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Heczko L, Liška V, Vyčítal O, Fiala O, Šůsová S, Hlaváč V, Souček P. Targeted panel sequencing of pharmacogenes and oncodrivers in colorectal cancer patients reveals genes with prognostic significance. Hum Genomics 2024; 18:83. [PMID: 39030589 PMCID: PMC11264515 DOI: 10.1186/s40246-024-00644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Colorectal cancer is still the second leading cause of cancer-related deaths and thus biomarkers allowing prediction of the resistance of patients to therapy and estimating their prognosis are needed. We designed a panel of 558 genes with pharmacogenomics records related to 5-fluorouracil resistance, genes important for sensitivity to other frequently used drugs, major oncodrivers, and actionable genes. We performed a target enrichment sequencing of DNA from tumors and matched blood samples of patients, and compared the results with patient prognosis stratified by systemic adjuvant chemotherapy. RESULTS The median number of detected variants per tumor sample was 18.5 with 4 classified as having a high predicted functional effect and 14.5 moderate effect. APC, TP53, and KRAS were the most frequent mutated genes (64%, 59%, and 42% of mutated samples, respectively) followed by FAT4 (23%), FBXW7, and PIK3CA (16% for both). Patients with advanced stage III had more frequently APC, TP53, or KRAS mutations than those in stages I or II. KRAS mutation counts followed an increasing trend with grade (G1 < G2 < G3). The response to adjuvant therapy was worse in carriers of frameshift mutations in APC or 12D variant in KRAS, but none of these oncodrivers had prognostic value. Carriage of somatic mutations in any of the genes ABCA13, ANK2, COL7A1, NAV3, or UNC80 had prognostic relevance for worse overall survival (OS) of all patients. In contrast, mutations in FLG, GLI3, or UNC80 were prognostic in the same direction for patients untreated, and mutations in COL6A3, LRP1B, NAV3, RYR1, RYR3, TCHH, or TENM4 for patients treated with adjuvant therapy. The first association was externally validated. From all germline variants with high or moderate predicted functional effects (median 326 per patient), > 5% frequency and positive Manhattan plot based on 3-year RFS, rs72753407 in NFACS, rs34621071 in ERBB4, and rs2444274 in RIF1 were significantly associated with RFS, OS or both. CONCLUSIONS The present study identified several putative somatic and germline genetic events with prognostic potential for colorectal cancer that should undergo functional characterization.
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Affiliation(s)
- Lucie Heczko
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
| | - Václav Liška
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Vyčítal
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Fiala
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Simona Šůsová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Viktor Hlaváč
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
| | - Pavel Souček
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 1655/76, Pilsen, 323 00, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
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Gabriel PE, Cancel-Tassin G, Audenet F, Masson-Lecomte A, Allory Y, Roumiguié M, Pradère B, Loriot Y, Léon P, Traxer O, Xylinas E, Rouprêt M, Neuzillet Y, Seisen T. A collaborative review of the microsatellite instability/deficient mismatch repair phenotype in patients with upper tract urothelial carcinoma. BJU Int 2024. [PMID: 38813615 DOI: 10.1111/bju.16405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
OBJECTIVE To perform a collaborative review of the literature exploring the microsatellite instability/deficient mismatch repair (MSI/dMMR) phenotype in patients with upper tract urothelial carcinoma (UTUC). METHOD A collaborative review of the literature available on Medline was conducted by the Cancer Committee of the French Association of Urology to report studies describing the genetic mechanisms, investigation, prevalence and impact of the MSI/dMMR phenotype in UTUC patients. RESULTS The predominant genetic mechanism leading to the MSI/dMMR phenotype in UTUC patients is related to the constitutional mutation of one allele of the MMR genes MLH1, MSH2, MSH6 and PMS2 within Lynch syndrome. Indications for its investigation currently remain limited to patients with a clinical suspicion for sporadic UTUC to refer only those with a positive testing for germline DNA sequencing to screen for this syndrome. With regard to technical aspects, despite the interest of MSIsensor, only PCR and immunohistochemistry are routinely used to somatically investigate the MSI and dMMR phenotypes, respectively. The prevalence of the MSI/dMMR phenotype in UTUC patients ranges from 1.7% to 57%, depending on the study population, investigation method and definition of a positive test. Younger age and a more balanced male to female ratio at initial diagnosis are the main specific clinical characteristics of UTUC patients with an MSI/dMMR phenotype. Despite the conflicting results available in the literature, these patients may have a better prognosis, potentially related to more favourable pathological features. Finally, they may also have lower sensitivity to chemotherapy but greater sensitivity to immunotherapy. CONCLUSION Our collaborative review summarises the available data from published studies exploring the MSI/dMMR phenotype in UTUC patients, the majority of which are limited by a low level of evidence.
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Affiliation(s)
- Pierre-Etienne Gabriel
- GRC 5 Predictive Onco-Uro, Sorbonne University, AP-HP, Urology, Pitie-Salpetriere Hospital, Paris, France
| | | | - François Audenet
- Department of urology, Georges Pompidou European Hospital, APHP, Centre, Université Paris Cité, Paris, France
| | | | - Yves Allory
- Department of Pathology, Institut Curie, Saint-Cloud, Paris, France
| | | | - Benjamin Pradère
- Department of Urology, La Croix Du Sud Hospital, Quint Fonsegrives, France
| | - Yohann Loriot
- Department of Oncology, Gustave Roussy, Villejuif, France
| | | | - Olivier Traxer
- Department of Urology, Tenon Hospital, AP-HP, Paris, France
| | - Evanguelos Xylinas
- Department of Urology, Bichat-Claude Bernard Hospital, AP-HP, Université de Paris, Paris, France
| | - Morgan Rouprêt
- GRC 5 Predictive Onco-Uro, Sorbonne University, AP-HP, Urology, Pitie-Salpetriere Hospital, Paris, France
| | - Yann Neuzillet
- Department of Urology, Foch Hospital, University of Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, Suresnes, France
| | - Thomas Seisen
- GRC 5 Predictive Onco-Uro, Sorbonne University, AP-HP, Urology, Pitie-Salpetriere Hospital, Paris, France
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Qiu Q, Tan D, Chen Q, Zhou R, Zhao X, Wen W, Yang P, Li J, Gong Z, Zhang D, Wang M. Clinical implications of PD-L1 expression and pathway-related molecular subtypes in advanced Asian colorectal cancer patients. Am J Cancer Res 2024; 14:796-808. [PMID: 38455414 PMCID: PMC10915335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
The expression level of PD-L1 does not accurately predict the prognosis of advanced colorectal cancer (CRC) patients, but it still reflects the tumor microenvironment to some extent. By stratifying PD-L1 status, gene subtypes in PD-L1 positivity-related pathological pathways were analyzed for their relationship to MSI or TMB to provide more individualized treatment options for CRCs. A total of 752 advanced CRCs were included, and their genomic variance was measured by a targeted next generation sequencing panel in this study. MSI and TMB were both measured by NGS, while PD-L1 expression level was measured using the PD-L1 colon 22C3 pharmDx kit. We found RTK/RAS pathway was positively related to high PD-L1 expression, with BRAF V600E and most KRAS mutations (G12 and G13) subtypes showing a significant correlation. Conversely, the Wnt and p53 pathways were negatively related to high PD-L1 expression, with APC C-terminal alterations and other non-inactivation mutations in TP53 making a primary contribution with significant statistical significance. Major subtypes showing a significantly higher proportion of TMB-H or MSI-H were irrespective of PD-L1 status. These findings demonstrate pathological pathways associated with high PD-L1 expression, suggesting that pathway-induced oncogenic constructive PD-L1 upregulation may be the reason for the corresponding patients' primary resistance to immune checkpoint inhibitors (ICIs), rather than a lack of pre-existing immune responses.
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Affiliation(s)
- Qingqing Qiu
- Department of General Surgery, RuiJin Hospital Lu Wan Branch, Shanghai Jiaotong University School of MedicineShanghai 200020, China
| | - Dan Tan
- Department of General Surgery, RuiJin Hospital Lu Wan Branch, Shanghai Jiaotong University School of MedicineShanghai 200020, China
| | - Qiaofeng Chen
- Department of General Surgery, RuiJin Hospital Lu Wan Branch, Shanghai Jiaotong University School of MedicineShanghai 200020, China
| | - Ru Zhou
- Department of General Surgery, RuiJin Hospital Lu Wan Branch, Shanghai Jiaotong University School of MedicineShanghai 200020, China
| | - Xiaokai Zhao
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Wei Wen
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Pengmin Yang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Jieyi Li
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Ziying Gong
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Daoyun Zhang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd.Jiaxing 314000, Zhejiang, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd.Jiaxing 314000, Zhejiang, China
| | - Mingliang Wang
- Department of General Surgery, RuiJin Hospital Lu Wan Branch, Shanghai Jiaotong University School of MedicineShanghai 200020, China
- Department of General Surgery, RuiJin Hospital, Shanghai Jiaotong University School of MedicineShanghai 200025, China
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Ding W, Yang P, Zhao X, Wang X, Liu H, Su Q, Wang X, Li J, Gong Z, Zhang D, Wang X. Unraveling EGFR-TKI resistance in lung cancer with high PD-L1 or TMB in EGFR-sensitive mutations. Respir Res 2024; 25:40. [PMID: 38238740 PMCID: PMC10797755 DOI: 10.1186/s12931-023-02656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although EGFR-TKI resistance mechanisms in non-small cell lung cancer (NSCLC) have been extensively studied, certain patient subgroups remain with unclear mechanisms. This retrospective study analysed mutation data of NSCLC patients with EGFR-sensitive mutations and high programmed death-ligand 1 (PD-L1) expression or high TMB to identify primary resistance mechanisms. METHODS Hybrid capture-based next-generation sequencing (NGS) was used to analyse mutations in 639 genes in tumor tissues and blood samples from 339 NSCLC patients. PD-L1 immunohistochemical staining was also performed on the same cell blocks. Molecular and pathway profiles were compared among patient subgroups. RESULTS TMB was significantly higher in lung cancer patients with EGFR-sensitive mutations and high PD-L1 expression. Compared with the high-expression PD-L1 or high TMB and low-expression or TMB groups, the top 10 genes exhibited differences in both gene types and mutation rates. Pathway analysis revealed a significant mutations of the PI3K signaling pathway in the EGFR-sensitive mutation group with high PD-L1 expression (38% versus 12%, p < 0.001) and high TMB group (31% versus 13%, p < 0.05). Notably, PIK3CA and PTEN mutations emerged as the most important differentially mutated genes within the PI3K signaling pathway. CONCLUSIONS Our findings reveal that the presence of PI3K signaling pathway mutations may be responsible for inducing primary resistance to EGFR-TKIs in NSCLC patients with EGFR-sensitive mutations along with high PD-L1 expression or high TMB. This finding is of great significance in guiding subsequent precision treatments in NSCLC.
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Affiliation(s)
- Wuwu Ding
- Department of Pathology, Deyang Pelple's Hospital, No.173 Taishan Road, Jingyang District, Deyang City, Sichuan Province, 618300, China
| | - Pengmin Yang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China
| | - Xiaokai Zhao
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China
| | - Xiaozhi Wang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
| | - Huaqing Liu
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
| | - Qing Su
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
| | - Xintao Wang
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China
| | - Jieyi Li
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China
| | - Ziying Gong
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China
| | - Daoyun Zhang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd, Jiaxing, 314000, China.
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Building 5, 3556 Linggongtang Road, Nanhu District, Jiaxing, Zhejiang, 314000, China.
| | - Xinwei Wang
- Department of Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Affiliated Cancer Hospital of Nanjing Medical University, No.42 Baiziting, Xuanwu District, Nanjing, 210009, China.
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5
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Heczko L, Hlaváč V, Holý P, Dvořák P, Liška V, Vyčítal O, Fiala O, Souček P. Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases. Cancer Cell Int 2023; 23:295. [PMID: 38008721 PMCID: PMC10676609 DOI: 10.1186/s12935-023-03135-x] [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: 10/02/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Colorectal cancer is a highly prevalent and deadly. The most common metastatic site is the liver. We performed a whole exome sequencing analysis of a series of metachronous colorectal cancer liver metastases (mCLM) and matched non-malignant liver tissues to investigate the genomic profile of mCLM and explore associations with the patients' prognosis and therapeutic modalities. METHODS DNA samples from mCLM and non-malignant liver tissue pairs (n = 41) were sequenced using whole exome target enrichment and their germline and somatic genetic variability, copy number variations, and mutational signatures were assessed for associations with relapse-free (RFS) and overall survival (OS). RESULTS Our genetic analysis could stratify all patients into existing targeted therapeutic regimens. The most commonly mutated genes in mCLM were TP53, APC, and KRAS together with PIK3CA and several passenger genes like ABCA13, FAT4, PCLO, and UNC80. Patients with somatic alterations in genes from homologous recombination repair, Notch, and Hedgehog pathways had significantly prolonged RFS, while those with altered MYC pathway genes had poor RFS. Additionally, alterations in the JAK-STAT pathway were prognostic of longer OS. Patients bearing somatic variants in VIPR2 had significantly shorter OS and those with alterations in MUC16 prolonged OS. Carriage of the KRAS-12D variant was associated with shortened survival in our and external datasets. On the other hand, tumor mutation burden, mismatch repair deficiency, microsatellite instability, mutational signatures, or copy number variation in mCLM had no prognostic value. CONCLUSIONS The results encourage further molecular profiling for personalized treatment of colorectal cancer liver metastases discerning metachronous from synchronous scenarios.
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Affiliation(s)
- Lucie Heczko
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
| | - Viktor Hlaváč
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Petr Holý
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
| | - Pavel Dvořák
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Václav Liška
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Vyčítal
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Fiala
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Souček
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic.
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
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Yang LP, Jiang TJ, He MM, Ling YH, Wang ZX, Wu HX, Zhang Z, Xu RH, Wang F, Yuan SQ, Zhao Q. Comprehensive genomic characterization of sporadic synchronous colorectal cancer: Implications for treatment optimization and clinical outcome. Cell Rep Med 2023; 4:101222. [PMID: 37794586 PMCID: PMC10591049 DOI: 10.1016/j.xcrm.2023.101222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Sporadic synchronous colorectal cancer (SCRC) refers to multiple primary CRC tumors detected simultaneously in an individual without predisposing hereditary conditions, which accounts for the majority of multiple CRCs while lacking a profound understanding of the genomic landscape and evolutionary dynamics to optimize its treatment. In this study, 103 primary tumor samples from 51 patients with SCRC undergo whole-exome sequencing. The germline and somatic mutations and evolutionary and clinical features are comprehensively investigated. Somatic genetic events are largely inconsistent between paired tumors. Compared with solitary CRC, SCRCs have higher prevalence of tumor mutation burden high (TMB-H; 33.3%) and microsatellite-instability high (MSI-H; 29.4%) and different mutation frequencies in oncogenic signaling pathways. Moreover, neutrally evolving SCRC tumors are associated with higher intratumoral heterogeneity and better prognosis. These findings unveil special molecular features, carcinogenesis, and prognosis of sporadic SCRC. Strategies for targeted therapy and immunotherapy should be optimized accordingly.
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Affiliation(s)
- Lu-Ping Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Teng-Jia Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Ming-Ming He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Yi-Hong Ling
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Zi-Xian Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Hao-Xiang Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Zhen Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Feng Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Shu-Qiang Yuan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China.
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China.
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7
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Peng H, Ying J, Zang J, Lu H, Zhao X, Yang P, Wang X, Li J, Gong Z, Zhang D, Wang Z. Specific Mutations in APC, with Prognostic Implications in Metastatic Colorectal Cancer. Cancer Res Treat 2023; 55:1270-1280. [PMID: 37114476 PMCID: PMC10582542 DOI: 10.4143/crt.2023.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
PURPOSE Loss-of-function mutations in the adenomatous polyposis coli (APC) gene are common in metastatic colorectal cancer (mCRC). However, the characteristic of APC specific mutations in mCRC is poorly understood. Here, we explored the clinical and molecular characteristics of N-terminal and C-terminal side APC mutations in Chinese patients with mCRC. MATERIALS AND METHODS Hybrid capture-based next-generation sequencing was performed on tumor tissues from 275 mCRC pati-ents to detect mutations in 639 tumor-associated genes. The prognostic value and gene-pathway difference between APC specific mutations in mCRC patients were analyzed. RESULTS APC mutations were highly clustered, accounting for 73% of all mCRC patients, and most of them were truncating mutations. The tumor mutation burden of the N-terminal side APC mutations group (n=76) was significantly lower than that of the C-terminal side group (n=123) (p < 0.001), further confirmed by the public database. Survival analysis showed that mCRC patients with N-terminus side APC mutations had longer overall survival than C-terminus side. Tumor gene pathway analysis showed that gene mutations in the RTK/RAS, Wnt and transforming growth factor β signaling pathways of the C-terminal group were significantly higher than those of the N-terminal group (p < 0.05). Additionally, KRAS, AMER1, TGFBR2, and ARID1A driver mutations were more common in patients with C-terminal side APC mutations. CONCLUSION APC specific mutations have potential function as mCRC prognostic biomarkers. There are obvious differences in the gene mutation patterns between the C-terminus and N-terminus APC mutations group, which may have certain guiding significance for the subsequent precise treatment of mCRC.
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Affiliation(s)
- Huan Peng
- Division of Colorectal Surgery, Department of Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai,
China
| | - Jun Ying
- Division of Colorectal Surgery, Department of Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai,
China
| | - Jia Zang
- Division of Colorectal Surgery, Department of Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai,
China
| | - Hao Lu
- Division of Colorectal Surgery, Department of Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai,
China
| | - Xiaokai Zhao
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Pengmin Yang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Xintao Wang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Jieyi Li
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Ziying Gong
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Daoyun Zhang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing,
China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing,
China
| | - Zhiguo Wang
- Division of Colorectal Surgery, Department of Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai,
China
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8
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Yakushina V, Kavun A, Veselovsky E, Grigoreva T, Belova E, Lebedeva A, Mileyko V, Ivanov M. Microsatellite Instability Detection: The Current Standards, Limitations, and Misinterpretations. JCO Precis Oncol 2023; 7:e2300010. [PMID: 37315263 DOI: 10.1200/po.23.00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Valentina Yakushina
- OncoAtlas LLC, Moscow, Russian Federation
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russian Federation
| | | | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russian Federation
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russian Federation
- Lomonosov Moscow State University, Moscow, Russian Federation
| | | | | | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
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9
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Styk J, Pös Z, Pös O, Radvanszky J, Turnova EH, Buglyó G, Klimova D, Budis J, Repiska V, Nagy B, Szemes T. Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook. EPMA J 2023; 14:143-165. [PMID: 36866160 PMCID: PMC9971410 DOI: 10.1007/s13167-023-00312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Zuzana Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Slovgen Ltd, 841 04 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Daniela Klimova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Medirex Group Academy, NPO, 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
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10
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Relative Risk of Bladder and Kidney Cancer in Lynch Syndrome: Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:cancers15020506. [PMID: 36672455 PMCID: PMC9856836 DOI: 10.3390/cancers15020506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/17/2023] Open
Abstract
Background: The association between Lynch syndrome (LS) and a higher risk of upper tract urothelial carcinoma is well established, but its effect on the risk of bladder and kidney cancers remains controversial. This review aimed to compare the relative risk (RR) of bladder and kidney cancer in confirmed LS germline mutation carriers compared to the general population. Methods: Medline, Embase, Cochrane Central, and Google Scholar were searched on 14 July 2022 for studies published in English that reported on the rates of urological cancer in adults with confirmed LS germline mutation. The quality of included studies was assessed using Cochrane’s tool to evaluate risk of bias in cohort studies. Random effects meta-analysis estimated the pooled relative risk of bladder and kidney cancer in LS carriers compared to the general population. The quality of the overall evidence was evaluated using GRADE. Results: Of the 1839 records identified, 5 studies involving 7120 participants from 3 continents were included. Overall, LS carriers had a statistically significantly higher RR of developing bladder cancer (RR: 7.48, 95% CI: 3.70, 15.13) and kidney cancer (RR: 3.97, 95% CI: 1.23, 12.81) compared to unaffected participants (p < 0.01). The quality of the evidence was assessed as “low” due to the inclusion of cohort studies, the substantial heterogeneity, and moderate-to-high risk of bias. Conclusion: Lynch syndrome is associated with a significant increase in the relative risk of kidney and bladder cancer. Clinicians should adopt a lower threshold for germline mutation genetic testing in individuals who present with bladder cancer. Further studies evaluating the role and cost-effectiveness of novel urine-based laboratory tests are needed. High-quality studies in histologically proven renal cell carcinoma and their underlying germline mutations are necessary to strengthen the association with LS.
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11
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Wen X, Pu H, Liu Q, Guo Z, Luo D. Circulating Tumor DNA-A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques. Cancers (Basel) 2022; 14:6025. [PMID: 36551512 PMCID: PMC9775401 DOI: 10.3390/cancers14246025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer is the second leading cause of death in the world and seriously affects the quality of life of patients. The diagnostic techniques for tumors mainly include tumor biomarker detection, instrumental examination, and tissue biopsy. In recent years, liquid technology represented by circulating tumor DNA (ctDNA) has gradually replaced traditional technology with its advantages of being non-invasive and accurate, its high specificity, and its high sensitivity. ctDNA may carry throughout the circulatory system through tumor cell necrosis, apoptosis, circulating exosome secretion, etc., carrying the characteristic changes in tumors, such as mutation, methylation, microsatellite instability, gene rearrangement, etc. In this paper, ctDNA mutation and methylation, as the objects to describe the preparation process before ctDNA analysis, and the detection methods of two gene-level changes, including a series of enrichment detection techniques derived from PCR, sequencing-based detection techniques, and comprehensive detection techniques, are combined with new materials. In addition, the role of ctDNA in various stages of cancer development is summarized, such as early screening, diagnosis, molecular typing, prognosis prediction, recurrence monitoring, and drug guidance. In summary, ctDNA is an ideal biomarker involved in the whole process of tumor development.
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Affiliation(s)
- Xiaosha Wen
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Huijie Pu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Quan Liu
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Zifen Guo
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Dixian Luo
- Laboratory Medicine Centre, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
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12
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Detecting mismatch repair deficiency in solid neoplasms: immunohistochemistry, microsatellite instability, or both? Mod Pathol 2022; 35:1515-1528. [PMID: 35668150 DOI: 10.1038/s41379-022-01109-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022]
Abstract
In managing patients with solid tumors, the value of detecting the status of tumor DNA mismatch repair function is widely recognized. Mismatch repair protein immunohistochemistry and molecular microsatellite instability testing constitute the two major test modalities currently in use, yet each is associated with caveats and limitations that can be consequential. Most notably, the traditional approach of defining mismatch repair protein immunohistochemistry abnormality by complete loss of staining in all tumor cells is evolving. Partial or clonal loss is becoming recognized as a manifestation of gene abnormality; in some cases, such clonal loss is associated with germline pathogenic variants. The current criteria and cutoff values for defining microsatellite instability-high are developed primarily according to colorectal tumors. Non-colorectal cases, and occasionally even colorectal tumors, that are mismatch repair-deficient by immunohistochemistry but not microsatellite instability-high by current standards are being recognized. Emerging data suggest that these immunohistochemistry abnormal / non-microsatellite instability-high cases warrant further genetic workup for Lynch syndrome detection. Whether these tumors respond to immunotherapy is a question still to be addressed. It is imperative that pathologists as well as clinicians and investigators be aware of such intricacies regarding routine immunohistochemistry and microsatellite instability testing and the results they generate. This review summarizes our current understanding of the advantages and limitations of these tests and offer our view on what constitutes the most optimal strategy in test selection and how best to utilize case context to enhance the interpretation of the test results.
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13
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Liquid Biopsy as a Source of Nucleic Acid Biomarkers in the Diagnosis and Management of Lynch Syndrome. Int J Mol Sci 2022; 23:ijms23084284. [PMID: 35457101 PMCID: PMC9029375 DOI: 10.3390/ijms23084284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited cancer predisposition disorder, which may manifest as colorectal cancer (CRC), endometrial cancer (EC) or other malignancies of the gastrointestinal and genitourinary tract as well as the skin and brain. Its genetic cause is a defect in one of the four key DNA mismatch repair (MMR) loci. Testing of patients at risk is currently based on the absence of MMR protein staining and detection of mutations in cancer tissue and the germline, microsatellite instability (MSI) and the hypermethylated state of the MLH1 promoter. If LS is shown to have caused CRC, lifetime follow-up with regular screening (most importantly, colonoscopy) is required. In recent years, DNA and RNA markers extracted from liquid biopsies have found some use in the clinical diagnosis of LS. They have the potential to greatly enhance the efficiency of the follow-up process by making it minimally invasive, reproducible, and time effective. Here, we review markers reported in the literature and their current clinical applications, and we comment on possible future directions.
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14
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A Fluorescent “Turn-On” Clutch Probe for Plasma Cell-Free DNA Identification from Lung Cancer Patients. NANOMATERIALS 2022; 12:nano12081262. [PMID: 35457970 PMCID: PMC9027387 DOI: 10.3390/nano12081262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 12/19/2022]
Abstract
Early diagnosis of cancer is of paramount significance for the therapeutic intervention of cancers. Although the detection of circulating cell-free DNA (cfDNA) has emerged as a promising, minimally invasive approach for early cancer diagnosis, there is an urgent need to develop a highly sensitive and rapid method to precisely identify plasma cfDNA from clinical samples. Herein, we report a robust fluorescent “turn-on” clutch probe based on non-emissive QDs-Ru complexes to rapidly recognize EGFR gene mutation in plasma cfDNA from lung cancer patients. In this system, the initially quenched emission of QDs is recovered while the red emission of Ru(II) complexes is switched on. This is because the Ru(II) complexes can specifically intercalate into the double-stranded DNA (dsDNA) to form Ru-dsDNA complexes and simultaneously liberate free QDs from the QDs-Ru complexes, which leads to the occurrence of an overlaid red fluorescence. In short, the fluorescent “turn-on” clutch probe offers a specific, rapid, and sensitive paradigm for the recognition of plasma cfDNA biomarkers from clinical samples, providing a convenient and low-cost approach for the early diagnosis of cancer and other gene-mutated diseases.
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15
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Sensitive detection of microsatellite instability in tissues and liquid biopsies: Recent developments and updates. Comput Struct Biotechnol J 2021; 19:4931-4940. [PMID: 34527197 PMCID: PMC8433064 DOI: 10.1016/j.csbj.2021.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
Microsatellite instability (MSI), a phenotype displayed as deletions/insertions of repetitive genomic sequences, has drawn great attention due to its application in cancer including diagnosis, prognosis and immunotherapy response prediction. Several methods have been developed for the detection of MSI, facilitating the MSI classification of cancer patients. In view of recent interest in minimally-invasive detection of MSI via liquid biopsy samples, which requires methods with high sensitivity to identify small fractions of altered DNA in the presence of large amount of wild type copies, sensitive MSI detection approaches are emerging. Here we review the available MSI detection methods and their detection limits and focus on recently developed next-generation-sequencing based approaches and bioinformatics algorithms available for MSI analysis in various cancer types.
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16
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Gilson P, Merlin JL, Harlé A. Detection of Microsatellite Instability: State of the Art and Future Applications in Circulating Tumour DNA (ctDNA). Cancers (Basel) 2021; 13:cancers13071491. [PMID: 33804907 PMCID: PMC8037825 DOI: 10.3390/cancers13071491] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Microsatellite instability (MSI) is a molecular fingerprint for defects in the mismatch repair system (dMMR) and is associated with higher risks of cancers. MSI/dMMR tumours are characterized by the accumulation of mutations throughout the genome, and particularly in microsatellite (MS) DNA repeat sequences. MSI stands as a major biomarker for familial cancer risk assessment, cancer prognosis, and therapeutic choices. Standard-of-care classification of MSI/dMMR tumours is most frequently achieved using immunohistochemistry or PCR-based assay directed against a set of five MS regions. However, novel molecular methods based on tumour tissue or plasma samples have been developed and could enter in the future trends of MSI testing. Here, we provide insights into these emerging approaches and discuss their advantages and limitations. Abstract Microsatellite instability (MSI) is a molecular scar resulting from a defective mismatch repair system (dMMR) and associated with various malignancies. MSI tumours are characterized by the accumulation of mutations throughout the genome and particularly clustered in highly repetitive microsatellite (MS) regions. MSI/dMMR status is routinely assessed in solid tumours for the initial screening of Lynch syndrome, the evaluation of cancer prognosis, and treatment decision-making. Currently, pentaplex PCR-based methods and MMR immunohistochemistry on tumour tissue samples are the standard diagnostic methods for MSI/dMMR. Other tissue methods such as next-generation sequencing or real-time PCR-based systems have emerged and represent viable alternatives to standard MSI testing in specific settings. The evolution of the standard molecular techniques has offered the opportunity to extend MSI determination to liquid biopsy based on the analysis of cell-free DNA (cfDNA) in plasma. This review aims at synthetizing the standard and emerging techniques used on tumour tissue samples for MSI/dMMR determination. We also provide insights into the MSI molecular techniques compatible with liquid biopsy and the potential clinical consequences for patients with solid cancers.
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Affiliation(s)
- Pauline Gilson
- Correspondence: ; Tel.: +33-(0)3-8365-6035; Fax: +33-(0)3-8365-6152
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17
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Tieng FYF, Abu N, Lee LH, Ab Mutalib NS. Microsatellite Instability in Colorectal Cancer Liquid Biopsy-Current Updates on Its Potential in Non-Invasive Detection, Prognosis and as a Predictive Marker. Diagnostics (Basel) 2021; 11:544. [PMID: 33803882 PMCID: PMC8003257 DOI: 10.3390/diagnostics11030544] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly-diagnosed cancer in the world and ranked second for cancer-related mortality in humans. Microsatellite instability (MSI) is an indicator for Lynch syndrome (LS), an inherited cancer predisposition, and a prognostic marker which predicts the response to immunotherapy. A recent trend in immunotherapy has transformed cancer treatment to provide medical alternatives that have not existed before. It is believed that MSI-high (MSI-H) CRC patients would benefit from immunotherapy due to their increased immune infiltration and higher neo-antigenic loads. MSI testing such as immunohistochemistry (IHC) and PCR MSI assay has historically been a tissue-based procedure that involves the testing of adequate tissue with a high concentration of cancer cells, in addition to the requirement for paired normal tissues. The invasive nature and specific prerequisite of such tests might hinder its application when surgery is not an option or when the tissues are insufficient. The application of next-generation sequencing, which is highly sensitive, in combination with liquid biopsy, therefore, presents an interesting possibility worth exploring. This review aimed to discuss the current body of evidence supporting the potential of liquid biopsy as a tool for MSI testing in CRC.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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