Computational Biology
The Computational Biology group was established recently at MSMF with a mandate to utilize computational and statistical techniques including Artificial Intelligence (AI) and Machine Learning (ML) algorithms for processing clinical, molecular, and medical image data to generate hypotheses for validation and translation to the clinic as diagnostics, prognostics or therapeutics. Currently, the group is working on projects in the area of head and neck and oncology and neuro-oncology towards identifying novel biomarkers through integrating multi-omic data. In another realm of research, members of the computational biology group analyze images of routinely acquired histopathology slides to uncover hidden patterns that link to a clinically meaningful subtype in brain tumors or to therapy sensitivity in lung carcinoma. All these projects could potentially lead to a diagnostic or prognostic test in the clinic that can aid the clinicians in augmenting the disease management regime.
People
Dr. Sujan K Dhar
Tahmina Mazumdar
Dr Akhila L
Dept of Histopathology, NH
M.V Ram Bhupal Reddy (MSc MTech, Genetic Engineering)
Senior Research Fellow (SRF, ICMR fellowship)
PhD scholar, Vellore Institute of Technology (VIT), Vellore
rambhupal.reddy@ms-mf.org
Project: ‘Molecular profile specifying resistance/response to cytotoxic andtargeted chemotherapy in Head and Neck cancer’. The main aim of the study is to identifymarkers/pathway that can predict response/resistance to a specific treatment, using the meta-analysis approach, and evaluate their efficacy to improvedisease outcome in head and neck cancer using in vitro and in vivo models. The study attempts to be a step towards the development of personalizedtherapy approach in HNSCC.
Vaishnav Vasudevan
(MSc, Biomedical Genetics)
Senior Research Fellow (SRF)
Project: “Phase IIb/III study to determine the efficacy of curcumin and metformin to reduce the incidence of second primary tumours of aero-digestive tract in patients with history of head and neck squamous cell carcinoma” funded by National Cancer Grid (NCG). Also working on, profiling the expression of the EGFR/TGFß pathway and immune response in HNSCC tumours and its correlation with clinical, pathological and prognostic parameters.
Safeena Kulsum(MSc, MTech Biotechnology)
Senior Research Fellow
safeena.kulsum@ms-mf.org
Project: “Molecular signatures specifying cancer stem-like cells from oral squamous cell carcinoma and their relevance in chemo resistance” (RGYI Grant, Department of Biotechnology, Govt of India). Project involves in re-visiting the concept of oral Cancer stem cells (CSCs) in drug resistance/ treatment failure and whether the drug-resistance CSC-markers can be explored for application in a clinical format. In addition, the strategy of targeting the CSC-fibroblast niche towards reversal of metastasis and chemo resistance in Head and Neck squamous cell carcinoma is also being investigated.
Alumni
Anuradha Panigrahi
Intern , PhD Student, NMIMS Mumbai
Vijeta Joshi
Intern, Educator, Aakash Institute
Dr Anjana Muralidharan P (BDS, MDS Oral & Maxillofacial Pathology)
Clinical Trial Co-ordinator
Project: Working on a project titled, “Phase IIb/III study to determine the efficacy of curcumin and metformin to reduce the incidence of second primary tumors of aero-digestive tract in patients with history of head and neck squamous cell carcinoma”. The project is a clinical trial funded by National Cancer Grid (NCG
N Reddy Harsha Vardhan(MSc MTech, Genetic Engineering)
Senior Research Fellow
Project: Program Support in Head and Neck Oncology (DBT, Govt of India). The study aims to address a major need for developing integrated, pathway based approach to determine treatment resistance/response for laryngo-pharyngeal cancer, which is one of the major cancers in India. An integrated approach to explore the genome, transcriptome and proteome of tissues and the body fluids is the strategy employed in the project. Also working on the “Detection of Metastasis in early stage cancer patients based on Circulating tumour cell profile” that involves enumeration/characterization of Circulating Tumor Cells (CTCs) at a cellular/molecular level, their correlation with prognosis, as an initial step towards identifying potential markers that can enable their clinical application.
Dr ShaliniSubramanyan MDS
KRISHNADEVARAYA COLLEGE OF DENTAL SCIENCES AND HOSPITAL, BANGALORE
Internship (6 months)
Project: THE SALIVARY ANALYSIS OF TELOMERASE LEVELS IN ORAL SQUAMOUS CELL CARCINOMA PATIENTS
Dr Nandini Mohan (MDS)
AECS MAARUTI COLLEGE OF DENTAL SCIENCES AND RESEARCH CENTRE, Bangalore
Internship (6 months)
Project: EXPRESSION OF BETA HUMAN CHORIONIC GONADOTROPIN IN SERUM AND TISSUE SECTIONS OF PREOPERATIVE ORAL SQUAMOUS CELL CARCINOMA PATIENTS
Ms. P. AMSAVALLI (B Tech Biotechnology)
Anna University, Chennai
Internship (3 months)
Project: DETECTION OF CIRCULATING TUMOUR CELLS USING CANCER STEM CELL MARKERS AND CORRELATION WITH METASTASIS IN HEAD AND NECK CANCER
Ms. S.R.SARANYA (B Tech Biotechnology)
Anna University, Chennai
Internship (3 months)
Project: DETECTION OF CIRCULATING TUMOUR CELLS USING CANCER STEM CELL MARKERS AND CORRELATION WITH METASTASIS IN HEAD AND NECK CANCER
Ms. UtkarshaPaithane, B.Tech + M.Tech Biotechnology
Amity University, Noida
Internship (3 months)
Project: Estimation of circulating DNA and correlation with metastasis in patients with head and neck squamous cell carcinoma
Short-term Interns
Ms RenukaRamanathan (X), Mr Anand Rao Tadipatri (Class Xth), Pradyumna Rao: Class XIIth
Research Projects
- Proteogenomic Integration for discovery of differntial biomarkers in Glioblastoma: Glioblastoma is an aggressive form of brain cancer with median survival less than 18 months. In this project, we are analyzing transcriptomics and proteomics data generated from a set of glioblastoma and lower-grade glioma patients using a combination of de novo assembly and alignment-based pipelines to arrive at novel peptides differentially expressed in glioblastoma and other related clinical phenotypes. Dr Ravi Sirdeshmukh, Dr Abhishek Kumar, Institute of Bioinformatics.
- AI-enabled computational model for IDH1 mutation detection from H&E-stained glioma histopathology images : Mutations in the IDH gene are known to indicate better prognosis for patients suffering from lower-grade glioma. Current pathology practice of detecting the mutation using immunohistochemistry can only detect the canonical mutations. In this project, we aim to develop an artificial neural network-based computational model that can detect both canonical and non-canonical mutations from histopathology images that are generated as part of the standard of care. Dr Akhila L, Pathology, NH
- Determination of COVID-19 severity indicators from the systematic analysis of public data: Through successive waves of COVID-19, it is now well-established that around 5-10% of infected patients progress to severe form of the disease and other factors like age and pre-existing illnesses increases the chance of severity. In this study, we have analyzed a plethora of publicly available data to establish a set of cytokine markers like IL-6 and IL-10 that be used as a prognostic indicators. We also showed that inflammation and hypercoagulopathy are the pre-dominant risk factors of severity for SARS-CoV-2 infected patients suffering from diabetes.
Patents
- Tumor microenvironment platform comprising oral carcinoma for predicting drug sensitivity, drug resistance, and disease progression. File Number: 202141048345/TEMP/E-1/54650/2021-CHE. Filed Date: 23RD OCTOBER 2021
- Compositions and methods for treating coronavirus infection with different levels of disease severity. File Number: 202041036866. Filed Date: 27TH AUGUST 2020
- Antibodies against Lipocalin-2 and uses thereof. File Number: 202021000274. Filed Date: 03RD JANUARY 2019