Discovery of therapeutically relevant alterations in human genome – a functional genomics approach
Researcher:
Dr. Pratik Chandrani
Funding:
DBT-Wellcome, Terry Fox foundation, Tata Memorial Centre
Collaborators:
Dr. Kumar Prabhash, Tata Memorial Hospital

Lung cancer remains the leading cause of cancer related deaths across the globe. According to the Globocan, around 2 million new lung cancer cases were reported and the numbers of deaths due to lung cancer were more than 1.7 million contributing to 18.6% of all cancer related deaths in 2018. In India, lung cancer constitutes 6.9 per cent of all new cancer cases and 9.3 per cent of all cancer related deaths in both sexes, it is the commonest cancer and cause of cancer related mortality in men. Our pioneering work (involving a large cohort of 1000 odd samples) establishes that while EGFR mutations are present in over 30% of East Asian and 10% of Caucasian lung adenocarcinoma patients, they are only found in about 23-25% of Indian lung adenocarcinoma patients (PLoS One 2013 Apr; PLoS One 2013 Oct; Ind J Cancer 2013; F1000Res 2015). Similarly, KRAS mutations are present at 60% lower frequency in Indian lung adenocarcinoma patients than compared to the Caucasian population (Br J Cancer 2014). Our more recent work establishes landscape of actionable mutations beyond EGFR and KRAS in Indian lung cancer patients (Annals of Oncology 2016). Taken together, these study forms a crucial basis to rationalize targeted therapy in India and to adopt genetic testing in a clinical diagnostic laboratory at an affordable pricing—as the genetic test developed in collaboration with Dr. Kumar Prabhash and Dr. Anuradha Choughule to genotype EGFR mutations has been able to remarkably reduce its cost from ~$200 to $12 per test (!) that is now being offered at the Tata Memorial Hospital on routine basis—enabling and transforming the way EGFR mutation profiling is been carried out at an affordable cost for every lung cancer patient. Our other seminal contribution from ACTREC includes an in-depth functional characterization of FGFR1 and FGFR3 alterations as novel candidate therapeutic targets in lung cancer (PLoS One 2011; Annals of Oncology 2016). Using elegant genetic, biochemical and mouse-xenograft based mechanistic characterization led to the discovery of FGFR3 activating mutations in lung adenocarcinoma patients of Indian origin. Our work thus opens a possibility for cancer treatment.


Figure: Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Left panel reflect first comprehensive landscape of therapeutically relevant alterations in lung aenocarcinomapatients of Indian origin. Right upper panel shows that the novel FGFR3 mutations derived from lung cancer patients forms FGFR inhibitor sensitive tumors; lower panel shows the drug is specific. (Annals of Oncology. 2017).

Understanding the complexities of human lung cancer genome
Researcher:
Asim Joshi, Ph.D-SRF
Funding:
DST-SERB
Collaborator:
Dr. Kumar Prabhash, Tata Memorial Hospital

Treatment with tyrosine kinase inhibitors (TKIs) is the standard of care for lung cancer patients positive for mutations in the EGFR gene. Unfortunately, within a year or so, a vast majority of patients develop resistance against TKIs treatment. Although numerous mechanisms of resistance have been described, in about 30% of cases the mechanism of resistance remains unknown. In this project, we propose to identify genetic alterations contributing to the EGFR TKI resistance by characterizing the genome of TKI-sensitive and TKI-resistant tumor from the same patient. I anticipate this study to have significant impact on the management of lung cancer and help in better selection of patients for the treatment.


Figure: The schema for identification of novel resistance mechanisms using primary tumors from EGFR mutated non-small cell lung cancer patients

An Integrative Approach to understand Resistance to Tyrosine Kinase Inhibitors in Human Lung Cancer.
Researcher:
Supriya Hait, Ph.D-JRF
Funding:
SERB DST
Collaborators:
Dr. Kumar Prabhash, Tata Memorial Hospital

Lung cancer resistance is the major obstacle to targeted therapies involving tyrosine kinase inhibitors (TKI). In Indian lung adenocarcinoma patients, activating mutations like EGFR kinase domain mutations and ALK rearrangement occurs at the rate of 23% and 5-7%, respectively. The TKIs Erlotinib and Crizotinib are the FDA approved drug of choice for patients with EGFR mutation and ALK rearrangement with response rate of 74% and 60% respectively. Numerous biological mechanisms of acquired resistance have been elucidated wherein the known genetic mechanisms accounts for 60% in EGFR mutants and 28-49% in ALK rearranged patients. However, epigenetic mechanism underlying resistance remains comparatively less explored. I aim to characterize mutational landscape of 450 epigenetic regulators by performing Whole Exome sequencing of TKI sensitive and resistant primary tumors followed by in depth targeted resequencing of these factors using cell line models established during the course of this study. Next, we will perturb the expression of candidate epigenetic regulators by performing overexpression and knockdown studies using TKI sensitive and resistant cell lines. This study would further the understanding of epigenetic mechanisms of acquired resistance in lung adenocarcinoma patients to help develop specific targeted treatments to overcome the resistance.



Figure:CT scan images of chest of EGFR mutant lung adenocarcinoma patient before and after treatment with Gefitinib. As seen in the scan, the tumor regresses after 1-2 months of gefitinib treatment. However, after 12 months, the disease progresses after initial benefit with Gefitinib treatment. [Representative image taken from internet. Source unknown.]


Establishing cell-free nucleic acid as diagnostic and monitoring tool in non-small cell lung carcinoma (NSCLC)
Researcher:
Vichitra Behel, Ph.D-JRF
Dr. Kumar Prabhash Lab, Department of Medical Oncology, Tata Memorial Hospital
Collaborators:
Dr. Amit Dutt, ACTREC-TMC, Navi Mumbai

Treatment of cancers like NSCLC has revolutionized in the last decade owing to the identification of driver mutations targetable by tyrosine kinase inhibitors. However, a major challenge in the treatment of patients with NSCLC is acquired resistance to therapy. Therefore, there is a need for timely disease monitoring and early detection of disease progression. As tissue biopsy cannot be performed repeatedly for disease monitoring, liquid biopsy, which detects circulating tumor DNA (ctDNA) in patient’s blood, can be used as an alternative. In lung cancer, various studies have shown successful mutation detection and disease monitoring using ctDNA. Therefore, in this study we aim to establish cell-free DNA as a diagnostic and monitoring tool in NSCLC. An early detection of acquired resistance and disease progression with this tool will help in delivering timely and effective treatment to patients with NSCLC.


Publications:

  1. Dutt A, Ramos AH, Hammerman PS, Mermel C, Cho J, Sharifnia T, Chande A, Tanaka KE, Stransky N, Greulich H, Gray NS, Meyerson M. Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer. PloS one. PMID: 21666749
  2. Choughule A, Noronha V, Joshi A, Desai S, Jambhekar N, Utture S, Thavamanni A, Prabhash K, Dutt A. Epidermal growth factor receptor mutation subtypes and geographical distribution among Indian non-small cell lung cancer patients. Indian journal of cancer. PloS one. PMID: 23979200
  3. Noronha V, Prabhash K, Thavamani A, Chougule A, Purandare N, Joshi A, Sharma R, Desai S, Jambekar N, Dutt A, Mulherkar R. EGFR mutations in Indian lung cancer patients: clinical correlation and outcome to EGFR targeted therapy. PloS one. PMID: 23620765
  4. Chougule A, Prabhash K, Noronha V, Joshi A, Thavamani A, Chandrani P, Upadhyay P, Utture S, Desai S, Jambhekar N, Dutt A. Frequency of EGFR mutations in 907 lung adenocarcioma patients of Indian ethnicity. PloS one. PMID: 24124538
  5. Choughule A, Sharma R, Trivedi V, Thavamani A, Noronha V, Joshi A, Desai S, Chandrani P, Sundaram P, Utture S, Jambhekar N, Gupta S, Aich J, Prabhash K, Dutt A. Coexistence of KRAS mutation with mutant but not wild-type EGFR predicts response to tyrosine-kinase inhibitors in human lung cancer. British journal of cancer. PMID: 25117816
  6. Ramteke MP, Patel KJ, Godbole M, Vyas M, Karve K, Choughule A, Prabhash K, Dutt A. CRE: a cost effective and rapid approach for PCR-mediated concatenation of KRAS and EGFR exons: Rapid way to detect EGFR and KRAS mutations. F1000Research. PMID: 27127615
  7. Chandrani P, Prabhash K, Prasad R, Sethunath V, Ranjan M, Iyer P, Aich J, Dhamne H, Iyer DN, Upadhyay P, Mohanty B, Chandna P, Kumar R, Joshi A, Noronha V, Patil V, Ramaswamy A, Karpe A, Thorat R, Chaudhari P, Ingle A, Choughule A, Dutt A. Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Annals of oncology : Official Journal of the European Society for Medical Oncology. PMID: 27998968
  8. Noronha V, Choughule A, Patil VM, Joshi A, Kumar R, Susan Joy Philip D, Banavali S, Dutt A, Prabhash K. Epidermal growth factor receptor exon 20 mutation in lung cancer: types, incidence, clinical features and impact on treatment. OncoTargets and therapy. PMID: 28652772
  9. Veldore VH, Choughule A, Routhu T, Mandloi N, Noronha V, Joshi A, Dutt A, Gupta R, Vedam R, Prabhash K. Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer. Lung Cancer (Auckland, N.Z.) PMID:  29379323
  10. Balaji SA, Shanmugam A, Chougule A, Sridharan S, Prabhash K, Arya A, Chaubey A, Hariharan A, Kolekar P, Sen M, Ravichandran A, Katragadda S, Sankaran S, Bhargava S, Kulkarni P, Rao S, Sunkavalli C, Banavali S, Joshi A, Noronha V, Dutt A, Bahadur U, Hariharan R, Veeramachaneni V, Gupta V. Analysis of solid tumor mutation profiles in liquid biopsy. Cancer medicine. PMID:  30264478