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Zhu L, Jiang Q, Meng J, Zhao H, Lin J. Pan-cancer analysis of COL15A1: an immunological and prognostic biomarker. Discov Oncol 2024; 15:325. [PMID: 39088036 PMCID: PMC11294514 DOI: 10.1007/s12672-024-01200-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/26/2024] [Indexed: 08/02/2024] Open
Abstract
Collagen, type XV, alpha 1 (COL15A1) belongs to the collagen superfamily, which can influence disease progression by modulating immune pathways. Although the growing number of investigations demonstrating the indispensable role of COL15A1 in the progression of certain tumors, no pan-cancer assessment of COL15A1 is accessible to date. Therefore, the available data was used to explore the role of COL15A1 in 33 types of tumors and to investigate their potential immune function. Numerous bioinformatics approaches were used to research the potential oncogenic role of COL15A1, including analysis of tumor prognosis, microsatellite instability (MSI), tumor mutational burden (TMB), single nucleotide polymorphism (SNP), drug sensitivity, immune cell infiltration, and the correlation between cancer stem cells (CSCs) and COL15A1 expression. The outcome implies that most tumors had a high expression of COL15A1, and COL15A1 manifested different relationships with prognosis in different tumors, including both positive and negative correlations. COL15A1 was also found to have a significant correlation with MSI, TMB, and immune infiltrating cells. Our study suggests that COL15A1 may serve as a prognostic marker for malignancy because of its differential expression in tissues and their function in tumor immunity.
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Affiliation(s)
- Lei Zhu
- Graduate School, Dalian Medical University, Dalian, Liaoning, China
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, Liaoning, China
| | - Qianheng Jiang
- School of Stomatology, China Medical University, Shenyang, Liaoning, China
| | - Jun Meng
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, Liaoning, China
| | - Haichun Zhao
- Department of General Surgery, Panjin Liao-Oil Field Gem Flower Hospital, Panjin, Liaoning, China
| | - Jie Lin
- Department of General Surgery, Liaoning Provincial Cancer Hospital, Shenyang, Liaoning, China.
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2
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Yin X, Wu Y, Song J. Characteristics of the immune environment in prostate cancer as an adjunct to immunotherapy. Health Sci Rep 2024; 7:e2148. [PMID: 38988627 PMCID: PMC11233410 DOI: 10.1002/hsr2.2148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/20/2024] [Accepted: 05/06/2024] [Indexed: 07/12/2024] Open
Abstract
Background and Aims The tumor microenvironment (TME) exerts an important role in carcinogenesis and progression. Several investigations have suggested that immune cell infiltration (ICI) is of high prognostic importance for tumor progression and patient survival in many tumors, particularly prostate cancer. The pattern of immune infiltration of PCa, on the other hand, has not been thoroughly understood. Methods The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets on PCa were obtained, and several datasets were merged into one data set using the "ComBat" algorithm. The ICI profiles of PCa patients were then to be uncovered by two computer techniques. The unsupervised clustering method was utilized to identify three ICI patterns in tumor samples, and Principal Component Analysis (PCA) was conducted to estimate the ICI score. Results Three different clusters of three ICIs were identified in 1341 PCa samples, which also correlated with different clinical features/characteristics and biological pathways. Patients with PCa are classified into high and low subtypes based on the ICI scores extracted from immune-associated signature genes. High ICI score subtypes are associated with a worse prognosis, which may intrigue the activation of cancer-related and immune-related pathways such as pathways involving Toll-like receptors, T-cell receptors, JAK-STAT, and natural killer cells. The ICI score was linked to tumor mutation load and immune/cancer-relevant signaling pathways, which explain prostate cancer's poor prognosis. Conclusion The findings of this study not only advanced our knowledge of the mechanism of immune response in the prostate tumor microenvironment but also provided a novel biomarker, that is, the ICI score, for disease prognosis and guiding precision immunotherapy.
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Affiliation(s)
- Xinhai Yin
- Department of Oral and Maxillofacial Surgery Guizhou Provincial People's Hospital Guiyang China
| | - Yadong Wu
- Department of Oral and Maxillofacial Surgery the Affiliated Stomatological Hospital of Guizhou Medical University Guiyang China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery the Affiliated Stomatological Hospital of Guizhou Medical University Guiyang China
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3
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Long Y, Wu Y, Peng J, Song J, Li N. Pyroptosis-related gene signatures are associated with prognosis and tumor microenvironment infiltration in head and neck cancer. Health Sci Rep 2023; 6:e1622. [PMID: 37841942 PMCID: PMC10568974 DOI: 10.1002/hsr2.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Background and Aims Recent studies have highlighted the biological significance of pyroptosis in cancer development. Nevertheless, it is still uncertain if pyroptosis also plays a part in immune modulation and the creation of the tumor microenvironment (TME). Methods The pyroptosis regulatory genes (PRGs) were comprehensively assessed in 1938 head and neck cancer samples, and systematically correlated these modification patterns with the infiltration characteristics of TME cells. The unsupervised consensus analysis method was used to identify specific pyroptosis clusters. The single-sample gene set enrichment analysis and CIBERSOFT algorithms were used to evaluate the infiltration levels of various immune cell subsets. A principal component analysis algorithm was used to construct the pyrolysis potential index (PPI) to quantify the pyrolysis regulation patterns in head and neck squamous cell carcinoma (HNSC). Results Pyrophosphate regulatory genes (PRGs) are often upregulated in tumors due to mutations. PRGs relate to various clinical outcomes and pathways. Molecular subtyping identified pyroptosis patterns, which align with three tumor immunophenotypes: immune-inflamed, immune-excluded, and immune-desert. The PPI measures pyrolysis roles, showing higher PPI in tumor samples linked to subtypes and clinical characteristics. Lower PPI correlates with longer survival, increased immune activity, more tumor mutations, high PD-L1 expression, and mutations in significant genes like PIK3CA. Such patients also experience enhanced immune responses in immunotherapy trials. Conclusion We conducted a comprehensive examination of pyroptosis in HNSC and developed a PPI indicator that shows a strong correlation with the variety and intricacy of the TME.
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Affiliation(s)
- Yan Long
- Department of Medical CosmetologyGuizhou Provincial People's HospitalGuiyangGuizhouChina
| | - Yadong Wu
- Department of Oral and Maxillofacial SurgeryThe Affiliated Stomatological Hospital of Guizhou Medical UniversityGuiyangChina
| | - Juxiang Peng
- Department of OrthodonticsGuiyang Stomatological HospitalGuiyangGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial SurgeryThe Affiliated Stomatological Hospital of Guizhou Medical UniversityGuiyangChina
| | - Na Li
- The Obstetrics and Gynecology DepartmentThe Second Affiliated Hospital of Zunyi Medical UniversityZunyiChina
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4
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Tsunedomi R, Shindo Y, Nakajima M, Yoshimura K, Nagano H. The tumor immune microenvironment in pancreatic cancer and its potential in the identification of immunotherapy biomarkers. Expert Rev Mol Diagn 2023; 23:1121-1134. [PMID: 37947389 DOI: 10.1080/14737159.2023.2281482] [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: 02/21/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Pancreatic cancer (PC) has an extremely poor prognosis, even with surgical resection and triplet chemotherapy treatment. Cancer immunotherapy has been recently approved for tumor-agnostic treatment with genome analysis, including in PC. However, it has limited efficacy. AREAS COVERED In addition to the low tumor mutation burden, one of the difficulties of immunotherapy in PC is the presence of abundant stromal cells in its microenvironment. Among stromal cells, cancer-associated fibroblasts (CAFs) play a major role in immunotherapy resistance, and CAF-targeted therapies are currently under development, including those in combination with immunotherapies. Meanwhile, microbiomes and tumor-derived exosomes (TDEs) have been shown to alter the behavior of distant receptor cells in PC. This review discusses the role of CAFs, microbiomes, and TDEs in PC tumor immunity. EXPERT OPINION Elucidating the mechanisms by which CAFs, microbiomes, and TDEs are involved in the tumorigenesis of PC will be helpful for developing novel immunotherapeutic strategies and identifying companion biomarkers for immunotherapy. Spatial single-cell analysis of the tumor microenvironment will be useful for identifying biomarkers of PC immunity. Furthermore, given the complexity of immune mechanisms, artificial intelligence models will be beneficial for predicting the efficacy of immunotherapy.
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Affiliation(s)
- Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yoshitaro Shindo
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Masao Nakajima
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Kiyoshi Yoshimura
- Division of Medical Oncology, Department of Medicine, Showa University School of Medicine, Shinagawa, Tokyo, Japan
- Department of Clinical Immuno-Oncology, Clinical Research Institute for Clinical Pharmacology and Therapeutics, Showa University, Setagaya, Tokyo, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
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5
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Imamura T, Ashida R, Ohshima K, Uesaka K, Sugiura T, Ohgi K, Yamada M, Otsuka S, Hatakeyama K, Nagashima T, Sugino T, Urakami K, Akiyama Y, Yamaguchi K. Characterization of pancreatic cancer with ultra-low tumor mutational burden. Sci Rep 2023; 13:4359. [PMID: 36928600 PMCID: PMC10020557 DOI: 10.1038/s41598-023-31579-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
In pancreatic cancer (PC), Tumor mutation burden (TMB) has been reported to be lower than in other cancers, with its clinical significance remaining unclear. We analyzed the dataset of whole-exome sequencing and gene expression profiling of 93 resected PC cases. The median TMB was 0.24. The TMB was classified as High (≥ 5.0), Low (< 5.0, ≥ 1.0), or Ultra-low (< 1.0). Nineteen samples (20%) were classified as TMB-low, and 74 (80%) were classified as TMB-ultra-low; no samples were TMB-high. TMB-ultra-low PC had significantly fewer borderline resectable lesions (P = 0.028) and fewer adenosquamous carcinomas (P = 0.003) than TBM-low PC. Furthermore, the TMB-ultra-low PC showed significantly lower detection rates of driver mutations and copy number variations. Microsatellite instability was not significantly correlated with the TMB status. The TMB-ultra-low PC had a significantly better prognosis than TBM-low PC (P = 0.023). A multivariate analysis identified TMB-ultra-low PC as an independent favorable prognostic factor (hazard ratio, 2.11; P = 0.019). A gene expression analysis showed that TMB-ultra-low PC was associated with reduced TP53 inactivation (P = 0.003) and reduced chromosomal instability (P = 0.001) compared to TBM-low PC. TMB-ultra-low PC had specific gene expression signatures and a better prognosis than TMB-low PC.
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Affiliation(s)
- Taisuke Imamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Ryo Ashida
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan.
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Katsuhisa Ohgi
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Mihoko Yamada
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Shimpei Otsuka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- SRL, Inc., Tokyo, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
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6
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Hatakeyama K, Nagashima T, Ohshima K, Ohnami S, Ohnami S, Shimoda Y, Naruoka A, Maruyama K, Iizuka A, Ashizawa T, Kenmotsu H, Mochizuki T, Urakami K, Akiyama Y, Yamaguchi K. Impact of somatic mutations and transcriptomic alterations on cancer aneuploidy. Biomed Res 2023; 44:187-197. [PMID: 37779031 DOI: 10.2220/biomedres.44.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Aneuploidy has been recognized as one of hallmark of tumorigenesis since the early 20th century. Recent developments in structural variation analysis in the human genome have revealed the diversity of aneuploidy in cancer. However, the effects of gene mutation and expression in tumors on aneuploidy remain poorly understood. Here, we performed whole exome analysis of over 5,000 Japanese cancer cases and investigated the impact of somatic mutations and gene expression alterations on aneuploidy. First, we evaluated tumor content and genomic alterations that could influence aneuploidy. Next, we compared the aneuploidy frequency in 18 cancer types and observed that TP53 mutations were associated with the aneuploidy on specific chromosomes in colorectal and gastric cancers. Finally, we used expression analysis to isolate pathways involved in aneuploidy accumulation from tumors without TP53 mutations. Chromosomal instability and cell cycle aberration were associated with aneuploidy in TP53 wild-type tumors, and 26 commonly upregulated genes were identified in aneuploidy-high solid tumors without TP53 mutations. Among them, two cancer-related genes (CENPA and PBK) were involved in aneuploidy. Our integrated analysis revealed that both TP53 mutations and transcriptomic alterations independent of somatic mutations affect aneuploidy accumulation. Our findings will facilitate further understanding of diverse aneuploidies in the tumorigenesis.
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Affiliation(s)
- Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
- SRL Inc., Shinjuku-ku, Tokyo 163-0409 Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Akira Iizuka
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Tadashi Ashizawa
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hos- pital, Sunto-gun, Shizuoka, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777 Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka 411-8777 Japan
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7
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Matsubayashi H, Oishi T, Sasaki K, Abe M, Kiyozumi Y, Higashigawa S, Niiya F, Sato J, Ishiwatari H, Imai K, Hotta K, Kishida Y, Takada K, Ono H, Yamazaki K, Yasui H, Kenmotsu H, Kado N, Kagawa H, Shiomi A, Sugiura T, Bando E, Nishimura S, Hatakeyama K, Serizawa M, Harada R, Sugino T. Discordance of microsatellite instability and mismatch repair immunochemistry occurs depending on the cancer type. Hum Pathol 2022; 135:54-64. [PMID: 36596344 DOI: 10.1016/j.humpath.2022.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/12/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023]
Abstract
Microsatellite instability (MSI) and deficiency of mismatch repair (dMMR) are key markers for predicting the response of immune checkpoint inhibitors (ICIs) and screening for Lynch syndrome (LS). This study examined the incidences of and factors associated with the concordance of MSI and MMR in human cancers. A total of 518 formalin-fixed cancer tissues were analyzed for MSI and MMR immunohistochemistry (IHC). MSI was analyzed by a PCR-based method using Promega markers. Concordance with MMR expression and factors associated with concordance were analyzed. In 2 colorectal cancer samples, MMR IHC failed due to inadequate staining conditions. In the remaining 516 cancers, a high level of MSI (MSI-H) was identified in 113 cases, and dMMR was identified in 112. The concordance of MSI and MMR IHC was 98.3%. Only 9 cases (4 pancreatobiliary, 3 colorectal, and 2 endometrial cancers) were discordant. Of the 113 MSI-H cases, 4 (3.5%) were proficient MMR (pMMR); of the 403 microsatellite stability (MSS) cases, 5 (1.2%) were dMMR. The independent factors associated with MSI-H/dMMR included meeting Amsterdam II criteria, assay purpose, and sampling method. Multivariate analysis revealed that cancer type (gastrointestinal cancers or others) was associated with concordance of MSI and MMR IHC. Three LS cases with pancreatic or endometrial cancer demonstrated MSS and dMMR, and one biliary cancer showed MSI-H and pMMR. Discordance between MSI and MMR IHC occasionally occurs in pancreaticobiliary and endometrial cancers. When suspected, both MSI and MMR IHC should be done to judge the ICI indication and screen for LS.
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Affiliation(s)
- Hiroyuki Matsubayashi
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan; Division of Endoscopy, Shizuoka, 411-8777, Japan.
| | - Takuma Oishi
- Division of Pathology, Shizuoka, 411-8777, Japan
| | - Keiko Sasaki
- Division of Pathology, Shizuoka, 411-8777, Japan
| | - Masato Abe
- Division of Pathology, Shizuoka, 411-8777, Japan
| | - Yoshimi Kiyozumi
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan
| | | | | | - Junya Sato
- Division of Endoscopy, Shizuoka, 411-8777, Japan
| | | | | | | | | | | | - Hiroyuki Ono
- Division of Endoscopy, Shizuoka, 411-8777, Japan
| | | | - Hirofumi Yasui
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan; Division of Gastrointestinal Oncology, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan; Division of Thoracic Oncology, Shizuoka, 411-8777, Japan
| | - Nobuhiro Kado
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan; Division of Gynecology, Shizuoka, 411-8777, Japan
| | - Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka, 411-8777, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka, 411-8777, Japan
| | - Teichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka, 411-8777, Japan
| | - Etsuro Bando
- Division of Gastric Surgery, Shizuoka, 411-8777, Japan
| | - Seiichiro Nishimura
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan; Division of Breast Surgery, Shizuoka, 411-8777, Japan
| | - Keiichi Hatakeyama
- Division of Clinical Research Center, Shizuoka Cancer Center, Shizuoka, 411-8777, Japan
| | - Masakuni Serizawa
- Division of Clinical Research Center, Shizuoka Cancer Center, Shizuoka, 411-8777, Japan
| | - Rina Harada
- Division of Genetic Medicine Promotion, Shizuoka, 411-8777, Japan
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8
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Kagawa H, Hatakeyama K, Shiomi A, Hino H, Manabe S, Yamaoka Y, Nagashima T, Ohshima K, Urakami K, Yamaguchi K. Consensus molecular subtyping improves the clinical usefulness of canonical tumor markers for colorectal cancer. Biomed Res 2022; 43:201-209. [PMID: 36517022 DOI: 10.2220/biomedres.43.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transcriptome-based classification, such as consensus molecular subtyping, is expected to be applied to colorectal cancer (CRC). However, the relationship between molecular profiles and classical tumor markers, which are already used in clinical practice, has not been analyzed in a large cohort and remains unclear. We classified more than 1,500 Japanese patients with CRC based on consensus molecular subtyping and investigated the clinically available blood carcinoembryonic antigen (CEA) concentrations of each subgroup. To precisely distinguish CRCs, we allocated them to five subgroups, including tumors that were difficult to classify using the consensus molecular subtypes (CMSs), and extracted a heterogeneous population with somatic mutations and expression profiles that differed from those of the CMSs 1-4. For patients allocated to the CMS4 subgroup of stage III CRCs, elevated blood CEA concentrations may identify a subgroup with highly aggressive disease and contribute to improving therapeutic decisions. Furthermore, gene expression and pathway analyses of tumor and non-tumor tissues revealed that tumor immunity was "cold" in this subgroup with high CEA concentrations. The combination of emerging molecular profiling and classical tumor markers may have greater clinical utility than either used alone.
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Affiliation(s)
- Hiroyasu Kagawa
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital.,Department of Surgery, Keio University School of Medicine
| | | | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Hitoshi Hino
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Shoichi Manabe
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Yusuke Yamaoka
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital
| | - Takeshi Nagashima
- SRL Inc.,Medical Genetics Division, Shizuoka Cancer Center Research Institute
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
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9
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A scoping review and meta-analysis on the prevalence of pan-tumour biomarkers (dMMR, MSI, high TMB) in different solid tumours. Sci Rep 2022; 12:20495. [PMID: 36443366 PMCID: PMC9705554 DOI: 10.1038/s41598-022-23319-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 10/29/2022] [Indexed: 11/29/2022] Open
Abstract
Immune checkpoint inhibitors have been approved in the USA for tumours exhibiting mismatch repair deficiency (dMMR), microsatellite instability (MSI), or high tumour mutational burden (TMB), with regulatory and reimbursement applications in multiple other countries underway. As the estimated budget impacts of future reimbursements depend on the size of the potential target population, we performed a scoping review and meta-analysis of the prevalence of these pan-tumour biomarkers in different cancers. We systematically searched Medline/Embase and included studies reporting the prevalence of dMMR/MSI/high TMB in solid tumours published 01/01/2018-31/01/2021. Meta-analyses were performed separately for the pan-cancer prevalence of each biomarker, and by cancer type and stage where possible. The searches identified 3890 papers, with 433 prevalence estimates for 32 different cancer types from 201 studies included in meta-analyses. The pooled overall prevalence of dMMR, MSI and high TMB (≥ 10 mutations/Mb) in pan-cancer studies was 2.9%, 2.7% and 14.0%, respectively. The prevalence profiles of dMMR/MSI and high TMB differed across cancer types. For example, endometrial, colorectal, small bowel and gastric cancers showed high prevalence of both dMMR and MSI (range: 8.7-26.8% and 8.5-21.9%, respectively) and high TMB (range: 8.5-43.0%), while cervical, esophageal, bladder/urothelial, lung and skin cancers showed low prevalence of dMMR and MSI (< 5%), but high prevalence of high TMB (range: 23.7-52.6%). For other cancer types, prevalence of all three biomarkers was generally low (< 5%). This structured review of dMMR/MSI/high TMB prevalence across cancers and for specific cancer types and stages provide timely evidence to inform budget impact forecasts in health technology assessments for drug approvals based on these pan-tumour biomarkers.
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10
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Hatakeyama K, Muramatsu K, Nagashima T, Kawanishi Y, Fukumura R, Ohshima K, Shimoda Y, Kenmotsu H, Mochizuki T, Urakami K, Akiyama Y, Sugino T, Yamaguchi K. Tumor cell enrichment by tissue suspension enables detection of mutations with low variant allele frequency and estimation of germline mutations. Sci Rep 2022; 12:2953. [PMID: 35194076 PMCID: PMC8863826 DOI: 10.1038/s41598-022-06885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
Targeted sequencing offers an opportunity to select specific drugs for cancer patients based on alterations in their genome. However, accurate sequencing cannot be performed in cancers harboring diffuse tumor cells because of low tumor content. We performed tumor cell enrichment using tissue suspension of formalin-fixed, paraffin-embedded (FFPE) tissue sections with low tumor cell content. The enriched fractions were used to efficiently identify mutations by sequencing a target panel of cancer-related genes. Tumor-enriched and residual fractions were isolated from FFPE tissue sections of intestinal and diffuse gastric cancers harboring diffuse tumor cells and DNA of suitable quality was isolated for next-generation sequencing. Sequencing of a target panel of cancer-related genes using the tumor-enriched fraction increased the number of detectable mutations and variant allele frequency. Furthermore, mutation analysis of DNA isolated from tumor-enriched and residual fractions allowed us to estimate germline mutations without a blood reference. This approach of tumor cell enrichment will not only enhance the success rate of target panel sequencing, but can also improve the accuracy of detection of somatic mutations in archived specimens.
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Affiliation(s)
- Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Koji Muramatsu
- Division of Pathology, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc, Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Yuichi Kawanishi
- SRL & Shizuoka Cancer Center Collaborative Laboratories Inc, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ryutaro Fukumura
- SRL & Shizuoka Cancer Center Collaborative Laboratories Inc, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc, Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Hirotsugu Kenmotsu
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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11
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Liang CW, Fang PW, Huang HY, Lo CM. Deep Convolutional Neural Networks Detect Tumor Genotype from Pathological Tissue Images in Gastrointestinal Stromal Tumors. Cancers (Basel) 2021; 13:5787. [PMID: 34830948 PMCID: PMC8616403 DOI: 10.3390/cancers13225787] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022] Open
Abstract
Gastrointestinal stromal tumors (GIST) are common mesenchymal tumors, and their effective treatment depends upon the mutational subtype of the KIT/PDGFRA genes. We established deep convolutional neural network (DCNN) models to rapidly predict drug-sensitive mutation subtypes from images of pathological tissue. A total of 5153 pathological images of 365 different GISTs from three different laboratories were collected and divided into training and validation sets. A transfer learning mechanism based on DCNN was used with four different network architectures, to identify cases with drug-sensitive mutations. The accuracy ranged from 87% to 75%. Cross-institutional inconsistency, however, was observed. Using gray-scale images resulted in a 7% drop in accuracy (accuracy 80%, sensitivity 87%, specificity 73%). Using images containing only nuclei (accuracy 81%, sensitivity 87%, specificity 73%) or cytoplasm (accuracy 79%, sensitivity 88%, specificity 67%) produced 6% and 8% drops in accuracy rate, respectively, suggesting buffering effects across subcellular components in DCNN interpretation. The proposed DCNN model successfully inferred cases with drug-sensitive mutations with high accuracy. The contribution of image color and subcellular components was also revealed. These results will help to generate a cheaper and quicker screening method for tumor gene testing.
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Affiliation(s)
- Cher-Wei Liang
- Department of Pathology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243, Taiwan; (C.-W.L.); (P.-W.F.)
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Pei-Wei Fang
- Department of Pathology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243, Taiwan; (C.-W.L.); (P.-W.F.)
| | - Hsuan-Ying Huang
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung 833, Taiwan;
| | - Chung-Ming Lo
- Graduate Institute of Library, Information and Archival Studies, National Chengchi University, Taipei 116, Taiwan
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12
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Chen X, Ou Z, Wang L, Zhang Z, Fan X, Liu H, Wang W, Zhang Y, Zhu J, Liang X, Lou F, Cao S, Yao Y, Wang H, Yao X. Association of tumor mutational burden with genomic alterations in Chinese urothelial carcinoma. Mol Carcinog 2021; 61:311-321. [PMID: 34729830 DOI: 10.1002/mc.23368] [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: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
The tumor mutational burden (TMB) calculated by whole-exome sequencing (WES) is a promising biomarker for the response to immune checkpoint inhibition (ICIs) in solid tumors. However, WES is not feasible in the routine clinical setting. In addition, the characteristics of the TMB in Chinese urothelial carcinoma (UC) are unclear. The aim of this study was to demonstrate the reliability of an Acornmed 808 panel and analyze the characteristics of the TMB in Chinese UC. An Acornmed 808 panel was designed and virtually validated using UC data from the cancer genome atlas (TCGA). Comprehensive analysis of sequencing and clinical data was performed to explore the characteristics of the TMB for 143 Chinese UC patients. Compared to the TMB calculated with random 808-, 500-, and 250-gene panels, the TMB calculated with the Acornmed 808 panel was closer to that calculated by WES. There were marked disparities in the mutational landscape and TMB between Chinese and TCGA UC data. The TMB was negatively associated with copy number variation (CNV). In contrast, the TMB was positive correlation with numbers of mutated DDR genes. Exposure to aristolochic acid signature was observed only in the TMB-high groups. The Acornmed 808 panel is a clinically practical method to assess the TMB. The TMB was associated with the DDR gene status and CNV counts and might be a biomarker for further stratification of UC patients. The study suggested that patients with high TMB may have a unique carcinogenic mechanism.
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Affiliation(s)
- Xusheng Chen
- Department of Geniturinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Zhenyu Ou
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Wang
- Department of Oncology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhenting Zhang
- Department of Geniturinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xiaodong Fan
- Department of Urology, Ningbo Urology & Nephrology Hospital, Ningbo, Zhejiang, China
| | - Huanhuan Liu
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Wenping Wang
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Yanrui Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Jun Zhu
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Ye Yao
- Department of College of Art and Science, Ohio State University, Columbus, Ohio, USA
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, PR China
| | - Xin Yao
- Department of Geniturinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, China
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13
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Erkizan HV, Sukhadia S, Natarajan TG, Marino G, Notario V, Lichy JH, Wadleigh RG. Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma. Sci Rep 2021; 11:14814. [PMID: 34285259 PMCID: PMC8292420 DOI: 10.1038/s41598-021-94064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal cancer has a strikingly low survival rate mainly due to the lack of diagnostic markers for early detection and effective therapies. In the U.S., 75% of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) are of African descent. African American ESCC (AA ESCC) is particularly aggressive, and its biological underpinnings remain poorly understood. We sought to identify the genomic abnormalities by conducting whole exome sequencing of 10 pairs of matched AA esophageal squamous cell tumor and control tissues. Genomic analysis revealed diverse somatic mutations, copy number alterations (SCNAs), and potential cancer driver genes. Exome variants created two subgroups carrying either a high or low tumor mutation burden. Somatic mutational analysis based on the Catalog of Somatic Mutations in Cancer (COSMIC) detected SBS16 as the prominent signature in the high mutation rate group suggesting increased DNA damage. SBS26 was also detected, suggesting possible defects in mismatch repair and microsatellite instability. We found SCNAs in multiple chromosome segments, encoding MYC on 8q24.21, PIK3CA and SOX2 on 3q26, CCND1, SHANK2, CTTN on 11q13.3, and KRAS on 12p12. Amplifications of EGFRvIII and EGFRvIVa mutants were observed in two patients, representing a novel finding in ESCC that has potential clinical relevance. This present exome sequencing, which to our knowledge, represents the first comprehensive exome analysis exclusively in AA ESCC, and highlights novel mutated loci that might explain the aggressive nature of AA ESCC and lead to the development of diagnostic and prognostic markers as well as therapeutic targets.
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Affiliation(s)
- Hayriye Verda Erkizan
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.
| | | | | | - Gustavo Marino
- Hepatology and Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Jack H Lichy
- Pathology and Laboratory Service, Veterans Affairs Medical Center, Washington, DC, USA
| | - Robert G Wadleigh
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.,Hematology and Medical Oncology, Veterans Affairs Medical Center, Washington, DC, USA
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14
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TP53 variant allele frequency correlates with the chemotherapy response score in ovarian/fallopian tube/peritoneal high-grade serous carcinoma. Hum Pathol 2021; 115:76-83. [PMID: 34153306 DOI: 10.1016/j.humpath.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022]
Abstract
Molecular findings in ovarian, fallopian tube, and peritoneal high-grade serous carcinoma (HGSCa) are emerging as potential prognostic indicators. The chemotherapy response score (CRS) has been proposed as a histologic-based prognostic factor in patients with HGSCa treated with neoadjuvant chemotherapy (NACT). No study details the relationship between the mutational landscape of HGSCa and the CRS. This study addresses this issue using next-generation sequencing (NGS). We retrospectively identified 25 HGSCas treated with NACT and pathology material available to calculate the CRS. All cases had NGS on the primary debulking specimen post-NACT. The three-tier Böhm CRS was applied to the omentum or adnexa and calculated as a combined score. Tumor mutation burden (TMB) and TP53 variant allele frequency (VAF) were calculated and used in correlative analysis. All cases had at least one mutation, most commonly TP53 (25 cases, 100%). Other mutations were BRCA2 (one case, 4%), ARID1A (two cases, 8%), and 1 (4%) of each of the following: ERBB2, NTRK3, STK11, NTRK2, TSC1, PIK3CA, NF1, NOTCH3, CDK2, SMAD4, and PMS2. TMB ranged from 2.58 to 7.75 (median 3.84). There was no statistically significant relationship between the TMB and omental CRS, R-squared = 0.011 (P = 0.62); adnexal CRS, R-squared = 0.005 (P = 0.74); or with the combined CRS, R-squared = 0.009 (P = 0.65). Statistically significant correlation was found between the TP53 VAF and the omental CRS (R-squared = 0.28, P = 0.007), adnexal CRS (R-squared = 0.26, P = 0.01), and the combined CRS (R-squared = 0.33, P = 0.0026). The TP53 VAF was adjusted for percent of tumor present on the slide resulting in an average per cell TP53 mutational load, resulting in similar results with a statistically significant correlation between the average per cell TP53 mutational load and the omental CRS (R-squared = 0.27, P = 0.02), adnexal CRS (R-squared = 0.16, P = 0.05), and the combined CRS (R-squared = 0.23, P = 0.02). In summary, NGS confirmed TP53 mutations in all cases of HGSCa. TMB showed no correlation with the CRS. TP53 VAF and average per cell TP53 mutational load showed significant correlation with the CRS, whether graded on the adnexa or omentum or as a combined score, indicating concordance between molecular and histological findings following NACT.
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15
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Pan JW, Zabidi MMA, Chong BK, Meng MY, Ng PS, Hasan SN, Sandey B, Bahnu S, Rajadurai P, Yip CH, Rueda OM, Caldas C, Chin SF, Teo SH. Germline APOBEC3B deletion increases somatic hypermutation in Asian breast cancer that is associated with Her2 subtype, PIK3CA mutations and immune activation. Int J Cancer 2021; 148:2489-2501. [PMID: 33423300 DOI: 10.1002/ijc.33463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
A 30-kb deletion that eliminates the coding region of APOBEC3B (A3B) is >5 times more common in women of Asian descent compared to European descent. This polymorphism creates a chimera with the APOBEC3A (A3A) coding region and A3B 3'UTR, and it is associated with an increased risk for breast cancer in Asian women. Here, we explored the relationship between the A3B deletion polymorphism with tumour characteristics in Asian women. Using whole exome and whole transcriptome sequencing data of 527 breast tumours, we report that germline A3B deletion polymorphism leads to expression of the A3A-B hybrid isoform and increased APOBEC-associated somatic hypermutation. Hypermutated tumours, regardless of A3B germline status, were associated with the Her2 molecular subtype and PIK3CA mutations. Compared to nonhypermutated tumours, hypermutated tumours also had higher neoantigen burden, tumour heterogeneity and immune activation. Taken together, our results suggest that the germline A3B deletion polymorphism, via the A3A-B hybrid isoform, contributes to APOBEC mutagenesis in a significant proportion of Asian breast cancers. In addition, APOBEC somatic hypermutation, regardless of A3B background, may be an important clinical biomarker for Asian breast cancers.
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Affiliation(s)
- Jia-Wern Pan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - Boon-Keat Chong
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Mei-Yee Meng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Pei-Sze Ng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Siti Norhidayu Hasan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Bethan Sandey
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Saira Bahnu
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | | | - Cheng-Har Yip
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
- Cambridge Breast Cancer Research Unit, CRUK Cambridge Cancer Centre, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Soo-Hwang Teo
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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16
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BMP4 and PHLDA1 are plausible drug-targetable candidate genes for KRAS G12A-, G12D-, and G12V-driven colorectal cancer. Mol Cell Biochem 2021; 476:3469-3482. [PMID: 33982211 PMCID: PMC8342352 DOI: 10.1007/s11010-021-04172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/28/2021] [Indexed: 11/21/2022]
Abstract
Despite the frequent detection of KRAS driver mutations in patients with colorectal cancer (CRC), no effective treatments that target mutant KRAS proteins have been introduced into clinical practice. In this study, we identified potential effector molecules, based on differences in gene expression between CRC patients carrying wild-type KRAS (n = 390) and those carrying KRAS mutations in codon 12 (n = 240). CRC patients with wild-type KRAS harboring mutations in HRAS, NRAS, PIK3CA, PIK3CD, PIK3CG, RALGDS, BRAF, or ARAF were excluded from the analysis. At least 11 promising candidate molecules showed greater than two-fold change between the KRAS G12 mutant and wild-type and had a Benjamini-Hochberg-adjusted P value of less than 1E-08, evidence of significantly differential expression between these two groups. Among these 11 genes examined in cell lines transfected with KRAS G12 mutants, BMP4, PHLDA1, and GJB5 showed significantly higher expression level in KRAS G12A, G12D, and G12V transfected cells than in the wild-type transfected cells. We expect that this study will lead to the development of novel treatments that target signaling molecules functioning with KRAS G12-driven CRC.
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17
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Comprehensive omic characterization of breast cancer in Mexican-Hispanic women. Nat Commun 2021; 12:2245. [PMID: 33854067 PMCID: PMC8046804 DOI: 10.1038/s41467-021-22478-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is a heterogeneous pathology, but the genomic basis of its variability remains poorly understood in populations other than Caucasians. Here, through DNA and RNA portraits we explored the molecular features of breast cancers in a set of Hispanic-Mexican (HM) women and compared them to public multi-ancestry datasets. HM patients present an earlier onset of the disease, particularly in aggressive clinical subtypes, compared to non-Hispanic women. The age-related COSMIC signature 1 was more frequent in HM women than in those from other ancestries. We found the AKT1E17K hotspot mutation in 8% of the HM women and identify the AKT1/PIK3CA axis as a potentially druggable target. Also, HM luminal breast tumors present an enhanced immunogenic phenotype compared to Asiatic and Caucasian tumors. This study is an initial effort to include patients from Hispanic populations in the research of breast cancer etiology and biology to further understand breast cancer disparities. Cancers in different populations have been shown to be genetically distinct. Here, the authors sequence breast cancers from Mexican-Hispanic patients and find that these patients have a higher percentage of Akt1 mutations compared to Caucasian and Asian populations, suggesting these are clinically actionable.
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18
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Naruoka A, Ohnami S, Nagashima T, Serizawa M, Hatakeyama K, Ohshima K, Ohnami S, Urakami K, Horiuchi Y, Kiyozumi Y, Matsubayashi H, Abe M, Ohishi T, Kameya T, Sugino T, Onitsuka T, Isaka M, Ohde Y, Sugiura T, Ito T, Uesaka K, Akiyama Y, Kusuhara M, Yamaguchi K. Genomic profiling of multiple tissues in two patients with multiple endocrine neoplasia type 1. Biomed Res 2021; 42:89-94. [PMID: 33840689 DOI: 10.2220/biomedres.42.89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant tumor syndrome. This hereditary cancer is caused by germline variants in MEN1. Two patients with MEN1 were identified via whole exome sequencing and gene expression profile analysis, conducted for 5,063 patients with various types of cancers. We obtained multiple tumors from each patient; tumors derived from these two MEN1 patients had a loss of the normal MEN1 allele and frequently chromosomal copy number changes. Thus, we investigated whether structural variants were present in the MEN1 patient genomes. Whole-genome sequencing revealed no catastrophic rearrangements, and the tumor samples had very low somatic variants. The two patients had germline variants in MEN1 and some chromosomal copy number changes including on chromosome 11. The only pathogenic variant detected was the MEN1 germline variant, and chromosomal rearrangements led to tumorigenesis in somatic cells. Furthermore, the MEN1 tumor samples displayed a specific signature characterized by T:A>C:G transition. Studies of multiple tumors obtained from single patients are rare in hereditary cancer syndromes, and our results provide insights that the second hit of the tumor suppressor gene MEN1 may be caused by a gross genome rearrangement, not a small insertion and deletion, nor a change in epigenetic regulation.
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Affiliation(s)
- Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute.,SRL Inc
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
| | | | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
| | - Yasue Horiuchi
- Division of Genetic Counseling, Shizuoka Cancer Center Hospital
| | | | | | - Masato Abe
- Division of Pathology, Shizuoka Cancer Center Hospital
| | - Takuma Ohishi
- Division of Pathology, Shizuoka Cancer Center Hospital
| | - Toru Kameya
- Division of Pathology, Shizuoka Cancer Center Hospital
| | | | - Tetsuro Onitsuka
- Division of Head and Neck Surgery, Shizuoka Cancer Center Hospital
| | - Mitsuhiro Isaka
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital
| | - Takaaki Ito
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute
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19
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Hatakeyama K, Nagashima T, Notsu A, Ohshima K, Ohnami S, Ohnami S, Shimoda Y, Naruoka A, Maruyama K, Iizuka A, Ashizawa T, Kenmotsu H, Mochizuki T, Urakami K, Akiyama Y, Yamaguchi K. Mutational concordance analysis provides supportive information for double cancer diagnosis. BMC Cancer 2021; 21:181. [PMID: 33607950 PMCID: PMC7893960 DOI: 10.1186/s12885-021-07899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Mutation analysis using next-generation sequencing highlights the features of tumors with somatic alterations. However, the mutation profile of double cancer remains unclear. Here, we analyzed tumors derived from the same patient using whole exome sequencing (WES) to investigate the coherence of somatic mutations in double cancer. Methods First, the tumor mutational burden (TMB) was investigated using WES of 5521 tumor specimens from a Japanese pan-cancer cohort. The frequencies of mutation concordance were then compared in these cancers. Finally, we calculated the expected value of mutational concordance fitting a Poisson distribution to determine the relationship between double and metastatic cancers. Results In all, 44, 58, and 121 paired samples were diagnosed as double cancer, multifocal lesions (derived from identical tissues), and metastasis, respectively. Our analysis revealed that common somatic mutations were almost entirely absent in double cancer, whereas primary tumors and metastatic foci harbored several identical alterations. Concordance of the mutation profile in the same patient reflects the tumor origin and development, suggesting the potential for identifying double cancer based on common somatic mutations. Furthermore, according to a Poisson distribution, double cancer could be discriminated based on paired samples from the same patient. The probability of double cancer with more than 10 mutations was ≤1 part-per-billion (ppb, 10− 9). In multifocal lesions, 74% of tumor pairs accumulated ≤10 common mutations, implying a difference in tumor origin within identical tissues. Conclusions These findings indicate that counting common somatic mutations can indicate the differences in origin between tumors derived from the same patient. Our mutation coherence analysis can thus provide beneficial information for diagnosing double cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07899-1.
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Affiliation(s)
- Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.,SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Akifumi Notsu
- Clinical Research Center, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.,SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Akira Iizuka
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Tadashi Ashizawa
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Genetic Medicine Promotion, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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20
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Sakai K, Tsuboi M, Kenmotsu H, Yamanaka T, Takahashi T, Goto K, Daga H, Ohira T, Ueno T, Aoki T, Nakagawa K, Yamazaki K, Hosomi Y, Kawaguchi K, Okumura N, Takiguchi Y, Sekine A, Haruki T, Yamamoto H, Sato Y, Akamatsu H, Seto T, Saeki S, Sugio K, Nishio M, Okabe K, Yamamoto N, Nishio K. Tumor mutation burden as a biomarker for lung cancer patients treated with pemetrexed and cisplatin (the JIPANG-TR). Cancer Sci 2020; 112:388-396. [PMID: 33185928 PMCID: PMC7780021 DOI: 10.1111/cas.14730] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/11/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022] Open
Abstract
The JIPANG study is a randomized phase III study of pemetrexed/cisplatin (Pem/Cis) versus vinorelbine/cisplatin (Vnr/Cis) for completely resected stage II-IIIA non-squamous non-small cell lung cancer (Ns-NSCLC). This study did not meet the primary endpoint (recurrence-free survival, RFS) but Pem/Cis had a similar efficacy to Vnr/Cis with a better tolerability. Tumor mutation burden (TMB) is thought to have a predictive value of immune checkpoint inhibitors. However, the relevance of TMB to cytotoxic chemotherapy remains unknown. This exploratory study investigates the relationship between tumor mutation profiles and clinical outcome of Pem/Cis. Formalin-fixed, paraffin-embedded tumor tissues (n = 389) were obtained from the patients. Mutation status of tissue DNA was analyzed by targeted deep sequencing. Epidermal growth factor receptor (EGFR) mutations were detected frequently in Ns-NSCLC (139/374). Patients without any EGFR mutations experienced longer RFS in the Pem/Cis arm versus Vnr/Cis arms. Pem/Cis in patients with high TMB (≥12-16 mut/Mb) tended to have improved survival. In patients with wild-type EGFR, TMB ≥ 12 mut/Mb was significantly associated with improved RFS with Pem/Cis versus Vnr/Cis (not reached vs 52.5 months; hazard ratio (HR) 0.477). It could be proposed that TMB was predictive of RFS benefit with Pem/Cis versus Vnr/Cis in Ns-NSCLC. Further investigation is required to determine whether TMB combined with EGFR mutation status could be used as a predictive biomarker.
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Affiliation(s)
- Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
| | - Masahiro Tsuboi
- Division of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center, Nagaizumi-cho Sunto-gun, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Japan
| | - Toshiaki Takahashi
- Division of Thoracic Oncology, Shizuoka Cancer Center, Nagaizumi-cho Sunto-gun, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Haruko Daga
- Department of Medical Oncology, Osaka City General Hospital, Osaka, Japan
| | - Tatsuo Ohira
- Department of Surgery, Tokyo Medical University, Tokyo, Japan
| | - Tsuyoshi Ueno
- Department of Thoracic Surgery, National Hospital Organization, Shikoku Cancer Center, Matsuyama, Japan
| | - Tadashi Aoki
- Department of Chest Surgery, Niigata Cancer Center Hospital, Niigata, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Koji Yamazaki
- Department of Thoracic Surgery, Kyushu Medical Center, Clinical Research Institute, National Hospital Organization, Fukuoka, Japan
| | - Yukio Hosomi
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Koji Kawaguchi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norihito Okumura
- Department of Thoracic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Yuichi Takiguchi
- Department of Medical Oncology, Chiba University Hospital, Chiba, Japan
| | - Akimasa Sekine
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Yokohama, Japan
| | - Tomohiro Haruki
- Division of General Thoracic Surgery, Department of Surgery, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Hiromasa Yamamoto
- Department of General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Hospital, Okayama, Japan
| | - Yuki Sato
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Hiroaki Akamatsu
- Internal Medicine III, Wakayama Medical University, Wakayama, Japan
| | - Takashi Seto
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Sho Saeki
- Department of Respiratory Medicine, Kumamoto University Hospital, Kumamoto, Japan
| | - Kenji Sugio
- Department of Thoracic and Breast Surgery, Oita University, Oita, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazunori Okabe
- Department of Thoracic Surgery, National Hospital Organization Yamaguchi Ube Medical Center, Yamaguchi, Japan
| | | | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
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21
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Hatakeyama K, Nagashima T, Ohshima K, Ohnami S, Ohnami S, Shimoda Y, Naruoka A, Maruyama K, Iizuka A, Ashizawa T, Mochizuki T, Urakami K, Akiyama Y, Yamaguchi K. Characterization of tumors with ultralow tumor mutational burden in Japanese cancer patients. Cancer Sci 2020; 111:3893-3901. [PMID: 32662546 PMCID: PMC7540986 DOI: 10.1111/cas.14572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Tumor mutational burden analysis using whole‐exome sequencing highlights features of tumors with various mutations or known driver alterations. Cancers with few changes in the exon regions have unclear characteristics, even though low‐mutated tumors are often detected in pan‐cancer analysis. In the present study, we analyzed tumors with low tumor mutational burden listed in the Japanese version of The Cancer Genome Atlas, a data set of 5020 primary solid tumors. Our analysis revealed that detection rates of known driver mutations and copy number variation were decreased in samples with tumor mutational burden below 1.0 (ultralow tumor), compared with those in samples with low tumor mutational burden (≤5 mutations/Mb). This trend was also observed in The Cancer Genome Atlas data set. In the ultralow tumor mutational burden tumors, expression analysis showed decreased TP53 inactivation and chromosomal instability. TP53 inactivation frequently correlated with PI3K/mTOR‐related gene expression, implying suppression of the PI3K/mTOR pathway in ultralow tumor mutational burden tumors. In common with mutational burden, the T cell‐inflamed gene expression profiling signature was a potential marker for prediction of an immune checkpoint inhibitor response, and some ultralow tumor mutational burden tumor populations highly expressed this signature. Our analysis focused on how these tumors could provide insight into tumors with low somatic alteration that are difficult to detect solely using whole‐exome sequencing.
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Affiliation(s)
- Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL Inc, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL Inc, Tokyo, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akira Iizuka
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tadashi Ashizawa
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
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22
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Zhang Y, Wang L, Li R, Liu B. The emerging development of tumor mutational burden in patients with NSCLC. Future Oncol 2020; 16:469-481. [PMID: 32048882 DOI: 10.2217/fon-2019-0650] [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: 01/10/2023] Open
Abstract
Immunocheckpoint inhibitors (ICIs) which target PD-1 and CTLA-4 have dramatically changed the history of non-small-cell lung cancer treatment. Multiple biomarkers especially tumor mutational burden (TMB) have been raised to be potential predictors of response to ICIs. However, great value of TMB has been observed in patients who receive ICIs monotherapy instead of ICIs combination therapy from latest exploratory studies. Thus, the innovative concept of TMB needs to be identified. This study uncovers specific aspects of TMB including signatures of TMB, factors related with variation, racial differences, heterogeneity between tissue TMB and blood-based TMB. Additionally, more and more factors are found valuable in clinical trials, suggesting that more markers should be further investigated as interesting candidates for response prediction beyond TMB.
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Affiliation(s)
- Yu Zhang
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Lifeng Wang
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Rutian Li
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Baorui Liu
- The Comprehensive Cancer Center of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
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23
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Wang HL, Liu PF, Yue J, Jiang WH, Cui YL, Ren H, Wang H, Zhuang Y, Liu Y, Jiang D, Dong Q, Zhang H, Mi JH, Xu ZM, Tian CJ, Zhang ZZ, Wang XW, Su MN, Lu W. Somatic gene mutation signatures predict cancer type and prognosis in multiple cancers with pan-cancer 1000 gene panel. Cancer Lett 2019; 470:181-190. [PMID: 31765737 DOI: 10.1016/j.canlet.2019.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
Most cancers are caused by somatic mutations. Some common mutations in the same cancer type can form a "signature" to specifically predict the prognosis or to distinguish it from other cancers. In this study, 710 somatic cell mutations were identified in 142 cases, including digestive, lung and urogenital cancers, and the digestive cancers were further divided into liver, stomach, intestinal, esophageal and cardia cancer. The above mutations were located in 166 genes. In addition, a group of high-frequency mutation genes with specific characteristics were screened to form predictive signatures for each cancer. Verification using TCGA suggested that the signatures could predict the stages, progression-free survival, and overall survival of digestive, intestinal, and liver cancers (P < 0.05). The validation cases further confirmed the predictive role of digestive and liver cancers signatures in diagnosis and prognosis. Overall, this study established predictive signatures for different cancer systems and their subtypes. These findings enable a better understanding in cancer genome, and contribute to the personalized diagnosis and treatment.
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Affiliation(s)
- Hai-Long Wang
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Peng-Fei Liu
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Jie Yue
- Department of Esophageal Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wen-Hua Jiang
- Department of Radiotherapy, Tianjin Medical University Second Hospital, Tianjin, China
| | - Yun-Long Cui
- Department of Hepatobiliary Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - He Ren
- Department of Pathology, Center of Tumour Immunology and Cytotherapy, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Han Wang
- Department of Applied Statistics, College of Science, Hebei University of Technology, Tianjin, China
| | - Yan Zhuang
- Department of Colorectal Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yong Liu
- Department of Gastric Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Da Jiang
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qian Dong
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Zhang
- Division of Biostatistics, Department of Prevebtive Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Jia-Hui Mi
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Zan-Mei Xu
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Cai-Juan Tian
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Zhen-Zhen Zhang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Xiao-Wei Wang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Mei-Na Su
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co.,Ltd, Tianjin, China
| | - Wei Lu
- Department of Hepatobiliary Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
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24
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Rapid Acquisition of Alectinib Resistance in ALK-Positive Lung Cancer With High Tumor Mutation Burden. J Thorac Oncol 2019; 14:2009-2018. [DOI: 10.1016/j.jtho.2019.07.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 12/28/2022]
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25
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Hatakeyama K, Nagashima T, Ohshima K, Ohnami S, Ohnami S, Shimoda Y, Serizawa M, Maruyama K, Naruoka A, Akiyama Y, Urakami K, Kusuhara M, Mochizuki T, Yamaguchi K. Mutational burden and signatures in 4000 Japanese cancers provide insights into tumorigenesis and response to therapy. Cancer Sci 2019; 110:2620-2628. [PMID: 31152682 PMCID: PMC6676127 DOI: 10.1111/cas.14087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/26/2019] [Accepted: 05/30/2019] [Indexed: 01/05/2023] Open
Abstract
Tumor mutational burden (TMB) and mutational signatures reflect the process of mutation accumulation in cancer. However, the significance of these emerging characteristics remains unclear. In the present study, we used whole‐exome sequencing to analyze the TMB and mutational signature in solid tumors of 4046 Japanese patients. Eight predominant signatures—microsatellite instability, smoking, POLE, APOBEC, UV, mismatch repair, double‐strand break repair, and Signature 16—were observed in tumors with TMB higher than 1.0 mutation/Mb, whereas POLE and UV signatures only showed moderate correlation with TMB, suggesting the extensive accumulation of mutations due to defective POLE and UV exposure. The contribution ratio of Signature 16, which is associated with hepatocellular carcinoma in drinkers, was increased in hypopharynx cancer. Tumors with predominant microsatellite instability signature were potential candidates for treatment with immune checkpoint inhibitors such as pembrolizumab and were found in 2.8% of cases. Furthermore, based on microarray analysis, tumors with predominant signatures were classified into 2 subgroups depending on the expression of immune‐related genes reflecting differences in the immune context of the tumor microenvironment. Tumor subpopulations differing in the content of infiltrating immune cells might respond differently to immunotherapeutics. An understanding of cancer characteristics based on TMB and mutational signatures could provide new insights into mutation‐driven tumorigenesis.
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Affiliation(s)
- Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan.,Corporate Project Office, SRL Inc., Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan.,Corporate Project Office, SRL Inc., Tokyo, Japan
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Masatoshi Kusuhara
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan.,Regional Resource Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Nagaizumi, Japan
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