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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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Colombino M, Rozzo C, Paliogiannis P, Casula M, Manca A, Doneddu V, Fedeli MA, Sini MC, Palomba G, Pisano M, Ascierto PA, Caracò C, Lissia A, Cossu A, Palmieri G. Comparison of BRAF Mutation Screening Strategies in a Large Real-Life Series of Advanced Melanoma Patients. J Clin Med 2020; 9:E2430. [PMID: 32751423 DOI: 10.3390/jcm9082430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
Malignant melanoma (MM) is one of the deadliest skin cancers. BRAF mutation status plays a predominant role in the management of MM patients. The aim of this study was to compare BRAF mutational testing performed by conventional nucleotide sequencing approaches with either real-time polymerase chain reaction (rtPCR) or next-generation sequencing (NGS) assays in a real-life, hospital-based series of advanced MM patients. Consecutive patients with AJCC (American Joint Committee on Cancer) stage IIIC and IV MM from Sardinia, Italy, who were referred for molecular testing, were enrolled into the study. Initial screening was performed to assess the mutational status of the BRAF and NRAS genes, using the conventional methodologies recognized by the nationwide guidelines, at the time of the molecular classification, required by clinicians: at the beginning, Sanger-based sequencing (SS) and, after, pyrosequencing. The present study was then focused on BRAF mutation detecting approaches only. BRAF wild-type cases with available tissue and adequate DNA were further tested with rtPCR (Idylla™) and NGS assays. Globally, 319 patients were included in the study; pathogenic BRAF mutations were found in 144 (45.1%) cases examined with initial screening. The rtPCR detected 11 (16.2%) and 3 (4.8%) additional BRAF mutations after SS and pyrosequencing, respectively. NGS detected one additional BRAF-mutated case (2.1%) among 48 wild-type cases previously tested with pyrosequencing and rtPCR. Our study evidenced that rtPCR and NGS were able to detect additional BRAF mutant cases in comparison with conventional sequencing methods; therefore, we argue for the preferential utilization of the aforementioned assays (NGS and rtPCR) in clinical practice, to eradicate false-negative cases and improve the accuracy of BRAF detection.
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Kyrochristos ID, Peristeri DV, Ziogas DE, Lykoudis EG, Roukos DH. Precise predictive and therapeutic strategy for breast cancer. Future Oncol 2018; 14:1777-1780. [PMID: 29846090 DOI: 10.2217/fon-2018-0277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Ioannis D Kyrochristos
- Center for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, 45110, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, 45500, Greece
| | - Dimitra V Peristeri
- Department of Surgery, Ioannina University Hospital, Ioannina, 45500, Greece
| | - Demosthenes E Ziogas
- Center for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, 45110, Greece.,Department of Surgery, 'G Hatzikosta' General Hospital, Ioannina, 45001, Greece
| | - Efstathios G Lykoudis
- Department of Plastic Surgery, Ioannina University Hospital, Ioannina, 45500, Greece
| | - Dimitrios H Roukos
- Department of Surgery, Ioannina University Hospital, Ioannina, 45500, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, 11527, Greece
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