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Yamamoto H, Watanabe Y, Arai H, Umemoto K, Tateishi K, Sunakawa Y. Microsatellite instability: A 2024 update. Cancer Sci 2024; 115:1738-1748. [PMID: 38528657 PMCID: PMC11145116 DOI: 10.1111/cas.16160] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Deficient mismatch repair (dMMR) results in microsatellite instability (MSI), a pronounced mutator phenotype. High-frequency MSI (MSI-H)/dMMR is gaining increasing interest as a biomarker for advanced cancer patients to determine their eligibility for immune checkpoint inhibitors (ICIs). Various methods based on next-generation sequencing (NGS) have been developed to assess the MSI status. Comprehensive genomic profiling (CGP) testing can precisely ascertain the MSI status as well as genomic alterations in a single NGS test. The MSI status can be also ascertained through the liquid biopsy-based CGP assays. MSI-H has thus been identified in various classes of tumors, resulting in a greater adoption of immunotherapy, which is hypothesized to be effective against malignancies that possess a substantial number of mutations and/or neoantigens. NGS-based studies have also characterized MSI-driven carcinogenesis, including significant rates of fusion kinases in colorectal cancers (CRCs) with MSI-H that are targets for therapeutic kinase inhibitors, particularly in MLH1-methylated CRCs with wild-type KRAS/BRAF. NTRK fusion is linked to the colorectal serrated neoplasia pathway. Recent advances in investigations of MSI-H malignancies have resulted in the development of novel diagnostic or therapeutic techniques, such as a synthetic lethal therapy that targets the Werner gene. DNA sensing in cancer cells is required for antitumor immunity induced by dMMR, opening up novel avenues and biomarkers for immunotherapy. Therefore, clinical relevance exists for analyses of MSI and MSI-H-associated genomic alterations in malignancy. In this article, we provide an update on MSI-driven carcinogenesis, with an emphasis on unique landscapes of diagnostic and immunotherapeutic strategies.
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Affiliation(s)
- Hiroyuki Yamamoto
- Department of BioinformaticsSt. Marianna University Graduate School of MedicineKawasakiJapan
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yoshiyuki Watanabe
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
- Department of Internal MedicineKawasaki Rinko General HospitalKawasakiJapan
| | - Hiroyuki Arai
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Kumiko Umemoto
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
| | - Keisuke Tateishi
- Department of GastroenterologySt. Marianna University School of MedicineKawasakiJapan
| | - Yu Sunakawa
- Department of Clinical OncologySt. Marianna University School of MedicineKawasakiJapan
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2
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Beech C, Hechtman JF. Molecular Approach to Colorectal Carcinoma: Current Evidence and Clinical Application. Clin Lab Med 2024; 44:221-238. [PMID: 38821642 DOI: 10.1016/j.cll.2023.08.011] [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] [Indexed: 06/02/2024]
Abstract
Colorectal carcinoma is one of the most common cancer types in men and women, responsible for both the third highest incidence of new cancer cases and the third highest cause of cancer deaths. In the last several decades, the molecular mechanisms surrounding colorectal carcinoma's tumorigenesis have become clearer through research, providing new avenues for diagnostic testing and novel approaches to therapeutics. Laboratories are tasked with providing the most current information to help guide clinical decisions. In this review, we summarize the current knowledge surrounding colorectal carcinoma tumorigenesis and highlight clinically relevant molecular testing.
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Affiliation(s)
- Cameron Beech
- Department of Pathology, Yale New Haven Hospital, New Haven, CT, USA
| | - Jaclyn F Hechtman
- Molecular and GI Pathologist, NeoGenomics Laboratories, Fort Myers, FL, USA.
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3
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Qi C, Zhou T, Bai Y, Chen H, Yuan J, Zhao F, Liu C, Ma M, Bei T, Chen S, Zhao X, Chen C, Shen L. China special issue on gastrointestinal tumors-NTRK fusion in a large real-world population and clinical utility of circulating tumor DNA genotyping to guide TRK inhibitor treatment. Int J Cancer 2023; 153:1916-1927. [PMID: 36946696 DOI: 10.1002/ijc.34522] [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: 09/16/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are rare oncogenic drivers and targets of TRK inhibitors in solid tumors. Little is known about NTRK fusion in Chinese patients with pan-cancer. Our study investigated the prevalence and genomic features of NTRK1/2/3 gene fusions in 67 883 Chinese patients with pan-cancer using next-generation sequencing (NGS) data and circulating tumor DNA (ctDNA) NGS to guide TRK inhibitor treatment and resistance monitoring. The prevalence of NTRK fusion (tissue NGS) in the pan-cancer population was 0.18%, with 46 unique NTRK-fusion partner pairs, of which 33 were not previously reported. NTRK2 breakpoint occurred more frequently in intron 15 than intron 12. In colorectal cancers (CRCs), compared to NTRK-negative tumors, NTRK-positive tumors displayed higher tumor mutational burden (TMB) levels (54.6 vs 17.7 mut/Mb, P < .0001). In microsatellite instability-high (MSI-H) CRC, patients with NTRK fusion had a significantly lower TMB than NTRK-negative cases (69.3 vs 79.9 mut/Mb, P = .012). The frequency of NTRK fusion in a ctDNA NGS cohort of 20 954 patients with cancer was similar to that of the tissue NGS cohort. In eight NTRK fusion ctDNA-positive patients, larotrectinib induced objective response in 75% of patients and median progression-free survival was 16.3 months. Blood samples collected from a patient with disease progression after larotrectinib treatment revealed NTRK3 G623R as the potential resistance mechanism. Our study revealed previously unreported NTRK fusion partners, associations of NTRK fusion with MSI and TMB, and the potential utility of ctDNA to screen candidates for TRK inhibitors and monitor drug resistance.
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Affiliation(s)
- Changsong Qi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Early Drug Development Center, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Ting Zhou
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuezong Bai
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Hui Chen
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Jiajia Yuan
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Feilong Zhao
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Chang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Early Drug Development Center, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Mingyang Ma
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Ting Bei
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Shiqing Chen
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | | | - Chunzhu Chen
- Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
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4
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Kobayashi Y, Niida A, Nagayama S, Saeki K, Haeno H, Takahashi KK, Hayashi S, Ozato Y, Saito H, Hasegawa T, Nakamura H, Tobo T, Kitagawa A, Sato K, Shimizu D, Hirata H, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Mizuno S, Kawazu M, Kohsaka S, Ueno T, Mano H, Ishihara S, Uemura M, Mori M, Doki Y, Eguchi H, Oshima M, Suzuki Y, Shibata T, Mimori K. Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers. Br J Cancer 2023; 129:1105-1118. [PMID: 37596408 PMCID: PMC10539316 DOI: 10.1038/s41416-023-02395-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Intratumor heterogeneity (ITH) in microsatellite instability-high (MSI-H) colorectal cancer (CRC) has been poorly studied. We aimed to clarify how the ITH of MSI-H CRCs is generated in cancer evolution and how immune selective pressure affects ITH. METHODS We reanalyzed public whole-exome sequencing data on 246 MSI-H CRCs. In addition, we performed a multi-region analysis from 6 MSI-H CRCs. To verify the process of subclonal immune escape accumulation, a novel computational model of cancer evolution under immune pressure was developed. RESULTS Our analysis presented the enrichment of functional genomic alterations in antigen-presentation machinery (APM). Associative analysis of neoantigens indicated the generation of immune escape mechanisms via HLA alterations. Multiregion analysis revealed the clonal acquisition of driver mutations and subclonal accumulation of APM defects in MSI-H CRCs. Examination of variant allele frequencies demonstrated that subclonal mutations tend to be subjected to selective sweep. Computational simulations of tumour progression with the interaction of immune cells successfully verified the subclonal accumulation of immune escape mutations and suggested the efficacy of early initiation of an immune checkpoint inhibitor (ICI) -based treatment. CONCLUSIONS Our results demonstrate the heterogeneous acquisition of immune escape mechanisms in MSI-H CRCs by Darwinian selection, providing novel insights into ICI-based treatment strategies.
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Affiliation(s)
- Yuta Kobayashi
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Satoshi Nagayama
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-Ku, Tokyo, 135-8550, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, 611-0041, Japan
| | - Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 227-8561, Japan
| | - Hiroshi Haeno
- Division of Integrated Research, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda City, Chiba, 278-0022, Japan
| | - Kazuki K Takahashi
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
| | - Shuto Hayashi
- Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuki Ozato
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takanori Hasegawa
- Division of Health Medical Data Science, Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Akihiro Kitagawa
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Kuniaki Sato
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, 811-1395, Japan
| | - Dai Shimizu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Shinichi Mizuno
- Division of Cancer Research, Center for Advanced Medical Innovation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Masaki Mori
- Faculty of Medicine, Tokai University, Isegahara, 259-1193, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kadoma-Cho, Kanazawa, 920-1164, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Sirokane-dai, Minato-Ku, Tokyo, 108-8639, Japan
- Division of Cancer Genomics, National Cancer Center Japan, Research Institute 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan.
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5
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Romanko AA, Mulkidjan RS, Tiurin VI, Saitova ES, Preobrazhenskaya EV, Krivosheyeva EA, Mitiushkina NV, Shestakova AD, Belogubova EV, Ivantsov AO, Iyevleva AG, Imyanitov EN. Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples. Int J Mol Sci 2023; 24:14203. [PMID: 37762506 PMCID: PMC10531831 DOI: 10.3390/ijms241814203] [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: 07/27/2023] [Revised: 08/26/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5'/3'-end expression imbalances is potentially capable of detecting the entire spectrum of NTRK gene fusions. Archival tumor specimens obtained from 8075 patients were subjected to manual dissection of tumor cells, DNA/RNA isolation, and cDNA synthesis. The 5'/3'-end expression imbalances in NTRK genes were analyzed by real-time PCR. Further identification of gene rearrangements was performed by variant-specific PCR for 44 common NTRK fusions, and, whenever necessary, by RNA-based next-generation sequencing (NGS). cDNA of sufficient quality was obtained in 7424/8075 (91.9%) tumors. NTRK rearrangements were detected in 7/6436 (0.1%) lung carcinomas, 11/137 (8.0%) pediatric tumors, and 13/851 (1.5%) adult non-lung malignancies. The highest incidence of NTRK translocations was observed in pediatric sarcomas (7/39, 17.9%). Increased frequency of NTRK fusions was seen in microsatellite-unstable colorectal tumors (6/48, 12.5%), salivary gland carcinomas (5/93, 5.4%), and sarcomas (7/143, 4.9%). None of the 1293 lung carcinomas with driver alterations in EGFR/ALK/ROS1/RET/MET oncogenes had NTRK 5'/3'-end expression imbalances. Variant-specific PCR was performed for 744 tumors with a normal 5'/3'-end expression ratio: there were no rearrangements in 172 EGFR/ALK/ROS1/RET/MET-negative lung cancers and 125 pediatric tumors, while NTRK3 fusions were detected in 2/447 (0.5%) non-lung adult malignancies. In conclusion, this study describes a diagnostic pipeline that can be used as a cost-efficient alternative to conventional methods of NTRK1-3 analysis.
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Affiliation(s)
- Aleksandr A. Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Rimma S. Mulkidjan
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Vladislav I. Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Evgeniya S. Saitova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Elena V. Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Elena A. Krivosheyeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Natalia V. Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Anna D. Shestakova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Evgeniya V. Belogubova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Alexandr O. Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Aglaya G. Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
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6
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Xu Y, Shi X, Wang W, Zhang L, Cheung S, Rudolph M, Brega N, Dong X, Qian L, Wang L, Yuan S, Tan DSW, Wang K. Prevalence and clinico-genomic characteristics of patients with TRK fusion cancer in China. NPJ Precis Oncol 2023; 7:75. [PMID: 37567953 PMCID: PMC10421940 DOI: 10.1038/s41698-023-00427-3] [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: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Neurotrophic tyrosine kinase (NTRK) fusions involving NTRK1, NTRK2, and NTRK3 were found in a broad range of solid tumors as driver gene variants. However, the prevalence of NTRK fusions in Chinese solid tumor patients is rarely reported. Based on the next-generation sequencing data from 10,194 Chinese solid tumor patients, we identified approximately 0.4% (40/10,194) of Chinese solid tumor patients with NTRK fusion. NTRK fusions were most frequently detected in soft tissue sarcoma (3.0%), especially in the fibrosarcoma subtype (12.7%). A total of 29 NTRK fusion patterns were identified, of which 11 were rarely reported. NTRK fusion mostly co-occurred with TP53 (38%), CDKN2A (23%), and ACVR2A (18%) and rarely with NTRK amplification (5.0%) and single nucleotide variants (2.5%). DNA-based NTRK fusion sequencing exhibited a higher detection rate than pan-TRK immunohistochemistry (100% vs. 87.5%). Two patients with NTRK fusions showed clinical responses to larotrectinib, supporting the effective response of NTRK fusion patients to TRK inhibitors.
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Affiliation(s)
- Yujun Xu
- Department of Imaging Interventional Therapy, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University; Department of Imaging Interventional Therapy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, China
| | | | | | - Lin Zhang
- OrigiMed Co. Ltd, 201114, Shanghai, China
| | - Shinghu Cheung
- Precision Molecular Oncology, Research and Early Development - Oncology, Pharmaceuticals, Bayer U.S. LLC, Cambridge, USA
| | - Marion Rudolph
- Translational Sciences Oncology, Research and Early Development - Oncology, Pharmaceuticals, Bayer AG, Berlin, Germany
| | | | | | - Lili Qian
- OrigiMed Co. Ltd, 201114, Shanghai, China
| | - Liwei Wang
- OrigiMed Co. Ltd, 201114, Shanghai, China
| | | | - Daniel Shao Weng Tan
- National Cancer Centre Singapore, Duke-NUS Medical School, 169610, Singapore, Singapore.
| | - Kai Wang
- OrigiMed Co. Ltd, 201114, Shanghai, China.
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7
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Heinrich K, Fischer LE, De Toni EN, Markwardt D, Roessler D, Beyer G, Günther M, Ormanns S, Klauschen F, Kunz WG, Fröhling S, Brummer T, Heinemann V, Westphalen CB. Case of a Patient With Pancreatic Cancer With Sporadic Microsatellite Instability Associated With a BRAF Fusion Achieving Excellent Response to Immunotherapy. JCO Precis Oncol 2023; 7:e2200650. [PMID: 37364232 PMCID: PMC10309529 DOI: 10.1200/po.22.00650] [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: 11/23/2022] [Revised: 03/04/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
In this case report, we discuss a case of pancreatic cancer bearing a BRAF fusion, leading to MAPK activation, MLHph, and finally MSI.
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Affiliation(s)
- Kathrin Heinrich
- Department of Medicine III and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Laura E. Fischer
- Department of Medicine III and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
| | - Enrico N. De Toni
- Department of Medicine II and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
| | - Daniel Markwardt
- Department of Medicine II and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
| | - Daniel Roessler
- Department of Medicine II and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
| | - Georg Beyer
- Department of Medicine II and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
| | - Michael Günther
- Institute of Pathology, Ludwig Maximilians University (LMU), Munich, Germany
| | - Steffen Ormanns
- Institute of Pathology, Ludwig Maximilians University (LMU), Munich, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Pathology, Ludwig Maximilians University (LMU), Munich, Germany
| | - Wolfgang G. Kunz
- Department of Radiology and Comprehensive Cancer Center (CCC Munich LMU), University Hospital, LMU Munich, Munich, Germany
| | - Stefan Fröhling
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKTZ), Heidelberg, Germany
- DKTK, Heidelberg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Heinemann
- Department of Medicine III and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - C. Benedikt Westphalen
- Department of Medicine III and Comprehensive Cancer Centre (CCC), LMU University Hospital Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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8
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Ishino T, Kawashima S, Tanji E, Ueno T, Ueda Y, Ogasawara S, Sato K, Mano H, Ishihara S, Kato N, Kawazu M, Togashi Y. Somatic mutations can induce a noninflamed tumour microenvironment via their original gene functions, despite deriving neoantigens. Br J Cancer 2023; 128:1166-1175. [PMID: 36732592 PMCID: PMC10006227 DOI: 10.1038/s41416-023-02165-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Identifying biomarkers to predict immune checkpoint inhibitor (ICI) efficacy is warranted. Considering that somatic mutation-derived neoantigens induce strong immune responses, patients with a high tumour mutational burden reportedly tend to respond to ICIs. However, there are several conflicting data. Therefore, we focused on the original function of neoantigenic mutations and their impact on the tumour microenvironment (TME). METHODS We evaluated 88 high-frequency microsatellite instability (MSI-H) colorectal cancers and analysed the function of the identified neoantigenic mutations and their influence on programmed cell death 1 (PD-1) blockade efficacy. The results were validated using The Cancer Genome Atlas (TCGA) datasets. RESULTS We identified frameshift mutations in RNF43 as a common neoantigenic gene mutation in MSI-H tumours. However, loss-of-function RNF43 mutations induced noninflamed TME by activating the WNT/β-catenin signalling pathway. In addition, loss of RNF43 function induced resistance to PD-1 blockade even in neoantigen-rich tumours. TCGA dataset analyses demonstrated that passenger rather than driver gene mutations were related to the inflamed TME in diverse cancer types. CONCLUSIONS We propose a novel concept of "paradoxical neoantigenic mutations" that can induce noninflamed TME through their original gene functions, despite deriving neoantigens, suggesting the significance of qualities as well as quantities in neoantigenic mutations.
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Affiliation(s)
- Takamasa Ishino
- Department of Tumor Microenvironment, Okayama University, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.,Division of Cell Therapy, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba, 260-8717, Japan.,Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1‑8‑1 Inohana, Chuo‑ku, Chiba, 260‑8670, Japan
| | - Shusuke Kawashima
- Division of Cell Therapy, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba, 260-8717, Japan.,Department of Dermatology, Graduate School of Medicine, Chiba University, 1‑8‑1 Inohana, Chuo‑ku, Chiba, 260‑8670, Japan
| | - Etsuko Tanji
- Division of Cell Therapy, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba, 260-8717, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute; 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Youki Ueda
- Department of Tumor Microenvironment, Okayama University, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Sadahisa Ogasawara
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1‑8‑1 Inohana, Chuo‑ku, Chiba, 260‑8670, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute; 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1‑8‑1 Inohana, Chuo‑ku, Chiba, 260‑8670, Japan
| | - Masahito Kawazu
- Division of Cell Therapy, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba, 260-8717, Japan. .,Division of Cellular Signaling, National Cancer Center Research Institute; 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yosuke Togashi
- Department of Tumor Microenvironment, Okayama University, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan. .,Division of Cell Therapy, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba, 260-8717, Japan.
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9
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Mei WJ, Mi M, Qian J, Xiao N, Yuan Y, Ding PR. Clinicopathological characteristics of high microsatellite instability/mismatch repair-deficient colorectal cancer: A narrative review. Front Immunol 2022; 13:1019582. [PMID: 36618386 PMCID: PMC9822542 DOI: 10.3389/fimmu.2022.1019582] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancers (CRCs) with high microsatellite instability (MSI-H) and deficient mismatch repair (dMMR) show molecular and clinicopathological characteristics that differ from those of proficient mismatch repair/microsatellite stable CRCs. Despite the importance of MSI-H/dMMR status in clinical decision making, the testing rates for MSI and MMR in clinical practice remain low, even in high-risk populations. Additionally, the real-world prevalence of MSI-H/dMMR CRC may be lower than that reported in the literature. Insufficient MSI and MMR testing fails to identify patients with MSI-H/dMMR CRC, who could benefit from immunotherapy. In this article, we describe the current knowledge of the clinicopathological features, molecular landscape, and radiomic characteristics of MSI-H/dMMR CRCs. A better understanding of the importance of MMR/MSI status in the clinical characteristics and prognosis of CRC may help increase the rates of MMR/MSI testing and guide the development of more effective therapies based on the unique features of these tumors.
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Affiliation(s)
- Wei-Jian Mei
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Mi Mi
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Qian
- Global Medical Affairs, MSD China, Shanghai, China
| | - Nan Xiao
- Global Medical Affairs, MSD China, Shanghai, China
| | - Ying Yuan
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, China,Cancer Center of Zhejiang University, Hangzhou, China,*Correspondence: Ying Yuan, ; Pei-Rong Ding,
| | - Pei-Rong Ding
- Department of Colorectal Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, China,*Correspondence: Ying Yuan, ; Pei-Rong Ding,
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10
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Akhoundova D, Hussung S, Sivakumar S, Töpfer A, Rechsteiner M, Kahraman A, Arnold F, Angst F, Britschgi C, Zoche M, Moch H, Weber A, Sokol E, Fritsch RM. ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer. Int J Cancer 2022; 151:2161-2171. [PMID: 36053834 PMCID: PMC9804412 DOI: 10.1002/ijc.34257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 01/05/2023]
Abstract
c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials.
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Affiliation(s)
- Dilara Akhoundova
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Saskia Hussung
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Smruthy Sivakumar
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Antonia Töpfer
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Fabian Arnold
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Florian Angst
- Institute of Diagnostic and Interventional RadiologyUniversity Hospital of ZurichZurichSwitzerland
| | - Christian Britschgi
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Martin Zoche
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Holger Moch
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Achim Weber
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Ethan Sokol
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Ralph M. Fritsch
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
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11
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Yamada A, Yamamoto Y, Minamiguchi S, Kamada M, Sunami T, Ohashi S, Seno H, Kawada K, Muto M. Clinicopathological and molecular characterization of deficient mismatch repair colorectal cancer. Hum Pathol 2022; 130:1-9. [PMID: 36150551 DOI: 10.1016/j.humpath.2022.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
Tumors demonstrating deficient mismatch repair (dMMR) account for 12%-15% of colorectal cancers (CRCs), but their characteristics have not been fully elucidated. The aim of this study was to characterize dMMR CRCs in terms of clinicopathological findings and molecular alterations. Immunostaining for mismatch repair (MMR) proteins was performed to determine MMR status, and then MLH1 promoter methylation and genetic variants of 25 genes involved in colorectal carcinogenesis were analyzed by next-generation sequencing in dMMR tumors. Coexistence of precancerous lesions was histologically evaluated to characterize the type of precursors. Immunohistochemistry revealed 34 dMMR tumors in 492 CRCs. Among dMMR CRCs, there were 25 MLH1 methylation-positive, 16 BRAF V600E variant-positive, and 7 KRAS variant-positive tumors. Positive MLH1 methylation was associated with BRAF V600E, older age, and right-side tumor location. MLH1 methylated BRAF/KRAS wild-type tumors were distinct in that all 5 tumors possessed variants in ligand-independent WNT signaling genes including APC, AXIN2, and CTNNB1. Among 10 dMMR CRCs that presented with precancerous lesions, 4 BRAF variant-positive, 1 KRAS variant-positive, and 2 BRAF/KRAS wild-type MLH1 methylated tumors coexisted with serrated lesions, whereas 1 MLH1 methylated BRAF/KRAS wild-type tumor and 2 MLH1 unmethylated tumors accompanied conventional adenomas. The present study characterized distinct subgroups of dMMR CRCs based on molecular alterations including MLH1 methylation and variants in BRAF, KRAS, and ligand-independent WNT signaling genes. The existence of distinct precursor lesions including serrated lesion and conventional adenoma further illustrates the involvement of heterogeneous carcinogenetic pathways in the development of dMMR CRCs.
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Affiliation(s)
- Atsushi Yamada
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto, 606-8507, Japan; Department of Clinical Data Science Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
| | - Yoshihiro Yamamoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Sachiko Minamiguchi
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Mayumi Kamada
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, 53 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tomohiko Sunami
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto, 606-8507, Japan; Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Shinya Ohashi
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kenji Kawada
- Department of Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Manabu Muto
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto, 606-8507, Japan; Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
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12
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Zhang Z, Pang J, Chen L, Chen J, Li J, Liu H, Wang J, Wu H, Liang Z. Pan-tropomyosin receptor kinase immunohistochemistry is a feasible routine screening strategy for NTRK fusions in mismatch repair-deficient colorectal carcinomas. Hum Pathol 2022; 129:21-31. [PMID: 35977594 DOI: 10.1016/j.humpath.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022]
Abstract
We have previously revealed the high enrichment of NTRK fusion in mismatch repair deficient (dMMR) CRCs. Optimized diagnostic approaches are urgently needed to identify dMMR CRCs that could benefit from TRK inhibitor therapy. A consecutive cohort of 240 surgically resected dMMR CRCs from 2015 to 2021 was collected for pan-TRK immunohistochemistry (IHC) using pan-TRK clone EPR17341 (VENTANA). We analyzed the sensitivity and specificity of pan-TRK IHC with sequential DNA/RNA-based Next Generation Sequencing (NGS) as the reference method and further explored IHC staining patterns and their correlation with fusion variants in dMMR CRCs. Of 240 dMMR CRCs, 15 (6.2%) were stained positive for pan-TRK IHC, and the sensitivity and specificity were both 100%. Five staining patterns were revealed, which correlated with fusion variants. Diffuse and strong positivity in membrane and cytoplasm were detected in all 6 cases with TPM3-NTRK1 fusions (6/15, 40%). Weak granular cytoplasmic staining, including diffuse or focal positivity, was found in 6 NTRK3 fusions (3 ETV6-NTRK3 and 3 EML4-NTRK3) (6/15, 40%). Diffuse and strong nuclear positivity was noticed in 2 LMNA-NTRK1 fusions (2/15, 13.3%). Intense granular cytoplasmic staining was observed in the only case with PLEKHA6-NTRK1 fusion (1/15, 6.7%). Interestingly, pan-TRK positivity was observed in one case with precursor lesions in both precancerous and cancerous regions, whereas MLH1 loss was restricted to the cancerous region. In summary, an optimized multi-step algorithm using pan-TRK IHC as a screening method was proposed to identify CRC patients harboring NTRK fusions.
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Affiliation(s)
- Zijuan Zhang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junyi Pang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Longyun Chen
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jingci Chen
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junjie Li
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hangqi Liu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jing Wang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Huanwen Wu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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13
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Turpin A, Neuzillet C, Colle E, Dusetti N, Nicolle R, Cros J, de Mestier L, Bachet JB, Hammel P. Therapeutic advances in metastatic pancreatic cancer: a focus on targeted therapies. Ther Adv Med Oncol 2022; 14:17588359221118019. [PMID: 36090800 PMCID: PMC9459481 DOI: 10.1177/17588359221118019] [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: 04/17/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022] Open
Abstract
Mortality from pancreatic ductal adenocarcinoma (PDAC) is increasing worldwide and effective new treatments are urgently needed. The current treatment of metastatic PDAC in fit patients is based on two chemotherapy combinations (FOLFIRINOX and gemcitabine plus nab-paclitaxel) which were validated more than 8 years ago. Although almost all treatments targeting specific molecular alterations have failed so far when administered to unselected patients, encouraging results were observed in the small subpopulations of patients with germline BRCA 1/2 mutations, and somatic gene fusions (neurotrophic tyrosine receptor kinase, Neuregulin 1, which are enriched in KRAS wild-type PDAC), KRAS G12C mutations, or microsatellite instability. While targeted tumor metabolism therapies and immunotherapy have been disappointing, they are still under investigation in combination with other drugs. Optimizing pharmacokinetics and adapting available chemotherapies based on molecular signatures are other promising avenues of research. This review evaluates the current expectations and limits of available treatments and analyses the existing trials. A permanent search for actionable vulnerabilities in PDAC tumor cells and microenvironments will probably result in a more personalized therapeutic approach, keeping in mind that supportive care must also play a major role if real clinical efficacy is to be achieved in these patients.
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Affiliation(s)
- Anthony Turpin
- Department of Medical Oncology, CNRS UMR9020,
Inserm UMR-S 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to
Therapies, University Lille, CHU Lille, Lille, France
| | - Cindy Neuzillet
- Department of Medical Oncology, Curie
Institute, Versailles Saint-Quentin University, Paris-Saclay University,
Saint-Cloud, France
| | - Elise Colle
- Department of Digestive and Medical Oncology,
Hospital Paul Brousse (AP-HP), Villejuif, University of Paris Saclay,
France
| | - Nelson Dusetti
- Cancer Research Center of Marseille, CRCM,
Inserm, CNRS, Paoli-Calmettes Institut, Aix-Marseille University, Marseille,
France
| | - Rémy Nicolle
- Centre de Recherche sur l’Inflammation, INSERM,
U1149, CNRS, ERL 8252, Université de Paris Cité, Paris, France
| | - Jérôme Cros
- Department of Pathology, University of Paris
Cité, Hospital Beaujon (AP-HP), Clichy, France
| | - Louis de Mestier
- Department of Gastroenterology and
Pancreatology, University of Paris Cité, Hospital Beaujon (AP-HP), Clichy,
France
| | - Jean-Baptiste Bachet
- Department of Gastroenterology and Digestive
Oncology, Pitié-Salpêtrière Hospital, Sorbonne University, UPMC University,
Paris, France
| | - Pascal Hammel
- Department of Digestive and Medical Oncology,
Hôpital Paul Brousse (AP-HP), 12 Avenue Paul Vaillant-Couturier, Villejuif
94800, University of Paris Saclay, France
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14
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Bang H, Lee MS, Sung M, Choi J, An S, Kim SH, Lee SE, Choi YL. NTRK Fusions in 1113 Solid Tumors in a Single Institution. Diagnostics (Basel) 2022; 12:diagnostics12061450. [PMID: 35741260 PMCID: PMC9222038 DOI: 10.3390/diagnostics12061450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Most NTRK fusions occur at very low frequencies in various common cancers. Recent recommendations on NTRK testing recommend immunohistochemistry (IHC) as the initial test for tumor types with a low frequency of NTRK fusions. This study investigated the accuracy of an IHC assay to detect NTRK fusions and characterize the clinicopathological and molecular features of NTRK-rearranged tumors. This retrospective study was conducted on 1113 solid tumor samples known to harbor no oncogenic driver alterations, including 510 non-small cell lung cancers (NSCLC), 503 colorectal cancers (CRC), and 79 inflammatory myofibroblastic tumors (IMT). Additionally, 21 ALK expression-positive cases were included. TRK expression was evaluated using a pan-Trk IHC assay, and positive cases were validated using NGS. TRK expression was observed in three NSCLCs (0.6%), six CRCs (1.2%), and six IMTs (6%). NTRK fusions were finally detected in two NSCLCs (0.4%), six CRCs (1.2%), and one IMT (1%). In NSCLC and CRC, the majority of NTRK fusions were readily discernible due to diffuse moderate-to-strong cytoplasmic staining on pan-Trk IHC. In IMT, focal weak nuclear staining indicated the presence of NTRK fusion. Therefore, the utility of pan-Trk IHC should be assessed considering that the difference in performance depends on tumor type.
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Affiliation(s)
- Heejin Bang
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
| | - Mi-Sook Lee
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Minjung Sung
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
| | - Juyoung Choi
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
| | - Sungbin An
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Seok-Hyung Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Seung Eun Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
- Correspondence: (S.E.L.); (Y.-L.C.); Tel.: +82-2-2030-5644 (S.E.L.); +82-2-3410-2800 (Y.-L.C.); Fax: +82-2-2030-5629 (S.E.L.); +82-2-3410-6396 (Y.-L.C.)
| | - Yoon-La Choi
- Laboratory of Theranotics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea; (M.-S.L.); (M.S.); (J.C.); (S.A.)
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
- Correspondence: (S.E.L.); (Y.-L.C.); Tel.: +82-2-2030-5644 (S.E.L.); +82-2-3410-2800 (Y.-L.C.); Fax: +82-2-2030-5629 (S.E.L.); +82-2-3410-6396 (Y.-L.C.)
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15
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Rahi H, Olave MC, Fritchie KJ, Greipp PT, Halling KC, Kipp BR, Graham RP. Gene Fusions in Gastrointestinal Tract cancers. Genes Chromosomes Cancer 2022; 61:285-297. [PMID: 35239225 DOI: 10.1002/gcc.23035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
Fusion genes have been identified a wide array of human neoplasms including hematologic and solid tumors, including gastrointestinal tract neoplasia. A fusion gene is the product of parts of two genes which are joined together following a deletion, translocation or chromosomal inversion. Together with single nucleotide variants, insertions, deletions, and amplification, fusion genes represent one of the key genomic mechanisms for tumor development. Detecting fusions in the clinic is accomplished by a variety of techniques including break-apart fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), and next-generation sequencing (NGS). Some recurrent gene fusions have been successfully targeted by small molecule or monoclonal antibody therapies (i.e. targeted therapies), while others are used for as biomarkers for diagnostic and prognostic purposes. The purpose of this review article is to discuss the clinical utility of detection of gene fusions in carcinomas and neoplasms arising primarily in the digestive system. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hamed Rahi
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Maria C Olave
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karen J Fritchie
- Division of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Patricia T Greipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
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16
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Kawazu M, Ueno T, Saeki K, Sax N, Togashi Y, Kanaseki T, Chida K, Kishigami F, Sato K, Kojima S, Otsuka M, Kawazoe A, Nishinakamura H, Yuka M, Yamamoto Y, Yamashita K, Inoue S, Tanegashima T, Matsubara D, Tane K, Tanaka Y, Iinuma H, Hashiguchi Y, Hazama S, Khor SS, Tokunaga K, Tsuboi M, Niki T, Eto M, Shitara K, Torigoe T, Ishihara S, Aburatani H, Haeno H, Nishikawa H, Mano H. HLA Class I Analysis Provides Insight Into the Genetic and Epigenetic Background of Immune Evasion in Colorectal Cancer With High Microsatellite Instability. Gastroenterology 2022; 162:799-812. [PMID: 34687740 DOI: 10.1053/j.gastro.2021.10.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS A detailed understanding of antitumor immunity is essential for optimal cancer immune therapy. Although defective mutations in the B2M and HLA-ABC genes, which encode molecules essential for antigen presentation, have been reported in several studies, the effects of these defects on tumor immunity have not been quantitatively evaluated. METHODS Mutations in HLA-ABC genes were analyzed in 114 microsatellite instability-high colorectal cancers using a long-read sequencer. The data were further analyzed in combination with whole-exome sequencing, transcriptome sequencing, DNA methylation array, and immunohistochemistry data. RESULTS We detected 101 truncating mutations in 57 tumors (50%) and loss of 61 alleles in 21 tumors (18%). Based on the integrated analysis that enabled the immunologic subclassification of microsatellite instability-high colorectal cancers, we identified a subtype of tumors in which lymphocyte infiltration was reduced, partly due to reduced expression of HLA-ABC genes in the absence of apparent genetic alterations. Survival time of patients with such tumors was shorter than in patients with other tumor types. Paradoxically, tumor mutation burden was highest in the subtype, suggesting that the immunogenic effect of accumulating mutations was counterbalanced by mutations that weakened immunoreactivity. Various genetic and epigenetic alterations, including frameshift mutations in RFX5 and promoter methylation of PSMB8 and HLA-A, converged on reduced expression of HLA-ABC genes. CONCLUSIONS Our detailed immunogenomic analysis provides information that will facilitate the improvement and development of cancer immunotherapy.
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Affiliation(s)
- Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Saeki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | | | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Keigo Chida
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Fumishi Kishigami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan; Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masafumi Otsuka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Akihito Kawazoe
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan; Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Hitomi Nishinakamura
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Maeda Yuka
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | | | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Tokiyoshi Tanegashima
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan; Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Matsubara
- Division of Integrative Pathology, Jichi Medical University, Shimotsukeshi, Japan
| | - Kenta Tane
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan; Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Hisae Iinuma
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yojiro Hashiguchi
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Shoichi Hazama
- Department of Digestive Surgery and Surgical Oncology, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Toshiro Niki
- Division of Integrative Pathology, Jichi Medical University, Shimotsukeshi, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohei Shitara
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Toshihiko Torigoe
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Haeno
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan; Research Institute, National Cancer Center Research Institute, Tokyo, Japan
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17
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Huang L, Zhu H, Luo Z, Luo C, Luo L, Nong B, Zhang S, Wan C, Wang Y, Songyang Z, Xiong Y. FPIA: A database for gene fusion profiling and interactive analyses. Int J Cancer 2022; 150:1504-1511. [PMID: 34985769 DOI: 10.1002/ijc.33921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/05/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022]
Abstract
As one of the hallmarks of cancer, gene fusions play an important role in tumorigenesis, and have been established as biomarkers and therapeutic targets. Although recent years have witnessed the development of gene fusion databases, a tool with interactive analytic functions is still lacking. Here, we introduce FPIA (Fusion Profiling Interactive Analysis), a web server to perform interactive and customizable analysis on fusion genes. With this platform, researchers can easily explore fusion-associated biological and molecular differences including gene expression, tumor purity and ploidy, mutation, copy number variations, protein expression, immune cell infiltration, stemness, telomere length, microsatellite instability, survival, and novel peptides based on 33 cancer types from TCGA data. Currently, it contains 31 633 fusion events from 6910 patients. FPIA complements the existing gene fusion annotation databases with its multi-omics analytic capacity, integrated analysis features, customized analysis selection, and user-friendly design. The comprehensive data analyses by FPIA will greatly facilitate data mining, hypothesis generation, and therapeutic target discovery. FPIA is available at http://bioinfo-sysu.com/fpia.
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Affiliation(s)
- Lu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Huiming Zhu
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chukun Luo
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Linjiang Luo
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Baoting Nong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Shiyu Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chengcheng Wan
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yanzhi Wang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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18
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Ukkola I, Nummela P, Kero M, Tammio H, Tuominen J, Kairisto V, Kallajoki M, Haglund C, Peltomäki P, Kytölä S, Ristimäki A. Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers. Virchows Arch 2022; 480:807-817. [PMID: 35237889 PMCID: PMC9023403 DOI: 10.1007/s00428-022-03302-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 01/09/2023]
Abstract
Gene fusions can act as oncogenic drivers and offer targets for cancer therapy. Since fusions are rare in colorectal cancer (CRC), their universal screening seems impractical. Our aim was to investigate gene fusions in 62 CRC cases with deficient MLH1 (dMLH1) and BRAFV600E wild-type (wt) status from a consecutive real-life series of 2079 CRCs. First, gene fusions were analysed using a novel FusionPlex Lung v2 RNA-based next-generation sequencing (NGS) panel, and these results were compared to a novel Idylla GeneFusion assay and pan-TRK immunohistochemistry (IHC). NGS detected seven (7/62, 11%) NTRK1 fusions (TPM3::NTRK1, PLEKHA6::NTRK1 and LMNA::NTRK1, each in two cases, and IRF2BP2::NTRK1 in one case). In addition, two ALK, four RET and seven BRAF fusions were identified. Idylla detected seven NTRK1 expression imbalances, in line with the NGS results (overall agreement 100%). Furthermore, Idylla detected the two NGS-identified ALK rearrangements as one specific ALK fusion and one ALK expression imbalance, whilst only two of the four RET fusions were discovered. However, Idylla detected several expression imbalances of ALK (n = 7) and RET (n = 1) that were found to be fusion negative with the NGS. Pan-TRK IHC showed clearly detectable, fusion partner-dependent staining patterns in the seven NTRK1 fusion cases. Overall agreement for pan-TRK antibody clone EPR17341 was 98% and for A7H6R 100% when compared to the NGS. Of the 62 CRCs, 43 were MLH1 promoter hypermethylated (MLH1ph) and 39 were RASwt. All fusion cases were both MLH1ph and RASwt. Our results show that kinase fusions (20/30, 67%) and most importantly targetable NTRK1 fusions (7/30, 23%) are frequent in CRCs with dMLH1/BRAFV600Ewt/MLH1ph/RASwt. NGS was the most comprehensive method in finding the fusions, of which a subset can be screened by Idylla or IHC, provided that the result is confirmed by NGS.
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Affiliation(s)
- Iiris Ukkola
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, P.O. Box 400, 00029, HUS, Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pirjo Nummela
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mia Kero
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, P.O. Box 400, 00029, HUS, Helsinki, Finland
| | - Hanna Tammio
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jenni Tuominen
- Department of Genomics, Laboratory of Molecular Haematology and Pathology, Turku University Central Hospital, Turku, Finland
| | - Veli Kairisto
- Department of Genomics, Laboratory of Molecular Haematology and Pathology, Turku University Central Hospital, Turku, Finland
| | - Markku Kallajoki
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Caj Haglund
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Cancer Medicine Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Soili Kytölä
- Department of Genetics, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, P.O. Box 400, 00029, HUS, Helsinki, Finland.
- Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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19
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NTRK insights: best practices for pathologists. Mod Pathol 2022; 35:298-305. [PMID: 34531526 PMCID: PMC8860742 DOI: 10.1038/s41379-021-00913-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/21/2022]
Abstract
Since the discovery of an oncogenic tropomyosin-receptor kinase (TRK) fusion protein in the early 1980s, our understanding of neurotrophic tropomyosin-receptor kinase (NTRK) fusions, their unique patterns of frequency in different tumor types, and methods to detect them have grown in scope and depth. Identification of these molecular alterations in the management of patients with cancer has become increasingly important with the emergence of histology-agnostic, US Food and Drug Administration-approved, effective TRK protein inhibitors. Herein, we review the biology of TRK in normal and malignant tissues, as well as the prevalence and enrichment patterns of these fusions across tumor types. Testing methods currently used to identify NTRK1-3 fusions will be reviewed in detail, with attention to newer assays including RNA-based next-generation sequencing. Recently proposed algorithms for NTRK fusion testing will be compared, and practical insights provided on how testing can best be implemented and communicated within the multidisciplinary healthcare team.
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20
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Wang J, Li R, Li J, Yi Y, Liu X, Chen J, Zhang H, Lu J, Li C, Wu H, Liang Z. Comprehensive analysis of oncogenic fusions in mismatch repair deficient colorectal carcinomas by sequential DNA and RNA next generation sequencing. J Transl Med 2021; 19:433. [PMID: 34657620 PMCID: PMC8522100 DOI: 10.1186/s12967-021-03108-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Background Colorectal carcinoma (CRC) harboring oncogenic fusions has been reported to be highly enriched in mismatch repair deficient (dMMR) tumors with MLH1 hypermethylation (MLH1me+) and wild-type BRAF and RAS. In this study, dMMR CRCs were screened for oncogene fusions using sequential DNA and RNA next generation sequencing (NGS). Results Comprehensive analysis of fusion variants, genetic profiles and clinicopathological features in fusion-positive dMMR CRCs was performed. Among 193 consecutive dMMR CRCs, 39 cases were identified as MLH1me+BRAF/RAS wild-type. Eighteen fusion-positive cases were detected by DNA NGS, all of which were MLH1me+ and BRAF/RAS wild-type. RNA NGS was sequentially conducted in the remaining 21 MLH1me+BRAF/RAS wild-type cases lacking oncogenic fusions by DNA NGS, and revealed four additional fusions, increasing the proportion of fusion-positive tumors from 46% (18/39) to 56% (22/39) in MLH1me+BRAF/RAS wild-type dMMR cases. All 22 fusions were found to involve RTK-RAS pathway. Most fusions affected targetable receptor tyrosine kinases, including NTRK1(9/22, 41%), NTRK3(5/22, 23%), ALK(3/22, 14%), RET(2/22, 9%) and MET(1/22, 5%), whilst only two fusions affected mitogen-activated protein kinase cascade components BRAF and MAPK1, respectively. RNF43 was identified as the most frequently mutated genes, followed by APC, TGFBR2, ATM, BRCA2 and FBXW7. The vast majority (19/22, 86%) displayed alterations in key WNT pathway components, whereas none harbored additional mutations in RTK-RAS pathway. In addition, fusion-positive tumors were typically diagnosed in elder patients and predominantly right-sided, and showed a significantly higher preponderance of hepatic flexure localization (P < 0.001) and poor differentiation (P = 0.019), compared to fusion-negative MLH1me+ CRCs. Conclusions We proved that sequential DNA and RNA NGS was highly effective for fusion detection in dMMR CRCs, and proposed an optimized practical fusion screening strategy. We further revealed that dMMR CRCs harboring oncogenic fusion was a genetically and clinicopathologically distinctive subgroup, and justified more precise molecular subtyping for personalized therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03108-6.
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Affiliation(s)
- Jing Wang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruiyu Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junjie Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Xiaoding Liu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jingci Chen
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Cami Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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21
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Imyanitov E, Kuligina E. Molecular testing for colorectal cancer: Clinical applications. World J Gastrointest Oncol 2021; 13:1288-1301. [PMID: 34721767 PMCID: PMC8529925 DOI: 10.4251/wjgo.v13.i10.1288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/19/2021] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
Molecular genetic analysis is an integral part of colorectal cancer (CRC) management. The choice of systemic therapy for CRC is largely based on the results of tumor molecular testing. Evaluation of the KRAS and NRAS gene status is mandatory for consideration of anti-epidermal growth factor receptor (EGFR) therapy. Tumors with the BRAF V600E substitution are characterized by aggressive behaviour, may require intensified cytotoxic regimens and benefit from combined BRAF and EGFR inhibition. The inactivation of DNA mismatch repair (MMR), or MUTYH gene, or DNA polymerase epsilon results in excessive tumor mutational burden; these CRCs are highly antigenic and therefore sensitive to immune checkpoint inhibitors. Some CRCs are characterized by overexpression of the HER2 oncogene and respond to the appropriate targeted therapy. There are CRCs with clinical signs of hereditary predisposition to this disease, which require germline genetic testing. Liquid biopsy is an emerging technology that has the potential to assist CRC screening, control the efficacy of surgical intervention and guide disease monitoring. The landscape of CRC molecular diagnosis is currently undergoing profound changes due to the increasing use of next generation sequencing.
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Affiliation(s)
- Evgeny Imyanitov
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg 194100, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, Saint-Petersburg 191015, Russia
| | - Ekaterina Kuligina
- Department of Tumor Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
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22
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Beech C, Hechtman JF. Molecular Approach to Colorectal Carcinoma: Current Evidence and Clinical Application. Surg Pathol Clin 2021; 14:429-441. [PMID: 34373094 DOI: 10.1016/j.path.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Colorectal carcinoma is one of the most common cancer types in men and women, responsible for both the third highest incidence of new cancer cases and the third highest cause of cancer deaths. In the last several decades, the molecular mechanisms surrounding colorectal carcinoma's tumorigenesis have become clearer through research, providing new avenues for diagnostic testing and novel approaches to therapeutics. Laboratories are tasked with providing the most current information to help guide clinical decisions. In this review, we summarize the current knowledge surrounding colorectal carcinoma tumorigenesis and highlight clinically relevant molecular testing.
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Affiliation(s)
- Cameron Beech
- Department of Pathology, Yale New Haven Hospital, New Haven, CT, USA
| | - Jaclyn F Hechtman
- Molecular and GI Pathologist, NeoGenomics Laboratories, Fort Myers, FL, USA.
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23
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Kim JH, Hong JH, Choi YL, Lee JA, Seo MK, Lee MS, An SB, Sung MJ, Cho NY, Kim SS, Shin YK, Kim S, Kang GH. NTRK oncogenic fusions are exclusively associated with the serrated neoplasia pathway in the colorectum and begin to occur in sessile serrated lesions. J Pathol 2021; 255:399-411. [PMID: 34402529 DOI: 10.1002/path.5779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 01/16/2023]
Abstract
Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are emerging tissue-agnostic drug targets in malignancies including colorectal carcinomas (CRCs), but their detailed landscape in the context of various colorectal carcinogenesis pathways remains to be investigated. In this study, pan-tropomyosin receptor kinase (TRK) protein expression was assessed by immunohistochemistry (IHC) in retrospectively collected colorectal epithelial tumor tissues, including 441 CRCs [133 microsatellite instability-high (MSI-high) and 308 microsatellite stable (MSS)] and 595 premalignant colorectal lesions (330 serrated lesions and 265 conventional adenomas). TRK-positive cases were then subjected to next-generation sequencing and/or fluorescence in situ hybridization to confirm NTRK rearrangements. TRK IHC positivity was not observed in any of the MSS CRCs, conventional adenomas, traditional serrated adenomas, or hyperplastic polyps, whereas TRK positivity was observed in 11 of 58 (19%) MLH1-methylated MSI-high CRCs, 4 of 23 (17%) sessile serrated lesions with dysplasia (SSLDs), and 5 of 132 (4%) sessile serrated lesions (SSLs). The 11 TRK-positive MSI-high CRCs commonly harbored CpG island methylator phenotype-high (CIMP-high), MLH1 methylation, BRAF/KRAS wild-type, and NTRK1 or NTRK3 fusion (TPM3-NTRK1, TPR-NTRK1, LMNA-NTRK1, SFPQ-NTRK1, ETV6-NTRK3, or EML4-NTRK3). Both NTRK1 or NTRK3 rearrangement and BRAF/KRAS wild-type were detected in all nine TRK-positive SSL(D)s, seven of which demonstrated MSS and/or CIMP-low. TRK expression was selectively observed in distorted serrated crypts within SSLs and was occasionally localized at the base of serrated crypts. NTRK fusions were detected only in SSLs of patients aged ≥50 years, whereas BRAF mutation was found in younger age-onset SSLs. In conclusion, NTRK-rearranged colorectal tumors develop exclusively through the serrated neoplasia pathway and can be initiated from non-dysplastic SSLs without BRAF/KRAS mutations prior to full occurrence of MSI-high/CIMP-high. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hoon Hong
- Central Laboratory, LOGONE Bio-Convergence Research Foundation, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Pathology and Translational Genomics, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mi-Kyoung Seo
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mi-Sook Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sung Bin An
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Min Jung Sung
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Su Kim
- Central Laboratory, LOGONE Bio-Convergence Research Foundation, Seoul, Republic of Korea
| | - Young Kee Shin
- Central Laboratory, LOGONE Bio-Convergence Research Foundation, Seoul, Republic of Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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24
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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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25
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Kelly AD, Wiklund T, Kononen J, Creeden J. STRN-ALK Fusion-Positive Case of Breast Cancer With Response to Alectinib. JCO Precis Oncol 2021; 5:PO.21.00142. [PMID: 34423228 PMCID: PMC8373546 DOI: 10.1200/po.21.00142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
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26
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Genomic context of NTRK1/2/3 fusion-positive tumours from a large real-world population. NPJ Precis Oncol 2021; 5:69. [PMID: 34285332 PMCID: PMC8292342 DOI: 10.1038/s41698-021-00206-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/22/2021] [Indexed: 12/28/2022] Open
Abstract
Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are rare oncogenic drivers in solid tumours. This study aimed to interrogate a large real-world database of comprehensive genomic profiling data to describe the genomic landscape and prevalence of NTRK gene fusions. NTRK fusion-positive tumours were identified from the FoundationCORE® database of >295,000 cancer patients. We investigated the prevalence and concomitant genomic landscape of NTRK fusions, predicted patient ancestry and compared the FoundationCORE cohort with entrectinib clinical trial cohorts (ALKA-372-001 [EudraCT 2012-000148-88]; STARTRK-1 [NCT02097810]; STARTRK-2 [NCT02568267]). Overall NTRK fusion-positive tumour prevalence was 0.30% among 45 cancers with 88 unique fusion partner pairs, of which 66% were previously unreported. Across all cases, prevalence was 0.28% and 1.34% in patients aged ≥18 and <18 years, respectively; prevalence was highest in patients <5 years (2.28%). The highest prevalence of NTRK fusions was observed in salivary gland tumours (2.62%). Presence of NTRK gene fusions did not correlate with other clinically actionable biomarkers; there was no co-occurrence with known oncogenic drivers in breast, or colorectal cancer (CRC). However, in CRC, NTRK fusion-positivity was associated with spontaneous microsatellite instability (MSI); in this MSI CRC subset, mutual exclusivity with BRAF mutations was observed. NTRK fusion-positive tumour types had similar frequencies in FoundationCORE and entrectinib clinical trials. NTRK gene fusion prevalence varied greatly by age, cancer type and histology. Interrogating large datasets drives better understanding of the characteristics of very rare molecular subgroups of cancer and allows identification of genomic patterns and previously unreported fusion partners not evident in smaller datasets.
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27
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Pursuit of Gene Fusions in Daily Practice: Evidence from Real-World Data in Wild-Type and Microsatellite Instable Patients. Cancers (Basel) 2021; 13:cancers13133376. [PMID: 34282766 PMCID: PMC8269381 DOI: 10.3390/cancers13133376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/26/2022] Open
Abstract
Agnostic biomarkers such as gene fusions allow to address cancer patients to targeted therapies; however, the low prevalence of these alterations across common malignancies poses challenges and needs a feasible and sensitive diagnostic process. RNA-based targeted next generation sequencing was performed on 125 samples of patients affected either by colorectal carcinoma, melanoma, or lung adenocarcinoma lacking genetic alterations in canonical driver genes, or by a colorectal carcinoma with microsatellite instability. Gene fusion rates were compared with in silico data from MSKCC datasets. For NTRK gene fusion detection we also employed a multitarget qRT-PCR and pan-TRK immunohistochemistry. Gene fusions were detected in 7/55 microsatellite instable colorectal carcinomas (12.73%), and in 4/70 of the "gene driver free" population (5.71%: 3/28 melanomas, 10.7%, and 1/12 lung adenocarcinomas, 8.3%). Fusion rates were significantly higher compared with the microsatellite stable and "gene driver positive" MSKCC cohorts. Pan-TRK immunohistochemistry showed 100% sensitivity, 91.7% specificity, and the occurrence of heterogeneous and/or subtle staining patterns. The enrichment of gene fusions in this "real-world" cohort highlights the feasibility of a workflow applicable in clinical practice. The heterogeneous expression in NTRK fusion positive tumours unveils challenging patterns to recognize and raises questions on the effective translation of the chimeric protein.
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28
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Yonemaru J, Hashimoto T, Takayanagi D, Naka T, Yatabe Y, Kanemitsu Y, Shiraishi K, Sekine S. NTRK fusion-positive colorectal cancer in Japanese population. Pathol Int 2021; 71:355-359. [PMID: 33631044 DOI: 10.1111/pin.13082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
Abstract
ALK, ROS1 and NTRK fusions are involved in the tumorigenesis of various organs, including colorectal cancer. This study aims to clarify the prevalence of these fusions in colorectal cancer in the Japanese population. Immunohistochemical analysis of 1012 specimens of colorectal cancer revealed two NTRK-positive cases (0.2%) whereas no ALK- or ROS1-positive cases were identified. Reverse transcription polymerase chain reaction (RT-PCR) detected an LMNA-NTRK1 fusion in a case of adenosquamous carcinoma and a TPM3-NTRK1 fusion in a case of tubular adenocarcinoma. Both NTRK1 fusion-positive cases lacked activating mutations in KRAS and BRAF and were mismatch repair-deficient with loss of MLH1 and PMS2 expression and MLH1 promoter methylation. Our results show that receptor tyrosine kinase fusions are rare but present in colorectal cancers in Japanese patients, with a prevalence similar to that reported in other countries.
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Affiliation(s)
- Junpei Yonemaru
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Taiki Hashimoto
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Daisuke Takayanagi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Tomoaki Naka
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yukihide Kanemitsu
- Department of Colorectal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigeki Sekine
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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29
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Guo M, Xiao ZD, Dai Z, Zhu L, Lei H, Diao LT, Xiong Y. The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers. Nucleic Acids Res 2021; 48:12618-12631. [PMID: 33275145 PMCID: PMC7736799 DOI: 10.1093/nar/gkaa1119] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
The majority of the human genome encodes long noncoding RNA (lncRNA) genes, critical regulators of various cellular processes, which largely outnumber protein-coding genes. However, lncRNA-involved fusions have not been surveyed and characterized yet. Here, we present a systematic study of the lncRNA fusion landscape across cancer types and identify >30 000 high-confidence tumor-specific lncRNA fusions (using 8284 tumor and 6946 normal samples). Fusions positively correlated with DNA damage and cancer stemness and were specifically low in microsatellite instable (MSI)-High or virus-infected tumors. Moreover, fusions distribute differently among cancer molecular subtypes, but with shared enrichment in tumors that are microsatellite stable (MSS), with high somatic copy number alterations (SCNA), and with poor survival. Importantly, we find a potentially new mechanism, mediated by enhancer RNAs (eRNA), which generates secondary fusions that form densely connected fusion networks with many fusion hubs targeted by FDA-approved drugs. Finally, we experimentally validate functions of two tumor-promoting chimeric proteins derived from mRNA-lncRNA fusions, KDM4B-G039927 and EPS15L1-lncOR7C2-1. The EPS15L1 fusion protein may regulate (Gasdermin E) GSDME, critical in pyroptosis and anti-tumor immunity. Our study completes the fusion landscape in cancers, sheds light on fusion mechanisms, and enriches lncRNA functions in tumorigenesis and cancer progression.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhen-Dong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510006, China
| | - Ling Zhu
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Lei
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Li-Ting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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30
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Perna C, Navarro A, Ruz-Caracuel I, Caniego-Casas T, Cristóbal E, Leskelä S, Longo F, Caminoa A, Santón A, Ferreiro R, Pizarro D, Palacios-Berraquero ML, Palacios J. Molecular Heterogeneity of High Grade Colorectal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13020233. [PMID: 33435234 PMCID: PMC7826680 DOI: 10.3390/cancers13020233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to its low frequency, high grade colorectal carcinomas (HG-CRCs) are underrepresented in molecular series. We intended to further characterize the pathological and molecular features of these tumors. In addition, morphologically different areas when present, were analyzed separately to study tumor heterogeneity. We found that most (72.5%) of HG-CRCs showed mismatch repair (MMR) deficiency. MMR status conditioned the frequency and the clonality of the molecular alterations found. Thus, whereas BRAF mutations and gene fusions were observed only in MMR deficient (MMRd) tumors, TP53, KRAS, and gene amplifications predominated in MMR proficient (MMRp) tumors. In MMRp tumors, gene amplification was a mechanism of progression, whereas the accumulation of mutations in genes of different pathways such as NOTCH, MMR or PIK3CA was involved in the clonal diversity of MMRd HG-CRC. In summary, intertumor and intratumor molecular heterogeneity in HG-CRCs is mainly due to MMR status. Abstract High grade colorectal carcinomas (HG-CRCs), which comprise 15% of colorectal carcinomas, are underrepresented in reported molecular studies. Clinicopathological, immunohistochemical, and molecular features of 40 HG-CRCs are described. Moreover, glandular and solid areas of 25 tumors were separately analyzed. The expression of MLH1, PMS2, MSH2, MSH6, p53, E-cadherin, CDX2, CK20, CD8, PDL1, PAN-TRK, c-MET, SMARCB1, ARID1A, SMARCA2, and SMARCA4 was analyzed by immunohistochemistry. Promoter MLH1 methylation was analyzed in tumors with MLH1/PMS2 loss. Next-generation sequencing was used to screen 161 genes for hotspot mutations, copy number variations and gene fusions. In this series, 72.5% of HG-CRCs showed mismatch repair deficiency (MMRd). MMR deficient tumor and MMR proficient (MMRp) tumors showed striking molecular differences. Thus, whereas BRAF mutations were only observed in MMRd tumors, mutations in KRAS and TP53 were more frequent in MMR proficient tumors. Moreover, gene fusions (NTRK1 and MET) were detected only in MMRd tumors, whereas gene amplification (MYC, CCND1 and EGFR) predominated in MMRp/TP53-mutated tumors. Loss of expression of proteins involved in chromatin remodeling, such as ARID1A, was observed only in MMRd HG-CRCs, which also showed more frequently PD-L1 expression and a higher number of tumor infiltrating lymphocytes. The separate analysis of glandular and solid areas indicated that the clonal or subclonal nature of the molecular alterations also depended on MMR status. Mutations in genes such as TP53 and KRAS were always clonal in MMRp-CRCs but occurred as subclonal events in MMRd-CRCs. Gene amplification was implicated in the progression of MMRp tumors, but not in MMRd tumors, in which clonal diversity was due to accumulation of mutations in genes of different pathways such as NOTCH, MMR, or PIK3CA. In summary, intertumor and intratumor molecular heterogeneity in HG-CRCs is mainly due to MMR status.
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Affiliation(s)
- Cristian Perna
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- Departamento de Medicina y Especialidades Médicas, Facultad de Medicina, Universidad de Alcalá, 28029 Madrid, Spain
| | - Antonia Navarro
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
| | - Ignacio Ruz-Caracuel
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
| | - Tamara Caniego-Casas
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
| | - Eva Cristóbal
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
| | - Susanna Leskelä
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
| | - Federico Longo
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Alejandra Caminoa
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
| | - Almudena Santón
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
| | - Reyes Ferreiro
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - David Pizarro
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
| | | | - José Palacios
- Department of Pathology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, 28034 Madrid, Spain; (C.P.); (A.N.); (I.R.-C.); (T.C.-C.); (E.C.); (S.L.); (A.C.); (A.S.); (D.P.)
- Departamento de Medicina y Especialidades Médicas, Facultad de Medicina, Universidad de Alcalá, 28029 Madrid, Spain
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain; (F.L.); (R.F.)
- Correspondence: ; Tel.: +34-913-368-337
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31
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Singh H, Li YY, Spurr LF, Shinagare AB, Abhyankar R, Reilly E, Brais LK, Nag A, Ducar MD, Thorner AR, Shapiro GI, Keller RB, Siletti C, Clark JW, Farago AF, Lin JJ, Demetri GD, Gujrathi R, Kulke MH, MacConaill LE, Ligon AH, Sicinska E, Meyerson ML, Meyerhardt JA, Cherniack AD, Wolpin BM, Ng K, Giannakis M, Hornick JL, Cleary JM. Molecular Characterization and Therapeutic Targeting of Colorectal Cancers Harboring Receptor Tyrosine Kinase Fusions. Clin Cancer Res 2021; 27:1695-1705. [PMID: 33414136 DOI: 10.1158/1078-0432.ccr-20-4073] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Receptor tyrosine kinase fusions in colorectal cancers are rare, but potentially therapeutically relevant. We describe clinical, molecular, and pathologic attributes of RTK fusion-associated colorectal cancer. EXPERIMENTAL DESIGN We identified all cases with RTK fusions in patients with colorectal cancer seen at Dana-Farber Cancer Institute (Boston, MA) who underwent OncoPanel testing between 2013 and 2018. Clinical, histologic, and molecular features were extracted from the patient charts and molecular testing results. RESULTS We identified 12 driver oncogenic fusions in various RTKs. These fusions occurred exclusively in BRAF and RAS wild-type tumors and were enriched in right-sided and mismatch repair-deficient (MMR-D) colorectal cancers. All of the MMR-D colorectal cancers with RTK fusions were found in tumors with acquired MMR-D due to MLH1 promoter hypermethylation and one was associated with a sessile serrated polyp. Molecular profiles of MMR-D colorectal cancer with RTK fusions largely resembled BRAF V600E-mutated MMR-D colorectal cancer, rather than those secondary to Lynch syndrome. We describe two patients with fusion-associated microsatellite stable (MSS) colorectal cancer who derived clinical benefit from therapeutic targeting of their translocation. The first harbored an ALK-CAD fusion and received sequential crizotinib and alectinib therapy for a total of 7.5 months until developing an ALK L1196Q gatekeeper mutation. The second patient, whose tumor contained an ROS1-GOPC fusion, continues to benefit from entrectinib after 9 months of therapy. CONCLUSIONS RTK fusions in colorectal cancer are a rare, but important disease subgroup that occurs in RAS and BRAF wild-type tumors. Despite enrichment in acquired MMR-D tumors, RTK fusions also occur in MSS colorectal cancer and provide an important therapeutic target.
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Affiliation(s)
- Harshabad Singh
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Liam F Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Atul B Shinagare
- Department of Radiology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Ritika Abhyankar
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Emma Reilly
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Lauren K Brais
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Anwesha Nag
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew D Ducar
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Early Drug Development Center, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rachel B Keller
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Cheta Siletti
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jeffrey W Clark
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Anna F Farago
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Division of Sarcoma, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rahul Gujrathi
- Department of Radiology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew H Kulke
- Department of Medical Oncology, Boston University Medical Center, Boston, Massachusetts
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Azra H Ligon
- Division of Clinical Cytogenetics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew L Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jeffrey A Meyerhardt
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Brian M Wolpin
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Kimmie Ng
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Marios Giannakis
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - James M Cleary
- Division of Gastrointestinal Cancers, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
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32
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Wang J, Li R, He Y, Yi Y, Wu H, Liang Z. Next-generation sequencing reveals heterogeneous genetic alterations in key signaling pathways of mismatch repair deficient colorectal carcinomas. Mod Pathol 2020; 33:2591-2601. [PMID: 32620917 DOI: 10.1038/s41379-020-0612-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
Colorectal carcinoma (CRC) with deficient mismatch repair (dMMR) is an etiologically heterogeneous molecular entity. We investigated the genetic profile, focusing on key signaling pathways and molecular diversity of dMMR CRCs. In this study, next-generation sequencing was applied to 156 consecutive dMMR CRCs and 225 randomly selected proficient MMR (pMMR) CRCs diagnosed between July 2015 and December 2019 at Peking Union Medical College Hospital. Genetic alterations and MLH1 promoter hypermethylation (MLH1me+) were analyzed. Among the most frequently mutated genes, RNF43, ARID1A, PIK3CA, ATM, and BRCA2 mutants were enriched in dMMR CRCs, whereas APC and TP53 mutations were enriched in pMMR CRCs. In dMMR group, RNF43, APC, ARID1A, and BRCA2 mutations were largely microsatellite instability events. WNT pathway was commonly altered regardless of MMR status. Compared to pMMR CRCs, dMMR CRCs had remarkably more prevalent PI3K, RTK-RAS, TGFβ, and DNA damage repair pathway alterations and more multiple mutations in WNT and PI3K pathways. Within dMMR tumors, mutual exclusivity occurred between CTNNB1 mutation and APC or RNF43 mutation, while coexistence existed between BRAF and RNF43 mutation, as well as RAS and APC mutation. MLH1me+ dMMR CRCs had significantly more frequent RNF43 mutations but less frequent KRAS, APC, and CTNNB1 mutations comparing to MLH1-unmethylated dMMR CRCs. RNF43/BRAF comutations were detected in MLH1me+ dMMR CRCs, whereas RAS/APC comutations were largely detected in Lynch syndrome-associated cases. RNF43 mutation was independently associated with MLH1me+ rather than BRAF mutations. dMMR CRCs bearing receptor tyrosine kinase fusion demonstrated no additional RTK-RAS mutations, significantly fewer PI3K alterations and more TGFBR2 mutations than other dMMR tumors. Our study revealed that dMMR CRCs had distinctive gene mutation spectra and signaling pathway interaction patterns compared to proficient mismatch repair (pMMR) CRCs, and molecular heterogeneity was evident for these divergent oncogenic pathways. These findings justify the use of individualized therapy targeted to dMMR CRC subgroups.
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Affiliation(s)
- Jing Wang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruiyu Li
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangzhige He
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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33
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Tsang ES, Grisdale CJ, Pleasance E, Topham JT, Mungall K, Reisle C, Choo C, Carreira M, Bowlby R, Karasinska JM, MacMillan D, Williamson LM, Chuah E, Moore RA, Mungall AJ, Zhao Y, Tessier-Cloutier B, Ng T, Sun S, Lim HJ, Schaeffer DF, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM, Loree JM. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Clin Cancer Res 2020; 27:522-531. [PMID: 33148671 DOI: 10.1158/1078-0432.ccr-20-1900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. EXPERIMENTAL DESIGN Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches. RESULTS In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1). CONCLUSIONS Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Marcus Carreira
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Daniel MacMillan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,Pancreas Centre BC, Vancouver, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Assessment of Predictive Biomarkers of the Response to Pazopanib Based on an Integrative Analysis of High-grade Soft-tissue Sarcomas: Analysis of a Tumor Sample from a Responder and Patients with Other Soft-tissue Sarcomas. Clin Orthop Relat Res 2020; 478:2461-2476. [PMID: 32567826 PMCID: PMC7594915 DOI: 10.1097/corr.0000000000001322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Soft-tissue sarcomas are a rare group of malignant tumors that usually are treated with surgical excision and radiation therapy, but recently, pazopanib, an oral tyrosine kinase inhibitor, has been used in patients with metastases who do not respond to standard chemotherapy regimens. Based on patients with advanced soft-tissue sarcomas who had received prior chemotherapy, several clinical studies have reported the survival and sensitivity (approximately 5% to 10% sensitive) of patients with soft-tissue sarcomas treated with pazopanib. Recently, next-generation sequencing (NGS) technologies have been used to provide a wide genetic information and to develop personalized medicine in cancer treatment. However, there are few reports and no genetic analyses of patients with soft-tissue sarcomas who had a complete response (CR) to pazopanib. QUESTIONS/PURPOSES We described the clinicopathologic features of a patient with a rare, advanced soft-tissue sarcoma who achieved a CR to pazopanib treatment. Furthermore, integrative analyses using NGS and arrays were performed to elucidate characteristic alterations, including gene mutations, copy number changes, and protein expression that were associated with response to pazopanib. Additionally, functional analyses consisting of in vitro and in vivo assays were also performed to elucidate whether the identified alterations were associated with oncogenic abilities and drug responses. METHODS In a sample from a 70-year-old woman with an advanced soft-tissue sarcoma treated for 1 month with 800 mg of oral pazopanib daily, CT scans demonstrated a CR to treatment. To our knowledge, there have been no patients with soft-tissue sarcomas among several clinical trials of pazopanib that have achieved a CR and therefore, our patient is considered to be extremely rare. We performed an integrative analysis including whole-exome sequencing, transcriptome sequencing, and phosphorylation profiling of receptor tyrosine kinases (RTK) using tumor samples from a patient with a CR matched to normal samples. From here on we will refer to this patient as having a CR, although a short term high-grade partial response may be more accurate. These analyses were performed using NGS and the phosphoreceptor tyrosine kinase (phospho-RTK) array. As a validation study, we also performed target sequencing using three samples from patients with long-term stable disease and two samples from patients with progressive disease who responded to pazopanib treatment. In addition, characteristic gene alterations that were identified according to the response to pazopanib in one patient with a CR, in three patients with long-term stable disease, and in 27 patients with high-grade soft-tissue sarcomas with different histologic subtypes and different responses to pazopanib were verified by quantitative real-time polymerase chain reaction. We conducted a focus formation assay to evaluate the transforming activities of these genomic alterations. RESULTS In the patient with a CR to pazopanib, we identified several somatic mutations including Fms related receptor tyrosine kinase 1 (FLT1) p.G38S, platelet-derived growth factor receptor alpha (PDGFRA) p.T83S, and platelet-derived growth factor receptor beta (PDGFRB) exon 13 skipping. Amplification at chromosome 12q13-14 encompassing GLI family zinc finger 1 (GLI1) and cyclin-dependent kinase-4 (CDK4) was also detected. Furthermore, an elevated PDGFRB phosphorylation level was observed in the tumor. In target sequencing analyses in five patients, one of three patients with long-term stable disease had 12q13-14 amplification. The mRNA expression of GLI1, CDK4, and pazopanib targets including PDGFRA, PDGFRB, vascular endothelial growth factor receptor (VEGFR)1-3, and stem cell factor receptor (KIT) in samples from the patient with a CR, and 27 patients with high-grade soft-tissue sarcomas was verified. The expression of GLI1 was characteristically increased in the patient with a CR and in those with long-term stable disease relative to other patients with soft-tissue sarcomas. Overexpression of GLI1 showed strong transforming potential in 3T3 cells. Moreover, the overexpression of GLI1 upregulated the expression of the PDGFRB protein and promoted phosphorylation, which was dose-dependently inhibited by pazopanib. However, inhibition of GLI1-induced transformation by pazopanib was limited in the focus formation assay; therefore, mechanisms other than PDGFRB activation may contribute to transformation. CONCLUSIONS We identified several gene alterations that might be associated with a CR and long-term stable disease in patients who received pazopanib for advanced soft-tissue sarcomas. We therefore believe that this distinct molecular profile warrants further investigation to identify predictive biomarkers of the response to pazopanib. CLINICAL RELEVANCE Our findings identify molecular mechanisms that possibly explain the high sensitivity of soft-tissue sarcomas to pazopanib and may lead to the development of predictive biomarkers and novel therapies in patients with this and other types of soft-tissue sarcomas.
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35
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Ryan ÉJ, Creavin B, Sheahan K. Delivery of Personalized Care for Locally Advanced Rectal Cancer: Incorporating Pathological, Molecular Genetic, and Immunological Biomarkers Into the Multimodal Paradigm. Front Oncol 2020; 10:1369. [PMID: 32923389 PMCID: PMC7456909 DOI: 10.3389/fonc.2020.01369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Approximately one-third of all newly diagnosed colorectal cancer (CRC) is composed of rectal cancer, with the incidence rising in younger patients. The principal neoadjuvant treatments consist of neoadjuvant short-course radiotherapy and long-course chemoradiation. Locally advanced rectal cancer (LARC) is particularly challenging to manage given the anatomical constrictions of the pelvis and the risk for local recurrence. In appropriately treated patients, 5- and 10-year overall survival is estimated at 60 and 50%, respectively. The prognosis for LARC has improved in recent years with more access to screening, advances in surgical techniques, and perioperative care. Furthermore, the refinement of the multidisciplinary team with combined-modality management strategies has improved outcomes. These advancements have been augmented by significant improvements in the understanding of the underlying tumor biology. However, there are many instances where patient outcomes do not match those for their tumor stage and accurate prognostic information for individual patients can be difficult to estimate owing to the heterogeneous nature of LARC. Many new combinations of chemotherapy with radiotherapy, including total neoadjuvant therapy with targeted therapies that aim to diminish toxicity and increase survival, are being evaluated in clinical trials. Despite these advances, local recurrence and distant metastasis remain an issue, with one-third of LARC patients dying within 5 years of initial treatment. Although much of the new pathological, molecular genetics, and immunological biomarkers allow refinement in the classification and prognostication of CRC, the relative importance of each of these factors with regards to the development and progression of LARC remains incompletely understood. These factors are often insufficiently validated and seldom consider the individual characteristics of the host, the tumor and its location, the local available expertise, or the probable location of recurrence. Appreciating the mechanisms behind these differences will allow for a more comprehensive, personalized approach and more informed treatment options, leading to ultimately superior outcomes. This review aims to first outline the current multidisciplinary context in which LARC care should be delivered and then discuss how some key prognosticators, including novel histopathological, molecular genetics, and immunological biomarkers, might fit into the wider context of personalized LARC management in the coming years.
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Affiliation(s)
- Éanna J. Ryan
- School of Medicine, University College Dublin, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ben Creavin
- School of Medicine, University College Dublin, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kieran Sheahan
- School of Medicine, University College Dublin, Dublin, Ireland
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36
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Vaňková B, Vaněček T, Ptáková N, Hájková V, Dušek M, Michal M, Švajdler P, Daum O, Daumová M, Michal M, Mezencev R, Švajdler M. Targeted next generation sequencing of MLH1-deficient, MLH1 promoter hypermethylated, and BRAF/RAS-wild-type colorectal adenocarcinomas is effective in detecting tumors with actionable oncogenic gene fusions. Genes Chromosomes Cancer 2020; 59:562-568. [PMID: 32427409 DOI: 10.1002/gcc.22861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Oncogenic gene fusions represent attractive targets for therapy of cancer. However, the frequency of actionable genomic rearrangements in colorectal cancer (CRC) is very low, and universal screening for these alterations seems to be impractical and costly. To address this problem, several large scale studies retrospectivelly showed that CRC with gene fusions are highly enriched in groups of tumors defined by MLH1 DNA mismatch repair protein deficiency (MLH1d), and hypermethylation of MLH1 promoter (MLH1ph), and/or the presence of microsatellite instability, and BRAF/KRAS wild-type status (BRAFwt/KRASwt). In this study, we used targeted next generation sequencing (NGS) to explore the occurence of potentially therapeutically targetable gene fusions in an unselected series of BRAFwt/KRASwt CRC cases that displayed MLH1d/MLH1ph. From the initially identified group of 173 MLH1d CRC cases, 141 cases (81.5%) displayed MLH1ph. BRAFwt/RASwt genotype was confirmed in 23 of 141 (~16%) of MLH1d/MLH1ph cases. Targeted NGS of these 23 cases identified oncogenic gene fusions in nine patients (39.1%; CI95: 20.5%-61.2%). Detected fusions involved NTRK (four cases), ALK (two cases), and BRAF genes (three cases). As a secondary outcome of NGS testing, we identified PIK3K-AKT-mTOR pathway alterations in two CRC cases, which displayed PIK3CA mutation. Altogether, 11 of 23 (~48%) MLH1d/MLH1ph/BRAFwt/RASwt tumors showed genetic alterations that could induce resistance to anti-EGFR therapy. Our study confirms that targeted NGS of MLH1d/MLH1ph and BRAFwt/RASwt CRCs could be a cost-effective strategy in detecting patients with potentially druggable oncogenic kinase fusions.
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Affiliation(s)
- Bohuslava Vaňková
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Tomáš Vaněček
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Nikola Ptáková
- Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic.,Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Martin Dušek
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Michael Michal
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | | | - Ondřej Daum
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Magdaléna Daumová
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Michal Michal
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
| | - Roman Mezencev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marián Švajdler
- Šikl's Department of Pathology, The Faculty of Medicine and Faculty Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Bioptická Laboratoř, s.r.o, Pilsen, Czech Republic
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37
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Ouali K, Pellat A, Cohen R, Svrcek M, Penault-Llorca F, André T. [NTRK Fusions: A new way of treatment for gastro-intestinal tumor?]. Bull Cancer 2020; 107:447-457. [PMID: 32067719 DOI: 10.1016/j.bulcan.2019.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/11/2019] [Accepted: 11/16/2019] [Indexed: 11/25/2022]
Abstract
The advent of molecular biology resulted in the discovery of new oncogenes that have led to the development of targeted therapies for the management of cancer patients. The development of these therapies has improved the prognosis of patients in various tumour localizations. The TRK receptor (tropomyosin receptor kinase) is a transmembrane receptor with a tyrosine kinase activity that plays a role in both cell proliferation and the physiology of the nervous system. Fusions involving the NTRK gene, which codes for this receptor, have been found in different types of solid tumours and lead to its constitutional activation. These fusions, however uncommon, are mainly found in rare pediatric tumours but can also be encountered in digestive cancers with high prevalence (such as colorectal cancer, especially in case of microsatellite instability, with a frequency of 2.5 to 38.5 %) or in aggressive cancers (such as pancreatic cancer). Therapies targeting TRK, such as larotrectinib or entrectinib, have shown significant response rates, usually greater than 6 months, for tumours from various primary sites presenting NTRK fusions and refractory to standard therapies. These fusions can be detected by different methods: immunohistochemistry, FISH (fluorescence in situ hybridization) as well as NGS (next generation sequencing). The intent of this review is to report on current knowledge on NTRK fusions in oncology and to discuss the role of these fusions in digestive cancers and potential therapeutic implications.
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Affiliation(s)
- Kaïssa Ouali
- AP-HP, hôpital Saint-Antoine, service d'oncologie médicale, 75012 Paris, France
| | - Anna Pellat
- AP-HP, hôpital Saint-Antoine, service d'oncologie médicale, 75012 Paris, France; Sorbonne université, Paris, France
| | - Romain Cohen
- AP-HP, hôpital Saint-Antoine, service d'oncologie médicale, 75012 Paris, France; Sorbonne université, Paris, France
| | - Magali Svrcek
- Sorbonne université, Paris, France; AP-HP, hôpital Saint-Antoine, département d'anatomo-pathologie, 75012 Paris, France
| | | | - Thierry André
- AP-HP, hôpital Saint-Antoine, service d'oncologie médicale, 75012 Paris, France; Sorbonne université, Paris, France.
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38
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Sveen A, Kopetz S, Lothe RA. Biomarker-guided therapy for colorectal cancer: strength in complexity. Nat Rev Clin Oncol 2020; 17:11-32. [PMID: 31289352 PMCID: PMC7577509 DOI: 10.1038/s41571-019-0241-1] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
The number of molecularly stratified treatment options available to patients with colorectal cancer (CRC) is increasing, with a parallel rise in the use of biomarkers to guide prognostication and treatment decision-making. The increase in both the number of biomarkers and their use has resulted in a progressively complex situation, evident both from the extensive interactions between biomarkers and from their sometimes complex associations with patient prognosis and treatment benefit. Current and emerging biomarkers also reflect the genomic complexity of CRC, and include a wide range of aberrations such as point mutations, amplifications, fusions and hypermutator phenotypes, in addition to global gene expression subtypes. In this Review, we provide an overview of current and emerging clinically relevant biomarkers and their role in the management of patients with CRC, illustrating the intricacies of biomarker interactions and the growing treatment opportunities created by the availability of comprehensive molecular profiling.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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39
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Abstract
Rectal cancer accounts for one-third of newly diagnosed colorectal cancer cases. Given its anatomical location and risk for local recurrence, a multidisciplinary treatment program including surgery, radiation therapy, and chemotherapy has demonstrated improved outcomes in localized disease. Genetic analysis has become part of the standard approach for management of advanced disease and new trials are considering tailored therapies for locally advanced disease. This review describes molecular subsets of colorectal cancer; implications for clinical management, including patterns of metastatic spread and response to therapies; and emerging matched therapies. During the last decade, significant biological differences have been noted based on colorectal cancer primary location and here we focus on rectal cancers and relevant markers for this disease. As more treatment for localized rectal cancer is shifted to the neoadjuvant setting and more targeted regimens are developed for metastatic disease, radiologists will increasingly see patients defined by molecular subsets and their awareness of the genetics of rectal cancer will help further refine our understanding of this disease.
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Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 E 66th Street, 10th Floor, New York, NY, 10065, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 E 66th Street, 10th Floor, New York, NY, 10065, USA.
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40
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Pagani F, Randon G, Guarini V, Raimondi A, Prisciandaro M, Lobefaro R, Di Bartolomeo M, Sozzi G, de Braud F, Gasparini P, Pietrantonio F. The Landscape of Actionable Gene Fusions in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20215319. [PMID: 31731495 PMCID: PMC6861915 DOI: 10.3390/ijms20215319] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
The treatment scenario of metastatic colorectal cancer (mCRC) has been rapidly enriched with new chemotherapy combinations and biological agents that lead to a remarkable improvement in patients’ outcome. Kinase gene fusions account for less than 1% of mCRC overall but are enriched in patients with high microsatellite instability, RAS/BRAF wild-type colorectal cancer. mCRC patients harboring such alterations show a poor prognosis with standard treatments that could be reversed by adopting novel therapeutic strategies. Moving forward to a positive selection of mCRC patients suitable for targeted therapy in the era of personalized medicine, actionable gene fusions, although rare, represent a peculiar opportunity to disrupt a tumor alteration to achieve therapeutic goal. Here we summarize the current knowledge on potentially actionable gene fusions in colorectal cancer available from retrospective experiences and promising preliminary results of new basket trials.
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Affiliation(s)
- Filippo Pagani
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Giovanni Randon
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Vincenzo Guarini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Alessandra Raimondi
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Michele Prisciandaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Riccardo Lobefaro
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Maria Di Bartolomeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
| | - Gabriella Sozzi
- Unit of Molecular Cytogenetics, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milano, Italy; (G.S.); (P.G.)
| | - Filippo de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Patrizia Gasparini
- Unit of Molecular Cytogenetics, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milano, Italy; (G.S.); (P.G.)
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milano, Italy; (F.P.); (G.R.); (V.G.); (A.R.); (M.P.); (R.L.); (M.D.B.); (F.d.B.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
- Correspondence:
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41
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Sai E, Miwa Y, Takeyama R, Kojima S, Ueno T, Yashiro M, Seto Y, Mano H. Identification of candidates for driver oncogenes in scirrhous-type gastric cancer cell lines. Cancer Sci 2019; 110:2643-2651. [PMID: 31222839 PMCID: PMC6676123 DOI: 10.1111/cas.14111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023] Open
Abstract
Scirrhous‐type gastric cancer (SGC) is one of the most intractable cancer subtypes in humans, and its therapeutic targets have been rarely identified to date. Exploration of somatic mutations in the SGC genome with the next‐generation sequencers has been hampered by markedly increased fibrous tissues. Thus, SGC cell lines may be useful resources for searching for novel oncogenes. Here we have conducted whole exome sequencing and RNA sequencing on 2 SGC cell lines, OCUM‐8 and OCUM‐9. Interestingly, most of the mutations thus identified have not been reported. In OCUM‐8 cells, a novel CD44‐IGF1R fusion gene is discovered, the protein product of which ligates the amino‐terminus of CD44 to the transmembrane and tyrosine‐kinase domains of IGF1R. Furthermore, both CD44 and IGF1R are markedly amplified in the OCUM‐8 genome and abundantly expressed. CD44‐IGF1R has a transforming ability, and the suppression of its kinase activity leads to rapid cell death of OCUM‐8. To the best of our knowledge, this is the first report describing the transforming activity of IGF1R fusion genes. However, OCUM‐9 seems to possess multiple oncogenic events in its genome. In particular, a novel BORCS5‐ETV6 fusion gene is identified in the OCUM‐9 genome. BORCS5‐ETV6 possesses oncogenic activity, and suppression of its message partially inhibits cell growth. Prevalence of these novel fusion genes among SGC awaits further investigation, but we validate the significance of cell lines as appropriate reagents for detailed genomic analyses of SGC.
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Affiliation(s)
- Eirin Sai
- Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiyuki Miwa
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Reina Takeyama
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Shinya Kojima
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Toshihide Ueno
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
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42
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Sun J, Fei F, Zhang M, Li Y, Zhang X, Zhu S, Zhang S. The role of mSEPT9 in screening, diagnosis, and recurrence monitoring of colorectal cancer. BMC Cancer 2019; 19:450. [PMID: 31088406 PMCID: PMC6518628 DOI: 10.1186/s12885-019-5663-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background The application of circulating, cell-free, methylated Septin9 (mSEPT9) DNA in screening and recurrence monitoring is highly promising. CpG island methylator phenotype (CIMP) is associated with microsatellite instability (MSI). The present study was performed to determine the diagnostic accuracy of mSEPT9 for colorectal cancer (CRC) and to evaluate its utility in CRC screening and recurrence monitoring. Methods For screening and diagnosis of CRC, peripheral mSEPT9 detection and fecal occult blood test (FOBT) were performed in 650 subjects, then the level of CEA, CA19–9 and CA724 was quantified in 173 subjects. Clinicopathological parameters and mismatch repair protein were detected among subjects with CRC. For recurrence monitoring of CRC, the sensitivity of mSEPT9 of 70 subjects was compared with tumor markers and contrast enhanced computed tomography (CECT). Results Seventy-three percent of CRC patients were mSEPT9-positive at 94.5% specificity, and 17.1% of patients with intestinal polyps and adenoma were mSEPT9-positive at 94.5% specificity, which were higher than FOBT for the screening of CRC. The sensitivity and specificity of mSEPT9 for diagnosis and recurrence monitoring were higher than that of CEA, CA19–9 and CA724. The combined detection of mSEPT9 and CECT enhanced the sensitivity for recurrence monitoring. Pre-therapeutic levels of mSEPT9 were strongly associated with TNM stage, Dukes stages and mismatch repair deficiency (dMMR). Conclusions mSEPT9 analysis might be popularized as a routine biomarker for CRC screening. The combined detection of mSEPT9 and CECT can play an important role for recurrence monitoring. CIMP was highly associated with the pathological stage of CRC and dMMR. Electronic supplementary material The online version of this article (10.1186/s12885-019-5663-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Sun
- Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China
| | - Fei Fei
- Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China.,Nankai University School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China
| | - Mingqing Zhang
- Department of colorectal surgery, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China
| | - Yuwei Li
- Department of colorectal surgery, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China
| | - Xipeng Zhang
- Department of colorectal surgery, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China
| | - Siwei Zhu
- Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, People's Republic of China. .,Nankai University School of Medicine, Nankai University, Tianjin, 300071, People's Republic of China.
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43
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Valeri N. Streamlining Detection of Fusion Genes in Colorectal Cancer: Having "Faith" in Precision Oncology in the (Tissue) "Agnostic" Era. Cancer Res 2019; 79:1041-1043. [PMID: 30877101 DOI: 10.1158/0008-5472.can-19-0305] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/16/2022]
Abstract
The FDA recently granted tissue-agnostic approval for the first-in-class TRK inhibitor larotrectinib for patients whose tumors harbor fusions in neurotrophic receptor tyrosine kinases. These fusion genes have a frequency of less than 1% in unselected patients with colorectal cancer. Using a multiomics approach and a clinically annotated cohort of patients with colorectal cancer, Cocco and colleagues showed that patients with sporadic, RAS/BRAF wild-type, mismatch repair-deficient colorectal cancer tumors with MLH1 promoter methylation present fusions in kinase genes in 42% of cases and suggested a diagnostic framework to improve the selection of patients eligible for gene fusion testing.See related article by Cocco et al., p. 1047.
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Affiliation(s)
- Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Department of Medicine, The Royal Marsden NHS Trust, London, United Kingdom
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44
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Kohsaka S, Tatsuno K, Ueno T, Nagano M, Shinozaki-Ushiku A, Ushiku T, Takai D, Ikegami M, Kobayashi H, Kage H, Ando M, Hata K, Ueda H, Yamamoto S, Kojima S, Oseto K, Akaike K, Suehara Y, Hayashi T, Saito T, Takahashi F, Takahashi K, Takamochi K, Suzuki K, Nagayama S, Oda Y, Mimori K, Ishihara S, Yatomi Y, Nagase T, Nakajima J, Tanaka S, Fukayama M, Oda K, Nangaku M, Miyazono K, Miyagawa K, Aburatani H, Mano H. Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. Cancer Sci 2019; 110:1464-1479. [PMID: 30737998 PMCID: PMC6447855 DOI: 10.1111/cas.13968] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 12/17/2022] Open
Abstract
Tumor molecular profiling is becoming a standard of care for patients with cancer, but the optimal platform for cancer sequencing remains undetermined. We established a comprehensive assay, the Todai OncoPanel (TOP), which consists of DNA and RNA hybridization capture‐based next‐generation sequencing panels. A novel method for target enrichment, named the junction capture method, was developed for the RNA panel to accurately and cost‐effectively detect 365 fusion genes as well as aberrantly spliced transcripts. The TOP RNA panel can also measure the expression profiles of an additional 109 genes. The TOP DNA panel was developed to detect single nucleotide variants and insertions/deletions for 464 genes, to calculate tumor mutation burden and microsatellite instability status, and to infer chromosomal copy number. Clinically relevant somatic mutations were identified in 32.2% (59/183) of patients by prospective TOP testing, signifying the clinical utility of TOP for providing personalized medicine to cancer patients.
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Affiliation(s)
- Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masaaki Nagano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aya Shinozaki-Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daiya Takai
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Masachika Ikegami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kobayashi
- Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hidenori Kage
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mizuo Ando
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Hata
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki Ueda
- Biological Data Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kumiko Oseto
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
| | - Keisuke Akaike
- Department of Orthopedic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Nagayama
- Gastroenterological Center, Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sakae Tanaka
- Department of Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Oda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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45
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Namba S, Sato K, Kojima S, Ueno T, Yamamoto Y, Tanaka Y, Inoue S, Nagae G, Iinuma H, Hazama S, Ishihara S, Aburatani H, Mano H, Kawazu M. Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer. Cancer Sci 2019; 110:1096-1104. [PMID: 30637877 PMCID: PMC6398885 DOI: 10.1111/cas.13937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 12/11/2022] Open
Abstract
The silencing of tumor suppressor genes by promoter CpG island (CGI) methylation is an important cause of oncogenesis. Silencing of MLH1 and BRCA1, two examples of oncogenic events, results from promoter CGI methylation. Interestingly, both MLH1 and BRCA1 have a divergent promoter, from which another gene on the opposite strand is also transcribed. Although studies have shown that divergent transcription is an important factor in transcriptional regulation, little is known about its implication in aberrant promoter methylation in cancer. In this study, we analyzed the methylation status of CGI in divergent promoters using a recently enriched transcriptome database. We measured the extent of CGI methylation in 119 colorectal cancer (CRC) clinical samples (65 microsatellite instability high [MSI‐H] CRC with CGI methylator phenotype, 28 MSI‐H CRC without CGI methylator phenotype and 26 microsatellite stable CRC) and 21 normal colorectal tissues using Infinium MethylationEPIC BeadChip. We found that CGI within divergent promoters are less frequently methylated than CGI within unidirectional promoters in normal cells. In the genome of CRC cells, CGI within unidirectional promoters are more vulnerable to aberrant methylation than CGI within divergent promoters. In addition, we identified three DNA sequence motifs that correlate with methylated CGI. We also showed that methylated CGI are associated with genes whose expression is low in normal cells. Thus, we here provide fundamental observations regarding the methylation of divergent promoters that are essential for the understanding of carcinogenesis and development of cancer prevention strategies.
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Affiliation(s)
- Shinichi Namba
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhito Sato
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Inoue
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hisae Iinuma
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Shoichi Hazama
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Soichiro Ishihara
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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46
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A germline HLTF mutation in familial MDS induces DNA damage accumulation through impaired PCNA polyubiquitination. Leukemia 2019; 33:1773-1782. [PMID: 30696947 DOI: 10.1038/s41375-019-0385-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/27/2018] [Accepted: 12/27/2018] [Indexed: 02/08/2023]
Abstract
Although several causal genes of familial myelodysplastic syndromes (MDS) have been identified, the genetic landscape and the molecular pathogenesis are not totally understood. To explore novel driver genes and their pathogenetic significance, we performed whole-exome sequence analysis of four individuals from a familial MDS pedigree and 10 candidate single-nucleotide variants (C9orf43, CYP7B1, EFHB, ENTPD7, FAM160B2, HELZ2, HLTF, INPP5J, ITPKB, and RYK) were identified. Knockdown screening revealed that Hltf downregulation enhanced colony-forming capacity of primary murine bone marrow (BM) stem/progenitor cells. γH2AX immunofluorescent staining assay revealed increased DNA damage in a human acute myeloid leukemia (AML) cell line ectopically expressing HLTF E259K, which was not observed in cells expressing wild-type HLTF. Silencing of HLTF in human AML cells also led to DNA damage, indicating that HLTF E259K is a loss-of-function mutation. Molecularly, we found that an E259K mutation reduced the binding capacity of HLTF with ubiquitin-conjugating enzymes, methanesulfonate sensitive 2 and ubiquitin-conjugating enzyme E2N, resulting in impaired polyubiquitination of proliferating cell nuclear antigen (PCNA) in HLTF E259K-transduced cells. In summary, our results indicate that a familial MDS-associated HLTF E259K germline mutation induces accumulation of DNA double-strand breaks, possibly through impaired PCNA polyubiquitination.
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