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Sánchez-Ramón S, Fuentes-Antrás J, Rider NL, Pérez-Segura P, de la Fuente-Muñoz E, Fernández-Arquero M, Neves E, Pérez de Diego R, Ocaña A, Guevara-Hoyer K. Exploring gastric cancer genetics: A turning point in common variable immunodeficiency. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100203. [PMID: 38283086 PMCID: PMC10818086 DOI: 10.1016/j.jacig.2023.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 01/30/2024]
Abstract
Background Gastric cancer (GC) stands as a prominent cause of cancer-related mortality and ranks second among the most frequently diagnosed malignancies in individuals with common variable immunodeficiency (CVID). Objective We sought to conduct a comprehensive, large-scale genetic analysis to explore the CVID-associated germline variant landscape within gastric adenocarcinoma samples and to seek to delineate the transcriptomic similarities between GC and CVID. Methods We investigated the presence of CVID-associated germline variants in 1591 GC samples and assessed their impact on tumor mutational load. The progression of GC was evaluated in patients with and without these variants. Transcriptomic similarities were explored by matching differentially expressed genes in GC to healthy gastric tissue with a CVID transcriptomic signature. Results CVID-associated germline variants were found in 60% of GC samples. Our analysis revealed a significant association between the presence of CVID-related genetic variants and higher tumor mutational load in GC (P < .0001); high GC mutational load seems to be linked to immunotherapy response and worse prognosis. Transcriptomic similarities unveiled key genes and pathways implicated in innate immune responses and tumorigenesis. We identified upregulated genes related to oncogene drivers, inflammation, tumor suppression, DNA repair, and downregulated immunomodulatory genes shared between GC and CVID. Conclusions Our findings contribute to a deeper understanding of potential molecular modulators of GC and shed light on the intricate interplay between immunodeficiency and cancer. This study underscores the clinical relevance of CVID-related variants in influencing GC progression and opens avenues for further exploration into novel therapeutic approaches.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Jesús Fuentes-Antrás
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicholas L. Rider
- Division of Clinical Informatics, Pediatrics, Allergy and Immunology, Liberty University College of Osteopathic Medicine and Collaborative Health Partners, Lynchburg, Va
| | - Pedro Pérez-Segura
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário de Santo António, Porto, Portugal
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Alberto Ocaña
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
| | - Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
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Fu M, Huang Y, Peng X, Li X, Luo N, Zhu W, Yang F, Chen Z, Ma S, Zhang Y, Li Q, Hu G. Development of Tumor Mutation Burden-Related Prognostic Model and Novel Biomarker Identification in Stomach Adenocarcinoma. Front Cell Dev Biol 2022; 10:790920. [PMID: 35399509 PMCID: PMC8983817 DOI: 10.3389/fcell.2022.790920] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Stomach adenocarcinoma (STAD) is one of the most common tumors. Tumor mutation burden (TMB) has been linked to immunotherapy response. We wanted to see if there was any link between TMB and cancer prognosis. Methods: The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to obtain mutation data, gene expression profiles, and clinical data. We looked at the differences in gene expression and immune markers between low and high TMB groups, built an immune prognostic model, and created a dynamic nomograph App that may be used in the clinic. Simultaneously, We ran the immunotherapy prediction and model comparison at the same time. Finally, model gene mutation and copy number variation (CNV) were displayed. The cellular functional experiments were used to investigate the potential role of GLP2R in gastric cancer. Results: Firstly, basic mutation information and differences in immune infiltration in STAD are revealed. Secondly, the prognostic model developed by us has good accuracy, and the corresponding dynamic nomograph Apps online and immunotherapy prediction facilitate clinical transformation. Furthermore, GLP2R knockdown significantly inhibited the proliferation, migration of gastric cancer cells in vitro. Conclusion: Our findings imply that TMB plays a significant role in the prognosis of STAD patients from a biological perspective. GLP2R may serve as a potential target for gastric cancer.
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Affiliation(s)
- Min Fu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongbiao Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohong Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjun Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziqi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengling Ma
- Department of Medical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yuanyuan Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
| | - Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
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Zhang AZ, Yuan X, Liang WH, Zhang HJ, Li Y, Xie YF, Li JF, Jiang CH, Li FP, Shen XH, Pang LJ, Zou H, Zhou WH, Li F, Hu JM. Immune Infiltration in Gastric Cancer Microenvironment and Its Clinical Significance. Front Cell Dev Biol 2022; 9:762029. [PMID: 35252217 PMCID: PMC8893596 DOI: 10.3389/fcell.2021.762029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy has developed rapidly and has gradually become one of the important methods for treatment of gastric cancer (GC). The research on tumor infiltrating immune cells (TIICs) and immune-related genes in the tumor microenvironment (TME) greatly encourages the development of immunotherapy. The devolution algorithm (CIBERSORT) was applied to infer the proportion of 22 TIICs based on gene expression profiles of GC tissues, which were downloaded from TCGA and GEO. TCGA was utilized to analyze the differential expression of immune-related genes, and explore the potential molecular functions of these genes. We have observed the enrichment of multiple TIICs in microenvironment of GC. Some of these cells were closely related to tumor mutational burden (TMB), microsatellite instability (MSI), Fuhrman grade, and TNM staging. Survival analysis showed that the infiltration level of CD8+ T cells, activated CD4+ memory T cells and M2 macrophages were significantly related to the prognosis of GC patients. The functional enrichment analysis of immune-related genes revealed that these genes were mainly associated with cytokine activation and response. Four significant modules were screened by PPI network and 20 key genes were screened from the modules. The expression levels of CALCR and PTH1R are strikingly related to the expression of immune checkpoint and the prognosis of GC patients. The type and number of TIICs in microenvironment of GC, as well as immune-related genes are closely related to tumor progression, and can be used as important indicators for patient prognosis assessment.
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Affiliation(s)
- An Zhi Zhang
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
- Department of Pathology, Jiaxing University Affiliated Women and Children Hospital (Jiaxing Maternity and Child Health Care Hospital), Jiaxing University, Jiaxing, China
| | - Xin Yuan
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Wei Hua Liang
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Hai Jun Zhang
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Ya Li
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Yu Fang Xie
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Jiang Fen Li
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Chen Hao Jiang
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Fan Ping Li
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Xi Hua Shen
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Li Juan Pang
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Hong Zou
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
| | - Wen Hu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Feng Li
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jian Ming Hu
- Department of Pathology/NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, China
- *Correspondence: Jian Ming Hu,
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Kou F, Wu L, Guo Y, Zhang B, Li B, Huang Z, Ren X, Yang L. Somatic copy number alterations are predictive of progression-free survival in patients with lung adenocarcinoma undergoing radiotherapy. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0728. [PMID: 34448554 PMCID: PMC9196051 DOI: 10.20892/j.issn.2095-3941.2020.0728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE Lung cancer is the most common cause of cancer-related deaths worldwide. Somatic copy number alterations (SCNAs) have been used to predict responses to therapies in many cancers, including lung cancer. However, little is known about whether they are predictive of radiotherapy outcomes. We aimed to understand the prognostic value and biological functions of SCNAs. METHODS We analyzed the correlation between SCNAs and clinical outcomes in The Cancer Genome Atlas data for 486 patients with non-small cell lung cancer who received radiotherapy. Gene set enrichment analyses were performed to investigate the potential mechanisms underlying the roles of SCNAs in the radiotherapy response. Our results were validated in 20 patients with lung adenocarcinoma (LUAD) receiving radiotherapy. RESULTS SCNAs were a better predictor of progression-free survival (PFS) in LUAD (P = 0.024) than in lung squamous carcinoma (P = 0.18) in patients treated with radiotherapy. Univariate and multivariate regression analyses revealed the superiority of SCNAs in predicting PFS in patients with LUAD. Patients with stage I cancer and low SCNA levels had longer PFS than those with high SCNA levels (P = 0.022). Our prognostic nomogram also showed that combining SCNAs and tumor/node/metastasis provided a better model for predicting long-term PFS. Additionally, high SCNA may activate the cell cycle pathway and induce tumorigenesis. CONCLUSIONS SCNAs may be used to predict PFS in patients with early-stage LUAD with radiotherapy, in combination with TNM, with the aim of predicting long-term PFS. Therefore, SCNAs are a novel predictive biomarker for radiotherapy in patients with LUAD.
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Affiliation(s)
- Fan Kou
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Lei Wu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Yan Guo
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Bailu Zhang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Baihui Li
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Ziqi Huang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Xiubao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China
| | - Lili Yang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
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Pei SN, Liao CK, Chen YS, Tseng CH, Hung CM, Chiu CC, Hsieh MC, Tsai YF, Liao HY, Liu WC, Rau KM. A Novel Combination of Bevacizumab with Chemotherapy Improves Therapeutic Effects for Advanced Biliary Tract Cancer: A Retrospective, Observational Study. Cancers (Basel) 2021; 13:cancers13153831. [PMID: 34359732 PMCID: PMC8345065 DOI: 10.3390/cancers13153831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Biliary tract cancer (BTC) is a heterogenous collection of biliary tract cancer at different primary sites, and the prognosis of advanced BTC is dismal. Systemic chemotherapy with gemcitabine and cisplatin (GC) has been the reference regimen since 2010. How to improve therapeutic effects of GC regimen is an urgent mission at present. METHODS Bevacizumab with a reduced dosage and modified schedule (10 mg/Kg/triweekly, 1 day before GS at the first 2 cycles) was combined with standard GC for patients with advanced BTC. Tumor response was assessed using Response Evaluation Criteria in Solid Tumors version 1.1 every 2 months. Kaplan-Meier curves were estimated for time-to-treatment failure (TTF), progression-free survival (PFS) and overall survival (OS). RESULT A total of thirty cases of advanced BTC accepted this treatment, and the overall response rate (ORR) was 50.0%, and the disease control rate was 80.0% for all patients. The median TTF was 5.8 months, the median PFS was 8.4 months, and the median OS was 13.6 months. Most responses were noted at the first evaluation. Adverse effects (AEs) were mostly tolerable. CONCLUSIONS After modifying the schedule, adding bevacizumab to a traditional GC regimen could increase the ORR with a shorter time-to-response, a better PFS and OS than GC alone but without the addition of AE. This regimen can be applied to patients with advanced BTC, especially those who are with a big tumor burden and who need a rapid response.
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Affiliation(s)
- Sung-Nan Pei
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
| | - Chun-Kai Liao
- Division of Hematology and Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan;
| | - Yaw-Sen Chen
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
- Division of General Surgery, Department of Surgery, E-Da Hospital, Kaohsiung 824, Taiwan
| | - Cheng-Hao Tseng
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
- Division of Gastroenterology and Hepatology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan
| | - Chao-Ming Hung
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
- Department of General Surgery, E-Da Cancer Hospital, Kaohsiung 824, Taiwan
| | - Chong-Chi Chiu
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
- Department of General Surgery, E-Da Cancer Hospital, Kaohsiung 824, Taiwan
| | - Meng-Che Hsieh
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
| | - Yu-Fen Tsai
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
| | - Hsiu-Yun Liao
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
| | - Wei-Ching Liu
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
| | - Kun-Ming Rau
- Department of Hematology-Oncology, E-Da Cancer Hospital, Kaohsiung 824, Taiwan; (S.-N.P.); (M.-C.H.); (Y.-F.T.); (H.-Y.L.); (W.-C.L.)
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan; (Y.-S.C.); (C.-H.T.); (C.-M.H.); (C.-C.C.)
- Kaohsiung Nan-Ping Cancer Prevention and Education Association, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-6150022
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Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:cancers12113304. [PMID: 33182397 PMCID: PMC7697455 DOI: 10.3390/cancers12113304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The use of next generation technologies has helped to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. Nonetheless, the sequencing of all protein-coding genes of an individual may lead to doubtful assignments of causality for non-pathological variants, so it is mandatory to perform comprehensive studies and screening of additional patients for new mutations. Here we describe a novel DNMT3A germline variant identified by whole-exome sequencing in a patient with multiple paragangliomas and papillary thyroid carcinoma. The increased methylation of DNMT3A target genes observed in the proband’s sample points towards a gain-of-function effect of the variant, contrasting with the inactivation caused by loss-of-function alterations commonly seen in other neoplasia and in patients with Tatton-Brown-Rahman syndrome. This finding stresses the diverse molecular outcomes and suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants. Abstract Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.
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He Y, Wang X. Identification of molecular features correlating with tumor immunity in gastric cancer by multi-omics data analysis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1050. [PMID: 33145269 PMCID: PMC7575957 DOI: 10.21037/atm-20-922] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Although immunotherapy has achieved success in treating various refractory malignancies including gastric cancers (GCs) with DNA mismatch repair deficiency, only a subset of cancer patients are responsive to immunotherapy. Therefore, the identification of useful biomarkers or interventional targets for improving cancer immunotherapy response is urgently needed. Methods We investigated the associations between various molecular features and immune signatures using three multi-omics GC datasets. These molecular features included genes, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), proteins, and pathways, and the immune signatures included CD8+ T cell infiltration, immune cytolytic activity (ICA), and PD-L1 expression. Moreover, we investigated the association between gene mutations and survival prognosis in a gastrointestinal (GI) cancer cohort receiving immunotherapy and two GC cohorts not receiving such a therapy. Results The mutations of some important oncogenes and tumor suppressor genes were appreciably associated with immune signatures in GC, including PIK3CA, MTOR, RNF213, TP53, ARID1A, PTEN, ATM, and CDH1. Moreover, a number of genes exhibited a significant expression correlation with immune signatures in GC, including CXCL9, CXCL13, CXCR6, CCL5, GUCY2C, MAP3K9, NEK3, PAK6, STK35, and WNK2. We identified several proteins whose expression had a significant positive correlation with immune signatures in GC. These proteins included caspase-7, PI3K-p85, PREX1, Lck, Bcl-2, and transglutaminase. In contrast, acetyl-CoA carboxylase (ACC) had a significant inverse expression correlation with immune signatures in GC, suggesting that inhibiting ACC could enhance antitumor immunity in GC. Furthermore, we identified numerous miRNAs and lncRNAs with a significant expression correlation with GC immunity, including hsa-miR-150, 155, 142, 342, 146, 101, 511, 29, AC022706.1, LINC01871, and AC006033.2. We also identified numerous cancer-associated pathways whose activity was associated with GC immunity, including mTOR, PI3K-AKT, MAPK, HIF-1, and VEGF signaling pathways. Interestingly, we found seven genes (ARID1A, BCOR, MTOR, CREBBP, SPEN, NOTCH4, and TET1) whose mutations were associated with better OS in GI cancer patients receiving anti-PD-1/PD-L1 immunotherapy but were not associated with OS in GC patients without immunotherapy. Conclusions The molecular features significantly associated with GC immunity could be useful biomarkers for stratifying GC patients responsive to immunotherapy or intervention targets for promoting antitumor immunity and immunotherapy response in GC.
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Affiliation(s)
- Yin He
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China.,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
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Li L, Li M, Wang X. Cancer type-dependent correlations between TP53 mutations and antitumor immunity. DNA Repair (Amst) 2020; 88:102785. [DOI: 10.1016/j.dnarep.2020.102785] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023]
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