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Georgoulias G, Zaravinos A. Genomic landscape of the immunogenicity regulation in skin melanomas with diverse tumor mutation burden. Front Immunol 2022; 13:1006665. [PMID: 36389735 PMCID: PMC9650672 DOI: 10.3389/fimmu.2022.1006665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Skin melanoma cells are tightly interconnected with their tumor microenvironment (TME), which influences their initiation, progression, and sensitivity/resistance to therapeutic interventions. An immune-active TME favors patient response to immune checkpoint inhibition (ICI), but not all patients respond to therapy. Here, we assessed differential gene expression in primary and metastatic tumors from the TCGA-SKCM dataset, compared to normal skin samples from the GTEx project and validated key findings across 4 independent GEO datasets, as well as using immunohistochemistry in independent patient cohorts. We focused our attention on examining the expression of various immune receptors, immune-cell fractions, immune-related signatures and mutational signatures across cutaneous melanomas with diverse tumor mutation burdens (TMB). Globally, the expression of most immunoreceptors correlated with patient survival, but did not differ between TMBhigh and TMBlow tumors. Melanomas were enriched in "naive T-cell", "effector memory T-cell", "exhausted T-cell", "resting Treg T-cell" and "Th1-like" signatures, irrespective of their BRAF, NF1 or RAS mutational status. Somatic mutations in IDO1 and HLA-DRA were frequent and could be involved in hindering patient response to ICI therapies. We finally analyzed transcriptome profiles of ICI-treated patients and associated their response with high levels of IFNγ, Merck18, CD274, CD8, and low levels of myeloid-derived suppressor cells (MDSCs), cancer-associated fibroblasts (CAFs) and M2 macrophages, irrespective of their TMB status. Overall, our findings highlight the importance of pre-existing T-cell immunity in ICI therapeutic outcomes in skin melanoma and suggest that TMBlow patients could also benefit from such therapies.
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Affiliation(s)
- George Georgoulias
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia, Cyprus
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Liu SP, Li XM, Liu DM, Xie SH, Zhang SB, Li Y, Xie ZF. LAMP2 as a Biomarker Related to Prognosis and Immune Infiltration in Esophageal Cancer and Other Cancers: A Comprehensive Pan-Cancer Analysis. Front Oncol 2022; 12:884448. [PMID: 35530327 PMCID: PMC9069144 DOI: 10.3389/fonc.2022.884448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
Esophageal cancer (ESCA) is a common malignant tumor with poor prognosis. Accumulating evidence indicates an important role of lysosomal-associated membrane protein 2 (LAMP2) in the progression and development of various cancers. In this study, we obtained RNA-sequencing raw count data and the corresponding clinical information for ESCA samples from The Cancer Genome Atlas and Gene Expression Omnibus databases. We comprehensively investigated the expression and prognostic significance of LAMP2 and relationships between LAMP2 expression and prognosis, different clinicopathological parameters, and immune cell infiltration in ESCA. We also obtained the differentially expressed genes between the high LAMP2 expression and low LAMP2 expression groups in ESCA and performed a functional enrichment analysis of the 250 linked genes most positively related to LAMP2 expression. Moreover, we performed the pan-cancer analysis of LAMP2 to further analyze the role of LAMP2 in 25 commonly occurring types of human cancer. We also verified and compared the expression of LAMP2 in 40 samples of human ESCA tissue and adjacent tissues. The results indicated that LAMP2 expression was significantly upregulated in ESCA and various human cancers. In addition, LAMP2 expression was associated with certain clinicopathological parameters, prognosis, and immune infiltration in ESCA and the other types of cancer. Our study represents a comprehensive pan-cancer analysis of LAMP2 and supports the potential use of the modulation of LAMP2 in the management of ESCA and various cancers.
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Affiliation(s)
- Shan-peng Liu
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiao-min Li
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Dan-man Liu
- Breast Surgery Clinics, Guangdong Province Women and Children Hospital, Guangzhou, China
| | - Shu-huan Xie
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Shao-bo Zhang
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yu Li
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Ze-feng Xie
- Thoracic Surgery Department, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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Xing R, Zhou Y, Yu J, Yu Y, Nie Y, Luo W, Yang C, Xiong T, Wu WKK, Li Z, Bing Y, Lin S, Zhang Y, Hu Y, Li L, Han L, Yang C, Huang S, Huang S, Zhou R, Li J, Wu K, Fan D, Tang G, Dou J, Zhu Z, Ji J, Fang X, Lu Y. Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer. Nat Commun 2019; 10:2037. [PMID: 31048690 PMCID: PMC6497673 DOI: 10.1038/s41467-019-09644-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/22/2019] [Indexed: 01/22/2023] Open
Abstract
Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification. Structural variations in gastric cancer impact progression. Here, the authors perform whole-genome sequencing on 168 gastric cancer patients and identified tandem-duplications of super-enhancer ZFP36L2 in 10% of gastric cancer, and mutational signatures in tumors with cadherin 1 mutations that associated with poor prognoses.
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Affiliation(s)
- Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Yong Zhou
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Yingyan Yu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Wen Luo
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Chao Yang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Teng Xiong
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - William K K Wu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Zhongwu Li
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yang Bing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Shuye Lin
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yaping Zhang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yingqi Hu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Lin Li
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumours, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, 200025, Shanghai, China
| | - Lijuan Han
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Chen Yang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Shaogang Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Suiping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Rui Zhou
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jing Li
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Guangbo Tang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Jianhua Dou
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Zhenggang Zhu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jiafu Ji
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Xiaodong Fang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China.
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China. .,Department of Medical Oncology, Beijing Hospital, 100730, Beijing, China.
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Sawas T, Killcoyne S, Iyer PG, Wang KK, Smyrk TC, Kisiel JB, Qin Y, Ahlquist DA, Rustgi AK, Costa RJ, Gerstung M, Fitzgerald RC, Katzka DA. Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts. Gastroenterology 2018; 155:1720-1728.e4. [PMID: 30165050 PMCID: PMC6298575 DOI: 10.1053/j.gastro.2018.08.036] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/06/2018] [Accepted: 08/20/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Most patients with esophageal adenocarcinoma (EAC) present with de novo tumors. Although this could be due to inadequate screening strategies, the precise reason for this observation is not clear. We compared survival of patients with prevalent EAC with and without synchronous Barrett esophagus (BE) with intestinal metaplasia (IM) at the time of EAC diagnosis. METHODS Clinical data were studied using Cox proportional hazards regression to evaluate the effect of synchronous BE-IM on EAC survival independent of age, sex, TNM stage, and tumor location. We analyzed data from a cohort of patients with EAC from the Mayo Clinic (n=411; 203 with BE and IM) and a multicenter cohort from the United Kingdom (n=1417; 638 with BE and IM). RESULTS In the Mayo cohort, BE with IM had a reduced risk of death compared to patients without BE and IM (hazard ratio [HR] 0.44; 95% CI, 0.34-0.57; P<.001). In a multivariable analysis, BE with IM was associated with longer survival independent of patient age or sex, tumor stage or location, and BE length (adjusted HR, 0.66; 95% CI, 0.5-0.88; P=.005). In the United Kingdom cohort, patients BE and IM had a reduced risk of death compared with those without (HR, 0.59; 95% CI, 0.5-0.69; P<.001), with continued significance in multivariable analysis that included patient age and sex and tumor stage and tumor location (adjusted HR, 0.77; 95% CI, 0.64-0.93; P=.006). CONCLUSION Two types of EAC can be characterized based on the presence or absence of BE. These findings could increase our understanding the etiology of EAC, and be used in management and prognosis of patients.
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Affiliation(s)
- Tarek Sawas
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Sarah Killcoyne
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Prasad G Iyer
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Kenneth K Wang
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Division of Pathology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Yi Qin
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - David A Ahlquist
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Anil K Rustgi
- University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rui J Costa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, United Kingdom; Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom.
| | - David A Katzka
- Divisions of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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