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Austin AL, Broaddus RR, Souers RJ, Kane ME, Kolhe R, Miller DV, Moncur JT, Ramkissoon S, Tafe LJ, Trembath DG, Graham RP. Current laboratory testing practices for mismatch repair deficiency and microsatellite instability testing: A survey-based review of current laboratory practices. Am J Clin Pathol 2024:aqae094. [PMID: 39078096 DOI: 10.1093/ajcp/aqae094] [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: 02/19/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES To describe mismatch repair (MMR) and microsatellite instability (MSI) testing practices in laboratories using the College of American Pathologists (CAP) MSI/MMR proficiency testing programs prior to the 2022 publication of the MSI/MMR practice guidelines copublished by CAP and the Association of Molecular Pathology (AMP). METHODS Data from supplemental questionnaires provided with the 2020-B MSI/MMR programs to 542 laboratories across different practice settings were reviewed. Questionnaires contained 21 questions regarding the type of testing performed, specimen/tumor types used for testing, and clinical practices for checkpoint blockade therapy. RESULTS Domestic laboratories test for MSI/MMR more often than international laboratories (P = .04) and academic hospitals/medical centers test more frequently than nonhospital sites/clinics (P = .03). The most commonly used testing modality is immunohistochemistry, followed by polymerase chain reaction, then next-generation sequencing. Most laboratories (72.6%; 347/478) reported awareness of the use of immune checkpoint inhibitor therapy for patients with high MSI or MMR-deficient results. CONCLUSIONS The results demonstrate the state of MMR and MSI testing in laboratories prior to the publication of the CAP/AMP best practice guidelines, highlighting differences between various laboratory types. The findings indicate the importance of consensus guidelines and provide a baseline for comparison after their implementation.
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Affiliation(s)
- Amy L Austin
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD, US
| | - Russell R Broaddus
- Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, US
| | - Rhona J Souers
- Biostatistics Department, College of American Pathologists, Northfield, IL, US
| | - Megan E Kane
- Proficiency Testing Department, College of American Pathologists, Northfield, IL, US
| | - Ravindra Kolhe
- Pathology, Medical College of Georgia at Augusta University, Augusta, GA, US
| | - Dylan V Miller
- EM and Immunostains Laboratory, Intermountain Central Laboratory, Murray, UT, US
| | - Joel T Moncur
- Office of the Director, The Joint Pathology Center, Silver Spring, MD, US
| | | | - Laura J Tafe
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, US
| | - Dimitri G Trembath
- Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, US
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2
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Kim M, Shim HS, Kim S, Lee IH, Kim J, Yoon S, Kim HD, Park I, Jeong JH, Yoo C, Cheon J, Kim IH, Lee J, Hong SH, Park S, Jung HA, Kim JW, Kim HJ, Cha Y, Lim SM, Kim HS, Lee CK, Kim JH, Chun SH, Yun J, Park SY, Lee HS, Cho YM, Nam SJ, Na K, Yoon SO, Lee A, Jang KT, Yun H, Lee S, Kim JH, Kim WS. Clinical Practice Recommendations for the Use of Next-Generation Sequencing in Patients with Solid Cancer: A Joint Report from KSMO and KSP. Cancer Res Treat 2024; 56:721-742. [PMID: 38037319 PMCID: PMC11261187 DOI: 10.4143/crt.2023.1043] [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: 09/13/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.
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Affiliation(s)
- Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Shinkyo Yoon
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyung-Don Kim
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Inkeun Park
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Ho Jeong
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Oncology,Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jieun Lee
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sook Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jin Won Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Han Jo Kim
- Division of Oncology and Hematology, Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Yongjun Cha
- Division of Medical Oncology, Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Choong-kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jee Hung Kim
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Chun
- Division of Medical Oncology, Department of Internal Medicine, Bucheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jina Yun
- Division of Hematology/Oncology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Mee Cho
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Soo Jeong Nam
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Korea
| | - Sun Och Yoon
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
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3
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Kim M, Shim HS, Kim S, Lee IH, Kim J, Yoon S, Kim HD, Park I, Jeong JH, Yoo C, Cheon J, Kim IH, Lee J, Hong SH, Park S, Jung HA, Kim JW, Kim HJ, Cha Y, Lim SM, Kim HS, Lee CK, Kim JH, Chun SH, Yun J, Park SY, Lee HS, Cho YM, Nam SJ, Na K, Yoon SO, Lee A, Jang KT, Yun H, Lee S, Kim JH, Kim WS. Clinical practice recommendations for the use of next-generation sequencing in patients with solid cancer: a joint report from KSMO and KSP. J Pathol Transl Med 2024; 58:147-164. [PMID: 39026440 PMCID: PMC11261170 DOI: 10.4132/jptm.2023.11.01] [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: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 07/20/2024] Open
Abstract
In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.
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Affiliation(s)
- Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyung-Don Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Inkeun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jieun Lee
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sook Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jin Won Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Han Jo Kim
- Division of Oncology and Hematology, Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Yongjun Cha
- Division of Medical Oncology, Center for Colorectal Cancer, National Cancer Center, Goyang, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jee Hung Kim
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Hoon Chun
- Division of Medical Oncology, Department of Internal Medicine, Bucheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jina Yun
- Division of Hematology/Oncology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Mee Cho
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Soo Jeong Nam
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Korea
| | - Sun Och Yoon
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
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4
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Gustav M, Reitsam NG, Carrero ZI, Loeffler CML, van Treeck M, Yuan T, West NP, Quirke P, Brinker TJ, Brenner H, Favre L, Märkl B, Stenzinger A, Brobeil A, Hoffmeister M, Calderaro J, Pujals A, Kather JN. Deep learning for dual detection of microsatellite instability and POLE mutations in colorectal cancer histopathology. NPJ Precis Oncol 2024; 8:115. [PMID: 38783059 PMCID: PMC11116442 DOI: 10.1038/s41698-024-00592-z] [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: 11/07/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated testing costs, systematic screening for these mutations is not commonly pursued. Notably, the histopathological phenotype resulting from POLE mutations is theorized to resemble that of MSI. This resemblance not only could facilitate their detection by a transformer-based Deep Learning (DL) system trained on MSI pathology slides, but also indicates the possibility for MSS patients with POLE mutations to access enhanced treatment options, which might otherwise be overlooked. To harness this potential, we trained a Deep Learning classifier on a large dataset with the ground truth for microsatellite status and subsequently validated its capabilities for MSI and POLE detection across three external cohorts. Our model accurately identified MSI status in both the internal and external resection cohorts using pathology images alone. Notably, with a classification threshold of 0.5, over 75% of POLE driver mutant patients in the external resection cohorts were flagged as "positive" by a DL system trained on MSI status. In a clinical setting, deploying this DL model as a preliminary screening tool could facilitate the efficient identification of clinically relevant MSI and POLE mutations in colorectal tumors, in one go.
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Affiliation(s)
- Marco Gustav
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | | | - Zunamys I Carrero
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Chiara M L Loeffler
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marko van Treeck
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicholas P West
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Titus J Brinker
- Digital Biomarkers for Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Loëtitia Favre
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Bruno Märkl
- Pathology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | | | - Alexander Brobeil
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julien Calderaro
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Anaïs Pujals
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany.
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
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Wilbur HC, Le DT, Agarwal P. Immunotherapy of MSI Cancer: Facts and Hopes. Clin Cancer Res 2024; 30:1438-1447. [PMID: 38015720 DOI: 10.1158/1078-0432.ccr-21-1935] [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: 04/19/2023] [Revised: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
Microsatellite instability (MSI) is a tumor molecular phenotype that evolves from loss of function in the mismatch repair (MMR) proteins through deleterious germline mutations, epigenetic inactivation, or somatic biallelic mutations. This phenotype is characterized by genomic hyper-mutability, increased neoantigen expression, and a favorable, immune-rich tumor microenvironment. These features confer a greater likelihood of response to treatment with the class of agents known as immune checkpoint inhibitors (ICI) and, potentially, other immune-based therapeutics. MSI as a predictive biomarker for response to treatment with ICIs ultimately led to the first tissue-agnostic approval of pembrolizumab for advanced, previously treated MSI or deficient MMR (dMMR) tumors. Nevertheless, response to ICIs in dMMR/MSI tumors is not universal. Identifying predictors of response and elucidating mechanisms of immune escape will be crucial to continued successful treatment of this subset. In this review, we aim to describe the pathogenesis and key immunologic features of dMMR/MSI tumors, provide a brief overview of the currently approved treatments, and discuss promising novel immune-based therapeutics currently under investigation.
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Affiliation(s)
- H Catherine Wilbur
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Dung T Le
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Parul Agarwal
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
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6
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Dasgupta S, Gayen S, Chakraborty T, Afrose N, Pal R, Mahata S, Nasare V, Roy S. Potential role of immune cell therapy in gynecological cancer and future promises: a comprehensive review. Med Oncol 2024; 41:98. [PMID: 38536512 DOI: 10.1007/s12032-024-02337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 05/31/2024]
Abstract
Gynecological malignancies are most leading causes of death among women worldwide. The high prevalence of gynecologic malignancies remains significant, necessitating to turn the novel treatment approach like immunotherapy, wherein cancer cells are killed by the invasion of immune system. In recent year, immunotherapy has mostly an advanced treatment approach to repressing the tumor cells survival, proliferation, and invasion via the activation of immune systems. Moreover, various types of immune cells including T-cells, B-cells, and dendritic cells are associated with the immunotherapeutic strategy in cancer treatment. Although the significant role of T-cells against cancer is well established, while B-cells and dendritic cells also play an important role against different gynecological cancer by regulating the immune system. This review focuses on that arena and highlight the role of immune cells in the treatment of gynaecological cancer. Various immune cell-based anticancer therapies such as T-cell therapies, Adoptive Cellular transfer, B-cell therapies as well as approaches to Dendritic Cell therapies have been discussed in detail. Furthermore, the clinical settings and future avenues regarding immunotherapy on gynecological cancer have also been reviewed and illuminated in the recent study.
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Affiliation(s)
- Sandipan Dasgupta
- Department of Pharmaceutical Technology, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Sakuntala Gayen
- NSHM Knowledge Campus, Kolkata - Group of Institutions, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Tania Chakraborty
- NSHM Knowledge Campus, Kolkata - Group of Institutions, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Naureen Afrose
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Ranita Pal
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, Kolkata, West Bengal, India
| | - Sutapa Mahata
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, Kolkata, West Bengal, India
| | - Vilas Nasare
- Department of Pathology and Cancer Screening, Chittaranjan National Cancer Institute, Kolkata, West Bengal, India
| | - Souvik Roy
- NSHM Knowledge Campus, Kolkata - Group of Institutions, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India.
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7
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Qin Y, Huo M, Liu X, Li SC. Biomarkers and computational models for predicting efficacy to tumor ICI immunotherapy. Front Immunol 2024; 15:1368749. [PMID: 38524135 PMCID: PMC10957591 DOI: 10.3389/fimmu.2024.1368749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Numerous studies have shown that immune checkpoint inhibitor (ICI) immunotherapy has great potential as a cancer treatment, leading to significant clinical improvements in numerous cases. However, it benefits a minority of patients, underscoring the importance of discovering reliable biomarkers that can be used to screen for potential beneficiaries and ultimately reduce the risk of overtreatment. Our comprehensive review focuses on the latest advancements in predictive biomarkers for ICI therapy, particularly emphasizing those that enhance the efficacy of programmed cell death protein 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) inhibitors and cytotoxic T-lymphocyte antigen-4 (CTLA-4) inhibitors immunotherapies. We explore biomarkers derived from various sources, including tumor cells, the tumor immune microenvironment (TIME), body fluids, gut microbes, and metabolites. Among them, tumor cells-derived biomarkers include tumor mutational burden (TMB) biomarker, tumor neoantigen burden (TNB) biomarker, microsatellite instability (MSI) biomarker, PD-L1 expression biomarker, mutated gene biomarkers in pathways, and epigenetic biomarkers. TIME-derived biomarkers include immune landscape of TIME biomarkers, inhibitory checkpoints biomarkers, and immune repertoire biomarkers. We also discuss various techniques used to detect and assess these biomarkers, detailing their respective datasets, strengths, weaknesses, and evaluative metrics. Furthermore, we present a comprehensive review of computer models for predicting the response to ICI therapy. The computer models include knowledge-based mechanistic models and data-based machine learning (ML) models. Among the knowledge-based mechanistic models are pharmacokinetic/pharmacodynamic (PK/PD) models, partial differential equation (PDE) models, signal networks-based models, quantitative systems pharmacology (QSP) models, and agent-based models (ABMs). ML models include linear regression models, logistic regression models, support vector machine (SVM)/random forest/extra trees/k-nearest neighbors (KNN) models, artificial neural network (ANN) and deep learning models. Additionally, there are hybrid models of systems biology and ML. We summarized the details of these models, outlining the datasets they utilize, their evaluation methods/metrics, and their respective strengths and limitations. By summarizing the major advances in the research on predictive biomarkers and computer models for the therapeutic effect and clinical utility of tumor ICI, we aim to assist researchers in choosing appropriate biomarkers or computer models for research exploration and help clinicians conduct precision medicine by selecting the best biomarkers.
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Affiliation(s)
- Yurong Qin
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
| | - Miaozhe Huo
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
| | - Xingwu Liu
- School of Mathematical Sciences, Dalian University of Technology, Dalian, Liaoning, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, China
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8
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Chuwdhury GS, Guo Y, Chiang CL, Lam KO, Kam NW, Liu Z, Dai W. ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction. Brief Bioinform 2024; 25:bbae024. [PMID: 38343325 PMCID: PMC10859690 DOI: 10.1093/bib/bbae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Neoantigens are derived from somatic mutations in the tumors but are absent in normal tissues. Emerging evidence suggests that neoantigens can stimulate tumor-specific T-cell-mediated antitumor immune responses, and therefore are potential immunotherapeutic targets. We developed ImmuneMirror as a stand-alone open-source pipeline and a web server incorporating a balanced random forest model for neoantigen prediction and prioritization. The prediction model was trained and tested using known immunogenic neopeptides collected from 19 published studies. The area under the curve of our trained model was 0.87 based on the testing data. We applied ImmuneMirror to the whole-exome sequencing and RNA sequencing data obtained from gastrointestinal tract cancers including 805 tumors from colorectal cancer (CRC), esophageal squamous cell carcinoma (ESCC) and hepatocellular carcinoma patients. We discovered a subgroup of microsatellite instability-high (MSI-H) CRC patients with a low neoantigen load but a high tumor mutation burden (> 10 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study identified a subset of MSI-H patients who may not benefit from this treatment with lower neoantigen load for major histocompatibility complex I (P < 0.0001) and II (P = 0.0008) molecules, respectively. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as a potential actionable target in ESCC. This is so far the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction.
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Affiliation(s)
- Gulam Sarwar Chuwdhury
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Yunshan Guo
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chi-Leung Chiang
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Ka-On Lam
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Ngar-Woon Kam
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Wei Dai
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
- University of Hong Kong-Shenzhen Hospital, Shenzhen, P. R. China
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9
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Taieb J, Bennouna J, Penault-Llorca F, Basile D, Samalin E, Zaanan A. Treatment of gastric adenocarcinoma: A rapidly evolving landscape. Eur J Cancer 2023; 195:113370. [PMID: 37948843 DOI: 10.1016/j.ejca.2023.113370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 11/12/2023]
Abstract
Gastric adenocarcinoma (GC) and gastroesophageal junction adenocarcinoma represent frequent and severe diseases whose management has radically changed over the last 10 years. With the advent of second- and third-line standard therapies for metastatic GC patients in the 2010s, the molecular dismemberment of the disease and positive trials with immunotherapy and targeted agents will mark the 2020s. New treatment options have emerged in the neoadjuvant, adjuvant, and metastatic setting. In addition to improved multimodal treatment in operable patients, new subgroups have emerged depending on molecular alterations (HER2, Microsatellite instability) or expression of specific proteins in the tumour (PDL1, Claudin 18.2) making immunohistochemistry central in profiling the tumour for an optimal individualised management. The aim of this review is to describe the current standards of management of early and late stage GC and the molecular markers needed today to optimally manage our patients together with future perspectives on this disease.
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Affiliation(s)
- Julien Taieb
- Department of Gastroenterology and Digestive Oncology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Institut du Cancer Paris CARPEM, Université Paris Cité, Paris, Hôpital Européen Georges Pompidou, Department of Tumor and Cancer Genomic Medicine, Paris, France.
| | - Jaafar Bennouna
- Department of Medical Oncology, Hopital Foch, Suresnes, France
| | | | - Debora Basile
- Department of Medical Oncology, San Giovanni di Dio Hospital, Crotone, Italy
| | - Emmanuelle Samalin
- Department of Medical Oncology, Institut du Cancer de Montpellier, Univ. Montpellier (ICM), Montpellier, France
| | - Aziz Zaanan
- Department of Gastroenterology and Digestive Oncology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Institut du Cancer Paris CARPEM, Université Paris Cité, Paris, Hôpital Européen Georges Pompidou, Department of Tumor and Cancer Genomic Medicine, Paris, France
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10
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Van Dingenen L, Segers C, Wouters S, Mysara M, Leys N, Kumar-Singh S, Malhotra-Kumar S, Van Houdt R. Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer. Front Cell Infect Microbiol 2023; 13:1298264. [PMID: 38035338 PMCID: PMC10687483 DOI: 10.3389/fcimb.2023.1298264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT.
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Affiliation(s)
- Lena Van Dingenen
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Charlotte Segers
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Shari Wouters
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Science, School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Rob Van Houdt
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
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11
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Ozer M, Vegivinti CTR, Syed M, Ferrell ME, Gonzalez Gomez C, Cheng S, Holder-Murray J, Bruno T, Saeed A, Sahin IH. Neoadjuvant Immunotherapy for Patients with dMMR/MSI-High Gastrointestinal Cancers: A Changing Paradigm. Cancers (Basel) 2023; 15:3833. [PMID: 37568648 PMCID: PMC10417711 DOI: 10.3390/cancers15153833] [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: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Immune checkpoint inhibitors have revolutionized the management of mismatch repair-deficient (MMR-D)/microsatellite instability-high (MSI-H) gastrointestinal cancers, particularly colorectal cancer. Cancers with the MMR-D/MSI-H genotype often carry a higher tumor mutation burden with frameshift alterations, leading to increased mutation-associated neoantigen (MANA) generation. The dramatic response seen with immune checkpoint inhibitors (ICIs), which are orchestrated by MANA-primed effector T cells, resulted in the rapid development of these novel therapeutics within the landscape of MSI-H gastrointestinal cancers. Recently, several clinical trials have utilized ICIs as potential neoadjuvant therapies for MSI-H gastrointestinal cancers and demonstrated deep clinical and pathological responses, creating opportunities for organ preservation. However, there are potential challenges to the neoadjuvant use of ICIs for certain disease types due to the clinical risk of overtreatment for a disease that can be cured through a surgery-only approach. In this review article, we discuss neoadjuvant management approaches with ICI therapy for patients with MSI-H gastrointestinal cancers, including those with oligometastatic disease. We also elaborate on potential challenges and opportunities for the neoadjuvant utilization of ICIs and provide further insight into the changing treatment paradigm of MMR-D/MSI-H gastrointestinal cancers.
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Affiliation(s)
- Muhammet Ozer
- Department of Gastrointestinal Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Masood Syed
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Morgan E. Ferrell
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Cyndi Gonzalez Gomez
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Svea Cheng
- Department of Medicine, University of Pittsburg School of Medicine, Pittsburgh, PA 15213, USA
| | - Jennifer Holder-Murray
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tullia Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anwaar Saeed
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ibrahim Halil Sahin
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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12
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Constantin M, Mătanie C, Petrescu L, Bolocan A, Andronic O, Bleotu C, Mitache MM, Tudorache S, Vrancianu CO. Landscape of Genetic Mutations in Appendiceal Cancers. Cancers (Basel) 2023; 15:3591. [PMID: 37509254 PMCID: PMC10377024 DOI: 10.3390/cancers15143591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
In appendiceal cancers, the most frequently mutated genes are (i) KRAS, which, when reactivated, restores signal transduction via the RAS-RAF-MEK-ERK signaling pathway and stimulates cell proliferation in the early stages of tumor transformation, and then angiogenesis; (ii) TP53, whose inactivation leads to the inhibition of programmed cell death; (iii) GNAS, which, when reactivated, links the cAMP pathway to the RAS-RAF-MEK-ERK signaling pathway, stimulating cell proliferation and angiogenesis; (iv) SMAD4, exhibiting typical tumor-suppressive activity, blocking the transmission of oncogenic TGFB signals via the SMAD2/SMAD3 heterodimer; and (v) BRAF, which is part of the RAS-RAF-MEK-ERK signaling pathway. Diverse mutations are reported in other genes, which are part of secondary or less critical signaling pathways for tumor progression, but which amplify the phenotypic diversity of appendiceal cancers. In this review, we will present the main genetic mutations involved in appendix tumors and their roles in cell proliferation and survival, and in tumor invasiveness, angiogenesis, and acquired resistance to anti-growth signals.
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Affiliation(s)
- Marian Constantin
- Institute of Biology of Romanian Academy, 060031 Bucharest, Romania
- The Research Institute of the University of Bucharest (ICUB), 050095 Bucharest, Romania
| | - Cristina Mătanie
- Department of Anatomy, Animal Physiology and Biophysics (DAFAB), Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Livia Petrescu
- Department of Anatomy, Animal Physiology and Biophysics (DAFAB), Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Alexandra Bolocan
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Octavian Andronic
- Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Coralia Bleotu
- Life, Environmental and Earth Sciences Division, The Research Institute of the University of Bucharest (ICUB), 050095 Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania
| | | | - Sorin Tudorache
- Faculty of Medicine, "Titu Maiorescu" University, 040441 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- The Research Institute of the University of Bucharest (ICUB), 050095 Bucharest, Romania
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
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13
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Kwon MJ, Lee JY, Kim EJ, Ko EJ, Ryu CS, Cho HJ, Jun HH, Kim JW, Kim NK. Genetic variants of MUC4 are associated with susceptibility to and mortality of colorectal cancer and exhibit synergistic effects with LDL-C levels. PLoS One 2023; 18:e0287768. [PMID: 37384668 PMCID: PMC10310026 DOI: 10.1371/journal.pone.0287768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
As a disease with high mortality and prevalence rates worldwide, colorectal cancer (CRC) has been thoroughly investigated. Mucins are involved in the induction of CRC and the regulation of intestinal homeostasis but a member of the mucin gene family MUC4 has a controversial role in CRC. MUC4 has been associated with either decreased susceptibility to or a worse prognosis of CRC. In our study, the multifunctional aspects of MUC4 were elucidated by genetic polymorphism analysis in a case-control study of 420 controls and 464 CRC patients. MUC4 rs1104760 A>G polymorphism had a protective effect on CRC risk (AG, AOR = 0.537; GG, AOR = 0.297; dominant model, AOR = 0.493; recessive model, AOR = 0.382) and MUC4 rs2688513 A>G was associated with an increased mortality rate of CRC (5 years, GG, adjusted HR = 6.496; recessive model, adjusted HR = 5.848). In addition, MUC4 rs1104760 A>G showed a high probability of being a potential biomarker for CRC patients with low-density lipoprotein cholesterol (LDL-C) in the risk range while showing a significant synergistic effect with the LDL-C level. This is the first study to indicate a significant association between MUC4 genetic polymorphisms and CRC prevalence, suggesting a functional genetic variant with the LDL-C level, for CRC prevention.
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Affiliation(s)
- Min Jung Kwon
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Eo Jin Kim
- Division of Hematology/Oncology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
| | - Hye Jung Cho
- Department of Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Hak Hoon Jun
- Department of Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jong Woo Kim
- Department of Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
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14
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Yakushina V, Kavun A, Veselovsky E, Grigoreva T, Belova E, Lebedeva A, Mileyko V, Ivanov M. Microsatellite Instability Detection: The Current Standards, Limitations, and Misinterpretations. JCO Precis Oncol 2023; 7:e2300010. [PMID: 37315263 DOI: 10.1200/po.23.00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Valentina Yakushina
- OncoAtlas LLC, Moscow, Russian Federation
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russian Federation
| | | | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russian Federation
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russian Federation
- Lomonosov Moscow State University, Moscow, Russian Federation
| | | | | | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
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15
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Şenocak Taşçı E, Yıldız İ, Erdamar S, Özer L. Discrepancy among microsatellite instability detection methodologies in non-colorectal cancer: Report of 3 cases. World J Clin Cases 2023; 11:3105-3113. [PMID: 37215411 PMCID: PMC10198076 DOI: 10.12998/wjcc.v11.i13.3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 04/04/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Microsatellite instability (MSI) is a predictive biomarker for cancer immunotherapy. The tumor-agnostic nature of MSI makes it a denominator for immunotherapy in several solid tumors. It can be assessed using next-generation sequencing (NGS), fluorescent multiplex PCR, and immunohistochemistry (IHC).
CASE SUMMARY Here, we report 3 cases with discordant MSI results detected using different methods. A cholangiocellular carcinoma case revealed proficient mismatch repair (MMR) by IHC but high MSI (MSI-H) by liquid NGS. A cervical cancer case revealed deficient MMR by IHC, microsatellite stable by PCR, and MSI-H by NGS. Lastly, an endometrial cancer case revealed proficient MMR by IHC but MSI-H by NGS.
CONCLUSION IHC for MMR status is the first choice due to several advantages. However, in cases of indeterminate IHC results, molecular testing by MSI-PCR is preferred. Recently, NGS-based MSI assays are being widely used to detect MSI-H tumors. All three methods have high accuracy; however, the inconsistencies between them may lead to misdiagnosis.
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Affiliation(s)
- Elif Şenocak Taşçı
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - İbrahim Yıldız
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - Sibel Erdamar
- Department of Pathology, Acıbadem MAA University, Istanbul 12345, Turkey
| | - Leyla Özer
- Department of Medical Oncology, Acıbadem MAA University, Istanbul 12345, Turkey
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16
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Zhang R, Clark SD, Guo B, Zhang T, Jeansonne D, Jeyaseelan SJ, Francis J, Huang W. Challenges in the combination of radiotherapy and immunotherapy for breast cancer. Expert Rev Anticancer Ther 2023; 23:375-383. [PMID: 37039098 PMCID: PMC10929662 DOI: 10.1080/14737140.2023.2188196] [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: 05/03/2022] [Accepted: 03/03/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION Immunotherapy (IT) is showing promise in the treatment of breast cancer, but IT alone only benefits a minority of patients. Radiotherapy (RT) is usually included in the standard of care for breast cancer patients and is traditionally considered as a local form of treatment. The emerging knowledge of RT-induced systemic immune response, and the observation that the rare abscopal effect of RT on distant cancer metastases can be augmented by IT, have increased the enthusiasm for combinatorial immunoradiotherapy (IRT) for breast cancer patients. However, IRT largely follows the traditional sole RT and IT protocols and does not consider patient specificity, although patients' responses to treatment remain heterogeneous. AREAS COVERED This review discusses the rationale of IRT for breast cancer, the current knowledge, challenges, and future directions. EXPERT OPINION The synergy between RT and the immune system has been observed but not well understood at the basic level. The optimal dosages, timing, target, and impact of biomarkers are largely unknown. There is an urgent need to design efficacious pre-clinical and clinical trials to optimize IRT for cancer patients, maximize the synergy of radiation and immune response, and explore the abscopal effect in depth, taking into account patients' personal features.
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Affiliation(s)
- Rui Zhang
- Medical Physics Program, Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA, USA
- Department of Radiation Oncology, Mary Bird Perkins Cancer Center, Baton Rouge, LA, USA
| | - Samantha D Clark
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Beibei Guo
- Department of Experimental Statistics, Louisiana State University, Baton Rouge, LA, USA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Duane Jeansonne
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Samithamby J Jeyaseelan
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Joseph Francis
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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17
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Poveda-Rogers C, Morrissette JJD. Greater expectations: meeting clinical needs through broad and rapid genomic testing. Clin Chem Lab Med 2023; 61:654-661. [PMID: 36473133 DOI: 10.1515/cclm-2022-1016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Cancer describes a group of diseases driven by genetic and genomic changes that can occur across hundreds of different genes. Knowledge of the specific variants present in a patient's cancer can help to predict response to different treatment options, confirm disease diagnosis, and understand a patient's prognosis and risks, which ultimately leads to improved survival outcomes. The advent of next-generation sequencing (NGS) technology has allowed pathologists to simultaneously profile the sequences of many genes in a single reaction, but not all NGS assays are built the same. While those used for broad genomic profiling are useful to probe large regions of the genome and gather more information about a patient's tumor, it comes at the cost of relatively long turnaround times (TAT), which may be detrimental to patient care. Conversely, NGS assays used for rapid genomic profiling provide faster results, but may miss detection of variants that are clinically informative. Determining which type of genomic profiling to order depends on a number of factors including the severity of a patient's illness, standard of care paradigms, and success or failure of previous therapies. Ultimately, the ideal clinical diagnostic laboratory will be able to offer both options to best meet the clinical needs of its patients.
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Affiliation(s)
- Corey Poveda-Rogers
- Hospital of the University of Pennsylvania, Pathology and Laboratory Medicine, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Hospital of the University of Pennsylvania, Pathology and Laboratory Medicine, Philadelphia, PA, USA
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18
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Malhotra R, Javle V, Tanwar N, Gowda P, Varghese L, K A, Madhusudhan N, Jaiswal N, K. S. B, Chatterjee M, Prabhash K, Sreekanthreddy P, Rishi KD, Goswami HM, Veldore VH. An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing. Front Oncol 2023; 13:1002792. [PMID: 36994199 PMCID: PMC10040847 DOI: 10.3389/fonc.2023.1002792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 03/16/2023] Open
Abstract
IntroductionThe concept of personalized medicine in cancer has emerged rapidly with the advancement of genome sequencing and the identification of clinically relevant variants that contribute to disease prognosis and facilitates targeted therapy options. In this study, we propose to validate a whole exome-based tumor molecular profiling for DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissue.MethodsThe study included 166 patients across 17 different cancer types. The scope of this study includes the identification of single-nucleotide variants (SNVs), insertions/deletions (INDELS), copy number alterations (CNAs), gene fusions, tumor mutational burden (TMB), and microsatellite instability (MSI). The assay yielded a mean read depth of 200×, with >80% of on-target reads and a mean uniformity of >90%. Clinical maturation of whole exome sequencing (WES) (DNA and RNA)- based assay was achieved by analytical and clinical validations for all the types of genomic alterations in multiple cancers. We here demonstrate a limit of detection (LOD) of 5% for SNVs and 10% for INDELS with 97.5% specificity, 100% sensitivity, and 100% reproducibility.ResultsThe results were >98% concordant with other orthogonal techniques and appeared to be more robust and comprehensive in detecting all the clinically relevant alterations. Our study demonstrates the clinical utility of the exome-based approach of comprehensive genomic profiling (CGP) for cancer patients at diagnosis and disease progression.DiscussionThe assay provides a consolidated picture of tumor heterogeneity and prognostic and predictive biomarkers, thus helping in precision oncology practice. The primary intended use of WES (DNA+RNA) assay would be for patients with rare cancers as well as for patients with unknown primary tumors, and this category constitutes nearly 20–30% of all cancers. The WES approach may also help us understand the clonal evolution during disease progression to precisely plan the treatment in advanced stage disease.
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Affiliation(s)
| | - Vyomesh Javle
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Pooja Gowda
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Linu Varghese
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | - Anju K
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | - Nupur Jaiswal
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
| | | | | | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | | | | | | | - Vidya H. Veldore
- 4baseCare Onco Solutions Pvt. Ltd., Bangalore, India
- *Correspondence: Vidya H. Veldore,
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19
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Sahin IH, Zhang J, Saridogan T, Gorantla V, Rhree J, Malhotra M, Thomas R, Hsu D, Saeed A. Neoadjuvant Immune Checkpoint Inhibitor Therapy for Patients With Microsatellite Instability-High Colorectal Cancer: Shedding Light on the Future. JCO Oncol Pract 2023; 19:251-259. [PMID: 36862965 DOI: 10.1200/op.22.00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized the treatment paradigm of mismatch repair-deficient/microsatellite instability-high (MMMR-D/MSI-H) colorectal cancer (CRC). Unique molecular features of MMR-D/MSI-H CRC with frameshift alterations, which result in mutation-associated neoantigen (MANA) generation, create an ideal molecular framework for MANA-driven T-cell priming and antitumor immunity. These biologic characteristics of MMR-D/MSI-H CRC resulted in rapid drug development with ICIs for patients with MMR-D/MSI-H CRC. Observed deep and durable responses with the use of ICIs in advanced-stage disease have stimulated the development of clinical trials with ICIs for patients with early-stage MMR-D/MSI-H CRC. Most recently, neoadjuvant dostarlimab monotherapy for nonoperative management of MMR-D/MSI-H rectal cancer and neoadjuvant NICHE trial with nivolumab and ipilimumab for MMR-D/MSI-H colon cancer resulted in groundbreaking results. Although nonoperative management of patients with MMR-D/MSI-H rectal cancer with ICIs will potentially define our current therapeutic approach, therapeutic goals of neoadjuvant ICI therapy for patients with MMR-D/MSI-H colon cancer may differ given that nonoperative management has not been well established for colon cancer. Herein, we overview recent advancements in ICI-based therapies for patients with early-stage MMR-D/MSI-H colon and rectal cancer and elaborate on the future treatment paradigm of this unique subgroup of CRC.
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Affiliation(s)
- Ibrahim Halil Sahin
- Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Janie Zhang
- Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Turcin Saridogan
- Department of Medicine, Hacettepe University of School of Medicine, Ankara, Turkey
| | | | - John Rhree
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | - Roby Thomas
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Dennis Hsu
- Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Anwaar Saeed
- Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,University of Pittsburgh Medical Center, Pittsburgh, PA
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20
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Biswas K, Mohammed A, Sharan SK, Shoemaker RH. Genetically engineered mouse models for hereditary cancer syndromes. Cancer Sci 2023; 114:1800-1815. [PMID: 36715493 PMCID: PMC10154891 DOI: 10.1111/cas.15737] [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: 12/14/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Advances in molecular diagnostics have led to improved diagnosis and molecular understanding of hereditary cancers in the clinic. Improving the management, treatment, and potential prevention of cancers in carriers of predisposing mutations requires preclinical experimental models that reflect the key pathogenic features of the specific syndrome associated with the mutations. Numerous genetically engineered mouse (GEM) models of hereditary cancer have been developed. In this review, we describe the models of Lynch syndrome and hereditary breast and ovarian cancer syndrome, the two most common hereditary cancer predisposition syndromes. We focus on Lynch syndrome models as illustrative of the potential for using mouse models to devise improved approaches to prevention of cancer in a high-risk population. GEM models are an invaluable tool for hereditary cancer models. Here, we review GEM models for some hereditary cancers and their potential use in cancer prevention studies.
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Affiliation(s)
- Kajal Biswas
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
| | - Altaf Mohammed
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Robert H Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
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21
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Han S, Chok AY, Peh DYY, Ho JZM, Tan EKW, Koo SL, Tan IBH, Ong JCA. The distinct clinical trajectory, metastatic sites, and immunobiology of microsatellite-instability-high cancers. Front Genet 2022; 13:933475. [DOI: 10.3389/fgene.2022.933475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/17/2022] [Indexed: 12/03/2022] Open
Abstract
Microsatellite-instability-high (MSI-H) cancers form a spectrum of solid organ tumors collectively known as Lynch Syndrome cancers, occurring not only in a subset of colorectal, endometrial, small bowel, gastric, pancreatic, and biliary tract cancers but also in prostate, breast, bladder, and thyroid cancers. Patients with Lynch Syndrome harbor germline mutations in mismatch repair genes, with a high degree of genomic instability, leading to somatic hypermutations and, therefore, oncogenesis and cancer progression. MSI-H cancers have unique clinicopathological characteristics compared to their microsatellite-stable (MSS) counterparts, marked by a higher neoantigen load, immune cell infiltration, and a marked clinical response to immune checkpoint blockade. Patients with known Lynch Syndrome may be detected early through surveillance, but some patients present with disseminated metastatic disease. The treatment landscape of MSI-H cancers, especially colorectal cancers, has undergone a paradigm shift and remains to be defined, with immune checkpoint blockade coming to the forefront of treatment strategies in the stage IV setting. We summarize in this review the clinical features of MSI-H cancers with a specific interest in the pattern of spread or recurrence, disease trajectory, and treatment strategies. We also summarize the tumor-immune landscape and genomic profile of MSI-H cancers and potential novel therapeutic strategies.
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22
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Rogers JE, Yamashita K, Sewastjanow Silva M, Ajani JA. Current Immune Checkpoint Inhibitor Genetic Biomarker Exploration in Gastrointestinal Tumors. Cancers (Basel) 2022; 14:4804. [PMID: 36230726 PMCID: PMC9563283 DOI: 10.3390/cancers14194804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/16/2022] [Accepted: 09/24/2022] [Indexed: 11/19/2022] Open
Abstract
Immune checkpoint inhibitors have revolutionized cancer management. Some patients with gastrointestinal (GI) tract malignancy have experienced remarkable results. Here, in our review, we discuss predictive/prognostic GI tumor biomarkers that appear to correlate with benefits with this strategy. Remarkable progress has been made in certain subsets of patients including the potential for solid tumor patients to avoid local therapies such as radiation and/or surgery (organ preservation), which come with acute and chronic risks that have historically been the only curable strategies for these GI tumors. These results provide new and exciting strategies for solid tumor management. Unfortunately, immune checkpoint inhibitors can correlate with biomarkers, but benefits occur in a small subset of patients with GI malignancies. Most frequently, immune checkpoint inhibitors fail to induce response in GI malignancies due to the "cold" tumor microenvironment that protects cancer. Translational strategies are needed to develop effective combination strategies and novel biomarkers to overcome the intrinsic resistance.
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Affiliation(s)
- Jane E. Rogers
- U.T. M.D. Anderson Cancer Center Pharmacy Clinical Programs, Houston, TX 77030, USA
| | - Kohei Yamashita
- U.T. M.D. Anderson Cancer Center Department of Gastrointestinal Medical Oncology, Houston, TX 77030, USA
| | - Matheus Sewastjanow Silva
- U.T. M.D. Anderson Cancer Center Department of Gastrointestinal Medical Oncology, Houston, TX 77030, USA
| | - Jaffer A. Ajani
- U.T. M.D. Anderson Cancer Center Department of Gastrointestinal Medical Oncology, Houston, TX 77030, USA
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23
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Microsatellite Instability: From the Implementation of the Detection to a Prognostic and Predictive Role in Cancers. Int J Mol Sci 2022; 23:ijms23158726. [PMID: 35955855 PMCID: PMC9369169 DOI: 10.3390/ijms23158726] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 02/07/2023] Open
Abstract
Microsatellite instability (MSI) has been identified in several tumors arising from either germline or somatic aberration. The presence of MSI in cancer predicts the sensitivity to immune checkpoint inhibitors (ICIs), particularly PD1/PD-L1 inhibitors. To date, the predictive role of MSI is currently used in the selection of colorectal cancer patients for immunotherapy; moreover, the expansion of clinical trials into other cancer types may elucidate the predictive value of MSI for non-colorectal tumors. In clinical practice, several assays are used for MSI testing, including immunohistochemistry (IHC), polymerase chain reaction (PCR) and next-generation sequencing (NGS). In this review, we provide an overview of MSI in various cancer types, highlighting its potential predictive/prognostic role and the clinical trials performed. Finally, we focus on the comparison data between the different assays used to detect MSI in clinical practice.
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24
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Gindin T, Hsiao SJ. Analytical Principles of Cancer Next Generation Sequencing. Clin Lab Med 2022; 42:395-408. [DOI: 10.1016/j.cll.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Abstract
Cancer cells shed naked DNA molecules into the circulation. This circulating tumor DNA (ctDNA) has become the predominant analyte for liquid biopsies to understand the mutational landscape of cancer. Coupled with next-generation sequencing, ctDNA can serve as an alternative substrate to tumor tissues for mutation detection and companion diagnostic purposes. In fact, recent advances in precision medicine have rapidly enabled the use of ctDNA to guide treatment decisions for predicting response and resistance to targeted therapies and immunotherapies. An advantage of using ctDNA over conventional tissue biopsies is the relatively noninvasive approach of obtaining peripheral blood, allowing for simple repeated and serial assessments. Most current clinical practice using ctDNA has endeavored to identify druggable and resistance mutations for guiding systemic therapy decisions, albeit mostly in metastatic disease. However, newer research is evaluating potential for ctDNA as a marker of minimal residual disease in the curative setting and as a useful screening tool to detect cancer in the general population. Here we review the history of ctDNA and liquid biopsies, technologies to detect ctDNA, and some of the current challenges and limitations in using ctDNA as a marker of minimal residual disease and as a general blood-based cancer screening tool. We also discuss the need to develop rigorous clinical studies to prove the clinical utility of ctDNA for future applications in oncology.
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26
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Li Z, Jia Y, Zhu H, Yuan H, Xing X, Xin Y, Ma T, Pang F, Zhang Y, Hu Y, Jia S, Ji J. Genomic landscape of microsatellite instability in Chinese tumors: a comparison of Chinese and TCGA cohorts. Int J Cancer 2022; 151:1382-1393. [PMID: 35567574 DOI: 10.1002/ijc.34119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/22/2022] [Accepted: 04/26/2022] [Indexed: 11/09/2022]
Abstract
Microsatellite instability (MSI) is an important biomarker for predicting the response to immunotherapy and prognosis that mainly results from a defective DNA mismatch repair (MMR) system and strongly correlates with high tumor mutation burden (TMB). Herein, we developed a novel method that integrates MSI score, MMR mutation status and TMB level to identify MSI status from next-generation sequencing (NGS) data. The novel method displays a sensitivity of 96.80%, a specificity of 99.96% and an overall accuracy of 99.89%, compared with current standards. Using our novel method, we analyzed 11,395 Chinese patients across 30 cancer types. High microsatellite instability (MSI-H) was detected in 210 (1.84%) samples in 18 of 30 cancer types assessed. Mutations in ACVR2A (73%), KMT2D (68%), KMT2B (66%) and MMR-related genes (MLH1, MSH2, MSH6 and PMS2) were enriched in MSI-H samples. Furthermore, MSI-H samples were more likely to have high TMB (P<0.01), high PD-L1 expression (P<0.05), and more tumor-infiltrating immune cells than microsatellite-stable (MSS) samples. Compared with the TCGA patients, the prevalence of MSI-H in the Chinese cohort was significantly lower in colorectal, gastric and pancreatic cancer, while significantly higher in urinary and prostate cancer. Mutations in ACVR2A (73% vs 28%, p <0.01) and MMR-related genes (51.4% vs 21.3%, p <0.01) were significantly higher in the Chinese population. Thus, our study suggests the fraction of MSI-H attributable to MMR inactivation mutations were lower in European than in Chinese patients, while the proportion of MSI-H due to other events may be higher. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ziyu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yongning Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Honglin Zhu
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Hongling Yuan
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Xiaofang Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Molecular Diagnostics, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yaqun Xin
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Tonghui Ma
- Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Fei Pang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yan Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ying Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Biobank, Peking University Cancer Hospital and Institute, Beijing, China
| | - Shuqin Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Molecular Diagnostics, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
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27
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Current Role of Immunotherapy in Gastric, Esophageal and Gastro-Esophageal Junction Cancers—A Report from the Western Canadian Gastrointestinal Cancer Consensus Conference. Curr Oncol 2022; 29:3160-3170. [PMID: 35621647 PMCID: PMC9139288 DOI: 10.3390/curroncol29050257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022] Open
Abstract
Gastric, esophageal and gastro-esophageal junction cancers are associated with inferior outcomes. For early-stage disease, perioperative chemotherapy or chemoradiation followed by surgery is the standard treatment. For most patients with advanced upper gastrointestinal tract cancers, platinum-based chemotherapy remains a standard treatment. Recently, several randomized clinical trials have demonstrated the benefit of immunotherapy involving checkpoint inhibitors alone or in combination with chemotherapy in patients with gastro-esophageal cancer and have changed the treatment landscape. The Western Canadian Gastrointestinal Cancer Consensus Conference (WCGCCC), involving experts from four Western Canadian provinces, convened virtually on 16 June 2021 and developed the recommendations on the role of immunotherapy in patients with gastro-esophageal cancer.
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28
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Zito Marino F, Amato M, Ronchi A, Panarese I, Ferraraccio F, De Vita F, Tirino G, Martinelli E, Troiani T, Facchini G, Pirozzi F, Perrotta M, Incoronato P, Addeo R, Selvaggi F, Lucido FS, Caraglia M, Savarese G, Sirica R, Casillo M, Lieto E, Auricchio A, Cardella F, Docimo L, Galizia G, Franco R. Microsatellite Status Detection in Gastrointestinal Cancers: PCR/NGS Is Mandatory in Negative/Patchy MMR Immunohistochemistry. Cancers (Basel) 2022; 14:cancers14092204. [PMID: 35565332 PMCID: PMC9102010 DOI: 10.3390/cancers14092204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Microsatellite instability (MSI) detection has a high impact on eligibility for immune checkpoint inhibitors in gastrointestinal cancers. The appropriate detection of MSI represents the major critical issue in clinical practice, thus a better understanding of the limits related to MSI testing is needed to avoid misinterpretations. This study addresses the discordance between IHC and PCR/NGS testing in a large retrospective series of colorectal and gastric cancers in order to improve diagnosis. Our findings show a disagreement between negative/patchy expression IHC and PCR/NGS results, suggesting that molecular testing is mandatory in this subset of tumors. Abstract Background: Microsatellite instability (MSI) is a predictive biomarker for immune checkpoint inhibitors. The main goal was to investigate the discordance between IHC and PCR/NGS for MSI testing in gastrointestinal cancers. Methods: Two series were analyzed through IHC for mismatch-repair-system proteins (MMRP) and PCR, with one series of 444 colorectal cancers (CRC) and the other of 176 gastric cancers (GC). All cases with discordant results between IHC and PCR were analyzed by NGS. IHC staining was evaluated as follows: proficient MMR (pMMR), with all MMR positive; deficient MMR (dMMR), with the loss of one heterodimer; and cases with the loss/patchy expression of one MMR (lo-paMMR). Cases with instability in at least two markers by PCR were MSI-high (MSI-H) and with instability in one marker, MSI-low (MSI-L). Cases without instability were evaluated as microsatellite-stable (MSS). Results: In the CRC cohort, 15 out of 444 cases were dMMR and 46 lo-paMMR. Among the 15 dMMR, 13 were MSI-H and 2 MSS. Among the 46 lo-paMMR, 13 were MSI-H and 33 were MSS. In the GC cohort, 13 out of 176 cases were dMMR and 6 cases lo-paMMR. Among the 13 dMMR, 12 were MSI-H and only 1 was MSS. All six lo-paMMR cases were MSS. All NGS results were in agreement with PCR. Conclusions: In clinical practice, MMR–IHC could be used as a screening test and additional molecular analysis is mandatory exclusively in cases carrying loss/patchy MMR-IHC.
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Affiliation(s)
- Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
| | - Martina Amato
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
| | - Iacopo Panarese
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
| | - Franca Ferraraccio
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
| | - Ferdinando De Vita
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.D.V.); (G.T.); (E.M.); (T.T.); (M.C.)
| | - Giuseppe Tirino
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.D.V.); (G.T.); (E.M.); (T.T.); (M.C.)
| | - Erika Martinelli
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.D.V.); (G.T.); (E.M.); (T.T.); (M.C.)
| | - Teresa Troiani
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.D.V.); (G.T.); (E.M.); (T.T.); (M.C.)
| | - Gaetano Facchini
- Medical Oncology Unit, SM delle Grazie Hospital, 80078 Pozzuoli, Naples, Italy;
| | - Felice Pirozzi
- General Surgery Unit, Santa Maria delle Grazie Hospital, 80078 Pozzuoli, Naples, Italy;
| | - Michele Perrotta
- Hepatology and Interventional Ultrasound Unit, San Giovanni di Dio Hospital, 80027 Frattamaggiore, Naples, Italy;
| | - Pasquale Incoronato
- Medical Oncology Unit, ASL Napoli 2 Nord Hospital, 80014 Giugliano, Naples, Italy;
| | - Raffaele Addeo
- Medical Oncology Unit, San Giovanni di Dio Hospital, 80027 Frattamaggiore, Naples, Italy;
| | - Francesco Selvaggi
- Department of Advanced Medical and Surgical Sciences, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.S.); (F.S.L.); (L.D.)
| | - Francesco Saverio Lucido
- Department of Advanced Medical and Surgical Sciences, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.S.); (F.S.L.); (L.D.)
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.D.V.); (G.T.); (E.M.); (T.T.); (M.C.)
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale srl, 80013 Casalnuovo, Naples, Italy; (G.S.); (R.S.); (M.C.)
| | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale srl, 80013 Casalnuovo, Naples, Italy; (G.S.); (R.S.); (M.C.)
| | - Marika Casillo
- AMES, Centro Polidiagnostico Strumentale srl, 80013 Casalnuovo, Naples, Italy; (G.S.); (R.S.); (M.C.)
| | - Eva Lieto
- Department of Translational Medical Science, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.L.); (A.A.); (F.C.)
| | - Annamaria Auricchio
- Department of Translational Medical Science, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.L.); (A.A.); (F.C.)
| | - Francesca Cardella
- Department of Translational Medical Science, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.L.); (A.A.); (F.C.)
| | - Ludovico Docimo
- Department of Advanced Medical and Surgical Sciences, Università degli Studi della Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.S.); (F.S.L.); (L.D.)
| | - Gennaro Galizia
- Department of Surgical Sciences, School of Medicine, Second University of Naples, Place Miraglia, 3th Building, West Side, 4th Floor, 80138 Naples, Italy;
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy; (F.Z.M.); (M.A.); (A.R.); (I.P.); (F.F.)
- Correspondence: ; Tel.: +39-0815664000
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29
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Kang SY, Kim DG, Ahn S, Ha SY, Jang KT, Kim KM. Comparative analysis of microsatellite instability by next-generation sequencing, MSI PCR and MMR immunohistochemistry in 1942 solid cancers. Pathol Res Pract 2022; 233:153874. [PMID: 35405622 DOI: 10.1016/j.prp.2022.153874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 11/25/2022]
Abstract
Checkpoint inhibitor approval for microsatellite instability-high (MSI-H) tumours has made MSI as a therapeutically important biomarker. Next-generation sequencing (NGS)-based MSI detection is being widely used for assessing MSI. However, MSI tumours detected using NGS and their relevance to MSI-polymerase chain reaction (PCR) and mismatch repair deficiency (dMMR) are unclear. In 1942 solid cancer cases tested using NGS-based comprehensive cancer panel with 523 genes (1.94 mb), the MSI score, tumour mutation burden (TMB; ≥ 10 mutations/mb), and frameshift mutations were analysed. GeneScan analyses of five mononucleotide markers (MSI-PCR) and MMR protein immunohistochemistry (IHC) were compared with the NGS-MSI results. With a ≥ 12% MSI score as a cut-off for MSI-H, two MSS cases were classified as MSI-H. With a ≥ 20% cut-off, 10 cases categorised as MSS by NGS were MSI-H/dMMR by MSI-PCR and MMR IHC. To avoid discrepant cases, we adopted a high MSI cut-off and a borderline MSI category. Finally, MSI-H (≥ 20%), borderline MSI (≥ 7% and < 20%), and MSS (< 7%) were found in 35 (1.8%), 24 (1.2%), and 1883 (97%) cases, respectively. All MSI-H cases by NGS were MSI-H/dMMR by MSI-PCR and MMR IHC. Of the 24 borderline MSI cases by NGS, MSI-H/dMMR was 9 (37.5%) cases, MSS/dMMR was 1 (4.2%) case, and 11 (45.8%) of them had high TMB. All MSS cases by NGS were MSS/pMMR by MSI-PCR/IHC, and 257 (13.6%) had high TMB. With those arbitrary cut-off points, 10 (0.5%) MSS cases using NGS were discrepant with MSI-PCR or MMR IHC, and all were borderline MSI cases. The mean number of frameshift mutations was significantly higher in the MSI-H group (28.3) than in the borderline MSI (7.7) or MSS (1.3) groups (p < 0.001). In conclusion, to facilitate therapeutic decision-making for NGS, cut-off points for MSI can be defined based on MSI-PCR/dMMR confirmation.
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Affiliation(s)
- So Young Kang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Deok Geun Kim
- Department of Clinical Genomic Center, Samsung Medical Center, Seoul, Republic of Korea; Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Soomin Ahn
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Clinical Genomic Center, Samsung Medical Center, Seoul, Republic of Korea; Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea.
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Artificial Intelligence for Predicting Microsatellite Instability Based on Tumor Histomorphology: A Systematic Review. Int J Mol Sci 2022; 23:ijms23052462. [PMID: 35269607 PMCID: PMC8910565 DOI: 10.3390/ijms23052462] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Microsatellite instability (MSI)/defective DNA mismatch repair (dMMR) is receiving more attention as a biomarker for eligibility for immune checkpoint inhibitors in advanced diseases. However, due to high costs and resource limitations, MSI/dMMR testing is not widely performed. Some attempts are in progress to predict MSI/dMMR status through histomorphological features on H&E slides using artificial intelligence (AI) technology. In this study, the potential predictive role of this new methodology was reviewed through a systematic review. Studies up to September 2021 were searched through PubMed and Embase database searches. The design and results of each study were summarized, and the risk of bias for each study was evaluated. For colorectal cancer, AI-based systems showed excellent performance with the highest standard of 0.972; for gastric and endometrial cancers they showed a relatively low but satisfactory performance, with the highest standard of 0.81 and 0.82, respectively. However, analyzing the risk of bias, most studies were evaluated at high-risk. AI-based systems showed a high potential in predicting the MSI/dMMR status of different cancer types, and particularly of colorectal cancers. Therefore, a confirmation test should be required only for the results that are positive in the AI test.
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31
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Haghighi L, Razmjou E, Rafiei-Sefiddashti R, Meamar AR, Akhlaghi L. Entamoeba histolytica and Probable Effect on Production Microsatellite Instability in Colorectal Cancer. Curr Microbiol 2022; 79:111. [PMID: 35175421 DOI: 10.1007/s00284-022-02782-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/23/2022] [Indexed: 11/28/2022]
Abstract
The mortality rate of Entamoeba histolytica is still high and approximately 100,000 per year. Environmental factors and different pathogens can cause microsatellite instability (MSI) positive, which may be one reason for colorectal cancer. MSI status can play an essential role in treatment. Moreover, E. histolytica might be one of the pathogens which raise the incidence of colorectal cancer. Therefore, the probable relationship of E. histolytica with MSI production was evaluated. Four hundred samples of colorectal biopsies based on pathological reports were divided into four groups: colitis, polyps, hyperplasia or dysplasia, and adenocarcinoma. The prevalence of E. histolytica was examined with PCR and immunohistochemical staining (IHC) for the light chain lectin HK-9. The adenocarcinoma formalin-fixed paraffin-embedded colorectal tumours sections were tested for MSI genes. We detected E. histolytica in 6% and 4% of colitis samples by PCR and IHC technique, respectively. However, it did not identify in polyp and hyperplasia samples. The MSI test was examined in the colorectal cancer group, which became positive in 19%. Entamoeba histolytica was detected in 26.3% (5/19) of MSI-positive and 2.5% (2/81) of MSI-negative cases by IHC technique however was not identified by PCR assay in this group. It is concluded PCR and IHC assay is recommended as complementary tests in colitis biopsies. Simultaneous PCR and IHC negative results could confirm the non-existence of the parasite with more confidence. Consequently, E. histolytica might be one of the biotic factors which raise the incidence of colorectal cancer because of the coincidence of the IHC positive results in MSI-positive adenocarcinoma.
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Affiliation(s)
- Leila Haghighi
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Elham Razmjou
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Raheleh Rafiei-Sefiddashti
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ahmad Reza Meamar
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Lame Akhlaghi
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Healey Bird B, Nally K, Ronan K, Clarke G, Amu S, Almeida AS, Flavin R, Finn S. Cancer Immunotherapy with Immune Checkpoint Inhibitors-Biomarkers of Response and Toxicity; Current Limitations and Future Promise. Diagnostics (Basel) 2022; 12:124. [PMID: 35054292 PMCID: PMC8775044 DOI: 10.3390/diagnostics12010124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
Immune checkpoint inhibitors are monoclonal antibodies that are used to treat over one in three cancer patients. While they have changed the natural history of disease, prolonging life and preserving quality of life, they are highly active in less than 40% of patients, even in the most responsive malignancies such as melanoma, and cause significant autoimmune side effects. Licenced biomarkers include tumour Programmed Death Ligand 1 expression by immunohistochemistry, microsatellite instability, and tumour mutational burden, none of which are particularly sensitive or specific. Emerging tumour and immune tissue biomarkers such as novel immunohistochemistry scores, tumour, stromal and immune cell gene expression profiling, and liquid biomarkers such as systemic inflammatory markers, kynurenine/tryptophan ratio, circulating immune cells, cytokines and DNA are discussed in this review. We also examine the influence of the faecal microbiome on treatment outcome and its use as a biomarker of response and toxicity.
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Affiliation(s)
- Brian Healey Bird
- School of Medicine, University College Cork, T12 K8AF Cork, Ireland
- Bon Secours Hospital, T12 K8AF Cork, Ireland
| | - Ken Nally
- School of Biochemistry and Cell Biology, University College Cork, T12 K8AF Cork, Ireland;
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (G.C.); (A.S.A.)
| | - Karine Ronan
- Department of Oncology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland;
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (G.C.); (A.S.A.)
- Department of Psychiatry, University College Cork, T12 K8AF Cork, Ireland
| | - Sylvie Amu
- Cancer Research at UCC, University College Cork, T12 K8AF Cork, Ireland;
| | - Ana S. Almeida
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (G.C.); (A.S.A.)
| | - Richard Flavin
- Department of Histopathology, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (R.F.); (S.F.)
- St. James’s Hospital Dublin, D08 NHY1 Dublin, Ireland
| | - Stephen Finn
- Department of Histopathology, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (R.F.); (S.F.)
- St. James’s Hospital Dublin, D08 NHY1 Dublin, Ireland
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Huebner T, Steffens M, Scholl C. Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe. Mol Diagn Ther 2021; 26:89-103. [PMID: 34905151 PMCID: PMC8766366 DOI: 10.1007/s40291-021-00567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
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Venetis K, Fusco N, Sajjadi E. Commentary: Mismatch Repair Deficiency and Microsatellite Instability in Triple-Negative Breast Cancer: A Retrospective Study of 440 Patients. Front Oncol 2021; 11:735476. [PMID: 34660298 PMCID: PMC8511768 DOI: 10.3389/fonc.2021.735476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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35
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Motta R, Cabezas-Camarero S, Torres-Mattos C, Riquelme A, Calle A, Figueroa A, Sotelo MJ. Immunotherapy in microsatellite instability metastatic colorectal cancer: Current status and future perspectives. J Clin Transl Res 2021; 7:511-522. [PMID: 34541365 PMCID: PMC8445628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/22/2021] [Accepted: 07/18/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most frequent and deadly malignancies worldwide. This specific pathology is composed of various molecular entities, with distinct immunological phenotypes. In addition to KRAS, NRAS, and BRAF mutation status, other druggable alterations such as those in HER2, MET, NTRK, ALK, and ROS1 have been identified in recent years offering new therapeutic options for some patients with CRC. AIM This review will focus on the molecular biology, immunological fingerprints, and current clinical evidence for the use of immunotherapy in patients with CRC. RELEVANCE FOR PATIENTS High microsatellite instability (MSI-H) and mutations in mismatch repair genes constitute a new molecular entity within CRC, which is characterized by a high mutational and neoantigen burden, frequent immune cell infiltration, and where immune checkpoint inhibitors have shown high response and survival rates compared to microsatellite stable (MSS) tumors. Indeed, the approval of pembrolizumab in MSI-H tumors was the first agnostic FDA approval in solid tumors. While monotherapy with anti-programmed cell death protein-1 agents achieves objective response rates (ORR) of around 30% and 1-year overall survival (OS) rates of 76%, anti-PD1, and anti-CTLA4 combinations achieve a 55% ORR and a 1-year OS rate of 85%. Several ongoing trials are evaluating the use of different immunotherapy combinations, both in the advanced and early settings and in MSI-h and MSS CRCs.
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Affiliation(s)
- Rodrigo Motta
- Department of Medical Oncology, Centro Oncologico Aliada; Lima, Peru
- Functional Unit of Health Technology, Instituto Nacional de Enfermedades Neoplasicas; Lima, Peru
| | | | - Cesar Torres-Mattos
- Department of Medical Oncology, Hospital Nacional Guillermo Almenara Irigoyen; Lima, Peru
- Oncological Research Unit, Clínica San Gabriel, Lima, Peru
| | - Alejandro Riquelme
- Department of Medical Oncology, Hospital Universitario Infanta Cristina; Madrid, Spain
| | - Ana Calle
- Department of Medical Oncology, Centro Oncologico Aliada; Lima, Peru
- Department of Medical Oncology, Hospital María Auxiliadora; Lima, Peru
| | - Alejandro Figueroa
- Department of Medical Oncology, Hospital Nacional Edgardo Rebagliati Martins; Lima, Peru
| | - Miguel J. Sotelo
- Department of Medical Oncology, Centro Oncologico Aliada; Lima, Peru
- Oncological Research Unit, Clínica San Gabriel, Lima, Peru
- Department of Medical Oncology, Hospital María Auxiliadora; Lima, Peru
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Tumour mutational burden, microsatellite instability, and actionable alterations in metastatic colorectal cancer: Next-generation sequencing results of TRIBE2 study. Eur J Cancer 2021; 155:73-84. [PMID: 34365081 DOI: 10.1016/j.ejca.2021.06.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND We performed a comprehensive genomic profiling of tumour samples from metastatic colorectal cancer (mCRC) patients enrolled in the TRIBE2 study to assess the concordance among different techniques to evaluate mismatch repair (MMR) and microsatellite instability (MSI) status, to characterize tumours according to the tumour mutational burden (TMB) and explore the clinical relevance of different TMB cutpoints, and to investigate the prevalence of alterations actionable with targeted approaches or immune checkpoint inhibitors. MATERIAL AND METHODS Tumour samples of 296 (44%) of 679 enrolled patients underwent 592-gene DNA next-generation sequencing (NGS). MMR status was assessed by immunohistochemistry (MMR-IHC), and MSI status was assessed by NGS (MSI-NGS). TMB was defined as low, intermediate, or high if <7, 7-16, or ≥17 mutations/megabase (mut/Mb) were found. The performance of TMB to predict MSI status was tested by receiver operating characteristic (ROC) curve. Actionable alterations included BRAF V600E, KRAS G12C, POLE mutations, HER2 amplification and mutations, and MSI-H. RESULTS Of 216 paired cases, concordance between MMR-IHC and MSI-NGS was 98.6%. Among 11 TMB-high tumours, eight (73%) were MSI-H and three (27%) were microsatellite stable and harboured POLE or MSH6 mutations. High TMB had a trend for a better outcome than low/intermediate TMB (hazard ratio for overall survival 0.45, 95% confidence interval 0.28-1.33; P = 0.106). No interaction effect between TMB and treatment arm was observed. Seventeen mut/Mb was identified as the optimal threshold of TMB for predicting MSI status. Actionable alterations were found in 62 (21%) of 296 patients. CONCLUSIONS Genomic profiling provides an overview of the genomic landscape of mCRC in a single analysis, including actionable targets and markers of immune sensitivity.
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Li P, Hou F, Wang S, Luo N, Qi Y, Wang Y. A novel NECTIN4-NTRK1 fusion identified in a lung squamous cell carcinoma patient with MSI-H. J Cancer Res Clin Oncol 2021; 147:2483-2486. [PMID: 33811536 DOI: 10.1007/s00432-021-03622-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Peng Li
- Department of Thoracic Surgery, Qingdao University, Qingdao, China
| | - Feng Hou
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Sai Wang
- Department of Thoracic Surgery, Qingdao University, Qingdao, China
| | - Ningning Luo
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Yongjie Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.
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Sajjadi E, Venetis K, Piciotti R, Invernizzi M, Guerini-Rocco E, Haricharan S, Fusco N. Mismatch repair-deficient hormone receptor-positive breast cancers: Biology and pathological characterization. Cancer Cell Int 2021; 21:266. [PMID: 34001143 PMCID: PMC8130151 DOI: 10.1186/s12935-021-01976-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/07/2021] [Indexed: 12/15/2022] Open
Abstract
The clinical outcome of patients with a diagnosis of hormone receptor (HR)+ breast cancer has improved remarkably since the arrival of endocrine therapy. Yet, resistance to standard treatments is a major clinical challenge for breast cancer specialists and a life-threatening condition for the patients. In breast cancer, mismatch repair (MMR) status assessment has been demonstrated to be clinically relevant not only in terms of screening for inherited conditions such as Lynch syndrome, but also for prognostication, selection for immunotherapy, and early identification of therapy resistance. Peculiar traits characterize the MMR biology in HR+ breast cancers compared to other cancer types. In these tumors, MMR genetic alterations are relatively rare, occurring in ~3 % of cases. On the other hand, modifications at the protein level can be observed also in the absence of gene alterations and vice versa. In HR+ breast cancers, the prognostic role of MMR deficiency has been confirmed by several studies, but its predictive value remains a matter of controversy. The characterization of MMR status in these patients is troubled by the lack of tumor-specific guidelines and/or companion diagnostic tests. For this reason, precise identification of MMR-deficient breast cancers can be problematic. A deeper understanding of the MMR biology and clinical actionability in HR+ breast cancer may light the path to effective tumor-specific diagnostic tools. For a precise MMR status profiling, the specific strengths and limitations of the available technologies should be taken into consideration. This article aims at providing a comprehensive overview of the current state of knowledge of MMR alterations in HR+ breast cancer. The available armamentarium for MMR testing in these tumors is also examined along with possible strategies for a tailored pathological characterization.
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Affiliation(s)
- Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Roberto Piciotti
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Marco Invernizzi
- Physical and Rehabilitative Medicine, Department of Health Sciences, University of Eastern Piedmont, Viale Piazza D'Armi, 1, 28100, Novara, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Svasti Haricharan
- Department of Tumor Microenvironment and Cancer Immunology, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, 92037, La Jolla, CA, USA
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122, Milan, Italy.
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Shioi S, Shimamoto A, Nakagami Y, Qin L, Shimokawa M, Oda S. Precision length determination and in silico simulation in PCR of microsatellite repeat sequences. Electrophoresis 2021; 42:1323-1332. [PMID: 33755214 DOI: 10.1002/elps.202100021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 11/05/2022]
Abstract
Despite being commonplace, polymerase chain reactions (PCRs) still contain many unknown aspects. One example is microsatellite PCR, which is now widely used for various purposes from ecology to cancer medicine. Since this category of repetitive DNA sequences induces polymerase slippage not only in vivo but also in vitro, microsatellite PCR products comprise a complex combination of DNA fragments with various lengths and have, therefore, been empirically interpreted. The primary obstacle for understanding microsatellite PCR was the intrinsic inaccuracy in sizing of DNA fragments in capillary electrophoresis (CE), which, however, has been overcome by elucidating intrinsic sizing errors in each fragment length range. Secondly, the slippage properties of the thermostable polymerases were first clarified in detail using primer extension assays. Furthermore, using the obtained slippage parameters and our original program, we have first reconstructed microsatellite PCR in silico. The entire processes of complex microsatellite PCR have, thus, been more clearly understood.
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Affiliation(s)
- Seijiro Shioi
- Cancer Genetics Laboratory, Clinical Research Institute, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Akiyoshi Shimamoto
- Cancer Genetics Laboratory, Clinical Research Institute, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Yuki Nakagami
- Department of Biostatistics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Lexin Qin
- Cancer Genetics Laboratory, Clinical Research Institute, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Mototsugu Shimokawa
- Department of Biostatistics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shinya Oda
- Cancer Genetics Laboratory, Clinical Research Institute, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
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40
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Mismatch Repair Status Characterization in Oncologic Pathology: Taking Stock of the Real-World Possibilities. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mismatch repair (MMR) system has a key role in supporting the DNA polymerase proofreading function and in maintaining genome stability. Alterations in the MMR genes are driving events of tumorigenesis, tumor progression, and resistance to therapy. These genetic scars may occur in either hereditary or sporadic settings, with different frequencies across tumor types. Appropriate characterization of the MMR status is a crucial task in oncologic pathology because it allows for both the tailored clinical management of cancer patients and surveillance of individuals at risk. The currently available MMR testing methods have specific strengths and weaknesses, and their application across different tumor types would require a tailored approach. This article highlights the indications and challenges in MMR status assessment for molecular pathologists, focusing on the possible strategies to overcome analytical and pre-analytical issues.
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41
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Tieng FYF, Abu N, Lee LH, Ab Mutalib NS. Microsatellite Instability in Colorectal Cancer Liquid Biopsy-Current Updates on Its Potential in Non-Invasive Detection, Prognosis and as a Predictive Marker. Diagnostics (Basel) 2021; 11:544. [PMID: 33803882 PMCID: PMC8003257 DOI: 10.3390/diagnostics11030544] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly-diagnosed cancer in the world and ranked second for cancer-related mortality in humans. Microsatellite instability (MSI) is an indicator for Lynch syndrome (LS), an inherited cancer predisposition, and a prognostic marker which predicts the response to immunotherapy. A recent trend in immunotherapy has transformed cancer treatment to provide medical alternatives that have not existed before. It is believed that MSI-high (MSI-H) CRC patients would benefit from immunotherapy due to their increased immune infiltration and higher neo-antigenic loads. MSI testing such as immunohistochemistry (IHC) and PCR MSI assay has historically been a tissue-based procedure that involves the testing of adequate tissue with a high concentration of cancer cells, in addition to the requirement for paired normal tissues. The invasive nature and specific prerequisite of such tests might hinder its application when surgery is not an option or when the tissues are insufficient. The application of next-generation sequencing, which is highly sensitive, in combination with liquid biopsy, therefore, presents an interesting possibility worth exploring. This review aimed to discuss the current body of evidence supporting the potential of liquid biopsy as a tool for MSI testing in CRC.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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Pestinger V, Smith M, Sillo T, Findlay JM, Laes JF, Martin G, Middleton G, Taniere P, Beggs AD. Use of an Integrated Pan-Cancer Oncology Enrichment Next-Generation Sequencing Assay to Measure Tumour Mutational Burden and Detect Clinically Actionable Variants. Mol Diagn Ther 2020; 24:339-349. [PMID: 32306292 PMCID: PMC7264086 DOI: 10.1007/s40291-020-00462-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The identification of tumour mutational burden (TMB) as a biomarker of response to programmed cell death protein 1 (PD-1) immunotherapy has necessitated the development of genomic assays to measure this. We carried out comprehensive molecular profiling of cancers using the Illumina TruSight Oncology 500 (TSO500) panel and compared these to whole-genome sequencing (WGS). METHODS Cancer samples derived from formalin-fixed material were profiled on the TSO500 panel, sequenced on an Illumina NextSeq 500 instrument and processed through the TSO500 Docker pipeline. Either FASTQ files (PierianDx) or vcf files (OncoKDM) were processed to understand clinical actionability. RESULTS In total, 108 samples (a mixture of colorectal, lung, oesophageal and control samples) were processed via the DNA panel. There was good correlation between TMB, single-nucleotide variants (SNVs), indels and copy-number variations as predicted by TSO500 and WGS (R2 > 0.9) and good reproducibility, with less than 5% variability between repeated controls. For the RNA panel, 13 samples were processed, with all known fusions observed via orthogonal techniques. For clinical actionability, 72 tier 1 variants and 297 tier 2 variants were detected, with clinical trials identified for all patients. CONCLUSIONS The TSO500 assay accurately measures TMB, microsatellite instability, SNVs, indels, copy-number/structural variation and gene fusions when compared to WGS and orthogonal technologies. Coupled with a clinical annotation pipeline, this provides a powerful methodology for identification of clinically actionable variants.
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Affiliation(s)
- Valerie Pestinger
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK
| | | | - Toju Sillo
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK
| | | | | | | | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK.
- Queen Elizabeth Hospital Birmingham, Birmingham, UK.
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Li K, Luo H, Huang L, Luo H, Zhu X. Microsatellite instability: a review of what the oncologist should know. Cancer Cell Int 2020; 20:16. [PMID: 31956294 PMCID: PMC6958913 DOI: 10.1186/s12935-019-1091-8] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/28/2019] [Indexed: 02/06/2023] Open
Abstract
The patients with high microsatellite instability (MSI-H)/mismatch repair deficient (dMMR) tumors recently have been reported that can benefit from immunotherapy, and MSI can be used as a genetic instability of a tumor detection index. However, many studies have shown that there are many heterogeneous phenomena in patients with MSI tumors in terms of immunotherapy, prognosis and chemotherapy sensitivity. Here we mainly review the research results of MSI detection methods, the mechanisms of MSI occurrence and its relationship with related tumors, aiming to make a brief analysis of the current research status of MSI and provide comparable reference and guidance value for further research in this field.
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Affiliation(s)
- Kai Li
- 1Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023 China.,2The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023 China.,3Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023 China
| | - Haiqing Luo
- 3Cancer Center, The Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023 China
| | - Lianfang Huang
- 1Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023 China.,2The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023 China
| | - Hui Luo
- 2The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023 China
| | - Xiao Zhu
- 1Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023 China.,2The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023 China
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