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Chen S, Huang M, Zhang L, Huang Q, Wang Y, Liang Y. Inflammatory response signature score model for predicting immunotherapy response and pan-cancer prognosis. Comput Struct Biotechnol J 2024; 23:369-383. [PMID: 38226313 PMCID: PMC10788202 DOI: 10.1016/j.csbj.2023.12.001] [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: 06/09/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 01/17/2024] Open
Abstract
Background Inflammatory responses influence the outcome of immunotherapy and tumorigenesis by modulating host immunity. However, systematic inflammatory response assessment models for predicting cancer immunotherapy (CIT) responses and survival across human cancers remain unexplored. Here, we investigated an inflammatory response score model to predict CIT responses and patient survival in a pan-cancer analysis. Methods We retrieved 12 CIT response gene expression datasets from the Gene Expression Omnibus database (GSE78220, GSE19423, GSE100797, GSE126044, GSE35640, GSE67501, GSE115821 and GSE168204), Tumor Immune Dysfunction and Exclusion database (PRJEB23709, PRJEB25780 and phs000452.v2.p1), European Genome-phenome Archive database (EGAD00001005738), and IMvigor210 cohort. The tumor samples from six cancers types: metastatic urothelial cancer, metastatic melanoma, gastric cancer, primary bladder cancer, renal cell carcinoma, and non-small cell lung cancer.We further established a binary classification model to predict CIT responses using the least absolute shrinkage and selection operator (LASSO) computational algorithm. Findings The model had high predictive accuracy in both the training and validation cohorts. During sub-group analysis, area under the curve (AUC) values of 0.82, 0.80, 0.71, 0.7, 0.67, and 0.64 were obtained for the non-small cell lung cancer, gastric cancer, metastatic urothelial cancer, primary bladder cancer, metastatic melanoma, and renal cell carcinoma cohorts, respectively. CIT response rates were higher in the high-scoring training cohort subjects (51%) than the low-scoring subjects (27%). The five-year survival rates in the high- and low score groups of the training cohorts were 62% and 21%, respectively, while those of the validation cohorts were 54% and 22%, respectively (P < 0·001 in all cases). Inflammatory response signature score derived from on-treatment tumor specimens are highly predictive of response to CIT in patients with metastatic melanoma. A significant correlation was observed between the inflammatory response scores and tumor purity. Regardless of the tumor purity, patients in the low score group had a significantly poorer prognosis than those in the high score group. Immune cell infiltration analysis indicated that in the high score cohort, tumor-infiltrating lymphocytes were significantly enriched, particularly effector and natural killer cells. Inflammatory response scores were positively correlated with immune checkpoint genes, suggesting that immune checkpoint inhibitors may have benefited patients with high scores. Analysis of signature scores across different cancer types from The Cancer Genome Atlas revealed that the prognostic performance of inflammatory response scores for survival in patients who have not undergone immunotherapy can be affected by tumor purity. Interleukin 21 (IL21) had the highest weight in the inflammatory response model, suggesting its vital role in the prediction mode. Since the number of metastatic melanoma patients (n = 429) was relatively large among CIT cohorts, we further performed a co-culture experiment using a melanoma cell line and CD8 + T cell populations generated from peripheral blood monocytes. The results showed that IL21 therapy combined with anti-PD1 (programmed cell death 1) antibodies (trepril monoclonal antibodies) significantly enhanced the cytotoxic activity of CD8 + T cells against the melanoma cell line. Conclusion In this study, we developed an inflammatory response gene signature model that predicts patient survival and immunotherapy response in multiple malignancies. We further found that the predictive performance in the non-small cell lung cancer and gastric cancer group had the highest value among the six different malignancy subgroups. When compared with existing signatures, the inflammatory response gene signature scores for on-treatment samples were more robust predictors of the response to CIT in metastatic melanoma.
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Affiliation(s)
- Shuzhao Chen
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), Shantou, Guangdong, China
| | - Mayan Huang
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Limei Zhang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Qianqian Huang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Yun Wang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
| | - Yang Liang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China
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Feng HR, Shen XN, Zhu XM, Zhong WT, Zhu DX, Zhao J, Chen YJ, Shen F, Liu K, Liang L. Unveiling major histocompatibility complex-mediated pan-cancer immune features by integrated single-cell and bulk RNA sequencing. Cancer Lett 2024; 597:217062. [PMID: 38878852 DOI: 10.1016/j.canlet.2024.217062] [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: 03/30/2024] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/25/2024]
Abstract
Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet persistent challenges such as low response rate and significant heterogeneity necessitate attention. The pivotal role of the major histocompatibility complex (MHC) in ICI efficacy, its intricate impacts and potentials as a prognostic marker, warrants comprehensive exploration. This study integrates single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, and spatial transcriptomic analyses to unveil pan-cancer immune characteristics governed by the MHC transcriptional feature (MHC.sig). Developed through scRNA-seq analysis of 663,760 cells across diverse cohorts and validated in 30 solid cancer types, the MHC.sig demonstrates a robust correlation between immune-related genes and infiltrating immune cells, highlighting its potential as a universal pan-cancer marker for anti-tumor immunity. Screening the MHC.sig for therapeutic targets using CRISPR data identifies potential genes for immune therapy synergy and validates its predictive efficacy for ICIs responsiveness across diverse datasets and cancer types. Finally, analysis of cellular communication patterns reveals interactions between C1QC+macrophages and malignant cells, providing insights into potential therapeutic agents and their sensitivity characteristics. This comprehensive analysis positions the MHC.sig as a promising marker for predicting immune therapy outcomes and guiding combinatorial therapeutic strategies.
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Affiliation(s)
- Hao-Ran Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Xiao-Nan Shen
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Xiao-Ming Zhu
- Department of Colorectal Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200082, People's Republic of China
| | - Wen-Tao Zhong
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510030, People's Republic of China
| | - De-Xiang Zhu
- Department of Colorectal Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Ji Zhao
- Department of Breast Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, People's Republic of China
| | - Yan-Jie Chen
- Department of Gastroenterology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, 361015, People's Republic of China; Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Feng Shen
- Department of Medical Oncology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, 361015, People's Republic of China.
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
| | - Li Liang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
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Liu J, Zhu P. A Novel Gene Signature Associated with Protein Post-translational Modification to Predict Clinical Outcomes and Therapeutic Responses of Colorectal Cancer. Mol Biotechnol 2024; 66:2106-2122. [PMID: 37592152 DOI: 10.1007/s12033-023-00852-6] [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: 07/11/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Accumulated evidence highlights the biological significance of diverse protein post-translational modifications (PTMs) in tumorigenicity and progression of colorectal cancer (CRC). In this study, ten PTM patterns (ubiquitination, methylation, phosphorylation, glycosylation, acetylation, SUMOylation, citrullination, neddylation, palmitoylation, and ADP-ribosylation) were analyzed for model construction. A post-translational modification index (PTMI) with a 14-gene signature was established. CRC patients with high PTMI had a worse prognosis after validating in nine independent datasets. By incorporating PTMI with clinical features, a nomogram with excellent predictive performance was constructed. Two molecular subtypes of CRC with obvious difference in survival time were identified by unsupervised clustering. Furthermore, PTMI was related to known immunoregulators and key tumor microenvironment components. Low-PTMI patients responded better to fluorouracil-based chemotherapy and immune checkpoint blockade therapy compared to high-PTMI patients, which was validated in multiple independent datasets. However, patients with high PTMI might be sensitive to bevacizumab. In short, we established a novel PTMI model by comprehensively analyzing diverse post-translational modification patterns, which can accurately predict clinical prognosis and treatment response of CRC patients.
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Affiliation(s)
- Jun Liu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Peng Zhu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong District, Chongqing, 400010, China.
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Zhang Y, Zhang C, He J, Lai G, Li W, Zeng H, Zhong X, Xie B. Comprehensive analysis of single cell and bulk RNA sequencing reveals the heterogeneity of melanoma tumor microenvironment and predicts the response of immunotherapy. Inflamm Res 2024; 73:1393-1409. [PMID: 38896289 DOI: 10.1007/s00011-024-01905-5] [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: 03/26/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Tumor microenvironment (TME) heterogeneity is an important factor affecting the treatment response of immune checkpoint inhibitors (ICI). However, the TME heterogeneity of melanoma is still widely characterized. METHODS We downloaded the single-cell sequencing data sets of two melanoma patients from the GEO database, and used the "Scissor" algorithm and the "BayesPrism" algorithm to comprehensively analyze the characteristics of microenvironment cells based on single-cell and bulk RNA-seq data. The prediction model of immunotherapy response was constructed by machine learning and verified in three cohorts of GEO database. RESULTS We identified seven cell types. In the Scissor+ subtype cell population, the top three were T cells, B cells and melanoma cells. In the Scissor- subtype, there are more macrophages. By quantifying the characteristics of TME, significant differences in B cells between responders and non-responders were observed. The higher the proportion of B cells, the better the prognosis. At the same time, macrophages in the non-responsive group increased significantly. Finally, nine gene features for predicting ICI response were constructed, and their predictive performance was superior in three external validation groups. CONCLUSION Our study revealed the heterogeneity of melanoma TME and found a new predictive biomarker, which provided theoretical support and new insights for precise immunotherapy of melanoma patients.
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Affiliation(s)
- Yuan Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Jing He
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Wenlong Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Haijiao Zeng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China.
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
- Research Center for Medicine and Social Development, Chongqing Medical University, Chongqing, China.
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Hu M, Coleman S, Judson-Torres RL, Tan AC. The classification of melanocytic gene signatures. Pigment Cell Melanoma Res 2024. [PMID: 39072997 DOI: 10.1111/pcmr.13189] [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: 02/20/2024] [Revised: 06/11/2024] [Accepted: 07/06/2024] [Indexed: 07/30/2024]
Abstract
Gene expression profiling technologies have revolutionized cell biology, enabling researchers to identify gene signatures linked to various biological attributes of melanomas, such as pigmentation status, differentiation state, proliferative versus invasive capacity, and disease progression. Although the discovery of gene signatures has significantly enhanced our understanding of melanocytic phenotypes, reconciling the numerous signatures reported across independent studies and different profiling platforms remains a challenge. Current methods for classifying melanocytic gene signatures depend on exact gene overlap and comparison with unstandardized baseline transcriptomes. In this study, we aimed to categorize published gene signatures into clusters based on their similar patterns of expression across clinical cutaneous melanoma specimens. We analyzed nearly 800 melanoma samples from six gene expression repositories and developed a classification framework for gene signatures that is resilient against biases in gene identification across profiling platforms and inconsistencies in baseline standards. Using 39 frequently cited published gene signatures, our analysis revealed seven principal classes of gene signatures that correlate with previously identified phenotypes: Differentiated, Mitotic/MYC, AXL, Amelanotic, Neuro, Hypometabolic, and Invasive. Each class is consistent with the phenotypes that the constituent gene signatures represent, and our classification method does not rely on overlapping genes between signatures. To facilitate broader application, we created WIMMS (what is my melanocytic signature, available at https://wimms.tanlab.org/), a user-friendly web application. WIMMS allows users to categorize any gene signature, determining its relationship to predominantly cited signatures and its representation within the seven principal classes.
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Affiliation(s)
- Min Hu
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Samuel Coleman
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA
| | - Robert L Judson-Torres
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
- Department of Dermatology, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Aik Choon Tan
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, USA
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
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6
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Quek C, Pratapa A, Bai X, Al-Eryani G, Pires da Silva I, Mayer A, Bartonicek N, Harvey K, Maher NG, Conway JW, Kasalo RJ, Ben Cheikh B, Braubach O, Palendira U, Saw RPM, Stretch JR, Shannon KF, Menzies AM, Scolyer RA, Long GV, Swarbrick A, Wilmott JS. Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy. Cell Rep 2024; 43:114392. [PMID: 38944836 DOI: 10.1016/j.celrep.2024.114392] [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: 10/13/2023] [Revised: 03/31/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024] Open
Abstract
Heterogeneous resistance to immunotherapy remains a major challenge in cancer treatment, often leading to disease progression and death. Using CITE-seq and matched 40-plex PhenoCycler tissue imaging, we performed longitudinal multimodal single-cell analysis of tumors from metastatic melanoma patients with innate resistance, acquired resistance, or response to immunotherapy. We established the multimodal integration toolkit to align transcriptomic features, cellular epitopes, and spatial information to provide deeper insights into the tumors. With longitudinal analysis, we identified an "immune-striving" tumor microenvironment marked by peri-tumor lymphoid aggregates and low infiltration of T cells in the tumor and the emergence of MITF+SPARCL1+ and CENPF+ melanoma subclones after therapy. The enrichment of B cell-associated signatures in the molecular composition of lymphoid aggregates was associated with better survival. These findings provide further insights into the establishment of microenvironmental cell interactions and molecular composition of spatial structures that could inform therapeutic intervention.
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Affiliation(s)
- Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
| | | | - Xinyu Bai
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ghamdan Al-Eryani
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - Inês Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, Australia
| | - Aaron Mayer
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Enable Medicine, Stanford, CA, USA
| | - Nenad Bartonicek
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - Kate Harvey
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Nigel G Maher
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jordan W Conway
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Rebecca J Kasalo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Head & Neck Cancer Institute, Chris O'Brien Lifehouse Cancer Centre, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital & NSW Health Pathology, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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Yu X, Song L, Cen L, Cao B, Tao R, Shen Y, Daga DA, Rodriguez PC, Conejo-Garcia JR, Wang X. A pan-cancer gamma delta T cell repertoire. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604205. [PMID: 39091790 PMCID: PMC11291071 DOI: 10.1101/2024.07.18.604205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
This report presents the largest collection of gamma-delta T cell receptor (γδ TCR) reads in human cancer to date, analyzing about 11,000 patient tumor samples across 33 cancer types using the TRUST4 algorithm. Despite γδ T cells being a small fraction of the T cell population, they play a key role in both innate and adaptive immunity. Our comprehensive analysis reveals their significant presence across all cancer types, specifically highlighting the diverse spectrum and clonality patterns of their γδ receptors. This research highlights the complex roles of γδ T cells in tumor tissues and their potential as prognostic biomarkers. We also demonstrate the utility of T cell receptor gamma (TRG) and delta (TRD) gene expression values from standard RNA-seq data. Ultimately, our work establishes a fundamental resource for future tumor-infiltrating γδ T cell research and may facilitate the development of novel γδ-T-cell-based therapeutic strategies. Together, we demonstrate the strong diversity and prognostic potential of γδ T cells in multiple cancer types. Highlights Comprehensive analysis of γδ TCRs from 11,473 tumor samplesSignificant variability and overall consistency in γδ gene expression and clonotypeγδ TCR expression and diversity as prognostic biomarkers across multiple cancersCentralized γδ TCR repertoire database for future therapeutic discovery.
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Wang X, Li T, Eljilany I, Sukrithan V, Ratan A, McCarter M, Carpten J, Colman H, Ikeguchi AP, Puzanov I, Arnold S, Churchman M, Hwu P, Rodriguez PC, Dalton WS, Weiner GJ, Tarhini AA. Multicellular immune ecotypes within solid tumors predict real-world therapeutic benefits with immune checkpoint inhibitors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.19.24310726. [PMID: 39072034 PMCID: PMC11275692 DOI: 10.1101/2024.07.19.24310726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Cancer initiation, progression, and immune evasion depend on the tumor microenvironment (TME). Thus, understanding the TME immune architecture is essential for understanding tumor metastasis and therapy response. This study aimed to create an immune cell states (CSs) atlas using bulk RNA-seq data enriched by eco-type analyses to resolve the complex immune architectures in the TME. Methods We employed EcoTyper, a machine-learning (ML) framework, to study the real-world prognostic significance of immune CSs and multicellular ecosystems, utilizing molecular data from 1,610 patients with multiple malignancies who underwent immune checkpoint inhibitor (ICI) therapy within the ORIEN Avatar cohort, a well-annotated real-world dataset. Results Our analysis revealed consistent ICI-specific prognostic TME carcinoma ecotypes (CEs) (including CE1, CE9, CE10) across our pan-cancer dataset, where CE1 being more lymphocyte-deficient and CE10 being more proinflammatory. Also, the analysis of specific immune CSs across different cancers showed consistent CD8+ and CD4+ T cell CS distribution patterns. Furthermore, survival analysis of the ORIEN ICI cohort demonstrated that ecotype CE9 is associated with the most favorable survival outcomes, while CE2 is linked to the least favorable outcomes. Notably, the melanoma-specific prognostic EcoTyper model confirmed that lower predicted risk scores are associated with improved survival and better response to immunotherapy. Finally, de novo discovery of ecotypes in the ORIEN ICI dataset identified Ecotype E3 as significantly associated with poorer survival outcomes. Conclusion Our findings offer important insights into refining the patient selection process for immunotherapy in real-world practice and guiding the creation of novel therapeutic strategies to target specific ecotypes within the TME.
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Affiliation(s)
- Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Tingyi Li
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Islam Eljilany
- Departments of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Vineeth Sukrithan
- Department of Internal Medicine, Ohio State University and Arthur G James Comprehensive Cancer Center, Columbus, OH 43210 USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Martin McCarter
- Department of Surgery, University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - John Carpten
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Howard Colman
- Department of Neurosurgery, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | | | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Susanne Arnold
- Department of Medical Oncology, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA
| | | | - Patrick Hwu
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | | | - George J. Weiner
- Department of Internal Medicine, Carver College of Medicine, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Ahmad A. Tarhini
- Departments of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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9
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Liu X, Chen C, Li J, Li L, Ma M. Identification of tumor-specific T cell signature predicting cancer immunotherapy response in bladder cancer by multi-omics analysis and experimental verification. Cancer Cell Int 2024; 24:255. [PMID: 39033098 PMCID: PMC11264995 DOI: 10.1186/s12935-024-03447-6] [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: 02/04/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Numerous gene signatures predicting the prognosis of bladder cancer have been identified. However, a tumor-specific T cell signature related to immunotherapy response in bladder cancer remains under investigation. METHODS Single-cell RNA and TCR sequencing from the Gene expression omnibus (GEO) database were used to identify tumor-specific T cell-related genes in bladder cancer. Subsequently, we constructed a tumor-specific T cell signature (TstcSig) and validated its clinical relevance for predicting immunotherapy response in multiple immunotherapy cohorts. Further analyses explored the immune characteristics of TstcSig in bladder cancer patients from other cohorts in the TCGA and GEO databases. Western blot (WB), multicolor immunofluorescence (MIF), qRT-PCR and flow cytometry assays were performed to validate the results of bioinformatics analysis. RESULTS The established TstcSig, based on five tumor-specific T cell-related genes, could predict outcomes in a bladder cancer immunotherapy cohort. This was verified using two additional immunotherapy cohorts and showed better predictive performance compared to 109 published T cell signatures. TstcSig was strongly correlated with immune characteristics such as immune checkpoint gene expression, tumor mutation burden, and T cell infiltration, as validated by single-cell and spatial transcriptomics datasets. Notably, the positive correlation between TstcSig and T cell infiltration was confirmed in the TCGA cohort. Furthermore, pan-cancer analysis demonstrated the heterogeneity of the prognostic value of TstcSig. Tumor-specific T cells highly expressed CD27, IFNG, GZMB and CXCL13 and secreted more effector cytokines for tumor cell killing, as validated experimentally. CONCLUSION We developed a five-gene signature (including VAMP5, TIGIT, LCK, CD27 and CACYBP) based on tumor-specific T cell-related genes to predict the immunotherapy response in bladder cancer patients.
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Affiliation(s)
- Xiufeng Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510080, People's Republic of China
| | - Chujun Chen
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, People's Republic of China
| | - Jiashan Li
- Department of ultrasound medicine, Jieshou People's Hospital, 339 Renmin Road, Jieshou, Fuyang, Anhui, 236500, China
| | - Linna Li
- Department of ultrasound medicine, Jieshou People's Hospital, 339 Renmin Road, Jieshou, Fuyang, Anhui, 236500, China
| | - Meng Ma
- Department of ultrasound medicine, Jieshou People's Hospital, 339 Renmin Road, Jieshou, Fuyang, Anhui, 236500, China.
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10
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Yang Y, Chen X, Pan J, Ning H, Zhang Y, Bo Y, Ren X, Li J, Qin S, Wang D, Chen MM, Zhang Z. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. Cell 2024:S0092-8674(24)00712-8. [PMID: 39047727 DOI: 10.1016/j.cell.2024.06.038] [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: 06/09/2023] [Revised: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
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Affiliation(s)
- Yu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jieying Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Huiheng Ning
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yaojun Zhang
- State Key Laboratory of Oncology in South China, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Min-Min Chen
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
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11
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Zhu J, Zhang J, Lou Y, Zheng Y, Zheng X, Cen W, Ye L, Zhang Q. Developing a machine learning-based prognosis and immunotherapeutic response signature in colorectal cancer: insights from ferroptosis, fatty acid dynamics, and the tumor microenvironment. Front Immunol 2024; 15:1416443. [PMID: 39076986 PMCID: PMC11284049 DOI: 10.3389/fimmu.2024.1416443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
Instruction Colorectal cancer (CRC) poses a challenge to public health and is characterized by a high incidence rate. This study explored the relationship between ferroptosis and fatty acid metabolism in the tumor microenvironment (TME) of patients with CRC to identify how these interactions impact the prognosis and effectiveness of immunotherapy, focusing on patient outcomes and the potential for predicting treatment response. Methods Using datasets from multiple cohorts, including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we conducted an in-depth multi-omics study to uncover the relationship between ferroptosis regulators and fatty acid metabolism in CRC. Through unsupervised clustering, we discovered unique patterns that link ferroptosis and fatty acid metabolism, and further investigated them in the context of immune cell infiltration and pathway analysis. We developed the FeFAMscore, a prognostic model created using a combination of machine learning algorithms, and assessed its predictive power for patient outcomes and responsiveness to treatment. The FeFAMscore signature expression level was confirmed using RT-PCR, and ACAA2 progression in cancer was further verified. Results This study revealed significant correlations between ferroptosis regulators and fatty acid metabolism-related genes with respect to tumor progression. Three distinct patient clusters with varied prognoses and immune cell infiltration were identified. The FeFAMscore demonstrated superior prognostic accuracy over existing models, with a C-index of 0.689 in the training cohort and values ranging from 0.648 to 0.720 in four independent validation cohorts. It also responses to immunotherapy and chemotherapy, indicating a sensitive response of special therapies (e.g., anti-PD-1, anti-CTLA4, osimertinib) in high FeFAMscore patients. Conclusion Ferroptosis regulators and fatty acid metabolism-related genes not only enhance immune activation, but also contribute to immune escape. Thus, the FeFAMscore, a novel prognostic tool, is promising for predicting both the prognosis and efficacy of immunotherapeutic strategies in patients with CRC.
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Affiliation(s)
- Junchang Zhu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jinyuan Zhang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yunwei Lou
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yijie Zheng
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xuzhi Zheng
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Cen
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lechi Ye
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiongying Zhang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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12
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Yu G, Liu R, Li J, Zhao G, Wang Y. The immunotherapy in gastrointestinal stromal tumors. Heliyon 2024; 10:e33617. [PMID: 39040340 PMCID: PMC11260923 DOI: 10.1016/j.heliyon.2024.e33617] [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: 01/03/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Using Tyrosine Kinase Inhibitors (TKIs) for gastrointestinal stromal tumors (GIST) has significantly reduced the risk of recurrence and prolonged survival. Immunotherapy has demonstrated efficacy in multiple solid tumors, but its effectiveness in GIST remains uncertain. Although early clinical studies indicate good tolerability of immunotherapy in patients, the efficacy is not as desired. Therefore, identifying the subset of GIST patients who benefit from immunotherapy and coordinating the relationship between immunotherapy and TKI treatment are crucial issues to be explored. In this review, we aims to provide a retrospective analysis of relevant literature and find that GIST patients exhibit a rich presence of tumor-infiltrating immune cells, which play critical roles in the immune surveillance and evasion processes of tumors. This review incorporates a selection of 48 articles published between 2002 and 2023, sourced from PubMed, EBSCO, and Google Scholar databases.
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Affiliation(s)
- Guilin Yu
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Ruibin Liu
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
- Department of Clinical Integration of Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Jiayao Li
- Liaoning Normal University Haihua College,Liaoning, China
| | - Guohua Zhao
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Yue Wang
- Department of General Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
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13
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Zemek RM, Anagnostou V, Pires da Silva I, Long GV, Lesterhuis WJ. Exploiting temporal aspects of cancer immunotherapy. Nat Rev Cancer 2024; 24:480-497. [PMID: 38886574 DOI: 10.1038/s41568-024-00699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/20/2024]
Abstract
Many mechanisms underlying an effective immunotherapy-induced antitumour response are transient and critically time dependent. This is equally true for several immunological events in the tumour microenvironment induced by other cancer treatments. Immune checkpoint therapy (ICT) has proven to be very effective in the treatment of some cancers, but unfortunately, with many cancer types, most patients do not experience a benefit. To improve outcomes, a multitude of clinical trials are testing combinations of ICT with various other treatment modalities. Ideally, those combination treatments should take time-dependent immunological events into account. Recent studies have started to map the dynamic cellular and molecular changes that occur during treatment with ICT, in the tumour and systemically. Here, we overlay the dynamic ICT response with the therapeutic response following surgery, radiotherapy, chemotherapy and targeted therapies. We propose that by combining treatments in a time-conscious manner, we may optimally exploit the interactions between the individual therapies.
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Affiliation(s)
- Rachael M Zemek
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inês Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Crown Princess Mary Cancer Centre Westmead, Blacktown Hospital, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia
| | - Willem Joost Lesterhuis
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
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14
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Yu K, Tian Q, Feng S, Zhang Y, Cheng Z, Li M, Zhu H, He J, Li M, Xiong X. Integration analysis of cell division cycle-associated family genes revealed potential mechanisms of gliomagenesis and constructed an artificial intelligence-driven prognostic signature. Cell Signal 2024; 119:111168. [PMID: 38599441 DOI: 10.1016/j.cellsig.2024.111168] [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: 02/26/2024] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Cell division cycle-associated (CDCA) gene family members are essential cell proliferation regulators and play critical roles in various cancers. However, the function of the CDCA family genes in gliomas remains unclear. This study aims to elucidate the role of CDCA family members in gliomas using in vitro and in vivo experiments and bioinformatic analyses. We included eight glioma cohorts in this study. An unsupervised clustering algorithm was used to identify novel CDCA gene family clusters. Then, we utilized multi-omics data to elucidate the prognostic disparities, biological functionalities, genomic alterations, and immune microenvironment among glioma patients. Subsequently, the scRNA-seq analysis and spatial transcriptomic sequencing analysis were carried out to explore the expression distribution of CDCA2 in glioma samples. In vivo and in vitro experiments were used to investigate the effects of CDCA2 on the viability, migration, and invasion of glioma cells. Finally, based on ten machine-learning algorithms, we constructed an artificial intelligence-driven CDCA gene family signature called the machine learning-based CDCA gene family score (MLCS). Our results suggested that patients with the higher expression levels of CDCA family genes had a worse prognosis, more activated RAS signaling pathways, and more activated immunosuppressive microenvironments. CDCA2 knockdown inhibited the proliferation, migration, and invasion of glioma cells. In addition, the MLCS had robust and favorable prognostic predictive ability and could predict the response to immunotherapy and chemotherapy drug sensitivity.
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Affiliation(s)
- Kai Yu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Qi Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Shi Feng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Yonggang Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Ziqi Cheng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Mingyang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Hua Zhu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Jianying He
- Department of Orthopedics, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.
| | - Xiaoxing Xiong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.
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15
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Liu Q, Ma F, Zhang G. Molecular subtyping of skin cutaneous melanoma based on inflammatory response. Heliyon 2024; 10:e33088. [PMID: 39005905 PMCID: PMC11239590 DOI: 10.1016/j.heliyon.2024.e33088] [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: 12/21/2023] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
The inflammatory response plays a crucial role in determining the prognosis and therapeutic response of skin cutaneous melanoma (SKCM). However, the molecular subtypes based on the inflammatory response and their clinical significance in SKCM have not been extensively studied. Clustering analyses to identify inflammation subtypes of SKCM based on the expression levels of inflammation response gene. We identified three subtypes: Inflammation_H, Inflammation_M, and Inflammation_L, which offer a more nuanced understanding of the complex relationship between inflammation and SKCM. The Inflammation_H subtype is associated with the most favourable prognosis, and is characterised by high levels of immune infiltrates and PD-L1 expression, low levels of stemness, high differentiation, and high genomic stability. In contrast, the Inflammation_L subtype has the least favourable prognosis, with the lowest levels of immune infiltrates and PD-L1 expression, high levels of stemness, low differentiation, and low genomic stability. In addition, the Inf-score, which is a linear risk scoring model based on the expression levels of inflammatory response genes, can be a useful tool for clinicians to assess SKCM prognosis and guide therapeutic decisions. This scoring model shows promise for clinical use in predicting patient outcomes and helps clinicians tailor treatments for individual patients. In conclusion, these findings represent a significant contribution to our understanding of the molecular subtypes of SKCM based on the levels of inflammatory response genes and their potential clinical significance. However, further studies are necessary to validate these findings and explore the underlying mechanisms of different subtypes.
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Affiliation(s)
- Qian Liu
- Big Data Institute, Central South University, Changsha, Hunan, China
| | - Fangyu Ma
- Health Management center Xiangya Hospital, Central South University, China
| | - Guanxiong Zhang
- The Department of Dermatology, Xiangya Hospital, Central South University, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, China
- Furong Laboratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, China
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16
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Sorino C, Iezzi S, Ciuffreda L, Falcone I. Immunotherapy in melanoma: advances, pitfalls, and future perspectives. Front Mol Biosci 2024; 11:1403021. [PMID: 39086722 PMCID: PMC11289331 DOI: 10.3389/fmolb.2024.1403021] [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: 03/18/2024] [Accepted: 05/16/2024] [Indexed: 08/02/2024] Open
Abstract
Cutaneous melanoma is the deadliest and most aggressive form of skin cancer owing to its high capacity for metastasis. Over the past few decades, the management of this type of malignancy has undergone a significant revolution with the advent of both targeted therapies and immunotherapy, which have greatly improved patient quality of life and survival. Nevertheless, the response rates are still unsatisfactory for the presence of side effects and development of resistance mechanisms. In this context, tumor microenvironment has emerged as a factor affecting the responsiveness and efficacy of immunotherapy, and the study of its interplay with the immune system has offered new promising clinical strategies. This review provides a brief overview of the currently available immunotherapeutic strategies for melanoma treatment by analyzing both the positive aspects and those that require further improvement. Indeed, a better understanding of the mechanisms involved in the immune evasion of melanoma cells, with particular attention on the role of the tumor microenvironment, could provide the basis for improving current therapies and identifying new predictive biomarkers.
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17
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Li L, Guo Y, Gong B, Wang S, Wang MM, Sun P, Jiang S, Yang L. Association between tertiary lymphoid structures and clinical outcomes in cancer patients treated with immune checkpoint inhibitors: an updated meta-analysis. Front Immunol 2024; 15:1385802. [PMID: 38994363 PMCID: PMC11236553 DOI: 10.3389/fimmu.2024.1385802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
Background Although numerous studies have reported the association between tertiary lymphoid structures (TLSs) and clinical outcomes in cancer patients treated with immune checkpoint inhibitors (ICIs), there remains a lack of a newer and more comprehensive meta-analysis. The main objective of this study is to explore prognostic biomarkers in immunotherapy-related patients, through analyzing the associations between tertiary lymphoid structures (TLSs) and clinical outcomes in cancer patients treated with ICIs, so as to investigate their prognostic value in cancer patients treated with ICIs. Methods A comprehensive search was conducted until February 2024 across PubMed, Embase, Web of Science, and the Cochrane Library databases to identify relevant studies evaluating the association between tertiary lymphoid structures and clinical outcomes in cancer patients treated with ICIs. The clinical outcomes were overall survival (OS), progression-free survival (PFS), and objective response rate (ORR). Results Thirteen studies were incorporated in this meta-analysis, among which nine evaluated the prognostic value of TLSs. The results showed the high levels of TLSs predicted a significantly prolonged OS (pooled HR = 0.35, 95% CI: 0.24-0.53, p < 0.001) and PFS (pooled HR = 0.47, 95% CI: 0.31-0.72, p < 0.001), while lower ORR (pooled OR = 3.78, 95% CI: 2.26-6.33, p < 0.001) in cancer patients treated with ICIs. Conclusion Our results indicated that high levels of TLSs could predict a favorable prognosis for cancer patients treated with ICIs and have the potential to become a prognostic biomarker of immunotherapy-related patients.
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Affiliation(s)
- Lingli Li
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, China
| | - Yusheng Guo
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, China
| | - Bingxin Gong
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, China
| | - Sichen Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | | | - Peng Sun
- Clinical & Technical Support, Philips Healthcare, Beijing, China
| | - Shanshan Jiang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Molecular Imaging, Wuhan, China
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Guo YA, Kulshrestha T, Chang MM, Kassam I, Revkov E, Rizzetto S, Tan AC, Tan DS, Tan IB, Skanderup AJ. Transcriptome Deconvolution Reveals Absence of Cancer Cell Expression Signature in Immune Checkpoint Blockade Response. CANCER RESEARCH COMMUNICATIONS 2024; 4:1581-1596. [PMID: 38722600 PMCID: PMC11203396 DOI: 10.1158/2767-9764.crc-23-0442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 06/28/2024]
Abstract
Immune checkpoint therapy (ICB) has conferred significant and durable clinical benefit to some patients with cancer. However, most patients do not respond to ICB, and reliable biomarkers of ICB response are needed to improve patient stratification. Here, we performed a transcriptome-wide meta-analysis across 1,486 tumors from ICB-treated patients and tumors with expected ICB outcomes based on microsatellite status. Using a robust transcriptome deconvolution approach, we inferred cancer- and stroma-specific gene expression differences and identified cell-type specific features of ICB response across cancer types. Consistent with current knowledge, stromal expression of CXCL9, CXCL13, and IFNG were the top determinants of favorable ICB response. In addition, we identified a group of potential immune-suppressive genes, including FCER1A, associated with poor response to ICB. Strikingly, PD-L1 expression in stromal cells, but not cancer cells, is correlated with ICB response across cancer types. Furthermore, the unbiased transcriptome-wide analysis failed to identify cancer-cell intrinsic expression signatures of ICB response conserved across tumor types, suggesting that cancer cells lack tissue-agnostic transcriptomic features of ICB response. SIGNIFICANCE Our results challenge the prevailing dogma that cancer cells present tissue-agnostic molecular markers that modulate immune activity and ICB response, which has implications on the development of improved ICB diagnostics and treatments.
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Affiliation(s)
- Yu Amanda Guo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
| | - Tanmay Kulshrestha
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
| | - Mei Mei Chang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
| | - Irfahan Kassam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
| | - Egor Revkov
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore 117417, Republic of Singapore
| | - Simone Rizzetto
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
| | - Aaron C. Tan
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Republic of Singapore
| | - Daniel S.W. Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Republic of Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Republic of Singapore
| | - Anders J. Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, #02-01 Genome, Singapore 138672, Republic of Singapore
- School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore 117417, Republic of Singapore
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Republic of Singapore
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19
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Feng S, Wang D, Jin Y, Huang S, Liang T, Sun W, Du X, Zhuo L, Shan C, Zhang W, Jing T, Zhao S, Hong R, You L, Liu G, Chen L, Ye D, Li X, Yang Y. Blockage of L2HGDH-mediated S-2HG catabolism orchestrates macrophage polarization to elicit antitumor immunity. Cell Rep 2024; 43:114300. [PMID: 38829739 DOI: 10.1016/j.celrep.2024.114300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/21/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
The high infiltration of tumor-associated macrophages (TAMs) in the immunosuppressive tumor microenvironment prominently attenuates the efficacy of immune checkpoint blockade (ICB) therapies, yet the underlying mechanisms are not fully understood. Here, we investigate the metabolic profile of TAMs and identify S-2-hydroxyglutarate (S-2HG) as a potential immunometabolite that shapes macrophages into an antitumoral phenotype. Blockage of L-2-hydroxyglutarate dehydrogenase (L2HGDH)-mediated S-2HG catabolism in macrophages promotes tumor regression. Mechanistically, based on its structural similarity to α-ketoglutarate (α-KG), S-2HG has the potential to block the enzymatic activity of 2-oxoglutarate-dependent dioxygenases (2-OGDDs), consequently reshaping chromatin accessibility. Moreover, S-2HG-treated macrophages enhance CD8+ T cell-mediated antitumor activity and sensitivity to anti-PD-1 therapy. Overall, our study uncovers the role of blockage of L2HGDH-mediated S-2HG catabolism in orchestrating macrophage antitumoral polarization and, further, provides the potential of repolarizing macrophages by S-2HG to overcome resistance to anti-PD-1 therapy.
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Affiliation(s)
- Shuang Feng
- Institute of Translational Medicine, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Duowei Wang
- Institute of Translational Medicine, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Yanyan Jin
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Shi Huang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Tong Liang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Wei Sun
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Xiuli Du
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Luoyi Zhuo
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Chun Shan
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Wenbo Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Tian Jing
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Sen Zhao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Ruisi Hong
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Linjun You
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Guilai Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Leilei Chen
- Institutes of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Dan Ye
- Institutes of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, P.R. China.
| | - Xianjing Li
- Institute of Translational Medicine, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China.
| | - Yong Yang
- Institute of Translational Medicine, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China; School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, Jiangsu, P.R. China.
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20
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Wang B, Wang K, Wu D, Sahni S, Jiang P, Ruppin E. Decoupling the correlation between cytotoxic and exhausted T lymphocyte states enhances melanoma immunotherapy response prediction. iScience 2024; 27:109926. [PMID: 38832027 PMCID: PMC11145333 DOI: 10.1016/j.isci.2024.109926] [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: 11/28/2023] [Revised: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Cytotoxic T lymphocyte (CTL) and terminal exhausted T lymphocyte (ETL) activities crucially influence immune checkpoint inhibitor (ICI) response. Despite this, the efficacy of ETL and CTL transcriptomic signatures for response prediction remains limited. Investigating this across the TCGA and publicly available single-cell cohorts, we find a strong positive correlation between ETL and CTL expression signatures in most cancers. We hence posited that their limited predictability arises due to their mutually canceling effects on ICI response. Thus, we developed DETACH, a computational method to identify a gene set whose expression pinpoints to a subset of melanoma patients where the CTL and ETL correlation is low. DETACH enhances CTL's prediction accuracy, outperforming existing signatures. DETACH signature genes activity also demonstrates a positive correlation with lymphocyte infiltration and the prevalence of reactive T cells in the tumor microenvironment (TME), advancing our understanding of the CTL cell state within the TME.
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Affiliation(s)
- Binbin Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Kun Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Di Wu
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Sahil Sahni
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
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21
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Xu M, Ma X, Wang Y, Yu Z, Zheng X, Dai H, Xue C. Developing a prognostic model for skin melanoma based on the persistent tumor mutation burden and determining IL17REL as a therapeutic target. J Cancer Res Clin Oncol 2024; 150:313. [PMID: 38900244 PMCID: PMC11189994 DOI: 10.1007/s00432-024-05843-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND One popular and well-established marker for the immune checkpoint blockade (ICB) response is tumor mutation burden (TMB). Persistent TMB (pTMB), a subset of TMB, provides a better indicator to predict patient ICB therapy outcomes, as shown by some studies. Immune checkpoint drugs have significantly changed how melanoma is treated in recent years. METHODS In this study, we integrated the TCGA-SKCM database and data of pTMB of TCGA from the paper that first mentioned pTMB and analyzed mutational and Immune characteristics associated with pTMB level in SKCM. Next, the predictive DEGs were identified the subgroups of pTMB by Cox regression and LASSO analyses to construct a pTMB-related signature. Finally, the expression and Biological functions of signature genes was detected, and further validated in vitro assay. RESULTS In the current research, we explored the mutational and immunological features related to the level of TMB in cutaneous melanoma (CM). The high-pTMB subgroup exhibited an increasing incidence of gene changes and higher levels of immune cell infiltration. Subsequently, we established a pTMB-related signature based on the predictive DEGs and found the biological features and immune-associated variables between two distinct risk groups. Lastly, the results of the clinical sample validation demonstrated that the expression of IL17REL was down-regulated in the collected samples of individuals with CM. The in vitro assay results indicated that IL17REL effectively suppressed the proliferation, clonality, and migration of CM cells. CONCLUSION In conclusion, we have developed a prediction model associated with TMB and subsequently validated the potential influence of IL17REL on Overall Survival (OS) in patients diagnosed with melanoma.
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Affiliation(s)
- Mingze Xu
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Xinyi Ma
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Yuchong Wang
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Ziqin Yu
- Department of Radiology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaoli Zheng
- Basic Medical School, Southwest Medical University, Luzhou, Sichuan, China
| | - Haiying Dai
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China.
| | - Chunyu Xue
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China.
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22
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Luo Y, Yang L, Wu H, Xu H, Peng J, Wang Y, Zhou F. Exploring the Molecular Mechanism of Comorbidity of Type 2 Diabetes Mellitus and Colorectal Cancer: Insights from Bulk Omics and Single-Cell Sequencing Validation. Biomolecules 2024; 14:693. [PMID: 38927096 PMCID: PMC11201668 DOI: 10.3390/biom14060693] [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: 03/08/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The relationship between type 2 diabetes mellitus (T2DM) and colorectal cancer (CRC) has long been extensively recognized, but their crosstalk mechanisms based on gene regulation remain elusive. In our study, for the first time, bulk RNA-seq and single-cell RNA-seq data were used to explore the shared molecular mechanisms between T2DM and CRC. Moreover, Connectivity Map and molecular docking were employed to determine potential drugs targeting the candidate targets. Eight genes (EVPL, TACSTD2, SOX4, ETV4, LY6E, MLXIPL, ENTPD3, UGP2) were identified as characteristic comorbidity genes for T2DM and CRC, with EVPL and ENTPD3 further identified as core comorbidity genes. Our results demonstrated that upregulation of EVPL and downregulation of ENTPD3 were intrinsic molecular features throughout T2DM and CRC and were significantly associated with immune responses, immune processes, and abnormal immune landscapes in both diseases. Single-cell analysis highlighted a cancer-associated fibroblast (CAF) subset that specifically expressed ENTPD3 in CRC, which exhibited high heterogeneity and unique tumor-suppressive features that were completely different from classical cancer-promoting CAFs. Furthermore, ENTPD3+ CAFs could notably predict immunotherapy response in CRC, holding promise to be an immunotherapy biomarker at the single-cell level. Finally, we identified that droperidol may be a novel drug simultaneously targeting EVPL and ENTPD3. In conclusion, previous studies have often focused solely on metabolic alterations common to T2DM and CRC. Our study establishes EVPL and ENTPD3 as characteristic molecules and immune biomarkers of comorbidity in T2DM and CRC patients, and emphasizes the importance of considering immunological mechanisms in the co-development of T2DM and CRC.
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Affiliation(s)
- Yongge Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
| | - Lei Yang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Han Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Hui Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Jin Peng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - You Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
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23
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Geels SN, Moshensky A, Sousa RS, Murat C, Bustos MA, Walker BL, Singh R, Harbour SN, Gutierrez G, Hwang M, Mempel TR, Weaver CT, Nie Q, Hoon DSB, Ganesan AK, Othy S, Marangoni F. Interruption of the intratumor CD8 + T cell:Treg crosstalk improves the efficacy of PD-1 immunotherapy. Cancer Cell 2024; 42:1051-1066.e7. [PMID: 38861924 PMCID: PMC11285091 DOI: 10.1016/j.ccell.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
PD-1 blockade unleashes potent antitumor activity in CD8+ T cells but can also promote immunosuppressive T regulatory (Treg) cells, which may worsen the response to immunotherapy. Tumor-Treg inhibition is a promising strategy to improve the efficacy of checkpoint blockade immunotherapy; however, our understanding of the mechanisms supporting tumor-Tregs during PD-1 immunotherapy is incomplete. Here, we show that PD-1 blockade increases tumor-Tregs in mouse models of melanoma and metastatic melanoma patients. Mechanistically, Treg accumulation is not caused by Treg-intrinsic inhibition of PD-1 signaling but depends on an indirect effect of activated CD8+ T cells. CD8+ T cells produce IL-2 and colocalize with Tregs in mouse and human melanomas. IL-2 upregulates the anti-apoptotic protein ICOS on tumor-Tregs, promoting their accumulation. Inhibition of ICOS signaling before PD-1 immunotherapy improves control over immunogenic melanoma. Thus, interrupting the intratumor CD8+ T cell:Treg crosstalk represents a strategy to enhance the therapeutic efficacy of PD-1 immunotherapy.
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Affiliation(s)
- Shannon N Geels
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Alexander Moshensky
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Rachel S Sousa
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Claire Murat
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, CA, USA
| | - Benjamin L Walker
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Rima Singh
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Stacey N Harbour
- Department of Pathology, University of Alabama, Birmingham, Birmingham, AL, USA
| | - Giselle Gutierrez
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA
| | - Michael Hwang
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Thorsten R Mempel
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Casey T Weaver
- Department of Pathology, University of Alabama, Birmingham, Birmingham, AL, USA
| | - Qing Nie
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute, Santa Monica, CA, USA
| | - Anand K Ganesan
- Department of Dermatology, University of California, Irvine, Irvine, CA, USA
| | - Shivashankar Othy
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Francesco Marangoni
- Institute for Immunology, University of California, Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
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24
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Li X, Feng X, Zhou J, Luo Y, Chen X, Zhao J, Chen H, Xiong G, Luo G. A muti-modal feature fusion method based on deep learning for predicting immunotherapy response. J Theor Biol 2024; 586:111816. [PMID: 38589007 DOI: 10.1016/j.jtbi.2024.111816] [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: 10/21/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Immune checkpoint therapy (ICT) has greatly improved the survival of cancer patients in the past few years, but only a small number of patients respond to ICT. To predict ICT response, we developed a multi-modal feature fusion model based on deep learning (MFMDL). This model utilizes graph neural networks to map gene-gene relationships in gene networks to low dimensional vector spaces, and then fuses biological pathway features and immune cell infiltration features to make robust predictions of ICT. We used five datasets to validate the predictive performance of the MFMDL. These five datasets span multiple types of cancer, including melanoma, lung cancer, and gastric cancer. We found that the prediction performance of multi-modal feature fusion model based on deep learning is superior to other traditional ICT biomarkers, such as ICT targets or tumor microenvironment-associated markers. In addition, we also conducted ablation experiments to demonstrate the necessity of fusing different modal features, which can improve the prediction accuracy of the model.
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Affiliation(s)
- Xiong Li
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Xuan Feng
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Juan Zhou
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Yuchao Luo
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Xiao Chen
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Jiapeng Zhao
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Haowen Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
| | - Guoming Xiong
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Guoliang Luo
- School of Software, East China Jiaotong University, Nanchang 330013, China
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25
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Luo L, Jiang M, Wu H, Liu Y, Wang H, Zhou C, Ren S, Chen X, Jiang T, Xu C. SIRPG expression positively associates with an inflamed tumor microenvironment and response to PD-1 blockade. Cancer Immunol Immunother 2024; 73:147. [PMID: 38833156 PMCID: PMC11150346 DOI: 10.1007/s00262-024-03737-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: 03/21/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND This study aimed to investigate the relationship between signal regulatory protein gamma (SIRPG) and tumor immune microenvironment phenotypes or T cell mediated-adaptive antitumor immunity, and its predictive value for response to PD-1 blockade in cancers. METHODS Pan-cancer analysis of SIRPG expression and immune deconvolution was performed using transcriptomic data across 33 tumor types. Transcriptomic and clinical data from 157 patients with non-small-cell lung cancer (NSCLC) and melanoma received PD-1 blockade were analyzed. Expression characteristics of SIRPG were investigated using single-cell RNA sequencing (scRNA-seq) data of 103,599 cells. The effect of SIRPG expression was evaluated via SIRPG knockdown or overexpression in Jurkat T cells. RESULTS The results showed that most cancers with high SIRPG expression had significantly higher abundance of T cells, B cells, NK cells, M1 macrophages and cytotoxic lymphocytes and increased expression level of immunomodulatory factors regulating immune cell recruitment, antigen presentation, T cell activation and cytotoxicity, but markedly lower abundance of neutrophils, M2 macrophages, and myeloid-derived suppressor cells. High SIRPG expression was associated with favorable response to PD-1 blockade in both NSCLC and melanoma. scRNA-seq data suggested SIRPG was mainly expressed in CD8+ exhausted T and CD4+ regulatory T cells, and positively associated with immune checkpoint expression including PDCD1 and CTLA4. In vitro test showed SIRPG expression in T cells could facilitate expression of PDCD1 and CTLA4. CONCLUSION High SIRPG expression is associated with an inflamed immune phenotype in cancers and favorable response to PD-1 blockade, suggesting it would be a promising predictive biomarker for PD-1 blockade and novel immunotherapeutic target.
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Affiliation(s)
- Libo Luo
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Hong Wu
- Department of Oncology and Cancer Institute, Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 1st Ring Road, Chengdu, 610072, China
| | - Yiqiang Liu
- Department of Oncology and Cancer Institute, Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 1st Ring Road, Chengdu, 610072, China
| | - Haowei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China.
| | - Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital and Thoracic Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China.
| | - Chuan Xu
- Department of Oncology and Cancer Institute, Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 1st Ring Road, Chengdu, 610072, China.
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26
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Pineda JMB, Bradley RK. DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers. eLife 2024; 12:RP89017. [PMID: 38829686 PMCID: PMC11147511 DOI: 10.7554/elife.89017] [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] [Indexed: 06/05/2024] Open
Abstract
Cancer immune evasion contributes to checkpoint immunotherapy failure in many patients with metastatic cancers. The embryonic transcription factor DUX4 was recently characterized as a suppressor of interferon-γ signaling and antigen presentation that is aberrantly expressed in a small subset of primary tumors. Here, we report that DUX4 expression is a common feature of metastatic tumors, with ~10-50% of advanced bladder, breast, kidney, prostate, and skin cancers expressing DUX4. DUX4 expression is significantly associated with immune cell exclusion and decreased objective response to PD-L1 blockade in a large cohort of urothelial carcinoma patients. DUX4 expression is a significant predictor of survival even after accounting for tumor mutational burden and other molecular and clinical features in this cohort, with DUX4 expression associated with a median reduction in survival of over 1 year. Our data motivate future attempts to develop DUX4 as a biomarker and therapeutic target for checkpoint immunotherapy resistance.
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Affiliation(s)
- Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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Chen Q, Gao F, Wu J, Zhang K, Du T, Chen Y, Cai R, Zhao D, Deng R, Tang J. Comprehensive pan-cancer analysis of mitochondrial outer membrane permeabilisation activity reveals positive immunomodulation and assists in identifying potential therapeutic targets for immunotherapy resistance. Clin Transl Med 2024; 14:e1735. [PMID: 38899748 PMCID: PMC11187817 DOI: 10.1002/ctm2.1735] [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: 01/25/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Mitochondrial outer membrane permeabilisation (MOMP) plays a pivotal role in cellular death and immune activation. A deeper understanding of the impact of tumour MOMP on immunity will aid in guiding more effective immunotherapeutic strategies. METHODS A comprehensive pan-cancer dataset comprising 30 cancer-type transcriptomic cohorts, 20 immunotherapy transcriptomic cohorts and three immunotherapy scRNA-seq datasets was collected and analysed to determine the influence of tumour MOMP activity on clinical prognosis, immune infiltration and immunotherapy effectiveness. Leveraging 65 scRNA-Seq datasets, the MOMP signature (MOMP.Sig) was developed to accurately reflect tumour MOMP activity. The clinical predictive value of MOMP.Sig was explored through machine learning models. Integration of the MOMP.Sig model and a pan-cancer immunotherapy CRISPR screen further investigated potential targets to overcome immunotherapy resistance, which subsequently underwent clinical validation. RESULTS Our research revealed that elevated MOMP activity reduces mortality risk in cancer patients, drives the formation of an anti-tumour immune environment and enhances the response to immunotherapy. This finding emphasises the potential clinical application value of MOMP activity in immunotherapy. MOMP.Sig, offering a more precise indicator of tumour cell MOMP activity, demonstrated outstanding predictive efficacy in machine-learning models. Moreover, with the assistance of the MOMP.Sig model, FOXO1 was identified as a core modulator that promotes immune resistance. Finally, these findings were successfully validated in clinical immunotherapy cohorts of skin cutaneous melanoma and triple-negative breast cancer patients. CONCLUSIONS This study enhances our understanding of MOMP activity in immune modulation, providing valuable insights for more effective immunotherapeutic strategies across diverse tumours.
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Affiliation(s)
- Qingshan Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Fenglin Gao
- Department of Respiratory and Critical Care MedicineThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Junwan Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Biotherapy Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Kaiming Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Tian Du
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yuhong Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Ruizhao Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Rong Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Jun Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
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Zhang P, Yang Z, Liu Z, Zhang G, Zhang L, Zhang Z, Fan J. Deciphering lung adenocarcinoma evolution: Integrative single-cell genomics identifies the prognostic lung progression associated signature. J Cell Mol Med 2024; 28:e18408. [PMID: 38837585 DOI: 10.1111/jcmm.18408] [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: 03/21/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 06/07/2024] Open
Abstract
We employed single-cell analysis techniques, specifically the inferCNV method, to dissect the complex progression of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) through minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC). This approach enabled the identification of Cluster 6, which was significantly associated with LUAD progression. Our comprehensive analysis included intercellular interaction, transcription factor regulatory networks, trajectory analysis, and gene set variation analysis (GSVA), leading to the development of the lung progression associated signature (LPAS). Interestingly, we discovered that the LPAS not only accurately predicts the prognosis of LUAD patients but also forecasts genomic alterations, distinguishes between 'cold' and 'hot' tumours, and identifies potential candidates suitable for immunotherapy. PSMB1, identified within Cluster 6, was experimentally shown to significantly enhance cancer cell invasion and migration, highlighting the clinical relevance of LPAS in predicting LUAD progression and providing a potential target for therapeutic intervention. Our findings suggest that LPAS offers a novel biomarker for LUAD patient stratification, with significant implications for improving prognostic accuracy and guiding treatment decisions.
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Affiliation(s)
- 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
| | - Zijun Yang
- 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
| | - Zuo Liu
- 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
| | - 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
| | - Jun Fan
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Huang F, Jin L, Zhang X, Wang M, Zhou C. Integrated pan-cancer analysis reveals the immunological and prognostic potential of RBFOX2 in human tumors. Front Pharmacol 2024; 15:1302134. [PMID: 38881877 PMCID: PMC11176534 DOI: 10.3389/fphar.2024.1302134] [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: 09/26/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Background The role of RNA-binding fox one homolog 2 (RBFOX2) in the progression of multiple tumors is increasingly supported by evidence. However, the unclearness pertaining to the expression of RBFOX2, its prognostic potential, and its correlation with the tumor microenvironment (TME) in pan-cancer persists. This study aims to comprehensively investigate the immunological prognostic value of RBFOX2. Methods The Cancer Genome Atlas Gene Expression Omnibus Genotype-Tissue Expression (GTEx), TIMER2.0, Kaplan-Meier (K-M) Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were utilized for a systematic analysis of RBFOX2. This analysis included studying its expression, prognostic value, DNA methylation, enrichment analysis, immune infiltration cells, and immune-related genes. Additionally, qRT-PCR, CCK-8, colony formation, transwell assays, and immunohistochemistry were employed to analyze the expression and biological function of RBFOX2 in liver cancer. Results Variations in RBFOX2 expression have been observed across diverse tumors and have been identified as indicators of unfavorable prognosis. It is closely linked to immune infiltration cells, immune checkpoints, chemokines, and chemokine receptors in the TME. Higher levels of RBFOX2 have been significantly associated with low response and poor prognosis in patients with non-small cell lung cancer (NSCLC) and melanoma who receive immunotherapy. Furthermore, the DNA methylation of RBFOX2 varies across different types of cancer and has shown better prognosis in patients with BLCA, BRCA, CESC, COAD, DLBC, HNSC, LAML, LGG, LUAD, PAAD, SKCM and THYM. Interestingly, RBFOX2 expression was found to be lower in hepatocellular carcinoma (HCC) patients' tumor tissues compared to their paired adjacent tissues. In vitro studies have shown that knockdown of RBFOX2 significantly promotes the growth and metastasis of liver cancer cells. Conclusion This study investigates the correlation between DNA methylation, prognostic value, and immune cell infiltration with the expression of RBFOX2 in pan-cancer and indicates its potential role to inhibit metastasis of liver cancer.
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Affiliation(s)
- Fengxian Huang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xinyue Zhang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, Xi'an, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
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Liu H, Shi K, Wei Z, Zhang Y, Li J. T cell-mediated tumor killing based signature to predict the prognosis and immunotherapy for glioblastoma. Heliyon 2024; 10:e31207. [PMID: 38813229 PMCID: PMC11133811 DOI: 10.1016/j.heliyon.2024.e31207] [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: 08/08/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Despite the significant advancements in cancer treatment brought by immune checkpoint inhibitors (ICIs), their effectiveness in treating glioblastoma (GBM) remains highly dissatisfactory. Immunotherapy relies on the fundamental concept of T cell-mediated tumor killing (TTK). Nevertheless, additional investigation is required to explore its potential in prognostic prediction and regulation of tumor microenvironment (TME) in GBM. TTK sensitivity related genes (referred to as GSTTKs) were obtained from the TISIDB. The training cohort was available from the TCGA-GBM, while the independent validation group was gathered from GEO database. Firstly, we examined differentially expressed GSTTKs (DEGs) with limma package. Afterwards, the prognostic DEGs were identified and the TTK signature was established with univariate and LASSO Cox analyses. Next, we examined the correlation between the TTK signature and outcome of GBM as well as immune phenotypes of TME. Furthermore, the evaluation of TTK signature in predicting the effectiveness of immunotherapy has also been conducted. We successfully developed a TTK signature with an independent predictive value. Patients who had a high score experienced a worse prognosis compared to patients with low scores. The TTK signature showed a strong positive association with the infiltration degree of immunocyte and the presence of various immune checkpoints. Moreover, individuals with a lower score exhibited increased responsiveness to ICIs and experienced improved prognosis. In conclusions, we successfully developed and verified a TTK signature that has the ability to predict the outcome and immune characteristics of GBM. Furthermore, the TTK signature has the potential to direct the personalized immunotherapy for GBM.
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Affiliation(s)
- Hongchao Liu
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Kangke Shi
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhihao Wei
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Yu Zhang
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Jiaqiong Li
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
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Zhang X, Li J, Yang L, Zhu Y, Gao R, Zhang T, Chen X, Fu J, He G, Shi H, Peng S, Wu X. Targeted proteomics-determined multi-biomarker profiles developed classifier for prognosis and immunotherapy responses of advanced cervical cancer. Front Immunol 2024; 15:1391524. [PMID: 38835778 PMCID: PMC11148239 DOI: 10.3389/fimmu.2024.1391524] [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: 02/26/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
Background Cervical cancer (CC) poses a global health challenge, with a particularly poor prognosis in cases of recurrence, metastasis, or advanced stages. A single biomarker is inadequate to predict CC prognosis or identify CC patients likely to benefit from immunotherapy, presumably owing to tumor complexity and heterogeneity. Methods Using advanced Olink proteomics, we analyzed 92 oncology-related proteins in plasma from CC patients receiving immunotherapy, based upon the comparison of protein expression levels of pre-therapy with those of therapy-Cycle 6 in the partial response (PR) group and progressive disease (PD) group, respectively. Results 55 proteins were identified to exhibit differential expression trends across pre-therapy and post-therapy in both PR and PD groups. Enriched GO terms and KEGG pathways were associated with vital oncological and immunological processes. A logistic regression model, using 5 proteins (ITGB5, TGF-α, TLR3, WIF-1, and ERBB3) with highest AUC values, demonstrated good predictive performance for prognosis of CC patients undergoing immunotherapy and showed potential across different cancer types. The effectiveness of these proteins in prognosis prediction was further validated using TCGA-CESC datasets. A negative correlation and previously unidentified roles of WIF-1 in CC immunotherapy was also first determined. Conclusion Our findings reveal multi-biomarker profiles effectively predicting CC prognosis and identifying patients benefitting most from immunotherapy, especially for those with limited treatment options and traditionally poor prognosis, paving the way for personalized immunotherapeutic treatments and improved clinical strategies.
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Affiliation(s)
- Xu Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liuke Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Youwei Zhu
- Clinical Center of Bio-Therapy at Zhongshan Hospital & Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Rongrong Gao
- Clinical Center for Biotherapy at Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tiancheng Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Xuwen Chen
- Shanghai Kelin Clinical Bioinformatics Institute, Shanghai, China
| | - Jun Fu
- LC-Bio Technology Co., Ltd, Hangzhou, China
| | - Gaoyang He
- LC-Bio Technology Co., Ltd, Hangzhou, China
| | - Huijuan Shi
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Shenjie Peng
- Shanghai Medical College of Fudan University, Fudan University, Shanghai, China
| | - XiaoHua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Wang L, Wei Y, Jin Z, Liu F, Li X, Zhang X, Bai X, Jia Q, Zhu B, Chu Q. IFN-α/β/IFN-γ/IL-15 pathways identify GBP1-expressing tumors with an immune-responsive phenotype. Clin Exp Med 2024; 24:102. [PMID: 38758367 PMCID: PMC11101573 DOI: 10.1007/s10238-024-01328-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: 01/24/2024] [Accepted: 03/09/2024] [Indexed: 05/18/2024]
Abstract
Immunotherapy is widely used in cancer treatment; however, only a subset of patients responds well to it. Significant efforts have been made to identify patients who will benefit from immunotherapy. Successful anti-tumor immunity depends on an intact cancer-immunity cycle, especially long-lasting CD8+ T-cell responses. Interferon (IFN)-α/β/IFN-γ/interleukin (IL)-15 pathways have been reported to be involved in the development of CD8+ T cells. And these pathways may predict responses to immunotherapy. Herein, we aimed to analyze multiple public databases to investigate whether IFN-α/β/IFN-γ/IL-15 pathways could be used to predict the response to immunotherapy. Results showed that IFN-α/β/IFN-γ/IL-15 pathways could efficiently predict immunotherapy response, and guanylate-binding protein 1 (GBP1) could represent the IFN-α/β/IFN-γ/IL-15 pathways. In public and private cohorts, we further demonstrated that GBP1 could efficiently predict the response to immunotherapy. Functionally, GBP1 was mainly expressed in macrophages and strongly correlated with chemokines involved in T-cell migration. Therefore, our study comprehensively investigated the potential role of GBP1 in immunotherapy, which could serve as a novel biomarker for immunotherapy and a target for drug development.
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Affiliation(s)
- Lei Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Yuxuan Wei
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Zheng Jin
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400032, People's Republic of China
- Research Institute, GloriousMed Clinical Laboratory (Shanghai) Co., Ltd, Shanghai, 201318, People's Republic of China
| | - Fangfang Liu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Xuchang Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Xiao Zhang
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Army Medical University, Shigatse, 857000, People's Republic of China
| | - Xiumei Bai
- Army 953 Hospital, Shigatse Branch of Xinqiao Hospital, Army Medical University, Shigatse, 857000, People's Republic of China
| | - Qingzhu Jia
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
- Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, People's Republic of China
| | - Bo Zhu
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, People's Republic of China
- Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, People's Republic of China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China.
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Kang J, Lee JH, Cha H, An J, Kwon J, Lee S, Kim S, Baykan MY, Kim SY, An D, Kwon AY, An HJ, Lee SH, Choi JK, Park JE. Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types. Nat Commun 2024; 15:4067. [PMID: 38744958 PMCID: PMC11094150 DOI: 10.1038/s41467-024-48310-4] [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: 05/26/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
The complexity of the tumor microenvironment poses significant challenges in cancer therapy. Here, to comprehensively investigate the tumor-normal ecosystems, we perform an integrative analysis of 4.9 million single-cell transcriptomes from 1070 tumor and 493 normal samples in combination with pan-cancer 137 spatial transcriptomics, 8887 TCGA, and 1261 checkpoint inhibitor-treated bulk tumors. We define a myriad of cell states constituting the tumor-normal ecosystems and also identify hallmark gene signatures across different cell types and organs. Our atlas characterizes distinctions between inflammatory fibroblasts marked by AKR1C1 or WNT5A in terms of cellular interactions and spatial co-localization patterns. Co-occurrence analysis reveals interferon-enriched community states including tertiary lymphoid structure (TLS) components, which exhibit differential rewiring between tumor, adjacent normal, and healthy normal tissues. The favorable response of interferon-enriched community states to immunotherapy is validated using immunotherapy-treated cancers (n = 1261) including our lung cancer cohort (n = 497). Deconvolution of spatial transcriptomes discriminates TLS-enriched from non-enriched cell types among immunotherapy-favorable components. Our systematic dissection of tumor-normal ecosystems provides a deeper understanding of inter- and intra-tumoral heterogeneity.
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Affiliation(s)
- Junho Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jun Hyeong Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Joonha Kwon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Division of Cancer Data Science, National Cancer Center, Bioinformatics Branch, Goyang, Republic of Korea
| | - Seongwoo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seongryong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Mert Yakup Baykan
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - So Yeon Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dohyeon An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ah-Young Kwon
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Hee Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-si, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
- Biomedical Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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Hou J, Xie S, Gao J, Jiang T, Zhu E, Yang X, Jin Z, Long H, Zhang A, Yang F, Wang L, Zha H, Jia Q, Zhu B, Wang X. NK cell transfer overcomes resistance to PD-(L)1 therapy in aged mice. Exp Hematol Oncol 2024; 13:48. [PMID: 38725070 PMCID: PMC11080179 DOI: 10.1186/s40164-024-00511-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Cancer is the leading cause of death among older adults. Although the integration of immunotherapy has revolutionized the therapeutic landscape of cancer, the complex interactions between age and immunotherapy efficacy remain incompletely defined. Here, we aimed to elucidate the relationship between aging and immunotherapy resistance. METHODS Flow cytometry was performed to evaluate the infiltration of immune cells in the tumor microenvironment (TME). In vivo T cell proliferation, cytotoxicity and migration assays were performed to evaluate the antitumor capacity of tumor antigen-specific CD8+ T cells in mice. Real-time quantitative PCR (qPCR) was used to investigate the expression of IFN-γ-associated gene and natural killer (NK)-associated chemokine. Adoptive NK cell transfer was adopted to evaluate the effects of NK cells from young mice in overcoming the immunotherapy resistance of aged mice. RESULTS We found that elderly patients with advanced non-small cell lung cancer (aNSCLC) aged ≥ 75 years exhibited poorer progression-free survival (PFS), overall survival (OS) and a lower clinical response rate after immunotherapy. Mechanistically, we showed that the infiltration of NK cells was significantly reduced in aged mice compared to younger mice. Furthermore, the aged NK cells could also suppress the activation of tumor antigen-specific CD8+ T cells by inhibiting the recruitment and activation of CD103+ dendritic cells (DCs). Adoptive transfer of NK cells from young mice to aged mice promoted TME remodeling, and reversed immunotherapy resistance. CONCLUSION Our findings revealed the decreased sensitivity of elderly patients to immunotherapy, as well as in aged mice. This may be attributed to the reduction of NK cells in aged mice, which inhibits CD103+ DCs recruitment and its CD86 expression and ultimately leads to immunotherapy resistance.
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Affiliation(s)
- Junlei Hou
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Shuanglong Xie
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Jianbao Gao
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Tao Jiang
- Shanghai Pulmonary Hospital, Shanghai, 200082, China
| | - Enjian Zhu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Xuezhi Yang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Zheng Jin
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Haixia Long
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Anmei Zhang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Fei Yang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Lujing Wang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Haoran Zha
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Xinxin Wang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
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Liu J, He X, Deng S, Zhao S, Zhang S, Chen Z, Xue C, Zeng L, Zhao H, Zhou Y, Bai R, Xu Z, Liu S, Zhou Q, Li M, Zhang J, Huang X, Chen R, Wang L, Lin D, Zheng J. QDPR deficiency drives immune suppression in pancreatic cancer. Cell Metab 2024; 36:984-999.e8. [PMID: 38642552 DOI: 10.1016/j.cmet.2024.03.015] [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: 05/24/2023] [Revised: 12/20/2023] [Accepted: 03/28/2024] [Indexed: 04/22/2024]
Abstract
The relevance of biopterin metabolism in resistance to immune checkpoint blockade (ICB) therapy remains unknown. We demonstrate that the deficiency of quinoid dihydropteridine reductase (QDPR), a critical enzyme regulating biopterin metabolism, causes metabolite dihydrobiopterin (BH2) accumulation and decreases the ratio of tetrahydrobiopterin (BH4) to BH2 in pancreatic ductal adenocarcinomas (PDACs). The reduced BH4/BH2 ratio leads to an increase in reactive oxygen species (ROS) generation and a decrease in the distribution of H3K27me3 at CXCL1 promoter. Consequently, myeloid-derived suppressor cells are recruited to tumor microenvironment via CXCR2 causing resistance to ICB therapy. We discovered that BH4 supplementation is capable to restore the BH4/BH2 ratio, enhance anti-tumor immunity, and overcome ICB resistance in QDPR-deficient PDACs. Tumors with lower QDPR expression show decreased responsiveness to ICB therapy. These findings offer a novel strategy for selecting patient and combining therapies to improve the effectiveness of ICB therapy in PDAC.
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Affiliation(s)
- Ji Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Xiaowei He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Shuang Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Sihan Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Shaoping Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Ziming Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Chunling Xue
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Lingxing Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Hongzhe Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Yifan Zhou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Ruihong Bai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Zilan Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Shaoqiu Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Quanbo Zhou
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialiang Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Xudong Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Rufu Chen
- Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liqin Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.
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Qu J, Wu B, Chen L, Wen Z, Fang L, Zheng J, Shen Q, Heng J, Zhou J, Zhou J. CXCR6-positive circulating mucosal-associated invariant T cells can identify patients with non-small cell lung cancer responding to anti-PD-1 immunotherapy. J Exp Clin Cancer Res 2024; 43:134. [PMID: 38698468 PMCID: PMC11067263 DOI: 10.1186/s13046-024-03046-3] [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: 02/19/2024] [Accepted: 04/13/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Mucosal-associated invariant T (MAIT) cells have been reported to regulate tumor immunity. However, the immune characteristics of MAIT cells in non-small cell lung cancer (NSCLC) and their correlation with the treatment efficacy of immune checkpoint inhibitors (ICIs) remain unclear. PATIENTS AND METHODS In this study, we performed single-cell RNA sequencing (scRNA-seq), flow cytometry, and multiplex immunofluorescence assays to determine the proportion and characteristics of CD8+MAIT cells in patients with metastatic NSCLC who did and did not respond to anti-PD-1 therapy. Survival analyses were employed to determine the effects of MAIT proportion and C-X-C chemokine receptor 6 (CXCR6) expression on the prognosis of patients with advanced NSCLC. RESULTS The proportion of activated and proliferating CD8+MAIT cells were significantly higher in responders-derived peripheral blood mononuclear cells (PBMCs) and lung tissues before anti-PD-1 therapy, with enhanced expression of cytotoxicity-related genes including CCL4, KLRG1, PRF1, NCR3, NKG7, GZMB, and KLRK1. The responders' peripheral and tumor-infiltrating CD8+MAIT cells showed an upregulated CXCR6 expression. Similarly, CXCR6+CD8+MAIT cells from responders showed higher expression of cytotoxicity-related genes, such as CST7, GNLY, KLRG1, NKG7, and PRF1. Patients with ≥15.1% CD8+MAIT cells to CD8+T cells ratio and ≥35.9% CXCR6+CD8+MAIT cells to CD8+MAIT cells ratio in peripheral blood showed better progression-free survival (PFS) after immunotherapy. The role of CD8+MAIT cells in lung cancer immunotherapy was potentially mediated by classical/non-classical monocytes through the CXCL16-CXCR6 axis. CONCLUSION CD8+MAIT cells are a potential predictive biomarker for patients with NSCLC responding to anti-PD-1 therapy. The correlation between CD8+MAIT cells and immunotherapy sensitivity may be ascribed to high CXCR6 expression.
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Affiliation(s)
- Jingjing Qu
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
| | - Binggen Wu
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
| | - Lijun Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P.R. China
| | - Zuoshi Wen
- Department of Cardiology, The First Affiliated Hospital, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
| | - Liangjie Fang
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
| | - Jing Zheng
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
| | - Qian Shen
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
| | - Jianfu Heng
- Department of Clinical Pharmaceutical Research Institution, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P. R. China.
| | - Jianya Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China.
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China.
| | - Jianying Zhou
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, P. R. China
- The Clinical Research Center for Respiratory Diseases of Zhejiang Province, Hangzhou, Zhejiang, 310003, P. R. China
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Shen D, Lewinger JP. A Regularized Cox Hierarchical Model for Incorporating Annotation Information in Predictive Omic Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.09.584239. [PMID: 38617211 PMCID: PMC11014500 DOI: 10.1101/2024.03.09.584239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Background Associated with high-dimensional omics data there are often "meta-features" such as biological pathways and functional annotations, summary statistics from similar studies that can be informative for predicting an outcome of interest. We introduce a regularized hierarchical framework for integrating meta-features, with the goal of improving prediction and feature selection performance with time-to-event outcomes. Methods A hierarchical framework is deployed to incorporate meta-features. Regularization is applied to the omic features as well as the meta-features so that high-dimensional data can be handled at both levels. The proposed hierarchical Cox model can be efficiently fitted by a combination of iterative reweighted least squares and cyclic coordinate descent. Results In a simulation study we show that when the external meta-features are informative, the regularized hierarchical model can substantially improve prediction performance over standard regularized Cox regression. We illustrate the proposed model with applications to breast cancer and melanoma survival based on gene expression profiles, which show the improvement in prediction performance by applying meta-features, as well as the discovery of important omic feature sets with sparse regularization at meta-feature level. Conclusions The proposed hierarchical regularized regression model enables integration of external meta-feature information directly into the modeling process for time-to-event outcomes, improves prediction performance when the external meta-feature data is informative. Importantly, when the external meta-features are uninformative, the prediction performance based on the regularized hierarchical model is on par with standard regularized Cox regression, indicating robustness of the framework. In addition to developing predictive signatures, the model can also be deployed in discovery applications where the main goal is to identify important features associated with the outcome rather than developing a predictive model.
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Affiliation(s)
- Dixin Shen
- Clinical Data Science, Gilead Sciences, Foster City, USA
| | - Juan Pablo Lewinger
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA
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Upadhye A, Meza Landeros KE, Ramírez-Suástegui C, Schmiedel BJ, Woo E, Chee SJ, Malicki D, Coufal NG, Gonda D, Levy ML, Greenbaum JA, Seumois G, Crawford J, Roberts WD, Schoenberger SP, Cheroutre H, Ottensmeier CH, Vijayanand P, Ganesan AP. Intra-tumoral T cells in pediatric brain tumors display clonal expansion and effector properties. NATURE CANCER 2024; 5:791-807. [PMID: 38228835 DOI: 10.1038/s43018-023-00706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Brain tumors in children are a devastating disease in a high proportion of patients. Owing to inconsistent results in clinical trials in unstratified patients, the role of immunotherapy remains unclear. We performed an in-depth survey of the single-cell transcriptomes and clonal relationship of intra-tumoral T cells from children with brain tumors. Our results demonstrate that a large fraction of T cells in the tumor tissue are clonally expanded with the potential to recognize tumor antigens. Such clonally expanded T cells display enrichment of transcripts linked to effector function, tissue residency, immune checkpoints and signatures of neoantigen-specific T cells and immunotherapy response. We identify neoantigens in pediatric brain tumors and show that neoantigen-specific T cell gene signatures are linked to better survival outcomes. Notably, among the patients in our cohort, we observe substantial heterogeneity in the degree of clonal expansion and magnitude of T cell response. Our findings suggest that characterization of intra-tumoral T cell responses may enable selection of patients for immunotherapy, an approach that requires prospective validation in clinical trials.
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Affiliation(s)
- Aditi Upadhye
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kevin E Meza Landeros
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | | | | | - Edwin Woo
- Southampton University Hospitals NHS Trust, Southampton, UK
| | - Serena J Chee
- Department of Respiratory Medicine, Liverpool Heart and Chest Hospital NHS Foundation Trust, Liverpool, UK
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Denise Malicki
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - David Gonda
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurological Surgery, University of California San Diego, La Jolla, CA, USA
| | - Michael L Levy
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurological Surgery, University of California San Diego, La Jolla, CA, USA
| | | | | | - John Crawford
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California Irvine, Irvine, CA, USA
- Children's Hospital Orange County, Irvine, CA, USA
| | - William D Roberts
- Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | | | - Christian H Ottensmeier
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Anusha-Preethi Ganesan
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Rady Children's Hospital, San Diego, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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Eum HH, Jeong D, Kim N, Jo A, Na M, Kang H, Hong Y, Kong JS, Jeong GH, Yoo SA, Lee HO. Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy. Br J Cancer 2024; 130:1388-1401. [PMID: 38424167 PMCID: PMC11014989 DOI: 10.1038/s41416-024-02617-7] [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] [Received: 06/08/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Immune checkpoint inhibitors unleash inhibitory signals on T cells conferred by tumors and surrounding stromal cells. Despite the clinical efficacy of checkpoint inhibitors, the lack of target expression and persistence of immunosuppressive cells limit the pervasive effectiveness of the therapy. These limitations may be overcome by alternative approaches that co-stimulate T cells and the immune microenvironment. METHODS We analyzed single-cell RNA sequencing data from multiple human cancers and a mouse tumor transplant model to discover the pleiotropic expression of the Interleukin 7 (IL-7) receptor on T cells, macrophages, and dendritic cells. RESULTS Our experiment on the mouse model demonstrated that recombinant IL-7 therapy induces tumor regression, expansion of effector CD8 T cells, and pro-inflammatory activation of macrophages. Moreover, spatial transcriptomic data support immunostimulatory interactions between macrophages and T cells. CONCLUSION These results indicate that IL-7 therapy induces anti-tumor immunity by activating T cells and pro-inflammatory myeloid cells, which may have diverse therapeutic applicability.
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Affiliation(s)
- Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Dasom Jeong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Areum Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Minsu Na
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Huiram Kang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yourae Hong
- Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jin-Sun Kong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Gi Heon Jeong
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seung-Ah Yoo
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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Mei J, Cai Y, Xu R, Li Q, Chu J, Luo Z, Sun Y, Shi Y, Xu J, Li D, Liang S, Jiang Y, Liu J, Qian Z, Zhou J, Wan M, Yang Y, Zhu Y, Zhang Y, Yin Y. Conserved immuno-collagenic subtypes predict response to immune checkpoint blockade. Cancer Commun (Lond) 2024; 44:554-575. [PMID: 38507505 PMCID: PMC11110954 DOI: 10.1002/cac2.12538] [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: 03/06/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) has revolutionized the treatment of various cancer types. Despite significant preclinical advancements in understanding mechanisms, identifying the molecular basis and predictive biomarkers for clinical ICB responses remains challenging. Recent evidence, both preclinical and clinical, underscores the pivotal role of the extracellular matrix (ECM) in modulating immune cell infiltration and behaviors. This study aimed to create an innovative classifier that leverages ECM characteristics to enhance the effectiveness of ICB therapy. METHODS We analyzed transcriptomic collagen activity and immune signatures in 649 patients with cancer undergoing ICB therapy. This analysis led to the identification of three distinct immuno-collagenic subtypes predictive of ICB responses. We validated these subtypes using the transcriptome data from 9,363 cancer patients from The Cancer Genome Atlas (TCGA) dataset and 1,084 in-house samples. Additionally, novel therapeutic targets were identified based on these established immuno-collagenic subtypes. RESULTS Our categorization divided tumors into three subtypes: "soft & hot" (low collagen activity and high immune infiltration), "armored & cold" (high collagen activity and low immune infiltration), and "quiescent" (low collagen activity and immune infiltration). Notably, "soft & hot" tumors exhibited the most robust response to ICB therapy across various cancer types. Mechanistically, inhibiting collagen augmented the response to ICB in preclinical models. Furthermore, these subtypes demonstrated associations with immune activity and prognostic predictive potential across multiple cancer types. Additionally, an unbiased approach identified B7 homolog 3 (B7-H3), an available drug target, as strongly expressed in "armored & cold" tumors, relating with poor prognosis. CONCLUSION This study introduces histopathology-based universal immuno-collagenic subtypes capable of predicting ICB responses across diverse cancer types. These findings offer insights that could contribute to tailoring personalized immunotherapeutic strategies for patients with cancer.
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Affiliation(s)
- Jie Mei
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuP. R. China
- The First Clinical Medicine CollegeNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Yun Cai
- Departments of GynecologyWuxi Maternal and Child Health Care Hospital, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
| | - Rui Xu
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuP. R. China
- The First Clinical Medicine CollegeNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Qing Li
- Departments of OncologyXuzhou Central HospitalThe Xuzhou School of Clinical Medicine of Nanjing Medical UniversityXuzhouJiangsuP. R. China
| | - Jiahui Chu
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuP. R. China
- The First Clinical Medicine CollegeNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Zhiwen Luo
- Department of Sports MedicineHuashan Hospital Affiliated to Fudan UniversityShanghaiP. R. China
| | - Yaying Sun
- Department of Sports MedicineShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiP. R. China
| | - Yuxin Shi
- Departments of OncologyThe Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
| | - Junying Xu
- Departments of OncologyThe Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
| | - Di Li
- Shanghai Outdo Biotech Co., Ltd., National Engineering Center for BiochipShanghaiP. R. China
| | - Shuai Liang
- Departments of OncologyThe Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
| | - Ying Jiang
- Departments of GynecologyWuxi Maternity and Child Health Care HospitalAffiliated Women's Hospital of Jiangnan UniversityWuxiJiangsuP. R. China
| | - Jiayu Liu
- Departments of GynecologyWuxi Maternity and Child Health Care HospitalAffiliated Women's Hospital of Jiangnan UniversityWuxiJiangsuP. R. China
| | - Zhiwen Qian
- Departments of GynecologyWuxi Maternal and Child Health Care Hospital, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
| | - Jiaofeng Zhou
- Department of PhysiologySchool of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Mengyun Wan
- Department of PhysiologySchool of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Yunlong Yang
- Department of Cellular and Genetic MedicineSchool of Basic Medical Sciences, Fudan UniversityShanghaiP. R. China
| | - Yichao Zhu
- Department of PhysiologySchool of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsuP. R. China
| | - Yan Zhang
- Departments of GynecologyWuxi Maternal and Child Health Care Hospital, Wuxi Medical Center, Nanjing Medical UniversityWuxiJiangsuP. R. China
- Departments of GynecologyWuxi Maternity and Child Health Care HospitalAffiliated Women's Hospital of Jiangnan UniversityWuxiJiangsuP. R. China
| | - Yongmei Yin
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuP. R. China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical UniversityNanjingJiangsuP. R. China
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Song P, Li Y, Zhang M, Lyu B, Cui Y, Gao S. Comprehensive Analysis of a Dendritic Cell Marker Genes Signature to Predict Prognosis and Immunotherapy Response in Lung Adenocarcinoma. J Immunother 2024:00002371-990000000-00101. [PMID: 38679823 DOI: 10.1097/cji.0000000000000521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 05/01/2024]
Abstract
With the development of immune checkpoints inhibitors (ICIs), immunotherapy has recently taken center stage in cancer treatment. Dendritic cells exert complicated and important functions in antitumor immunity. This study aims to construct a novel dendritic cell marker gene signature (DCMGS) to predict the prognosis and immunotherapy response of lung adenocarcinoma (LUAD). DC marker genes in LUAD were identified by analysis of single-cell RNA sequencing data. 6 genes (G0S2, KLF4, ALDH2, IER3, TXN, CD69) were screened as the most prognosis-related genes for constructing DCMGS on a training cohort from TCGA data set. Patients were divided into high-risk and low-risk groups by DCMGS risk score based on overall survival time. Then, the predictive ability of the risk model was validated in 6 independent cohorts. DCMGS was verified to be an independent prognostic factor in multivariate analysis. Furthermore, we performed pathway enrichment analysis to explore possible biological mechanisms of the powerful predictive ability of DCMGS, and immune cell infiltration landscape and inflammatory activities were exhibited to reflect the immune profile. Notably, we bridged DCMGS with expression of immune checkpoints and TCR/BCR repertoire diversity that can inflect immunotherapy response. Finally, the predictive ability of DCMGS in immunotherapy response was also validated by 2 cohorts that had received immunotherapy. As a result, the patients with lower DCMGS risk scores showed a better prognosis and immunotherapy response. In conclusion, DCMGS was suggested to be a promising prognostic indicator for LUAD and a desirable predictor for immunotherapy response.
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Affiliation(s)
- Peng Song
- Department of Thoracic Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuan Li
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Moyan Zhang
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baihan Lyu
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Yong Cui
- Department of Thoracic Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Chen D, Liu P, Lu X, Li J, Qi D, Zang L, Lin J, Liu Y, Zhai S, Fu D, Weng Y, Li H, Shen B. Pan-cancer analysis implicates novel insights of lactate metabolism into immunotherapy response prediction and survival prognostication. J Exp Clin Cancer Res 2024; 43:125. [PMID: 38664705 PMCID: PMC11044366 DOI: 10.1186/s13046-024-03042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Immunotherapy has emerged as a potent clinical approach for cancer treatment, but only subsets of cancer patients can benefit from it. Targeting lactate metabolism (LM) in tumor cells as a method to potentiate anti-tumor immune responses represents a promising therapeutic strategy. METHODS Public single-cell RNA-Seq (scRNA-seq) cohorts collected from patients who received immunotherapy were systematically gathered and scrutinized to delineate the association between LM and the immunotherapy response. A novel LM-related signature (LM.SIG) was formulated through an extensive examination of 40 pan-cancer scRNA-seq cohorts. Then, multiple machine learning (ML) algorithms were employed to validate the capacity of LM.SIG for immunotherapy response prediction and survival prognostication based on 8 immunotherapy transcriptomic cohorts and 30 The Cancer Genome Atlas (TCGA) pan-cancer datasets. Moreover, potential targets for immunotherapy were identified based on 17 CRISPR datasets and validated via in vivo and in vitro experiments. RESULTS The assessment of LM was confirmed to possess a substantial relationship with immunotherapy resistance in 2 immunotherapy scRNA-seq cohorts. Based on large-scale pan-cancer data, there exists a notably adverse correlation between LM.SIG and anti-tumor immunity as well as imbalance infiltration of immune cells, whereas a positive association was observed between LM.SIG and pro-tumorigenic signaling. Utilizing this signature, the ML model predicted immunotherapy response and prognosis with an AUC of 0.73/0.80 in validation sets and 0.70/0.87 in testing sets respectively. Notably, LM.SIG exhibited superior predictive performance across various cancers compared to published signatures. Subsequently, CRISPR screening identified LDHA as a pan-cancer biomarker for estimating immunotherapy response and survival probability which was further validated using immunohistochemistry (IHC) and spatial transcriptomics (ST) datasets. Furthermore, experiments demonstrated that LDHA deficiency in pancreatic cancer elevated the CD8+ T cell antitumor immunity and improved macrophage antitumoral polarization, which in turn enhanced the efficacy of immunotherapy. CONCLUSIONS We unveiled the tight correlation between LM and resistance to immunotherapy and further established the pan-cancer LM.SIG, holds the potential to emerge as a competitive instrument for the selection of patients suitable for immunotherapy.
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Affiliation(s)
- Dongjie Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Pengyi Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xiongxiong Lu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Jingfeng Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Debin Qi
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Longjun Zang
- Department of General Surgery, Taiyuan Central Hospital, Taiyuan, Shanxi, 030009, China
| | - Jiayu Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yihao Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Shuyu Zhai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Da Fu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Yuanchi Weng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Hongzhe Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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43
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Chen H, Yan D, Sun J, Zhou M. Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning. J Chem Inf Model 2024; 64:3579-3591. [PMID: 38545680 DOI: 10.1021/acs.jcim.4c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Exhausted T cells are a key component of immune cells that play a crucial role in the immune response against cancer and influence the efficacy of immunotherapy. Accurate assessment and measurement of T-cell exhaustion (TEX) are critical for understanding the heterogeneity of TEX in the tumor microenvironment (TME) and tailoring individualized immunotherapeutic strategies. In this study, we introduced DeepEpiTEX, a novel computational framework based on deep neural networks, for inferring the developmental hierarchy and functional states of exhausted T cells in the TME from epigenetic profiles. DeepEpiTEX was trained using various modalities of epigenetic data, including DNA methylation data, microRNA expression data, and long non-coding RNA expression data from 30 bulk solid cancer types in the TCGA pan-cancer cohort, and identified five optimal TEX subsets with significant survival differences across the majority of cancer types. The performance of DeepEpiTEX was further evaluated and validated in external multi-center and multi-type cancer cohorts, consistently demonstrating its generalizability and applicability in different experimental settings. In addition, we discovered the potential relationship between TEX subsets identified by DeepEpiTEX and the response to immune checkpoint blockade therapy, indicating that individuals with immune-favorable TEX subsets may experience the greatest benefits. In conclusion, our study sheds light on the role of epigenetic regulation in TEX and provides a powerful and promising tool for categorizing TEX in different disease settings.
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Affiliation(s)
- Hongyan Chen
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Dongxue Yan
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jie Sun
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Meng Zhou
- School of Biomedical Engineering, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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44
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Xiong G, Shan J, Chong Q, Cui Y. Tertiary lymphoid structures associated with enhanced anti-tumor immunity and favorable prognosis in cervical squamous carcinoma. Aging (Albany NY) 2024; 16:6898-6920. [PMID: 38709170 PMCID: PMC11087108 DOI: 10.18632/aging.205733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/13/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Cervical squamous carcinoma (CESC) is the main subtype of cervical cancer. Unfortunately, there are presently no effective treatment options for advanced and recurrent CESC. Tertiary lymphoid structures (TLSs) are clusters of lymphoid cells that resemble secondary lymphoid organs; nevertheless, there is no summary of the clinical importance of TLS in CESC. METHODS A large set of transcriptomic and single-cell RNA-sequencing (scRNA-seq) datasets were used to analyze the pattern of TLS and its immuno-correlations in CESC. Additionally, an independent in-house cohort was collected to validate the correlation between TLS and TME features. RESULTS In the current study, we found that the presence of TLS could predict better prognosis in CESC and was correlated with the activation of immunological signaling pathways and enrichment of immune cell subpopulations. In addition, TLS was associated with reduced proliferation activity in tumor cells, indicating the negative correlation between TLS and the degree of malignancy. Last but not least, in two independent immunotherapy cohorts, tumors with the presence of TLS were more sensitive to immunotherapy. CONCLUSION Overall, TLS is related to an inflamed TME and identified immune-hot tumors, which could be an indicator for the identification of immunological features in CESC.
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Affiliation(s)
- Guohai Xiong
- Department of Gynaecology, Yancheng Third People’s Hospital, Yancheng 224008, China
- Department of Gynaecology, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng 224008, China
| | - Jinmei Shan
- Department of Gynaecology, Yancheng Third People’s Hospital, Yancheng 224008, China
- Department of Gynaecology, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng 224008, China
| | - Qingguo Chong
- Department of Gynaecology, Yancheng Third People’s Hospital, Yancheng 224008, China
- Department of Gynaecology, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng 224008, China
| | - Yueqing Cui
- Department of Gynaecology, Yancheng Third People’s Hospital, Yancheng 224008, China
- Department of Gynaecology, The Yancheng School of Clinical Medicine of Nanjing Medical University, Yancheng 224008, China
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45
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Zheng K, Hai Y, Chen H, Zhang Y, Hu X, Ni K. Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model. J Transl Med 2024; 22:365. [PMID: 38632658 PMCID: PMC11025237 DOI: 10.1186/s12967-024-05186-8] [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: 12/31/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Molecular subtyping is expected to enable precise treatment. However, reliable subtyping strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE), we aimed to develop a novel TIDE-based subtyping strategy to guide personalized immunotherapy in the bladder cancer (BC). METHODS Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. Subsequently, consensus clustering was applied to classify BC patients based on TIDE marker-genes. Patients' clinicopathological, molecular features and signaling pathways of the different TIDE subtypes were well characterized. We also utilize the deconvolution algorithms to analyze the tumor microenvironment, and further explore the sensitivity and mechanisms of each subtype to immunotherapy. Furthermore, BC patient clinical information, real-world BC samples and urine samples were collected for the validation of our findings, which were used for RNA-seq analysis, H&E staining, immunohistochemistry and immunofluorescence staining, and enzyme-linked immunosorbent assay. Finally, we also explored the conservation of our novel TIDE subtypes in pan-cancers. RESULTS We identified 69 TIDE biomarker genes and classified BC samples into three subtypes using consensus clustering. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples and collected patient clinical data. This subtyping method was proved to be more efficient than previous known methods in identifying non-responders to immunotherapy. We also propose that combining our TIDE subtypes with known biomarkers can potentially improve the sensitivity and specificity of these biomarkers. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, we confirmed that the TIDE subtypes are conserved across the pan-tumors. CONCLUSIONS Our novel TIDE-based subtyping method can serve as a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized therapy decisions for selecting potential beneficiaries and excluding resistant patients of ICB therapy.
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Affiliation(s)
- Kun Zheng
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Youlong Hai
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Hongqi Chen
- Department of Urology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, 215200, Jiangsu, China
| | - Yukun Zhang
- Beijing University of Chinese Medicine East Hospital, Zaozhuang Hospital, Zaozhuang, 277000, Shandong, China
| | - Xiaoyong Hu
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Kai Ni
- Department of Urology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
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46
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Pereira MVA, Galvani RG, Gonçalves-Silva T, de Vasconcelo ZFM, Bonomo A. Tissue adaptation of CD4 T lymphocytes in homeostasis and cancer. Front Immunol 2024; 15:1379376. [PMID: 38690280 PMCID: PMC11058666 DOI: 10.3389/fimmu.2024.1379376] [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: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The immune system is traditionally classified as a defense system that can discriminate between self and non-self or dangerous and non-dangerous situations, unleashing a tolerogenic reaction or immune response. These activities are mainly coordinated by the interaction between innate and adaptive cells that act together to eliminate harmful stimuli and keep tissue healthy. However, healthy tissue is not always the end point of an immune response. Much evidence has been accumulated over the years, showing that the immune system has complex, diversified, and integrated functions that converge to maintaining tissue homeostasis, even in the absence of aggression, interacting with the tissue cells and allowing the functional maintenance of that tissue. One of the main cells known for their function in helping the immune response through the production of cytokines is CD4+ T lymphocytes. The cytokines produced by the different subtypes act not only on immune cells but also on tissue cells. Considering that tissues have specific mediators in their architecture, it is plausible that the presence and frequency of CD4+ T lymphocytes of specific subtypes (Th1, Th2, Th17, and others) maintain tissue homeostasis. In situations where homeostasis is disrupted, such as infections, allergies, inflammatory processes, and cancer, local CD4+ T lymphocytes respond to this disruption and, as in the healthy tissue, towards the equilibrium of tissue dynamics. CD4+ T lymphocytes can be manipulated by tumor cells to promote tumor development and metastasis, making them a prognostic factor in various types of cancer. Therefore, understanding the function of tissue-specific CD4+ T lymphocytes is essential in developing new strategies for treating tissue-specific diseases, as occurs in cancer. In this context, this article reviews the evidence for this hypothesis regarding the phenotypes and functions of CD4+ T lymphocytes and compares their contribution to maintaining tissue homeostasis in different organs in a steady state and during tumor progression.
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Affiliation(s)
- Marina V. A. Pereira
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- Laboratory of High Complexity, Fernandes Figueira National Institute for The Health of Mother, Child, and Adolescent, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rômulo G. Galvani
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Triciana Gonçalves-Silva
- National Center for Structural Biology and Bioimaging - CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zilton Farias Meira de Vasconcelo
- Laboratory of High Complexity, Fernandes Figueira National Institute for The Health of Mother, Child, and Adolescent, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Adriana Bonomo
- Laboratory on Thymus Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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47
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Wang Y, Pattarayan D, Huang H, Zhao Y, Li S, Wang Y, Zhang M, Li S, Yang D. Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer. Nat Commun 2024; 15:3178. [PMID: 38609378 PMCID: PMC11015024 DOI: 10.1038/s41467-024-47433-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: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Chemo-immunotherapy combinations have been regarded as one of the most practical ways to improve immunotherapy response in cancer patients. In this study, we integrate the transcriptomics data from anti-PD-1-treated tumors and compound-treated cancer cell lines to systematically screen for chemo-immunotherapy synergisms in silico. Through analyzing anti-PD-1 induced expression changes in patient tumors, we develop a shift ability score to measure if a chemotherapy or a small molecule inhibitor treatment can shift anti-PD-1 resistance in tumor cells. By applying shift ability analysis to 41,321 compounds and 16,853 shRNA treated cancer cell lines transcriptomic data, we characterize the landscape of chemo-immunotherapy synergism and experimentally validated a mitochondrial RNA-dependent mechanism for drug-induced immune activation in tumor. Our study represents an effort to mechanistically characterize chemo-immunotherapy synergism and will facilitate future pre-clinical and clinical studies.
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Affiliation(s)
- Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Dhamotharan Pattarayan
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Haozhe Huang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yueshan Zhao
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Sihan Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yifei Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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48
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Tian J, Quek C. Understanding the Tumor Microenvironment in Melanoma Patients with In-Transit Metastases and Its Impacts on Immune Checkpoint Immunotherapy Responses. Int J Mol Sci 2024; 25:4243. [PMID: 38673829 PMCID: PMC11050678 DOI: 10.3390/ijms25084243] [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: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Melanoma is the leading cause of global skin cancer-related death and currently ranks as the third most commonly diagnosed cancer in Australia. Melanoma patients with in-transit metastases (ITM), a type of locoregional metastasis located close to the primary tumor site, exhibit a high likelihood of further disease progression and poor survival outcomes. Immunotherapies, particularly immune checkpoint inhibitors (ICI), have demonstrated remarkable efficacy in ITM patients with reduced occurrence of further metastases and prolonged survival. The major challenge of immunotherapeutic efficacy lies in the limited understanding of melanoma and ITM biology, hindering our ability to identify patients who likely respond to ICIs effectively. In this review, we provided an overview of melanoma and ITM disease. We outlined the key ICI therapies and the critical immune features associated with therapy response or resistance. Lastly, we dissected the underlying biological components, including the cellular compositions and their communication networks within the tumor compartment, to enhance our understanding of the interactions between immunotherapy and melanoma, providing insights for future investigation and the development of drug targets and predictive biomarkers.
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Affiliation(s)
| | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia;
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Lauss M, Phung B, Borch TH, Harbst K, Kaminska K, Ebbesson A, Hedenfalk I, Yuan J, Nielsen K, Ingvar C, Carneiro A, Isaksson K, Pietras K, Svane IM, Donia M, Jönsson G. Molecular patterns of resistance to immune checkpoint blockade in melanoma. Nat Commun 2024; 15:3075. [PMID: 38594286 PMCID: PMC11004175 DOI: 10.1038/s41467-024-47425-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.
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Affiliation(s)
- Martin Lauss
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Bengt Phung
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Troels Holz Borch
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Joan Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Kari Nielsen
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Dermatology, Skåne University Hospital and Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Christian Ingvar
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Ana Carneiro
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital Comprehensive Cancer Center, 22185, Lund, Sweden
| | - Karolin Isaksson
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Surgery, Kristianstad Hospital, 29133, Kristianstad, Sweden
| | - Kristian Pietras
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Göran Jönsson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden.
- Lund University Cancer Center, LUCC, Lund, Sweden.
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50
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Bai X, Attrill GH, Gide TN, Ferguson PM, Nahar KJ, Shang P, Vergara IA, Palendira U, da Silva IP, Carlino MS, Menzies AM, Long GV, Scolyer RA, Wilmott JS, Quek C. Stroma-infiltrating T cell spatiotypes define immunotherapy outcomes in adolescent and young adult patients with melanoma. Nat Commun 2024; 15:3014. [PMID: 38589406 PMCID: PMC11002019 DOI: 10.1038/s41467-024-47301-9] [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: 04/16/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
The biological underpinnings of therapeutic resistance to immune checkpoint inhibitors (ICI) in adolescent and young adult (AYA) melanoma patients are incompletely understood. Here, we characterize the immunogenomic profile and spatial architecture of the tumor microenvironment (TME) in AYA (aged ≤ 30 years) and older adult (aged 31-84 years) patients with melanoma, to determine the AYA-specific features associated with ICI treatment outcomes. We identify two ICI-resistant spatiotypes in AYA patients with melanoma showing stroma-infiltrating lymphocytes (SILs) that are distinct from the adult TME. The SILhigh subtype was enriched in regulatory T cells in the peritumoral space and showed upregulated expression of immune checkpoint molecules, while the SILlow subtype showed a lack of immune activation. We establish a young immunosuppressive melanoma score that can predict ICI responsiveness in AYA patients and propose personalized therapeutic strategies for the ICI-resistant subgroups. These findings highlight the distinct immunogenomic profile of AYA patients, and individualized TME features in ICI-resistant AYA melanoma that require patient-specific treatment strategies.
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Affiliation(s)
- Xinyu Bai
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Grace H Attrill
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Tuba N Gide
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - Kazi J Nahar
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Ping Shang
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Ines Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Royal North Shore Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Royal North Shore Hospital, Sydney, NSW, Australia
- Mater Hospital, North Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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