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Dharavath B, Butle A, Pal A, Desai S, Upadhyay P, Rane A, Khandelwal R, Manavalan S, Thorat R, Sonawane K, Vaish R, Gera P, Bal M, D'Cruz AK, Nair S, Dutt A. Role of miR-944/MMP10/AXL- axis in lymph node metastasis in tongue cancer. Commun Biol 2023; 6:57. [PMID: 36650344 PMCID: PMC9845355 DOI: 10.1038/s42003-023-04437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Occult lymph-node metastasis is a crucial predictor of tongue cancer mortality, with an unmet need to understand the underlying mechanism. Our immunohistochemical and real-time PCR analysis of 208 tongue tumors show overexpression of Matrix Metalloproteinase, MMP10, in 86% of node-positive tongue tumors (n = 79; p < 0.00001). Additionally, global profiling for non-coding RNAs associated with node-positive tumors reveals that of the 11 significantly de-regulated miRNAs, miR-944 negatively regulates MMP10 by targeting its 3'-UTR. We demonstrate that proliferation, migration, and invasion of tongue cancer cells are suppressed by MMP10 knockdown or miR-944 overexpression. Further, we show that depletion of MMP10 prevents nodal metastases using an orthotopic tongue cancer mice model. In contrast, overexpression of MMP10 leads to opposite effects upregulating epithelial-mesenchymal-transition, mediated by a tyrosine kinase gene, AXL, to promote nodal and distant metastasis in vivo. Strikingly, AXL expression is essential and sufficient to mediate the functional consequence of MMP10 overexpression. Consistent with our findings, TCGA-HNSC data suggests overexpression of MMP10 or AXL positively correlates with poor survival of the patients. In conclusion, our results establish that the miR-944/MMP10/AXL- axis underlies lymph node metastases with potential therapeutic intervention and prediction of nodal metastases in tongue cancer patients.
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Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Ankita Pal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Risha Khandelwal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sujith Manavalan
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Kavita Sonawane
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Richa Vaish
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Poonam Gera
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Tissue Biorepository, Advanced Centre for Treatment Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Munita Bal
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Anil K D'Cruz
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
- Apollo Cancer Center, Apollo Hospitals, CBD Belapur, Navi Mumbai, 400614, India
| | - Sudhir Nair
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India.
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Rekhi B, Bal M, Dharavath B, Dutt A, Pai P. A Rare Case of A Low-Grade Inflammatory Leiomyosarcoma/Histiocyte-Rich Rhabdomyoblastic Tumor in the Neck of An Adolescent Male. Turk Patoloji Derg 2023; 39:154-160. [PMID: 35642345 PMCID: PMC10518194 DOI: 10.5146/tjpath.2022.01577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/19/2022] [Indexed: 11/18/2022] Open
Abstract
Inflammatory leiomyosarcoma (LMS) is a newly included rare tumor entity in the group of smooth muscle tumors in the recent WHO classification. Recent studies have shown skeletal muscle expression within this tumor and its proximity with histiocyte-rich rhabdomyoblastic tumor (HRRT). A 17-year-old male presented with a soft tissue lump over the back of his neck of one-year duration. Radiologically, a lesion measuring 5.9 cm in the largest dimension was seen, extending from the skull base up to the C2 vertebral level, abutting the occipital bone. The initial biopsy was reported as a fibrohistiocytic tumor at the referring laboratory. A microscopic review of the sections from the initial biopsy and subsequent resection revealed a well-circumscribed, cellular tumor composed of plump spindle and polygonal-shaped tumor cells with relatively bland nuclei, moderate to abundant eosinophilic cytoplasm and numerous interspersed histiocytes, including foam cells and lymphocytes. Immunohistochemically, the tumor cells were positive for desmin, MYOD1 and SMA, focally positive for myogenin, while negative for h-caldesmon, SOX10 and S100P. A diagnosis of inflammatory leiomyosarcoma/HRRT was offered. Subsequently, the tumor was tested for MYOD1 (L122R) mutation and was found to be negative. The patient underwent adjuvant radiation therapy and is free-of-disease at 12 months post-treatment. This case constitutes an extremely rare case of an inflammatory LMS/HRRT, identified in the neck region. This tumor should be differentiated from its close mimics, such as a spindle cell/sclerosing rhabdomyosarcoma, as the latter is treated more aggressively, including with chemotherapy, given its relatively poor prognosis.
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Affiliation(s)
- Bharat Rekhi
- Department of Pathology Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute (HBNI) University, Mumbai, India
| | - Munita Bal
- Department of Pathology Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute (HBNI) University, Mumbai, India
| | - Bhaskar Dharavath
- Homi Bhabha National Institute (HBNI) University, Mumbai, India; Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute (HBNI) University, Mumbai, India; Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Prathamesh Pai
- Department of Surgical Oncology (Head and Neck Disease Management Group), Tata Memorial Hospital, HBNI University, Mumbai, India
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Yadav N, Sunder R, Desai S, Dharavath B, Chandrani P, Godbole M, Dutt A. Progesterone modulates the DSCAM-AS1/miR-130a/ESR1 axis to suppress cell invasion and migration in breast cancer. Breast Cancer Res 2022; 24:97. [PMID: 36578092 PMCID: PMC9798554 DOI: 10.1186/s13058-022-01597-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A preoperative-progesterone intervention increases disease-free survival in patients with breast cancer, with an unknown underlying mechanism. We elucidated the role of non-coding RNAs in response to progesterone in human breast cancer. METHODS Whole transcriptome sequencing dataset of 30 breast primary tumors (10 tumors exposed to hydroxyprogesterone and 20 tumors as control) were re-analyzed to identify differentially expressed non-coding RNAs followed by real-time PCR analyses to validate the expression of candidates. Functional analyses were performed by genetic knockdown, biochemical, and cell-based assays. RESULTS We identified a significant downregulation in the expression of a long non-coding RNA, Down syndrome cell adhesion molecule antisense DSCAM-AS1, in response to progesterone treatment in breast cancer. The progesterone-induced expression of DSCAM-AS1 could be effectively blocked by the knockdown of progesterone receptor (PR) or treatment of cells with mifepristone (PR-antagonist). We further show that knockdown of DSCAM-AS1 mimics the effect of progesterone in impeding cell migration and invasion in PR-positive breast cancer cells, while its overexpression shows an opposite effect. Additionally, DSCAM-AS1 sponges the activity of miR-130a that regulates the expression of ESR1 by binding to its 3'-UTR to mediate the effect of progesterone in breast cancer cells. Consistent with our findings, TCGA analysis suggests that high levels of miR-130a correlate with a tendency toward better overall survival in patients with breast cancer. CONCLUSION This study presents a mechanism involving the DSCAM-AS1/miR-130a/ESR1 genomic axis through which progesterone impedes breast cancer cell invasion and migration. The findings highlight the utility of progesterone treatment in impeding metastasis and improving survival outcomes in patients with breast cancer.
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Affiliation(s)
- Neelima Yadav
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Pratik Chandrani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Medical Oncology Molecular Lab & Centre for Computational Biology, Bioinformatics and Crosstalk Lab, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India
| | - Mukul Godbole
- School of Biosciences and Technology, Faculty of Sciences and Health Sciences, MIT World Peace University, Pune, Maharashtra, 411038, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Rekhi B, Dodd L, Dharavath B, Dutt A. Cytomorphology of spindle cell/sclerosing rhabdomyosarcoma, including MYOD1 (LI22R) mutation result. Diagn Cytopathol 2022; 50:E367-E372. [PMID: 35929754 DOI: 10.1002/dc.25032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/07/2022]
Abstract
Spindle cell/sclerosing rhabdomyosarcoma (RMS), characterized by MYOD1 (L122R) mutation in a subset of cases is a newly described subtype of RMS. Presently, there is no documentation of cytomorphological features, especially of sclerosing RMS. Case 1: A 24-year-old male presented with pain and swelling in his wrist for a one-year duration. MRI revealed a well-defined soft tissue lesion measuring 5.3 cm, encasing the lower end of the ulna. Fine-needle aspiration cytology (FNAC) smears revealed clusters of tumor cells with round to oval to spindle-shaped nuclei, scant to moderate amount of cytoplasm with the wisps of the metachromatic stroma. Histopathological examination revealed a malignant tumor comprising cells with polygonal to spindle-shaped nuclei, arranged in a sclerotic stroma. Immunohistochemically, the tumor cells were positive for desmin, myogenin, and MYOD1. A diagnosis of sclerosing RMS was offered. Furthermore, the tumor revealed MYOD1 (L122R) mutation. Case 2: A 43-year-old male presented with a 4-month history of "nasal stuffiness" and pressure. Imaging revealed a poorly defined infiltrative lesion in his nasal cavity. FNAC smears revealed loose and tightly cohesive clusters of malignant cells with oval to spindle-shaped nuclei, a moderate amount of ill-defined bluish to finely vacuolated cytoplasm, and focal streak artifact with interspersed stromal fragments. Histopathological examination revealed a malignant tumor composed of oval to spindle-shaped nuclei, embedded in a variably hyalinized stroma. Immunohistochemically, the tumor cells were positive for desmin, and myogenin. Diagnosis of spindle cell/sclerosing RMS was offered. The present study constitutes one of the first documentation of cytomorphological features of two rare cases of spindle cell/sclerosing RMS. The differential diagnoses and treatment-related implications are presented.
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Affiliation(s)
- Bharat Rekhi
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute (HBNI) University, Mumbai, India
| | - Leslie Dodd
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Bhaskar Dharavath
- Homi Bhabha National Institute (HBNI) University, Mumbai, India
- Integrated Genmomics Laboratory, Advanced Centtre for Treatment, Research and Education in Cancer, Khargar, Navi Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute (HBNI) University, Mumbai, India
- Integrated Genmomics Laboratory, Advanced Centtre for Treatment, Research and Education in Cancer, Khargar, Navi Mumbai, India
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Noronha V, Chougule A, Chandrani P, Kaushal RK, Patil VM, Menon N, Kapoor A, Chopade S, Singh A, Shetty O, Dutt A, Banavali S, Prabhash K. Lung cancer with dual EGFR and ALK driver alterations at baseline: a retrospective observational cohort study. Acta Oncol 2022; 61:1143-1147. [PMID: 35972844 DOI: 10.1080/0284186x.2022.2109426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Vanita Noronha
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | | | - Pratik Chandrani
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | | | | | - Nandini Menon
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | | | - Sunil Chopade
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | - Ajaykumar Singh
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | - Amit Dutt
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | - Shripad Banavali
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
| | - Kumar Prabhash
- Tata Memorial Center, Homi Bhabha National Institute, Mumbai, India
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Joshi A, Butle A, Hait S, Mishra R, Trivedi V, Thorat R, Choughule A, Noronha V, Prabhash K, Dutt A. Osimertinib for lung cancer cells harboring low-frequency EGFR T790M mutation. Transl Oncol 2022; 22:101461. [PMID: 35653897 PMCID: PMC9156817 DOI: 10.1016/j.tranon.2022.101461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/25/2022] Open
Abstract
Osimertinib, a third-generation EGFR tyrosine kinase inhibitor, shows significant benefit among patients with EGFR T790M mutation at disease progression. We analyzed the whole exome sequence of 48 samples obtained from 16 lung cancer patients with a longitudinal follow-up: treatment-naïve-baseline primary tumors positive for EGFR activating-mutations, paired re-biopsies upon disease progression but negative for EGFR T790M mutation based on qPCR, and their matched normal blood samples. Our Next generation sequencing (NGS) analysis identified an additional set of 25% re-biopsy samples to harbor EGFR T790M mutation occurring at a low-allele frequency of 5% or less, undetectable by conventional qPCR-based assays. Notably, the clinical utility of osimertinib among patients harboring low-allele frequency of EGFR T790M in tissue biopsy upon disease progression remains less explored. We established erlotinib-resistant PC-9R cells and twenty single-cell sub-clones from erlotinib-sensitive lung cancer PC-9 cells using in vitro drug-escalation protocol. NGS and allele-specific PCR confirmed the low-allele frequency of EGFR T790M present at 5% with a 100-fold higher resistance to erlotinib in the PC-9R cells and its sub-clones. Additionally, luciferase tagged PC-9, and PC-9R cells were orthotopically injected through the intercostal muscle into NOD-SCID mice. The orthotopic lung tumors formed were observed by non-invasive bioluminescence imaging. Consistent with in vitro data, osimertinib, but not erlotinib, caused tumor regression in mice injected with PC-9R cells, while both osimertinib and erlotinib inhibited tumors in mice injected with PC-9 cells. Taken together, our findings could extend the benefit of osimertinib treatment to patients with low EGFR T790M mutation allele frequency on disease progression.
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Affiliation(s)
- Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210
| | - Supriya Hait
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210
| | - Vaishakhi Trivedi
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment Research and Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094.
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Behel V, Noronha V, Choughule A, Shetty O, Chandrani P, Kapoor A, Bondili SK, Bajpai J, Kumar R, Pai T, Bal M, Gurav M, Bapat P, Mittal N, Menon S, Patil V, Menon N, Dutt A, Prabhash K. Impact of Molecular Tumor Board on the Clinical Management of Patients With Cancer. JCO Glob Oncol 2022; 8:e2200030. [PMID: 35802838 PMCID: PMC9296182 DOI: 10.1200/go.22.00030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Multidisciplinary molecular tumor boards (MTBs) help in interpreting complex genomic data generated by molecular tumor profiling and improve patients' access to targeted therapies. The purpose of this study was to assess the impact of our institution's MTB on the clinical management of patients with cancer. METHODS This study was conducted at a tertiary cancer center in India. Cases to be discussed in the MTB were identified by molecular pathologists, scientists, or oncologists. On the basis of the clinical data and molecular test reports, a course of clinical management was recommended and made available to the treating oncologist. We determined the proportion of patients who were recommended a change in the clinical management. We also assessed compliance of the treating oncologists with MTB recommendations. RESULTS There were 339 discussions for 328 unique patients. The median age of the cohort was 54 years (range 17-87), and the majority of the patients were men (65.1%). Of 339 cases, 133 (39.2%) were recommended continuation of ongoing therapy while the remaining 206 (60.7%) were recommended a change in clinical management. Compliance with MTB recommendations for a change in clinical management was 58.5% (79 of 138 evaluable cases). Compliance and implementation for MTB's recommendation to start a new therapy in 104 evaluable cases were 60.5% and 44.2%, respectively. A total of 248 biopsies had at least one actionable mutation. A total of 646 mutations were identified in the cohort, with EGFR being the most frequently altered gene. CONCLUSION MTBs help in interpreting results of molecular tests, understanding the significance of molecular abnormalities, and assessing the benefits of available targeted therapies and clinical trials in the management of patients with targetable genetic alterations.
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Affiliation(s)
- Vichitra Behel
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Pratik Chandrani
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Akhil Kapoor
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
- Homi Bhabha Cancer Hospital, Varanasi, India
| | - Suresh Kumar Bondili
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Jyoti Bajpai
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Rajiv Kumar
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Trupti Pai
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Munita Bal
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Mamta Gurav
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Prachi Bapat
- Homi Bhabha National Institute, Mumbai, India
- Department of Molecular Pathology, Tata Memorial Hospital, Mumbai, India
| | - Neha Mittal
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Santosh Menon
- Homi Bhabha National Institute, Mumbai, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, India
| | - Vijay Patil
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Nandini Menon
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute, Mumbai, India
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
- Kumar Prabhash, Department of Medical Oncology, Tata Memorial Hospital, Dr. E Borges Road, Parel, Mumbai - 400 012, Maharashtra, India; e-mail:
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Desai S, Mishra R, Ahmad S, Hait S, Joshi A, Dutt A. TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants. Database (Oxford) 2022; 2022:6583650. [PMID: 35551364 PMCID: PMC9216475 DOI: 10.1093/database/baac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/05/2022] [Accepted: 04/12/2022] [Indexed: 02/05/2023]
Abstract
Cancer is a somatic disease. The lack of Indian-specific reference germline variation resources limits the ability to identify true cancer-associated somatic variants among Indian cancer patients. We integrate two recent studies, the GenomeAsia 100K and the Genomics for Public Health in India (IndiGen) program, describing genome sequence variations across 598 and 1029 healthy individuals of Indian origin, respectively, along with the unique variants generated from our in-house 173 normal germline samples derived from cancer patients to generate the Tata Memorial Centre-SNP database (TMC-SNPdb) 2.0. To show its utility, GATK/Mutect2-based somatic variant calling was performed on 224 in-house tumor samples to demonstrate a reduction in false-positive somatic variants. In addition to the ethnic-specific variants from GenomeAsia 100K and IndiGenomes databases, 305 132 unique variants generated from 173 in-house normal germline samples derived from cancer patients of Indian origin constitute the Indian specific, TMC-SNPdb 2.0. Of 305 132 unique variants, 11.13% were found in the coding region with missense variants (31.3%) as the most predominant category. Among the non-coding variations, intronic variants (49%) were the highest contributors. The non-synonymous to synonymous SNP ratio was observed to be 1.9, consistent with the previous version of TMC-SNPdb and literature. Using TMC SNPdb 2.0, we analyzed a whole-exome sequence from 224 in-house tumor samples (180 paired and 44 orphans). We show an average depletion of 3.44% variants per paired tumor and significantly higher depletion (P-value < 0.001) for orphan tumors (4.21%), demonstrating the utility of the rare, unique variants found in the ethnic-specific variant datasets in reducing the false-positive somatic mutations. TMC-SNPdb 2.0 is the most exhaustive open-source reference database of germline variants occurring across 1800 Indian individuals to analyze cancer genomes and other genetic disorders. The database and toolkit package is available for download at the following: Database URL http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNPdb2/TMCSNPdb2.html.
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Affiliation(s)
| | | | - Suhail Ahmad
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Supriya Hait
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Amit Dutt
- *Corresponding author: Tel: +91-22-27405056/30435056; Fax: +91-22-27405085;
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Desai S, Dharavath B, Manavalan S, Rane A, Redhu A, Sunder R, Butle A, Mishra R, Joshi A, Togar T, Apte S, Bala P, Chandrani P, Chopra S, Bashyam M, Banerjee A, Prabhash K, Nair S, Dutt A. Fusobacterium nucleatum is associated with inflammation and poor survival in early-stage HPV-negative tongue cancer. NAR Cancer 2022; 4:zcac006. [PMID: 35252868 PMCID: PMC8894079 DOI: 10.1093/narcan/zcac006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature. In addition, we identify a significant prevalence of Fusobacterium in head and neck tumors, comparable to colorectal tumors. The Fusobacterium-high subgroup of head and neck tumors occurs mutually exclusive to human papillomavirus, and is characterized by overexpression of miRNAs associated with inflammation, elevated innate immune cell fraction and nodal metastases. We validate the association of Fusobacterium with the inflammatory markers IL1B, IL6 and IL8, miRNAs hsa-mir-451a, hsa-mir-675 and hsa-mir-486-1, and MMP10 in the tongue tumor samples. A higher burden of Fusobacterium is also associated with poor survival, nodal metastases and extracapsular spread in tongue tumors defining a distinct subgroup of head and neck cancer.
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Sujith Manavalan
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Archana Kumari Redhu
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Trupti Togar
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Shruti Apte
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Pratyusha Bala
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad500039, Telangana, India
| | - Pratik Chandrani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Supriya Chopra
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
- Department of Radiation Oncology, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad500039, Telangana, India
| | - Anirban Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai 400012, Maharashtra, India
| | - Sudhir Nair
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, Maharashtra, India
| | - Amit Dutt
- To whom correspondence should be addressed. Tel: +91 22 27405056/30435056;
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Butle A, Joshi A, Noronha V, Prabhash K, Dutt A. Weekly osimertinib dosing prevents EGFR mutant tumor cells destined to home mouse lungs. Transl Oncol 2021; 14:101111. [PMID: 33993094 PMCID: PMC8236545 DOI: 10.1016/j.tranon.2021.101111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 02/05/2023] Open
Abstract
The recently conducted ADAURA trial concludes daily dosing of adjuvant osimertinib, a third-generation EGFR tyrosine kinase inhibitor (TKI), improves disease-free survival with stage IB/II/IIIA EGFR -mutated non-small cell lung cancer patients in comparison to placebo. We have developed a preclinical orthotopic mouse model, using luciferase tagged lung adenocarcinoma cells harboring EGFR TKI sensitive exon 19 deletion to model and extend trial implications comparing a weekly vs daily dosing outcome of osimertinib to a first-generation TKI- erlotinib. We find that 100% of mice in both the groups receiving osimertinib daily or weekly before injection of cells show a complete absence of homing of cells in mice's lungs from day three until day 18 post-injection of cells. On the other hand, 25% and 75% of mice receiving erlotinib daily and weekly before injecting cells show homing of cells to the lungs. The tumors observed in the lungs, when dissected at day 30, confirmed the colonization of the injected cells homing to the organ. Thus, our study establishes the efficacy of pretreatment with osimertinib in reducing tumor cells' homing to mouse lungs in an in vivo mouse model.
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Affiliation(s)
- Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210
| | - Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India 400012; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra, India 410210; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India 400094.
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Abstract
BACKGROUND Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate. RESULTS We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.0, to perform genomic analysis to understand the variability and dynamics of the virus. It adopts the recent clade nomenclature and demonstrates the clade prediction accuracy of 92.8%. IPD 2.0 also contains a SARS-CoV-2 updater module, allowing automatic upgrading of the variant database using genome sequences from GISAID. As a proof of principle, analyzing 208,911 SARS-CoV-2 genome sequences, we generate an extensive database of 2.58 million sample-wise variants. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil and data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. CONCLUSIONS A novel and dynamic feature of the SARS-CoV-2 module of IPD 2.0 makes it a contemporary tool to analyze the diverse and growing genomic strains of the virus and serve as a vital tool to help facilitate rapid genomic surveillance in a population to identify variants involved in breakthrough infections. IPD 2.0 is freely available from http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and the web-application is available at http://ipd.actrec.gov.in/ipdweb/ .
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
- Adjunct Faculty, Institute of Advanced Virology, Kerala State Council for Science, Technology and Environment, Govt. of Kerala, Thonnakkal, Kerala, 695317, India.
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Desai S, Rashmi S, Rane A, Dharavath B, Sawant A, Dutt A. An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Brief Bioinform 2021; 22:1065-1075. [PMID: 33479725 PMCID: PMC7929363 DOI: 10.1093/bib/bbaa437] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The analysis of the SARS-CoV-2 genome datasets has significantly advanced our understanding of the biology and genomic adaptability of the virus. However, the plurality of advanced sequencing datasets-such as short and long reads-presents a formidable computational challenge to uniformly perform quantitative, variant or phylogenetic analysis, thus limiting its application in public health laboratories engaged in studying epidemic outbreaks. We present a computational tool, Infectious Pathogen Detector (IPD), to perform integrated analysis of diverse genomic datasets, with a customized analytical module for the SARS-CoV-2 virus. The IPD pipeline quantitates individual occurrences of 1060 pathogens and performs mutation and phylogenetic analysis from heterogeneous sequencing datasets. Using IPD, we demonstrate a varying burden (5.055-999655.7 fragments per million) of SARS-CoV-2 transcripts across 1500 short- and long-read sequencing SARS-CoV-2 datasets and identify 4634 SARS-CoV-2 variants (~3.05 variants per sample), including 449 novel variants, across the genome with distinct hotspot mutations in the ORF1ab and S genes along with their phylogenetic relationships establishing the utility of IPD in tracing the genome isolates from the genomic data (as accessed on 11 June 2020). The IPD predicts the occurrence and dynamics of variability among infectious pathogens-with a potential for direct utility in the COVID-19 pandemic and beyond to help automate the sequencing-based pathogen analysis and in responding to public health threats, efficaciously. A graphical user interface (GUI)-enabled desktop application is freely available for download for the academic users at http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and for web-based processing at http://ipd.actrec.gov.in/ipdweb/ to generate an automated report without any prior computational know-how.
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | | | | | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aniket Sawant
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Amit Dutt
- Corresponding author: Dr Amit Dutt, Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai 410210, India. Tel.: +91-22-27405056/30435056; E-mail:
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Joshi A, Mishra R, Desai S, Chandrani P, Kore H, Sunder R, Hait S, Iyer P, Trivedi V, Choughule A, Noronha V, Joshi A, Patil V, Menon N, Kumar R, Prabhash K, Dutt A. Molecular characterization of lung squamous cell carcinoma tumors reveals therapeutically relevant alterations. Oncotarget 2021; 12:578-588. [PMID: 33796225 PMCID: PMC7984830 DOI: 10.18632/oncotarget.27905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/15/2021] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Unlike lung adenocarcinoma patients, there is no FDA-approved targeted-therapy likely to benefit lung squamous cell carcinoma patients. MATERIALS AND METHODS We performed survival analyses of lung squamous cell carcinoma patients harboring therapeutically relevant alterations identified by whole exome sequencing and mass spectrometry-based validation across 430 lung squamous tumors. RESULTS We report a mean of 11.6 mutations/Mb with a characteristic smoking signature along with mutations in TP53 (65%), CDKN2A (20%), NFE2L2 (20%), FAT1 (15%), KMT2C (15%), LRP1B (15%), FGFR1 (14%), PTEN (10%) and PREX2 (5%) among lung squamous cell carcinoma patients of Indian descent. In addition, therapeutically relevant EGFR mutations occur in 5.8% patients, significantly higher than as reported among Caucasians. In overall, our data suggests 13.5% lung squamous patients harboring druggable mutations have lower median overall survival, and 19% patients with a mutation in at least one gene, known to be associated with cancer, result in significantly shorter median overall survival compared to those without mutations. CONCLUSIONS We present the first comprehensive landscape of genetic alterations underlying Indian lung squamous cell carcinoma patients and identify EGFR, PIK3CA, KRAS and FGFR1 as potentially important therapeutic and prognostic target.
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Affiliation(s)
- Asim Joshi
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Rohit Mishra
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
| | - Sanket Desai
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Pratik Chandrani
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
- 5Centre for Computational Biology, Bioinformatics and Crosstalk Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
| | - Hitesh Kore
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
| | - Roma Sunder
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
| | - Supriya Hait
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Prajish Iyer
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Vaishakhi Trivedi
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Anuradha Choughule
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Vanita Noronha
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Amit Joshi
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Vijay Patil
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Nandini Menon
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Rajiv Kumar
- 3Department of Pathology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
| | - Kumar Prabhash
- 2Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, Maharashtra 400012, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
- Kumar Prabhash, email:
| | - Amit Dutt
- 1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India
- 4Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 410210, India
- Correspondence to: Amit Dutt, email:
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Kaur E, Nair J, Ghorai A, Mishra SV, Achareker A, Ketkar M, Sarkar D, Salunkhe S, Rajendra J, Gardi N, Desai S, Iyer P, Thorat R, Dutt A, Moiyadi A, Dutt S. Inhibition of SETMAR-H3K36me2-NHEJ repair axis in residual disease cells prevents glioblastoma recurrence. Neuro Oncol 2020; 22:1785-1796. [PMID: 32458986 PMCID: PMC7746947 DOI: 10.1093/neuonc/noaa128] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Residual disease of glioblastoma (GBM) causes recurrence. However, targeting residual cells has failed, due to their inaccessibility and our lack of understanding of their survival mechanisms to radiation therapy. Here we deciphered a residual cell-specific survival mechanism essential for GBM relapse. METHODS Therapy resistant residual (RR) cells were captured from primary patient samples and cell line models mimicking clinical scenario of radiation resistance. Molecular signaling of resistance in RR cells was identified using RNA sequencing, genetic and pharmacological perturbations, overexpression systems, and molecular and biochemical assays. Findings were validated in patient samples and an orthotopic mouse model. RESULTS RR cells form more aggressive tumors than the parental cells in an orthotopic mouse model. Upon radiation-induced damage, RR cells preferentially activated a nonhomologous end joining (NHEJ) repair pathway, upregulating Ku80 and Artemis while downregulating meiotic recombination 11 (Mre11) at protein but not RNA levels. Mechanistically, RR cells upregulate the Su(var)3-9/enhancer-of-zeste/trithorax (SET) domain and mariner transposase fusion gene (SETMAR), mediating high levels of H3K36me2 and global euchromatization. High H3K36me2 leads to efficiently recruiting NHEJ proteins. Conditional knockdown of SETMAR in RR cells induced irreversible senescence partly mediated by reduced H3K36me2. RR cells expressing mutant H3K36A could not retain Ku80 at double-strand breaks, thus compromising NHEJ repair, leading to apoptosis and abrogation of tumorigenicity in vitro and in vivo. Pharmacological inhibition of the NHEJ pathway phenocopied H3K36 mutation effect, confirming dependency of RR cells on the NHEJ pathway for their survival. CONCLUSIONS We demonstrate that the SETMAR-NHEJ regulatory axis is essential for the survival of clinically relevant radiation RR cells, abrogation of which prevents recurrence in GBM.
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Affiliation(s)
- Ekjot Kaur
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Jyothi Nair
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Atanu Ghorai
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Saket V Mishra
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Anagha Achareker
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Madhura Ketkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Debashmita Sarkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Sameer Salunkhe
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Jacinth Rajendra
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Nilesh Gardi
- Integrated Genomics Laboratory, ACTREC, Kharghar, Navi Mumbai, India
| | - Sanket Desai
- Integrated Genomics Laboratory, ACTREC, Kharghar, Navi Mumbai, India
| | - Prajish Iyer
- Integrated Genomics Laboratory, ACTREC, Kharghar, Navi Mumbai, India
| | - Rahul Thorat
- Laboratory Animal Facility, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Amit Dutt
- Integrated Genomics Laboratory, ACTREC, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Aliasgar Moiyadi
- Department of Neurosurgery, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Shilpee Dutt
- Integrated Genomics Laboratory, ACTREC, Kharghar, Navi Mumbai, India
- Corresponding Author: Dr. Shilpee Dutt, Principal Investigator, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India 410210 ()
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15
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Salunkhe S, Mishra SV, Ghorai A, Hole A, Chandrani P, Dutt A, Chilakapati M, Dutt S. Metabolic rewiring in drug resistant cells exhibit higher OXPHOS and fatty acids as preferred major source to cellular energetics. Biochim Biophys Acta Bioenerg 2020; 1861:148300. [PMID: 32858000 DOI: 10.1016/j.bbabio.2020.148300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023]
Abstract
Alteration in metabolic repertoire is associated with resistance phenotype. Although a common phenotype, not much efforts have been undertaken to design effective strategies to target the metabolic drift in cancerous cells with drug resistant properties. Here, we identified that drug resistant AML cell line HL-60/MX2 did not follow classical Warburg effect, instead these cells exhibited drastically low levels of aerobic glycolysis. Biochemical analysis confirmed reduced glucose consumption and lactic acid production by resistant population with no differences in glutamine consumption. Raman spectroscopy revealed increased lipid and cytochrome content in resistant cells which were also visualized as lipid droplets by Raman mapping, electron microscopy and lipid specific staining. Gene set enrichment analysis data from sensitive and resistant cell lines revealed significant enrichment of lipid metabolic pathways in HL-60/MX2 cells. Further, HL-60/MX2 possessed higher mitochondrial activity and increased OXPHOS suggesting the role of fatty acid metabolism as energy source which was confirmed by increased rate of fatty acid oxidation. Accordingly, OXPHOS inhibitor increased sensitivity of resistant cells to chemotherapeutic drug and fatty acid oxidation inhibitor Etomoxir reduced colony formation ability of resistant cells demonstrating the requirement of fatty acid metabolism and dependency on OXPHOS by resistant leukemic cells for survival and tumorigenicity.
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Affiliation(s)
- Sameer Salunkhe
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Saket V Mishra
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Atanu Ghorai
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Aarti Hole
- Chilakapati Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC), India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Murali Chilakapati
- Chilakapati Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India.
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16
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Desai S, Mishra SV, Joshi A, Sarkar D, Hole A, Mishra R, Dutt S, Chilakapati MK, Gupta S, Dutt A. Raman spectroscopy-based detection of RNA viruses in saliva: A preliminary report. J Biophotonics 2020; 13:e202000189. [PMID: 32609429 PMCID: PMC7361326 DOI: 10.1002/jbio.202000189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 02/05/2023]
Abstract
Several non-invasive Raman spectroscopy-based assays have been reported for rapid and sensitive detection of pathogens. We developed a novel statistical model for the detection of RNA viruses in saliva, based on an unbiased selection of a set of 65 Raman spectral features that mostly attribute to the RNA moieties, with a prediction accuracy of 91.6% (92.5% sensitivity and 88.8% specificity). Furthermore, to minimize variability and automate the downstream analysis of the Raman spectra, we developed a GUI-based analytical tool "RNA Virus Detector (RVD)." This conceptual framework to detect RNA viruses in saliva could form the basis for field application of Raman Spectroscopy in managing viral outbreaks, such as the ongoing COVID-19 pandemic. (http://www.actrec.gov.in/pi-webpages/AmitDutt/RVD/RVD.html).
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Saket V. Mishra
- Shilpee Dutt LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Asim Joshi
- Integrated Cancer Genomics LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Debashmita Sarkar
- Shilpee Dutt LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Arti Hole
- Chilkapati LaboratoryNavi MumbaiIndia
| | - Rohit Mishra
- Integrated Cancer Genomics LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Shilpee Dutt
- Shilpee Dutt LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Murali K. Chilakapati
- Chilkapati LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Sudeep Gupta
- Department of Medical OncologyAdvanced Centre for Treatment, Research, and Education in CancerNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
| | - Amit Dutt
- Integrated Cancer Genomics LaboratoryNavi MumbaiIndia
- Homi Bhabha National Institute, Training School Complex, Anushakti NagarMumbaiIndia
- Adjunct Faculty, Institute of Advanced VirologyKerala State Council for Science, Technology and Environment, Govt of KeralaThonnakkalKerala695317India
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17
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Dharavath B, Yadav N, Desai S, Sunder R, Mishra R, Ketkar M, Bhanshe P, Gupta A, Redhu AK, Patkar N, Dutt S, Gupta S, Dutt A. A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2. Heliyon 2020; 6:e04405. [PMID: 32665985 PMCID: PMC7341355 DOI: 10.1016/j.heliyon.2020.e04405] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 02/08/2023] Open
Abstract
Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.
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Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Neelima Yadav
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Madhura Ketkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Prasanna Bhanshe
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Anurodh Gupta
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Archana Kumari Redhu
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Nikhil Patkar
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sudeep Gupta
- Department of Medical Oncology, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Adjunct Faculty, Institute of Advanced Virology, Kerala State Council for Science, Technology and Environment, Govt of Kerala, Thonnakkal, Kerala, 695317, India
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18
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Togar T, Desai S, Mishra R, Terwadkar P, Ramteke M, Ranjan M, Kawle D, Sahoo B, Pal A, Upadhyay P, Dutt A. Identifying cancer driver genes from functional genomics screens. Swiss Med Wkly 2020; 150:w20195. [PMID: 32083704 DOI: 10.4414/smw.2020.20195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
With the emerging advances made in genomics and functional genomics approaches, there is a critical and growing unmet need to integrate plural datasets in order to identify driver genes in cancer. An integrative approach, with the convergence of multiple types of genetic evidence, can limit false positives through a posterior filtering strategy and reduce the need for multiple hypothesis testing to identify true cancer vulnerabilities. We performed a pooled shRNA screen against 906 human genes in the oral cancer cell line AW13516 in triplicate. The genes that were depleted in the screen were integrated with copy number alteration and gene expression data and ranked based on ROAST analysis, using an integrative scoring system, DepRanker, to compute a Rank Impact Score (RIS) for each gene. The RIS-based ranking of candidate driver genes was used to identify the putative oncogenes AURKB and TK1 as essential for oral cancer cell proliferation. We validated the findings, showing that shRNA mediated genetic knockdown of TK1 or pharmacological inhibition of AURKB by AZD-1152 HQPA in AW13516 cells could significantly impede their proliferation. Next we analysed alterations in AURKB and TK1 genes in head and neck cancer and their association with prognosis using data on 528 patients obtained from TCGA. Patients harbouring alterations in AURKB and TK1 genes were associated with poor survival. To summarise, we present DepRanker as a simple yet robust package with no third-party dependencies for the identification of potential driver genes from a pooled shRNA functional genomic screen by integrating results from RNAi screens with gene expression and copy number data. Using DepRanker, we identify AURKB and TK1 as potential therapeutic targets in oral cancer. DepRanker is in the public domain and available for download at http://www.actrec.gov.in/pi-webpages/AmitDutt/DepRanker/DepRanker.html.
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Affiliation(s)
- Trupti Togar
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India / Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Sanket Desai
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India / Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Rohit Mishra
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Prachi Terwadkar
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Manoj Ramteke
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Malika Ranjan
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Dhananjay Kawle
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Bikram Sahoo
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Ankita Pal
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Pawan Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India / Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India / Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
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19
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Noronha V, Patil VM, Joshi A, Menon N, Chougule A, Mahajan A, Janu A, Purandare N, Kumar R, More S, Goud S, Kadam N, Daware N, Bhattacharjee A, Shah S, Yadav A, Trivedi V, Behel V, Dutt A, Banavali SD, Prabhash K. Gefitinib Versus Gefitinib Plus Pemetrexed and Carboplatin Chemotherapy in EGFR-Mutated Lung Cancer. J Clin Oncol 2020; 38:124-136. [PMID: 31411950 DOI: 10.1200/jco.19.01154] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Standard first-line therapy for EGFR-mutant advanced non-small-cell lung cancer (NSCLC) is an epidermal growth factor receptor (EGFR)-directed oral tyrosine kinase inhibitor. Adding pemetrexed and carboplatin chemotherapy to an oral tyrosine kinase inhibitor may improve outcomes. PATIENTS AND METHODS This was a phase III randomized trial in patients with advanced NSCLC harboring an EGFR-sensitizing mutation and a performance status of 0 to 2 who were planned to receive first-line palliative therapy. Random assignment was 1:1 to gefitinib 250 mg orally per day (Gef) or gefitinib 250 mg orally per day plus pemetrexed 500 mg/m2 and carboplatin area under curve 5 intravenously every 3 weeks for four cycles, followed by maintenance pemetrexed (gefitinib plus chemotherapy [Gef+C]). The primary end point was progression-free survival (PFS); secondary end points included overall survival (OS), response rate, and toxicity. RESULTS Between 2016 and 2018, 350 patients were randomly assigned to Gef (n = 176) and Gef+C (n = 174). Twenty-one percent of patients had a performance status of 2, and 18% of patients had brain metastases. Median follow-up time was 17 months (range, 7 to 30 months). Radiologic response rates were 75% and 63% in the Gef+C and Gef arms, respectively (P = .01). Estimated median PFS was significantly longer with Gef+C than Gef (16 months [95% CI, 13.5 to 18.5 months] v 8 months [95% CI, 7.0 to 9.0 months], respectively; hazard ratio for disease progression or death, 0.51 [95% CI, 0.39 to 0.66]; P < .001). Estimated median OS was significantly longer with Gef+C than Gef (not reached v 17 months [95% CI, 13.5 to 20.5 months]; hazard ratio for death, 0.45 [95% CI, 0.31 to 0.65]; P < .001). Clinically relevant grade 3 or greater toxicities occurred in 51% and 25% of patients in the Gef+C and Gef arms, respectively (P < .001). CONCLUSION Adding pemetrexed and carboplatin chemotherapy to gefitinib significantly prolonged PFS and OS but increased toxicity in patients with NSCLC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Nandkumar Kadam
- Gunvati J. Kapoor Medical Relief Charitable Foundation, Mumbai, India
| | - Nilesh Daware
- Gunvati J. Kapoor Medical Relief Charitable Foundation, Mumbai, India
| | | | | | | | | | | | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
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20
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Sikder S, Kumari S, Kumar M, Sen S, Singhal NB, Chellappan S, Godbole M, Chandrani P, Dutt A, Gopinath KS, Kundu TK. Chromatin protein PC4 is downregulated in breast cancer to promote disease progression: Implications of miR-29a. Oncotarget 2019; 10:6855-6869. [PMID: 31839879 PMCID: PMC6901337 DOI: 10.18632/oncotarget.27325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/19/2019] [Indexed: 02/05/2023] Open
Abstract
The human transcriptional coactivator PC4 has numerous roles to play in the cell. Other than its transcriptional coactivation function, it facilitates chromatin organization, DNA damage repair, viral DNA replication, etc. Although it was found to be an essential protein in vivo, the importance of this multifunctional protein in the regulation of different cellular pathways has not been investigated in details, particularly in oncogenesis. In this study, PC4 downregulation was observed in a significant proportion of mammary tissues obtained from Breast cancer patient samples as well as in a subset of highly invasive and metastatic Breast cancer patient-derived cell lines. We have identified a miRNA, miR-29a which potentially reduce the expression of PC4 both in RNA and protein level. This miR-29a was found to be indeed overexpressed in a substantial number of Breast cancer patient samples and cell lines as well, suggesting one of the key mechanisms of PC4 downregulation. Stable Knockdown of PC4 in MCF7 cells induced its migratory as well as invasive properties. Furthermore, in an orthotopic breast cancer mice model system; we have shown that reduced expression of PC4 enhances the tumorigenic potential substantially. Absence of PC4 led to the upregulation of several genes involved in Epithelial to Mesenchymal Transition (EMT), indicating the possible mechanism of uniform tumour progression in the orthotropic mice. Collectively these data establish the role of PC4 in tumour suppression.
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Affiliation(s)
- Sweta Sikder
- 1Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sujata Kumari
- 1Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Manoj Kumar
- 1Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Shrinka Sen
- 1Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | | | - Mukul Godbole
- 3Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Mumbai, India
| | - Pratik Chandrani
- 3Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Mumbai, India
| | - Amit Dutt
- 3Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Mumbai, India
| | | | - Tapas K. Kundu
- 1Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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21
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Arora R, Rekhi B, Chandrani P, Krishna S, Dutt A. Merkel cell polyomavirus is implicated in a subset of Merkel cell carcinomas, in the Indian subcontinent. Microb Pathog 2019; 137:103778. [PMID: 31600537 PMCID: PMC7166130 DOI: 10.1016/j.micpath.2019.103778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Merkel cell carcinoma is a rare, lethal cancer histopathologically composed of cells showing similarity with mechanoreceptor Merkel cells. Merkel cell tumors manifest in two distinct forms. While a virus called Merkel cell polyomavirus is involved in the pathogenesis of one form of Merkel tumors, the other is driven by ultraviolet (UV)-linked mutations. In this study we investigated 18 cases, from the Indian population, of Merkel cell carcinoma for immunohistochemical (IHC) expression of Merkel cell polyomavirus (MCV) T antigen, including 12 cases tested by PCR, to identify viral etiopathology. We tested the tumors with two sensitive antibodies (CM2B4 and Ab3), targeting the viral large T antigen protein and with PCR primers targeting the N terminus of T antigen. Overall, we observed 38.8% (7/18) tumors displaying positive IHC expression of Merkel cell polyomavirus T antigen and 25% (3/12) tumors showing positive results, by both, immunohistochemistry and PCR. This constitutes the first report from India showing implication of MCV in Merkel cell carcinomas. Moreover, this is one of the larger series of Merkel cell carcinomas, tested for MCV, by both immunohistochemistry and PCR, in this part of the world. These results further indicate that a slightly more number of such cases in India are likely to be caused by UV-linked damage, as opposed to Merkel cell polyomavirus mediated tumorigenesis, which is definitely implicated in a subset of cases.
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Affiliation(s)
- Reety Arora
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India.
| | - Bharat Rekhi
- Department of Surgical Pathology, Tata Memorial Centre, Parel, Mumbai, Maharashtra, India.
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
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22
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Singh S, Kumar M, Kumar S, Sen S, Upadhyay P, Bhattacharjee S, M N, Tomar VS, Roy S, Dutt A, Kundu TK. The cancer-associated, gain-of-function TP53 variant P152Lp53 activates multiple signaling pathways implicated in tumorigenesis. J Biol Chem 2019; 294:14081-14095. [PMID: 31366730 PMCID: PMC6755804 DOI: 10.1074/jbc.ra118.007265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 06/21/2019] [Indexed: 02/05/2023] Open
Abstract
TP53 is the most frequently mutated tumor suppressor gene in many cancers, yet biochemical characterization of several of its reported mutations with probable biological significance have not been accomplished enough. Specifically, missense mutations in TP53 can contribute to tumorigenesis through gain-of-function of biochemical and biological properties that stimulate tumor growth. Here, we identified a relatively rare mutation leading to a proline to leucine substitution (P152L) in TP53 at the very end of its DNA-binding domain (DBD) in a sample from an Indian oral cancer patient. Although the P152Lp53 DBD alone bound to DNA, the full-length protein completely lacked binding ability at its cognate DNA motifs. Interestingly, P152Lp53 could efficiently tetramerize, and the mutation had only a limited impact on the structure and stability of full-length p53. Significantly, when we expressed this variant in a TP53-null cell line, it induced cell motility, proliferation, and invasion compared with a vector-only control. Also, enhanced tumorigenic potential was observed when P152Lp53-expressing cells were xenografted into nude mice. Investigating the effects of P152Lp53 expression on cellular pathways, we found that it is associated with up-regulation of several pathways, including cell-cell and cell-extracellular matrix signaling, epidermal growth factor receptor signaling, and Rho-GTPase signaling, commonly active in tumorigenesis and metastasis. Taken together, our findings provide a detailed account of the biochemical and cellular alterations associated with the cancer-associated P152Lp53 variant and establish it as a gain-of-function TP53 variant.
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Affiliation(s)
- Siddharth Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | | | - Shrinka Sen
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Sayan Bhattacharjee
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Naveen M
- BioCOS Life Sciences Pvt. Ltd., Bengaluru, India
| | - Vivek Singh Tomar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Amit Dutt
- Integrated Cancer Genomics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
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23
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Iyer P, Shrikhande SV, Ranjan M, Joshi A, Gardi N, Prasad R, Dharavath B, Thorat R, Salunkhe S, Sahoo B, Chandrani P, Kore H, Mohanty B, Chaudhari V, Choughule A, Kawle D, Chaudhari P, Ingle A, Banavali S, Gera P, Ramadwar MR, Prabhash K, Barreto SG, Dutt S, Dutt A. ERBB2 and KRAS alterations mediate response to EGFR inhibitors in early stage gallbladder cancer. Int J Cancer 2019; 144:2008-2019. [PMID: 30304546 PMCID: PMC6378102 DOI: 10.1002/ijc.31916] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/05/2023]
Abstract
The uncommonness of gallbladder cancer in the developed world has contributed to the generally poor understanding of the disease. Our integrated analysis of whole exome sequencing, copy number alterations, immunohistochemical, and phospho-proteome array profiling indicates ERBB2 alterations in 40% early-stage rare gallbladder tumors, among an ethnically distinct population not studied before, that occurs through overexpression in 24% (n = 25) and recurrent mutations in 14% tumors (n = 44); along with co-occurring KRAS mutation in 7% tumors (n = 44). We demonstrate that ERBB2 heterodimerizes with EGFR to constitutively activate the ErbB signaling pathway in gallbladder cells. Consistent with this, treatment with ERBB2-specific, EGFR-specific shRNA or with a covalent EGFR family inhibitor Afatinib inhibits tumor-associated characteristics of the gallbladder cancer cells. Furthermore, we observe an in vivo reduction in tumor size of gallbladder xenografts in response to Afatinib is paralleled by a reduction in the amounts of phospho-ERK, in tumors harboring KRAS (G13D) mutation but not in KRAS (G12V) mutation, supporting an essential role of the ErbB pathway. In overall, besides implicating ERBB2 as an important therapeutic target under neo-adjuvant or adjuvant settings, we present the first evidence that the presence of KRAS mutations may preclude gallbladder cancer patients to respond to anti-EGFR treatment, similar to a clinical algorithm commonly practiced to opt for anti-EGFR treatment in colorectal cancer.
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Affiliation(s)
- Prajish Iyer
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Shailesh V. Shrikhande
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Malika Ranjan
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Asim Joshi
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Nilesh Gardi
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Ratnam Prasad
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bhasker Dharavath
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
| | - Rahul Thorat
- Laboratory Animal FacilityAdvanced Centre for Treatment, Research and Education in Cancer, Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Sameer Salunkhe
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Shilpee laboratoryAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bikram Sahoo
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Pratik Chandrani
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Hitesh Kore
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Bhabani Mohanty
- Small Animal Imaging facilityAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Vikram Chaudhari
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Anuradha Choughule
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Dhananjay Kawle
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Pradip Chaudhari
- Small Animal Imaging facilityAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Arvind Ingle
- Laboratory Animal FacilityAdvanced Centre for Treatment, Research and Education in Cancer, Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Shripad Banavali
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Poonam Gera
- Tissue BiorepositoryAdvanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Mukta R. Ramadwar
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of PathologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Kumar Prabhash
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Department of Medical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Savio George Barreto
- Department of Gastrointestinal and Hepato‐Pancreato‐Biliary Surgical OncologyTata Memorial Centre, Ernest Borges MargMumbaiMaharashtraIndia
| | - Shilpee Dutt
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
- Shilpee laboratoryAdvanced Centre for Treatment Research Education In Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
| | - Amit Dutt
- Integrated Cancer Genomics LaboratoryAdvanced Centre for Treatment Research Education in Cancer (ACTREC), Tata Memorial CentreNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
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24
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Godbole M, Togar T, Patel K, Dharavath B, Yadav N, Janjuha S, Gardi N, Tiwary K, Terwadkar P, Desai S, Prasad R, Dhamne H, Karve K, Salunkhe S, Kawle D, Chandrani P, Dutt S, Gupta S, Badwe RA, Dutt A. Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1-NDRG1 axis in both PR-positive and -negative breast cancer cells. J Biol Chem 2018; 293:19263-19276. [PMID: 30337371 PMCID: PMC6298595 DOI: 10.1074/jbc.ra118.002894] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/13/2018] [Indexed: 02/05/2023] Open
Abstract
Preoperative progesterone intervention has been shown to confer a survival benefit to breast cancer patients independently of their progesterone receptor (PR) status. This observation raises the question how progesterone affects the outcome of PR-negative cancer. Here, using microarray and RNA-Seq-based gene expression profiling and ChIP-Seq analyses of breast cancer cells, we observed that the serum- and glucocorticoid-regulated kinase gene (SGK1) and the tumor metastasis-suppressor gene N-Myc downstream regulated gene 1 (NDRG1) are up-regulated and that the microRNAs miR-29a and miR-101-1 targeting the 3'-UTR of SGK1 are down-regulated in response to progesterone. We further demonstrate a dual-phase transcriptional and post-transcriptional regulation of SGK1 in response to progesterone, leading to an up-regulation of NDRG1 that is mediated by a set of genes regulated by the transcription factor AP-1. We found that NDRG1, in turn, inactivates a set of kinases, impeding the invasion and migration of breast cancer cells. In summary, we propose a model for the mode of action of progesterone in breast cancer. This model helps decipher the molecular basis of observations in a randomized clinical trial of the effect of progesterone on breast cancer and has therefore the potential to improve the prognosis of breast cancer patients receiving preoperative progesterone treatment.
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Affiliation(s)
- Mukul Godbole
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Trupti Togar
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | - Bhasker Dharavath
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | - Neelima Yadav
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | - Nilesh Gardi
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | | | - Sanket Desai
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
| | | | | | - Kunal Karve
- From the Integrated Cancer Genomics Laboratory and
| | - Sameer Salunkhe
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
- the Shilpee Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer
| | | | | | - Shilpee Dutt
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
- the Shilpee Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer
| | | | - Rajendra A Badwe
- the Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India and
| | - Amit Dutt
- From the Integrated Cancer Genomics Laboratory and
- the Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra 400094, India
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25
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Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell 2018; 34:792-806.e5. [PMID: 30449325 PMCID: PMC6248889 DOI: 10.1016/j.ccell.2018.09.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 02/08/2023]
Abstract
Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.
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Affiliation(s)
- Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Tarjani M Thaker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kate Senger
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Noelyn M Kljavin
- Molecular Oncology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037, India
| | - Sameer Phalke
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Prasanna Kumar
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc., Foster City, CA 94404, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ravi Gupta
- Bioinformatics Department, MeGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Arati Khanna-Gupta
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Sally E Trabucco
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ryan J Hartmaier
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ashish Singh
- Department of Medical Oncology, Christian Medical College and Hospital, Vellore 632004, India
| | | | | | - Amit Dutt
- ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Vijay Patil
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | - Amit Joshi
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | | | - James Ziai
- Pathology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Vedam Ramprasad
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA.
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26
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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 Med 2018; 7:5439-5447. [PMID: 30264478 PMCID: PMC6246960 DOI: 10.1002/cam4.1791] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/29/2018] [Accepted: 08/29/2018] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is increasingly gaining traction as an alternative to invasive solid tumor biopsies for prognosis, treatment decisions, and disease monitoring. Matched tumor-plasma samples were collected from 180 patients across different cancers with >90% of the samples below Stage IIIB. Tumors were profiled using next-generation sequencing (NGS) or quantitative PCR (qPCR), and the mutation status was queried in the matched plasma using digital platforms such as droplet digital PCR (ddCPR) or NGS for concordance. Tumor-plasma concordance of 82% and 32% was observed in advanced (Stage IIB and above) and early (Stage I to Stage IIA) stage samples, respectively. Interestingly, the overall survival outcomes correlated to presurgical/at-biopsy ctDNA levels. Baseline ctDNA stratified patients into three categories: (a) high ctDNA correlated with poor survival outcome, (b) undetectable ctDNA with good outcome, and (c) low ctDNA whose outcome was ambiguous. ctDNA could be a powerful tool for therapy decisions and patient management in a large number of cancers across a variety of stages.
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Affiliation(s)
- Sai A. Balaji
- Strand Life Sciences Pvt. Ltd.BangaloreKarnatakaIndia
- Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical FoundationBangaloreKarnatakaIndia
| | | | | | | | | | - Anuradha Arya
- Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical FoundationBangaloreKarnatakaIndia
| | - Aditya Chaubey
- Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical FoundationBangaloreKarnatakaIndia
| | - Arun Hariharan
- Strand Life Sciences Pvt. Ltd.BangaloreKarnatakaIndia
- Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical FoundationBangaloreKarnatakaIndia
| | | | - Manimala Sen
- Strand Life Sciences Pvt. Ltd.BangaloreKarnatakaIndia
| | | | | | | | | | | | - Suchitra Rao
- Mazumdar Shaw Medical CenterBangaloreKarnatakaIndia
| | | | | | - Amit Joshi
- Tata Memorial HospitalMumbaiMaharashtraIndia
| | | | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in CancerTata Memorial CentreKharghar, RaigadMaharashtraIndia
| | | | | | | | - Vaijayanti Gupta
- Strand Life Sciences Pvt. Ltd.BangaloreKarnatakaIndia
- Mazumdar Shaw Center for Translational Research, Mazumdar Shaw Medical FoundationBangaloreKarnatakaIndia
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27
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Salunkhe S, Chandran N, Chandrani P, Dutt A, Dutt S. CytoPred: 7-gene pair metric for AML cytogenetic risk prediction. Brief Bioinform 2018; 21:348-354. [PMID: 30380003 DOI: 10.1093/bib/bby100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 02/05/2023] Open
Abstract
Cytogenetic-based subjective prognostication of acute myeloid leukemia (AML) patients is a cumbersome process. Top scoring pair (TSP)-based decision tree using a robust analytical algorithm with statistical rigor offers a promising alternative. We describe CytoPred as a 7-gene pair signature based on the analysis of 2547 AML patient sample gene expression data using a modified TSP algorithm to estimate cytogenetic risk. The essential modification in TSP that helped computational encumbrance includes the filtration of gene pairs above random weighted guessers as well as sampling the gene pairs from the original gene pair pool to reduce overfitting issue. The CytoPred classifies AML cohort into clinically relevant `good' and `Int_poor' prognosis groups with distinct survival differences. The 7-gene pair was derived using 1248 AML patient samples in training set and 675 samples used for internal testing of the algorithm. The finest classifier 7-gene pair was picked from an initial pool size of 6.1 × 107 gene pairs that generated 57 687 decision trees. Further, for unbiased evaluation of CytoPred performance, we did an independent validation in 624 AML patient cohort. The CytoPred well qualifies the cutoffs for diagnostic application with 98.27% sensitivity and 99.27% specificity to predictive value in Int_poor class while 97.09% sensitivity and 91.74% specificity to predictive value for good class. Furthermore, CytoPred predicts almost identical survival probabilities like cytogenetics and its performance is not much influenced by various recurrent mutations as well as individual French-American-British (FAB) subtypes. In summary, we present a robust 7-gene pair-based metric to clinically prognosticate AML patients.
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Affiliation(s)
- Sameer Salunkhe
- Shilpee Dutt laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute,Training School Complex, Anushakti Nagar, Mumbai, India
| | - Naren Chandran
- Shilpee Dutt laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
- Homi Bhabha National Institute,Training School Complex, Anushakti Nagar, Mumbai, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
- Homi Bhabha National Institute,Training School Complex, Anushakti Nagar, Mumbai, India
| | - Shilpee Dutt
- Shilpee Dutt laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute,Training School Complex, Anushakti Nagar, Mumbai, India
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28
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Chatterjee S, Chaubal R, Maitra A, Gardi N, Dutt A, Gupta S, Badwe RA, Majumder PP, Pandey P. Pre-operative progesterone benefits operable breast cancer patients by modulating surgical stress. Breast Cancer Res Treat 2018; 170:431-438. [PMID: 29564740 DOI: 10.1007/s10549-018-4749-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/08/2018] [Indexed: 02/08/2023]
Abstract
PURPOSE We have reported a survival benefit of single injection of hydroxyprogesterone prior to surgery for primary tumour in patients with node-positive operable breast cancer. Hydroxyprogesterone was meant to recapitulate the luteal phase of menstrual cycle in these women. We wanted to understand the molecular basis of action of hydroxyprogesterone on primary breast tumours in a peri-operative setting. METHODS We performed whole transcriptome sequencing (RNA-Seq) of primary breast tumour samples collected from patients before and after hydroxyprogesterone exposure and controls. Paired breast cancer samples were obtained from patients who were given hydroxyprogesterone before surgery and a group of patients who were subjected to only surgery. RESULTS A test of significance between the two groups revealed 207 significantly altered genes, after correction for multiple hypothesis testing. We found significantly contrasting gene expression patterns in exposed versus unexposed groups; 142 genes were up-regulated post-surgery among exposed patients, and down-regulated post-surgery among unexposed patients. Significantly enriched pathways included genes that respond to progesterone, cellular stress, nonsense-mediated decay of proteins and negative regulation of inflammatory response. These results suggest that cellular stress is modulated by hydroxyprogesterone. Network analysis revealed that UBC, a mediator of stress response, to be a major node to which many of the significantly altered genes connect. CONCLUSIONS Our study suggests that pre-operative exposure to progesterone favourably modulates the effect of surgical stress, and this might underlie its beneficial effect when administered prior to surgery.
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Affiliation(s)
- Shatakshee Chatterjee
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India
| | - Rohan Chaubal
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India
| | - Nilesh Gardi
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Amit Dutt
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India
| | - Sudeep Gupta
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India.
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, 400012, India.
| | - Rajendra A Badwe
- Tata Memorial Centre/Hospital, Parel, Mumbai, 400012, India.
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai, 400012, India.
| | - Partha P Majumder
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India.
| | - Priyanka Pandey
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, 741251, West Bengal, India.
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29
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Rajendra J, Datta KK, Ud Din Farooqee SB, Thorat R, Kumar K, Gardi N, Kaur E, Nair J, Salunkhe S, Patkar K, Desai S, Goda JS, Moiyadi A, Dutt A, Venkatraman P, Gowda H, Dutt S. Enhanced proteasomal activity is essential for long term survival and recurrence of innately radiation resistant residual glioblastoma cells. Oncotarget 2018; 9:27667-27681. [PMID: 29963228 PMCID: PMC6021241 DOI: 10.18632/oncotarget.25351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/25/2018] [Indexed: 02/05/2023] Open
Abstract
Therapy resistance and recurrence in Glioblastoma is due to the presence of residual radiation resistant cells. However, because of their inaccessibility from patient biopsies, the molecular mechanisms driving their survival remain unexplored. Residual Radiation Resistant (RR) and Relapse (R) cells were captured using cellular radiation resistant model generated from patient derived primary cultures and cell lines. iTRAQ based quantitative proteomics was performed to identify pathways unique to RR cells followed by in vitro and in vivo experiments showing their role in radio-resistance. 2720 proteins were identified across Parent (P), RR and R population with 824 and 874 differential proteins in RR and R cells. Unsupervised clustering showed proteasome pathway as the most significantly deregulated pathway in RR cells. Concordantly, the RR cells displayed enhanced expression and activity of proteasome subunits, which triggered NFkB signalling. Pharmacological inhibition of proteasome activity led to impeded NFkB transcriptional activity, radio-sensitization of RR cells in vitro, and significantly reduced capacity to form orthotopic tumours in vivo. We demonstrate that combination of proteasome inhibitor with radio-therapy abolish the inaccessible residual resistant cells thereby preventing GBM recurrence. Furthermore, we identified first proteomic signature of RR cells that can be exploited for GBM therapeutics.
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Affiliation(s)
- Jacinth Rajendra
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Keshava K. Datta
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sheikh Burhan Ud Din Farooqee
- 3 Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Rahul Thorat
- 5 Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai, India
| | - Kiran Kumar
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Nilesh Gardi
- 4 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Ekjot Kaur
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Jyothi Nair
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Sameer Salunkhe
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Ketaki Patkar
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
| | - Sanket Desai
- 4 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Jayant Sastri Goda
- 8 Department of Radiation Oncology, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Aliasgar Moiyadi
- 6 Department of neurosurgery Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Amit Dutt
- 4 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Prasanna Venkatraman
- 3 Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Harsha Gowda
- 2 Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Shilpee Dutt
- 1 Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, India
- 7 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
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Abstract
This article traces the journey of one of the teams from India that has been actively managing and researching gallbladder cancer for more than a decade, providing insights into the work carried out and highlighting areas that warrant future research in this cancer traditionally known for its dismal outcomes.
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Affiliation(s)
- Savio G Barreto
- Hepatobiliary & Oesophagogastric Unit, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, Adelaide, South Australia, Australia
- College of Medicine & Public Health, Flinders University, South Australia, Australia
| | - Amit Dutt
- The Advanced Centre for Treatment, Research & Education in Cancer, Kharghar, Navi Mumbai, India & Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Bhawna Sirohi
- Department of Medical Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Shailesh V Shrikhande
- Department of Gastrointestinal & Hepato-Pancreato-Biliary Surgical Oncology, Tata Memorial Centre, Parel, Mumbai, India
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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 (Auckl) 2018; 9:1-11. [PMID: 29379323 PMCID: PMC5757203 DOI: 10.2147/lctt.s147841] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA), from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS) for EGFR mutation testing in non-small cell lung cancer (NSCLC). A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96%) between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically useful material for molecular testing in NSCLC.
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Affiliation(s)
| | | | | | | | | | - Amit Joshi
- Tata Memorial Centre, Parel, Mumbai, India
| | - Amit Dutt
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India
| | - Ravi Gupta
- MedGenome Labs Private Ltd,, Bangalore, India
| | - Ramprasad Vedam
- MedGenome Labs Private Ltd,, Bangalore, India
- Ramprasad Vedam, MedGenome Labs Private Ltd., 3 Floor, Narayana Netralaya Building, NH City, 258/A, Bommasandra Industrial Area, Bommasandra, Bangalore 560099, India, Email
| | - Kumar Prabhash
- Tata Memorial Centre, Parel, Mumbai, India
- Correspondence: Kumar Prabhash, Department of Medical Oncology, Tata Memorial Hospital, Dr E Borges Road, Parel, Mumbai 400 012, India, Email
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Godbole M, Chandrani P, Gardi N, Dhamne H, Patel K, Yadav N, Gupta S, Badwe R, Dutt A. miR-129-2 mediates down-regulation of progesterone receptor in response to progesterone in breast cancer cells. Cancer Biol Ther 2017; 18:801-805. [PMID: 28876975 PMCID: PMC5678702 DOI: 10.1080/15384047.2017.1373216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE Hormonal therapy is an important component of first line of treatment for breast cancer. Response to hormonal therapy is influenced by the progesterone receptor (PR)-status of breast cancer patients. However as an early effect, exposure to progesterone decreases expression of PR in breast cancer cells. An understanding of the mechanism underlying down-regulation of PR could help improve response to hormonal therapy. METHODS We performed small RNA sequencing of breast cancer cells for identification of microRNAs targeting PR in response to progesterone treatment. Biochemical approaches were used to validate the findings in breast cancer cells. RESULTS Analysis of small RNA sequencing of four breast cancer cell lines treated with progesterone revealed an up-regulation of miR-129-2 independent of the PR status of the cells. We show that miR-129-2 targets 3'UTR of PR to down-regulate its expression. Furthermore, inhibition of miR-129-2 expression rescues the down-regulation of PR in breast cancer cells. Also, the expression levels of miR-129-2 was observed to be elevated in patients with low expression of PR in the TCGA cohort (n = 359). CONCLUSION miR-129-2 mediates down-regulation of PR in breast cancer cells in response to progesterone, while anti-miR-129-2 could potentiate PR expression levels among patients with inadequate PR levels. Thus, modulation of activity of miR-129-2 could stabilize PR expression and potentially improve response to hormonal therapy under adjuvant or neo-adjuvant settings.
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Affiliation(s)
- Mukul Godbole
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
- Integrated Cancer Genomics Laboratory, Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Maharashtra, Mumbai, India
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
- Integrated Cancer Genomics Laboratory, Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Maharashtra, Mumbai, India
| | - Nilesh Gardi
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
- Integrated Cancer Genomics Laboratory, Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Maharashtra, Mumbai, India
| | - Hemant Dhamne
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
| | - Kuldeep Patel
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
| | - Neelima Yadav
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
- Integrated Cancer Genomics Laboratory, Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Maharashtra, Mumbai, India
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Maharashtra, Mumbai, India
- Sudeep Gupta Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai- 400012, India
| | - Rajendra Badwe
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Maharashtra, Mumbai, India
- Rajendra Badwe Department of Surgical Oncology, Tata Memorial Centre, Mumbai- 400012, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai, India
- Integrated Cancer Genomics Laboratory, Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Maharashtra, Mumbai, India
- CONTACT Amit Dutt Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
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Upadhyay P, Gardi N, Desai S, Chandrani P, Joshi A, Dharavath B, Arora P, Bal M, Nair S, Dutt A. Genomic characterization of tobacco/nut chewing HPV-negative early stage tongue tumors identify MMP10 asa candidate to predict metastases. Oral Oncol 2017; 73:56-64. [PMID: 28939077 PMCID: PMC5628952 DOI: 10.1016/j.oraloncology.2017.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/27/2017] [Accepted: 08/06/2017] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Nodal metastases status among early stage tongue squamous cell cancer patients plays a decisive role in the choice of treatment, wherein about 70% patients can be spared from surgery with an accurate prediction of negative pathological lymph node status. This underscores an unmet need for prognostic biomarkers to stratify the patients who are likely to develop metastases. MATERIALS AND METHODS We performed high throughput sequencing of fifty four samples derived from HPV negative early stage tongue cancer patients habitual of chewing betel nuts, areca nuts, lime or tobacco using whole exome (n=47) and transcriptome (n=17) sequencing that were analyzed using in-house computational tools. Additionally, gene expression meta-analyses were carried out for 253 tongue cancer samples. The candidate genes were validated using qPCR and immuno-histochemical analysis in an extended set of 50 early primary tongue cancer samples. RESULTS AND CONCLUSION Somatic analysis revealed a classical tobacco mutational signature C:G>A:T transversion in 53% patients that were mutated in TP53, NOTCH1, CDKN2A, HRAS, USP6, PIK3CA, CASP8, FAT1, APC, and JAK1. Similarly, significant gains at genomic locus 11q13.3 (CCND1, FGF19, ORAOV1, FADD), 5p15.33 (SHANK2, MMP16, TERT), and 8q24.3 (BOP1); and, losses at 5q22.2 (APC), 6q25.3 (GTF2H2) and 5q13.2 (SMN1) were observed in these samples. Furthermore, an integrated gene-expression analysis of 253 tongue tumors suggested an upregulation of metastases-related pathways and over-expression of MMP10 in 48% tumors that may be crucial to predict nodal metastases in early tongue cancer patients. In overall, we present the first descriptive portrait of somatic alterations underlying the genome of tobacco/nut chewing HPV-negative early tongue cancer, and identify MMP10 asa potential prognostic biomarker to stratify those likely to develop metastases.
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Affiliation(s)
- Pawan Upadhyay
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Nilesh Gardi
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India
| | - Sanket Desai
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Pratik Chandrani
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Asim Joshi
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Bhaskar Dharavath
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Priyanca Arora
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Munita Bal
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Sudhir Nair
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Amit Dutt
- Integrated Genomics Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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Bhat S, Gardi N, Hake S, Kotian N, Sawant S, Kannan S, Parmar V, Desai S, Dutt A, Joshi NN. Impact of intra-tumoral IL17A and IL32 gene expression on T-cell responses and lymph node status in breast cancer patients. J Cancer Res Clin Oncol 2017; 143:1745-1756. [PMID: 28470472 PMCID: PMC5863950 DOI: 10.1007/s00432-017-2431-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/20/2017] [Indexed: 02/08/2023]
Abstract
PURPOSE Pro-inflammatory cytokines such as Interleukin-17A (IL17A) and Interleukin-32 (IL32), known to enhance natural killer and T cell responses, are also elevated in human malignancies and linked to poor clinical outcomes. To address this paradox, we evaluated relation between IL17A and IL32 expression and other inflammation- and T cell response-associated genes in breast tumors. METHODS TaqMan-based gene expression analysis was carried out in seventy-eight breast tumors. The association between IL17A and IL32 transcript levels and T cell response genes, ER status as well as lymph node status was also examined in breast tumors from TCGA dataset. RESULTS IL17A expression was detected in 32.7% ER-positive and 84.6% ER-negative tumors, with higher expression in the latter group (26.2 vs 7.1-fold, p < 0.01). ER-negative tumors also showed higher expression of IL32 as opposed to ER-positive tumors (8.7 vs 2.5-fold, p < 0.01). Expression of both IL17A and IL32 genes positively correlated with CCL5, GNLY, TBX21, IL21 and IL23 transcript levels (p < 0.01). Amongst ER-positive tumors, higher IL32 expression significantly correlated with lymph node metastases (p < 0.05). Conversely, in ER-negative subtype, high IL17A and IL32 expression was seen in patients with negative lymph node status (p < 0.05). Tumors with high IL32 and IL17A expression showed higher expression of TH1 response genes studied, an observation validated by similar analysis in the TCGA breast tumors (n=1041). Of note, these tumors were characterized by low expression of a potentially immunosuppressive isoform of IL32 (IL32γ). CONCLUSION These results suggest that high expression of both IL17A and IL32 leads to enhancement of T cell responses. Our study, thus, provides basis for the emergence of strong T cell responses in an inflammatory milieu that have been shown to be associated with better prognosis in ER-negative breast cancer.
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Affiliation(s)
- Shreyas Bhat
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Nilesh Gardi
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Sujata Hake
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Nirupama Kotian
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sharada Sawant
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sadhana Kannan
- Epidemiology and Clinical Trials Unit, Clinical Research Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Vani Parmar
- Department of Surgical Oncology, Tata Memorial Hospital, Parel, Mumbai, Maharashtra, 400012, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Hospital, Parel, Mumbai, Maharashtra, 400012, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Amit Dutt
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Narendra N Joshi
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India.
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Godbole M, Tiwary K, Badwe R, Gupta S, Dutt A. Progesterone suppresses the invasion and migration of breast cancer cells irrespective of their progesterone receptor status - a short report. Cell Oncol (Dordr) 2017; 40:411-417. [PMID: 28653288 PMCID: PMC5537311 DOI: 10.1007/s13402-017-0330-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Pre-operative progesterone treatment of breast cancer has been shown to confer survival benefits to patients independent of their progesterone receptor (PR) status. The underlying mechanism and the question whether such an effect can also be observed in PR negative breast cancer cells remain to be resolved. METHODS We performed proteome profiling of PR-positive and PR-negative breast cancer cells in response to progesterone using a phospho-kinase array platform. Western blotting was used to validate the results. Cell-based phenotypic assays were conducted using PR-positive and PR-negative breast cancer cells to assess the effect of progesterone. RESULTS We found that progesterone induces de-phosphorylation of 12 out of 43 kinases tested, which are mostly involved in cellular invasion and migration regulation. Consistent with this observation, we found through cell-based phenotypic assays that progesterone inhibits the invasion and migration of breast cancer cells independent of their PR status. CONCLUSION Our results indicate that progesterone can inhibit breast cancer cell invasion and migration mediated by the de-phosphorylation of kinases. This inhibition appears to be independent of the PR status of the breast cancer cells. In a broader context, our study may provide a basis for an association between progesterone treatment and recurrence reduction in breast cancer patients, thereby providing a lead for modelling a randomized in vitro study.
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Affiliation(s)
- Mukul Godbole
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Kanishka Tiwary
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
| | - Rajendra Badwe
- Department of Surgical Oncology, Tata Memorial Centre, Tata Memorial Hospital, Mumbai, 400012, India.
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, 400012, India.
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India.
- Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India.
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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. Ann Oncol 2017; 28:597-603. [PMID: 27998968 PMCID: PMC5391708 DOI: 10.1093/annonc/mdw636] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths across the world. In this study, we present therapeutically relevant genetic alterations in lung adenocarcinoma of Indian origin. MATERIALS AND METHODS Forty-five primary lung adenocarcinoma tumors were sequenced for 676 amplicons using RainDance cancer panel at an average coverage of 1500 × (reads per million mapped reads). To validate the findings, 49 mutations across 23 genes were genotyped in an additional set of 363 primary lung adenocarcinoma tumors using mass spectrometry. NIH/3T3 cells over expressing mutant and wild-type FGFR3 constructs were characterized for anchorage independent growth, constitutive activation, tumor formation and sensitivity to FGFR inhibitors using in vitro and xenograft mouse models. RESULTS We present the first spectrum of actionable alterations in lung adenocarcinoma tumors of Indian origin, and shows that mutations of FGFR3 are present in 20 of 363 (5.5%) patients. These FGFR3 mutations are constitutively active and oncogenic when ectopically expressed in NIH/3T3 cells and using a xenograft model in NOD/SCID mice. Inhibition of FGFR3 kinase activity inhibits transformation of NIH/3T3 overexpressing FGFR3 constructs and growth of tumors driven by FGFR3 in the xenograft models. The reduction in tumor size in the mouse is paralleled by a reduction in the amounts of phospho-ERK, validating the in vitro findings. Interestingly, the FGFR3 mutations are significantly higher in a proportion of younger patients and show a trend toward better overall survival, compared with patients lacking actionable alterations or those harboring KRAS mutations. CONCLUSION We present the first actionable mutation spectrum in Indian lung cancer genome. These findings implicate FGFR3 as a novel therapeutic in lung adenocarcinoma.
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Affiliation(s)
- P. Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - K. Prabhash
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - V. Sethunath
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - M. Ranjan
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - J. Aich
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - H. Dhamne
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - D. N. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - B. Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Chandna
- AceProbe Technologies Pvt. Ltd, New Delhi, India
| | - R. Kumar
- Department of Pathology, Tata Memorial Hospital
| | - A. Joshi
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Noronha
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Patil
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Ramaswamy
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Karpe
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Thorat
- Department of Pathology, Tata Memorial Hospital
| | - P. Chaudhari
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Ingle
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Choughule
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Correspondence to: Dr Amit Dutt, Wellcome Trust/DBT India Alliance Intermediate Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai 410 210, India. Tel: +91-22-27405056; E-mail:
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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. Onco Targets Ther 2017; 10:2903-2908. [PMID: 28652772 PMCID: PMC5476719 DOI: 10.2147/ott.s133245] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND There are limited data available on the treatment and outcome of epidermal growth factor receptor (EGFR) exon 20-mutated lung cancer patients. Hence, we planned an analysis of the demographic details, clinical profile and survival of lung cancer patients with exon 20 mutations. We compared our results to patients with EGFR tyrosine kinase inhibitor (TKI)-sensitizing activating and EGFR/anaplastic lymphoma kinase (ALK)-negative mutations. METHODS This was a retrospective analysis of lung cancer patients who were treated at our center between January 2010 and August 2014. We reviewed the results of EGFR mutation testing by real-time polymerase chain reaction and Sanger sequencing. We also reviewed the data relating to baseline demographics, clinical profile, patient treatment and outcome measures in terms of response and overall survival (OS). RESULTS A total of 580 patients fulfilled the selection criteria. In all, 227 (39.1%) patients had EGFR TKI-sensitizing activating mutations, 20 (3.4%) patients had exon 20 insertion mutations and 333 patients were EGFR/ALK mutation negative (57.5%). The median OS was 5 months (95% confidence interval [CI] 0.17-9.8 months) in exon 20 insertion mutations, 16.1 months (95% CI 12.8-19.5 months) in EGFR TKI-sensitizing activating mutations and 10 months (95% CI 7.9-12.1 months) in EGFR/ALK mutation-negative patients. The median OS was significantly better for the EGFR TKI-sensitizing activating mutation group (P=0.000, log-rank test) and for the EGFR/ALK-negative group (P=0.037, log-rank test) compared to the exon 20-mutated group. CONCLUSION Exon 20 mutation results in a poorer OS prognosis compared to EGFR- and ALK-negative patients and patients harboring EGFR TKI-sensitizing activating mutations. The incidence of de novo exon 20 insertions was 3.4%. Different types of exon mutations seem to have different outcomes.
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Affiliation(s)
| | | | | | | | - Rajiv Kumar
- Department of Pathology, Tata Memorial Hospital
| | | | | | - Amit Dutt
- Dutt Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
| | - Kumar Prabhash
- Department of Medical Oncology-Molecular Laboratory
- Correspondence: Kumar Prabhash, Department of Medical Oncology, Medical Oncology Molecular Laboratory, Tata Memorial Hospital, 1108, HBB, Parel, Mumbai 400012, India Tel +91 92 2418 2898, Email
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Mittra I, Samant U, Sharma S, Raghuram GV, Saha T, Tidke P, Pancholi N, Gupta D, Prasannan P, Gaikwad A, Gardi N, Chaubal R, Upadhyay P, Pal K, Rane B, Shaikh A, Salunkhe S, Dutt S, Mishra PK, Khare NK, Nair NK, Dutt A. Cell-free chromatin from dying cancer cells integrate into genomes of bystander healthy cells to induce DNA damage and inflammation. Cell Death Discov 2017; 3:17015. [PMID: 28580170 PMCID: PMC5447133 DOI: 10.1038/cddiscovery.2017.15] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 02/05/2017] [Indexed: 02/08/2023] Open
Abstract
Bystander cells of the tumor microenvironment show evidence of DNA damage and inflammation that can lead to their oncogenic transformation. Mediator(s) of cell-cell communication that brings about these pro-oncogenic pathologies has not been identified. We show here that cell-free chromatin (cfCh) released from dying cancer cells are the key mediators that trigger both DNA damage and inflammation in the surrounding healthy cells. When dying human cancer cells were cultured along with NIH3T3 mouse fibroblast cells, numerous cfCh emerged from them and rapidly entered into nuclei of bystander NIH3T3 cells to integrate into their genomes. This led to activation of H2AX and inflammatory cytokines NFκB, IL-6, TNFα and IFNγ. Genomic integration of cfCh triggered global deregulation of transcription and upregulation of pathways related to phagocytosis, DNA damage and inflammation. None of these activities were observed when living cancer cells were co-cultivated with NIH3T3 cells. However, upon intravenous injection into mice, both dead and live cells were found to be active. Living cancer cells are known to undergo extensive cell death when injected intravenously, and we observed that cfCh emerging from both types of cells integrated into genomes of cells of distant organs and induced DNA damage and inflammation. γH2AX and NFκB were frequently co-expressed in the same cells suggesting that DNA damage and inflammation are closely linked pathologies. As concurrent DNA damage and inflammation is a potent stimulus for oncogenic transformation, our results suggest that cfCh from dying cancer cells can transform cells of the microenvironment both locally and in distant organs providing a novel mechanism of tumor invasion and metastasis. The afore-described pro-oncogenic pathologies could be abrogated by concurrent treatment with chromatin neutralizing/degrading agents suggesting therapeutic possibilities.
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Affiliation(s)
- Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
- Division of Laboratory Medicine, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
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| | - Urmila Samant
- Division of Laboratory Medicine, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Suvarna Sharma
- Division of Laboratory Medicine, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, India
| | - Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Tannistha Saha
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Pritishkumar Tidke
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Namrata Pancholi
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Deepika Gupta
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Preeti Prasannan
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Ashwini Gaikwad
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Nilesh Gardi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
| | - Rohan Chaubal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
| | - Kavita Pal
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Bhagyeshri Rane
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Alfina Shaikh
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Sameer Salunkhe
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
- DNA Repair and Chromatin Biology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Shilpee Dutt
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
- DNA Repair and Chromatin Biology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Pradyumna K Mishra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Naveen K Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Naveen K Nair
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 410210, India
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Rekhi B, Upadhyay P, Ramteke MP, Dutt A. MYOD1 (L122R) mutations are associated with spindle cell and sclerosing rhabdomyosarcomas with aggressive clinical outcomes. Mod Pathol 2016; 29:1532-1540. [PMID: 27562493 PMCID: PMC5133269 DOI: 10.1038/modpathol.2016.144] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 02/08/2023]
Abstract
Recurrent mutations in the myogenic transcription factor MYOD1 and PIK3CA were initially described in a subset of embryonal rhabdomyosarcomas. Recently, two independent studies demonstrated presence of MYODI (L122R) mutations as the basis to re-classify a spindle cell rhabdomyosarcoma, along with a sclerosing rhabdomyosarcoma, distinct from an embryonal rhabdomyosarcoma. We analyzed a much larger cohort of 49 primary rhabdomyosarcoma tumor samples of various subtypes, collected over a period of 9 years, for the presence of MYOD1 (L122R), PIK3CA (H1047), and PIK3CA (E542/E545) mutations, along with immunohistochemical analysis of desmin, myogenin, and MYOD1. Although activating PIK3CA mutations were absent across the sample set analyzed, we report 20% MYOD1 (L122R) mutation in rhabdomyosarcomas, found exclusively in 10 of 21 spindle cell and sclerosing rhabdomyosarcomas, occurring mostly in the head and neck region along with extremity sites (64%), than the paratesticular and intra-abdominal sites. Furthermore, while all 10 MYOD1 mutant spindle cell and sclerosing rhabdomyosarcoma samples showed diffuse and strong MYOD1 immunoexpression, 7 of 31 samples of rhabdomyosarcoma with wild-type MYOD1 were negative for MYOD1 expression. Clinically, a striking correlation was found between MYOD1 mutation and the clinical outcomes available for 15 of 21 cases: 5 of 7 patients with spindle cell and sclerosing rhabdomyosarcomas, harboring MYOD1 mutation, were alive-with-disease and 2 of 8 patients with spindle cell and sclerosing rhabdomyosarcomas, with mutant MYOD1, were free-of-disease. Taken together, we present the first report of MYOD1 (L122R) mutation in the largest cohort of 49 rhabdomyosarcomas reported so far, that are associated with a relatively aggressive clinical course. Moreover, consistent with the earlier two studies, this study further reinforces a relationship between spindle cell and the sclerosing rhabdomyosarcoma-now recognized as a single subtype, distinct from an embryonal rhabdomyosarcoma.
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Affiliation(s)
- Bharat Rekhi
- Department of Surgical Pathology, Tata Memorial Centre, Parel, Mumbai, Maharashtra, India
| | - Pawan Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar, Mumbai, India
| | - Manoj P Ramteke
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar, Mumbai, India
- Wellcome Trust/ DBT India Alliance Intermediate Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai, Maharashtra 410 210, India. E-mail:
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Upadhyay P, Nair S, Kaur E, Aich J, Dani P, Sethunath V, Gardi N, Chandrani P, Godbole M, Sonawane K, Prasad R, Kannan S, Agarwal B, Kane S, Gupta S, Dutt S, Dutt A. Notch pathway activation is essential for maintenance of stem-like cells in early tongue cancer. Oncotarget 2016; 7:50437-50449. [PMID: 27391340 PMCID: PMC5226594 DOI: 10.18632/oncotarget.10419] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/07/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Notch pathway plays a complex role depending on cellular contexts: promotes stem cell maintenance or induces terminal differentiation in potential cancer-initiating cells; acts as an oncogene in lymphocytes and mammary tissue or plays a growth-suppressive role in leukemia, liver, skin, and head and neck cancer. Here, we present a novel clinical and functional significance of NOTCH1 alterations in early stage tongue squamous cell carcinoma (TSCC). PATIENTS AND METHODS We analyzed the Notch signaling pathway in 68 early stage TSCC primary tumor samples by whole exome and transcriptome sequencing, real-time PCR based copy number, expression, immuno-histochemical, followed by cell based biochemical and functional assays. RESULTS We show, unlike TCGA HNSCC data set, NOTCH1 harbors significantly lower frequency of inactivating mutations (4%); is somatically amplified; and, overexpressed in 31% and 37% of early stage TSCC patients, respectively. HNSCC cell lines over expressing NOTCH1, when plated in the absence of attachment, are enriched in stem cell markers and form spheroids. Furthermore, we show that inhibition of NOTCH activation by gamma secretase inhibitor or shRNA mediated knockdown of NOTCH1 inhibits spheroid forming capacity, transformation, survival and migration of the HNSCC cells suggesting an oncogenic role of NOTCH1 in TSCC. Clinically, Notch pathway activation is higher in tumors of non-smokers compared to smokers (50% Vs 18%, respectively, P=0.026) and is also associated with greater nodal positivity compared to its non-activation (93% Vs 64%, respectively, P=0.029). CONCLUSION We anticipate that these results could form the basis for therapeutic targeting of NOTCH1 in tongue cancer.
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Affiliation(s)
- Pawan Upadhyay
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Sudhir Nair
- 2 Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre,Mumbai- 4100012, India
| | - Ekjot Kaur
- 3 Shilpee Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Jyotirmoi Aich
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Prachi Dani
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Vidyalakshmi Sethunath
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Nilesh Gardi
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Pratik Chandrani
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Mukul Godbole
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Kavita Sonawane
- 2 Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre,Mumbai- 4100012, India
| | - Ratnam Prasad
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Sadhana Kannan
- 4 Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Beamon Agarwal
- 5 Department of Pathology, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Shubhada Kane
- 6 Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai- 400012, India
| | - Sudeep Gupta
- 7 Department of Medical Oncology, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Mumbai- 400012, India
| | - Shilpee Dutt
- 3 Shilpee Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
| | - Amit Dutt
- 1 Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education In Cancer, Tata Memorial Centre, Navi Mumbai- 410210, India
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Kaur E, Sahu A, Hole AR, Rajendra J, Chaubal R, Gardi N, Dutt A, Moiyadi A, Krishna CM, Dutt S. Unique spectral markers discern recurrent Glioblastoma cells from heterogeneous parent population. Sci Rep 2016; 6:26538. [PMID: 27221528 PMCID: PMC4879554 DOI: 10.1038/srep26538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 05/04/2016] [Indexed: 02/08/2023] Open
Abstract
An inability to discern resistant cells from bulk tumour cell population contributes to poor prognosis in Glioblastoma. Here, we compared parent and recurrent cells generated from patient derived primary cultures and cell lines to identify their unique molecular hallmarks. Although morphologically similar, parent and recurrent cells from different samples showed variable biological properties like proliferation and radiation resistance. However, total RNA-sequencing revealed transcriptional landscape unique to parent and recurrent populations. These data suggest that global molecular differences but not individual biological phenotype could differentiate parent and recurrent cells. We demonstrate that Raman Spectroscopy a label-free, non-invasive technique, yields global information about biochemical milieu of recurrent and parent cells thus, classifying them into distinct clusters based on Principal-Component-Analysis and Principal-Component-Linear-Discriminant-Analysis. Additionally, higher lipid related spectral peaks were observed in recurrent population. Importantly, Raman spectroscopic analysis could further classify an independent set of naïve primary glioblastoma tumour tissues into non-responder and responder groups. Interestingly, spectral features from the non-responder patient samples show a considerable overlap with the in-vitro generated recurrent cells suggesting their similar biological behaviour. This feasibility study necessitates analysis of a larger cohort of naïve primary glioblastoma samples to fully envisage clinical utility of Raman spectroscopy in predicting therapeutic response.
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Affiliation(s)
- Ekjot Kaur
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Aditi Sahu
- Chilakapati Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Arti R. Hole
- Chilakapati Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Jacinth Rajendra
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Rohan Chaubal
- Integrated Cancer Genomics Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Nilesh Gardi
- Integrated Cancer Genomics Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - C. Murali Krishna
- Chilakapati Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai 410210, India
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Upadhyay P, Gardi N, Desai S, Sahoo B, Singh A, Togar T, Iyer P, Prasad R, Chandrani P, Gupta S, Dutt A. TMC-SNPdb: an Indian germline variant database derived from whole exome sequences. Database (Oxford) 2016; 2016:baw104. [PMID: 27402678 PMCID: PMC4940432 DOI: 10.1093/database/baw104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/08/2016] [Indexed: 02/05/2023]
Abstract
Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html.
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Affiliation(s)
- Pawan Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Nilesh Gardi
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Sanket Desai
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Bikram Sahoo
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Ankita Singh
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Trupti Togar
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Prajish Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Ratnam Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Pratik Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, Maharashtra 410012, India
| | - Amit Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment Research Education in Cancer (ACTREC)
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Iyer P, Barreto SG, Sahoo B, Chandrani P, Ramadwar MR, Shrikhande SV, Dutt A. Non-typhoidal Salmonella DNA traces in gallbladder cancer. Infect Agent Cancer 2016; 11:12. [PMID: 26941832 PMCID: PMC4776363 DOI: 10.1186/s13027-016-0057-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We earlier proposed a genetic model for gallbladder carcinogenesis and its dissemination cascade. However, the association of gallbladder cancer and 'inflammatory stimulus' to drive the initial cascade in the model remained unclear. A recent study suggested infection with Salmonella can lead to changes in the host signalling pathways in gallbladder cancer. FINDINGS We examined the whole exomes of 26 primary gall bladder tumour and paired normal samples for presence of 143 HPV (Human papilloma virus) types along with 6 common Salmonella serotypes (S. typhi Ty2, S. typhi CT18, S. typhimurium LT2, S. choleraesuis SCB67, S. paratyphi TCC, and S. paratyphi SPB7) using a computational subtraction pipeline based on the HPVDetector, we recently described. Based on our evaluation of 26 whole exome gallbladder primary tumours and matched normal samples: association of typhoidal Salmonella species were found in 11 of 26 gallbladder cancer samples, and non-typhoidal Salmonella species in 12 of 26 gallbladder cancer, with 6 samples were found co-infected with both. CONCLUSIONS We present the first evidence to support the association of non-typhoidal Salmonella species along with typhoidal strains in gallbladder cancer. Salmonella infection in the chronic carrier state fits the role of the 'inflammatory stimulus' in the genetic model for gallbladder carcinogenesis that may play a role in gallbladder cancer analogous to Helicobacter pylori in gastric cancer.
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Affiliation(s)
- Prajish Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Savio George Barreto
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology, and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta, The Medicity, Gurgaon, India
| | - Bikram Sahoo
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Pratik Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Mukta R. Ramadwar
- Department of Pathology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Shailesh V. Shrikhande
- Department of Gastrointestinal and Hepato-Pancreato-Biliary Surgical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
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Chandrani P, Upadhyay P, Iyer P, Tanna M, Shetty M, Raghuram GV, Oak N, Singh A, Chaubal R, Ramteke M, Gupta S, Dutt A. Integrated genomics approach to identify biologically relevant alterations in fewer samples. BMC Genomics 2015; 16:936. [PMID: 26572163 PMCID: PMC4647579 DOI: 10.1186/s12864-015-2138-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/23/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Several statistical tools have been developed to identify genes mutated at rates significantly higher than background, indicative of positive selection, involving large sample cohort studies. However, studies involving smaller sample sizes are inherently restrictive due to their limited statistical power to identify low frequency genetic variations. RESULTS We performed an integrated characterization of copy number, mutation and expression analyses of four head and neck cancer cell lines - NT8e, OT9, AW13516 and AW8507 - by applying a filtering strategy to prioritize for genes affected by two or more alterations within or across the cell lines. Besides identifying TP53, PTEN, HRAS and MET as major altered HNSCC hallmark genes, this analysis uncovered 34 novel candidate genes altered. Of these, we find a heterozygous truncating mutation in Nuclear receptor binding protein, NRBP1 pseudokinase gene, identical to as reported in other cancers, is oncogenic when ectopically expressed in NIH-3 T3 cells. Knockdown of NRBP1 in an oral carcinoma cell line bearing NRBP1 mutation inhibit transformation and survival of the cells. CONCLUSIONS In overall, we present the first comprehensive genomic characterization of four head and neck cancer cell lines established from Indian patients. We also demonstrate the ability of integrated analysis to uncover biologically important genetic variation in studies involving fewer or rare clinical specimens.
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Affiliation(s)
- Pratik Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Pawan Upadhyay
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Prajish Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Mayur Tanna
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Madhur Shetty
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Gorantala Venkata Raghuram
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Ninad Oak
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Ankita Singh
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Rohan Chaubal
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Manoj Ramteke
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, Maharashtra, India.
| | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, Maharashtra, 410210, India.
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Chandrani P, Kulkarni V, Iyer P, Upadhyay P, Chaubal R, Das P, Mulherkar R, Singh R, Dutt A. NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome. Br J Cancer 2015; 112:1958-65. [PMID: 25973533 PMCID: PMC4580395 DOI: 10.1038/bjc.2015.121] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool 'HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. METHODS We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a 'quick mode' to identify presence of HPV types and an 'integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. RESULTS On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. CONCLUSIONS HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.
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Affiliation(s)
- P Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - V Kulkarni
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Upadhyay
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Chaubal
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - P Das
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Mulherkar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - R Singh
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - A Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India
- E-mail:
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Abstract
This article alludes to the findings of Tomasetti and Vogelstein and argues that for clinicians and scientists no matter how difficult understanding the pathogenesis of cancer may be, they remain the only hope for patients suffering from the disease. Data citing wide differences in cancer incidence in different parts of the world is presented to drive home the point that 'Bad luck' is not a good enough explanation for cancer pathogenesis. There remains a lot to be uncovered in cancer and clinicians and scientists should strive to this end.
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Affiliation(s)
- Savio George Barreto
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta-The Medicity, Gurgaon, Haryana, India
| | - Merlyn Barreto
- Consultant Obstetrician and Gynaecologist, Gurgaon, Haryana, India
| | - Rohan Chaubal
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India
| | - Amit Dutt
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India
- Address for correspondence: Dr. Amit Dutt, Principal Investigator, Wellcome Trust/ DBT India Alliance Int Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai-410 210, Mumbai, India. E-mail:
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Mittra I, Khare NK, Raghuram GV, Chaubal R, Khambatti F, Gupta D, Gaikwad A, Prasannan P, Singh A, Iyer A, Singh A, Upadhyay P, Nair NK, Mishra PK, Dutt A. Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes. J Biosci 2015; 40:91-111. [PMID: 25740145 PMCID: PMC5779614 DOI: 10.1007/s12038-015-9508-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored.We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their own that are deleterious to healthy cells of the body. Fragmented DNA and chromatin (DNAfs and Cfs) isolated from blood of cancer patients and healthy volunteers are readily taken up by a variety of cells in culture to be localized in their nuclei within a few minutes. The intra-nuclear DNAfs and Cfs associate themselves with host cell chromosomes to evoke a cellular DNA-damage-repair-response (DDR) followed by their incorporation into the host cell genomes. Whole genome sequencing detected the presence of tens of thousands of human sequence reads in the recipient mouse cells. Genomic incorporation of DNAfs and Cfs leads to dsDNA breaks and activation of apoptotic pathways in the treated cells. When injected intravenously into Balb/C mice, DNAfs and Cfs undergo genomic integration into cells of their vital organs resulting in activation of DDR and apoptotic proteins in the recipient cells. Cfs have significantly greater activity than DNAfs with respect to all parameters examined, while both DNAfs and Cfs isolated from cancer patients are more active than those from normal volunteers. All the above pathological actions of DNAfs and Cfs described above can be abrogated by concurrent treatment with DNase I and/or anti-histone antibody complexed nanoparticles both in vitro and in vivo. Taken together, our results suggest that circulating DNAfs and Cfs are physiological, continuously arising, endogenous DNA damaging agents with implications to ageing and a multitude of human pathologies including initiation of cancer.
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Affiliation(s)
- Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India,
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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. F1000Res 2015; 4:160. [PMID: 27127615 PMCID: PMC4830212 DOI: 10.12688/f1000research.6663.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 02/05/2023] Open
Abstract
Molecular diagnostics has changed the way lung cancer patients are treated worldwide. Of several different testing methods available, PCR followed by directed sequencing and amplification refractory mutation system (ARMS) are the two most commonly used diagnostic methods worldwide to detect mutations at KRAS exon 2 and EGFR kinase domain exons 18-21 in lung cancer. Compared to ARMS, the PCR followed by directed sequencing approach is relatively inexpensive but more cumbersome to perform. Moreover, with a limiting amount of genomic DNA from clinical formalin-fixed, paraffin-embedded (FFPE) specimens or fine biopsies of lung tumors, multiple rounds of PCR and sequencing reactions often get challenging. Here, we report a cost-effective single multiplex-PCR based method, CRE (for Co-amplification of five K RAS and E GFR exons), followed by concatenation of the PCR product as a single linear fragment for direct sequencing. CRE is a robust protocol that can be adapted for routine use in clinical diagnostics with reduced variability, cost and turnaround time requiring a minimal amount of template DNA extracted from FFPE or fresh frozen tumor samples. As a proof of principle, CRE is able to detect the activating EGFR L858R and T790M EGFR mutations in lung cancer cell line and primary tumors.
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Affiliation(s)
- Manoj P. Ramteke
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
| | - Kuldeep J Patel
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
| | - Mukul Godbole
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
| | - Maulik Vyas
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
| | - Kunal Karve
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, Maharashtra, 400012, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, Maharashtra, 400012, India
| | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, 410210, India
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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. Br J Cancer 2014; 111:2203-4. [PMID: 25117816 PMCID: PMC4260019 DOI: 10.1038/bjc.2014.401] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- A Choughule
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - R Sharma
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - V Trivedi
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - A Thavamani
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - V Noronha
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - A Joshi
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - S Desai
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - P Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - P Sundaram
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
| | - S Utture
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - N Jambhekar
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - S Gupta
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
| | - J Aich
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
- E-mail: or E-mail: or ; E-mail:
| | - K Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Center, Mumbai, India
- E-mail: or E-mail: or ; E-mail:
| | - A Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Navi Mumbai, India
- E-mail: or E-mail: or ; E-mail:
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Abstract
Gallbladder cancer, although regarded as the most common malignancy of the biliary tract, continues to be associated with a dismal overall survival even in the present day. While complete surgical removal of the tumour offers a good chance of cure, only a fraction of the patients are amenable to curative surgery owing to their delayed presentation. Moreover, the current contribution of adjuvant therapies towards prolonging survival is marginal, at best. Thus, understanding the biology of the disease will not only enable a better appreciation of the pathways of progression but also facilitate the development of an accurate genetic model for gallbladder carcinogenesis and dissemination. This review provides an updated, evidence-based model of the pathways of carcinogenesis in gallbladder cancer and its dissemination. The model proposed could serve as the scaffolding for elucidation of the molecular mechanisms involved in gallbladder carcinogenesis. A better understanding of the pathways involved in gallbladder tumorigenesis will serve to identify patients at risk for the cancer (and who thus could be offered prophylactic cholecystectomy) as well as aid oncologists in planning the most suitable treatment for a particular patient, thereby setting us on the vanguard of transforming the current treatment paradigm for gallbladder cancer.
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Affiliation(s)
- S G Barreto
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology, and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta, The Medicity, Gurgaon
| | - A Dutt
- The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - A Chaudhary
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology, and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta, The Medicity, Gurgaon
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