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Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma
The genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutate...
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Published in: | Cancer Immunology, Immunotherapy : CII Immunotherapy : CII, 2024-06, Vol.73 (8), p.141, Article 141 |
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creator | Zhou, Yue Chu, Li Li, Shuyan Chu, Xiao Ni, Jianjiao Jiang, Shanshan Pang, Yechun Zheng, Danru Lu, Yujuan Lan, Fangcen Cai, Xiuyu Yang, Xi Zhu, Zhengfei |
description | The genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutated genes, including TP53, KMT2C, KMT2D, LRP1B, and FAT1. The most frequent mutation sites were ALOX12B (c.1565C >
T
), SLX4 (c.2786C >
T
), LRIG1 (c.746A >
G
), and SPEN (c.6915_6917del) (6.5%). Pathway analysis revealed dysregulation of cell cycle regulation, epigenetic regulation, PI3K/AKT signaling, and NOTCH signaling. A 17-mutated gene-related risk model was constructed using random survival forest analysis and showed significant prognostic value in both our cohort and the validation cohort. Based on the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression (ESTIMATE) algorithm, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm, and the MCPcounter algorithm, we found that the risk score calculated by the risk model was significantly correlated with stimulatory immune checkpoints (TNFSF4, ITGB2, CXCL10, CXCL9, and BTN3A1;
p
|
doi_str_mv | 10.1007/s00262-024-03725-2 |
format | article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_11150228</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3064376415</sourcerecordid><originalsourceid>FETCH-LOGICAL-c356t-b46caed7ed7fd1ee822f2319360a3cf8adb6abae5de3573f654698abfd66bb863</originalsourceid><addsrcrecordid>eNp9kctu1TAQhiNERUvhBVggS2y6CfUldpIVQkflIlWCBaytSTJJXCX2qS-n4ll4WdymlMICyZItzze_5_dfFK8Yfcsorc8DpVzxkvKqpKLmsuRPihNWiXzVSPb00fm4eB7CFaUVp237rDgWTSN4W1cnxc-v3k3WhWh6coAlIXEjmdC6NV-sKUI0zpJgJgsxeSQQgusNRBzIjYkzMeuaLJJMe4f2YLyzK9pITG5yKc7oLdnNxmJAss9iuRa2TgxuP8OEsJBwnWB1KZAel4X04HuTB4AXxdEIS8CX9_tp8f3Dxbfdp_Lyy8fPu_eXZS-kimVXqR5wqPMaB4bYcD5ywVqhKIh-bGDoFHSAckAhazEqWam2gW4clOq6RonT4t2mu0_dikOfZ_Sw6L03K_gf2oHRf1esmfXkDpoxJinnTVY4u1fw7jphiHo14dYMWMy-tKCqkg2XdZXRN_-gVy55m_3dUaJWFZOZ4huVvzUEj-PDNIzq2_D1Fr7O4eu78DXPTa8f-3ho-Z12BsQGhFyyE_o_b_9H9hcuoMEE</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3064376415</pqid></control><display><type>article</type><title>Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma</title><source>Springer Nature</source><source>Springer Nature - SpringerLink Journals - Fully Open Access </source><source>PubMed Central</source><creator>Zhou, Yue ; Chu, Li ; Li, Shuyan ; Chu, Xiao ; Ni, Jianjiao ; Jiang, Shanshan ; Pang, Yechun ; Zheng, Danru ; Lu, Yujuan ; Lan, Fangcen ; Cai, Xiuyu ; Yang, Xi ; Zhu, Zhengfei</creator><creatorcontrib>Zhou, Yue ; Chu, Li ; Li, Shuyan ; Chu, Xiao ; Ni, Jianjiao ; Jiang, Shanshan ; Pang, Yechun ; Zheng, Danru ; Lu, Yujuan ; Lan, Fangcen ; Cai, Xiuyu ; Yang, Xi ; Zhu, Zhengfei</creatorcontrib><description>The genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutated genes, including TP53, KMT2C, KMT2D, LRP1B, and FAT1. The most frequent mutation sites were ALOX12B (c.1565C >
T
), SLX4 (c.2786C >
T
), LRIG1 (c.746A >
G
), and SPEN (c.6915_6917del) (6.5%). Pathway analysis revealed dysregulation of cell cycle regulation, epigenetic regulation, PI3K/AKT signaling, and NOTCH signaling. A 17-mutated gene-related risk model was constructed using random survival forest analysis and showed significant prognostic value in both our cohort and the validation cohort. Based on the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression (ESTIMATE) algorithm, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm, and the MCPcounter algorithm, we found that the risk score calculated by the risk model was significantly correlated with stimulatory immune checkpoints (TNFSF4, ITGB2, CXCL10, CXCL9, and BTN3A1;
p
< 0.05). Additionally, it was significantly associated with markers that are important in predicting response to immunotherapy (CD274, IFNG, and TAMM2;
p
< 0.05). Furthermore, the results of immunofluorescence double staining showed that patients with high risk scores had a significantly higher level of M2 macrophage than those with low risk scores (
p
< 0.05). In conclusion, our study provides insights into the genomic landscape of ESCC and highlights the prognostic value of a genomic mutation signature associated with the immune microenvironment in southern Chinese patients with ESCC.</description><identifier>ISSN: 1432-0851</identifier><identifier>ISSN: 0340-7004</identifier><identifier>EISSN: 1432-0851</identifier><identifier>DOI: 10.1007/s00262-024-03725-2</identifier><identifier>PMID: 38832974</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>1-Phosphatidylinositol 3-kinase ; Adult ; Aged ; AKT protein ; Algorithms ; Asian People - genetics ; Biomarkers, Tumor - genetics ; Cancer Research ; Cell cycle ; China ; CXCL10 protein ; East Asian People ; Epigenetics ; Esophageal cancer ; Esophageal carcinoma ; Esophageal Neoplasms - genetics ; Esophageal Neoplasms - immunology ; Esophageal Neoplasms - mortality ; Esophageal Squamous Cell Carcinoma - genetics ; Esophageal Squamous Cell Carcinoma - immunology ; Esophageal Squamous Cell Carcinoma - mortality ; Esophageal Squamous Cell Carcinoma - pathology ; Female ; Genomics ; Genomics - methods ; Humans ; Immune checkpoint ; Immunofluorescence ; Immunology ; Immunotherapy ; Macrophages ; Male ; Medicine ; Medicine & Public Health ; Microenvironments ; Middle Aged ; Mutation ; Oncology ; p53 Protein ; Prognosis ; Squamous cell carcinoma ; Tumor Microenvironment - genetics ; Tumor Microenvironment - immunology ; Tumors</subject><ispartof>Cancer Immunology, Immunotherapy : CII, 2024-06, Vol.73 (8), p.141, Article 141</ispartof><rights>The Author(s) 2024</rights><rights>2024. The Author(s).</rights><rights>The Author(s) 2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c356t-b46caed7ed7fd1ee822f2319360a3cf8adb6abae5de3573f654698abfd66bb863</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11150228/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11150228/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38832974$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhou, Yue</creatorcontrib><creatorcontrib>Chu, Li</creatorcontrib><creatorcontrib>Li, Shuyan</creatorcontrib><creatorcontrib>Chu, Xiao</creatorcontrib><creatorcontrib>Ni, Jianjiao</creatorcontrib><creatorcontrib>Jiang, Shanshan</creatorcontrib><creatorcontrib>Pang, Yechun</creatorcontrib><creatorcontrib>Zheng, Danru</creatorcontrib><creatorcontrib>Lu, Yujuan</creatorcontrib><creatorcontrib>Lan, Fangcen</creatorcontrib><creatorcontrib>Cai, Xiuyu</creatorcontrib><creatorcontrib>Yang, Xi</creatorcontrib><creatorcontrib>Zhu, Zhengfei</creatorcontrib><title>Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma</title><title>Cancer Immunology, Immunotherapy : CII</title><addtitle>Cancer Immunol Immunother</addtitle><addtitle>Cancer Immunol Immunother</addtitle><description>The genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutated genes, including TP53, KMT2C, KMT2D, LRP1B, and FAT1. The most frequent mutation sites were ALOX12B (c.1565C >
T
), SLX4 (c.2786C >
T
), LRIG1 (c.746A >
G
), and SPEN (c.6915_6917del) (6.5%). Pathway analysis revealed dysregulation of cell cycle regulation, epigenetic regulation, PI3K/AKT signaling, and NOTCH signaling. A 17-mutated gene-related risk model was constructed using random survival forest analysis and showed significant prognostic value in both our cohort and the validation cohort. Based on the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression (ESTIMATE) algorithm, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm, and the MCPcounter algorithm, we found that the risk score calculated by the risk model was significantly correlated with stimulatory immune checkpoints (TNFSF4, ITGB2, CXCL10, CXCL9, and BTN3A1;
p
< 0.05). Additionally, it was significantly associated with markers that are important in predicting response to immunotherapy (CD274, IFNG, and TAMM2;
p
< 0.05). Furthermore, the results of immunofluorescence double staining showed that patients with high risk scores had a significantly higher level of M2 macrophage than those with low risk scores (
p
< 0.05). In conclusion, our study provides insights into the genomic landscape of ESCC and highlights the prognostic value of a genomic mutation signature associated with the immune microenvironment in southern Chinese patients with ESCC.</description><subject>1-Phosphatidylinositol 3-kinase</subject><subject>Adult</subject><subject>Aged</subject><subject>AKT protein</subject><subject>Algorithms</subject><subject>Asian People - genetics</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Cancer Research</subject><subject>Cell cycle</subject><subject>China</subject><subject>CXCL10 protein</subject><subject>East Asian People</subject><subject>Epigenetics</subject><subject>Esophageal cancer</subject><subject>Esophageal carcinoma</subject><subject>Esophageal Neoplasms - genetics</subject><subject>Esophageal Neoplasms - immunology</subject><subject>Esophageal Neoplasms - mortality</subject><subject>Esophageal Squamous Cell Carcinoma - genetics</subject><subject>Esophageal Squamous Cell Carcinoma - immunology</subject><subject>Esophageal Squamous Cell Carcinoma - mortality</subject><subject>Esophageal Squamous Cell Carcinoma - pathology</subject><subject>Female</subject><subject>Genomics</subject><subject>Genomics - methods</subject><subject>Humans</subject><subject>Immune checkpoint</subject><subject>Immunofluorescence</subject><subject>Immunology</subject><subject>Immunotherapy</subject><subject>Macrophages</subject><subject>Male</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Microenvironments</subject><subject>Middle Aged</subject><subject>Mutation</subject><subject>Oncology</subject><subject>p53 Protein</subject><subject>Prognosis</subject><subject>Squamous cell carcinoma</subject><subject>Tumor Microenvironment - genetics</subject><subject>Tumor Microenvironment - immunology</subject><subject>Tumors</subject><issn>1432-0851</issn><issn>0340-7004</issn><issn>1432-0851</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNp9kctu1TAQhiNERUvhBVggS2y6CfUldpIVQkflIlWCBaytSTJJXCX2qS-n4ll4WdymlMICyZItzze_5_dfFK8Yfcsorc8DpVzxkvKqpKLmsuRPihNWiXzVSPb00fm4eB7CFaUVp237rDgWTSN4W1cnxc-v3k3WhWh6coAlIXEjmdC6NV-sKUI0zpJgJgsxeSQQgusNRBzIjYkzMeuaLJJMe4f2YLyzK9pITG5yKc7oLdnNxmJAss9iuRa2TgxuP8OEsJBwnWB1KZAel4X04HuTB4AXxdEIS8CX9_tp8f3Dxbfdp_Lyy8fPu_eXZS-kimVXqR5wqPMaB4bYcD5ywVqhKIh-bGDoFHSAckAhazEqWam2gW4clOq6RonT4t2mu0_dikOfZ_Sw6L03K_gf2oHRf1esmfXkDpoxJinnTVY4u1fw7jphiHo14dYMWMy-tKCqkg2XdZXRN_-gVy55m_3dUaJWFZOZ4huVvzUEj-PDNIzq2_D1Fr7O4eu78DXPTa8f-3ho-Z12BsQGhFyyE_o_b_9H9hcuoMEE</recordid><startdate>20240604</startdate><enddate>20240604</enddate><creator>Zhou, Yue</creator><creator>Chu, Li</creator><creator>Li, Shuyan</creator><creator>Chu, Xiao</creator><creator>Ni, Jianjiao</creator><creator>Jiang, Shanshan</creator><creator>Pang, Yechun</creator><creator>Zheng, Danru</creator><creator>Lu, Yujuan</creator><creator>Lan, Fangcen</creator><creator>Cai, Xiuyu</creator><creator>Yang, Xi</creator><creator>Zhu, Zhengfei</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T5</scope><scope>H94</scope><scope>K9.</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20240604</creationdate><title>Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma</title><author>Zhou, Yue ; Chu, Li ; Li, Shuyan ; Chu, Xiao ; Ni, Jianjiao ; Jiang, Shanshan ; Pang, Yechun ; Zheng, Danru ; Lu, Yujuan ; Lan, Fangcen ; Cai, Xiuyu ; Yang, Xi ; Zhu, Zhengfei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c356t-b46caed7ed7fd1ee822f2319360a3cf8adb6abae5de3573f654698abfd66bb863</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>1-Phosphatidylinositol 3-kinase</topic><topic>Adult</topic><topic>Aged</topic><topic>AKT protein</topic><topic>Algorithms</topic><topic>Asian People - genetics</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Cancer Research</topic><topic>Cell cycle</topic><topic>China</topic><topic>CXCL10 protein</topic><topic>East Asian People</topic><topic>Epigenetics</topic><topic>Esophageal cancer</topic><topic>Esophageal carcinoma</topic><topic>Esophageal Neoplasms - genetics</topic><topic>Esophageal Neoplasms - immunology</topic><topic>Esophageal Neoplasms - mortality</topic><topic>Esophageal Squamous Cell Carcinoma - genetics</topic><topic>Esophageal Squamous Cell Carcinoma - immunology</topic><topic>Esophageal Squamous Cell Carcinoma - mortality</topic><topic>Esophageal Squamous Cell Carcinoma - pathology</topic><topic>Female</topic><topic>Genomics</topic><topic>Genomics - methods</topic><topic>Humans</topic><topic>Immune checkpoint</topic><topic>Immunofluorescence</topic><topic>Immunology</topic><topic>Immunotherapy</topic><topic>Macrophages</topic><topic>Male</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Microenvironments</topic><topic>Middle Aged</topic><topic>Mutation</topic><topic>Oncology</topic><topic>p53 Protein</topic><topic>Prognosis</topic><topic>Squamous cell carcinoma</topic><topic>Tumor Microenvironment - genetics</topic><topic>Tumor Microenvironment - immunology</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhou, Yue</creatorcontrib><creatorcontrib>Chu, Li</creatorcontrib><creatorcontrib>Li, Shuyan</creatorcontrib><creatorcontrib>Chu, Xiao</creatorcontrib><creatorcontrib>Ni, Jianjiao</creatorcontrib><creatorcontrib>Jiang, Shanshan</creatorcontrib><creatorcontrib>Pang, Yechun</creatorcontrib><creatorcontrib>Zheng, Danru</creatorcontrib><creatorcontrib>Lu, Yujuan</creatorcontrib><creatorcontrib>Lan, Fangcen</creatorcontrib><creatorcontrib>Cai, Xiuyu</creatorcontrib><creatorcontrib>Yang, Xi</creatorcontrib><creatorcontrib>Zhu, Zhengfei</creatorcontrib><collection>SpringerOpen</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Immunology Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Cancer Immunology, Immunotherapy : CII</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhou, Yue</au><au>Chu, Li</au><au>Li, Shuyan</au><au>Chu, Xiao</au><au>Ni, Jianjiao</au><au>Jiang, Shanshan</au><au>Pang, Yechun</au><au>Zheng, Danru</au><au>Lu, Yujuan</au><au>Lan, Fangcen</au><au>Cai, Xiuyu</au><au>Yang, Xi</au><au>Zhu, Zhengfei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma</atitle><jtitle>Cancer Immunology, Immunotherapy : CII</jtitle><stitle>Cancer Immunol Immunother</stitle><addtitle>Cancer Immunol Immunother</addtitle><date>2024-06-04</date><risdate>2024</risdate><volume>73</volume><issue>8</issue><spage>141</spage><pages>141-</pages><artnum>141</artnum><issn>1432-0851</issn><issn>0340-7004</issn><eissn>1432-0851</eissn><abstract>The genomic landscape of esophageal squamous cell cancer (ESCC), as well as its impact on the regulation of immune microenvironment, is not well understood. Thus, tumor samples from 92 patients were collected from two centers and subjected to targeted-gene sequencing. We identified frequently mutated genes, including TP53, KMT2C, KMT2D, LRP1B, and FAT1. The most frequent mutation sites were ALOX12B (c.1565C >
T
), SLX4 (c.2786C >
T
), LRIG1 (c.746A >
G
), and SPEN (c.6915_6917del) (6.5%). Pathway analysis revealed dysregulation of cell cycle regulation, epigenetic regulation, PI3K/AKT signaling, and NOTCH signaling. A 17-mutated gene-related risk model was constructed using random survival forest analysis and showed significant prognostic value in both our cohort and the validation cohort. Based on the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression (ESTIMATE) algorithm, the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm, and the MCPcounter algorithm, we found that the risk score calculated by the risk model was significantly correlated with stimulatory immune checkpoints (TNFSF4, ITGB2, CXCL10, CXCL9, and BTN3A1;
p
< 0.05). Additionally, it was significantly associated with markers that are important in predicting response to immunotherapy (CD274, IFNG, and TAMM2;
p
< 0.05). Furthermore, the results of immunofluorescence double staining showed that patients with high risk scores had a significantly higher level of M2 macrophage than those with low risk scores (
p
< 0.05). In conclusion, our study provides insights into the genomic landscape of ESCC and highlights the prognostic value of a genomic mutation signature associated with the immune microenvironment in southern Chinese patients with ESCC.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>38832974</pmid><doi>10.1007/s00262-024-03725-2</doi><oa>free_for_read</oa></addata></record> |
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subjects | 1-Phosphatidylinositol 3-kinase Adult Aged AKT protein Algorithms Asian People - genetics Biomarkers, Tumor - genetics Cancer Research Cell cycle China CXCL10 protein East Asian People Epigenetics Esophageal cancer Esophageal carcinoma Esophageal Neoplasms - genetics Esophageal Neoplasms - immunology Esophageal Neoplasms - mortality Esophageal Squamous Cell Carcinoma - genetics Esophageal Squamous Cell Carcinoma - immunology Esophageal Squamous Cell Carcinoma - mortality Esophageal Squamous Cell Carcinoma - pathology Female Genomics Genomics - methods Humans Immune checkpoint Immunofluorescence Immunology Immunotherapy Macrophages Male Medicine Medicine & Public Health Microenvironments Middle Aged Mutation Oncology p53 Protein Prognosis Squamous cell carcinoma Tumor Microenvironment - genetics Tumor Microenvironment - immunology Tumors |
title | Prognostic value of genomic mutation signature associated with immune microenvironment in southern Chinese patients with esophageal squamous cell carcinoma |
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