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Wang Z, Chen H, Sun L, Wang X, Xu Y, Tian S, Liu X. Uncovering the potential of APOD as a biomarker in gastric cancer: A retrospective and multi-center study. Comput Struct Biotechnol J 2024; 23:1051-1064. [PMID: 38455068 PMCID: PMC10918487 DOI: 10.1016/j.csbj.2024.02.015] [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: 10/21/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Gastric cancer (GC) poses a significant health challenge worldwide, necessitating the identification of predictive biomarkers to improve prognosis. Dysregulated lipid metabolism is a well-recognized hallmark of tumorigenesis, prompting investigation into apolipoproteins (APOs). In this study, we focused on apolipoprotein D (APOD) following comprehensive analyses of APOs in pan-cancer. Utilizing data from the TCGA-STAD and GSE62254 cohorts, we elucidated associations between APOD expression and multiple facets of GC, including prognosis, tumor microenvironment (TME), cancer biomarkers, mutations, and immunotherapy response, and identified potential anti-GC drugs. Single-cell analyses and immunohistochemical staining confirmed APOD expression in fibroblasts within the GC microenvironment. Additionally, we independently validated the prognostic significance of APOD in the ZN-GC cohort. Our comprehensive analyses revealed that high APOD expression in GC patients was notably associated with unfavorable clinical outcomes, reduced microsatellite instability and tumor mutation burden, alterations in the TME, and diminished response to immunotherapy. These findings provide valuable insights into the potential prognostic and therapeutic implications of APOD in GC.
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Affiliation(s)
- Zisong Wang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Hongshan Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Le Sun
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xuanyu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Yihang Xu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Sufang Tian
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xiaoping Liu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
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2
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Ma Y, Jiang Z, Pan L, Zhou Y, Xia R, Liu Z, Yuan L. Current development of molecular classifications of gastric cancer based on omics (Review). Int J Oncol 2024; 65:89. [PMID: 39092559 DOI: 10.3892/ijo.2024.5677] [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: 06/04/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Gastric cancer (GC) is a complex and heterogeneous disease with significant phenotypic and genetic variation. Traditional classification systems rely mainly on the evaluation of clinical pathological features and conventional biomarkers and might not capture the diverse clinical processes of individual GCs. The latest discoveries in omics technologies such as next‑generation sequencing, proteomics and metabolomics have provided crucial insights into potential genetic alterations and biological events in GC. Clustering strategies for identifying subtypes of GC might offer new tools for improving GC treatment and clinical trial outcomes by enabling the development of therapies tailored to specific subtypes. However, the feasibility and therapeutic significance of implementing molecular classifications of GC in clinical practice need to addressed. The present review examines the current molecular classifications, delineates the prevailing landscape of clinically relevant molecular features, analyzes their correlations with traditional GC classifications, and discusses potential clinical applications.
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Affiliation(s)
- Yubo Ma
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Zhengchen Jiang
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
| | - Libin Pan
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310005, P.R. China
| | - Ying Zhou
- Department of Pharmacy, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310005, P.R. China
| | - Ruihong Xia
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Zhuo Liu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China
| | - Li Yuan
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
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3
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Zhakula-Kostadinova N, Taylor AM. Patterns of Aneuploidy and Signaling Consequences in Cancer. Cancer Res 2024; 84:2575-2587. [PMID: 38924459 DOI: 10.1158/0008-5472.can-24-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Aneuploidy, or a change in the number of whole chromosomes or chromosome arms, is a near-universal feature of cancer. Chromosomes affected by aneuploidy are not random, with observed cancer-specific and tissue-specific patterns. Recent advances in genome engineering methods have allowed the creation of models with targeted aneuploidy events. These models can be used to uncover the downstream effects of individual aneuploidies on cancer phenotypes including proliferation, apoptosis, metabolism, and immune signaling. Here, we review the current state of research into the patterns of aneuploidy in cancer and their impact on signaling pathways and biological processes.
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Affiliation(s)
- Nadja Zhakula-Kostadinova
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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4
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Kim R, Kim S, Oh BBL, Yu WS, Kim CW, Hur H, Son SY, Yang MJ, Cho DS, Ha T, Heo S, Jang JY, Yun JS, Kwack KS, Kim JK, Huh J, Lim SG, Han SU, Lee HW, Park JE, Kim CH, Roh J, Koh YW, Lee D, Kim JH, Lee GH, Noh CK, Jung YJ, Park JW, Sheen S, Ahn MS, Choi YW, Kim TH, Kang SY, Choi JH, Baek SY, Lee KM, Il Kim S, Noh SH, Kim SH, Hwang H, Joo E, Lee S, Shin JY, Yun JY, Park J, Yi K, Kwon Y, Lee WC, Park H, Lim J, Yi B, Koo J, Koh JY, Lee S, Lee Y, Lee BR, Connolly-Strong E, Ju YS, Kwon M. Clinical application of whole-genome sequencing of solid tumors for precision oncology. Exp Mol Med 2024:10.1038/s12276-024-01288-x. [PMID: 39138315 DOI: 10.1038/s12276-024-01288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 08/15/2024] Open
Abstract
Genomic alterations in tumors play a pivotal role in determining their clinical trajectory and responsiveness to treatment. Targeted panel sequencing (TPS) has served as a key clinical tool over the past decade, but advancements in sequencing costs and bioinformatics have now made whole-genome sequencing (WGS) a feasible single-assay approach for almost all cancer genomes in clinical settings. This paper reports on the findings of a prospective, single-center study exploring the real-world clinical utility of WGS (tumor and matched normal tissues) and has two primary objectives: (1) assessing actionability for therapeutic options and (2) providing clarity for clinical questions. Of the 120 patients with various solid cancers who were enrolled, 95 (79%) successfully received genomic reports within a median of 11 working days from sampling to reporting. Analysis of these 95 WGS reports revealed that 72% (68/95) yielded clinically relevant insights, with 69% (55/79) pertaining to therapeutic actionability and 81% (13/16) pertaining to clinical clarity. These benefits include the selection of informed therapeutics and/or active clinical trials based on the identification of driver mutations, tumor mutational burden (TMB) and mutational signatures, pathogenic germline variants that warrant genetic counseling, and information helpful for inferring cancer origin. Our findings highlight the potential of WGS as a comprehensive tool in precision oncology and suggests that it should be integrated into routine clinical practice to provide a complete image of the genomic landscape to enable tailored cancer management.
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Affiliation(s)
| | - Seokhwi Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | | | - Woo Sik Yu
- Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Chang Woo Kim
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hoon Hur
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sang-Yong Son
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Min Jae Yang
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Dae Sung Cho
- Department of Urology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Taeyang Ha
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Subin Heo
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeon Yeob Jang
- Department of Otolaryngology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jae Sung Yun
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Kyu-Sung Kwack
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jai Keun Kim
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jimi Huh
- Department of Radiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sun Gyo Lim
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sang-Uk Han
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyun Woo Lee
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Ji Eun Park
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Chul-Ho Kim
- Department of Otolaryngology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jin Roh
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jang-Hee Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Gil Ho Lee
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Choong-Kyun Noh
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yun Jung Jung
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Ji Won Park
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seungsoo Sheen
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Mi Sun Ahn
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Yong Won Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Tae-Hwan Kim
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Seok Yun Kang
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Jin-Hyuk Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Soo Yeon Baek
- Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Kee Myung Lee
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sun Il Kim
- Department of Urology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sung Hyun Noh
- Department of Neurosurgery, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Se-Hyuk Kim
- Department of Neurosurgery, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | - Hyemin Hwang
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Minsuk Kwon
- Department of Hematology-Oncology, Ajou University School of Medicine, Gyeonggi-do, Republic of Korea.
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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5
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Matsuishi A, Nakajima S, Saito M, Saito K, Fukai S, Tsumuraya H, Kanoda R, Kikuchi T, Nirei A, Kaneta A, Okayama H, Mimura K, Hanayama H, Sakamoto W, Momma T, Saze Z, Kono K. The impact of CLDN18.2 expression on effector cells mediating antibody-dependent cellular cytotoxicity in gastric cancer. Sci Rep 2024; 14:17916. [PMID: 39095563 PMCID: PMC11297210 DOI: 10.1038/s41598-024-68970-y] [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: 05/03/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
Activating antibody-dependent cellular cytotoxicity (ADCC) by targeting claudin-18 isoform 2 (CLDN18.2) using zolbetuximab, a monoclonal antibody against CLDN18.2, has been considered a promising novel therapeutic strategy for gastric cancer (GC). However, the impact of CLDN18.2 expression on natural killer (NK) cells and monocytes/macrophages-crucial effector cells of ADCC-in GC has not been fully investigated. In the present study, we assessed the impact of CLDN18.2 expression on clinical outcomes, molecular features, and the frequencies of tumor-infiltrating NK cells and macrophages, as well as peripheral blood NK cells and monocytes, in GC by analyzing our own GC cohorts. The expression of CLDN18.2 did not significantly impact clinical outcomes of GC patients, while it was significantly and positively associated with Epstein-Barr virus (EBV) status and PD-L1 expression. The frequencies of tumor-infiltrating NK cells and macrophages, as well as peripheral blood NK cells and monocytes, were comparable between CLDN18.2-positive and CLDN18.2-negative GCs. Importantly, both CLDN18.2 expression and the number of tumor-infiltrating NK cells were significantly higher in EBV-associated GC compared to other molecular subtypes. Our findings support the effectiveness of zolbetuximab in CLDN18.2-positive GC, and offer a novel insight into the treatment of this cancer type, highlighting its potential effectiveness for CLDN18.2-positive/EBV-associated GC.
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Affiliation(s)
- Akira Matsuishi
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Shotaro Nakajima
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan.
- Department of Multidisciplinary Treatment of Cancer and Regional Medical Support, Fukushima Medical University School of Medicine, 1 Hikariga-oka, Fukushima City, Fukushima, 960-1295, Japan.
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Satoshi Fukai
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hideaki Tsumuraya
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Ryo Kanoda
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomohiro Kikuchi
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Azuma Nirei
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akinao Kaneta
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hirokazu Okayama
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kosaku Mimura
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
- Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroyuki Hanayama
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Wataru Sakamoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Zenichiro Saze
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
- Department of Multidisciplinary Treatment of Cancer and Regional Medical Support, Fukushima Medical University School of Medicine, 1 Hikariga-oka, Fukushima City, Fukushima, 960-1295, Japan
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6
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Dravillas CE, Coleman SS, Hoyd R, Caryotakis G, Denko L, Chan CH, Churchman ML, Denko N, Dodd RD, Eljilany I, Hardikar S, Husain M, Ikeguchi AP, Jin N, Ma Q, McCarter MD, Osman AE, Robinson LA, Singer EA, Tinoco G, Ulrich CM, Zakharia Y, Spakowicz D, Tarhini AA, Tan AC. The Tumor Microbiome as a Predictor of Outcomes in Patients with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors. CANCER RESEARCH COMMUNICATIONS 2024; 4:1978-1990. [PMID: 39015091 PMCID: PMC11307144 DOI: 10.1158/2767-9764.crc-23-0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/21/2023] [Accepted: 07/12/2024] [Indexed: 07/18/2024]
Abstract
Emerging evidence supports the important role of the tumor microbiome in oncogenesis, cancer immune phenotype, cancer progression, and treatment outcomes in many malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and its potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICI). Baseline tumor samples were collected from 71 patients with metastatic melanoma before treatment with ICIs. Bulk RNA sequencing (RNA-seq) was conducted on the formalin-fixed, paraffin-embedded and fresh frozen tumor samples. Durable clinical benefit (primary clinical endpoint) following ICIs was defined as overall survival >24 months and no change to the primary drug regimen (responders). We processed RNA-seq reads to carefully identify exogenous sequences using the {exotic} tool. The age of the 71 patients with metastatic melanoma ranged from 24 to 83 years, 59% were male, and 55% survived >24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNA-seq, including bacteria, fungi, and viruses. We found differences in gene expression and microbe abundances in immunotherapy-responsive versus nonresponsive tumors. Responders showed significant enrichment of bacteriophages in the phylum Uroviricota, and nonresponders showed enrichment of several bacteria, including Campylobacter jejuni. These microbes correlated with immune-related gene expression signatures. Finally, we found that models for predicting prolonged survival with immunotherapy using both microbe abundances and gene expression outperformed models using either dataset alone. Our findings warrant further investigation and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs. SIGNIFICANCE We analyzed the tumor microbiome and interactions with genes and pathways in metastatic melanoma treated with immunotherapy and identified several microbes associated with immunotherapy response and immune-related gene expression signatures. Machine learning models that combined microbe abundances and gene expression outperformed models using either dataset alone in predicting immunotherapy responses.
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Affiliation(s)
- Caroline E. Dravillas
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Samuel S. Coleman
- Department of Oncological Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
- Department of Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
| | - Rebecca Hoyd
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Griffin Caryotakis
- Department of Oncological Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
- Department of Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
| | - Louis Denko
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Carlos H.F. Chan
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa.
| | | | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Rebecca D. Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa.
| | - Islam Eljilany
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Sheetal Hardikar
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
| | - Marium Husain
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Alexandra P. Ikeguchi
- Department of Hematology/Oncology, Stephenson Cancer Center of University of Oklahoma, Oklahoma City, Oklahoma.
| | - Ning Jin
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.
| | - Martin D. McCarter
- Department of Surgery, University of Colorado School of Medicine, Aurora, Colorado.
| | - Afaf E.G. Osman
- Division of Hematology and Hematologic Malignancies, Department of Internal Medicine, University of Utah, Salt Lake City, Utah.
| | - Lary A. Robinson
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Eric A. Singer
- Division of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Gabriel Tinoco
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Cornelia M. Ulrich
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
| | - Yousef Zakharia
- Division of Oncology, Hematology and Blood and Marrow Transplantation, University of Iowa, Holden Comprehensive Cancer Center, Iowa City, Iowa.
| | - Daniel Spakowicz
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
| | - Ahmad A. Tarhini
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Aik Choon Tan
- Department of Oncological Science, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
- Department of Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
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7
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Jiang Z, Zhu M, Zhang L, Cui H, Jiang R, Yang Y. Antitumor immunity and prognosis value elicited by FAT3 and LRP1B co-mutation in endometrial cancer. Gynecol Oncol 2024; 187:1-11. [PMID: 38696842 DOI: 10.1016/j.ygyno.2024.04.023] [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: 12/17/2023] [Revised: 03/07/2024] [Accepted: 04/23/2024] [Indexed: 05/04/2024]
Abstract
OBJECTIVE FAT3 and LRP1B are two tumor suppressor genes with high mutation frequency in multiple cancer types, we sought to investigate the prognostic and immunological significance of these two genes in EC. METHODS Based on a cohort of 502 EC samples, we conducted a comprehensive analysis of its multidimensional data types including genomic, transcriptomic, and clinical information, the potential impact of FAT3 and LRP1B co-mutation on antitumor immune response and prognosis were systematically discussed. RESULTS We observed that FAT3 and LRP1B co-mutation was not only defined a dataset with prominently increased TMB, decreased tumor aneuploidy, and specially enriched in MSI-H subtype, but also manifested increased expression of immune-related markers, especially exclusive upregulation of PD-L1 levels and higher PD-L1+/CD8A+ proportion. Further analysis focused on lymphocyte infiltration and pathway enrichment explored the immune cell composition of the microenvironment and underlying molecular mechanisms affecting tumor development. Furthermore, EC patients with FAT3 and LRP1B co-mutation possessed significantly prolonged PFS and OS, and the co-mutation status was proved to be an independent prognostic factor. And a nomogram with high predictive performance was constructed by incorporating co-mutation with clinical features. More strikingly, the prognosis of MSI-H patients in EC with co-mutation was significantly improved, and their survival reached a level consistent with the POLE subtype. CONCLUSIONS In endometrial cancer, co-mutation of FAT3 and LRP1B not only leads to activation of the immune state, but also represents a subgroup with an improved prognosis, particularly in the MSI-H subtype.
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Affiliation(s)
- Zhansheng Jiang
- 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, China; Department of Integrative Oncology, Tianjin Medical University Cancer Institute and Hospital, China.
| | - Mingyu Zhu
- 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, China; Center for Precision Cancer Medicine & Translational Research, Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer, China
| | - Lu Zhang
- Center for Precision Cancer Medicine & Translational Research, Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer, China
| | - Haiyan Cui
- Center for Precision Cancer Medicine & Translational Research, Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer, China
| | - Richeng Jiang
- 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, China; Center for Precision Cancer Medicine & Translational Research, Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer, China.
| | - Yanfang Yang
- 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, China; Department of the second breast cancer, Tianjin Medical University Cancer Institute and Hospital, China.
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8
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Chen X, Agustinus AS, Li J, DiBona M, Bakhoum SF. Chromosomal instability as a driver of cancer progression. Nat Rev Genet 2024:10.1038/s41576-024-00761-7. [PMID: 39075192 DOI: 10.1038/s41576-024-00761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/31/2024]
Abstract
Chromosomal instability (CIN) refers to an increased propensity of cells to acquire structural and numerical chromosomal abnormalities during cell division, which contributes to tumour genetic heterogeneity. CIN has long been recognized as a hallmark of cancer, and evidence over the past decade has strongly linked CIN to tumour evolution, metastasis, immune evasion and treatment resistance. Until recently, the mechanisms by which CIN propels cancer progression have remained elusive. Beyond the generation of genomic copy number heterogeneity, recent work has unveiled additional tumour-promoting consequences of abnormal chromosome segregation. These mechanisms include complex chromosomal rearrangements, epigenetic reprogramming and the induction of cancer cell-intrinsic inflammation, emphasizing the multifaceted role of CIN in cancer.
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Affiliation(s)
- Xuelan Chen
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Albert S Agustinus
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Jun Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melody DiBona
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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9
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Kim JY, Hong N, Ham SW, Park S, Seo S, Kim H. Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH. PLoS One 2024; 19:e0307943. [PMID: 39074091 DOI: 10.1371/journal.pone.0307943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Notch ligands [jagged (JAG) and, delta-like (DLL) families] and receptors [NOTCH family] are key regulators of Notch signaling. NOTCH signaling contributes to vascular development, tissue homeostasis, angiogenesis, and cancer progression. To elucidate the universal functions of the JAG, DLL, and NOTCH families and their connections with various biological functions, we examined 15 types of cancer using The Cancer Genome Atlas clinical database. We selected the differentially expressed genes (DEGs), which were positively correlated to the JAG, DLL, and NOTCH families in each cancer. We selected positive and negative hallmark signatures across cancer types. These indicated biological features associated with angiogenesis, hypoxia, KRAS signaling, cell cycle, and MYC targets by gene ontology and gene set enrichment analyses using DEGs. Furthermore, we analyzed single-cell RNA sequencing data to examine the expression of JAG, DLL, and NOTCH families and enrichment of hallmark signatures. Positive signatures identified using DEGs, such as KRAS signaling and hypoxia, were enriched in clusters with high expression of JAG, DLL, and NOTCH families. We subsequently validated the correlation between the JAG, DLL, and NOTCH families and clinical stages, including treatment response, metastasis, and recurrence. In addition, we performed survival analysis to identify hallmark signatures that critically affect patient survival when combining the expression of JAG, DLL, and NOTCH families. By combining the DEG enrichment and hallmark signature enrichment in survival analysis, we suggested unexplored regulatory functions and synergistic effects causing synthetic lethality. Taken together, our observations demonstrate the functions of JAG, DLL, and NOTCH families in cancer malignancy and provide insights into their molecular regulatory mechanisms.
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Affiliation(s)
- Jung Yun Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Nayoung Hong
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Seok Won Ham
- MEDIFIC Inc., Hwaseong-si, Gyeonggi-do, Republic of Korea
| | - Sehyeon Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sunyoung Seo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hyunggee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
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10
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Chen H, Jing C, Shang L, Zhu X, Zhang R, Liu Y, Wang M, Xu K, Ma T, Jing H, Wang Z, Li X, Chong W, Li L. Molecular characterization and clinical relevance of metabolic signature subtypes in gastric cancer. Cell Rep 2024; 43:114424. [PMID: 38959111 DOI: 10.1016/j.celrep.2024.114424] [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: 12/04/2023] [Revised: 05/06/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
Metabolic reprogramming dictates tumor molecular attributes and therapeutic potentials. However, the comprehensive metabolic characteristics in gastric cancer (GC) remain obscure. Here, metabolic signature-based clustering analysis identifies three subtypes with distinct molecular and clinical features: MSC1 showed better prognosis and upregulation of the tricarboxylic acid (TCA) cycle and lipid metabolism, combined with frequent TP53 and RHOA mutation; MSC2 had moderate prognosis and elevated nucleotide and amino acid metabolism, enriched by intestinal histology and mismatch repair deficient (dMMR); and MSC3 exhibited poor prognosis and enhanced glycan and energy metabolism, accompanied by diffuse histology and frequent CDH1 mutation. The Shandong Provincial Hospital (SDPH) in-house dataset with matched transcriptomic, metabolomic, and spatial-metabolomic analysis also validated these findings. Further, we constructed the metabolic subtype-related prognosis gene (MSPG) scoring model to quantify the activity of individual tumors and found a positive correlation with cuproptosis signaling. In conclusion, comprehensive recognition of the metabolite signature can enhance the understanding of diversity and heterogeneity in GC.
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Affiliation(s)
- Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China.
| | - Changqing Jing
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Xingyu Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Ronghua Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Yuan Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Mingfei Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Kang Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Tianrong Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Haiyan Jing
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Ze Wang
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Xin Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China.
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan 250021, China; Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China.
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11
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Burdett NL, Willis MO, Pandey A, Twomey L, Alaei S, Bowtell DDL, Christie EL. Timing of whole genome duplication is associated with tumor-specific MHC-II depletion in serous ovarian cancer. Nat Commun 2024; 15:6069. [PMID: 39025846 PMCID: PMC11258338 DOI: 10.1038/s41467-024-50137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
Whole genome duplication is frequently observed in cancer, and its prevalence in our prior analysis of end-stage, homologous recombination deficient high grade serous ovarian cancer (almost 80% of samples) supports the notion that whole genome duplication provides a fitness advantage under the selection pressure of therapy. Here, we therefore aim to identify potential therapeutic vulnerabilities in primary high grade serous ovarian cancer with whole genome duplication by assessing differentially expressed genes and pathways in 79 samples. We observe that MHC-II expression is lowest in tumors which have acquired whole genome duplication early in tumor evolution, and further demonstrate that reduced MHC-II expression occurs in subsets of tumor cells rather than in canonical antigen-presenting cells. Early whole genome duplication is also associated with worse patient survival outcomes. Our results suggest an association between the timing of whole genome duplication, MHC-II expression and clinical outcome in high grade serous ovarian cancer that warrants further investigation for therapeutic targeting.
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Affiliation(s)
- Nikki L Burdett
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Box Hill Hospital, Eastern Health, Box Hill, VIC, 3128, Australia
| | | | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Laura Twomey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sara Alaei
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3168, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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12
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Skelly DA, Graham JP, Cheng M, Furuta M, Walter A, Stoklasek TA, Yang H, Stearns TM, Poirion O, Zhang JG, Grassmann JDS, Luo D, Flynn WF, Courtois ET, Chang CH, Serreze DV, Menghi F, Reinholdt LG, Liu ET. Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603136. [PMID: 39071392 PMCID: PMC11275897 DOI: 10.1101/2024.07.11.603136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy has been experimentally challenging because of variations in both host and tumor genomes, differences in the microbiome, and patient life exposures. Utilizing the Collaborative Cross (CC) multi-parent mouse genetic resource population, we developed an approach that fixes the tumor genomic configuration while varying host genetics. With this approach, we discovered that response to anti-PD-1 (aPD1) immunotherapy was significantly heritable in four distinct murine tumor models (H2 between 0.18-0.40). For the MC38 colorectal carcinoma system (H2 = 0.40), we mapped four significant ICI response quantitative trait loci (QTL) localized to mouse chromosomes (mChr) 5, 9, 15 and 17, and identified significant epistatic interactions between specific QTL pairs. Differentially expressed genes within these QTL were highly enriched for immune genes and pathways mediating allograft rejection and graft vs host disease. Using a cross species analytical approach, we found a core network of 48 genes within the four QTLs that showed significant prognostic value for overall survival in aPD1 treated human cohorts that outperformed all other existing validated immunotherapy biomarkers, especially in human tumors of the previously defined immune subtype 4. Functional blockade of two top candidate immune targets within the 48 gene network, GM-CSF and high affinity IL-2/IL-15 signaling, completely abrogated the MC38 tumor transcriptional response to aPD1 therapy in vivo. Thus, we have established a powerful cross species in vivo platform capable of uncovering host genetic factors that establish the tumor immune microenvironment configuration propitious for ICI response.
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Affiliation(s)
- Daniel A. Skelly
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - John P. Graham
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Mayuko Furuta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Andrew Walter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | | | | | - Olivier Poirion
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ji-Gang Zhang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Diane Luo
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - William F. Flynn
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Elise T. Courtois
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- OB/Gyn Department, UConn Health, Farmington, CT, USA
| | - Chih-Hao Chang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - David V. Serreze
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Edison T. Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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13
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Wang X, Liu X, Xiao R, Fang Y, Zhou F, Gu M, Luo X, Jiang D, Tang Y, You L, Zhao Y. Histone lactylation dynamics: Unlocking the triad of metabolism, epigenetics, and immune regulation in metastatic cascade of pancreatic cancer. Cancer Lett 2024; 598:217117. [PMID: 39019144 DOI: 10.1016/j.canlet.2024.217117] [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: 04/06/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Cancer cells rewire metabolism to sculpt the immune tumor microenvironment (TME) and propel tumor advancement, which intricately tied to post-translational modifications. Histone lactylation has emerged as a novel player in modulating protein functions, whereas little is known about its pathological role in pancreatic ductal adenocarcinoma (PDAC) progression. Employing a multi-omics approach encompassing bulk and single-cell RNA sequencing, metabolomics, ATAC-seq, and CUT&Tag methodologies, we unveiled the potential of histone lactylation in prognostic prediction, patient stratification and TME characterization. Notably, "LDHA-H4K12la-immuno-genes" axis has introduced a novel node into the regulatory framework of "metabolism-epigenetics-immunity," shedding new light on the landscape of PDAC progression. Furthermore, the heightened interplay between cancer cells and immune counterparts via Nectin-2 in liver metastasis with elevated HLS unraveled a positive feedback loop in driving immune evasion. Simultaneously, immune cells exhibited altered HLS and autonomous functionality across the metastatic cascade. Consequently, the exploration of innovative combination strategies targeting the metabolism-epigenetics-immunity axis holds promise in curbing distant metastasis and improving survival prospects for individuals grappling with challenges of PDAC.
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Affiliation(s)
- Xing Wang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Xiaohong Liu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Ruiling Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Yuan Fang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Feihan Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Minzhi Gu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Xiyuan Luo
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Decheng Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Yuemeng Tang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, PR China.
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14
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Fernandez-Mateos J, Cresswell GD, Trahearn N, Webb K, Sakr C, Lampis A, Stuttle C, Corbishley CM, Stavrinides V, Zapata L, Spiteri I, Heide T, Gallagher L, James C, Ramazzotti D, Gao A, Kote-Jarai Z, Acar A, Truelove L, Proszek P, Murray J, Reid A, Wilkins A, Hubank M, Eeles R, Dearnaley D, Sottoriva A. Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer. NATURE CANCER 2024:10.1038/s43018-024-00787-0. [PMID: 38997466 DOI: 10.1038/s43018-024-00787-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/23/2024] [Indexed: 07/14/2024]
Abstract
Cancer evolution lays the groundwork for predictive oncology. Testing evolutionary metrics requires quantitative measurements in controlled clinical trials. We mapped genomic intratumor heterogeneity in locally advanced prostate cancer using 642 samples from 114 individuals enrolled in clinical trials with a 12-year median follow-up. We concomitantly assessed morphological heterogeneity using deep learning in 1,923 histological sections from 250 individuals. Genetic and morphological (Gleason) diversity were independent predictors of recurrence (hazard ratio (HR) = 3.12 and 95% confidence interval (95% CI) = 1.34-7.3; HR = 2.24 and 95% CI = 1.28-3.92). Combined, they identified a group with half the median time to recurrence. Spatial segregation of clones was also an independent marker of recurrence (HR = 2.3 and 95% CI = 1.11-4.8). We identified copy number changes associated with Gleason grade and found that chromosome 6p loss correlated with reduced immune infiltration. Matched profiling of relapse, decades after diagnosis, confirmed that genomic instability is a driving force in prostate cancer progression. This study shows that combining genomics with artificial intelligence-aided histopathology leads to the identification of clinical biomarkers of evolution.
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Affiliation(s)
- Javier Fernandez-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Katharine Webb
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Chirine Sakr
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Lampis
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Christine Stuttle
- The Royal Marsden NHS Foundation Trust, London, UK
- Oncogenetics Team, The Institute of Cancer Research, London, UK
| | - Catherine M Corbishley
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- St. George's Hospital Healthcare NHS Trust, London, UK
| | | | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Lewis Gallagher
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Chela James
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | | | - Annie Gao
- Bob Champion Cancer Unit, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | | | - Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Lesley Truelove
- Bob Champion Cancer Unit, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Paula Proszek
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Julia Murray
- The Royal Marsden NHS Foundation Trust, London, UK
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alison Reid
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Anna Wilkins
- The Royal Marsden NHS Foundation Trust, London, UK
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Michael Hubank
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Ros Eeles
- The Royal Marsden NHS Foundation Trust, London, UK
- Oncogenetics Team, The Institute of Cancer Research, London, UK
| | - David Dearnaley
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK.
- Academic Urology Unit, The Royal Marsden NHS Foundation Trust, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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15
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Wang SW, Zheng QY, Hong WF, Tang BF, Hsu SJ, Zhang Y, Zheng XB, Zeng ZC, Gao C, Ke AW, Du SS. Mechanism of immune activation mediated by genomic instability and its implication in radiotherapy combined with immune checkpoint inhibitors. Radiother Oncol 2024; 199:110424. [PMID: 38997092 DOI: 10.1016/j.radonc.2024.110424] [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: 04/07/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
Various genetic and epigenetic changes associated with genomic instability (GI), including DNA damage repair defects, chromosomal instability, and mitochondrial GI, contribute to development and progression of cancer. These alterations not only result in DNA leakage into the cytoplasm, either directly or through micronuclei, but also trigger downstream inflammatory signals, such as the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. Apart from directly inducing DNA damage to eliminate cancer cells, radiotherapy (RT) exerts its antitumor effects through intracellular DNA damage sensing mechanisms, leading to the activation of downstream inflammatory signaling pathways. This not only enables local tumor control but also reshapes the immune microenvironment, triggering systemic immune responses. The combination of RT and immunotherapy has emerged as a promising approach to increase the probability of abscopal effects, where distant tumors respond to treatment due to the systemic immunomodulatory effects. This review emphasizes the importance of GI in cancer biology and elucidates the mechanisms by which RT induces GI remodeling of the immune microenvironment. By elucidating the mechanisms of GI and RT-induced immune responses, we aim to emphasize the crucial importance of this approach in modern oncology. Understanding the impact of GI on tumor biological behavior and therapeutic response, as well as the possibility of activating systemic anti-tumor immunity through RT, will pave the way for the development of new treatment strategies and improve prognosis for patients.
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Affiliation(s)
- Si-Wei Wang
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Liver Cancer Institute, Fudan University, Shanghai 200030, China
| | - Qiu-Yi Zheng
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Wei-Feng Hong
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Bu-Fu Tang
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Shu-Jung Hsu
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Yang Zhang
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Xiao-Bin Zheng
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Zhao-Chong Zeng
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Chao Gao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Liver Cancer Institute, Fudan University, Shanghai 200030, China.
| | - Ai-Wu Ke
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Liver Cancer Institute, Fudan University, Shanghai 200030, China.
| | - Shi-Suo Du
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai 200030, China.
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Luo Y, Tian W, Kang D, Wu L, Tang H, Wang S, Zhang C, Xie Y, Zhang Y, Xie J, Deng X, Zou H, Wu H, Lin H, Wei W. RNA modification gene WDR4 facilitates tumor progression and immunotherapy resistance in breast cancer. J Adv Res 2024:S2090-1232(24)00266-2. [PMID: 38960276 DOI: 10.1016/j.jare.2024.06.029] [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: 12/04/2023] [Revised: 06/30/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Growing interest toward RNA modification in cancer has inspired the exploration of gene sets related to multiple RNA modifications. However, a comprehensive elucidation of the clinical value of various RNA modifications in breast cancer is still lacking. OBJECTIVES This study aimed to provide a strategy based on RNA modification-related genes for predicting therapy response and survival outcomes in breast cancer patients. METHODS Genes related to thirteen RNA modification patterns were integrated for establishing a nine-gene-containing signature-RMscore. Alterations of tumor immune microenvironment and therapy response featured by different RMscore levels were assessed by bulk transcriptome, single-cell transcriptome and genomics analyses. The biological function of key RMscore-related molecules was investigated by cellular experiments in vitro and in vivo, using flow cytometry, immunohistochemistry and immunofluorescence staining. RESULTS This study has raised an effective therapy strategy for breast cancer patients after a well-rounded investigation of RNA modification-related genes. With a great performance of predicting patient prognosis, high levels of the RMscore proposed in this study represented suppressive immune microenvironment and therapy resistance, including adjuvant chemotherapy and PD-L1 blockade treatment. As the key contributor of the RMscore, inhibition of WDR4 impaired breast cancer progression significantly in vitro and in vivo, as well as participated in regulating cell cycle and mTORC1 signaling pathway via m7G modification. CONCLUSION Briefly, this study has developed promising and effective tactics to achieve the prediction of survival probabilities and treatment response in breast cancer patients.
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Affiliation(s)
- Yongzhou Luo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Wenwen Tian
- Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, No.78, Hengzhigang Road, Guangzhou 510095, China
| | - Da Kang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Linyu Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Sifen Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yi Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Yue Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Zou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China
| | - Hao Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
| | - Huan Lin
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Weidong Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651, East Dongfeng Road, Guangzhou 510060, China.
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Ye B, Li Z, Wang Q. A novel artificial intelligence network to assess the prognosis of gastrointestinal cancer to immunotherapy based on genetic mutation features. Front Immunol 2024; 15:1428529. [PMID: 38994371 PMCID: PMC11236566 DOI: 10.3389/fimmu.2024.1428529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have revolutionized gastrointestinal cancer treatment, yet the absence of reliable biomarkers hampers precise patient response prediction. Methods We developed and validated a genomic mutation signature (GMS) employing a novel artificial intelligence network to forecast the prognosis of gastrointestinal cancer patients undergoing ICIs therapy. Subsequently, we explored the underlying immune landscapes across different subtypes using multiomics data. Finally, UMI-77 was pinpointed through the analysis of drug sensitization data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. The sensitivity of UMI-77 to the AGS and MKN45 cell lines was evaluated using the cell counting kit-8 (CCK8) assay and the plate clone formation assay. Results Using the artificial intelligence network, we developed the GMS that independently predicts the prognosis of gastrointestinal cancer patients. The GMS demonstrated consistent performance across three public cohorts and exhibited high sensitivity and specificity for 6, 12, and 24-month overall survival (OS) in receiver operating characteristic (ROC) curve analysis. It outperformed conventional clinical and molecular features. Low-risk samples showed a higher presence of cytolytic immune cells and enhanced immunogenic potential compared to high-risk samples. Additionally, we identified the small molecule compound UMI-77. The half-maximal inhibitory concentration (IC50) of UMI-77 was inversely related to the GMS. Notably, the AGS cell line, classified as high-risk, displayed greater sensitivity to UMI-77, whereas the MKN45 cell line, classified as low-risk, showed less sensitivity. Conclusion The GMS developed here can reliably predict survival benefit for gastrointestinal cancer patients on ICIs therapy.
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Affiliation(s)
- Bicheng Ye
- School of Clinical Medicine, Yangzhou Polytechnic College, Yangzhou, China
| | - Zhongyan Li
- Department of Geriatric Medicine, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huai'an, China
| | - Qiqi Wang
- Department of Gastroenterology, Wenzhou Central Hospital, Wenzhou, China
- Department of Gastroenterology, The Dingli Clinical College of Wenzhou Medical University, Wenzhou, China
- Department of Gastroenterology, The Second Afliated Hospital of Shanghai University, Wenzhou, China
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Wu Q, Lu M, Ouyang H, Zhou T, Lei J, Wang P, Wang W. CDKL3 is a promising biomarker for diagnosis and prognosis prediction in patients with hepatocellular carcinoma. Exp Biol Med (Maywood) 2024; 249:10106. [PMID: 38993199 PMCID: PMC11237920 DOI: 10.3389/ebm.2024.10106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 07/13/2024] Open
Abstract
Cyclin-dependent kinase-like 3 (CDKL3) has been identified as an oncogene in certain types of tumors. Nonetheless, its function in hepatocellular carcinoma (HCC) is poorly understood. In this study, we conducted a comprehensive analysis of CDKL3 based on data from the HCC cohort of The Cancer Genome Atlas (TCGA). Our analysis included gene expression, diagnosis, prognosis, functional enrichment, tumor microenvironment and metabolic characteristics, tumor burden, mRNA expression-based stemness, alternative splicing, and prediction of therapy response. Additionally, we performed a cell counting kit-8 assay, TdT-mediated dUTP nick-end Labeling staining, migration assay, wound healing assay, colony formation assay, and nude mouse experiments to confirm the functional relevance of CDKL3 in HCC. Our findings showed that CDKL3 was significantly upregulated in HCC patients compared to controls. Various bioinformatic analyses suggested that CDKL3 could serve as a potential marker for HCC diagnosis and prognosis. Furthermore, CDKL3 was found to be involved in various mechanisms linked to the development of HCC, including copy number variation, tumor burden, genomic heterogeneity, cancer stemness, and alternative splicing of CDKL3. Notably, CDKL3 was also closely correlated with tumor immune cell infiltration and the expression of immune checkpoint markers. Additionally, CDKL3 was shown to independently function as a risk predictor for overall survival in HCC patients by multivariate Cox regression analysis. Furthermore, the knockdown of CDKL3 significantly inhibited cell proliferation in vitro and in vivo, indicating its role as an oncogene in HCC. Taken together, our findings suggest that CDKL3 shows promise as a biomarker for the detection and treatment outcome prediction of HCC patients.
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Affiliation(s)
- Qingsi Wu
- Department of Blood Transfusion, Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Microbiology and Parasitology, Hefei, Anhui, China
| | - Mengran Lu
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Huijuan Ouyang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Tingting Zhou
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Jingyuan Lei
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Panpan Wang
- School of Public Health, Department of Hygiene Inspection and Quarantine, Anhui Medical University, Hefei, Anhui, China
| | - Wei Wang
- Department of Gastroenterology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui, China
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Wang X, Chen J, Li C, Liu Y, Chen S, Lv F, Lan K, He W, Zhu H, Xu L, Ma K, Guo H. Integrated bulk and single-cell RNA sequencing identifies an aneuploidy-based gene signature to predict sensitivity of lung adenocarcinoma to traditional chemotherapy drugs and patients' prognosis. PeerJ 2024; 12:e17545. [PMID: 38938612 PMCID: PMC11210463 DOI: 10.7717/peerj.17545] [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: 02/04/2024] [Accepted: 05/19/2024] [Indexed: 06/29/2024] Open
Abstract
Background Patients with lung adenocarcinoma (LUAD) often develop a poor prognosis. Currently, researches on prognostic and immunotherapeutic capacity of aneuploidy-related genes in LUAD are limited. Methods Genes related to aneuploidy were screened based on bulk RNA sequencing data from public databases using Spearman method. Next, univariate Cox and Lasso regression analyses were performed to establish an aneuploidy-related riskscore (ARS) model. Results derived from bioinformatics analysis were further validated using cellular experiments. In addition, typical LUAD cells were identified by subtype clustering, followed by SCENIC and intercellular communication analyses. Finally, ESTIMATE, ssGSEA and CIBERSORT algorithms were employed to analyze the potential relationship between ARS and tumor immune environment. Results A five-gene ARS signature was developed. These genes were abnormally high-expressed in LUAD cell lines, and in particular the high expression of CKS1B promoted the proliferative, migratory and invasive phenotypes of LUAD cell lines. Low ARS group had longer overall survival time, higher degrees of inflammatory infiltration, and could benefit more from receiving immunotherapy. Patients in low ASR group responded more actively to traditional chemotherapy drugs (Erlotinib and Roscovitine). The scRNA-seq analysis annotated 17 cell subpopulations into seven cell clusters. Core transcription factors (TFs) such as CREB3L1 and CEBPD were enriched in high ARS cell group, while TFs such as BCLAF1 and UQCRB were enriched in low ARS cell group. CellChat analysis revealed that high ARS cell groups communicated with immune cells via SPP1 (ITGA4-ITGB1) and MK (MDK-NCl) signaling pathways. Conclusion In this research, integrative analysis based on the ARS model provided a potential direction for improving the diagnosis and treatment of LUAD.
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Affiliation(s)
- Xiaobin Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
| | - Jiakuan Chen
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
| | - Chaofan Li
- Department of Thoracic Surgery, The 986 Military Medical Hospital of the Air Force, Xi’an, China
| | - Yufei Liu
- Department of Thoracic Surgery, The 986 Military Medical Hospital of the Air Force, Xi’an, China
| | - Shiqun Chen
- Thoracic Surgery, Weinan Central Hospital, Weinan, China
| | - Feng Lv
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
| | - Ke Lan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
| | - Wei He
- Department of Thoracic Surgery, The 986 Military Medical Hospital of the Air Force, Xi’an, China
| | - Hongsheng Zhu
- Thoracic Surgery, Shaanxi Chenggu County Hospital, Chenggu, China
| | - Liang Xu
- Thoracic Surgery, Shaanxi Chenggu County Hospital, Chenggu, China
| | - Kaiyuan Ma
- Thoracic Surgery, Shaanxi Chenggu County Hospital, Chenggu, China
| | - Haihua Guo
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
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Klockner TC, Campbell CS. Selection forces underlying aneuploidy patterns in cancer. Mol Cell Oncol 2024; 11:2369388. [PMID: 38919375 PMCID: PMC11197905 DOI: 10.1080/23723556.2024.2369388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Aneuploidy, the presence of an aberrant number of chromosomes, has been associated with tumorigenesis for over a century. More recently, advances in karyotyping techniques have revealed its high prevalence in cancer: About 90% of solid tumors and 50-70% of hematopoietic cancers exhibit chromosome gains or losses. When analyzed at the level of specific chromosomes, there are strong patterns that are observed in cancer karyotypes both pan-cancer and for specific cancer types. These specific aneuploidy patterns correlate strongly with outcomes for tumor initiation, progression, metastasis formation, immune evasion and resistance to therapeutic treatment. Despite their prominence, understanding the basis underlying aneuploidy patterns in cancer has been challenging. Advances in genetic engineering and bioinformatic analyses now offer insights into the genetic determinants of aneuploidy pattern selection. Overall, there is substantial evidence that expression changes of particular genes can act as the positive selective forces for adaptation through aneuploidy. Recent findings suggest that multiple genes contribute to the selection of specific aneuploid chromosomes in cancer; however, further research is necessary to identify the most impactful driver genes. Determining the genetic basis and accompanying vulnerabilities of specific aneuploidy patterns is an essential step in selectively targeting these hallmarks of tumors.
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Affiliation(s)
- Tamara C. Klockner
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Chromosome Biology, University of Vienna, Vienna, Austria
- A Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Christopher S. Campbell
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Chromosome Biology, University of Vienna, Vienna, Austria
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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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Xu M, Ma X, Wang Y, Yu Z, Zheng X, Dai H, Xue C. Developing a prognostic model for skin melanoma based on the persistent tumor mutation burden and determining IL17REL as a therapeutic target. J Cancer Res Clin Oncol 2024; 150:313. [PMID: 38900244 PMCID: PMC11189994 DOI: 10.1007/s00432-024-05843-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND One popular and well-established marker for the immune checkpoint blockade (ICB) response is tumor mutation burden (TMB). Persistent TMB (pTMB), a subset of TMB, provides a better indicator to predict patient ICB therapy outcomes, as shown by some studies. Immune checkpoint drugs have significantly changed how melanoma is treated in recent years. METHODS In this study, we integrated the TCGA-SKCM database and data of pTMB of TCGA from the paper that first mentioned pTMB and analyzed mutational and Immune characteristics associated with pTMB level in SKCM. Next, the predictive DEGs were identified the subgroups of pTMB by Cox regression and LASSO analyses to construct a pTMB-related signature. Finally, the expression and Biological functions of signature genes was detected, and further validated in vitro assay. RESULTS In the current research, we explored the mutational and immunological features related to the level of TMB in cutaneous melanoma (CM). The high-pTMB subgroup exhibited an increasing incidence of gene changes and higher levels of immune cell infiltration. Subsequently, we established a pTMB-related signature based on the predictive DEGs and found the biological features and immune-associated variables between two distinct risk groups. Lastly, the results of the clinical sample validation demonstrated that the expression of IL17REL was down-regulated in the collected samples of individuals with CM. The in vitro assay results indicated that IL17REL effectively suppressed the proliferation, clonality, and migration of CM cells. CONCLUSION In conclusion, we have developed a prediction model associated with TMB and subsequently validated the potential influence of IL17REL on Overall Survival (OS) in patients diagnosed with melanoma.
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Affiliation(s)
- Mingze Xu
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Xinyi Ma
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Yuchong Wang
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Ziqin Yu
- Department of Radiology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaoli Zheng
- Basic Medical School, Southwest Medical University, Luzhou, Sichuan, China
| | - Haiying Dai
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China.
| | - Chunyu Xue
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China.
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Pu Y, Yang G, Zhou Y, Pan X, Guo T, Chai X. The Macrophage migration inhibitory factor is a vital player in Pan-Cancer by functioning as a M0 Macrophage biomarker. Int Immunopharmacol 2024; 134:112198. [PMID: 38733827 DOI: 10.1016/j.intimp.2024.112198] [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: 02/22/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The role of the macrophage migration inhibitory factor (MIF) has recently attracted considerable attention in cancer research; nonetheless, the insights provided by current investigations remain constrained. Our main objective was to investigate its role and the latent mechanisms within the pan-cancer realm. METHODS We used comprehensive pan-cancer bulk sequencing data and online network tools to investigate the association between MIF expression and patient prognosis, genomic instability, cancer cell stemness, DNA damage repair, and immune infiltration. Furthermore, we validated the relationship between MIF expression and M0 macrophages using single-cell datasets, the SpatialDB database, and fluorescence staining. Additionally, we assessed the therapeutic response using the ROC plotter tool. RESULTS We observed the upregulation of MIF expression across numerous cancer types. Notably, elevated MIF levels were associated with a decline in genomic stability. We found a significant correlation between increased MIF expression and increased expression of mismatch repair genes, stemness features, and homologous recombination genes across diverse malignancies. Subsequently, through an analysis using ESTIMATE and cytokine results, we revealed the involvement of MIF in immune suppression. Then, we validated MIF as a hallmark of the M0 macrophages involved in tumor immunity. Our study suggests an association with other immune-inhibitory cellular populations and restraint of CD8 + T cells. In addition, we conducted a comparative analysis of MIF expression before and after treatment in three distinct sets of therapy responders and non-responders. Intriguingly, we identified notable disparities in MIF expression patterns in bladder urothelial carcinoma and ovarian cancer following particular therapeutic interventions. CONCLUSION Comprehensive pan-cancer analysis revealed notable enrichment of MIF within M0 macrophages, exerting a profound influence on tumor-associated immunosuppression and the intricate machinery of DNA repair.
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Affiliation(s)
- Yuting Pu
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guifang Yang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yang Zhou
- Department of Intensive Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaogao Pan
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tuo Guo
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangping Chai
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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24
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Torkildsen CF, Austdal M, Jarmund AH, Kleinmanns K, Lamark EK, Nilsen EB, Stefansson I, Sande RK, Iversen AC, Thomsen LCV, Bjørge L. New immune phenotypes for treatment response in high-grade serous ovarian carcinoma patients. Front Immunol 2024; 15:1394497. [PMID: 38947323 PMCID: PMC11211251 DOI: 10.3389/fimmu.2024.1394497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024] Open
Abstract
Despite advances in surgical and therapeutic approaches, high-grade serous ovarian carcinoma (HGSOC) prognosis remains poor. Surgery is an indispensable component of therapeutic protocols, as removal of all visible tumor lesions (cytoreduction) profoundly improves the overall survival. Enhanced predictive tools for assessing cytoreduction are essential to optimize therapeutic precision. Patients' immune status broadly reflects the tumor cell biological behavior and the patient responses to disease and treatment. Serum cytokine profiling is a sensitive measure of immune adaption and deviation, yet its integration into treatment paradigms is underexplored. This study is part of the IMPACT trial (NCT03378297) and aimed to characterize immune responses before and during primary treatment for HGSOC to identify biomarkers for treatment selection and prognosis. Longitudinal serum samples from 22 patients were collected from diagnosis until response evaluation. Patients underwent primary cytoreductive surgery or neoadjuvant chemotherapy (NACT) based on laparoscopy scoring. Twenty-seven serum cytokines analyzed by Bio-Plex 200, revealed two immune phenotypes at diagnosis: Immune High with marked higher serum cytokine levels than Immune Low. The immune phenotypes reflected the laparoscopy scoring and allocation to surgical treatment. The five Immune High patients undergoing primary cytoreductive surgery exhibited immune mobilization and extended progression-free survival, compared to the Immune Low patients undergoing the same treatment. Both laparoscopy and cytoreductive surgery induced substantial and transient changes in serum cytokines, with upregulation of the inflammatory cytokine IL-6 and downregulation of the multifunctional cytokines IP-10, Eotaxin, IL-4, and IL-7. Over the study period, cytokine levels uniformly decreased in all patients, leading to the elimination of the initial immune phenotypes regardless of treatment choice. This study reveals distinct pre-treatment immune phenotypes in HGSOC patients that might be informative for treatment stratification and prognosis. This potential novel biomarker holds promise as a foundation for improved assessment of treatment responses in patients with HGSOC. ClinicalTrials.gov Identifier: NCT03378297.
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Affiliation(s)
- Cecilie Fredvik Torkildsen
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marie Austdal
- Department of Research, Stavanger University Hospital, Stavanger, Norway
| | - Anders Hagen Jarmund
- Department of Clinical and Molecular Medicine, and Centre of Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Katrin Kleinmanns
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Eva Karin Lamark
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Elisabeth Berge Nilsen
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - Ingunn Stefansson
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Ragnar Kvie Sande
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ann-Charlotte Iversen
- Department of Clinical and Molecular Medicine, and Centre of Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Liv Cecilie Vestrheim Thomsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Line Bjørge
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
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25
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Sawant A, Shi F, Lopes EC, Hu Z, Abdelfattah S, Baul J, Powers J, Hinrichs CS, Rabinowitz JD, Chan CS, Lattime EC, Ganesan S, White E. Immune Checkpoint Blockade Delays Cancer and Extends Survival in Murine DNA Polymerase Mutator Syndromes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597960. [PMID: 38915517 PMCID: PMC11195045 DOI: 10.1101/2024.06.10.597960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mutations in polymerases Pold1 and Pole exonuclease domains in humans are associated with increased cancer incidence, elevated tumor mutation burden (TMB) and response to immune checkpoint blockade (ICB). Although ICB is approved for treatment of several cancers, not all tumors with elevated TMB respond. Here we generated Pold1 and Pole proofreading mutator mice and show that ICB treatment of mice with high TMB tumors did not improve survival as only a subset of tumors responded. Similarly, introducing the mutator alleles into mice with Kras/p53 lung cancer did not improve survival, however, passaging mutator tumor cells in vitro without immune editing caused rejection in immune-competent hosts, demonstrating the efficiency by which cells with antigenic mutations are eliminated. Finally, ICB treatment of mutator mice earlier, before observable tumors delayed cancer onset, improved survival, and selected for tumors without aneuploidy, suggesting the use of ICB in individuals at high risk for cancer prevention. Highlights Germline somatic and conditional Pold1 and Pole exonuclease domain mutations in mice produce a mutator phenotype. Spontaneous cancers arise in mutator mice that have genomic features comparable to human tumors with these mutations.ICB treatment of mutator mice with tumors did not improve survival as only a subset of tumors respond. Introduction of the mutator alleles into an autochthonous mouse lung cancer model also did not produce immunogenic tumors, whereas passaging mutator tumor cells in vitro caused immune rejection indicating efficient selection against antigenic mutations in vivo . Prophylactic ICB treatment delayed cancer onset, improved survival, and selected for tumors with no aneuploidy.
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26
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Berland L, Gabr Z, Chang M, Ilié M, Hofman V, Rignol G, Ghiringhelli F, Mograbi B, Rashidian M, Hofman P. Further knowledge and developments in resistance mechanisms to immune checkpoint inhibitors. Front Immunol 2024; 15:1384121. [PMID: 38903504 PMCID: PMC11188684 DOI: 10.3389/fimmu.2024.1384121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
The past decade has witnessed a revolution in cancer treatment, shifting from conventional drugs (chemotherapies) towards targeted molecular therapies and immune-based therapies, in particular immune-checkpoint inhibitors (ICIs). These immunotherapies release the host's immune system against the tumor and have shown unprecedented durable remission for patients with cancers that were thought incurable, such as metastatic melanoma, metastatic renal cell carcinoma (RCC), microsatellite instability (MSI) high colorectal cancer and late stages of non-small cell lung cancer (NSCLC). However, about 80% of the patients fail to respond to these immunotherapies and are therefore left with other less effective and potentially toxic treatments. Identifying and understanding the mechanisms that enable cancerous cells to adapt to and eventually overcome therapy can help circumvent resistance and improve treatment. In this review, we describe the recent discoveries on the onco-immunological processes which govern the tumor microenvironment and their impact on the resistance to PD-1/PD-L1 checkpoint blockade.
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Affiliation(s)
- Léa Berland
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Zeina Gabr
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
- School of Life Science, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michelle Chang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Marius Ilié
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Laboratory of Clinical and Experimental Pathology, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Pasteur Hospital, Université Côte d’Azur, Nice, France
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
- Hospital-Integrated Biobank (BB-0033–00025), Pasteur Hospital, Nice, France
| | - Véronique Hofman
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Laboratory of Clinical and Experimental Pathology, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Pasteur Hospital, Université Côte d’Azur, Nice, France
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
- Hospital-Integrated Biobank (BB-0033–00025), Pasteur Hospital, Nice, France
| | - Guylène Rignol
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Laboratory of Clinical and Experimental Pathology, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Pasteur Hospital, Université Côte d’Azur, Nice, France
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
| | - François Ghiringhelli
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
- Department of Biology and Pathology of Tumors, Georges-Francois Leclerc Cancer Center-UNICANCER, Dijon, France
| | - Baharia Mograbi
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
| | - Mohamad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Paul Hofman
- Inserm U1081 Institute for Research on Cancer and Aging, Nice (IRCAN) Team 4, Université Côte d’Azur, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Nice, France
- Laboratory of Clinical and Experimental Pathology, Institut Hospitalo Universitaire (IHU) RespirERA, Federation Hospitalo Universitaire (FHU) OncoAge, Pasteur Hospital, Université Côte d’Azur, Nice, France
- Institut Hospitalo Universitaire (IHU) RespirERA, Nice, France
- Hospital-Integrated Biobank (BB-0033–00025), Pasteur Hospital, Nice, France
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27
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Rustgi N, Wu S, Samec T, Walker P, Xiu J, Lou E, Goel S, Saeed A, Moy RH. Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:1399-1409. [PMID: 38717153 PMCID: PMC11146286 DOI: 10.1158/2767-9764.crc-23-0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/26/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024]
Abstract
Cyclin E overexpression as a result of CCNE1 amplification is a critical driver of genomic instability in gastric cancer, but its clinical implication is largely unknown. Thus, we integrated genomic, transcriptomic, and immune profiling analysis of 7,083 esophagogastric tumors and investigated the impact of CCNE1 amplification on molecular features and treatment outcomes. We identified CCNE1 amplification in 6.2% of esophageal adenocarcinoma samples, 7.0% of esophagogastric junction carcinoma, 4.2% of gastric adenocarcinoma samples, and 0.8% of esophageal squamous cell carcinoma. Metastatic sites such as lymph node and liver showed an increased frequency of CCNE1 amplification relative to primary tumors. Consistent with a chromosomal instability phenotype, CCNE1 amplification was associated with decreased CDH1 mutation and increased TP53 mutation and ERBB2 amplification. We observed no differences in immune biomarkers such as PD-L1 expression and tumor mutational burden comparing CCNE1-amplified and nonamplified tumors, although CCNE1 amplification was associated with changes in immune populations such as decreased B cells and increased M1 macrophages from transcriptional analysis. Real-world survival analysis demonstrated that patients with CCNE1-amplified gastric cancer had worse survival after trastuzumab for HER2-positive tumors, but better survival after immunotherapy. These data suggest that CCNE1-amplified gastric cancer has a distinct molecular and immune profile with important therapeutic implications, and therefore further investigation of CCNE1 amplification as a predictive biomarker is warranted. SIGNIFICANCE Advanced gastric cancer has a relatively dismal outcome with a 5-year overall survival of less than 10%. Furthermore, while comprehensive molecular analyses have established molecular subtypes within gastric cancers, biomarkers of clinical relevance in this cancer type are lacking. Overall, this study demonstrates that CCNE1 amplification is associated with a distinct molecular profile in gastric cancer and may impact response to therapy, including targeted therapy and/or immunotherapy.
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Affiliation(s)
- Naryan Rustgi
- Department of Surgery, Division of Surgical Sciences, Columbia University Irving Medical Center, New York, New York
| | - Sharon Wu
- Caris Life Sciences, Phoenix, Arizona
| | | | | | | | - Emil Lou
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Sanjay Goel
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Anwaar Saeed
- Department of Medicine, Division of Hematology and Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Ryan H. Moy
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, New York
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28
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Chang TG, Cao Y, Sfreddo HJ, Dhruba SR, Lee SH, Valero C, Yoo SK, Chowell D, Morris LGT, Ruppin E. LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features. NATURE CANCER 2024:10.1038/s43018-024-00772-7. [PMID: 38831056 DOI: 10.1038/s43018-024-00772-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/24/2024] [Indexed: 06/05/2024]
Abstract
Despite the revolutionary impact of immune checkpoint blockade (ICB) in cancer treatment, accurately predicting patient responses remains challenging. Here, we analyzed a large dataset of 2,881 ICB-treated and 841 non-ICB-treated patients across 18 solid tumor types, encompassing a wide range of clinical, pathologic and genomic features. We developed a clinical score called LORIS (logistic regression-based immunotherapy-response score) using a six-feature logistic regression model. LORIS outperforms previous signatures in predicting ICB response and identifying responsive patients even with low tumor mutational burden or programmed cell death 1 ligand 1 expression. LORIS consistently predicts patient objective response and short-term and long-term survival across most cancer types. Moreover, LORIS showcases a near-monotonic relationship with ICB response probability and patient survival, enabling precise patient stratification. As an accurate, interpretable method using a few readily measurable features, LORIS may help improve clinical decision-making in precision medicine to maximize patient benefit. LORIS is available as an online tool at https://loris.ccr.cancer.gov/ .
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Affiliation(s)
- Tian-Gen Chang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hannah J Sfreddo
- Department of Surgery and Cancer Immunogenomics Research Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saugato Rahman Dhruba
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Se-Hoon Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Cristina Valero
- Department of Surgery and Cancer Immunogenomics Research Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luc G T Morris
- Department of Surgery and Cancer Immunogenomics Research Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
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29
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Zhao Y, He S, Zhao M, Huang Q. Surviving the Storm: The Role of Poly- and Depolyploidization in Tissues and Tumors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306318. [PMID: 38629780 PMCID: PMC11199982 DOI: 10.1002/advs.202306318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 03/18/2024] [Indexed: 06/27/2024]
Abstract
Polyploidization and depolyploidization are critical processes in the normal development and tissue homeostasis of diploid organisms. Recent investigations have revealed that polyaneuploid cancer cells (PACCs) exploit this ploidy variation as a survival strategy against anticancer treatment and for the repopulation of tumors. Unscheduled polyploidization and chromosomal instability in PACCs enhance malignancy and treatment resistance. However, their inability to undergo mitosis causes catastrophic cellular death in most PACCs. Adaptive ploid reversal mechanisms, such as multipolar mitosis, centrosome clustering, meiosis-like division, and amitosis, counteract this lethal outcome and drive cancer relapse. The purpose of this work is to focus on PACCs induced by cytotoxic therapy, highlighting the latest discoveries in ploidy dynamics in physiological and pathological contexts. Specifically, by emphasizing the role of "poly-depolyploidization" in tumor progression, the aim is to identify novel therapeutic targets or paradigms for combating diseases associated with aberrant ploidies.
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Affiliation(s)
- Yucui Zhao
- Cancer CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai201620China
- Department of Radiation OncologySecond Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Sijia He
- Cancer CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai201620China
| | - Minghui Zhao
- Cancer CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai201620China
- Department of Radiation OncologyFirst Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
| | - Qian Huang
- Cancer CenterShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai201620China
- Shanghai Key Laboratory of Pancreatic DiseasesShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai201620China
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30
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Munro V, Kelly V, Messner CB, Kustatscher G. Cellular control of protein levels: A systems biology perspective. Proteomics 2024; 24:e2200220. [PMID: 38012370 DOI: 10.1002/pmic.202200220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.
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Affiliation(s)
- Victoria Munro
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Van Kelly
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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31
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Ibarra-Arellano MA, Caprio LA, Hada A, Stotzem N, Cai L, Shah S, Melms JC, Wünneman F, Izar B, Schapiro D. micronuclAI: Automated quantification of micronuclei for assessment of chromosomal instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595722. [PMID: 38854106 PMCID: PMC11160592 DOI: 10.1101/2024.05.24.595722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Chromosomal instability (CIN) is a hallmark of cancer that drives metastasis, immune evasion and treatment resistance. CIN results from chromosome mis-segregation events during anaphase, as excessive chromatin is packaged in micronuclei (MN), that can be enumerated to quantify CIN. Despite recent advancements in automation through computer vision and machine learning, the assessment of CIN remains a predominantly manual and time-consuming task, thus hampering important work in the field. Here, we present micronuclAI , a novel pipeline for automated and reliable quantification of MN of varying size, morphology and location from DNA-only stained images. In micronucleAI , single-cell crops are extracted from high-resolution microscopy images with the help of segmentation masks, which are then used to train a convolutional neural network (CNN) to output the number of MN associated with each cell. The pipeline was evaluated against manual single-cell level counts by experts and against routinely used MN ratio within the complete image. The classifier was able to achieve a weighted F1 score of 0.937 on the test dataset and the complete pipeline can achieve close to human-level performance on various datasets derived from multiple human and murine cancer cell lines. The pipeline achieved a root-mean-square deviation (RMSE) value of 0.0041, an R 2 of 0.87 and a Pearson's correlation of 0.938 on images obtained at 10X magnification. We tested the approach in otherwise isogenic cell lines in which we genetically dialed up or down CIN rates, and also on a publicly available image data set (obtained at 100X) and achieved an RMSE value of 0.0159, an R 2 of 0.90, and a Pearson's correlation of 0.951. Given the increasing interest in developing therapies for CIN-driven cancers, this method provides an important, scalable, and rapid approach to quantifying CIN on routinely obtained images. We release a GUI-implementation for easy access and utilization of the pipeline.
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32
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Hayes BH, Wang M, Zhu H, Phan SH, Dooling LJ, Andrechak JC, Chang AH, Tobin MP, Ontko NM, Marchena T, Discher DE. Chromosomal instability induced in cancer can enhance macrophage-initiated immune responses that include anti-tumor IgG. eLife 2024; 12:RP88054. [PMID: 38805560 PMCID: PMC11132682 DOI: 10.7554/elife.88054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
Solid tumors generally exhibit chromosome copy number variation, which is typically caused by chromosomal instability (CIN) in mitosis. The resulting aneuploidy can drive evolution and associates with poor prognosis in various cancer types as well as poor response to T-cell checkpoint blockade in melanoma. Macrophages and the SIRPα-CD47 checkpoint are understudied in such contexts. Here, CIN is induced in poorly immunogenic B16F10 mouse melanoma cells using spindle assembly checkpoint MPS1 inhibitors that generate persistent micronuclei and diverse aneuploidy while skewing macrophages toward a tumoricidal 'M1-like' phenotype based on markers and short-term anti-tumor studies. Mice bearing CIN-afflicted tumors with wild-type CD47 levels succumb similar to controls, but long-term survival is maximized by SIRPα blockade on adoptively transferred myeloid cells plus anti-tumor monoclonal IgG. Such cells are the initiating effector cells, and survivors make de novo anti-cancer IgG that not only promote phagocytosis of CD47-null cells but also suppress tumor growth. CIN does not affect the IgG response, but pairing CIN with maximal macrophage anti-cancer activity increases durable cures that possess a vaccination-like response against recurrence.
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Affiliation(s)
- Brandon H Hayes
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
- Bioengineering Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
| | - Mai Wang
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Hui Zhu
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Steven H Phan
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Lawrence J Dooling
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Jason C Andrechak
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
- Bioengineering Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
| | - Alexander H Chang
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Michael P Tobin
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
- Bioengineering Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
| | - Nicholas M Ontko
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Tristan Marchena
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn, University of PennsylvaniaPhiladelphhiaUnited States
- Molecular and Cell Biophysics Lab, University of PennsylvaniaPhiladelphiaUnited States
- Bioengineering Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
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33
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Li B, Jin K, Liu Z, Su X, Xu Z, Liu G, Xu J, Chang Y, Wang Y, Zhu Y, Xu L, Wang Z, Liu H, Zhang W. RAD51 Expression as a Biomarker to Predict Efficacy of Platinum-Based Chemotherapy and PD-L1 Blockade for Muscle-Invasive Bladder Cancer. J Immunother 2024:00002371-990000000-00105. [PMID: 38800996 DOI: 10.1097/cji.0000000000000525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 04/11/2024] [Indexed: 05/29/2024]
Abstract
RAD51, a key recombinase that catalyzes homologous recombination (HR), is commonly overexpressed in multiple cancers. It is curial for DNA damage repair (DDR) to maintain genomic integrity which could further determine the therapeutic response. Herein, we attempt to explore the clinical value of RAD51 in therapeutic guidance in muscle-invasive bladder cancer (MIBC). In this retrospective study, a total of 823 patients with MIBC were included. Zhongshan hospital (ZSHS) cohort (n=134) and The Cancer Genome Atlas-Bladder Cancer (TCGA-BLCA) cohort (n=391) were included for the investigation of chemotherapeutic response. The IMvigor210 cohort (n=298) was utilized to interrogate the predictive efficacy of RAD51 status to programmed cell death ligand-1 (PD-L1) blockade. In addition, the association of RAD51 with genomic instability and tumor immune contexture was investigated. Patients with RAD51 overexpression were more likely to benefit from both platinum-based chemotherapy and immunotherapy rather than RAD51-low patients. The TMB high PD-L1 high RAD51 high subgroup possessed the best clinical benefits from PD-L1 blockade. RAD51-high tumors featured by genomic instability were correlated to highly inflamed and immunogenic contexture with activated immunotherapeutic pathway in MIBC. RAD51 could serve as a prognosticator for treatment response to platinum-based chemotherapy and PD-L1 inhibitor in MIBC patients. Besides, it could also improve the predictive efficacy of TMB and PD-L1.
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Affiliation(s)
- Bingyu Li
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kaifeng Jin
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhaopei Liu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaohe Su
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ziyue Xu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ge Liu
- Department of Biochemistry and Molecular Biology, NHC Key Laboratory of Glycoconjugate Research, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jingtong Xu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuan Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yiwei Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Le Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zewei Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hailong Liu
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Chen J, Kaya NA, Zhang Y, Kendarsari RI, Sekar K, Lee Chong S, Seshachalam VP, Ling WH, Jin Phua CZ, Lai H, Yang H, Lu B, Lim JQ, Ma S, Chew SC, Chua KP, Santiago Alvarez JJ, Wu L, Ooi L, Yaw-Fui Chung A, Cheow PC, Kam JH, Wei-Chieh Kow A, Ganpathi IS, Bunchaliew C, Thammasiri J, Koh PS, Bee-Lan Ong D, Lim J, de Villa VH, Dela Cruz RD, Loh TJ, Wan WK, Leow WQ, Yang Y, Liu J, Skanderup AJ, Pang YH, Ting Soon GS, Madhavan K, Kiat-Hon Lim T, Bonney G, Goh BKP, Chew V, Dan YY, Toh HC, Sik-Yin Foo R, Tam WL, Zhai W, Kah-Hoe Chow P. A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and 'bad apple' effect on clinical trajectory. J Hepatol 2024:S0168-8278(24)00352-0. [PMID: 38782118 DOI: 10.1016/j.jhep.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) is a highly fatal cancer characterized by high intra-tumor heterogeneity (ITH). A panoramic understanding of its tumor evolution, in relation to its clinical trajectory, may provide novel prognostic and treatment strategies. METHODS Through the Asia-Pacific Hepatocellular Carcinoma trials group (NCT03267641), we recruited one of the largest prospective cohorts of patients with HCC, with over 600 whole genome and transcriptome samples from 123 treatment-naïve patients. RESULTS Using a multi-region sampling approach, we revealed seven convergent genetic evolutionary paths governed by the early driver mutations, late copy number variations and viral integrations, which stratify patient clinical trajectories after surgical resection. Furthermore, such evolutionary paths shaped the molecular profiles, leading to distinct transcriptomic subtypes. Most significantly, although we found the coexistence of multiple transcriptomic subtypes within certain tumors, patient prognosis was best predicted by the most aggressive cell fraction of the tumor, rather than by overall degree of transcriptomic ITH level - a phenomenon we termed the 'bad apple' effect. Finally, we found that characteristics throughout early and late tumor evolution provide significant and complementary prognostic power in predicting patient survival. CONCLUSIONS Taken together, our study generated a comprehensive landscape of evolutionary history for HCC and provides a rich multi-omics resource for understanding tumor heterogeneity and clinical trajectories. IMPACT AND IMPLICATIONS This prospective study, utilizing comprehensive multi-sector, multi-omics sequencing and clinical data from surgically resected hepatocellular carcinoma (HCC), reveals critical insights into the role of tumor evolution and intra-tumor heterogeneity (ITH) in determining the prognosis of HCC. These findings are invaluable for oncology researchers and clinicians, as they underscore the influence of distinct evolutionary paths and the 'bad apple' effect, where the most aggressive tumor fraction dictates disease progression. These insights not only enhance prognostic accuracy post-surgical resection but also pave the way for personalized treatment strategies tailored to specific tumor evolutionary and transcriptomic profiles. The coexistence of multiple subtypes within the same tumor prompts a re-appraisal of the utilities of depending on single samples to represent the entire tumor and suggests the need for clinical molecular imaging. This research thus marks a significant step forward in the clinical understanding and management of HCC, underscoring the importance of integrating tumor evolutionary dynamics and multi-omics biomarkers into therapeutic decision-making. CLINICAL TRIAL NUMBER NCT03267641 (Observational cohort).
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Affiliation(s)
- Jianbin Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore.
| | - Neslihan Arife Kaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | - Ying Zhang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Raden Indah Kendarsari
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Karthik Sekar
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Shay Lee Chong
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Veerabrahma Pratap Seshachalam
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Wen Huan Ling
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Hannah Lai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Hechuan Yang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Bingxin Lu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Cell & Developmental Biology, Division of Biosciences, Faculty of Life Sciences, Bloomsbury, London WC1E 6AP, UK
| | - Jia Qi Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Siming Ma
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Sin Chi Chew
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - Khi Pin Chua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jacob Josiah Santiago Alvarez
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Lingyan Wu
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore
| | - London Ooi
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Alexander Yaw-Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Peng Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Juinn Huar Kam
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Alfred Wei-Chieh Kow
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Iyer Shridhar Ganpathi
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Chairat Bunchaliew
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | | | - Peng Soon Koh
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H de Villa
- Department of Surgery and Center for Liver Disease Management and Transplantation, The Medical City, Pasig City, Metro Manila, Philippines
| | | | - Tracy Jiezhen Loh
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Wei Keat Wan
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Wei Qiang Leow
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Yi Yang
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China
| | - Jin Liu
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Yin Huei Pang
- Department of Pathology, National University Health System, Singapore 119074, Republic of Singapore
| | - Gwyneth Shook Ting Soon
- Department of Pathology, National University Health System, Singapore 119074, Republic of Singapore
| | - Krishnakumar Madhavan
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Tony Kiat-Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Republic of Singapore
| | - Glenn Bonney
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119228, Republic of Singapore
| | - Brian K P Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth Duke-NUS Academic Medical Centre, Singapore, Republic of Singapore
| | - Yock Young Dan
- Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Hospital, Singapore, Republic of Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Center Singapore, 169610 Singapore, Republic of Singapore
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Cardiovascular Research Institute, National University of Singapore, National University Healthcare System, Singapore 119228, Republic of Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Republic of Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore.
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, P.R. China.
| | - Pierce Kah-Hoe Chow
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Republic of Singapore; Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Republic of Singapore; SingHealth-Duke-NUS Academic Surgery Program, Duke-NUS Graduate Medical School, Singapore 169857, Republic of Singapore.
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35
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Huang M, Cha Z, Liu R, Lin M, Gafoor NA, Kong T, Ge F, Chen W. Enhancing immunotherapy outcomes by targeted remodeling of the tumor microenvironment via combined cGAS-STING pathway strategies. Front Immunol 2024; 15:1399926. [PMID: 38817608 PMCID: PMC11137211 DOI: 10.3389/fimmu.2024.1399926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) represent a groundbreaking advance in the treatment of malignancies such as melanoma and non-small cell lung cancer, showcasing substantial therapeutic benefits. Nonetheless, the efficacy of ICIs is limited to a small subset of patients, primarily benefiting those with "hot" tumors characterized by significant immune infiltration. The challenge of converting "cold" tumors, which exhibit minimal immune activity, into "hot" tumors to enhance their responsiveness to ICIs is a critical and complex area of current research. Central to this endeavor is the activation of the cGAS-STING pathway, a pivotal nexus between innate and adaptive immunity. This pathway's activation promotes the production of type I interferon (IFN) and the recruitment of CD8+ T cells, thereby transforming the tumor microenvironment (TME) from "cold" to "hot". This review comprehensively explores the cGAS-STING pathway's role in reconditioning the TME, detailing the underlying mechanisms of innate and adaptive immunity and highlighting the contributions of various immune cells to tumor immunity. Furthermore, we delve into the latest clinical research on STING agonists and their potential in combination therapies, targeting this pathway. The discussion concludes with an examination of the challenges facing the advancement of promising STING agonists in clinical trials and the pressing issues within the cGAS-STING signaling pathway research.
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Affiliation(s)
- Mingqing Huang
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Zhuocen Cha
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
- Guizhou Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guizhou, China
| | - Rui Liu
- Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Mengping Lin
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Naif Abdul Gafoor
- International Education School of Kunming Medical University, Kunming, China
| | - Tong Kong
- Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
| | - Fei Ge
- Department of Breast Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China
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Zhou H, Shen Y, Zheng G, Zhang B, Wang A, Zhang J, Hu H, Lin J, Liu S, Luan X, Zhang W. Integrating single-cell and spatial analysis reveals MUC1-mediated cellular crosstalk in mucinous colorectal adenocarcinoma. Clin Transl Med 2024; 14:e1701. [PMID: 38778448 PMCID: PMC11111627 DOI: 10.1002/ctm2.1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mucinous colorectal adenocarcinoma (MCA) is a distinct subtype of colorectal cancer (CRC) with the most aggressive pattern, but effective treatment of MCA remains a challenge due to its vague pathological characteristics. An in-depth understanding of transcriptional dynamics at the cellular level is critical for developing specialised MCA treatment strategies. METHODS We integrated single-cell RNA sequencing and spatial transcriptomics data to systematically profile the MCA tumor microenvironment (TME), particularly the interactome of stromal and immune cells. In addition, a three-dimensional bioprinting technique, canonical ex vivo co-culture system, and immunofluorescence staining were further applied to validate the cellular communication networks within the TME. RESULTS This study identified the crucial intercellular interactions that engaged in MCA pathogenesis. We found the increased infiltration of FGF7+/THBS1+ myofibroblasts in MCA tissues with decreased expression of genes associated with leukocyte-mediated immunity and T cell activation, suggesting a crucial role of these cells in regulating the immunosuppressive TME. In addition, MS4A4A+ macrophages that exhibit M2-phenotype were enriched in the tumoral niche and high expression of MS4A4A+ was associated with poor prognosis in the cohort data. The ligand-receptor-based intercellular communication analysis revealed the tight interaction of MUC1+ malignant cells and ZEB1+ endothelial cells, providing mechanistic information for MCA angiogenesis and molecular targets for subsequent translational applications. CONCLUSIONS Our study provides novel insights into communications among tumour cells with stromal and immune cells that are significantly enriched in the TME during MCA progression, presenting potential prognostic biomarkers and therapeutic strategies for MCA. KEY POINTS Tumour microenvironment profiling of MCA is developed. MUC1+ tumour cells interplay with FGF7+/THBS1+ myofibroblasts to promote MCA development. MS4A4A+ macrophages exhibit M2 phenotype in MCA. ZEB1+ endotheliocytes engage in EndMT process in MCA.
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Affiliation(s)
- Haiyang Zhou
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Yiwen Shen
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guangyong Zheng
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Beibei Zhang
- Department of DermatologyTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Anqi Wang
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Jing Zhang
- Department of PathologyChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hao Hu
- Department of PathologyChanghai HospitalNaval Medical UniversityShanghaiChina
| | - Jiayi Lin
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Sanhong Liu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Xin Luan
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- School of PharmacyNaval Medical UniversityShanghaiChina
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Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024; 56:900-912. [PMID: 38388848 PMCID: PMC11096114 DOI: 10.1038/s41588-024-01665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
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Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Wu Z, Dong Z, Luo J, Hu W, Tong Y, Gao X, Yao W, Tian H, Wang X. A comprehensive comparison of molecular and phenotypic profiles between hepatitis B virus (HBV)-infected and non-HBV-infected hepatocellular carcinoma by multi-omics analysis. Genomics 2024; 116:110831. [PMID: 38513875 DOI: 10.1016/j.ygeno.2024.110831] [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: 08/01/2023] [Revised: 11/22/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Hepatitis B virus (HBV) infection is a major etiology of hepatocellular carcinoma (HCC). An interesting question is how different are the molecular and phenotypic profiles between HBV-infected (HBV+) and non-HBV-infected (HBV-) HCCs? Based on the publicly available multi-omics data for HCC, including bulk and single-cell data, and the data we collected and sequenced, we performed a comprehensive comparison of molecular and phenotypic features between HBV+ and HBV- HCCs. Our analysis showed that compared to HBV- HCCs, HBV+ HCCs had significantly better clinical outcomes, higher degree of genomic instability, higher enrichment of DNA repair and immune-related pathways, lower enrichment of stromal and oncogenic signaling pathways, and better response to immunotherapy. Furthermore, in vitro experiments confirmed that HBV+ HCCs had higher immunity, PD-L1 expression and activation of DNA damage response pathways. This study may provide insights into the profiles of HBV+ and HBV- HCCs, and guide rational therapeutic interventions for HCC patients.
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Affiliation(s)
- Zijie Wu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Zehua Dong
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Weiwei Hu
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yue Tong
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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Loda A, Semeraro F, Parolini S, Ronca R, Rezzola S. Cancer stem-like cells in uveal melanoma: novel insights and therapeutic implications. Biochim Biophys Acta Rev Cancer 2024; 1879:189104. [PMID: 38701937 DOI: 10.1016/j.bbcan.2024.189104] [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: 02/14/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Uveal melanoma (UM) is the most common primary ocular tumor in the adult population. Even though these primary tumors are successfully treated in 90% of cases, almost 50% of patients ultimately develop metastasis, mainly in the liver, via hematological dissemination, with a median survival spanning from 6 to 12 months after diagnosis. In this context, chemotherapy regimens and molecular targeted therapies have demonstrated poor response rates and failed to improve survival. Among the multiple reasons for therapy failure, the presence of cancer stem-like cells (CSCs) represents the main cause of resistance to anticancer therapies. In the last few years, the existence of CSCs in UM has been demonstrated both in preclinical and clinical studies, and new molecular pathways and mechanisms have been described for this subpopulation of UM cells. Here, we will discuss the state of the art of CSC biology and their potential exploitation as therapeutic target in UM.
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Affiliation(s)
- Alessandra Loda
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesco Semeraro
- Eye Clinic, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Silvia Parolini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy; National Center for Gene Therapy and Drugs based on RNA Technology - CN3, Padova, Italy; Consorzio Interuniversitario per le Biotecnologie (CIB), Italy
| | - Roberto Ronca
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy; Consorzio Interuniversitario per le Biotecnologie (CIB), Italy
| | - Sara Rezzola
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
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Chen D, Liu P, Lu X, Li J, Qi D, Zang L, Lin J, Liu Y, Zhai S, Fu D, Weng Y, Li H, Shen B. Pan-cancer analysis implicates novel insights of lactate metabolism into immunotherapy response prediction and survival prognostication. J Exp Clin Cancer Res 2024; 43:125. [PMID: 38664705 PMCID: PMC11044366 DOI: 10.1186/s13046-024-03042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Immunotherapy has emerged as a potent clinical approach for cancer treatment, but only subsets of cancer patients can benefit from it. Targeting lactate metabolism (LM) in tumor cells as a method to potentiate anti-tumor immune responses represents a promising therapeutic strategy. METHODS Public single-cell RNA-Seq (scRNA-seq) cohorts collected from patients who received immunotherapy were systematically gathered and scrutinized to delineate the association between LM and the immunotherapy response. A novel LM-related signature (LM.SIG) was formulated through an extensive examination of 40 pan-cancer scRNA-seq cohorts. Then, multiple machine learning (ML) algorithms were employed to validate the capacity of LM.SIG for immunotherapy response prediction and survival prognostication based on 8 immunotherapy transcriptomic cohorts and 30 The Cancer Genome Atlas (TCGA) pan-cancer datasets. Moreover, potential targets for immunotherapy were identified based on 17 CRISPR datasets and validated via in vivo and in vitro experiments. RESULTS The assessment of LM was confirmed to possess a substantial relationship with immunotherapy resistance in 2 immunotherapy scRNA-seq cohorts. Based on large-scale pan-cancer data, there exists a notably adverse correlation between LM.SIG and anti-tumor immunity as well as imbalance infiltration of immune cells, whereas a positive association was observed between LM.SIG and pro-tumorigenic signaling. Utilizing this signature, the ML model predicted immunotherapy response and prognosis with an AUC of 0.73/0.80 in validation sets and 0.70/0.87 in testing sets respectively. Notably, LM.SIG exhibited superior predictive performance across various cancers compared to published signatures. Subsequently, CRISPR screening identified LDHA as a pan-cancer biomarker for estimating immunotherapy response and survival probability which was further validated using immunohistochemistry (IHC) and spatial transcriptomics (ST) datasets. Furthermore, experiments demonstrated that LDHA deficiency in pancreatic cancer elevated the CD8+ T cell antitumor immunity and improved macrophage antitumoral polarization, which in turn enhanced the efficacy of immunotherapy. CONCLUSIONS We unveiled the tight correlation between LM and resistance to immunotherapy and further established the pan-cancer LM.SIG, holds the potential to emerge as a competitive instrument for the selection of patients suitable for immunotherapy.
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Affiliation(s)
- Dongjie Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Pengyi Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xiongxiong Lu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Jingfeng Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Debin Qi
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Longjun Zang
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan, Shanxi, 030009, China
| | - Jiayu Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yihao Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Shuyu Zhai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Da Fu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Yuanchi Weng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Hongzhe Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 2024; 43:113988. [PMID: 38517886 PMCID: PMC11063629 DOI: 10.1016/j.celrep.2024.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
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Affiliation(s)
- Elena Kuzmin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.
| | | | | | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Kento T Abe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael Schwartz
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Joseph Del Corpo
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Dongmei Zou
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Genevieve Morin
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Alain Pacis
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Yang Yang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Constanza Martinez
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
| | - Jarrett Barber
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Mathieu Bourgey
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Anne-Marie Fortier
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada
| | - Peter G Davison
- Department of Surgery, McGill University, Montreal, QC H3G 1A4, Canada; McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Sloan Kettering Institute, New York City, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
| | - Sidong Huang
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics (C3G), McGill University, Montreal, QC H3A 0G1, Canada
| | - Peter Van Loo
- The Francis Crick Institute, NW1 1AT London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada.
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Lechner A, Kumbrink J, Walz C, Jung A, Baumeister P, Flach S. Molecular characterization of the evolution of premalignant lesions in the upper aerodigestive tract. Front Oncol 2024; 14:1364958. [PMID: 38706595 PMCID: PMC11067708 DOI: 10.3389/fonc.2024.1364958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Early relapse and development of metastatic disease are some of the primary reasons for the poor prognosis of patients with head and neck squamous cell carcinoma (HNSCC). HNSCC is a heterogeneous disease which may develop in large premalignant fields of genetically altered cells. Yet knowing which individuals will progress and develop clinically significant cancers during their lifetimes remains one of the most important challenges of reducing HNSCC morbidity and mortality. To further elucidate the molecular mechanisms, we performed a focused analysis of the genome and immune microenvironment from multiple, matched normal squamous tissue, premalignant lesions, as well as primary and recurrent tumors from seven patients with p16-negative HNSCC. Methods We performed targeted panel Next Generation Sequencing (161 genes) to analyze somatic variants from sequentially collected, matched formalin-fixed paraffin-embedded tissue (normal, premalignant, HNSCC) from two patients. These samples plus samples from five additional patients were analyzed with the Nanostring PanCancer Immune Panel. In addition, we performed shallow whole genome sequencing (0.5x coverage on average) on samples from three of these patients. Patients were, apart from one case, primarily treated with curative-intent surgery, and received subsequent adjuvant treatment, if indicated. Results The most frequently mutated genes were TP53 and NOTCH1. Other mutated genes included NOTCH3 and CDKN2A, among others. A significant number of mutations were private to dysplasia and invasive carcinoma, respectively, however, almost 20% were shared between them. Increasing genomic instability was observed when comparing histologically normal squamous mucosa with higher levels of dysplasia. High-grade dysplasia showed similarly rearranged genomes as invasive carcinoma. Pathways related to interferon alpha and gamma response were upregulated even in moderate dysplastic lesions with increasing expression in higher grades of dysplasia and carcinoma. SPINK5, a known tumor suppressor gene in HNSCC, was already downregulated in low-grade dysplastic lesions, indicating an early deactivation in the evolution of the disease. Conclusion Genomic alterations as well as aberrant immune gene expression can be observed early in the evolution of tumors of the upper aerodigestive tract, highlighting the potential for targeting early mechanisms of disease progression.
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Affiliation(s)
- Axel Lechner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-Universität (LMU) Munich University Hospital, Munich, Germany
| | - Jörg Kumbrink
- Department of Pathology, LMU Munich University Hospital, Munich, Germany
| | - Christoph Walz
- Department of Pathology, LMU Munich University Hospital, Munich, Germany
| | - Andreas Jung
- Department of Pathology, LMU Munich University Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-Universität (LMU) Munich University Hospital, Munich, Germany
| | - Susanne Flach
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-Universität (LMU) Munich University Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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Chen E, Zou Z, Wang R, Liu J, Peng Z, Gan Z, Lin Z, Liu J. Predictive value of a stemness-based classifier for prognosis and immunotherapy response of hepatocellular carcinoma based on bioinformatics and machine-learning strategies. Front Immunol 2024; 15:1244392. [PMID: 38694506 PMCID: PMC11061862 DOI: 10.3389/fimmu.2024.1244392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
Objective Significant advancements have been made in hepatocellular carcinoma (HCC) therapeutics, such as immunotherapy for treating patients with HCC. However, there is a lack of reliable biomarkers for predicting the response of patients to therapy, which continues to be challenging. Cancer stem cells (CSCs) are involved in the oncogenesis, drug resistance, and invasion, as well as metastasis of HCC cells. Therefore, in this study, we aimed to create an mRNA expression-based stemness index (mRNAsi) model to predict the response of patients with HCC to immunotherapy. Methods We retrieved gene expression and clinical data of patients with HCC from the GSE14520 dataset and the Cancer Genome Atlas (TCGA) database. Next, we used the "one-class logistic regression (OCLR)" algorithm to obtain the mRNAsi of patients with HCC. We performed "unsupervised consensus clustering" to classify patients with HCC based on the mRNAsi scores and stemness subtypes. The relationships between the mRNAsi model, clinicopathological features, and genetic profiles of patients were compared using various bioinformatic methods. We screened for differentially expressed genes to establish a stemness-based classifier for predicting the patient's prognosis. Next, we determined the effect of risk scores on the tumor immune microenvironment (TIME) and the response of patients to immune checkpoint blockade (ICB). Finally, we used qRT-PCR to investigate gene expression in patients with HCC. Results We screened CSC-related genes using various bioinformatics tools in patients from the TCGA-LIHC cohort. We constructed a stemness classifier based on a nine-gene (PPARGC1A, FTCD, CFHR3, MAGEA6, CXCL8, CABYR, EPO, HMMR, and UCK2) signature for predicting the patient's prognosis and response to ICBs. Further, the model was validated in an independent GSE14520 dataset and performed well. Our model could predict the status of TIME, immunogenomic expressions, congenic pathway, and response to chemotherapy drugs. Furthermore, a significant increase in the proportion of infiltrating macrophages, Treg cells, and immune checkpoints was observed in patients in the high-risk group. In addition, tumor cells in patients with high mRNAsi scores could escape immune surveillance. Finally, we observed that the constructed model had a good expression in the clinical samples. The HCC tumor size and UCK2 genes expression were significantly alleviated and decreased, respectively, by treatments of anti-PD1 antibody. We also found knockdown UCK2 changed expressions of immune genes in HCC cell lines. Conclusion The novel stemness-related model could predict the prognosis of patients and aid in creating personalized immuno- and targeted therapy for patients in HCC.
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Affiliation(s)
- Erbao Chen
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhilin Zou
- Department of Ophthalmology, Affiliated Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Rongyue Wang
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jie Liu
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhen Peng
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhe Gan
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zewei Lin
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jikui Liu
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
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Lim RJ, Salehi-Rad R, Tran LM, Oh MS, Dumitras C, Crosson WP, Li R, Patel TS, Man S, Yean CE, Abascal J, Huang Z, Ong SL, Krysan K, Dubinett SM, Liu B. CXCL9/10-engineered dendritic cells promote T cell activation and enhance immune checkpoint blockade for lung cancer. Cell Rep Med 2024; 5:101479. [PMID: 38518770 PMCID: PMC11031384 DOI: 10.1016/j.xcrm.2024.101479] [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: 08/11/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Immune checkpoint blockade (ICB) with PD-1/PD-L1 inhibition has revolutionized the treatment of non-small cell lung cancer (NSCLC). Durable responses, however, are observed only in a subpopulation of patients. Defective antigen presentation and an immunosuppressive tumor microenvironment (TME) can lead to deficient T cell recruitment and ICB resistance. We evaluate intratumoral (IT) vaccination with CXCL9- and CXCL10-engineered dendritic cells (CXCL9/10-DC) as a strategy to overcome resistance. IT CXCL9/10-DC leads to enhanced T cell infiltration and activation in the TME and tumor inhibition in murine NSCLC models. The antitumor efficacy of IT CXCL9/10-DC is dependent on CD4+ and CD8+ T cells, as well as CXCR3-dependent T cell trafficking from the lymph node. IT CXCL9/10-DC, in combination with ICB, overcomes resistance and establishes systemic tumor-specific immunity in murine models. These studies provide a mechanistic understanding of CXCL9/10-DC-mediated host immune activation and support clinical translation of IT CXCL9/10-DC to augment ICB efficacy in NSCLC.
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Affiliation(s)
- Raymond J Lim
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ramin Salehi-Rad
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Linh M Tran
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Michael S Oh
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Camelia Dumitras
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William P Crosson
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rui Li
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tejas S Patel
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha Man
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cara E Yean
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jensen Abascal
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - ZiLing Huang
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephanie L Ong
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kostyantyn Krysan
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Steven M Dubinett
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Bin Liu
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Lauss M, Phung B, Borch TH, Harbst K, Kaminska K, Ebbesson A, Hedenfalk I, Yuan J, Nielsen K, Ingvar C, Carneiro A, Isaksson K, Pietras K, Svane IM, Donia M, Jönsson G. Molecular patterns of resistance to immune checkpoint blockade in melanoma. Nat Commun 2024; 15:3075. [PMID: 38594286 PMCID: PMC11004175 DOI: 10.1038/s41467-024-47425-y] [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: 07/27/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.
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Affiliation(s)
- Martin Lauss
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Bengt Phung
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Troels Holz Borch
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Joan Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Kari Nielsen
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Dermatology, Skåne University Hospital and Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Christian Ingvar
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Ana Carneiro
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital Comprehensive Cancer Center, 22185, Lund, Sweden
| | - Karolin Isaksson
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Surgery, Kristianstad Hospital, 29133, Kristianstad, Sweden
| | - Kristian Pietras
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Göran Jönsson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden.
- Lund University Cancer Center, LUCC, Lund, Sweden.
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46
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Zhang Y, Li D. An original aneuploidy-related gene model for predicting lung adenocarcinoma survival and guiding therapy. Sci Rep 2024; 14:8135. [PMID: 38584220 PMCID: PMC10999435 DOI: 10.1038/s41598-024-58020-y] [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: 11/02/2023] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Aneuploidy is a hallmark of cancers, but the role of aneuploidy-related genes in lung adenocarcinoma (LUAD) and their prognostic value remain elusive. Gene expression and copy number variation (CNV) data were enrolled from TCGA and GEO database. Consistency clustering analysis was performed for molecular cluster. Tumor microenvironment was assessed by the xCell and ESTIMATE algorithm. Limma package was used for selecting differentially expressed genes (DEGs). LASSO and stepwise multivariate Cox regression analysis were used to establish an aneuploidy-related riskscore (ARS) signature. GDSC database was conducted to predict drug sensitivity. A nomogram was designed by rms R package. TCGA-LUAD patients were stratified into 3 clusters based on CNV data. The C1 cluster displayed the optimal survival advantage and highest inflammatory infiltration. Based on integrated intersecting DEGs, we constructed a 6-gene ARS model, which showed effective prediction for patient's survival. Drug sensitivity test predicted possible sensitive drugs in two risk groups. Additionally, the nomogram exhibited great predictive clinical treatment benefits. We established a 6-gene aneuploidy-related signature that could effectively predict the survival and therapy for LUAD patients. Additionally, the ARS model and nomogram could offer guidance for the preoperative estimation and postoperative therapy of LUAD.
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Affiliation(s)
- Yalei Zhang
- Department of Thoracic Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510032, China.
| | - Dongmei Li
- Department of Thoracic Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510032, China
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47
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Sali R, Jiang Y, Attaranzadeh A, Holmes B, Li R. Morphological diversity of cancer cells predicts prognosis across tumor types. J Natl Cancer Inst 2024; 116:555-564. [PMID: 37982756 PMCID: PMC10995848 DOI: 10.1093/jnci/djad243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Intratumor heterogeneity drives disease progression and treatment resistance, which can lead to poor patient outcomes. Here, we present a computational approach for quantification of cancer cell diversity in routine hematoxylin-eosin-stained histopathology images. METHODS We analyzed publicly available digitized whole-slide hematoxylin-eosin images for 2000 patients. Four tumor types were included: lung, head and neck, colon, and rectal cancers, representing major histology subtypes (adenocarcinomas and squamous cell carcinomas). We performed single-cell analysis on hematoxylin-eosin images and trained a deep convolutional autoencoder to automatically learn feature representations of individual cancer nuclei. We then computed features of intranuclear variability and internuclear diversity to quantify tumor heterogeneity. Finally, we used these features to build a machine-learning model to predict patient prognosis. RESULTS A total of 68 million cancer cells were segmented and analyzed for nuclear image features. We discovered multiple morphological subtypes of cancer cells (range = 15-20) that co-exist within the same tumor, each with distinct phenotypic characteristics. Moreover, we showed that a higher morphological diversity is associated with chromosome instability and genomic aneuploidy. A machine-learning model based on morphological diversity demonstrated independent prognostic values across tumor types (hazard ratio range = 1.62-3.23, P < .035) in validation cohorts and further improved prognostication when combined with clinical risk factors. CONCLUSIONS Our study provides a practical approach for quantifying intratumor heterogeneity based on routine histopathology images. The cancer cell diversity score can be used to refine risk stratification and inform personalized treatment strategies.
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Affiliation(s)
- Rasoul Sali
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuming Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Armin Attaranzadeh
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brittany Holmes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
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48
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Boruah N, Hoyos D, Moses R, Hausler R, Desai H, Le AN, Good M, Kelly G, Raghavakaimal A, Tayeb M, Narasimhamurthy M, Doucette A, Gabriel P, Feldman MJ, Park J, de Rodas ML, Schalper KA, Goldfarb SB, Nayak A, Levine AJ, Greenbaum BD, Maxwell KN. Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588009. [PMID: 38617260 PMCID: PMC11014613 DOI: 10.1101/2024.04.03.588009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Pathogenic germline TP53 alterations cause Li-Fraumeni Syndrome (LFS), and breast cancer is the most common cancer in LFS females. We performed first of its kind multimodal analysis of LFS breast cancer (LFS-BC) compared to sporadic premenopausal BC. Nearly all LFS-BC underwent biallelic loss of TP53 with no recurrent oncogenic variants except ERBB2 (HER2) amplification. Compared to sporadic BC, in situ and invasive LFS-BC exhibited a high burden of short amplified aneuploid segments (SAAS). Pro-apoptotic p53 target genes BAX and TP53I3 failed to be up-regulated in LFS-BC as was seen in sporadic BC compared to normal breast tissue. LFS-BC had lower CD8+ T-cell infiltration compared to sporadic BC yet higher levels of proliferating cytotoxic T-cells. Within LFS-BC, progression from in situ to invasive BC was marked by an increase in chromosomal instability with a decrease in proliferating cytotoxic T-cells. Our study uncovers critical events in mutant p53-driven tumorigenesis in breast tissue.
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Affiliation(s)
- Nabamita Boruah
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Renyta Moses
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ryan Hausler
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Heena Desai
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anh N Le
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Madeline Good
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gregory Kelly
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ashvathi Raghavakaimal
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Maliha Tayeb
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mohana Narasimhamurthy
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Abigail Doucette
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peter Gabriel
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael J. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Jinae Park
- Departments of Medicine and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Shari B. Goldfarb
- Departments of Medicine and Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical Center, New York, NY
| | - Anupma Nayak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | | | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Medical Center, New York, NY:
| | - Kara N. Maxwell
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA
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49
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Fan Q, Wang Y, Cheng J, Pan B, Zang X, Liu R, Deng Y. Single-cell RNA-seq reveals T cell exhaustion and immune response landscape in osteosarcoma. Front Immunol 2024; 15:1362970. [PMID: 38629071 PMCID: PMC11018946 DOI: 10.3389/fimmu.2024.1362970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Background T cell exhaustion in the tumor microenvironment has been demonstrated as a substantial contributor to tumor immunosuppression and progression. However, the correlation between T cell exhaustion and osteosarcoma (OS) remains unclear. Methods In our present study, single-cell RNA-seq data for OS from the GEO database was analysed to identify CD8+ T cells and discern CD8+ T cell subsets objectively. Subgroup differentiation trajectory was then used to pinpoint genes altered in response to T cell exhaustion. Subsequently, six machine learning algorithms were applied to develop a prognostic model linked with T cell exhaustion. This model was subsequently validated in the TARGETs and Meta cohorts. Finally, we examined disparities in immune cell infiltration, immune checkpoints, immune-related pathways, and the efficacy of immunotherapy between high and low TEX score groups. Results The findings unveiled differential exhaustion in CD8+ T cells within the OS microenvironment. Three genes related to T cell exhaustion (RAD23A, SAC3D1, PSIP1) were identified and employed to formulate a T cell exhaustion model. This model exhibited robust predictive capabilities for OS prognosis, with patients in the low TEX score group demonstrating a more favorable prognosis, increased immune cell infiltration, and heightened responsiveness to treatment compared to those in the high TEX score group. Conclusion In summary, our research elucidates the role of T cell exhaustion in the immunotherapy and progression of OS, the prognostic model constructed based on T cell exhaustion-related genes holds promise as a potential method for prognostication in the management and treatment of OS patients.
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Affiliation(s)
- Qizhi Fan
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiyan Wang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun Cheng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Boyu Pan
- Department of Orthopedics, Third Hospital of Changsha, Changsha, China
| | - Xiaofang Zang
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Renfeng Liu
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Youwen Deng
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
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50
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Li GX, Chang RZ, Liu TT, Jin GN, Lu K, Yong TY, Li Z, Liu JH, Zhang B, Zhang WG, Ding ZY. GRIN2A mutation is a novel indicator of stratifying beneficiaries of immune checkpoint inhibitors in multiple cancers. Cancer Gene Ther 2024; 31:586-598. [PMID: 38267623 DOI: 10.1038/s41417-024-00730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/26/2024]
Abstract
Glutamate-NMDAR receptors (GRINs) have been reported to influence cancer immunogenicity; however, the relationship between GRIN alterations and the response to immune checkpoint inhibitors (ICIs) has not been determined. This study combined clinical characteristics and mutational profiles from multiple cohorts to form a discovery cohort (n = 901). The aim of this study was to investigate the correlation between the mutation status of the GRIN gene and the response to ICI therapy. Additionally, an independent ICI-treated cohort from the Memorial Sloan Kettering Cancer Center (MSKCC, N = 1513) was used for validation. Furthermore, this study explored the associations between GRIN2A mutations and intrinsic and extrinsic immunity using multiomics analysis. In the discovery cohort, patients with GRIN2A-MUTs had improved clinical outcomes, as indicated by a higher objective response rate (ORR: 36.8% vs 25.8%, P = 0.020), durable clinical benefit (DCB: 55.2% vs 38.7%, P = 0.005), prolonged progression-free survival (PFS: HR = 0.65; 95% CI 0.49 to 0.87; P = 0.003), and increased overall survival (OS: HR = 0.67; 95% CI 0.50 to 0.89; P = 0.006). Similar results were observed in the validation cohort, in which GRIN2A-MUT patients exhibited a significant improvement in overall survival (HR = 0.66; 95% CI = 0.49 to 0.88; P = 0.005; adjusted P = 0.045). Moreover, patients with GRIN2A-MUTs exhibited an increase in tumor mutational burden, high expression of costimulatory molecules, increased activity of antigen-processing machinery, and infiltration of various immune cells. Additionally, gene sets associated with cell cycle regulation and the interferon response were enriched in GRIN2A-mutated tumors. In conclusion, GRIN2A mutation is a novel biomarker associated with a favorable response to ICIs in multiple cancers.
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Affiliation(s)
- Gan-Xun Li
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui-Zhi Chang
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tong-Tong Liu
- Department of Anesthesiology, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Guan-Nan Jin
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Kan Lu
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tu-Ying Yong
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430071, Hubei, China
| | - Zifu Li
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430071, Hubei, China
| | - Ji-Hong Liu
- Department and Institute of Urology, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wan-Guang Zhang
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Ze-Yang Ding
- Hepatic Surgery Center, and Hubei Key Laboratory of Hepato-Biliary-Pancreatic Diseases, National Medical Center for Major Public Health Events, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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