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Aparicio T, Henriques J, Svrcek M, Zaanan A, Manfredi S, Casadei-Gardini A, Tougeron D, Gornet JM, Jary M, Terrebonne E, Piessen G, Afchain P, Lecaille C, Pocard M, Lecomte T, Rimini M, Di Fiore F, Le Brun Ly V, Cascinu S, Vernerey D, Laurent Puig P. Genomic profiling of small bowel adenocarcinoma: a pooled analysis from 3 databases. Br J Cancer 2024; 131:49-62. [PMID: 38745088 PMCID: PMC11231144 DOI: 10.1038/s41416-024-02687-7] [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: 09/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Small bowel adenocarcinoma is a rare disease. The genomic profiling tumours according to clinical characteristics and its impact on the prognosis remains unclear. METHODS A pooled analysis of clinical data, genomic profiling and MisMatch Repair (MMR) status from three databases was performed. RESULTS A total of 188 tumour samples were analysed. A predisposing disease was reported in 22.3%, mainly Lynch syndrome and Crohn's disease. The tumours were localized in 80.2% and metastatic in 18.8%. The most frequent mutations were KRAS (42.0%) among them 7/79 are G12C, TP53 (40.4%), APC (19.1%), PIK3CA (18.6%), SMAD4 (12.8%) and ERBB2 (9.6%). Mutation distribution differed according to predisposing disease for TP53, ERBB2, IDH1, FGFR3, FGFR1 and KDR. KRAS and SMAD4 mutations were more frequent in metastatic tumour, whereas ERBB2 mutations were absent in metastatic tumour. For localized tumour, APC mutation was independently associated with a poor overall survival (OS) (p = 0.0254). 31.8% of localized tumours and 11.3% of metastatic tumours were dMMR (29.8% of the entire cohort). A dMMR status was associated with a better OS (HR = 0.61 [0.39-0.96], p = 0.0316). CONCLUSIONS There is a different genomic profile according to the stage and predisposing disease. dMMR and APC mutation in localized tumour predict a better prognosis.
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Affiliation(s)
- Thomas Aparicio
- Department of Gastroenterology and Digestive Oncology, Saint Louis Hospital, APHP, Université de Paris Cité, Paris, France.
| | - Julie Henriques
- Methodology and Quality of Life Unit in Oncology, CHU Besançon, Hôpital Jean Minjoz, Besançon, France
- Bourgogne Franche-Comté University, INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Magali Svrcek
- Sorbonne Université, Department of Pathology, Saint Antoine Hospital, APHP, Paris, France
| | - Aziz Zaanan
- Department of Gastroenterology and Digestive Oncology, Georges Pompidou Hospital, APHP, Université de Paris Cité, Paris, France
| | - Sylvain Manfredi
- Digestive Cancer Registry of Burgundy, INSERM, LNC UMR1231, University Bourgogne Franche-Comté, Dijon-Bourgogne University Hospital, Dijon, France
| | | | - David Tougeron
- Department of Hepato-Gastroenterology, CHU de Poitiers, Poitiers, France
| | - Jean-Marc Gornet
- Department of Gastroenterology and Digestive Oncology, Saint Louis Hospital, APHP, Université de Paris Cité, Paris, France
| | - Marine Jary
- Department of Digestive and Hepatobiliary Surgery, University Hospital of Clermont-Ferrand, U1071 INSERM, Clermont-Auvergne University, Clermont-Ferrand, France
| | - Eric Terrebonne
- Department of Gastroenterology, CHU Haut-Lévêque, Pessac, France
| | - Guillaume Piessen
- Department of Digestive and Oncological Surgery, Claude Huriez University Hospital, University Lille, Lille, France
| | - Pauline Afchain
- Department of Oncology, Saint Antoine Hospital, APHP, Paris, France
| | - Cédric Lecaille
- Department of Gastroenterology, Polyclinic Bordeaux Nord, Bordeaux, France
| | - Marc Pocard
- Department of Digestive Surgery, Pitié-Salpétrière Hospital, APHP, Paris, France
| | - Thierry Lecomte
- Department of Hepato-Gastroenterology and Digestive Oncology, Trousseau Hospital, CHU Tours, Tours, France
| | - Margherita Rimini
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Frédéric Di Fiore
- Department of Digestive Oncology, CHU Charles Nicolle, Rouen, France
| | | | - Stefano Cascinu
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Dewi Vernerey
- Methodology and Quality of Life Unit in Oncology, CHU Besançon, Hôpital Jean Minjoz, Besançon, France
- Bourgogne Franche-Comté University, INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Pierre Laurent Puig
- Department of Biology, Georges Pompidou Hospital, APHP, Université de Paris Cité, Paris, France
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2
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Schaefer M, Reichl S, Ter Horst R, Nicolas AM, Krausgruber T, Piras F, Stepper P, Bock C, Samwald M. GPT-4 as a biomedical simulator. Comput Biol Med 2024; 178:108796. [PMID: 38909448 DOI: 10.1016/j.compbiomed.2024.108796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND Computational simulation of biological processes can be a valuable tool for accelerating biomedical research, but usually requires extensive domain knowledge and manual adaptation. Large language models (LLMs) such as GPT-4 have proven surprisingly successful for a wide range of tasks. This study provides proof-of-concept for the use of GPT-4 as a versatile simulator of biological systems. METHODS We introduce SimulateGPT, a proof-of-concept for knowledge-driven simulation across levels of biological organization through structured prompting of GPT-4. We benchmarked our approach against direct GPT-4 inference in blinded qualitative evaluations by domain experts in four scenarios and in two quantitative scenarios with experimental ground truth. The qualitative scenarios included mouse experiments with known outcomes and treatment decision support in sepsis. The quantitative scenarios included prediction of gene essentiality in cancer cells and progression-free survival in cancer patients. RESULTS In qualitative experiments, biomedical scientists rated SimulateGPT's predictions favorably over direct GPT-4 inference. In quantitative experiments, SimulateGPT substantially improved classification accuracy for predicting the essentiality of individual genes and increased correlation coefficients and precision in the regression task of predicting progression-free survival. CONCLUSION This proof-of-concept study suggests that LLMs may enable a new class of biomedical simulators. Such text-based simulations appear well suited for modeling and understanding complex living systems that are difficult to describe with physics-based first-principles simulations, but for which extensive knowledge is available as written text. Finally, we propose several directions for further development of LLM-based biomedical simulators, including augmentation through web search retrieval, integrated mathematical modeling, and fine-tuning on experimental data.
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Affiliation(s)
- Moritz Schaefer
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Stephan Reichl
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Rob Ter Horst
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Adele M Nicolas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Thomas Krausgruber
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Francesco Piras
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Peter Stepper
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Christoph Bock
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
| | - Matthias Samwald
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währingerstraße 25a, 1090, Vienna, Austria.
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3
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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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Zhu K, Yang X, Tai H, Zhong X, Luo T, Zheng H. HER2-targeted therapies in cancer: a systematic review. Biomark Res 2024; 12:16. [PMID: 38308374 PMCID: PMC10835834 DOI: 10.1186/s40364-024-00565-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
Abnormal alterations in human epidermal growth factor receptor 2 (HER2, neu, and erbB2) are associated with the development of many tumors. It is currently a crucial treatment for multiple cancers. Advanced in molecular biology and further exploration of the HER2-mediated pathway have promoted the development of medicine design and combination drug regimens. An increasing number of HER2-targeted drugs including specific monoclonal antibodies, tyrosine kinase inhibitors (TKIs), and antibody-drug conjugates (ADCs) have been approved by the U.S. Food and Drug Administration. The emergence of ADCs, has significantly transformed the treatment landscape for various tumors, such as breast, gastric, and bladder cancer. Classic monoclonal antibodies and novel TKIs have not only demonstrated remarkable efficacy, but also expanded their indications, with ADCs in particular exhibiting profound clinical applications. Moreover the concept of low HER2 expression signifies a breakthrough in HER2-targeted therapy, indicating that an increasing number of tumors and patients will benefit from this approach. This article, provides a comprehensive review of the underlying mechanism of action, representative drugs, corresponding clinical trials, recent advancements, and future research directions pertaining to HER2-targeted therapy.
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Affiliation(s)
- Kunrui Zhu
- Institute for Breast Health Medicine, Cance Center, Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xinyi Yang
- College of Clinical Medical, Guizhou Medical University, Guiyang, 550000, Guizhou Province, China
| | - Hebei Tai
- College of Clinical Medical, Guizhou Medical University, Guiyang, 550000, Guizhou Province, China
| | - Xiaorong Zhong
- Institute for Breast Health Medicine, Cance Center, Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ting Luo
- Institute for Breast Health Medicine, Cance Center, Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Hong Zheng
- Institute for Breast Health Medicine, Cance Center, Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Badia-Ramentol J, Gimeno-Valiente F, Duréndez E, Martínez-Ciarpaglini C, Linares J, Iglesias M, Cervantes A, Calon A, Tarazona N. The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice. Cancer Treat Rev 2023; 121:102643. [PMID: 37871463 DOI: 10.1016/j.ctrv.2023.102643] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Adjuvant chemotherapy following surgical intervention remains the primary treatment option for patients with localized colorectal cancer (CRC). However, a significant proportion of patients will have an unfavorable outcome after current forms of chemotherapy. While reflecting the increasing complexity of CRC, the clinical application of molecular biomarkers provides information that can be utilized to guide therapeutic strategies. Among these, caudal-related homeobox transcription factor 2 (CDX2) emerges as a biomarker of both prognosis and relapse after therapy. CDX2 is a key transcription factor that controls intestinal fate. Although rarely mutated in CRC, loss of CDX2 expression has been reported mostly in right-sided, microsatellite-unstable tumors and is associated with aggressive carcinomas. The pathological assessment of CDX2 by immunohistochemistry can thus identify patients with high-risk CRC, but the evaluation of CDX2 expression remains challenging in a substantial proportion of patients. In this review, we discuss the roles of CDX2 in homeostasis and CRC and the alterations that lead to protein expression loss. Furthermore, we review the clinical significance of CDX2 assessment, with a particular focus on its current use as a biomarker for pathological evaluation and clinical decision-making. Finally, we attempt to clarify the molecular implications of CDX2 deficiency, ultimately providing insights for a more precise evaluation of CDX2 protein expression.
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Affiliation(s)
- Jordi Badia-Ramentol
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - Elena Duréndez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | | | - Jenniffer Linares
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Iglesias
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain; Department of Pathology, Hospital del Mar, Barcelona, CIBERONC, Spain
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | - Alexandre Calon
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain.
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Kajiwara T, Nishina T, Yamashita R, Nakamura Y, Shiozawa M, Yuki S, Taniguchi H, Hara H, Ohta T, Esaki T, Shinozaki E, Takashima A, Yamamoto Y, Yamazaki K, Yoshino T, Hyodo I. Sidedness-Dependent Prognostic Impact of Gene Alterations in Metastatic Colorectal Cancer in the Nationwide Cancer Genome Screening Project in Japan (SCRUM-Japan GI-SCREEN). Cancers (Basel) 2023; 15:5172. [PMID: 37958346 PMCID: PMC10647889 DOI: 10.3390/cancers15215172] [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: 09/08/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The treatment strategies and prognoses of patients with metastatic colorectal cancer (CRC) differ according to the sidedness of the primary tumor. TP53 gain-of-function (GOF) and non-GOF variants have been reported to be differentially associated with prognosis by sidedness. We aimed to evaluate the sidedness-dependent prognostic impact of gene alterations in metastatic CRC. Patients enrolled between April 2017 and March 2019 were included in this study. Those excluded were individuals whose tumor tissues were obtained after chemotherapy and those who were enrolled in the study more than six months after starting first-line chemotherapy. Finally, we assessed 531 patients who underwent complete gene sequencing. The study revealed a significant difference in overall survival between individuals with left-sided CRC (n = 355) and right-sided colon cancer (CC) (n = 176) when considering the TP53 non-GOF variant, KRAS wild-type, NOTCH1 wild-type, NOTCH1 covariant, NOTCH3 sole variant, and MYC amplification. Multivariate analysis on each side revealed that the TP53 GOF and KRAS variants were independent poor prognostic factors for left-sided CRC (p = 0.03 and p < 0.01, respectively), and the TP53 non-GOF variant, BRAF V600E, and MYC amplification for right-sided CC (p < 0.05, p < 0.01, and p = 0.02, respectively). The NOTCH3 sole variant was an independent and favorable prognostic factor for left-sided CRC (p < 0.01). The prognostic significance of gene alterations differed between left-sided CRC and right-sided CC.
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Affiliation(s)
- Takeshi Kajiwara
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama 791-0280, Japan; (T.N.); (I.H.)
| | - Tomohiro Nishina
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama 791-0280, Japan; (T.N.); (I.H.)
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa 277-8577, Japan;
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (Y.N.); (T.Y.)
| | - Manabu Shiozawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama 241-8515, Japan;
| | - Satoshi Yuki
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo 060-8638, Japan;
| | - Hiroya Taniguchi
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan;
| | - Hiroki Hara
- Department of Gastroenterology, Saitama Cancer Center, Kitaadachi-gun, Saitama 362-0806, Japan;
| | - Takashi Ohta
- Department of Clinical Oncology, Kansai Rosai Hospital, Amagasaki 660-8511, Japan;
| | - Taito Esaki
- Department of Gastrointestinal and Medical Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka 811-1395, Japan;
| | - Eiji Shinozaki
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan;
| | - Atsuo Takashima
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan;
| | - Yoshiyuki Yamamoto
- Department of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan;
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shunto-gun, Shizuoka 411-8777, Japan;
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (Y.N.); (T.Y.)
| | - Ichinosuke Hyodo
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama 791-0280, Japan; (T.N.); (I.H.)
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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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Uchida S, Sugino T. ERBB2-Mutant Gastrointestinal Tumors Represent Heterogeneous Molecular Biology, Particularly in Microsatellite Instability, Tumor Mutation Burden, and Co-Mutated Genes: An In Silico Study. Curr Issues Mol Biol 2023; 45:7404-7416. [PMID: 37754252 PMCID: PMC10528499 DOI: 10.3390/cimb45090468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/28/2023] Open
Abstract
During recent years, activating mutations in ERBB2 have been reported in solid tumors of various organs, and clinical trials targeting ERBB2-mutant tumors have been conducted. However, no effective treatment has been established for gastrointestinal tumors targeting ERBB2 mutations. ERBB2-mutant tumors have a higher tumor mutation burden (TMB) and microsatellite instability (MSI) than ERBB2 non-mutant tumors, but not all ERBB2-mutant tumors are TMB- and MSI-high. Thus, a more detailed classification of ERBB2-mutant tumors based on the underlying molecular mechanisms is required. Herein, we classified ERBB2 mutations into three groups-group 1: both ERBB2 mutations and amplifications; group 2: ERBB2 mutations annotated as putative driver mutations but without amplifications; group 3: ERBB2 mutations annotated as non-driver mutations (passenger mutations or unknown significance) and those that were not amplified in gastrointestinal tumors. Esophageal adenocarcinoma, gastric cancer, and colorectal cancer presented significantly higher MSI and TMB in the ERBB2-mutant group than in the ERBB2-wild-type group. The proportions of TMB- and MSI-high tumors and frequency of co-mutated downstream genes differed among the groups. We identified TMB- and MSI-high groups; this classification is considered important for guiding the selection of drugs for ERBB2-mutant tumors with downstream genetic mutations.
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Affiliation(s)
- Shiro Uchida
- Division of Diagnostic Pathology, Kikuna Memorial Hospital, 4-4-27, Kikuna, Kohoku-ku, Yokohama 222-0011, Japan
- Division of Pathology, Shizuoka Cancer Center, Shizuoka 411-8777, Japan;
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka 411-8777, Japan;
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9
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Maki H, Jain AJ, Haddad A, Lendoire M, Chun YS, Vauthey J. Locoregional treatment for colorectal liver metastases aiming for precision medicine. Ann Gastroenterol Surg 2023; 7:543-552. [PMID: 37416742 PMCID: PMC10319606 DOI: 10.1002/ags3.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 07/08/2023] Open
Abstract
In patients with colorectal liver metastases (CLM), surgery is potentially curative. The use of novel surgical techniques and complementary percutaneous ablation allows for curative-intent treatment even in marginally resectable cases. Resection is used as part of a multidisciplinary approach, which for nearly all patients will include perioperative chemotherapy. Small CLM can be treated with parenchymal-sparing hepatectomy (PSH) and/or ablation. For small CLM, PSH results in better survival and higher rates of resectability of recurrent CLM than non-PSH. For patients with extensive bilateral distribution of CLM, two-stage hepatectomy or fast-track two-stage hepatectomy is effective. Our increasing knowledge of genetic alterations allows us to use them as prognostic factors alongside traditional risk factors (e.g. tumor diameter and tumor number) to select patients with CLM for resection and guide surveillance after resection. Alteration in RAS family genes (hereafter referred to as "RAS alteration") is an important negative prognostic factor, as are alterations in the TP53, SMAD4, FBXW7, and BRAF genes. However, APC alteration appears to improve prognosis. RAS alteration, increased number and diameter of CLM, and primary lymph node metastasis are well-known risk factors for recurrence after CLM resection. In patients free of recurrence 2 y after CLM resection, only RAS alteration is associated with recurrence. Thus, surveillance intensity can be stratified by RAS alteration status after 2 y. Novel diagnostic instruments and tools, such as circulating tumor DNA, may lead to further evolution of patient selection, prognostication, and treatment algorithms for CLM.
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Affiliation(s)
- Harufumi Maki
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Anish J. Jain
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Antony Haddad
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Mateo Lendoire
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Yun Shin Chun
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jean‐Nicolas Vauthey
- Department of Surgical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
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10
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Guo L, Dou Y, Xiang Y, Luo L, Xu X, Wang Q, Zhang Y, Liang T. Systematic analysis of cancer-specific synthetic lethal interactions provides insight into personalized anticancer therapy. FEBS J 2023; 290:1531-1548. [PMID: 36181326 DOI: 10.1111/febs.16643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
The concept of synthetic lethality has great potential for anticancer therapy as a new strategy to specifically kill cancer cells while sparing normal cells. To further understand the potential molecular interactions and gene characteristics involved in synthetic lethality, we performed a comprehensive analysis of predicted cancer-specific genetic interactions. Many genes were identified as cancer-associated genes that contributed to multiple biological processes and pathways, and the gene features were not random, indicating their potential roles in human carcinogenesis. Some relevant genes detected in multiple cancers were prone to be enriched in specific biological progresses and pathways, especially processes associated with DNA damage, chromosome-related functions and cancer pathways. These findings strongly implicated potential roles for these genes in cancer pathophysiology and functional relationships, as well as applications for future anticancer drug discovery. Further experimental validation indicated that the synthetic lethal interaction of APC and GFER may provide a potential anticancer strategy for patients with APC-mutant colon cancer. These results will contribute to further exploration of synthetic lethal interactions and broader application of the concept of synthetic lethality in anticancer therapeutics.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, China
| | - Yuyang Dou
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, China
| | - Yangyang Xiang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, China
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, China
| | - Xinru Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, China
| | - Qiushi Wang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, China
| | - Yuting Zhang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, China
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11
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Liu C, Jin Y, Zhang H, Yan J, Guo Y, Bao X, Zhao P. Effects of KMT2D mutation and its exon 39 mutation on the immune microenvironment and drug sensitivity in colorectal adenocarcinoma. Heliyon 2023; 9:e13629. [PMID: 36846668 PMCID: PMC9950945 DOI: 10.1016/j.heliyon.2023.e13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Background KMT2D mutation (KMT2DMT) was found to play an important role in cancer immunity and response to immune checkpoint inhibitors (ICIs). The present study aims to investigate the association between KMT2D exon 39 mutation (K-ex39MT) and molecular and clinical characteristics in colorectal adenocarcinoma (CRAD). Methods We performed profiling of KMT2DMT and K-ex39MT via Kaplan-Meier analysis, cBioportal, Immune-related functional analysis and correlation analysis with TCGA and MSK cohorts to explore their effects on the prognosis, immune landscape, molecular characteristics and drug sensitivity in CRAD. Panel gene sequencing of 30 in-house CRAD tissues and multiple immunofluorescences (mIF) were also used. Results In multi-cancer, patients with KMT2DMT have a worse overall survival (OS), and CRAD with K-ex39MT exhibited a greater degree of immune cellular infiltration. For CRAD, compared with KMT2D exon39 wild type (K-ex39WT), K-ex39MT patients had higher tumor mutational burden (TMB) and lower copy number alteration (CNA), and were accompanied by more immune cell infiltration including activated T cells, NK cells, Treg cells and exhausted T cells and enrichment of immune-related genes and pathways. In drug sensitivity prediction, K-ex39MT patients have a lower CTX-S score and IC50 of 5-Fluorouracil and irinotecan, and higher Tumor Immune Dysfunction and Rejection (TIDE) dysfunction score. Conclusions CRAD patients with K-ex39MT have more abundant immune cell infiltration and enrichment of immune-related pathways and signatures. And they may be more sensitive to some chemotherapies but less to cetuximab.
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Affiliation(s)
- Chuan Liu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China
| | - Yuzhi Jin
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China
| | - Junrong Yan
- Medical Department, Nanjing Geneseeq Technology Inc., Nanjing 210032, Jiangsu Province, People's Republic of China
| | - Yixuan Guo
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China,Corresponding author.
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang Province, People's Republic of China,Corresponding author.
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12
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Chen Y, Sun H, Deng Y, Ma Y, Huang H, Liu Y, Zhang Y, Zhang H, Ye S, E M, Guo H, Wu M, Wu C, Pu X, Chen X, Liang C, Ou Q, Weng H, Wu X, Shao Y, Gu A, Lin T. The clinical and genomic distinctions of Class1/2/3 BRAF-mutant colorectal cancer and differential prognoses. Biomark Res 2023; 11:11. [PMID: 36694231 PMCID: PMC9875443 DOI: 10.1186/s40364-022-00443-8] [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: 08/10/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
BRAF mutations are the oncogenic drivers in colorectal cancer and V600 mutations (Class1), which lead to RAS-independent active monomers, are the most common mutation types. BRAF non-V600 mutants can be further classified as RAS-independent active dimers (Class2) and RAS-dependent impaired kinase (Class3). We retrospectively reviewed the mutational profiles of 328 treatment-naïve colorectal tumors with BRAF mutations detected using capture-based hybrid next-generation sequencing targeting 400 + cancer-related genes. The clinical and genetic distinctions of patients harboring Class1/2/3 BRAF mutations were investigated, which revealed that tumors with Class1 BRAF mutations showed more unique genomic profiles than those with Class2/3 mutations. Also, by using an external dataset from cBioPortal, we demonstrated that patients with Class3 BRAF mutations had the best survival outcomes compared to the other two subgroups. These findings promoted the development of anti-BRAF strategies by distinguishing BRAF mutant subgroups.
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Affiliation(s)
- Yungchang Chen
- grid.54549.390000 0004 0369 4060Department of Medical Oncology, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Sichuan 610041 Chengdu, China
| | - Hao Sun
- grid.190737.b0000 0001 0154 0904Department of Gastrointestinal Cancer Center, Chongqing University Cancer Hospital, 400030 Chongqing, China
| | - Yanhong Deng
- grid.488525.6Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-sen University, 510655 Guangzhou, China
| | - Yutong Ma
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - He Huang
- grid.488530.20000 0004 1803 6191Department of Medical Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Yang Liu
- grid.54549.390000 0004 0369 4060Department of Pathology, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, 610041 Chengdu, China
| | - Yaru Zhang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - Hongyu Zhang
- grid.452859.70000 0004 6006 3273Department of Medical Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, 519000 Zhuhai, China
| | - Sheng Ye
- grid.412615.50000 0004 1803 6239Department of Medical Oncology, The First Affiliated Hospital of Sun Yat-sen University, 510080 Guangzhou, China
| | - Mingyan E
- grid.412651.50000 0004 1808 3502Department of Radiation Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, 150040 Harbin, Heilongjiang China
| | - Hongqiang Guo
- grid.414008.90000 0004 1799 4638Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 450008 Zhengzhou, China
| | - Mengmeng Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - Chunman Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - Xingxiang Pu
- grid.216417.70000 0001 0379 7164Department of Thoracic Medical Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Yuelu District, 410013 Changsha, China
| | - Xinggui Chen
- grid.410560.60000 0004 1760 3078Department of Medical Oncology, Cancer Center, Affiliated Hospital of Guangdong Medical University, 524023 Zhanjiang, China
| | - Chaoyong Liang
- grid.256607.00000 0004 1798 2653Department of Medical Oncology, Guangxi Medical University Cancer Hospital, 530021 Nanning, China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - Huawei Weng
- grid.488530.20000 0004 1803 6191Department of Medical Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc, 210000 Nanjing, China ,grid.89957.3a0000 0000 9255 8984School of Public Health, Nanjing Medical University, 211166 Nanjing, China
| | - Anxin Gu
- grid.412651.50000 0004 1808 3502Department of Radiation Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, 150040 Harbin, Heilongjiang China
| | - Tongyu Lin
- grid.54549.390000 0004 0369 4060Department of Medical Oncology, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, No. 55, Section 4, South Renmin Road, Sichuan 610041 Chengdu, China ,grid.488530.20000 0004 1803 6191Department of Medical Oncology, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
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13
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Chang YK, Tseng HH, Leung CM, Lu KC, Tsai KW. Targeted Next-Generation Sequencing-Based Multiple Gene Mutation Profiling of Patients with Rectal Adenocarcinoma Receiving or Not Receiving Neoadjuvant Chemoradiotherapy. Int J Mol Sci 2022; 23:ijms231810353. [PMID: 36142267 PMCID: PMC9499649 DOI: 10.3390/ijms231810353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
This study investigated whether oncogenic and tumor-suppressive gene mutations are involved in the differential outcomes of patients with rectal carcinoma receiving neoadjuvant chemoradiotherapy (nCRT). Genomic DNA was obtained from formalin-fixed paraffin-embedded (FFPE) specimens of patients with rectal carcinoma who received a complete nCRT course. Gene mutation status was examined in specimens from patients before and after nCRT by using the AmpliSeq platform. Our data revealed that the nonsynonymous p53, APC, KRAS, CDKN2A, and EGFR mutations were observed in 93.1%, 65.5%, 48.6%, and 31% of the patients with rectal adenocarcinoma, respectively. BRAF, FBXW7, PTEN, and SMAD4 mutations were observed in 20.7% of patients with rectal carcinoma. The following 12 gene mutations were observed more frequently in the patients exhibiting a complete response than in those demonstrating a poor response before nCRT: ATM, BRAF, CDKN2A, EGFR, FLT3, GNA11, KDR, KIT, PIK3CA, PTEN, PTPN11, SMAD4, and TP53. In addition, APC, BRAF, FBXW7, KRAS, SMAD4, and TP53 mutations were retained after nCRT. Our results indicate a complex mutational profile in rectal carcinoma, suggesting the involvement of BRAF, SMAD4, and TP53 genetic variants in the outcomes of patients with nCRT.
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Affiliation(s)
- You-Kang Chang
- Department of Radiation Oncology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei 23142, Taiwan
- College of Medicine, Tzu Chi University, Hualien City 97004, Taiwan
| | - Hui-Hwa Tseng
- Department of Anatomic Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 97004, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 81341, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 97004, Taiwan
- Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City 24205, Taiwan
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 23142, Taiwan
- Correspondence: ; Tel.: +886-2-266289779 (ext. 5796); Fax: +886-2-66281258
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14
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Russo V, Lallo E, Munnia A, Spedicato M, Messerini L, D’Aurizio R, Ceroni EG, Brunelli G, Galvano A, Russo A, Landini I, Nobili S, Ceppi M, Bruzzone M, Cianchi F, Staderini F, Roselli M, Riondino S, Ferroni P, Guadagni F, Mini E, Peluso M. Artificial Intelligence Predictive Models of Response to Cytotoxic Chemotherapy Alone or Combined to Targeted Therapy for Metastatic Colorectal Cancer Patients: A Systematic Review and Meta-Analysis. Cancers (Basel) 2022; 14:4012. [PMID: 36011003 PMCID: PMC9406544 DOI: 10.3390/cancers14164012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Tailored treatments for metastatic colorectal cancer (mCRC) have not yet completely evolved due to the variety in response to drugs. Therefore, artificial intelligence has been recently used to develop prognostic and predictive models of treatment response (either activity/efficacy or toxicity) to aid in clinical decision making. In this systematic review, we have examined the ability of learning methods to predict response to chemotherapy alone or combined with targeted therapy in mCRC patients by targeting specific narrative publications in Medline up to April 2022 to identify appropriate original scientific articles. After the literature search, 26 original articles met inclusion and exclusion criteria and were included in the study. Our results show that all investigations conducted on this field have provided generally promising results in predicting the response to therapy or toxic side-effects. By a meta-analytic approach we found that the overall weighted means of the area under the receiver operating characteristic (ROC) curve (AUC) were 0.90, 95% C.I. 0.80-0.95 and 0.83, 95% C.I. 0.74-0.89 in training and validation sets, respectively, indicating a good classification performance in discriminating response vs. non-response. The calculation of overall HR indicates that learning models have strong ability to predict improved survival. Lastly, the delta-radiomics and the 74 gene signatures were able to discriminate response vs. non-response by correctly identifying up to 99% of mCRC patients who were responders and up to 100% of patients who were non-responders. Specifically, when we evaluated the predictive models with tests reaching 80% sensitivity (SE) and 90% specificity (SP), the delta radiomics showed an SE of 99% and an SP of 94% in the training set and an SE of 85% and SP of 92 in the test set, whereas for the 74 gene signatures the SE was 97.6% and the SP 100% in the training set.
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Affiliation(s)
- Valentina Russo
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Eleonora Lallo
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Armelle Munnia
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Miriana Spedicato
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Romina D’Aurizio
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Elia Giuseppe Ceroni
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Giulia Brunelli
- Institute of Informatics and Telematics, National Research Council, 56124 Pisa, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Ida Landini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Marcello Ceppi
- Clinical Epidemiology Unit, IRCCS-Ospedale Policlinico San Martino, 16131 Genova, Italy
| | - Marco Bruzzone
- Clinical Epidemiology Unit, IRCCS-Ospedale Policlinico San Martino, 16131 Genova, Italy
| | - Fabio Cianchi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Fabio Staderini
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Mario Roselli
- Medical Oncology Unit, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Silvia Riondino
- Medical Oncology Unit, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Patrizia Ferroni
- BioBIM (InterInstitutional Multidisciplinary Biobank), IRCCS San Raffaele Roma, 00166 Rome, Italy
- Department of Human Sciences & Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Fiorella Guadagni
- BioBIM (InterInstitutional Multidisciplinary Biobank), IRCCS San Raffaele Roma, 00166 Rome, Italy
- Department of Human Sciences & Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Marco Peluso
- Research and Development Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
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15
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Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer. Nat Med 2022; 28:1646-1655. [PMID: 35970919 PMCID: PMC9801308 DOI: 10.1038/s41591-022-01930-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/29/2022] [Indexed: 01/03/2023]
Abstract
The incidence of rectal cancer is increasing in patients younger than 50 years. Locally advanced rectal cancer is still treated with neoadjuvant radiation, chemotherapy and surgery, but recent evidence suggests that patients with a complete response can avoid surgery permanently. To define correlates of response to neoadjuvant therapy, we analyzed genomic and transcriptomic profiles of 738 untreated rectal cancers. APC mutations were less frequent in the lower than in the middle and upper rectum, which could explain the more aggressive behavior of distal tumors. No somatic alterations had significant associations with response to neoadjuvant therapy in a treatment-agnostic manner, but KRAS mutations were associated with faster relapse in patients treated with neoadjuvant chemoradiation followed by consolidative chemotherapy. Overexpression of IGF2 and L1CAM was associated with decreased response to neoadjuvant therapy. RNA-sequencing estimates of immune infiltration identified a subset of microsatellite-stable immune hot tumors with increased response and prolonged disease-free survival.
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16
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van den Driest L, Johnson CH, Rattray NJW, Rattray Z. Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancer. Altern Lab Anim 2022; 50:282-292. [PMID: 35765262 DOI: 10.1177/02611929221107546] [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: 11/16/2022]
Abstract
Colorectal cancer (CRC) is a global cause of cancer-related mortality driven by genetic and environmental factors which influence therapeutic outcomes. The emergence of next-generation sequencing technologies enables the rapid and extensive collection and curation of genetic data for each cancer type into clinical gene expression biobanks. We report the application of bioinformatics tools for investigating the expression patterns and prognostic significance of three genes that are commonly dysregulated in colon cancer: adenomatous polyposis coli (APC); B-Raf proto-oncogene (BRAF); and Kirsten rat sarcoma viral oncogene homologue (KRAS). Through the use of bioinformatics tools, we show the patterns of APC, BRAF and KRAS genetic alterations and their role in patient prognosis. Our results show mutation types, the frequency of mutations, tumour anatomical location and differential expression patterns for APC, BRAF and KRAS for colorectal tumour and matched healthy tissue. The prognostic value of APC, BRAF and KRAS genetic alterations was investigated as a function of their expression levels in CRC. In the era of precision medicine, with significant advancements in biobanking and data curation, there is significant scope to use existing clinical data sets for evaluating the role of mutational drivers in carcinogenesis. This approach offers the potential for studying combinations of less well-known genes and the discovery of novel biomarkers, or for studying the association between various effector proteins and pathways.
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Affiliation(s)
- Lisa van den Driest
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 3527University of Strathclyde, Glasgow, UK
| | | | - Nicholas J W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 3527University of Strathclyde, Glasgow, UK
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, 3527University of Strathclyde, Glasgow, UK
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17
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Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules 2022; 12:biom12070878. [PMID: 35883434 PMCID: PMC9312989 DOI: 10.3390/biom12070878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer is one of the most prevalent cancer types. Although there have been breakthroughs in its treatments, a better understanding of the molecular mechanisms and genetic involvement in colorectal cancer will have a substantial role in producing novel and targeted treatments with better safety profiles. In this review, the main molecular pathways and driver genes that are responsible for initiating and propagating the cascade of signaling molecules reaching carcinoma and the aggressive metastatic stages of colorectal cancer were presented. Protein kinases involved in colorectal cancer, as much as other cancers, have seen much focus and committed efforts due to their crucial role in subsidizing, inhibiting, or changing the disease course. Moreover, notable improvements in colorectal cancer treatments with in silico studies and the enhanced selectivity on specific macromolecular targets were discussed. Besides, the selective multi-target agents have been made easier by employing in silico methods in molecular de novo synthesis or target identification and drug repurposing.
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18
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Lin Y, Liao X, Zhang Y, Wu G, Ye J, Luo S, He X, Luo M, Xie M, Zhang J, Li Q, Huang Y, Liao S, Li Y, Liang R. Homologous Recombination Pathway Alternation Predicts Prognosis of Colorectal Cancer With Chemotherapy. Front Pharmacol 2022; 13:920939. [PMID: 35734400 PMCID: PMC9207269 DOI: 10.3389/fphar.2022.920939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Chemotherapy is the basic treatment for colorectal cancer (CRC). However, colorectal cancer cells often develop resistance to chemotherapy drugs, leading to recurrence and poor prognosis. More and more studies have shown that the Homologous recombination (HR) pathway plays an important role in chemotherapy treatment for tumors. However, the relationship between HR pathway, chemotherapy sensitivity, and the prognosis of CRC patients is still unclear. Methods: We collected 35 samples of CRC patients after chemotherapy treatment from Guangxi Medical University Cancer Hospital, then collected mutation data and clinical prognosis data from the group. We also downloaded Mondaca-CRC, TCGA-CRC cohorts for chemotherapy treatment. Result: We found that HR mutant-type (HR-MUT) patients are less likely to experience tumor metastasis after receiving chemotherapy. Additionally, our univariate and multivariate cox regression models showed that HR-MUT can be used as an independent predictor of the prognosis of chemotherapy for CRC patients. The KM curve showed that patients with HR-MUT CRC had significantly prolonged overall survival (OS) time (log-rank p = 0.017; hazard ratio (HR) = 0.69). Compared to HR mutant-type (HR-WT), HR-MUT has a significantly lower IC50 value with several chemotherapeutic drugs. Pathway enrichment analysis further revealed that the HR-MUT displayed a significantly lower rate of DNA damage repair ability, tumor growth, metastasis activity, and tumor fatty acid metabolism activity than HR-WT, though its immune response activity was notably higher. Conclusion: These findings indicate that HR-MUT may be a relevant marker for CRC patients receiving chemotherapy, as it is closely related to improving OS time and reducing chemotherapy resistance.
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Affiliation(s)
- Yan Lin
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiaoli Liao
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yumei Zhang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Guobin Wu
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Jiazhou Ye
- Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Shanshan Luo
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xinxin He
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Min Luo
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingzhi Xie
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Jinyan Zhang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Qian Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yu Huang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Sina Liao
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yongqiang Li
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Rong Liang, ; Yongqiang Li,
| | - Rong Liang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Rong Liang, ; Yongqiang Li,
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19
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Li J, Ji Y, Chen N, Wang H, Fang C, Yin X, Jiang Z, Dong Z, Zhu D, Fu J, Zhou W, Jiang R, He L, Hantao Z, Shi G, Cheng L, Su X, Dai L, Deng H. A specific upregulated lncRNA in colorectal cancer promotes cancer progression. JCI Insight 2022; 7:158855. [PMID: 35617032 PMCID: PMC9462503 DOI: 10.1172/jci.insight.158855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNA (lncRNA) plays a crucial role in the pathogenesis of various diseases, including colorectal cancer (CRC). The gene mutations of Adenomatous polyposis coli (APC) were found in most colorectal cancer patients. They are functioned as an important inducer of tumorigenesis. Based on our microarray results, we identified a specific upregulated lncRNA in colorectal cancer (SURC). Further analysis showed that high SURC expression correlated with poorer disease-free survival and overall survival in patients with colorectal cancer. Besides, we found that mutated APC genes can promote the transcription of SURC by reducing the degradation of β-catenin protein in colorectal cancer. Functional assays revealed that knockdown of SURC impaired CRC cell proliferation, colony formation, cell cycle and tumor growth. Additionally, SURC can promote CCND2 expression by inhibiting the expression of miR-185-5p in CRC cells. In conclusion, we demonstrate that SURC is a specific upregulated lncRNA in CRC and the SURC/miR-185-5p/CCND2 axis may be targetable for CRC diagnosis and therapy.
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Affiliation(s)
- Junshu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Ji
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Na Chen
- School of Pharmacy, Chengdu Medical College, Chengdu, China
| | - Huiling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaonan Yin
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyuan Jiang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zhexu Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wencheng Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ruiyi Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling He
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhang Hantao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaolan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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20
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Okamoto T, Natsume Y, Doi M, Nosato H, Iwaki T, Yamanaka H, Yamamoto M, Kawachi H, Noda T, Nagayama S, Sakanashi H, Yao R. Integration of human inspection and AI-based morphological typing of PDOs reveals inter-patient heterogeneity of colorectal cancer. Cancer Sci 2022; 113:2693-2703. [PMID: 35585758 PMCID: PMC9357621 DOI: 10.1111/cas.15396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogenous disease, and patients have differences in therapeutic response. However, the mechanisms underlying inter-patient heterogeneity in the response to chemotherapeutic agents remain to be elucidated, and molecular tumor characteristics are required to select patients for specific therapies. Patient-derived organoids (PDOs) established from CRCs recapitulate various biological characteristics of tumor tissues, including cellular heterogeneity and the response to chemotherapy. PDOs established from CRCs exhibit various morphologies, but there are no criteria for defining these morphologies, which hampers the analysis of their biological significance. Here, we developed an artificial intelligence (AI)-based classifier to categorize PDOs based on microscopic images according to their similarity in appearance and classified tubular adenocarcinoma-derived PDOs into six types. Transcriptome analysis identified differential expression of genes related to cell adhesion in some of the morphological types. Genes involved in ribosome biogenesis were also differentially expressed and were most highly expressed in morphological types exhibiting CRC stem cell properties. We identified an RNA polymerase I inhibitor, CX-5641, to be an upstream regulator of these type-specific gene sets. Notably, PDO types with increased expression of genes involved in ribosome biogenesis were resistant to CX-5461 treatment. Taken together, these results uncover the biological significance of the morphology of PDOs and provide novel indicators by which to categorize CRCs. Therefore, the AI-based classifier is a useful tool to support PDO-based cancer research.
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Affiliation(s)
- Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hirokazu Nosato
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Toshiyuki Iwaki
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Mayuko Yamamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute; Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tetsuo Noda
- Director's office, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Hidenori Sakanashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
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21
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Lin A, Zhou N, Zhu W, Zhang J, Wei T, Guo L, Luo P, Zhang J. Genomic and immunological profiles of small-cell lung cancer between East Asians and Caucasian. Cancer Cell Int 2022; 22:173. [PMID: 35488336 PMCID: PMC9052616 DOI: 10.1186/s12935-022-02588-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 12/05/2022] Open
Abstract
The characterization of immunological and genomic differences in small-cell lung cancer (SCLC) between East Asian (EA) and Caucasian patients can reveal important clinical therapies for EA patients with SCLC. By sequencing and analyzing a molecular and immunological dataset of 98-SCLC patients of EA ancestry, immunogenicity, including DNA damage repair alterations and tumor mutation burden (TMB), was found to be significantly higher in the EA cohort than in the Caucasian cohort. The epithelial-mesenchymal transition (EMT) was the signaling signature with the predominant frequency of mutations across all patients in the EA cohort. Analysis of tumor-infiltrated immune cells revealed that resting lymphocytes were significantly enriched in the EA cohort. Compound-targeting analysis showed that topoisomerase inhibitors might be capable of targeting TP53 and RB1 comutations in EA SCLC patients. EA SCLC patients who harbored COL6A6 mutations had poor survival, while Caucasian SCLC patients with OTOF, ANKRD30B, and TECPR2 mutations were identified to have a shorter survival.
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Affiliation(s)
- Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Ningning Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Jiexia Zhang
- Department of Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Ting Wei
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
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22
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Johnson H, El-Schich Z, Ali A, Zhang X, Simoulis A, Wingren AG, Persson JL. Gene-Mutation-Based Algorithm for Prediction of Treatment Response in Colorectal Cancer Patients. Cancers (Basel) 2022; 14:cancers14082045. [PMID: 35454952 PMCID: PMC9030299 DOI: 10.3390/cancers14082045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose: Despite the high mortality of metastatic colorectal cancer (mCRC), no new biomarker tools are available for predicting treatment response. We developed gene-mutation-based algorithms as a biomarker classifier to predict treatment response with better precision than the current predictive factors. Methods: Random forest machine learning (ML) was applied to identify the candidate algorithms using the MSK Cohort (n = 471) as a training set and validated in the TCGA Cohort (n = 221). Logistic regression, progression-free survival (PFS), and univariate/multivariate Cox proportional hazard analyses were performed and the performance of the candidate algorithms was compared with the established risk parameters. Results: A novel 7-Gene Algorithm based on mutation profiles of seven KRAS-associated genes was identified. The algorithm was able to distinguish non-progressed (responder) vs. progressed (non-responder) patients with AUC of 0.97 and had predictive power for PFS with a hazard ratio (HR) of 16.9 (p < 0.001) in the MSK cohort. The predictive power of this algorithm for PFS was more pronounced in mCRC (HR = 16.9, p < 0.001, n = 388). Similarly, in the TCGA validation cohort, the algorithm had AUC of 0.98 and a significant predictive power for PFS (p < 0.001). Conclusion: The novel 7-Gene Algorithm can be further developed as a biomarker model for prediction of treatment response in mCRC patients to improve personalized therapies.
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Affiliation(s)
| | - Zahra El-Schich
- Department of Biomedical Sciences, Malmö University, SE-206 06 Malmö, Sweden; (Z.E.-S.); (A.G.W.)
| | - Amjad Ali
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden;
| | - Xuhui Zhang
- Department of Bio-Diagnosis, Institute of Basic Medical Sciences, Beijing 100005, China;
| | - Athanasios Simoulis
- Department of Clinical Pathology and Cytology, Skåne University Hospital, SE-205 02 Malmö, Sweden;
| | - Anette Gjörloff Wingren
- Department of Biomedical Sciences, Malmö University, SE-206 06 Malmö, Sweden; (Z.E.-S.); (A.G.W.)
| | - Jenny L. Persson
- Department of Biomedical Sciences, Malmö University, SE-206 06 Malmö, Sweden; (Z.E.-S.); (A.G.W.)
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden;
- Correspondence: ; Tel.: +46-0706391199
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23
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Chen X, Hu M, Chen Y, Li A, Hua Y, Jiang H, Li H, Lin M. Targeted deep sequencing reveals APC mutations as predictors of overall survival in Chinese colorectal patients receiving adjuvant chemotherapy. Scand J Gastroenterol 2022; 57:465-472. [PMID: 34978498 DOI: 10.1080/00365521.2021.2022189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objective: Targeted deep sequencing was used to characterize the mutational spectrum of APC in Chinese colorectal tumors in comparison to that in Caucasians from The Cancer Genome Atlas (TCGA) and to investigate whether APC mutations can predict overall survival in CRC patients receiving adjuvant chemotherapy.Methods: A total of 315 Chinese CRC patients including 241 stage II/III patients receiving fluorouracil-based adjuvant chemotherapy were included in this study. Next generation sequencing was carried out to detect somatic mutations on all APC exons. The associations between APC mutations and overall survival were determined by the Cox proportional hazards model.Results:APC was mutated in 221 of 315 colorectal tumors (70.2%). Chinese CRC had a much higher frequency of missense mutations (16.2% vs. 2.4%), but a lower frequency of nonsense (41.0% vs. 54.2%) and frameshift mutations (10.5% vs. 18.4%) than Caucasian CRC. Among stage II/III patients receiving fluorouracil-based adjuvant chemotherapy, APC mutations showed a significant association with worse survival (HR = 1.69; 95% CI, 1.10-2.62; p = .0179). Of the mutation types, frameshift mutations conferred the highest risk of death (HR = 2.88; 95% CI, 1.54-5.37; p =.0009). Among individual mutation sites, Arg232Ter, the most frequent mutation in Chinese CRC, exhibited the strongest negative impact on survival (HR = 2.65; 95% CI, 1.16-6.03; p =.0202).Conclusion:APC overall mutation was an independent predictor for overall survival of stage II/III CRC patients receiving fluorouracil-based chemotherapy.
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Affiliation(s)
- Xin Chen
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Mengjun Hu
- Department of Pathology, Zhuji People's Hospital, Shaoxing, China
| | - Ying Chen
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Ajian Li
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Yutong Hua
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Huihong Jiang
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Huaguang Li
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
| | - Moubin Lin
- Department of General Surgery, Yangpu Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China.,Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai, China
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24
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Currais P, Rosa I, Claro I. Colorectal cancer carcinogenesis: From bench to bedside. World J Gastrointest Oncol 2022; 14:654-663. [PMID: 35321283 PMCID: PMC8919024 DOI: 10.4251/wjgo.v14.i3.654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/18/2021] [Accepted: 02/20/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) remains one of the main causes of cancer death in developed countries. Yet, it is potentially preventable, by removing the precursor lesions - adenomas or serrated lesions. Several studies proved that this intervention reduces CRC mortality and that the first colonoscopy’s results can guide surveillance strategies. More recently, it became clear that several carcinogenesis pathways may lead to sporadic CRC. CRC is a heterogeneous disease, characterized by multiple molecular subtypes. Three main pathways have been implicated in the development of CRC: Chromosomal instability, microsatellite instability, and the “serrated” pathways, with overlapping features between them. This and other molecular and genetic based CRC classifications are known to have clinical implications, spanning from familial risk assessment to therapy choices. The authors review basic science data and provide insight on current implications for the management of patients with CRC.
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Affiliation(s)
- Pedro Currais
- Department of Gastroenterology, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, Lisboa 1099-023, Portugal
| | - Isadora Rosa
- Department of Gastroenterology, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, Lisboa 1099-023, Portugal
| | - Isabel Claro
- Department of Gastroenterology, Instituto Portugues de Oncologia de Lisboa Francisco Gentil, Lisboa 1099-023, Portugal
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25
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Son HY, Jeong HK, Apostolopoulos V, Kim CW. MUC1 expressing tumor growth was retarded after human mucin 1 (MUC1) plasmid DNA immunization. Int J Immunopathol Pharmacol 2022; 36:3946320221112358. [PMID: 35839304 PMCID: PMC9289905 DOI: 10.1177/03946320221112358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Introduction Naked DNA is one of the attractive tools for vaccination studies. We studied naked DNA
vaccination against the human tumor antigen, mucin, which is encoded by the
MUC1 gene. Methods We constructed the pcDNA3.0-MUC1 (pcDNA-MUC1) plasmid expressing an underglycosylated
MUC1 protein. BALB/c mice were immunized intradermally thrice at 2-weeks intervals with
pcDNA-MUC1. Two weeks after the last immunization, tumor challenge experiments were
performed using either the CT26 or TA3HA tumor cell lines, both of which transduce human
MUC1. Results Immune cell population monitoring from pcDNA-MUC1-immunized animals indicated that
immune cell activation was induced by MUC1-specific immunization. Using intracellular
fluorescence activated cell sorting and enzyme-linked immunosorbent spot assay, we
reported that interferon-γ secreting CD8+ T cells were mainly involved in
MUC1-specific immunization. In all mice immunized with MUC1 DNA, tumor
growth inhibition was observed, whereas control mice developed tumors
(p < 0.001). Conclusion Our results suggest that intradermal immunization with MUC1 DNA
induces MUC1-specific CD8+ T cell infiltration into tumors, elicits
tumor-specific Th1-type immune response, and inhibits tumor growth.
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Affiliation(s)
- Hye-Youn Son
- Department of Breast and Endocrine Surgery, Center for Medical Innovation, 58927Seoul National University Hospital, Seoul, South Korea
| | - Hwan-Kyu Jeong
- School of Biosystems and Biomedical Sciences, 34973Korea University, Seoul, South Korea
| | - Vasso Apostolopoulos
- Institute for Health and Sport, 5399Victoria University, Melbourne, Vic, Australia
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26
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Manca P, Corallo S, Busico A, Lonardi S, Corti F, Antoniotti C, Procaccio L, Clavarezza M, Smiroldo V, Tomasello G, Murialdo R, Sartore-Bianchi A, Racca P, Pagani F, Randon G, Martinetti A, Sottotetti E, Palermo F, Perrone F, Tamborini E, Prisciandaro M, Raimondi A, Di Bartolomeo M, Morano F, Pietrantonio F. The Added Value of Baseline Circulating Tumor DNA Profiling in Patients with Molecularly Hyperselected, Left-sided Metastatic Colorectal Cancer. Clin Cancer Res 2021; 27:2505-2514. [PMID: 33547199 DOI: 10.1158/1078-0432.ccr-20-4699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/08/2021] [Accepted: 01/29/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The routine use of liquid biopsy is not recommended for the choice of initial treatment for patients with metastatic colorectal cancer (mCRC). EXPERIMENTAL DESIGN We included patients with left-sided, RAS/BRAF wild-type, HER2-negative, and microsatellite stable mCRC, treated with upfront panitumumab/FOLFOX-4 in the Valentino study. We performed amplicon-based genomic profiling of 14 genes in baseline plasma samples and compared these data with tumor tissue ultra-deep sequencing results. Specific gene mutations in circulating tumor DNA (ctDNA) and their clonality were associated with progression-free survival (PFS), overall survival (OS), and radiological dynamics. RESULTS Ten and 15 of 120 patients had a mutation of RAS and PIK3CA in ctDNA, with a positive concordance with tissue deep sequencing of only 31.3% and 47.1%, respectively. Presence of RAS or PIK3CA mutations in baseline ctDNA was associated with worse median PFS [8 vs. 12.8 months; HR, 2.49; 95% confidence interval (CI), 1.28-4.81; P = 0.007 and 8.5 vs. 12.9 months; HR, 2.86; 95% CI, 1.63-5.04; P < 0.001] and median OS (17.1 vs. 36.5 months; HR, 2.26; 95% CI, 1.03-4.96; P = 0.042 and 21.1 vs. 38.9 months; HR, 2.18; 95% CI, 1.16-4.07; P = 0.015). RAS mutations in ctDNA were associated with worse RECIST response, early tumor shrinkage, and depth of response, while PIK3CA mutations were not. Patients with higher levels of RAS/PIK3CA variant allele fraction (VAF) in ctDNA had the worst outcomes (VAF ≥ 5% vs. all wild-type: median PFS, 7.7 vs. 13.1 months; HR, 4.02; 95% CI, 2.03-7.95; P < 0.001 and median OS, 18.8 vs. 38.9 months; HR, 4.07; 95% CI, 2.04-8.12; P < 0.001). CONCLUSIONS Baseline ctDNA profiling may add value to tumor tissue testing to refine the molecular hyperselection of patients with mCRC for upfront anti-EGFR-based strategies.
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Affiliation(s)
- Paolo Manca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Corallo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Lonardi
- Unit of Medical Oncology 1, Department of Clinical and Experimental Oncology & Early Phase Clinical Trial Unit, Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - Francesca Corti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Carlotta Antoniotti
- Unit of Medical Oncology, Azienda Ospedaliero-Universitaria Pisana, Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Letizia Procaccio
- Unit of Medical Oncology 1, Department of Clinical and Experimental Oncology & Early Phase Clinical Trial Unit, Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - Matteo Clavarezza
- Medical Oncology Unit, Ente Ospedaliero Ospedali Galliera, Genoa, Italy
| | - Valeria Smiroldo
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Gianluca Tomasello
- Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Roberto Murialdo
- Department of Internal Medicine (Di.M.I.), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan & Department of Oncology and Hemato-Oncology, Università degli Studi di Milano (La Statale), Milan, Italy
| | - Patrizia Racca
- Medical Oncology Division 1, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Filippo Pagani
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonia Martinetti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisa Sottotetti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Palermo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Prisciandaro
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandra Raimondi
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Di Bartolomeo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Morano
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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