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Liu Y, Qi L, Ye B, Wang A, Lu J, Qu L, Luo P, Wang L, Jiang A. MOICS, a novel classier deciphering immune heterogeneity and aid precise management of clear cell renal cell carcinoma at multiomics level. Cancer Biol Ther 2024; 25:2345977. [PMID: 38659199 PMCID: PMC11057626 DOI: 10.1080/15384047.2024.2345977] [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: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
Recent studies have indicated that the tumor immune microenvironment plays a pivotal role in the initiation and progression of clear cell renal cell carcinoma (ccRCC). However, the characteristics and heterogeneity of tumor immunity in ccRCC, particularly at the multiomics level, remain poorly understood. We analyzed immune multiomics datasets to perform a consensus cluster analysis and validate the clustering results across multiple internal and external ccRCC datasets; and identified two distinctive immune phenotypes of ccRCC, which we named multiomics immune-based cancer subtype 1 (MOICS1) and subtype 2 (MOICS2). The former, MOICS1, is characterized by an immune-hot phenotype with poor clinical outcomes, marked by significant proliferation of CD4+ and CD8+ T cells, fibroblasts, and high levels of immune inhibitory signatures; the latter, MOICS2, exhibits an immune-cold phenotype with favorable clinical characteristics, characterized by robust immune activity and high infiltration of endothelial cells and immune stimulatory signatures. Besides, a significant negative correlation between immune infiltration and angiogenesis were identified. We further explored the mechanisms underlying these differences, revealing that negatively regulated endopeptidase activity, activated cornification, and neutrophil degranulation may promote an immune-deficient phenotype, whereas enhanced monocyte recruitment could ameliorate this deficiency. Additionally, significant differences were observed in the genomic landscapes between the subtypes: MOICS1 exhibited mutations in TTN, BAP1, SETD2, MTOR, MUC16, CSMD3, and AKAP9, while MOICS2 was characterized by notable alterations in the TGF-β pathway. Overall, our work demonstrates that multi-immune omics remodeling analysis enhances the understanding of the immune heterogeneity in ccRCC and supports precise patient management.
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Affiliation(s)
- Ying Liu
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Bicheng Ye
- School of Clinical Medicine, Medical College of Yangzhou Polytechnic College, Yangzhou, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Juan Lu
- Vocational Education Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
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Salihoglu R, Balkenhol J, Dandekar G, Liang C, Dandekar T, Bencurova E. Cat-E: A comprehensive web tool for exploring cancer targeting strategies. Comput Struct Biotechnol J 2024; 23:1376-1386. [PMID: 38596315 PMCID: PMC11001601 DOI: 10.1016/j.csbj.2024.03.024] [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: 01/27/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Identifying potential cancer-associated genes and drug targets from omics data is challenging due to its diverse sources and analyses, requiring advanced skills and large amounts of time. To facilitate such analysis, we developed Cat-E (Cancer Target Explorer), a novel R/Shiny web tool designed for comprehensive analysis with evaluation according to cancer-related omics data. Cat-E is accessible at https://cat-e.bioinfo-wuerz.eu/. Cat-E compiles information on oncolytic viruses, cell lines, gene markers, and clinical studies by integrating molecular datasets from key databases such as OvirusTB, TCGA, DrugBANK, and PubChem. Users can use all datasets and upload their data to perform multiple analyses, such as differential gene expression analysis, metabolic pathway exploration, metabolic flux analysis, GO and KEGG enrichment analysis, survival analysis, immune signature analysis, single nucleotide variation analysis, dynamic analysis of gene expression changes and gene regulatory network changes, and protein structure prediction. Cancer target evaluation by Cat-E is demonstrated here on lung adenocarcinoma (LUAD) datasets. By offering a user-friendly interface and detailed user manual, Cat-E eliminates the need for advanced computational expertise, making it accessible to experimental biologists, undergraduate and graduate students, and oncology clinicians. It serves as a valuable tool for investigating genetic variations across diverse cancer types, facilitating the identification of novel diagnostic markers and potential therapeutic targets.
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Affiliation(s)
- Rana Salihoglu
- Department of Bioinformatics, University of Wurzburg, 97074 Wurzburg, Germany
| | - Johannes Balkenhol
- Department of Bioinformatics, University of Wurzburg, 97074 Wurzburg, Germany
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University Hospital of Wurzburg, 97080 Wurzburg, Germany
| | - Gudrun Dandekar
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital of Wurzburg, 97080 Wurzburg, Germany
| | - Chunguang Liang
- Department of Bioinformatics, University of Wurzburg, 97074 Wurzburg, Germany
- Institute of Immunology, Jena University Hospital, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Wurzburg, 97074 Wurzburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, University of Wurzburg, 97074 Wurzburg, Germany
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Zhu Z, Cao H, Yan H, Liu H, Hong Z, Sun A, Liu T, Mao F. Prognostic iron-metabolism signature robustly stratifies single-cell characteristics of hepatocellular carcinoma. Comput Struct Biotechnol J 2024; 23:929-941. [PMID: 38375529 PMCID: PMC10875160 DOI: 10.1016/j.csbj.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Cancer immunotherapy has shown to be a promising method in treating hepatocellular carcinoma (HCC), but suboptimal responses in patients are attributed to cellular and molecular heterogeneity. Iron metabolism-related genes (IRGs) are important in maintaining immune system homeostasis and have the potential to help develop new strategies for HCC treatment. Herein, we constructed and validated the iron-metabolism gene prognostic index (IPX) using univariate Cox proportional hazards regression and LASSO Cox regression analysis, successfully categorizing HCC patients into two groups with distinct survival risks. Then, we performed single-sample gene set enrichment analysis, weighted correlation network analysis, gene ontology enrichment analysis, cellular lineage analysis, and SCENIC analysis to reveal the key determinants underlying the ability of this model based on bulk and single-cell transcriptomic data. We identified several driver transcription factors specifically activated in specific malignant cell sub-populations to contribute to the adverse survival outcomes in the IPX-high subgroup. Within the tumor microenvironment (TME), T cells displayed significant diversity in their cellular characteristics and experienced changes in their developmental paths within distinct clusters identified by IPX. Interestingly, the proportion of Treg cells was increased in the high-risk group compared with the low-risk group. These results suggest that iron-metabolism could be involved in reshaping the TME, thereby disrupting the cell cycle of immune cells. This study utilized IRGs to construct a novel and reliable model, which can be used to assess the prognosis of patients with HCC and further clarify the molecular mechanisms of IRGs in HCC at single-cell resolution.
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Affiliation(s)
- Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Huang Cao
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
| | - Hongyu Yan
- School of Medicine, Xiamen University, Xiamen, Fujian 361100, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Hanzhi Liu
- The Third Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Zaifa Hong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361103, China
| | - Anran Sun
- Oncology Research Center, Foresea Life Insurance Guangzhou General Hospital, Guangzhou, Guangdong 511300, China
- Research Center for Translational Medicine, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, China
| | - Tong Liu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
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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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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Ma S, Pan X, Gan J, Guo X, He J, Hu H, Wang Y, Ning S, Zhi H. DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma. Epigenetics 2024; 19:2318506. [PMID: 38439715 PMCID: PMC10936651 DOI: 10.1080/15592294.2024.2318506] [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: 07/26/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (CpGct) in glioma tissues. We identified eight prognosis-related CpGct to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight CpGct might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient's prognosis.
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Affiliation(s)
- Shuangyue Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Gan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaxin Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaheng He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoyu Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuncong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Southworth E, Thomson JP, Croy I, Churchman M, Arends MJ, Hollis RL, Gourley C, Herrington CS. Whole exome sequencing reveals diverse genomic relatedness between paired concurrent endometrial and ovarian carcinomas. Eur J Cancer 2024; 208:114205. [PMID: 38986422 DOI: 10.1016/j.ejca.2024.114205] [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: 05/13/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
INTRODUCTION Concurrent non-serous endometrial and ovarian tumours are often managed clinically as two separate primary tumours, but almost all exhibit evidence of a genomic relationship. METHODOLOGY This study investigates the extent of relatedness using whole exome sequencing, which was performed on paired non-serous endometrial and ovarian carcinomas from 27 patients with concurrent tumours in a cohort with detailed clinicopathological annotation. Four whole exome sequencing-derived parameters (mutation, mutational burden, mutational signatures and mutant allele tumour heterogeneity scores) were used to develop a novel unsupervised model for the assessment of genomic similarity to infer genomic relatedness of paired tumours. RESULTS This novel model demonstrated genomic relatedness across all four parameters in all tumour pairs. Mutations in PTEN, ARID1A, CTNNB1, KMT2D and PIK3CA occurred most frequently and 24 of 27 (89 %) tumour pairs shared identical mutations in at least one of these genes, with all pairs sharing mutations in a number of other genes. Ovarian endometriosis, CTNNB1 exon 3 mutation, and progression and death from disease were present across the similarity ranking. Mismatch repair deficiency was associated with less genomically similar pairs. DISCUSSION Although there was diversity across the cohort, the presence of genomic similarity in all paired tumours supports the hypothesis that concurrent non-serous endometrial and ovarian carcinomas are genomically related and may have arisen from a common origin.
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Affiliation(s)
- Emily Southworth
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - John P Thomson
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian Croy
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Mark J Arends
- Edinburgh Pathology, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert L Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - C Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Pathology, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
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Zhou X, Ying H, Sun Y, Zhang W, Luo P, Zhu S, Zhang J. Homologous recombination deficiency (HRD) is associated with better prognosis and possibly causes a non-inflamed tumour microenvironment in nasopharyngeal carcinoma. J Pathol Clin Res 2024; 10:e12391. [PMID: 39104056 DOI: 10.1002/2056-4538.12391] [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: 01/09/2024] [Revised: 06/18/2024] [Accepted: 06/30/2024] [Indexed: 08/07/2024]
Abstract
Homologous recombination deficiency (HRD) score is a reliable indicator of genomic instability. The significance of HRD in nasopharyngeal carcinoma (NPC), particularly its influence on prognosis and the immune microenvironment, has yet to be adequately explored. Understanding HRD status comprehensively can offer valuable insights for guiding precision treatment. We utilised three cohorts to investigate HRD status in NPC: the Zhujiang cohort from local collection and the Hong Kong (SRA288429) and Singapore (SRP035573) cohorts from public datasets. The GATK (genome analysis toolkit) best practice process was employed to investigate germline and somatic BRCA1/2 mutations and various bioinformatics tools and algorithms to examine the association between HRD status and clinical molecular characteristics. We found that individuals with a negative HRD status (no-HRD) exhibited a higher risk of recurrence [hazard ratio (HR), 1.43; 95% confidence interval (CI), 2.03-333.76; p = 0.012] in the Zhujiang cohort, whereas, in the Singapore cohort, they experienced a higher risk of mortality (HR, 26.04; 95% CI, 1.43-34.21; p = 0.016) compared with those in the HRD group. In vitro experiments demonstrated that NPC cells with BRCA1 knockdown exhibit heightened sensitivity to chemoradiotherapy. Furthermore, the HRD group showed significantly higher tumour mutational burden and tumour neoantigen burden levels than the no-HRD group. Immune infiltration analysis indicated that HRD tissues tend to have a non-inflamed tumour microenvironment. In conclusion, patients with HRD exhibit a comparatively favourable prognosis in NPC, possibly associated with a non-inflammatory immune microenvironment. These findings have positive implications for treatment stratification, enabling the selection of more precise and effective therapeutic approaches and aiding in the prediction of treatment response and prognosis to a certain extent.
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Affiliation(s)
- Xinyi Zhou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Haoxuan Ying
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Yujie Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Wenda Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Shuhan Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
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Liu S, Wang S, Guo J, Wang C, Zhang H, Lin D, Wang Y, Hu X. Crosstalk among disulfidptosis-related lncRNAs in lung adenocarcinoma reveals a correlation with immune profile and clinical prognosis. Noncoding RNA Res 2024; 9:772-781. [PMID: 38590434 PMCID: PMC10999374 DOI: 10.1016/j.ncrna.2024.03.006] [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: 12/17/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Disulfidptosis refers to a specific programmed cell death process characterized by the accumulation of disulfides. It has recently been reported in several cancers. However, the impact of disulfidptosis-related long non-coding RNAs (lncRNAs) on malignant tumors has remained largely unknown. In the present work, we screened prognostic disulfidptosis-related lncRNAs and studied their effects on lung adenocarcinoma. Relevant clinical data of lung adenocarcinoma cases were retrieved from The Cancer Genome Atlas (TCGA) database. RNA sequencing was used to identify differentially expressed disulfidptosis-related lncRNAs within lung adenocarcinoma. In addition, prognostic disulfidptosis-related lncRNAs were obtained through univariate Cox regression analysis. LASSO-COX was used to construct new disulfidptosis-related lncRNA signatures. Different statistical approaches were used to validate the practicability and accuracy of the disulfidptosis-related lncRNAs signatures. Furthermore, several bioinformatic approaches were used to study relevant heterogeneities in biological processes and pathways of diverse risk groups. Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) was conducted to analyze the expression of disulfidptosis-related lncRNAs. Finally, seven disulfidptosis-related lncRNA signatures were identified in lung adenocarcinoma cells. The prognosis prediction model constructed efficiently predicted patient survival. Subgroup analysis revealed significant differences in immune cell proportion, including T follicular helper cells and M0 macrophages. In addition, in vitro experimental results demonstrated significant differences in disulfidptosis-related lncRNAs. Altogether, the six disulfidptosis-related lncRNA signatures could serve as a potential prognostic biomarker for lung adenocarcinoma. Furthermore, these can be used as a prediction model in individualized immunotherapy for lung adenocarcinoma.
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Affiliation(s)
- Shifeng Liu
- Department of Interventional Medical Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Song Wang
- Department of Interventional Medical Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jian Guo
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Congxiao Wang
- Department of Interventional Medical Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hao Zhang
- Department of Interventional Medical Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dongliang Lin
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi'an, China
| | - Xiaokun Hu
- Department of Interventional Medical Center, The Affiliated Hospital of Qingdao University, Qingdao, China
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He Z, Chen M, Luo Z. Bioinformatics analysis of the tumor microenvironment in melanoma - Constructing a prognostic model based on CD8+ T cell-related genes: An observational study. Medicine (Baltimore) 2024; 103:e38924. [PMID: 39121331 PMCID: PMC11315512 DOI: 10.1097/md.0000000000038924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/21/2024] [Indexed: 08/11/2024] Open
Abstract
This research endeavor seeks to explore the microenvironment of melanoma tumors and construct a prognostic model by focusing on genes specific to CD8+ T cells. The single-cell sequencing data of melanoma underwent processing with the Seurat package, subsequent to which cell communication network analysis was conducted using the iTALK package and transcription factor analysis was performed using the SCENIC package. Univariate COX and LASSO regression analyses were utilized to pinpoint genes linked to the prognosis of melanoma patients, culminating in the creation of a prognostic model through multivariate COX analysis. The model was validated using the GSE65904 and GSE35640 datasets. Multi-omics analysis was conducted utilizing the maftools, limma, edgeR, ChAMP, and clusterProfiler packages. The examination of single-cell sequencing data revealed the presence of 8 cell types, with the transcription factors RFXAP, CLOCK, MGA, RBBP, and ZNF836 exhibiting notably high expression levels in CD8+ T cells as determined by the SCENIC package. Utilizing these transcription factors and their associated target genes, a prognostic model was developed through COX and LASSO analyses, incorporating the genes GPR171, FAM174A, and BPI. This study validated the model with independent datasets and conducted additional analysis involving multi-omics and immune infiltration to identify a more favorable prognosis for patients in the low-risk group. The findings provide valuable insights into the tumor microenvironment of melanoma and establish a reliable prognostic model. The integration of multi-omics and immune infiltration analyses enhances our understanding of the pathogenesis of melanoma. The identification of specific genes holds promise as potential biomarkers for individuals with melanoma, serving as important indicators for predicting patient outcomes and determining their response to immunotherapy.
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Affiliation(s)
- Zhenghao He
- Department of Plastic Surgery, the First Affiliated Hospital of Jinan University, Guangdong, Guangzhou, China
- Department of Plastic Surgery, Zhongshan City People’s Hospital, Guangdong, Zhongshan, China
| | - Manli Chen
- Department of Plastic Surgery, Zhongshan City People’s Hospital, Guangdong, Zhongshan, China
| | - Zhijun Luo
- Department of Plastic Surgery, Zhongshan City People’s Hospital, Guangdong, Zhongshan, China
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Wei C, Ma Y, Wang M, Wang S, Yu W, Dong S, Deng W, Bie L, Zhang C, Shen W, Xia Q, Luo S, Li N. Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census. NPJ Precis Oncol 2024; 8:176. [PMID: 39117688 PMCID: PMC11310399 DOI: 10.1038/s41698-024-00660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across nine cancer types and identified distinct monocyte/TAM composition patterns. Using spatial analysis from clinical study tissues, we assessed TAM functions in shaping the tumor microenvironment (TME) and influencing immunotherapy. Two specific TAM clusters (pro-inflammatory and pro-tumor) and four TME subtypes showed distinct immunological features, genomic profiles, immunotherapy responses, and cancer prognosis. Pro-inflammatory TAMs resided in immune-enriched niches with exhausted CD8+ T cells, while pro-tumor TAMs were restricted to niches associated with a T-cell-excluded phenotype and hypoxia. We developed a machine learning model to predict immune checkpoint blockade response by integrating TAMs and clinical data. Our study comprehensively characterizes the common features of TAMs and highlights their interaction with the TME.
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Affiliation(s)
- Chen Wei
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Yijie Ma
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Mengyu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Siyi Wang
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenyue Yu
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Shuailei Dong
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wenying Deng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Liangyu Bie
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chi Zhang
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Shen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Qingxin Xia
- Department of Pathology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Suxia Luo
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Ning Li
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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12
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Guan P, Chen J, Mo C, Fukawa T, Zhang C, Cai X, Li M, Hong JH, Chan JY, Ng CCY, Lee JY, Wong SF, Liu W, Zeng X, Wang P, Xiao R, Rajasegaran V, Myint SS, Lim AMS, Yeong JPS, Tan PH, Ong CK, Xu T, Du Y, Bai F, Yao X, Teh BT, Tan J. Comprehensive molecular characterization of collecting duct carcinoma for therapeutic vulnerability. EMBO Mol Med 2024:10.1038/s44321-024-00102-5. [PMID: 39122888 DOI: 10.1038/s44321-024-00102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 08/12/2024] Open
Abstract
Collecting duct carcinoma (CDC) is an aggressive rare subtype of kidney cancer with unmet clinical needs. Little is known about its underlying molecular alterations and etiology, primarily due to its rarity, and lack of preclinical models. This study aims to comprehensively characterize molecular alterations in CDC and identify its therapeutic vulnerabilities. Through whole-exome and transcriptome sequencing, we identified KRAS hotspot mutations (G12A/D/V) in 3/13 (23%) of the patients, in addition to known TP53, NF2 mutations. 3/13 (23%) patients carried a mutational signature (SBS22) caused by aristolochic acid (AA) exposures, known to be more prevalent in Asia, highlighting a geologically specific disease etiology. We further discovered that cell cycle-related pathways were the most predominantly dysregulated pathways. Our drug screening with our newly established CDC preclinical models identified a CDK9 inhibitor LDC000067 that specifically inhibited CDC tumor growth and prolonged survival. Our study not only improved our understanding of oncogenic molecular alterations of Asian CDC, but also identified cell-cycle machinery as a therapeutic vulnerability, laying the foundation for clinical trials to treat patients with such aggressive cancer.
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Affiliation(s)
- Peiyong Guan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jianfeng Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Chengqiang Mo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Tomoya Fukawa
- Department of Urology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Chao Zhang
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China
| | - Xiuyu Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Mei Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jing Han Hong
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Jing Yi Lee
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Suet Far Wong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Wei Liu
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Xian Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Peili Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Rong Xiao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Abner Ming Sun Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Luma Medical Centre, Singapore, Republic of Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Tao Xu
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Yiqing Du
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xin Yao
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China.
| | - Bin Tean Teh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Republic of Singapore.
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- Hainan Academy of Medical Science, Hainan Medical University, Haikou, PR China.
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13
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Wu Z, Zhang Y, Cheng Y, Li J, Li F, Wang C, Shi L, Qin G, Zhan W, Cai Y, Xie X, Ling J, Hu H, Zhang J, Deng Y. PD-1 blockade plus COX inhibitors in dMMR metastatic colorectal cancer: Clinical, genomic, and immunologic analyses from the PCOX trial. MED 2024; 5:998-1015.e6. [PMID: 38795703 DOI: 10.1016/j.medj.2024.05.002] [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: 12/15/2023] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND Approximately 20% of patients with DNA mismatch repair deficiency (dMMR) metastatic colorectal cancer do not respond to anti-programmed death-1 (PD-1) ligand therapy, and baseline biomarkers of response are lacking. METHODS We conducted a phase 2 study to evaluate the efficacy of cyclooxygenase (COX) inhibitors in combination with anti-PD-1 therapy in patients with dMMR metastatic colorectal cancer. The primary endpoint was objective response rate. The secondary endpoints included progression-free survival (PFS), overall survival (OS), disease control rate, duration of response, and safety. FINDINGS A total of 30 patients were enrolled, and the objective response rate was 73.3%, meeting the predefined endpoint of 68%. The median PFS and median OS were not reached at a median follow-up period of 50.8 months. Disease control was achieved in 28 patients (93.3%). The median duration of response was not reached. The combination was well tolerated. Multiomics analysis revealed that the antigen processing and presentation pathway was positively associated with treatment response and PFS. Higher TAPBP expression was predictive of better PFS (log-rank p = 0.003), and this prognostic significance was confirmed in an immunotherapy validation cohort. CONCLUSIONS Thus, COX inhibitors combined with PD-1 blockade may be effective and safe treatment options for patients with dMMR metastatic colorectal cancer, and TAPBP may serve as a biomarker for immune checkpoint inhibitor therapy (this study was registered at ClinicalTrials.gov: NCT03638297). FUNDING Funded by the National Natural Science Foundation of China (81974369) and the program of Guangdong Provincial Clinical Research Center for Digestive Diseases (2020B1111170004).
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Affiliation(s)
- Zehua Wu
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Yuanzhe Zhang
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Department of Radiology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yi Cheng
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Jianxia Li
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Fangqian Li
- Department of Radiology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Chao Wang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Lishuo Shi
- Clinical Research Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Ge Qin
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Weixiang Zhan
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Yue Cai
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaoyu Xie
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Jiayu Ling
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Huabin Hu
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Jianwei Zhang
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Yanhong Deng
- Department of Medical Oncology, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
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14
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Yang J, Zhang L, Zhu B, Wu H, Peng M. Immunogenomic profiles and therapeutic options of the pan-programmed cell death-related lncRNA signature for patients with bladder cancer. Sci Rep 2024; 14:18500. [PMID: 39122807 DOI: 10.1038/s41598-024-68859-w] [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: 03/28/2023] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Programmed cell death (PCD) is a process that eliminates infected, damaged, or possibly neoplastic cells to sustain homeostatic multicellular organisms. Although long noncoding RNAs (lncRNAs) are involved in various types of PCD and regulate tumor growth, invasion, and migration, the role of PCD-related lncRNAs in bladder cancer still lacks systematic exploration. In this research, we integrated multiple types of PCD as pan-PCD and identified eight pan-PCD-related lncRNAs (LINC00174, HCP5, HCG27, UCA1, SNHG15, GHRLOS, CYB561D2, and AGAP11). Then, we generated a pan-PCD-related lncRNA prognostic signature (PPlncPS) with excellent predictive power and reliability, which performed equally well in the E-MTAB-4321 cohort. In comparison with the low-PPlncPS score group, the high-PPlncPS score group had remarkably higher levels of angiogenesis, matrix, cancer-associated fibroblasts, myeloid cell traffic, and protumor cytokine signatures. In addition, the low-PPlncPS score group was positively correlated with relatively abundant immune cell infiltration, upregulated expression levels of immune checkpoints, and high tumor mutation burden (TMB). Immunogenomic profiles revealed that patients with both low PPlncPS scores and high TMB had the best prognosis and may benefit from immune checkpoint inhibitors. Furthermore, for patients with high PPlncPS scores, docetaxel, staurosporine, and luminespib were screened as potential therapeutic candidates. In conclusion, we generated a pan-PCD-related lncRNA signature, providing precise and individualized prediction for clinical prognosis and some new insights into chemotherapy and immune checkpoint inhibitor therapy for bladder cancer.
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Affiliation(s)
- Jia Yang
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Lusi Zhang
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Bin Zhu
- Department of Urology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Hongtao Wu
- Department of Urology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
| | - Mou Peng
- Department of Urology, the Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, 410011, Hunan, China.
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15
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Shelton V, Detroja R, Liu T, Isaev K, Silva A, Passerini V, Bakhtiari M, Calvente L, Hong M, He MY, Modi S, Hershenfeld SA, Ludvigsen M, Madsen C, Hamilton-Dutoit S, d'Amore FA, Brodtkorb M, Johnson NA, Baetz T, LeBrun D, Tobin JWD, Gandhi MK, Mungall AJ, Xu W, Ben-Neriah S, Steidl C, Delabie J, Tremblay-LeMay R, Jegede O, Weigert O, Kahl B, Evens AM, Kridel R. Identification of genetic subtypes in follicular lymphoma. Blood Cancer J 2024; 14:128. [PMID: 39112453 PMCID: PMC11306633 DOI: 10.1038/s41408-024-01111-w] [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: 02/28/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Follicular lymphoma (FL) exhibits considerable variability in biological features and clinical trajectories across patients. To dissect the diversity of FL, we utilized a Bernoulli mixture model to identify genetic subtypes in 713 pre-treatment tumor tissue samples. Our analysis revealed the existence of five subtypes with unique genetic profiles that correlated with clinicopathological characteristics. The clusters were enriched in specific mutations as follows: CS (CREBBP and STAT6), TT (TNFAIP3 and TP53), GM (GNA13 and MEF2B), Q (quiescent, for low mutation burden), and AR (mutations of mTOR pathway-related genes). The subtype Q was enriched for patients with stage I disease and associated with a lower proliferative history than the other subtypes. The AR subtype was unique in its enrichment for IgM-expressing FL cases and was associated with advanced-stage and more than 4 nodal sites. The existence of subtypes was validated in an independent cohort of 418 samples from the GALLIUM trial. Notably, patients assigned to the TT subtype consistently experienced inferior progression-free survival when treated with immunochemotherapy. Our findings offer insight into core pathways distinctly linked with each FL cluster and are expected to be informative in the era of targeted therapies.
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Affiliation(s)
- Victoria Shelton
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Rajesh Detroja
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Ting Liu
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Keren Isaev
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Anjali Silva
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Verena Passerini
- Department of Internal Medicine III, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
| | - Mehran Bakhtiari
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Lourdes Calvente
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Michael Hong
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Michael Y He
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | - Saloni Modi
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada
| | | | - Maja Ludvigsen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Charlotte Madsen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Francesco Annibale d'Amore
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Tara Baetz
- Department of Oncology, Queen's University, Kingston, ON, Canada
| | - David LeBrun
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Josh W D Tobin
- Mater Research University of Queensland, Brisbane, QLD, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Maher K Gandhi
- Mater Research University of Queensland, Brisbane, QLD, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | | | | | - Jan Delabie
- Laboratory and Medicine Program, University Health Network, Toronto, ON, Canada
| | | | | | - Oliver Weigert
- Department of Internal Medicine III, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brad Kahl
- Washington University, St. Louis, MO, USA
| | | | - Robert Kridel
- Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.
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16
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Zhang H, Sun L, Liu J, Wang J, Meng L, Gao Y, Li J, Zhou Q. Immune-related gene signature improves prognosis prediction in patients with breast cancer and associates it with tumor immunity and inflammatory response. BMC Womens Health 2024; 24:446. [PMID: 39113010 PMCID: PMC11304607 DOI: 10.1186/s12905-024-03289-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/01/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND The prognostic potential of immune-related genes, particularly immune checkpoint inhibitors (ICIs) and long non-coding RNAs (lncRNAs), is gaining attention for evaluating the prognosis of breast cancer patients. METHODS We analyzed 23 datasets to identify 15 ICI-related mRNAs and 5 immune-related lncRNAs, creating a robust immune score (IS). This score was used to classify patients into high and low IS groups and assess their survival outcomes. RESULTS Patients with high IS showed significantly poorer overall survival (OS) and progression-free survival (PFS) compared to those with low IS. Multivariate Cox regression analysis confirmed IS as an independent prognostic factor. Additionally, high IS was associated with higher mutation loads and neoantigen profiles, while low IS correlated with enhanced immune cell infiltration. CONCLUSIONS The immune score developed from ICI-related mRNAs and lncRNAs effectively predicts the prognosis of breast cancer patients and highlights the differential immune and inflammatory responses between patients with varying levels of immune score. This underscores the relevance of IS in guiding therapeutic decisions and tailoring patient management strategies in clinical settings.
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Affiliation(s)
- Haiping Zhang
- Department of Breast Surgery, Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Lu Sun
- Department of Chemoradiotherapy, Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Jingjing Liu
- Department of Chemoradiotherapy, Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Jing Wang
- Department of Breast Surgery, Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Lingchao Meng
- Department of Pathology, Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Yuan Gao
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei Province, China
| | - Jingwu Li
- Department of Breast Center, Tangshan People's Hospital, Tangshan, Hebei, 063001, China.
- Hebei Key Laboratory of Molecular Oncology, Tangshan, Hebei, 063001, China.
| | - Qi Zhou
- Department of Breast Surgery, Tangshan People's Hospital, Tangshan, Hebei, 063001, China.
- Hebei Key Laboratory of Molecular Oncology, Tangshan, Hebei, 063001, China.
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17
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Zhang S, Jiang Y, Shi L, Wei T, Lai Z, Feng X, Li S, Tang D. Identification and analysis of key genes related to efferocytosis in colorectal cancer. BMC Med Genomics 2024; 17:198. [PMID: 39107816 PMCID: PMC11304617 DOI: 10.1186/s12920-024-01967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
The impact of efferocytosis-related genes (ERGs) on the diagnosis of colorectal cancer (CRC) remains unclear. In this study, efferocytosis-associated biomarkers for the diagnosis of CRC were identified by integrating data from transcriptome sequencing and public databases. Finally, the expression of biomarkers was validated by real-time quantitative polymerase chain reaction (RT-qPCR). Our study may provide a reference for CRC diagnosis. BACKGROUND It has been shown that some efferocytosis related genes (ERGs) are associated with the development of cancer. However, it is still uncertain how ERGs may influence the diagnosis of colorectal cancer (CRC). METHODS In our study, the CRC cohorts were gained from transcriptome sequencing and the gene expression omnibus (GEO) database (GSE71187). Efferocytosis related biomarkers with diagnostic utility for CRC were identified through combining differentially expressed analysis, machine learning algorithms, and receiver operating characteristic (ROC) analysis. Then, infiltration abundance of immune cells between CRC and control was evaluated. The regulatory networks (including mRNA-miRNA-lncRNA and miRNA/transcription factors (TF)-mRNA networks) were created. Finally, the expression of biomarkers was validated via real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained. ELMO3 was highly expressed in CRC group, while P2RY12 and PDK4 was lowly expressed. Besides, the infiltrating abundance of 3 immune cells between CRC and control groups was significantly differential, namely activated CD4 memory T cells, macrophages M0, and resting mast cells. We then constructed a mRNA-miRNA-lncRNA network containing 3 mRNAs, 33 miRNAs, and 22 lncRNAs, and a miRNA/TF-mRNA network including 3 mRNAs, 33 miRNAs, and 7 TFs. Additionally, RT-qPCR results revealed that the expression trends of all biomarkers were consistent with the transcriptome sequencing data and GSE71187. CONCLUSION Taken together, this study provides three efferocytosis related biomarkers (ELMO3, P2RY12, and PDK4) for diagnosis of CRC, providing a scientific reference for further studies of CRC.
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Affiliation(s)
- Shengliang Zhang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Ying Jiang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Lei Shi
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Tianning Wei
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Zhiwen Lai
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Xuan Feng
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Shiyuan Li
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Detao Tang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China.
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Luo Z, Li Y, Xu B, Yu T, Luo M, You P, Niu X, Li J. Overexpression of ESYT3 improves radioimmune responses through activating cGAS-STING pathway in lung adenocarcinoma. Exp Hematol Oncol 2024; 13:77. [PMID: 39103908 DOI: 10.1186/s40164-024-00546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/26/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Radiotherapy can modulate systemic antitumor immunity, while immune status in the tumor microenvironment also influences the efficacy of radiotherapy, but relevant molecular mechanisms are poorly understood in lung adenocarcinoma (LUAD). METHODS In this study, we innovatively proposed a radiotherapy response classification for LUAD, and discovered ESYT3 served as a tumor suppressor and radioimmune response sensitizer. ESYT3 expression was measured both in radioresistant and radiosensitive LUAD tissues and cells. The influence of ESYT3 on radiotherapy sensitivity and resistance was then investigated. Interaction between ESYT3 and STING was evaluated through multiple immunofluorescent staining and coimmunoprecipitation, and downstream molecules were further analyzed. In vivo models were constructed to assess the combination treatment efficacy of ESYT3 overexpression with radiotherapy. RESULTS We found that radioresistant subtype presented immunosuppressive state and activation of DNA damage repair pathways than radiosensitive subtype. ESYT3 expression was remarkably attenuated both in radioresistant LUAD tissues and cells. Clinically, low ESYT3 expression was linked with radioresistance. Overexpression of ESYT3 enabled to alleviate radioresistance, and sensitize LUAD cells to DNA damage induced by irradiation. Mechanically, ESYT3 directly interacted with STING, and activated cGAS-STING signaling, subsequently increasing the generation of type I IFNs as well as downstream chemokines CCL5 and CXCL10, thus improving radioimmune responses. The combination treatment of ESYT3 overexpression with radiotherapy had a synergistic anticancer effect in vitro and in vivo. CONCLUSIONS In summary, low ESYT3 expression confers resistance to radiotherapy in LUAD, and its overexpression can improve radioimmune responses through activating cGAS-STING-dependent pathway, thus providing an alternative combination therapeutic strategy for LUAD patients.
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Affiliation(s)
- Zan Luo
- Department of Radiation Oncology, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China
- Jiangxi Key Laboratory of Oncology, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China
| | - Ying Li
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, Hubei, China
| | - Bin Xu
- Laboratory of Tumor Metastasis, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Health Committee Key (JHCK), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China.
| | - Tenghua Yu
- Department of Breast Surgery, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China
| | - Mingming Luo
- Jiangxi Clinical Research Center for Cancer, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China
| | - PeiMeng You
- Department of Radiation Oncology, Jiangxi Key Laboratory of Translational Cancer Research, Cancer Hospital of Nanchang University, Jiangxi Cancer Hospital of Nanchang University), Nanchang, Jiangxi, 330029, China
| | - Xing Niu
- Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, Hong Kong, Hong Kong, 999077, China.
- China Medical University, Shenyang, Liaoning, 110122, China.
| | - Junyu Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China.
- Jiangxi Key Laboratory of Oncology, The Second Affiliated Hospital of Nanchang Medical College), Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, China.
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Xu S, Cao L, Chen R, Ye C, Li Q, Jiang Q, Yan F, Wan M, Zhang X, Ruan J. Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma. Oncologist 2024; 29:e1061-e1072. [PMID: 38842680 PMCID: PMC11299938 DOI: 10.1093/oncolo/oyae132] [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: 07/20/2023] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Patients with intrahepatic cholangiocarcinoma (ICC) are prone to recurrence and poor survival. Targeted therapy related to isocitrate dehydrogenase (IDH) is an extremely important treatment. IDH1 and IDH2 mutations are generally thought to have similar effects on the tumor landscape. However, it is doubtful whether these 2 mutations have exactly the same effects on tumor cells and the tumor microenvironment. METHODS All collected tumor samples were subjected to simultaneous whole-exon sequencing and proteome sequencing. RESULTS IDH1 mutations accounted for 12.2%, and IDH2 mutations accounted for 5.5%, all missense mutations. Tumors with IDH mutations had lower proportions of KRAS and TP53 mutations. Mutated genes were obviously enriched in the kinase pathway in the tumors with IDH2 mutations. The signaling pathways were mainly enriched in the activation of cellular metabolic activities and an increase of inhibitory immune cells in the tumors with IDH mutations. Moreover, tumors had unique enrichment in DNA repair in IDH1 mutants and secretion of biological molecules in IDH2 mutants. Inhibitory immune cells might be more prominent in IDH2 mutants, and the expression of immune checkpoints PVR and HLA-DQB1 was more prominent in IDH1 mutants. IDH mutants were more related to metabolism-related and inflammation-immune response clusters, and some belonged to the DNA replication and repair cluster. CONCLUSIONS These results revealed the differential IDH1 and IDH2 mutation-related landscapes, and we have provided an important reference database to guide ICC treatment.
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Affiliation(s)
- Shuaishuai Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Linping Cao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, People’s Republic of China
| | - Ruyin Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Chanqi Ye
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Qiong Li
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Qi Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Feifei Yan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, and Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou, People’s Republic of China
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, People’s Republic of China
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Liang A, Wu Z, Zhuo T, Zhu Y, Li Z, Chen S, Dai L, Wang Y, Tan X, Chen M. TONSL promotes lung adenocarcinoma progression, immune escape and drug sensitivity. Clin Transl Oncol 2024:10.1007/s12094-024-03627-w. [PMID: 39097545 DOI: 10.1007/s12094-024-03627-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/19/2024] [Indexed: 08/05/2024]
Abstract
PURPOSE The tonsoku-like DNA repair protein (TONSL) encoded by the TONSL gene, located on chromosome 8q24.3, is crucial for repairing DNA double-strand breaks through homologous recombination. However, TONSL overexpression in lung adenocarcinoma (LUAD) promotes tumor development, leading to a poor prognosis. METHODS TONSL was verified as a reliable prognostic marker for LUAD using bioinformatics, and clinical features related to LUAD prognosis were screened from the TCGA database to establish the relationship between risk factors and TONSL expression. In addition, TONSL expression in normal and LUAD tissues was verified using real-time quantitative polymerase chain reaction and immunohistochemistry. To elucidate the possible functions of TONSL, TONSL-related differentially expressed genes were screened, and functional enrichment analysis was performed. Subsequently, siRNA was used to knock down TONSL expression in lung cancer cells for cytobehavioral experiments. The effects of TONSL expression on tumor immune escape were analyzed using the ESTIMATE algorithm and tumor immune-infiltration analysis. In addition, the half-maximal inhibitory concentration of LUAD with varying TONSL expression levels in response to first-line chemotherapeutic drugs and epidermal growth factor receptor-tyrosine kinase inhibitors was analyzed for drug sensitivity. RESULTS Up-regulation of TONSL in LUAD promotes the proliferation, migration, and invasion of lung cancer cells, thereby contributing to a poor prognosis. Furthermore, TONSL overexpression promotes immune escape and drug sensitivity in LUAD. CONCLUSION TONSL serves as a reliable prognostic marker for LUAD, and its up-regulation is associated with increased immune escape and drug sensitivity. These findings suggest that TONSL holds potential as a novel therapeutic target for LUAD.
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Affiliation(s)
- Anru Liang
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zuotao Wu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ting Zhuo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yongjie Zhu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zihao Li
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Sirong Chen
- Department of Radiotherapy, Guangxi Medical University Cancer Hospital, No. 71 Hedi Rd, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Lei Dai
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yongyong Wang
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiang Tan
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Mingwu Chen
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Xiao L, He R, Hu K, Song G, Han S, Lin J, Chen Y, Zhang D, Wang W, Peng Y, Zhang J, Yu P. Exploring a specialized programmed-cell death patterns to predict the prognosis and sensitivity of immunotherapy in cutaneous melanoma via machine learning. Apoptosis 2024; 29:1070-1089. [PMID: 38615305 DOI: 10.1007/s10495-024-01960-7] [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] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
The mortality and therapeutic failure in cutaneous melanoma (CM) are mainly caused by wide metastasis and chemotherapy resistance. Meanwhile, immunotherapy is considered a crucial therapy strategy for CM patients. However, the efficiency of currently available methods and biomarkers in predicting the response of immunotherapy and prognosis of CM is limited. Programmed cell death (PCD) plays a significant role in the occurrence, development, and therapy of various malignant tumors. In this research, we integrated fourteen types of PCD, multi-omics data from TCGA-SKCM and other cohorts in GEO, and clinical CM patients to develop our analysis. Based on significant PCD patterns, two PCD-related CM clusters with different prognosis, tumor microenvironment (TME), and response to immunotherapy were identified. Subsequently, seven PCD-related features, especially CD28, CYP1B1, JAK3, LAMP3, SFN, STAT4, and TRAF1, were utilized to establish the prognostic signature, namely cell death index (CDI). CDI accurately predicted the response to immunotherapy in both CM and other cancers. A nomogram with potential superior predictive ability was constructed, and potential drugs targeting CM patients with specific CDI have also been identified. Given all the above, a novel CDI gene signature was indicated to predict the prognosis and exploit precision therapeutic strategies of CM patients, providing unique opportunities for clinical intelligence and new management methods for the therapy of CM.
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Affiliation(s)
- Leyang Xiao
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
- The Second Clinical Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Ruifeng He
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
- The Second Clinical Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Kaibo Hu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
- The Second Clinical Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Gelin Song
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
- The Second Clinical Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Shengye Han
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
- The Second Clinical Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
| | - Jitao Lin
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Yixuan Chen
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, Hong Kong
| | - Wuming Wang
- Department of Thoracic Surgery, Jiangxi Provincial Chest Hospital, Nanchang, 330006, People's Republic of China
| | - Yating Peng
- Department of Dermatology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Jing Zhang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China.
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, 332000, People's Republic of China.
| | - Peng Yu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China.
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, 332000, People's Republic of China.
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22
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Zhu Y, Li Z, Wu Z, Zhuo T, Dai L, Liang G, Peng H, Lu H, Wang Y. MIS18A upregulation promotes cell viability, migration and tumor immune evasion in lung adenocarcinoma. Oncol Lett 2024; 28:376. [PMID: 38910901 PMCID: PMC11190817 DOI: 10.3892/ol.2024.14509] [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: 02/03/2024] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Lung adenocarcinoma (LUAD) presents a significant global health challenge owing to its poor prognosis and high mortality rates. Despite its involvement in the initiation and progression of a number of cancer types, the understanding of the precise impact of MIS18 kinetochore protein A (MIS18A) on LUAD remains incomplete. In the present study, the role of MIS18A in LUAD was investigated by analyzing the genomic and clinical data from multiple public datasets. The expression of MIS18A was validated using reverse transcription-quantitative polymerase chain reaction, and in vitro experiments involving small interfering RNA-induced downregulation of MIS18A in lung cancer cells were conducted to further explore its impact. These findings revealed that elevated MIS18A expression in LUAD was associated with advanced clinical features and poor prognosis. Functional analysis also revealed the role of MIS18A in regulating the cell cycle and immune-related pathways. Moreover, MIS18A altered the immune microenvironment in LUAD, influencing its response to immunotherapy and drug sensitivity. The results of the in vitro experiments indicated that suppression of MIS18A expression reduced the proliferative and migratory capacities of LUAD cells. In summary, MIS18A possesses potential as a biomarker and may serve as a possible therapeutic target for LUAD, with significant implications for tumor progression by influencing both cell cycle dynamics and immune infiltration.
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Affiliation(s)
- Yongjie Zhu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zihao Li
- Department of Thoracic Surgery, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi Zhuang Autonomous Region 545026, P.R. China
| | - Zuotao Wu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ting Zhuo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Lei Dai
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Guanbiao Liang
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Huajian Peng
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Honglin Lu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yongyong Wang
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Gong H, Zhang P, Liu Q, Tian Y, Chen F, Qian S, Tu C, Tan Y, Hu X, Zhang B. XRCC2 driven homologous recombination subtypes and therapeutic targeting in lung adenocarcinoma metastasis. NPJ Precis Oncol 2024; 8:169. [PMID: 39090304 PMCID: PMC11294482 DOI: 10.1038/s41698-024-00658-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is a leading cause of cancer mortality, with many patients facing poor prognosis, particularly those with metastatic or drug-resistant tumors. Homologous recombination genes (HRGs) are crucial in tumor progression and therapy resistance, but their clinical significance in LUAD is not well understood. In this study, we systematically characterize key HRGs in LUAD patients, identifying two distinct HR subtypes associated with different outcomes and biological functions. We establish a 5-gene scoring system (XRCC2, RAD51, BRCA1, FANCA, and CHEK1) that reliably predicts patient outcomes and immunotherapy responses in LUAD. Bioinformatics analysis and clinical validation highlight XRCC2 as a crucial biomarker in LUAD. Functional investigations through in vivo and in vitro experiments reveal the role of XRCC2 in promoting lung cancer migration and invasion. Mechanistically, XRCC2 stabilizes vimentin (VIM) protein expression through deubiquitylation. We predict c-MYC as a potential regulator of XRCC2 and demonstrate that inhibiting c-MYC with compound 10058-F4 reduces XRCC2 and VIM expression. Preclinical studies show the synergistic inhibition of metastasis in vivo when combining 10058-F4 with doxorubicin (Dox). Our findings present a potential personalized predictive tool for LUAD prognosis, identifying XRCC2 as a critical biomarker. The c-Myc-XRCC2-VIM axis emerges as a promising therapeutic target for overcoming lung metastasis. This study provides valuable insights into LUAD, proposing a prognostic tool for further clinical validation and unveiling a potential therapeutic strategy for combating lung metastasis by targeting c-Myc-XRCC2-VIM.
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Affiliation(s)
- Han Gong
- The 1st Department of Thoracic Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 4100013, China
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Peihe Zhang
- Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiang Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yuxuan Tian
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Fuxin Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Siyi Qian
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xingming Hu
- The 1st Department of Thoracic Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 4100013, China.
| | - Bin Zhang
- The 1st Department of Thoracic Surgery of Hunan Cancer Hospital & the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 4100013, China.
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha, China.
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Wang D, Zhang J, Wang J, Cai Z, Jin S, Chen G. Identification of collagen subtypes of gastric cancer for distinguishing patient prognosis and therapeutic response. CANCER INNOVATION 2024; 3:e125. [PMID: 38948250 PMCID: PMC11212290 DOI: 10.1002/cai2.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 07/02/2024]
Abstract
Background Gastric cancer is a highly heterogeneous disease, presenting a major obstacle to personalized treatment. Effective markers of the immune checkpoint blockade response are needed for precise patient classification. We, therefore, divided patients with gastric cancer according to collagen gene expression to indicate their prognosis and treatment response. Methods We collected data for 1250 patients with gastric cancer from four cohorts. For the TCGA-STAD cohort, we used consensus clustering to stratify patients based on expression levels of 44 collagen genes and compared the prognosis and clinical characteristics between collagen subtypes. We then identified distinct transcriptomic and genetic alteration signatures for the subtypes. We analyzed the associations of collagen subtypes with the responses to chemotherapy, immunotherapy, and targeted therapy. We also established a platform-independent collagen-subtype predictor. We verified the findings in three validation cohorts (GSE84433, GSE62254, and GSE15459) and compared the collagen subtyping method with other molecular subtyping methods. Results We identified two subtypes of gastric adenocarcinoma: a high-expression collagen subtype (CS-H) and a low-expression collagen subtype (CS-L). Collagen subtype was an independent prognostic factor, with better overall survival in the CS-L subgroup. The inflammatory response, angiogenesis, and phosphoinositide 3-kinase (PI3K)/Akt pathways were transcriptionally active in the CS-H subtype, while DNA repair activity was significantly greater in the CS-L subtype. PIK3CA was frequently amplified in the CS-H subtype, while PIK3C2A, PIK3C2G, and PIK3R1 were frequently deleted in the CS-L subtype. CS-H subtype tumors were more sensitive to fluorouracil, while CS-L subtype tumors were more sensitive to immune checkpoint blockade. CS-L subtype was predicted to be more sensitive to HER2-targeted drugs, and CS-H subtype was predicted to be more sensitive to vascular endothelial growth factor and PI3K pathway-targeting drugs. Collagen subtyping also has the potential to be combined with existing molecular subtyping methods for better patient classification. Conclusions We classified gastric cancers into two subtypes based on collagen gene expression and validated these subtypes in three validation cohorts. The collagen subgroups differed in terms of prognosis, clinical characteristics, transcriptome, and genetic alterations. The subtypes were closely related to patient responses to chemotherapy, immunotherapy, and targeted therapy.
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Affiliation(s)
- Di Wang
- Department of Molecular Pathology, Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouChina
| | - Jing Zhang
- Department of Pathology, Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouChina
| | - Jianchao Wang
- Department of Pathology, Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouChina
| | - Zhonglin Cai
- Department of UrologyGongli Hospital of Shanghai Pudong New AreaShanghaiChina
| | - Shanfeng Jin
- Department of Molecular Pathology, Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouChina
| | - Gang Chen
- Department of Pathology, Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouChina
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Wu W, Li A, He H, Ye S, Zhou Z, Quan JH, Tan W. Long noncoding RNA LINC01550 inhibits colorectal cancer malignancy by suppressing the Wnt/β-catenin signaling pathway. J Biochem Mol Toxicol 2024; 38:e23774. [PMID: 39041324 DOI: 10.1002/jbt.23774] [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: 02/21/2024] [Revised: 05/20/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024]
Abstract
Colorectal cancer (CRC) is a common gastrointestinal malignancy. Long noncoding RNAs (lncRNAs) are associated with the progression of various cancers, including CRC. Herein, we explored the function of lncRNA LINC01550 in CRC. LINC01550 expression in CRC was analyzed using The Cancer Genome Atlas (TCGA). The diagnostic value of LINC01550 was evaluated using ROC curves. The relationship between clinicopathological variables and LINC01550 expression was explored, and its prognostic value was assessed using Kaplan-Meier and Cox regression analyses. The relationship between LINC01550 expression and immune cell infiltration was analyzed using CIBERSORT. Tumor-associated mutations and drug sensitivity were compared between high and low LINC01550 expression groups. The effects of LINC01550 overexpression on CRC cells were investigated using CCK-8, flow cytometry, wound healing, Transwell, qRT-PCR, and western blot assays. LINC01550 was downregulated in CRC tissues, and the low expression of LINC01550 was correlated with advanced stage and metastasis. CRC patients with low LINC01550 expression had poorer overall survival. LINC01550 expression was an independent risk factor for CRC prognosis. APC and TP53 mutations were more frequent in the low LINC01550 expression group, while the high LINC01550 expression group was significantly more sensitive to 5-fluorouracil, irinotecan, trametinib, gemcitabine, rapamycin, and XAV939. LINC01550 overexpression suppressed the proliferation, migration, invasion, and epithelial-mesenchymal transition of HCT-116 and HT-29 cells and promoted apoptosis. LINC01550 exerted these effects by inhibiting Wnt/β-catenin signaling. Our results suggest LINC01550 as a diagnostic and prognostic predictor in CRC that acts as a tumor suppressor and a potential therapeutic target.
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Affiliation(s)
- Weiyun Wu
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Aiting Li
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Huanjin He
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Shicai Ye
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhuliang Zhou
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Juan-Hua Quan
- Laboratory of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wenkai Tan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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Nagelberg AL, Sihota TS, Chuang YC, Shi R, Chow JLM, English J, MacAulay C, Lam S, Lam WL, Lockwood WW. Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response. Br J Cancer 2024; 131:534-550. [PMID: 38890444 PMCID: PMC11300780 DOI: 10.1038/s41416-024-02755-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: 09/20/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Identification of driver mutations and development of targeted therapies has considerably improved outcomes for lung cancer patients. However, significant limitations remain with the lack of identified drivers in a large subset of patients. Here, we aimed to assess the genomic landscape of lung adenocarcinomas (LUADs) from individuals without a history of tobacco use to reveal new genetic drivers of lung cancer. METHODS Integrative genomic analyses combining whole-exome sequencing, copy number, and mutational information for 83 LUAD tumors was performed and validated using external datasets to identify genetic variants with a predicted functional consequence and assess association with clinical outcomes. LUAD cell lines with alteration of identified candidates were used to functionally characterize tumor suppressive potential using a conditional expression system both in vitro and in vivo. RESULTS We identified 21 genes with evidence of positive selection, including 12 novel candidates that have yet to be characterized in LUAD. In particular, SNF2 Histone Linker PHD RING Helicase (SHPRH) was identified due to its frequency of biallelic disruption and location within the familial susceptibility locus on chromosome arm 6q. We found that low SHPRH mRNA expression is associated with poor survival outcomes in LUAD patients. Furthermore, we showed that re-expression of SHPRH in LUAD cell lines with inactivating alterations for SHPRH reduces their in vitro colony formation and tumor burden in vivo. Finally, we explored the biological pathways associated SHPRH inactivation and found an association with the tolerance of LUAD cells to DNA damage. CONCLUSIONS These data suggest that SHPRH is a tumor suppressor gene in LUAD, whereby its expression is associated with more favorable patient outcomes, reduced tumor and mutational burden, and may serve as a predictor of response to DNA damage. Thus, further exploration into the role of SHPRH in LUAD development may make it a valuable biomarker for predicting LUAD risk and prognosis.
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Affiliation(s)
- Amy L Nagelberg
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tianna S Sihota
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yu-Chi Chuang
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Justine L M Chow
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - John English
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Calum MacAulay
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada.
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
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Liu C, Liu L. Identification and immunoassay of prognostic genes associated with the complement system in acute myeloid leukemia. J Formos Med Assoc 2024; 123:904-915. [PMID: 38341328 DOI: 10.1016/j.jfma.2024.01.024] [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: 09/21/2023] [Revised: 01/12/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Studies have associated the development of pulmonary leukemia with the activation of the complement system. However, the roles and mechanisms of complement system-related genes (CSRGs) in acute myeloid leukemia (AML) have not been investigated extensively. This study used The Cancer Genome Atlas (TCGA)-AML and GSE37642 datasets. Differentially expressed CSRGs (CSRDEGs) were identified by overlapping genes differentially expressed between the high and low CSRG score groups and key module genes identified in a weighted gene co-expression network analysis. Univariate and multivariate Cox analyses identified CSRG-related biomarkers, which were used to build a prognostic model. After gene set enrichment analysis (GSEA), immune-related and drug-sensitivity analyses were performed in the high- and low-risk groups. Four prognosis-related biomarkers were identified and used to develop a prognostic model: MEOX2, IGFBP5, CH25H, and RAB3B. The model's performance was verified in a test cohort (a subset of samples from the TCGA-AML dataset) and a validation cohort (GSE37642). The GSEA revealed that the high-risk group was mainly enriched for Golgi organization and cytokine-cytokine receptor interactions, and the low-risk group was mainly enriched in the hedgehog signaling pathway and spliceosome. Lastly, two immune cells were found to show differential infiltration between risk groups, which correlated with the risk scores. M1 macrophage infiltration was significantly positively correlated with RAB3B expression. Sensitivity to 36 drugs differed significantly between risk groups. This study screened four CSRG-related biomarkers (MEOX2, IGFBP5, CH25H, and RAB3B) to provide a basis for predicting AML prognosis.
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Affiliation(s)
- Chen Liu
- Department of Hematology, First Affiliated Hospital of Chongqing Medical University, ChongQing, 400016, China.
| | - Lin Liu
- Department of Hematology, First Affiliated Hospital of Chongqing Medical University, ChongQing, 400016, China.
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Sun X, Li J, Gao X, Huang Y, Pang Z, Lv L, Li H, Liu H, Zhu L. Disulfidptosis‑related lncRNA prognosis model to predict survival therapeutic response prediction in lung adenocarcinoma. Oncol Lett 2024; 28:342. [PMID: 38855504 PMCID: PMC11157670 DOI: 10.3892/ol.2024.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/19/2024] [Indexed: 06/11/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer, and disulfidptosis is a newly discovered mechanism of programmed cell death. However, the effects of disulfidptosis-related lncRNAs (DR-lncRNAs) in LUAD have yet to be fully elucidated. The aim of the present study was to identify and validate a novel lncRNA-based prognostic marker that was associated with disulfidptosis. RNA-sequencing and associated clinical data were obtained from The Cancer Genome Atlas database. Univariate Cox regression and lasso algorithm analyses were used to identify DR-lncRNAs and to establish a prognostic model. Kaplan-Meier curves, receiver operating characteristic curves, principal component analysis, Cox regression, nomograms and calibration curves were used to assess the reliability of the prognostic model. Functional enrichment analysis, immune infiltration analysis, somatic mutation analysis, tumor microenvironment and drug predictions were applied to the risk model. Reverse transcription-quantitative PCR was subsequently performed to validate the mRNA expression levels of the lncRNAs in normal cells and tumor cells. These analyses enabled a DR-lncRNA prognosis signature to be constructed, consisting of nine lncRNAs; U91328.1, LINC00426, MIR1915HG, TMPO-AS1, TDRKH-AS1, AL157895.1, AL512363.1, AC010615.2 and GCC2-AS1. This risk model could serve as an independent prognostic tool for patients with LUAD. Numerous immune evaluation algorithms indicated that the low-risk group may exhibit a more robust and active immune response against the tumor. Moreover, the tumor immune dysfunction exclusion algorithm suggested that immunotherapy would be more effective in patients in the low-risk group. The drug-sensitivity results showed that patients in the high-risk group were more sensitive to treatment with crizotinib, erlotinib or savolitinib. Finally, the expression levels of AL157895.1 were found to be lower in A549. In summary, a novel DR-lncRNA signature was constructed, which provided a new index to predict the efficacy of therapeutic interventions and the prognosis of patients with LUAD.
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Affiliation(s)
- Xiaoming Sun
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Jia Li
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Xuedi Gao
- Department of Ophthamology, Jinan Mingshui Eye Hospital, Jinan, Shandong 250200, P.R. China
| | - Yubin Huang
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Zhanyue Pang
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Lin Lv
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Hao Li
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Haibo Liu
- Department of Thoracic Surgery, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Liangming Zhu
- Department of Thoracic Surgery, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
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29
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Liang P, Peng M, Tao J, Wang B, Wei J, Lin L, Cheng B, Xiong S, Li J, Li C, Yu Z, Li C, Wang J, Li H, Chen Z, Fan J, Liang W, He J. Development of a genome atlas for discriminating benign, preinvasive, and invasive lung nodules. MedComm (Beijing) 2024; 5:e644. [PMID: 39036344 PMCID: PMC11258453 DOI: 10.1002/mco2.644] [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: 12/26/2023] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/23/2024] Open
Abstract
To tackle misdiagnosis in lung cancer screening with low-dose computed tomography (LDCT), we aimed to compile a genome atlas for differentiating benign, preinvasive, and invasive lung nodules and characterize their molecular pathogenesis. We collected 432 lung nodule tissue samples from Chinese patients, spanning benign, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IA). We performed comprehensive sequencing, examining somatic variants, gene expressions, and methylation levels. Our findings uncovered EGFR and TP53 mutations as key drivers in - early lung cancer development, with EGFR mutation frequency increasing with disease progression. Both EGFR mutations and EGF/EGFR hypo-methylation activated the EGFR pathway, fueling cancer growth. Transcriptome analysis identified four lung nodule subtypes (G1-4) with distinct molecular features and immune cell infiltrations: EGFR-driven G1, EGFR/TP53 co-mutation G2, inflamed G3, stem-like G4. Estrogen/androgen response was associated with the EGFR pathway, proposing a new therapy combining tyrosine kinase inhibitors with antiestrogens. Preinvasive nodules exhibited stem cell pathway enrichment, potentially hindering invasion. Epigenetic regulation of various genes was essential for lung cancer initiation and development. This study provides insights into the molecular mechanism of neoplastic progression and identifies potential diagnostic biomarkers and therapeutic targets for lung cancer.
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Affiliation(s)
- Peng Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Minhua Peng
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinsheng Tao
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Bo Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinwang Wei
- Department of Data ScienceGenomicare Biotechnology (Shanghai) Co., Ltd.ShanghaiChina
- Department of Data ScienceShanghai CreateCured Biotechnology Co., Ltd.ShanghaiChina
| | - Lixuan Lin
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Bo Cheng
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Shan Xiong
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianfu Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Caichen Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Ziwen Yu
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Chunyan Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jun Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Hui Li
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Zhiwei Chen
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- AnchorDx Inc.FremontCaliforniaUSA
| | - Jian‐Bing Fan
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- Department of PathologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianxing He
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
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30
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Hwang HW, Shin HT, An HY, Byun JW. Genomic progression for local invasion of cutaneous squamous cell carcinoma from the superficial to the deep portion. Int J Cancer 2024; 155:532-544. [PMID: 38739001 DOI: 10.1002/ijc.34952] [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: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. While many treatments exist, our understanding of its genomic progression, especially from the epidermis to the deep dermis, remains limited. This study aims to identify genetic mutations associated with the progression of cSCC into the deep dermis, providing insights into its aggressive behavior and high-risk features. We performed high-depth whole-exome sequencing on 12 cSCC tissues, along with paired normal tissues from six patients, using microdissection techniques. The mutational analysis focused on identifying alterations enriched during cSCC progression. Gene Ontology enrichment analysis, immunohistochemical assays, and external single-cell RNA data were utilized for validation. A total of 8863 non-synonymous somatic mutations were identified in 4092 genes across the superficial and deep portions of cSCCs. Analysis of deep portion mutations revealed a significant correlation with gene ontology biological processes, particularly cell junction organization, and cell-cell adhesion. Clonal mutations in these processes were more prevalent in the deep portions, indicating their impact on the cSCC mutation landscape. Genetic evolution analysis identified 29 causal genes associated with dermal invasion in cSCC. We highlight somatic mutations in cSCC, revealing heterogeneity between superficial and deep regions. Altered genes in cell junction organization and cell-cell adhesion emerged as pivotal in dermal invasion. We identified 29 causal genes primarily in deep tumor regions. Our findings emphasize analyzing multiple tumor regions to capture varied mutational landscapes. These insights advance our understanding of cSCC progression, emphasizing genetic and cellular changes during tumor evolution.
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Affiliation(s)
- Hye Won Hwang
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), Inha University School of Medicine, Incheon, Republic of Korea
| | - Hye Young An
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Ji Won Byun
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
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31
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Abulimiti M, Jia ZY, Wu Y, Yu J, Gong YH, Guan N, Xiong DQ, Ding N, Uddin N, Wang J. Exploring and clinical validation of prognostic significance and therapeutic implications of copper homeostasis-related gene dysregulation in acute myeloid leukemia. Ann Hematol 2024; 103:2797-2826. [PMID: 38879648 DOI: 10.1007/s00277-024-05841-6] [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: 05/09/2024] [Accepted: 06/08/2024] [Indexed: 07/28/2024]
Abstract
The patterns and biological functions of copper homeostasis-related genes (CHRGs) in acute myeloid leukemia (AML) remain unclear. We explored the patterns and biological functions of CHRGs in AML. Using independent cohorts, including TCGA-GTEx, GSE114868, GSE37642, and clinical samples, we identified 826 common differentially expressed genes. Specifically, 12 cuproptosis-related genes (e.g., ATP7A, ATP7B) were upregulated, while 17 cuproplasia-associated genes (e.g., ATOX1, ATP7A) were downregulated in AML. We used LASSO-Cox, Kaplan-Meier, and Nomogram analyses to establish prognostic risk models, effectively stratifying patients with AML into high- and low-risk groups. Subgroup analysis revealed that high-risk patients exhibited poorer overall survival and involvement in fatty acid metabolism, apoptosis, and glycolysis. Immune infiltration analysis indicated differences in immune cell composition, with notable increases in B cells, cytotoxic T cells, and memory T cells in the low-risk group, and increased monocytes and neutrophils in the high-risk group. Single-cell sequencing analysis corroborated the expression characteristics of critical CHRGs, such as MAPK1 and ATOX1, associated with the function of T, B, and NK cells. Drug sensitivity analysis suggested potential therapeutic agents targeting copper homeostasis, including Bicalutamide and Sorafenib. PCR validation confirmed the differential expression of 4 cuproptosis-related genes (LIPT1, SLC31A1, GCSH, and PDHA1) and 9 cuproplasia-associated genes (ATOX1, CCS, CP, MAPK1, SOD1, COA6, PDK1, DBH, and PDE3B) in AML cell line. Importantly, these genes serve as potential biomarkers for patient stratification and treatment. In conclusion, we shed light on the expression patterns and biological functions of CHRGs in AML. The developed risk models provided prognostic implications for patient survival, offering valuable information on the regulatory characteristics of CHRGs and potential avenues for personalized treatment in AML.
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Affiliation(s)
| | - Zheng-Yi Jia
- School of Pharmacy, Xinjiang Medical University, Urumqi, 830011, China
| | - Yun Wu
- Department of General Medicine, The First Affiliated Hospital of the Xinjiang Medical University, Urumqi, 830011, China
| | - Jing Yu
- Department of Teaching and Research, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Yue-Hong Gong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Na Guan
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Dai-Qin Xiong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nan Ding
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Jie Wang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China.
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Quan S, Li N, Lian S, Wang Y, Liu Y, Liu J, Zhang Z, Gao D, Li Y. SLC4A4 as a novel biomarker involved in immune system response and lung adenocarcinoma progression. Int Immunopharmacol 2024; 140:112756. [PMID: 39083932 DOI: 10.1016/j.intimp.2024.112756] [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: 05/07/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Altered expression and activity of solute carrier family 4 member 4 (SLC4A4) could affect the growth, survival and metastasis of tumor cells. Currently, the role of SLC4A4 in lung adenocarcinoma (LUAD) immunotherapy and prognosis was not entirely clear. METHODS We analyzed SLC4A4 expression in LUAD tissues and cell lines using quantitative reverse transcription-polymerase chain reaction, Western blotting, and immunohistochemistry. The effects of SLC4A4 overexpression on angiogenesis, cell migration, invasion, and epithelial-mesenchymal transition were examined. Public databases helped construct a risk model evaluating SLC4A4's expression on LUAD prognosis and immunotherapy response. Additionally, a xenograft model, flow cytometry, and enzyme-linked immunosorbent assay further explored SLC4A4's role in tumor immune microenvironment infiltration. RESULTS Upregulation of SLC4A4 promoted apoptosis in the LUAD cell line and significantly inhibited the migration and invasive ability of cancer cells (P<0.01). A total of 10 key genes (including SIGLEC6, RHOV, PIR, MOB3B, MIR3135B, LPAR6, KRT8, ITGA2, CPS1, and C6) were screened according to SLC4A4 expression, immune score and stromal score, and a prognostic model with good outcome was constructed (AUC values of which in the training cohort at 1,3, and 5 years reached 0.73, 0.73, and 0.72, respectively). Importantly, we demonstrated that high expression of SLC4A4 was able to increase the proliferation level and cytokine secretion of CD8+ T cells for the purpose of promoting the immune system response to LUAD. CONCLUSION Our study revealed that SLC4A4 can serve as a prognostic indicator for LUAD, providing new insights into the treatment and diagnosis of LUAD.
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Affiliation(s)
- Siyu Quan
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Na Li
- Nephrology Department, Jinan Zhangqiu District People's Hospital, Jinan 250200, China
| | - Shihai Lian
- Out-patient Department, Zaozhuang Municipal Hospital, Zaozhuang 277102, China
| | - Yuanyuan Wang
- The Department of Hospital Infection, Jinan Fifth People's Hospital, Jinan 250022, China
| | - Yang Liu
- Thoracic Surgery, PLA 80th Group Army Hospital, Weifang 261011, China
| | - Jianbo Liu
- Department of Thoracic Surgery, The Fourth People's Hospital of Heze, Heze 274100, China
| | - Zewei Zhang
- Department of Thoracic Surgery, Gaoqing County People's Hospital, Gaoqing 256399, China
| | - Dejun Gao
- Department of Thoracic Surgery, The Second People's Hospital of Liaocheng, Liaocheng 252600, China
| | - Yun Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.
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Fridland S, Kim HS, Chae YK. Differential impact of intratumor heterogeneity (ITH) on survival outcomes in early-stage lung squamous and adenocarcinoma based on tumor mutational burden (TMB). Transl Lung Cancer Res 2024; 13:1481-1494. [PMID: 39118891 PMCID: PMC11304137 DOI: 10.21037/tlcr-24-226] [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: 03/20/2024] [Accepted: 06/06/2024] [Indexed: 08/10/2024]
Abstract
Background Molecular biomarkers are reshaping patient stratification and treatment decisions, yet their precise use and best implementation remain uncertain. Intratumor heterogeneity (ITH), an area of increasing research interest with prognostic value across various conditions, lacks defined clinical relevance in certain non-small cell lung cancer (NSCLC) subtypes. Exploring the relationship between ITH and tumor mutational burden (TMB) is crucial, as their interplay might reveal distinct patient subgroups. This study evaluates how the ITH-TMB dynamic affects prognosis across the two main histological subtypes of NSCLC, squamous cell and adenocarcinoma, with a specific focus on early-stage cases to address their highly unmet clinical needs. Methods We stratify a cohort of 741 early-stage NSCLC patients from The Cancer Genome Atlas (TCGA) based on ITH and TMB and evaluate differences in clinical outcomes. Additionally, we compare driver mutations and the tumor microenvironment (TME) between high and low ITH groups. Results In lung squamous cell carcinoma (LUSC), high ITH predicts an extended progression-free survival (PFS) (median: 21 vs. 14 months, P=0.01), while in lung adenocarcinoma (LUAD), high ITH predicts a reduced PFS (median: 15 vs. 20 months, P=0.04). This relationship is driven by the low TMB subset of patients. Additionally, we found that CD8 T cells were enriched in better-performing subgroups, regardless of histologic subtype or ITH status. Conclusions There are significant differences in clinical outcomes, driver mutations, and the TME between high and low ITH groups among early-stage NSCLC patients. These differences may have treatment implications, necessitating further validation in other NSCLC datasets.
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Affiliation(s)
- Stanislav Fridland
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hye Sung Kim
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Young Kwang Chae
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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Ordi O, Saco A, Peñuelas N, Blanco-Irazuegui O, Del Pino M, Carreras-Dieguez N, Marimon L, Rodrigo-Calvo MT, Morató A, Sisuashvili L, Bustamante M, Cruells A, Darecka K, Vega N, Alós S, Trias I, Fusté P, Parra G, Gut M, Munmany M, Torné A, Jares P, Rakislova N. Whole-exome sequencing of vulvar squamous cell carcinomas reveals an impaired prognosis in patients with TP53 mutations and concurrent CCND1 gains. Mod Pathol 2024:100574. [PMID: 39089654 DOI: 10.1016/j.modpat.2024.100574] [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: 01/23/2024] [Revised: 07/03/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
Very little information is available on the mutational landscape of vulvar squamous cell carcinoma (VSCC), a disease that mainly affects older women. Studies focusing on the mutational patterns of the currently recognized etiopathogenic types of this tumor [human papillomavirus (HPV)-associated (HPV-A), HPV-independent (HPV-I) with TP53 mutation (HPV-I/TP53mut), and HPV-I with wild-type TP53 (HPV-I/TP53wt]) are particularly rare, and there is almost no information on the prognostic implications of these abnormalities. Whole-exome DNA sequencing of 60 VSCC and matched normal tissues from each patient was performed. HPV detection, immunohistochemistry (IHC) for p16, p53, and mismatch repair proteins were also performed. Ten tumors (16.7%) were classified as HPV-A, 37 (61.7%) as HPV-I/TP53mut, and 13 (21.6%) as HPV-I/TP53wt. TP53 was the most frequently mutated gene (66.7%), followed by FAT1 (28.3%), CDKN2A (25.0%), RNF213 (23.3%), NFE2L2 (20%) and PIK3CA (20%). All the 60 tumors (100%) were DNA mismatch repair proficient. Seventeen tumors (28.3%) showed CCND1 gain. Bivariate analysis, adjusted for FIGO stage, revealed that TP53 mutation, CCND1 gain, and the combination of the two alterations were strongly associated with impaired recurrence-free survival (hazard ratio=4.4, p<0.001) and disease-specific survival (hazard ratio=6.1, p=0.002). Similar results were obtained when p53 IHC status was used instead of TP53 status and when considering only HPV-I VSCC. However, in the latter category, p53 IHC maintained its prognostic impact only in combination with CCND1 gains. All tumors carried at least one potentially actionable genomic alteration. In conclusion, VSCCs with CCND1 gain represent a prognostically adverse category among HPV-I/TP53mut tumors. All patients with VSCCs are potential candidates for targeted therapy.
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Affiliation(s)
- Oriol Ordi
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain; Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain
| | - Adela Saco
- Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Nuria Peñuelas
- Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain
| | - Odei Blanco-Irazuegui
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain
| | - Marta Del Pino
- Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain; Department of Obstetrics and Gynecology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Núria Carreras-Dieguez
- Department of Obstetrics and Gynecology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Lorena Marimon
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain; Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | | | - Alba Morató
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain; Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain
| | - Lia Sisuashvili
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Mariona Bustamante
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain
| | - Adrià Cruells
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain
| | - Katarzyna Darecka
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Naiara Vega
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Silvia Alós
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Isabel Trias
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Pere Fusté
- Department of Obstetrics and Gynecology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Genis Parra
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643 Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; Facultat de Biologia, Universitat de Barcelona (UB), Av. Diagonal, 643 Barcelona, Spain
| | - Meritxell Munmany
- Department of Obstetrics and Gynecology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Aureli Torné
- Department of Obstetrics and Gynecology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain
| | - Natalia Rakislova
- Departament de Fonaments Clínics. Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), c. Casanova, 143, 08036 Barcelona, Spain; Barcelona Institute of Global Health (ISGlobal)-University of Barcelona, Barcelona, Spain; Department of Pathology, Hospital Clínic of Barcelona-University of Barcelona, Barcelona, Spain.
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Wang Y, Yao J, Zhang Z, Wei L, Wang S. Generation of novel lipid metabolism-based signatures to predict prognosis and immunotherapy response for colorectal adenocarcinoma. Sci Rep 2024; 14:17158. [PMID: 39060344 PMCID: PMC11282063 DOI: 10.1038/s41598-024-67549-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: 01/12/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Lipid metabolism reprogramming involves in epithelial-mesenchymal transition (EMT), cancer stemness and immune checkpoints (ICs), which influence the metastasis of cancer. This study aimed to generate lipid metabolism-based signatures to predict prognosis, immunotherapy and chemotherapy response for colorectal adenocarcinoma (COAD). Transcriptome data and clinical information of COAD patients were collected from the cancer genome atlas (TCGA) database. The expression of EMT-, stem cell-, and IC-related genes were assessed between COAD and control samples. Modules and genes correlated EMT, ICs and stemness signatures were identified through weighted gene co-expression network analysis (WGCNA). Prognostic signatures were generated and then the distribution of risk genes was evaluated using single-cell RNA sequencing (scRNA-seq) data from GSE132465 dataset. COAD patients exhibited increased EMT score and stemness along with decreased ICs. Next, 12 hub genes (PIK3CG, ALOX5AP, PIK3R5, TNFAIP8L2, DPEP2, PIK3CD, PIK3R6, GGT5, ELOVL4, PTGIS, CYP7B1 and PRKD1) were found within green and yellow modules correlated with EMT, stemness and ICs. Lipid metabolism-based prognostic signatures were generated based on PIK3CG, GGT5 and PTGIS. Patients with high-risk group had poor prognosis, elevated ESTIMATEScore and StromalScore, 100% mutation rate and higher TIDE score. Samples in low-risk group had more immunogenicity on ICIs. Notably, PIK3CG was expressed in B cells, while GGT5 and PTGIS were expressed in stromal cells. This study generates lipid metabolism-based signatures correlated with EMT, stemness and ICs for predicting prognosis of COAD, and provides potential therapeutic targets for immunotherapy in COAD.
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Affiliation(s)
- Yi Wang
- Department of Oncology and Hematology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215127, China
| | - Jun Yao
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215127, China
| | - Zhe Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215127, China
| | - Luxin Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215127, China
| | - Sheng Wang
- Department of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215127, China.
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Xu S, Zhang Y, Yang Y, Dong K, Zhang H, Luo C, Liu SM. A m 6A regulators-related classifier for prognosis and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1374465. [PMID: 39119345 PMCID: PMC11306056 DOI: 10.3389/fimmu.2024.1374465] [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: 01/22/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background Increasing evidence have highlighted the biological significance of mRNA N6-methyladenosine (m6A) modification in regulating tumorigenicity and progression. However, the potential roles of m6A regulators in tumor microenvironment (TME) formation and immune cell infiltration in liver hepatocellular carcinoma (LIHC or HCC) requires further clarification. Method RNA sequencing data were obtained from TCGA-LIHC databases and ICGC-LIRI-JP databases. Consensus clustering algorithm was used to identify m6A regulators cluster subtypes. Weighted gene co-expression network analysis (WGCNA), LASSO regression, Random Forest (RF), and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) were applied to identify candidate biomarkers, and then a m6Arisk score model was constructed. The correlations of m6Arisk score with immunological characteristics (immunomodulators, cancer immunity cycles, tumor-infiltrating immune cells (TIICs), and immune checkpoints) were systematically evaluated. The effective performance of nomogram was evaluated using concordance index (C-index), calibration plots, decision curve analysis (DCA), and receiver operating characteristic curve (ROC). Results Two distinct m6A modification patterns were identified based on 23 m6A regulators, which were correlated with different clinical outcomes and biological functions. Based on the constructed m6Arisk score model, HCC patients can be divided into two distinct risk score subgroups. Further analysis indicated that the m6Arisk score showed excellent prognostic performance. Patients with a high m6Arisk score was significantly associated with poorer clinical outcome, lower drug sensitivity, and higher immune infiltration. Moreover, we developed a nomogram model by incorporating the m6Arisk score and clinicopathological features. The application of the m6Arisk score for the prognostic stratification of HCC has good clinical applicability and clinical net benefit. Conclusion Our findings reveal the crucial role of m6A modification patterns for predicting HCC TME status and prognosis, and highlight the good clinical applicability and net benefit of m6Arisk score in terms of prognosis, immunophenotype, and drug therapy in HCC patients.
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Affiliation(s)
- Shaohua Xu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Yi Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kexin Dong
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hanfei Zhang
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis & Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China
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Wen B, Zhang P, Xie J, Zhou Z, Zhang G, Zhang L, Zhang Z. Deciphering the prognostic role of endoplasmic reticulum stress in lung adenocarcinoma: integrating prognostic prediction and immunotherapy strategies. Clin Exp Med 2024; 24:169. [PMID: 39052154 PMCID: PMC11272744 DOI: 10.1007/s10238-024-01439-4] [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: 06/09/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Endoplasmic reticulum stress (ERS) is a critical factor influencing lung adenocarcinoma (LUAD) progression and patient outcomes. In this study, we analyzed gene expression data from LUAD samples sourced from The Cancer Genomic Atlas and Gene Expression Omnibus databases. Utilizing advanced statistical methods including LASSO and Cox regression, we developed a ERS-associated signature (ERAS) based on ten ERS-related genes. This model stratified patients into high- and low-risk groups, with the high-risk group exhibiting decreased survival rates, elevated tumor mutational burden, and heightened chemotherapy sensitivity. Additionally, we observed lower immune and ESTIMATE scores in the high-ERAS group, indicating a potentially compromised immune response. Experimental validation through quantitative real-time polymerase chain reaction confirmed the utility of our model. Furthermore, we constructed a nomogram to predict 1-, 3-, and 5-year survival rates, providing clinicians with a valuable tool for personalized patient management. In conclusion, our study demonstrates the efficacy of the ERAS in identifying high-ERAS LUAD patients, offering promising implications for improved prognostication and treatment strategies.
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Affiliation(s)
- Bing Wen
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Department of Cardiothoracic Surgery, The Second People's Hospital of Yibin, Yibin, Sichuan, China
| | - Pengpeng Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiping Xie
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhaokai Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lianmin Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| | - Zhenfa Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
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Zhou R, Jia X, Li Z, Huang S, Feng W, Zhu X. Identifying an immunosenescence-associated gene signature in gastric cancer by integrating bulk and single-cell sequencing data. Sci Rep 2024; 14:17055. [PMID: 39048596 PMCID: PMC11269723 DOI: 10.1038/s41598-024-68054-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: 03/11/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
It has been believed that immunosenescence plays a crucial role in tumorigenesis and cancer therapy. Nevertheless, there is still a lack of understanding regarding its role in determining clinical outcomes and therapy selection for gastric cancer patients, due to the lack of a feasible immunosenescence signature. Therefore, this research aims to develop a gene signature based on immunosenescence, which is used for stratification of gastric cancer. By integrative analysis of bulk transcriptome and single-cell data, we uncovered immunosenescence features in gastric cancer. Random forest algorithm was used to select hub genes and multivariate Cox algorithm was applied to construct a scoring system to evaluate the prognosis and the response to immunotherapy and chemotherapy. The Cancer Genome Atlas of Stomach Adenocarcinoma (TCGA-STAD) cohort was implemented as the training cohort and two independent cohorts from the Gene Expression Omnibus (GEO) database were used for validation. The model was further tested by our Fudan cohort. In this study, immunosenescence was identified as a hallmark of gastric cancer that is linked with transcriptomic features, genomic variations, and distinctive tumor microenvironment (TME). Four immunosenescence genes, including APOD, ADIPOR2, BRAF, and C3, were screened out to construct a gene signature for risk stratification. Higher risk scores indicated strong predictive power for poorer overall survival. Notably, the risk score signature could reliably predict response to chemotherapy and immunotherapy, with patients with high scores benefiting from immunotherapy and patients with low scores responding to chemotherapy. We report immunosenescence as a hitherto unheralded hallmark of gastric cancer that affects prognosis and treatment efficiency.
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Affiliation(s)
- Runye Zhou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xiya Jia
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shenglin Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wanjing Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xiaodong Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China.
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Cai Z, Jiang Z, Li S, Mo S, Wang S, Liang M, Tan X, Zhong W, Zhang L, Deng J, Zhong C, Lu J. RNA modification Regulators' Co-Expression Score (RMRCoeS) predicts biochemical recurrence and therapy response in prostate cancer: A multi-omics and experimental validation study. Int Immunopharmacol 2024; 139:112723. [PMID: 39053228 DOI: 10.1016/j.intimp.2024.112723] [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: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Owing to the heterogeneity of prostate cancer (PCa), the clinical indicators traditionally fall short of meeting the requirements for personalized medicine. The realm of RNA modification has emerged as an increasingly relevant domain, shedding light on its pivotal role in tumor heterogeneity. However, the specific contributions of RNA modification regulators within the context of PCa remain largely unexplored. METHODS In this study, we undertook a literature review to summarize the common 8 types of RNA modifications (ac4c, AI, APA, m1A, m5c, m6A, m7G, Ψ) encompassing a total of 84 regulators. Moreover, we integrated multi-center cohorts with Ridge regression to develop the Regulators' Co-Expression Score (RMRCoeS). Then we assessed the role of RMRCoeS in several clinical aspects such as biochemical recurrence (BCR), responses to chemotherapy, androgen receptor signaling inhibitor (ARSI) therapy and immunotherapy in PCa. Finally, we validated the cancer-promoting performance of five hub genes through immunohistochemistry and in vitro assays. RESULTS Within the mutation landscape of RNA modification regulators, we observed a relatively low overall mutation rate. Remarkably, RMRCoeS, comprising 81 RNA modification regulators, exhibited a notable capability for accurately predicting the prognosis and therapeutic responses in PCa patients subjected to BCR, chemotherapy, ARSI therapy, and immunotherapy. A high RMRCoeS was indicative of a poor prognosis and unfavorable therapy responses. Functional enrichment analysis unveiled that RMRCoeS may exert its influence on PCa progression through various metabolic pathways. Furthermore, a higher RMRCoeS showed a positive correlation with elevated CNV mutations. Lastly, we validated the oncogene effects of CPSF4, WBSCR22, RPUSD3, TRMT61A, and NSUN5-five hub regulators-within the context of PCa. CONCLUSION The function of different RNA modifications is interconnected. Comprising eight distinct RNA modifications' regulators, RMRCoeS exhibits multifaceted roles in various aspects of PCa, including disease progression, prognosis, and responses to multiple therapies. Furthermore, we provide the initial validation of the oncogene effect associated with WBSCR22, RPUSD3, TRMT61A and NSUN5 in PCa. Our findings offer novel insights into the significance of RNA modifications in PCa personalized medicine.
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Affiliation(s)
- Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Zhaojun Jiang
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Songbo Li
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, The Second People's Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi 541002, China
| | - Shanshan Mo
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Shuo Wang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, China
| | - Min Liang
- Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Xiao Tan
- Department of Urology, School of Clinical Medicine, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa 999078, Macau
| | - Le Zhang
- Institute for Integrative Genome Biology, University of California, Riverside 92507, CA, USA
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Chuanfan Zhong
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Jianming Lu
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
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Atzeni R, Massidda M, Pieroni E, Rallo V, Pisu M, Angius A. A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer. Int J Mol Sci 2024; 25:8044. [PMID: 39125613 DOI: 10.3390/ijms25158044] [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: 06/10/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Accurate detection and analysis of somatic variants in cancer involve multiple third-party tools with complex dependencies and configurations, leading to laborious, error-prone, and time-consuming data conversions. This approach lacks accuracy, reproducibility, and portability, limiting clinical application. Musta was developed to address these issues as an end-to-end pipeline for detecting, classifying, and interpreting cancer mutations. Musta is based on a Python command-line tool designed to manage tumor-normal samples for precise somatic mutation analysis. The core is a Snakemake-based workflow that covers all key cancer genomics steps, including variant calling, mutational signature deconvolution, variant annotation, driver gene detection, pathway analysis, and tumor heterogeneity estimation. Musta is easy to install on any system via Docker, with a Makefile handling installation, configuration, and execution, allowing for full or partial pipeline runs. Musta has been validated at the CRS4-NGS Core facility and tested on large datasets from The Cancer Genome Atlas and the Beijing Institute of Genomics. Musta has proven robust and flexible for somatic variant analysis in cancer. It is user-friendly, requiring no specialized programming skills, and enables data processing with a single command line. Its reproducibility ensures consistent results across users following the same protocol.
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Affiliation(s)
- Rossano Atzeni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy
| | - Matteo Massidda
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
| | - Enrico Pieroni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy
| | - Vincenzo Rallo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
| | - Massimo Pisu
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy
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Zhao J, Shen F, Hu YM, Yin K, Chen Y, Chen YJ, Hu QC, Liang L. Prognostic value and microenvironmental crosstalk of exosome-related signatures in human epidermal growth factor receptor 2 positive breast cancer. Open Life Sci 2024; 19:20220899. [PMID: 39071494 PMCID: PMC11282918 DOI: 10.1515/biol-2022-0899] [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: 07/27/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 07/30/2024] Open
Abstract
This study aimed to determine the prognostic value and microenvironmental crosstalk of exosome-related signatures in human epidermal growth factor receptor 2 positive breast cancer (HER2+ BC). Transcriptome sequencing and clinicopathological data were downloaded from the Cancer Genome Atlas. The 10X single cell sequencing dataset was downloaded from the National Center for Biotechnology Information Gene Expression Omnibus. Exosomes-Related Genes were extracted from the ExoCarta and Gene Set Enrichment Analysis databases. FGF9, SF3B4, and EPCAM were found and deemed the most accurate predictive signatures. Patients with HER2+ BC were subtyped into three groupings by exosome prognostic gene (EPGs). The expression of SF3B4 was positively linked with the infiltration of macrophages, neutrophils, and CD4+ T cells. The expression characteristics of EPGs were associated with the biological process of "response to xenobiotic stimuli." Interactions were relatively high between malignant epithelial cells and fibroblasts, endothelial cells, monocytes, and macrophages. Malignant epithelial cells interact more with fibroblasts and endothelial cells. The migration inhibitory factor pathway was the primary outgoing signaling pattern, while the C-C motif chemokine ligand pathway was the primary incoming signaling pattern for communication between malignant epithelial cells and macrophages. This study described the role of exosome signatures in the prognosis and microenvironment of HER2+ BC and provided a basis for future research.
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Affiliation(s)
- Ji Zhao
- Department of Breast Surgery, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Feng Shen
- Department of Medical Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, 361015, People’s Republic of China
| | - Yue-Mei Hu
- Department of Pathology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Kai Yin
- Department of Breast Surgery, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People’s Republic of China
| | - Ying Chen
- Department of Radiation Oncology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 Xianxia Road, Changning District, Shanghai, 200336, People’s Republic of China
| | - Yan-Jie Chen
- Department of Gastroenterology, Zhongshan Hospital (Xiamen), Fudan University, No. 668, Jinhu Road, Huli District, Xiamen, 361015, People’s Republic of China
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Xuhui District, Shanghai200032, People’s Republic of China
| | - Qun-Chao Hu
- Department of Radiation Oncology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 Xianxia Road, Changning District, Shanghai, 200336, People’s Republic of China
| | - Li Liang
- Department of Medical Oncology, Zhongshan Hospital Fudan University, No. 180, Fenglin Road, Xuhui District, Shanghai, 200032, People’s Republic of China
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Wang Z, Weng Z, Lin L, Wu X, Liu W, Zhuang Y, Jian J, Zhuo C. Characterize molecular signatures and establish a prognostic signature of gastric cancer by integrating single-cell RNA sequencing and bulk RNA sequencing. Discov Oncol 2024; 15:301. [PMID: 39044041 PMCID: PMC11266334 DOI: 10.1007/s12672-024-01168-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
Gastric cancer is a significant global health concern with complex molecular underpinnings influencing disease progression and patient outcomes. Various molecular drivers were reported, and these studies offered potential avenues for targeted therapies, biomarker discovery, and the development of precision medicine strategies. However, it was posed that the heterogeneity of the disease and the complexity of the molecular interactions are still challenging. By seamlessly integrating data from single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq), we embarked on characterizing molecular signatures and establishing a prognostic signature for this complex malignancy. We offered a holistic view of gene expression landscapes in gastric cancer, identified 226 candidate marker genes from 3 different dimensions, and unraveled key players' risk stratification and treatment decision-making. The convergence of molecular insights in gastric cancer progression occurs at multiple biological scales simultaneously. The focal point of this study lies in developing a prognostic model, and we amalgamated four molecular signatures (COL4A1, FKBP10, RNASE1, SNCG) and three clinical parameters using advanced machine-learning techniques. The model showed high predictive accuracy, with the potential to revolutionize patient care by using clinical variables. This will strengthen the reliability of the model and enable personalized therapeutic strategies based on each patient's unique molecular profile. In summary, our research sheds light on the molecular underpinnings of gastric cancer, culminating in a powerful prognostic tool for gastric cancer. With a firm foundation in biological insights and clinical implications, our study paves the way for future validations and underscores the potential of integrated molecular analysis in advancing precision oncology.
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Affiliation(s)
- Zhiwei Wang
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Zhiyan Weng
- Department of Endocrinology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Endocrinology, Binhai Campus of the First Affiliated Hospital, National Regional Medical Center, Fujian Medical University, Fuzhou, 350212, China
- Clinical Research Center for Metabolic Diseases of Fujian Province, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Luping Lin
- Department of Abdominal Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Xianyi Wu
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Wenju Liu
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Yong Zhuang
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Jinliang Jian
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China
| | - Changhua Zhuo
- Department of Gastrointestinal Surgical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350011, China.
- Fujian Key Laboratory of Translational Cancer Medicine, Fujian Provincial Key Laboratory of Tumor Biotherapy, Fuzhou, 350011, China.
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Stigliani A, Ialchina R, Yao J, Czaplinska D, Dai Y, Andersen HB, Rennie S, Andersson R, Pedersen SF, Sandelin A. Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance. Cell Rep 2024; 43:114409. [PMID: 38944837 DOI: 10.1016/j.celrep.2024.114409] [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: 02/13/2023] [Revised: 12/11/2023] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
Harsh environments in poorly perfused tumor regions may select for traits driving cancer aggressiveness. Here, we investigated whether tumor acidosis interacts with driver mutations to exacerbate cancer hallmarks. We adapted mouse organoids from normal pancreatic duct (mN10) and early pancreatic cancer (mP4, KRAS-G12D mutation, ± p53 knockout) from extracellular pH 7.4 to 6.7, representing acidic niches. Viability was increased by acid adaptation, a pattern most apparent in wild-type (WT) p53 organoids, and exacerbated upon return to pH 7.4. This led to increased survival of acid-adapted organoids treated with gemcitabine and/or erlotinib, and, in WT p53 organoids, acid-induced attenuation of drug effects. New genetic variants became dominant during adaptation, yet they were unlikely to be its main drivers. Transcriptional changes induced by acid and drug adaptation differed overall, but acid adaptation increased the expression of gemcitabine resistance genes. Thus, adaptation to acidosis increases cancer cell viability after chemotherapy.
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Affiliation(s)
- Arnaud Stigliani
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Renata Ialchina
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Jiayi Yao
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Dominika Czaplinska
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Yifan Dai
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Henriette Berg Andersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Robin Andersson
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, DK2100 Copenhagen Ø, Denmark.
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, DK2200 Copenhagen N, Denmark.
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Miao Y, Chen Q, Liu X, Bu J, Zhang Z, Liu T, Yue Z, Huang L, Sun S, Li H, Yang A, Yang Z, Chen C. Comprehensive analysis of endoplasmic reticulum stress related signature in head and neck squamous carcinoma. Sci Rep 2024; 14:16972. [PMID: 39043683 PMCID: PMC11266686 DOI: 10.1038/s41598-024-65090-5] [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: 04/19/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024] Open
Abstract
Head and neck squamous carcinoma (HNSC) is a prevalent malignant disease, with the majority of patients being diagnosed at an advanced stage. Endoplasmic reticulum stress (ERS) is considered to be a process that promotes tumorigenesis and impacts the tumor microenvironment (TME) in various cancers. The study aims to investigate the predictive value of ERS in HNSC and explore the correlation between ERS-related genes and TME. A series of bioinformatics analyses were carried out based on mRNA and scRNA-seq data from the TCGA and GEO databases. We conducted RT-qPCR and western blot to validate the signature, and performed cell functional experiments to investigate the in vitro biological functions of the gene. We identified 63 ERS-related genes that were associated with outcome and stage in HNSC. A three-gene signature (ATF6, TRIB3, and UBXN6) was developed, which presents predictive value in the prognosis and immunotherapy response of HNSC patients. The high-risk group exhibited a worse prognosis but may benefit from immunotherapy. Furthermore, there was a significant correlation between the signature and immune infiltration. In the high-risk group, fibroblasts were more active in intercellular communication, and more T cells were observed at the end of the sequential phase. The genes in the ERS-related signature were overexpressed in HNSC cells, and the knockdown of TRIB3 significantly inhibited cell proliferation and migration. This study established a novel ERS-related signature that has potential implications for HNSC therapy and the understanding of TME.
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Affiliation(s)
- Yu Miao
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China
| | - Qiaorong Chen
- Department of Head and Neck Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510060, People's Republic of China
| | - Xinyu Liu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510060, People's Republic of China
| | - Jian Bu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510060, People's Republic of China
| | - Zhuoqi Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510060, People's Republic of China
| | - Tongjing Liu
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China
| | - Zhenjie Yue
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China
| | - Lizhen Huang
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China
| | - Shuaishuai Sun
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China
| | - Hao Li
- The Second Clinical College of Hainan Medical University, Haikou, 570100, People's Republic of China
| | - Ankui Yang
- Department of Head and Neck Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Zhongyuan Yang
- Department of Head and Neck Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, People's Republic of China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.
| | - Cuifang Chen
- Department of Otorhinolaryngology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, 16th Floor, No. 2 Inpatient Building, Qingyuan, People's Republic of China.
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Yoshida T, Nakamoto T, Atsumi N, Ohe C, Sano T, Yasukochi Y, Tsuta K, Kinoshita H. Impact of LAG-3/FGL1 pathway on immune evasive contexture and clinical outcomes in advanced urothelial carcinoma. J Immunother Cancer 2024; 12:e009358. [PMID: 39043605 PMCID: PMC11268076 DOI: 10.1136/jitc-2024-009358] [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] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Anti-programmed death-1 (PD-1)/anti-PD-ligand-1 (PD-L1) pathway inhibition is a standard regimen for advanced urothelial carcinoma (UC); however, its limited efficacy has been reflected in reported medium response rates. This study explored the role of next-generation coinhibitory receptors (IRs; lymphocyte activation gene 3 (LAG-3), T-cell immunoglobulin and mucin domain 3 (TIM-3), and T-cell immunoreceptor with Ig and ITIM domains (TIGIT)) and their ligands (LGs) in the response to PD-(L)1 blockade therapy and the oncological outcomes in patients with UC. METHODS We investigated metastatic UC cases who underwent PD-(L)1 therapy (cohort 1: n=348, cohort 2: n=89, and cohort 4: n=29) or advanced UC cases involving surgery (cohort 3: n=293 and cohort 5: n=90). We assessed the mRNA expression profiles and corresponding clinical information regarding IRs and LGs using cohorts 1, 2, and 3. Additionally, we elucidated the spatial features of these targeted markers using multiplex immunohistochemistry (mIHC) on formalin-fixed paraffin-embedded samples from cohorts 4 and 5. Survival, differential expressed gene, and Gene Set Enrichment analyses were performed. For mIHC, quantitative analyses were also performed to correlate immune and tumor cell densities with patient survival. RESULTS LAG-3 expression was strongly associated with the responsiveness of PD-(L)1 blockade compared with the expression of TIM-3 and TIGIT. In tumors with high LAG-3 levels, the increased expression of fibrinogen-like protein 1 (FGL1) had a significantly negative effect on the response to PD-(L)1 blockade and overall survival. Moreover, high FGL1 levels were associated with elevated CD4+ regulatory T-cell gene signatures and the upregulation of CD39 and neuropilin-1, with both indicating CD8+ T-cell exhaustion. mIHC analyses revealed that patients with stromal CD8+LAG-3+cellshigh-tumor FGL1+cellshigh exhibited a significant negative correlation with survival rates compared with those with stromal CD8+LAG-3+cellshigh-tumor FGL1+cellslow. CONCLUSIONS LAG-3 expression and high FGL1 coexpression are important predictive factors of adverse oncological outcomes related to the presence of immunosuppressive contextures. These findings are hypothesis-generating, warranting further mechanistic and clinical studies aimed to evaluate LAG-3/FGL1 blockade in UC.
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Affiliation(s)
- Takashi Yoshida
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
- Graduate School of Engineering, Tottori University, Tottori, Japan
- Department of Urology, Osaka Saiseikai-Noe Hospital, Osaka, Japan
- Corporate Sponsored Research Programs for Multicellular Interactions in Cancer, Kansai Medical University, Osaka, Japan
| | - Takahiro Nakamoto
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
- Department of Pathology, Kansai Medical University, Osaka, Japan
| | - Naho Atsumi
- Corporate Sponsored Research Programs for Multicellular Interactions in Cancer, Kansai Medical University, Osaka, Japan
- Department of Pathology, Kansai Medical University, Osaka, Japan
| | - Chisato Ohe
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Takeshi Sano
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
| | - Yoshiki Yasukochi
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Koji Tsuta
- Corporate Sponsored Research Programs for Multicellular Interactions in Cancer, Kansai Medical University, Osaka, Japan
- Department of Pathology, Kansai Medical University, Osaka, Japan
| | - Hidefumi Kinoshita
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
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Xiang H, Luo R, Wang Y, Yang B, Xu S, Huang W, Tang S, Fang R, Chen L, Zhu N, Yu Z, Akesu S, Wei C, Xu C, Zhou Y, Gu J, Zhao J, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pan-melanoma. Cell Discov 2024; 10:78. [PMID: 39039072 PMCID: PMC11263678 DOI: 10.1038/s41421-024-00688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/03/2024] [Indexed: 07/24/2024] Open
Abstract
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.
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Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Na Zhu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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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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Zhang H, Huang W, Chen M, Liu Y, Yan B, Mou S, Jiang W, Mei H. Research on molecular characteristics of ADME-related genes in kidney renal clear cell carcinoma. Sci Rep 2024; 14:16834. [PMID: 39039118 PMCID: PMC11263354 DOI: 10.1038/s41598-024-67516-6] [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: 02/17/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
Genes involved in drug absorption, distribution, metabolism, and excretion (ADME) are named ADME genes. However, the comprehensive role of ADME genes in kidney renal clear cell carcinoma (KIRC) remains unclear. Using the clinical and gene expression data of KIRC patients downloaded from The Cancer Genome Atlas (TCGA), ArrayExpress, and the Gene Expression Omnibus (GEO) databases, we cluster patients into two patterns, and the population with a relatively poor prognosis demonstrated higher level of immunosuppressive cell infiltration and higher proportion of glycolytic subtypes. Then, 17 ADME genes combination identified through the least absolute shrinkage and selection operator algorithm (LASSO, 1000 times) was utilized to calculate the ADME score. The ADME score was found to be an independent predictor of prognosis in KIRC and to be tightly associated with the infiltration level of immune cells, metabolic properties, tumor-related signaling pathways, genetic variation, and responses to chemotherapeutics. Our work revealed the characteristics of ADME in KIRC. Assessing the ADME profiles of individual patients can deepen our comprehension of tumor microenvironment (TME) features in KIRC and can aid in developing more personalized and effective therapeutic strategies.
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Affiliation(s)
- Haiyu Zhang
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Department of Urology, Shantou University Medical College, Shantou, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weisheng Huang
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Department of Urology, Shantou University Medical College, Shantou, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mutong Chen
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Department of Urology, Shantou University Medical College, Shantou, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhan Liu
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bing Yan
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shuanzhu Mou
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wendong Jiang
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hongbing Mei
- Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.
- Department of Urology, Shantou University Medical College, Shantou, China.
- Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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Huang X, Du G, Yang Y, Su P, Chen S, Cai C, Huang T, Zeng Y, Tao Y, Tian D, Zhang N. Advancing bladder cancer management: development of a prognostic model and personalized therapy. Front Immunol 2024; 15:1430792. [PMID: 39104534 PMCID: PMC11298345 DOI: 10.3389/fimmu.2024.1430792] [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: 05/10/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Background Bladder cancer (BLCA) was recognized as a significant public health challenge due to its high incidence and mortality rates. The influence of molecular subtypes on treatment outcomes was well-acknowledged, necessitating further exploration of their characterization and application. This study was aimed at enhancing the understanding of BLCA by mapping its molecular heterogeneity and developing a robust prognostic model using single-cell and bulk RNA sequencing data. Additionally, immunological characteristics and personalized treatment strategies were investigated through the risk score. Methods Single-cell RNA sequencing (scRNA-seq) data from GSE135337 and bulk RNA-seq data from several sources, including GSE13507, GSE31684, GSE32894, GSE69795, and TCGA-BLCA, were utilized. Molecular subtypes, particularly the basal-squamous (Ba/Sq) subtype associated with poor prognosis, were identified. A prognostic model was constructed using LASSO and Cox regression analyses focused on genes linked with the Ba/Sq subtype. this model was validated across internal and external datasets to ensure predictive accuracy. High- and low-risk groups based on the risk score derived from TCGA-BLCA data were analyzed to examine their immune-related molecular profiles and treatment responses. Results Six molecular subtypes were identified, with the Ba/Sq subtype being consistently associated with poor prognosis. The prognostic model, based on basal-squamous subtype-related genes (BSSRGs), was shown to have strong predictive performance across diverse clinical settings with AUC values at 1, 3, and 5 years indicating robust predictability in training, testing, and entire datasets. Analysis of the different risk groups revealed distinct immune infiltration and microenvironments. Generally higher tumor mutation burden (TMB) scores and lower tumor immune dysfunction and exclusion (TIDE) scores were exhibited by the low-risk group, suggesting varied potentials for systemic drug response between the groups. Finally, significant differences in potential systemic drug response rates were also observed between risk groups. Conclusions The study introduced and validated a new prognostic model for BLCA based on BSSRGs, which was proven effective in prognosis prediction. The potential for personalized therapy, optimized by patient stratification and immune profiling, was highlighted by our risk score, aiming to improve treatment efficacy. This approach was promised to offer significant advancements in managing BLCA, tailoring treatments based on detailed molecular and immunological insights.
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Affiliation(s)
- Xiang Huang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guotu Du
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ying Yang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Peng Su
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shicheng Chen
- Department of Urology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Chongjiong Cai
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Department of Urology, Renhuai People’s Hospital, Zunyi, China
| | - Tianyu Huang
- Department of Nursing, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yu Zeng
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yonggang Tao
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Demei Tian
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Neng Zhang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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50
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Peng Z, Fang W, Wu B, He M, Li S, Wei J, Hao Y, Jin L, Liu M, Zhang X, Wei Y, Ge Y, Wei Y, Qian H, Zhang Y, Jiang J, Chang Z, Rao Y, Zhang X, Cui CP, Zhang L. Targeting Smurf1 to block PDK1-Akt signaling in KRAS-mutated colorectal cancer. Nat Chem Biol 2024:10.1038/s41589-024-01683-5. [PMID: 39039255 DOI: 10.1038/s41589-024-01683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 06/23/2024] [Indexed: 07/24/2024]
Abstract
The phosphoinositide 3-kinase (PI3K)-Akt axis is one of the most frequently activated pathways and is demonstrated as a therapeutic target in Kirsten rat sarcoma viral oncogene homolog (KRAS)-mutated colorectal cancer (CRC). Targeting the PI3K-Akt pathway has been a challenging undertaking through the decades. Here we unveiled an essential role of E3 ligase SMAD ubiquitylation regulatory factor 1 (Smurf1)-mediated phosphoinositide-dependent protein kinase 1 (PDK1) neddylation in PI3K-Akt signaling and tumorigenesis. Upon growth factor stimulation, Smurf1 immediately triggers PDK1 neddylation and the poly-neural precursor cell expressed developmentally downregulated protein 8 (poly-Nedd8) chains recruit methyltransferase SET domain bifurcated histone lysine methyltransferase 1 (SETDB1). The cytoplasmic complex of PDK1 assembled with Smurf1 and SETDB1 (cCOMPASS) consisting of PDK1, Smurf1 and SETDB1 directs Akt membrane attachment and T308 phosphorylation. Smurf1 deficiency dramatically reduces CRC tumorigenesis in a genetic mouse model. Furthermore, we developed a highly selective Smurf1 degrader, Smurf1-antagonizing repressor of tumor 1, which exhibits efficient PDK1-Akt blockade and potent tumor suppression alone or combined with PDK1 inhibitor in KRAS-mutated CRC. The findings presented here unveil previously unrecognized roles of PDK1 neddylation and offer a potential strategy for targeting the PI3K-Akt pathway and KRAS mutant cancer therapy.
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Affiliation(s)
- Zhiqiang Peng
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- Shanghai Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Wei Fang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- Shanghai Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
| | - Bo Wu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Ming He
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Shaohua Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- Shanghai Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
| | - Jun Wei
- Shanghai Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
| | - Yang Hao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lujia Jin
- Department of Gastrointestinal Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Mingqiu Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yange Wei
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yingwei Ge
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yinghua Wei
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangjun Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Junyi Jiang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhijie Chang
- School of Medicine, Tsinghua University, Beijing, China
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
| | - Xueli Zhang
- Shanghai Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.
| | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Lingqiang Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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