisms with polycystic ovary syndrome (PCOS) in South Indian population. Meta Gene 17: 202-205.
- Srividya, Giridhar B.H., Vishwanath S. and Anirban Chakraborty. 2018. Profiling of germline mutations in major hotspot codons of TP53 using PCR-RFLP. Pathology and Oncology Research (in press)
- Karanth Padyana Anupama, Anirban Chakraborty, Iddya Karunasagar, Indrani Karunasagar Biswajit Maiti. 2019. Loop-mediated isothermal amplification assay as a point-of-care diagnostic tool for Vibrio parahaemolyticus: Recent developments and improvements. Expert Review of Molecular Diagnostics 19: 229-239
- Srividya Arjuna, Gunimala Chakraborty, Rajesh Venkataram, Pandyanda Nanjappa Dechamma, Anirban Chakraborty. 2020. Detection of epidermal growth factor receptor T790M mutation by allele-specific loop mediated isothermal amplification. Journal of Carcinogenesis 19: 3
- Srividya Arjuna, Rajesh Venkataram, Gunimala Chakraborty, Nishith Babu, Audrey D'Cruz, Giridhar Belur Hosmane, Anirban Chakraborty. 2020. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Scientific Reports 10:17559
- Leonard Clinton D'Souza, Shruti Mishra, Anirban Chakraborty, Anusmita Shekher, Anurag Sharma, Subash Chandra Gupta. 2020. Oxidative Stress and Cancer Development: Are non-coding RNAs the missing links? Antioxidants and Redox Signaling 33 (17): 1209-1229
- Venkataram R, Arjuna S, Hosmane GB, Chakraborty A. 2021. Quantitative analysis of cell-free DNA by droplet digital PCR reveals the presence of EGFR mutations in non-malignant lung pathologies. Monaldi Archives for Chest Disease 91:1748
- Harshitha KP, Dechamma PN, Nishith B, Krithika Kalladka, Shanti Priya Dias, Gunimala Chakraborty, Sudhindra M Rao, Anirban Chakraborty. 2021. TP53 Codon 72 polymorphism and Type 2 Diabetes: A case-control study in South Indian Population. Molecular Biology Reports 48:5093-5097
- Bharti Mittal, Dechamma Pandyanda Nanjappa, Gunimala Chakraborty, Anirban Chakraborty, Arati Khanna-Gupta. 2021. A patient with Lesch-Nyhan Syndrome presenting with anesthetic challenges: not an exception, but the rule. Gene Reports 24:101289
- Dechamma Pandyanda Nanjappa, Nishith Babu, Arati Khanna-Gupta, Marie-Françoise O'Donohue, Patrick Sips, Anirban Chakraborty. 2021. Poly (A)-specific ribonuclease (PARN): More than just "mRNA stock clearing". Life Sciences 285:119953
- Rathika Damodara Shenoy, Vikram Shetty, Annelies Dheedene, Björn Menten, Dechamma Pandyanda Nanjappa, Gunimala Chakraborty, Patrick Sips, Anne de Paepe, Bert Callewaert, Anirban Chakraborty. 2021. Phenotypic and molecular heterogeneity in Mandibulofacial Dysostoses: A case series from India. The Cleft Palate-Craniofacial Journal (in press)
- Audrey D'Cruz, Dechamma Pandyanda Nanjappa, Sahana Maben, Pushparaja Shetty, Anirban Chakraborty. 2021. Non-invasive saliva-based detection of gene mutations in oral cancer patients by Oral Rub and Rinse technique. Asian Pacific Journal of Cancer Prevention (in press)
- Jazeela, K., Chakraborty, A., Karunasagar, I., Deekshit, V.K (2020) Non-Typhoidal Salmonella: A Potential Anti-Cancer Agent. Journal of Applied Microbiology 128: 2-14.
- Srividya, A., Maiti, B., Chakraborty, A., Chakraborty, G. (2019). Loop Mediated Isothermal Amplification: A promising tool for screening genetic mutations. Molecular Diagnosis & Therapy 23(6), 723-733.
- Srividya, Giridhar, B.H., Vishwanath, S., Chakraborty, A. (2019) Profiling of germline mutations in major hotspot codons of TP53 using PCR-RFLP. Pathology Oncology Research 25(4), 1373-1377.
- Dwivedi, S., Sharma, R., Shetty, P.K., Chakraborty, A. (2018) Association of INS VNTR polymorphisms with polycystic ovary syndrome (PCOS) in South Indian population. Meta Gene 17: 202-205
- Bennett, A.H., O'Donohue, M.F., Gundry, S.R., Chan, A.T., Widrick, J., Draper, I., Chakraborty, A., Zhou, Y., Zon, L.I., Gleizes, P., Beggs, A.H., Gupta, V. (2018) RNA helicase, DDX27 regulates skeletal muscle growth and regeneration by modulation of translational processes. PLoS Genetics 14(3): e1007226
- Chakraborty, A., Uechi, T., Nakajima, Y., Gazda, H.T., O'Donohue, M., Gleizes, P., Kenmochi, N. (2018) Cross talk between TP53 and c-Myc in the pathophysiology of Diamond-Blackfan anemia: Evidence from RPL11-deficient in vivo and in vitro models. Biochemical and Biophysical Research Communications 495: 1839-1845.
- Yadav, G.V., Chakraborty, A., Uechi, T., Kenmochi, N. (2014) Ribosomal protein deficiency causes Tp53-independent erythropoiesis failure in zebrafish. The International Journal of Biochemistry & Cell Biology 49: 1-7.
- Higa-Nakamine, S., Suzuki, T., Uechi, T., Chakraborty, A., Nakajima, Y., Nakamura, M., Hirano, N., Suzuki T., Kenmochi, N. (2012) Loss of ribosomal RNA modification causes developmental defects in zebrafish. Nucleic Acids Research 40:391-398.
- Chakraborty, A., Uechi, T., Kenmochi, N. (2011) Guarding the Translation Apparatus: Defective Ribosome Biogenesis and the p53 Signaling pathway. Wiley Interdisciplinary Reviews: RNA, 2: 507-522.
- Chakraborty, A., Uechi, T., Higa, S., Torihara, H., Kenmochi, N. (2009) Loss of ribosomal protein L11 affects zebrafish embryonic development through a p53-dependent apoptotic response. PLoS ONE 4(1): e4152.
Conference publications- 20
All Publications: Google Scholar: https://scholar.google.co.in/citations?user=g-vUFywAAAAJ&hl=en
ResearchGate: www.researchgate.net/profile/Anirban_Chakraborty12
Extramural Funding
- The association of ACE2 and TMPRSS2 gene polymorphisms with susceptibility and severity to COVID-19 in Indian population and validation using zebrafish model system, Principal Investigator, Funded by ICMR, 2021-2024
- Combating cancer through alternative approaches: Investigating the antitumor properties of non-typhoidal Salmonella in transgenic zebrafish cancer models, Principal Investigator, Funded by ICMR, 2021-2024
- Investigating the mechanisms of genetic disorders using the zebrafish model system (GEN-ZEMO), Principal Investigator, Funded by DST-BELSPO, 2018-2021
- RNases and cancer: decoding the role of poly(A)-specific ribonuclease (PARN) in tumorigenesis, funded by DST-SERB, 2017-2020
- Ribosomal defects and craniofacial deformities: A systematic genetic analysis of Treacher Collins syndrome (TCS) and TCS-like cases in India-Genotyping of patients, funded by NitteDU, 2018-2020
- Screening of gene mutations that interferes with response to CCRT in esophageal cancer patients: AS-LAMP assays using cell free DNA, funded by NitteDU, 2019-2021Genetic markers of Tuberculosis among Indo-Tibetan and Indian Population, funded by NitteDU, 2019-2021
- Impact of interaction with children on blood hormonal levels among institutionalized elderly, funded by NitteDU, 2019-2021
- In vitro cytotoxicity evaluation of denture materials used in the fabrication of RPD, funded by NitteDU, 2018-2020
- Effects of Titanium Surfaces on cell viability and cytokine expression in vitro, funded by NitteDU, 2018-2020
- Generation of transgenic zebrafish models for elucidating the molecular mechanisms of Mycobacterium infection, funded by NitteDU, 2018-2020
- Non-invasive detection of DNA methylation in lung cancer patients by droplet digital PCR, Principal Investigator, Funded by Nitte (Deemed to be University), 2020-2022
- Genetic testing of non-small cell lung cancers: Development of AS-LAMP assays for detection of EGFR and KRAS mutations, Principal Investigator, Funded by Nitte (Deemed to be University), 2016-2019
- Gene environment interaction in the development of asthma and allergic diseases: A study using Indian population, Principal Investigator, Funded by Nitte (Deemed to be University), 2016-2019
Dr. GUNIMALA CHAKRABORTY
- DesignationAssociate Professor G-II
- Email gunimala@nitte.edu.in
- Contact No..
- Joining date 01-05-2018
Over the past 12 years I have worked on development of many new diagnostic techniques for a bacterial, viral pathogen as well as a parasite affecting humans using my expertise on LAMP technique and characterization (identification and function) of cytokines under different stress/infection. At present my research area and interest focusses on development of rapid molecular detection techniques, development of transgenic zebrafish lines for human diseases, Human /animal parasitology, and Molecular Immunology.
Doctor of Philosophy (Applied Biochemistry and Bioscience), University of Miyazaki, Japan, 2007
Master of Science (Aquaculture), West Bengal University of Animal Sciences, Kolkata, 2003
Associate Professor - Grade I, Nitte Centre for Science Education and Research, Mangaluru (2018-till date)
DST women Scientist, Nitte Centre for Science Education and Research, Mangaluru (2015 –2018)
Postdoctoral Fellow, (Infectious Diseases and Parasitology), Faculty of Medicine, University of Miyazaki, Japan (2010-2012).
Postdoctoral Fellow, (Biochemistry and Applied Science), Faculty of Agriculture, University of Miyazaki, Japan (2007 - 2009).
Zebrafish Model system: Transgenesis and disease modelling
Molecular detection techniques
Molecular Genetics
Bioinformatics
Human/animal parasitology
DST women Scientist Fellow awarded by Department of Science and Technology, Govt. of India, 2015 -2018.
Postdoctoral Fellow by University of Miyazaki, Department of Infectious Diseases and Parasitology, Faculty of Medicine, Japan,2010-2012
Postdoctoral Fellow awarded by Japan Society for Promotion of Science, Japan, 2007 - 2009
Rotary Yoneyama Fellowship for the doctoral studies awarded by Yoneyama Foundation of Japan, April 2005-March 2007
North East Council (NEC) Fellowship during B.F.Sc. program, awarded by Manipur State Fisheries Department, India ,1997-2001
- Coordinator, Institutional Editorial committee
- Member, Institutional committee against substance abuse
- Member coordinator, Institutional Committee against sexual harassment
Member, Society of Biological Chemist (India)
Undergraduate
Cell based assays in Biomedical Science, Genetic Engineering, Good Laboratory Practices
Postgraduate
Medical Biotechnology, Application Biotechnology in Food Science, Research Ethics & IPR
Cell based assays in Biomedical Science, Genetic Engineering, Good Laboratory Practices
Postgraduate
Medical Biotechnology, Application Biotechnology in Food Science, Research Ethics & IPR
• PG: 04 completed and 02 ongoing
• UG: 04 completed
- Punja HK, Nanjappa DP, Babu N, Kalladka K, Dias BS, Chakraborty G, Rao SM, Chakraborty A. TP53 codon 72 polymorphism and type 2 diabetes: a case-control study in South Indian population. Molecular Biology Reports. 2021 Jun 28:1-5
- Mittal B, Nanjappa DP, Chakraborty G, Chakraborty A, Khanna-Gupta A. A patient with Lesch-Nyhan Syndrome presenting with anesthetic challenges: not an exception, but the rule. Gene Reports. 2021 Jul 23:101289
- Arjuna S, Venkataram R, Dechamma PN, Chakraborty G, Babu N, D'Cruz A, Hosmane GB, Chakraborty A. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Scientific reports. 2020 Oct 16;10(1):1-7
- Prabhakara Aprathi, Pandyanda Nanjappa Dechamma, Babu Nishith, Kalladka Krithika, Chakraborty Anirban, Chakraborty Gunimala*. Exposure to mosquito repellents causes profound development defects and induces oxidative stress in zebrafish. Journal of Health and Allied Sciences NU, :2020;10:122-127
- Shreya Kunder,Babu Nishith Pandyanda Nanjappa Dechamma, Kalladka Krithika, Chakraborty Gunimala, Chakraborty Anirban*. Evaluation of toxicity and antioxidant property of Cassia fistula stem bark extracts in zebrafish. Journal of Health and Allied Sciences NU:2020; 10:109-115
- Dinesh Deeksha, Pandyanda Nanjappa Dechamma, Babu Nishith, Kalladka Krithika, Chakraborty Gunimala, Chakraborty Anirban*. 2020.Evaluation of toxicity and anti-angiogenic activity of Murraya koenigii leaf extracts in zebrafish. J Health Allied Sci NU:2020; 10:79-85
- Srividya Arjuna, Gunimala Chakraborty, Rajesh Venkataram, Pandyanda Nanjappa Dechamma, Anirban Chakraborty.2020. Detection of epidermal growth factor receptor T790M mutation by allele-specific loop mediated isothermal amplification. Journal of Carcinogenesis
Extramural Funding
- Liquid Biopsy for Lung Cancer: Development of LAMP assays using cell-free DNA for screening of gene mutations that interfere with response to TKIs in patients Principal Investigator, funded by ICMR, Govt. of India, 2020-2023
- The association of ACE2 and TMPRSS2 gene polymorphisms with susceptibility and severity to COVID-19 in Indian population and validation using zebrafish model system Co-Principal Investigator, funded by ICMR (covid Research), Govt. of India,2021-2024
Dr. ARSHDEEP SIDHU
- DesignationAssistant Professor (G-II)
- Email a.sidhu@nitte.edu.in
- Contact No..
- Joining date 02-01-2020
The focus of my research is to understand the functioning of disordered and hybrid proteins, with respect to age associated diseases like neurodegeneration and cancer. A parallel interest is to develop amyloid based bio-nanocomposites for diverse applications. During my postdoc at Erasmus Medical Center, Rotterdam and PhD, I gained expertise in protein conformation studies using atomic force microscopy by single molecule imaging and analysis of DNA repair proteins (BRCA2-RAD51), study of polymorphism in self-assembled amyloids (α-synuclein) and functionalization of amyloids with gold nanoparticles (conductive nanowires). I joined NUCSER in 2020.
Doctor of Philosophy (Nanobiophysics), University of Twente, The Netherlands, 2016
Master of Science (Human Genomics), Panjab University, India, 2007
Best debater on "Impact of Nanotechnology on Society", 2014
Immunology foundation fellowship, 2009
EMBO travel award, 2009
UGC-NET lectureship, 2007
Gold medal Panjab University, 2007
Member: Student Welfare Committee, NUCSER
Coordinator, Departmental Journal Club and Work-Discussions, NUCSER
Member, Indian Biophysical Society
Undergraduate-
Human pathology
Postgraduate-
Genetic Engineering
PhD: 02 (ongoing)
UG students: 03 (completed)
Journal publications-
Arshdeep Sidhu, Małgorzata Grosbart, Humberto Sánchez, Bram Verhagen, Nick L L van der Zon, Dejan Ristić, Sarah E van Rossum-Fikkert, Claire Wyman (2020) Conformational flexibility and oligomerization of BRCA2 regions induced by RAD51 interaction. Nucleic Acids Research. (In press) https://doi.org/10.1093/nar/gkaa648 [IF: 11.501]
Sidhu, A*., Vaneyck, J., Blum, C., Segers-Nolten, I., Subramaniam, V. (2018) Polymorph-specific distribution of binding sites determines thioflavin-T fluorescence intensity in α-synuclein fibrils. Amyloid 25(3), 189-196.
Sidhu, A., Ristic, D., Sánchez, H., Wyman, C. (2018) The recombination mediator BRCA2: Architectural plasticity of recombination intermediates revealed by single-molecule imaging (SFM/TIRF). Methods in Enzymology 600: 347-374.
Sidhu, A., Segers-Nolten, I., Raussens, V., Claessens, M. M., Subramaniam, V. (2017). Distinct Mechanisms Determine α-Synuclein Fibril Morphology during Growth and Maturation. ACS chemical neuroscience 8(3), 538-547.
Sidhu, A., Segers-Nolten, I., Subramaniam, V. (2016). Conformational Compatibility Is Essential for Heterologous Aggregation of α-Synuclein. ACS chemical neuroscience 7(6), 719-727.
Raiss, C.C., Braun, T.S., Konings, I.B., Grabmayr, H., Hassink, G.C., Sidhu, A., le Feber, J., Bausch, A.R., Jansen, C., Subramaniam, V., Claessens, M.M. (2016). Functionally different α-synuclein inclusions yield insight into Parkinson's disease pathology. Scientific reports 6, 23116 .
Sidhu, A., Segers-Nolten, I., Subramaniam, V. (2014). Solution conditions define morphological homogeneity of α-synuclein fibrils. Biochimica et biophysica acta 1844(12), 2127-2134.
Sidhu, A., Surolia, A., Robertson, A. D., Sundd, M. (2011). A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip. Journal of molecular biology 411(5), 1037-1048.
Sidhu, A., Sundd, M. (2009) Protein biotechnology and its applications. Biotechnology applications, ed. C.S.K Mishra.; 213-230.
Conference publications- 01
