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Tanwar NA, Malhotra R, Satheesh AP, Khuntia SP, Sreekanthreddy P, Varghese L, Kolla S, Chandrani P, Choughule A, Pange P, Gupta V, Noronha V, Patil VM, Pramanik R, Kumar S, Nayak SP, Babu S, Shetty R, Kantharaju M, Chinder PS, Korlimarla A, Srinath BS, Prabhash K, Rishi KD, Goswami HM, Veldore VH. Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From India. JCO Glob Oncol 2023; 9:e2300047. [PMID: 38085046 PMCID: PMC10846780 DOI: 10.1200/go.23.00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/12/2023] [Accepted: 07/22/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE The purpose of this study was to understand the impact of population diversity and geographic variation on tumor mutation burden (TMB) scores across cancers and its implication on stratification of patients for immune checkpoint inhibitor (ICI) therapy. MATERIALS AND METHODS This retrospective study used whole-exome sequencing (WES) to profile 1,233 Indian patients with cancer across 30 different cancer types and to estimate their TMB scores. A WES-based pipeline was adopted, along with an indigenously developed strategy for arriving at true somatic mutations. A robust unsupervised machine learning approach was used to understand the distribution of TMB scores across different populations and within the population. RESULTS The results of the study showed a biphasic distribution of TMB scores in most cancers, with different threshold scores across cancer types. Patients with cancer in India had higher TMB scores compared with the Caucasian patients. We also observed that the TMB score value at 90th percentile (predicting high efficacy to ICI) was high in four different cancer types (sarcoma, ovary, head and neck, and breast) in the Indian cohort as compared with The Cancer Genome Atlas or public cohort. However, in lung and colorectal cancers, the TMB score distribution was similar between the two population cohorts. CONCLUSION The findings of this study indicate that it is crucial to benchmark both cancer-specific and population-specific TMB distributions to establish a TMB threshold for each cancer in various populations. Additional prospective studies on much larger population across different cancers are warranted to validate this observation to become the standard of care.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Anuradha Choughule
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | | | | | | | | | - Suresh Babu
- Fortis Cancer Research Centre, Bangalore, India
| | | | | | | | - Aruna Korlimarla
- Sri Shankara Cancer Hospital & Research Centre, Bangalore, India
| | - BS Srinath
- Sri Shankara Cancer Hospital & Research Centre, Bangalore, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
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Wang C, He Y, He Y, Liang W, Zhou C, Wu M, Meng Z, Li W, Cao J. Prognostic and biological function value of OSBPL3 in colorectal cancer analyzed by multi-omic data analysis. BMC Gastroenterol 2023; 23:270. [PMID: 37550605 PMCID: PMC10408063 DOI: 10.1186/s12876-023-02824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies in the world. This study proposes to reveal prognostic biomarkers for the prognosis and treatment of CRC patients. METHODS Differential analysis of OSBPL3 was performed in pan-cancer, and the correlation between clinical stage and OSBPL3 was analyzed. Multiple omics analysis was used to compare the relationship between survival of patients and copy number variation, single nucleotide variant, and methylation status. Survival differences between high and low OSBPL3 expression groups were analyzed. Differentially expressed genes (DEGs) between high and low OSBPL3 expression groups were obtained, and functional enrichment analysis was implemented. Correlations between immune cells and OSBPL3 was analyzed. Drug sensitivity between the two OSBPL3 expression groups was compared. Moreover, the expression of OSBPL3 was verified by immunohistochemistry and real-time quantitative PCR. RESULTS OSBPL3 was differentially expressed in 13 tumors and had some correlations with T and N stages. OSBPL3 expression was regulated by methylation and higher OSBPL3 expression was associated with poorer prognosis in CRC. 128 DEGs were obtained and they were mainly involved in signaling receptor activator activity, aspartate and glutamate metabolism. T cell gamma delta and T cell follicular helper were significantly different in the high and low OSBPL3 expression groups. Moreover, OSBPL3 showed negative correlations with multiple drugs. OSBPL3 was significantly upregulated in CRC samples compared to normal samples. CONCLUSIONS A comprehensive analysis demonstrated that OSBPL3 had potential prognostic value, and guiding significance for CRC chemotherapeutic.
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Affiliation(s)
- Chengxing Wang
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yaoming He
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yu He
- National Drug Clinical Trial Institution, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Weijun Liang
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Chaorong Zhou
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Meimei Wu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Zijie Meng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Wanglin Li
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
| | - Jie Cao
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
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Malhotra R, Javle V, Tanwar N, Gowda P, Varghese L, K A, Madhusudhan N, Jaiswal N, K. S. B, Chatterjee M, Prabhash K, Sreekanthreddy P, Rishi KD, Goswami HM, Veldore VH. An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing. Front Oncol 2023; 13:1002792. [PMID: 36994199 PMCID: PMC10040847 DOI: 10.3389/fonc.2023.1002792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 03/16/2023] Open
Abstract
IntroductionThe concept of personalized medicine in cancer has emerged rapidly with the advancement of genome sequencing and the identification of clinically relevant variants that contribute to disease prognosis and facilitates targeted therapy options. In this study, we propose to validate a whole exome-based tumor molecular profiling for DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissue.MethodsThe study included 166 patients across 17 different cancer types. The scope of this study includes the identification of single-nucleotide variants (SNVs), insertions/deletions (INDELS), copy number alterations (CNAs), gene fusions, tumor mutational burden (TMB), and microsatellite instability (MSI). The assay yielded a mean read depth of 200×, with >80% of on-target reads and a mean uniformity of >90%. Clinical maturation of whole exome sequencing (WES) (DNA and RNA)- based assay was achieved by analytical and clinical validations for all the types of genomic alterations in multiple cancers. We here demonstrate a limit of detection (LOD) of 5% for SNVs and 10% for INDELS with 97.5% specificity, 100% sensitivity, and 100% reproducibility.ResultsThe results were >98% concordant with other orthogonal techniques and appeared to be more robust and comprehensive in detecting all the clinically relevant alterations. Our study demonstrates the clinical utility of the exome-based approach of comprehensive genomic profiling (CGP) for cancer patients at diagnosis and disease progression.DiscussionThe assay provides a consolidated picture of tumor heterogeneity and prognostic and predictive biomarkers, thus helping in precision oncology practice. The primary intended use of WES (DNA+RNA) assay would be for patients with rare cancers as well as for patients with unknown primary tumors, and this category constitutes nearly 20–30% of all cancers. The WES approach may also help us understand the clonal evolution during disease progression to precisely plan the treatment in advanced stage disease.
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Affiliation(s)
| | - Vyomesh Javle
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Pooja Gowda
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Linu Varghese
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Anju K
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Nupur Jaiswal
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | | | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | | | | | | | - Vidya H. Veldore
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
- *Correspondence: Vidya H. Veldore,
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Naves MPC, de Morais CR, de Freitas V, Ribeiro DL, Lopes DS, Antunes LMG, de Melo Rodrigues V, de Rezende AAA, Spanó MA. Mutagenic and genotoxic activities of Phospholipase A 2 Bothropstoxin-I from Bothrops jararacussu in Drosophila melanogaster and human cell lines. Int J Biol Macromol 2021; 182:1602-1610. [PMID: 34033823 DOI: 10.1016/j.ijbiomac.2021.05.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 11/29/2022]
Abstract
Phospholipase A2 Bothropstoxin-I (PLA2 BthTX-I) is a myotoxic Lys49-PLA2 from Bothrops jararacussu snake venom. In order to evaluate the DNA damage caused by BthTX-I, we used the Somatic Mutation and Recombination Test (SMART) in Drosophila melanogaster and Comet assay in HUVEC and DU-145 cells. For SMART, different concentrations of BthTX-I (6.72 to 430 μg/mL) were used and no significant changes in the survival rate were observed. Significant frequency of mutant spots was observed for the ST cross at the highest concentration of BthTX-I due to recombinogenic activity. In the HB cross, BthTX-I increased the number of mutant spots at intermediate concentrations, being 53.75 μg/mL highly mutagenic and 107.5 μg/mL predominantly recombinogenic. The highest concentrations were neither mutagenic nor recombinogenic, which could indicate cytotoxicity in the wing cells of D. melanogaster. In vitro, all BthTX-I concentrations (1 to 50 μg/mL) induced decrease in HUVEC cell viability, as well as in DU-145 cells at concentrations of 10, 25, and 50 μg/mL. The comet assay showed that in HUVEC and DU-145 cells, all BthTX-I concentrations promoted increase of DNA damage. Further studies should be performed to elucidate the mechanism of action of PLA2 BthTX-I and its possible use in therapeutic strategies against cancer.
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Affiliation(s)
| | - Cássio Resende de Morais
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil
| | - Vitor de Freitas
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil
| | - Diego Luis Ribeiro
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Daiana Silva Lopes
- Multidisciplinary Institute in Health, Federal University of Bahia, Vitória da Conquista, BA, Brazil
| | - Lusânia Maria Greggi Antunes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Mário Antônio Spanó
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
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