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Dharavath B, Butle A, Chaudhary A, Pal A, Desai S, Chowdhury A, Thorat R, Upadhyay P, Nair S, Dutt A. Recurrent UBE3C-LRP5 translocations in head and neck cancer with therapeutic implications. NPJ Precis Oncol 2024; 8:63. [PMID: 38438481 PMCID: PMC10912599 DOI: 10.1038/s41698-024-00555-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional characterization of UBE3C-LRP5 translocation in head and neck cancer. Our whole transcriptome sequencing and RT-PCR analysis of 151 head and neck cancer tumor samples identified the LRP5-UBE3C and UBE3C-LRP5 fusion transcripts in 5.3% of patients of Indian origin (n = 151), and UBE3C-LRP5 fusion transcripts in 1.2% of TCGA-HNSC patients (n = 502). Further, whole genome sequencing identified the breakpoint of UBE3C-LRP5 translocation. We demonstrate that UBE3C-LRP5 fusion is activating in vitro and in vivo, and promotes the proliferation, migration, and invasion of head and neck cancer cells. In contrast, depletion of UBE3C-LRP5 fusion suppresses the clonogenic, migratory, and invasive potential of the cells. The UBE3C-LRP5 fusion activates the Wnt/β-catenin signaling by promoting nuclear accumulation of β-catenin, leading to upregulation of Wnt/β-catenin target genes, MYC, CCND1, TCF4, and LEF1. Consistently, treatment with the FDA-approved drug, pyrvinium pamoate, significantly reduced the transforming ability of cells expressing the fusion protein and improved survival in mice bearing tumors of fusion-overexpressing cells. Interestingly, fusion-expressing cells upon knockdown of CTNNB1, or LEF1 show reduced proliferation, clonogenic abilities, and reduced sensitivity to pyrvinium pamoate. Overall, our study suggests that the UBE3C-LRP5 fusion is a promising therapeutic target for head and neck cancer and that pyrvinium pamoate may be a potential drug candidate for treating head and neck cancer harboring this translocation.
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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
- Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, Maharashtra, 441108, India
| | - Akshita Chaudhary
- 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
| | - Aniket Chowdhury
- 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
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, 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.
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India.
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Cho-Clark MJ, Sukumar G, Vidal NM, Raiciulescu S, Oyola MG, Olsen C, Mariño-Ramírez L, Dalgard CL, Wu TJ. Comparative transcriptome analysis between patient and endometrial cancer cell lines to determine common signaling pathways and markers linked to cancer progression. Oncotarget 2021; 12:2500-2513. [PMID: 34966482 PMCID: PMC8711572 DOI: 10.18632/oncotarget.28161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/08/2023] Open
Abstract
The rising incidence and mortality of endometrial cancer (EC) in the United States calls for an improved understanding of the disease's progression. Current methodologies for diagnosis and treatment rely on the use of cell lines as models for tumor biology. However, due to inherent heterogeneity and differential growing environments between cell lines and tumors, these comparative studies have found little parallels in molecular signatures. As a consequence, the development and discovery of preclinical models and reliable drug targets are delayed. In this study, we established transcriptome parallels between cell lines and tumors from The Cancer Genome Atlas (TCGA) with the use of optimized normalization methods. We identified genes and signaling pathways associated with regulating the transformation and progression of EC. Specifically, the LXR/RXR activation, neuroprotective role for THOP1 in Alzheimer's disease, and glutamate receptor signaling pathways were observed to be mostly downregulated in advanced cancer stage. While some of these highlighted markers and signaling pathways are commonly found in the central nervous system (CNS), our results suggest a novel function of these genes in the periphery. Finally, our study underscores the value of implementing appropriate normalization methods in comparative studies to improve the identification of accurate and reliable markers.
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Affiliation(s)
- Madelaine J. Cho-Clark
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sorana Raiciulescu
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Mario G. Oyola
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Cara Olsen
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20814, USA
| | - Clifton L. Dalgard
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - T. John Wu
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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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] [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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4
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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. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2020; 1861:148300. [PMID: 32858000 DOI: 10.1016/j.bbabio.2020.148300] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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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5
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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] [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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6
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Schuh A, Dreau H, Knight SJL, Ridout K, Mizani T, Vavoulis D, Colling R, Antoniou P, Kvikstad EM, Pentony MM, Hamblin A, Protheroe A, Parton M, Shah KA, Orosz Z, Athanasou N, Hassan B, Flanagan AM, Ahmed A, Winter S, Harris A, Tomlinson I, Popitsch N, Church D, Taylor JC. Clinically actionable mutation profiles in patients with cancer identified by whole-genome sequencing. Cold Spring Harb Mol Case Stud 2018; 4:a002279. [PMID: 29610388 PMCID: PMC5880257 DOI: 10.1101/mcs.a002279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) efforts have established catalogs of mutations relevant to cancer development. However, the clinical utility of this information remains largely unexplored. Here, we present the results of the first eight patients recruited into a clinical whole-genome sequencing (WGS) program in the United Kingdom. We performed PCR-free WGS of fresh frozen tumors and germline DNA at 75× and 30×, respectively, using the HiSeq2500 HTv4. Subtracted tumor VCFs and paired germlines were subjected to comprehensive analysis of coding and noncoding regions, integration of germline with somatically acquired variants, and global mutation signatures and pathway analyses. Results were classified into tiers and presented to a multidisciplinary tumor board. WGS results helped to clarify an uncertain histopathological diagnosis in one case, led to informed or supported prognosis in two cases, leading to de-escalation of therapy in one, and indicated potential treatments in all eight. Overall 26 different tier 1 potentially clinically actionable findings were identified using WGS compared with six SNVs/indels using routine targeted NGS. These initial results demonstrate the potential of WGS to inform future diagnosis, prognosis, and treatment choice in cancer and justify the systematic evaluation of the clinical utility of WGS in larger cohorts of patients with cancer.
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Affiliation(s)
- Anna Schuh
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Samantha J L Knight
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kate Ridout
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Tuba Mizani
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
| | - Dimitris Vavoulis
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Richard Colling
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford OX3 9DU, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Pavlos Antoniou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Erika M Kvikstad
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Melissa M Pentony
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Angela Hamblin
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Andrew Protheroe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, United Kingdom
| | - Marina Parton
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
| | - Ketan A Shah
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Zsolt Orosz
- Breast Unit, Royal Marsden NHS Foundation Trust and Kingston NHS Foundation Trust, London SW3 6JJ, United Kingdom
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, United Kingdom
| | - Nick Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Bass Hassan
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Adrienne M Flanagan
- University College London, Cancer Institute and Royal National Orthopaedic NHS Hospital, London WC1E 6BT, United Kingdom
| | - Ahmed Ahmed
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Stuart Winter
- Department of Ear Nose and Throat-Head and Neck Surgery, Oxford University Hospitals, Oxford OX3 9DU, United Kingdom
| | - Adrian Harris
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ian Tomlinson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Niko Popitsch
- The Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - David Church
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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7
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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] [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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8
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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] [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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