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Ohe C, Yoshida T, Amin MB, Smith SC, Shiohara M, Tsujio N, Kato M, Uno R, Tsuzuki T, Kohashi K. Comparison of Histologic Parameters and Predictive Gene Signatures in Clear Cell Renal Cell Carcinoma Response to Systemic Therapy. Pathol Int 2025. [PMID: 40432277 DOI: 10.1111/pin.70012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 02/24/2025] [Accepted: 04/07/2025] [Indexed: 05/29/2025]
Abstract
Growing experience has correlated the histomorphological characteristics of clear cell renal cell carcinoma (ccRCC), ranging from cytoplasmic features to architectural patterns and tumor immune microenvironment, with clinical outcomes. However, further assessment is needed to determine which of these histologic parameters best correlate with outcomes of interest, especially response to tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs). Herein, we evaluated four histologic parameters: (i) World Health Organization (WHO)/International Society of Urological Pathology (ISUP) grade; (ii) clear and eosinophilic cytological phenotypes; (iii) immunophenotypes; and (iv) vascularity-based architectural classification, using hematoxylin and eosin-stained whole slide images for The Cancer Genome Atlas (TCGA) ccRCC cohort (n = 433). We then correlated these parameters with gene expression signatures associated with TKI and ICI response. Multivariate analysis found that the cytological phenotype and vascularity-based architectural classification were independently associated with an angiogenesis-related gene signature (both p < 0.05). Conversely, WHO/ISUP grade and immunophenotype were independently associated with effector T-cell and immune checkpoint gene signatures (both p < 0.05). In conclusion, histologic parameters, including cytological features, architectural patterns, and tumor immune microenvironment, are associated with gene signatures related to therapy response, with different parameters informative for TKIs versus ICIs. These findings may help guide prospective validation studies.
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Affiliation(s)
- Chisato Ohe
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
| | - Takashi Yoshida
- Department of Urology and Andrology, Kansai Medical University, Osaka, Japan
- Department of Urology, Osaka Saiseikai-Noe Hospital, Osaka, Japan
- Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Mahul B Amin
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
- Department of Urology, University of Southern California, Los Angeles, California, USA
| | - Steven C Smith
- Departments of Pathology and Urology, School of Medicine and VCU Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Masanori Shiohara
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Nozomi Tsujio
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Masahiro Kato
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Rena Uno
- Department of Pathology, Hyogo Cancer Center, Hyogo, Japan
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Kenichi Kohashi
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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2
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Shu L, Tao T, Xiao D, Liu S, Tao Y. The role of B cell immunity in lung adenocarcinoma. Genes Immun 2025:10.1038/s41435-025-00331-9. [PMID: 40360749 DOI: 10.1038/s41435-025-00331-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 04/07/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025]
Abstract
Lung cancer is the deadliest cancer globally. Non-small cell lung cancer (NSCLC), including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma, constitutes a significant portion of cases. Adenocarcinoma, the most prevalent type, has seen a rising incidence. Immune checkpoint inhibitors (ICIs) have improved outcomes in lung adenocarcinoma (LUAD), yet response rates remain unsatisfactory. PD-1/PD-L1 inhibitors are primary ICIs for LUAD, targeting the PD-1/PD-L1 pathway between CD8+ T cells and tumor cells. However, LUAD presents a "cold tumor" phenotype with fewer CD8+ T cells and lower PD-1 expression, leading to resistance to ICIs. Thus, understanding the function of other immune cell in tumor microenvironment is crucial for developing novel immunotherapies for LUAD. B cells, which is part of the adaptive immune system, have gained attention for its role in cancer immunology. While research on B cells lags behind T cells, recent studies reveal their close correlation with prognosis and immunotherapy effectiveness in various solid tumors, including lung cancer. B cells show higher abundance, activity, and prognostic significance in LUAD than that in LUSC. This review summarizes the difference of B cell immunity between LUAD and other lung cancers, outlines the role of B cell immunity in LUAD.
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Affiliation(s)
- Long Shu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Tania Tao
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan, China.
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, School of Basic Medicine, Central South University, Changsha, Hunan, China.
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3
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Liu Y, Sinjab A, Min J, Han G, Paradiso F, Zhang Y, Wang R, Pei G, Dai Y, Liu Y, Cho KS, Dai E, Basi A, Burks JK, Rajapakshe KI, Chu Y, Jiang J, Zhang D, Yan X, Guerrero PA, Serrano A, Li M, Hwang TH, Futreal A, Ajani JA, Solis Soto LM, Jazaeri AA, Kadara H, Maitra A, Wang L. Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics. Cancer Cell 2025; 43:905-924.e6. [PMID: 40154487 PMCID: PMC12074878 DOI: 10.1016/j.ccell.2025.03.004] [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: 03/19/2024] [Revised: 08/09/2024] [Accepted: 03/03/2025] [Indexed: 04/01/2025]
Abstract
Cancer-associated fibroblasts (CAFs) are a multifaceted cell population essential for shaping the tumor microenvironment (TME) and influencing therapy responses. Characterizing the spatial organization and interactions of CAFs within complex tissue environments provides critical insights into tumor biology and immunobiology. In this study, through integrative analyses of over 14 million cells from 10 cancer types across 7 spatial transcriptomics and proteomics platforms, we discover, validate, and characterize four distinct spatial CAF subtypes. These subtypes are conserved across cancer types and independent of spatial omics platforms. Notably, they exhibit distinct spatial organizational patterns, neighboring cell compositions, interaction networks, and transcriptomic profiles. Their abundance and composition vary across tissues, shaping TME characteristics, such as levels, distribution, and state composition of tumor-infiltrating immune cells, tumor immune phenotypes, and patient survival. This study enriches our understanding of CAF spatial heterogeneity in cancer and paves the way for novel approaches to target and modulate CAFs.
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Affiliation(s)
- Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jimin Min
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Francesca Paradiso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuanyuan Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yibo Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA
| | - Yang Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyung Serk Cho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Akshay Basi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kimal I Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiahui Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paola A Guerrero
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tae Hyun Hwang
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA.
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA; The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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4
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Yang Z, Su W, Wei X, Pan Y, Xing M, Niu L, Feng B, Kong W, Ren X, Huang F, Zhou J, Zhao W, Qiu Y, Liao T, Chen Q, Qu S, Wang Y, Guan Q, Li D, Zen K, Chen Y, Qin C, Wang Y, Zhou X, Xiang J, Yao B. Hypoxia inducible factor-1α drives cancer resistance to cuproptosis. Cancer Cell 2025; 43:937-954.e9. [PMID: 40054467 DOI: 10.1016/j.ccell.2025.02.015] [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: 01/23/2024] [Revised: 12/09/2024] [Accepted: 02/11/2025] [Indexed: 03/20/2025]
Abstract
Cuproptosis represents a new type of cell death that intricately associated with copper homeostasis and protein lipoylation. The cuproptosis suppression has been characterized in the hypoxic tumor microenvironment (TME). Here we reveal that hypoxia inducible factor-1α (HIF-1α) is a driver of cuproptosis resistance in solid tumor. We found that HIF-1α activates pyruvate dehydrogenase kinase 1 and 3 (PDK1/3), resulting in decreased expression of dihydrolipoamide S-acetyltransferase (DLAT) (target of copper), and promotes the accumulation of metallothionein, which sequesters mitochondrial copper, leading to resistance to cuproptosis under hypoxic conditions. Furthermore, we discovered that high levels of copper reduce ubiquitination and increase the stability of HIF-1α protein without affecting its mRNA levels. Inhibition of HIF-1α increases the susceptibility of cancer to cuproptosis in vivo. This study unveils the multifaceted role of HIF-1α in cuproptosis and demonstrates the molecular mechanism of hypoxia-promoted carcinogenesis.
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Affiliation(s)
- Zhou Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Su
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yitong Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mengying Xing
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Lili Niu
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University, Shanghai, China
| | - Baijie Feng
- Department of Medical Oncology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Weiyu Kong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaohan Ren
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Huang
- National Experimental Teaching Center of Basic Medical Science, Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Jingwan Zhou
- National Experimental Teaching Center of Basic Medical Science, Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Wei Zhao
- Department of Clinical Laboratory, School of Clinical Medicine and the First Affiliated Hospital of Chengdu Medical College, Department of Clinical Biochemistry, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yingyi Qiu
- National Experimental Teaching Center of Basic Medical Science, Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Chen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shuang Qu
- Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunjun Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing Guan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Duanshu Li
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Zen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yun Chen
- Research Center of Surgery, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China; Department of Immunology, School of Basic Medical Sciences, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xiang Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Jun Xiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Bing Yao
- National Experimental Teaching Center of Basic Medical Science, Department of Medical Genetics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China; Department of General Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Nanjing, China; State Key Laboratory Cultivation Base of Biomarkers for Cancer Precision Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, NHC Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China.
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5
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Moore WH, Silk M, Bhattacharji P, Pua BB, Mammarappallil J, Sterman DH, Chachoua A. Early experience with PEF in the setting of recalcitrant stage IV lung cancer. Lung Cancer 2025; 204:108575. [PMID: 40409026 DOI: 10.1016/j.lungcan.2025.108575] [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: 02/24/2025] [Revised: 04/29/2025] [Accepted: 05/02/2025] [Indexed: 05/25/2025]
Abstract
BACKGROUND Advanced-stage non-small cell lung cancer treatment has evolved with the introduction of molecularly targeted therapy, immunotherapy and combination frontline therapies. Despite these advancements, most patients experience treatment failure, resulting in poor prognosis characterized by low median progression-free survival (PFS) and overall survival (OS). Second-line chemotherapy has demonstrated minimally improved survival compared to best supportive care. Exploring new mechanisms to enhance treatment response in this patient population is critical. OBJECTIVE This retrospective study aims to assess if there is survival benefit in a cohort of patients with stage IV lung cancer who have failed previous systemic therapy treated with pulsed electrical fields (PEF) therapy compared to a propensity-matched cohort. METHODS A retrospective review of patients treated with PEF at three academic institutions from January 1, 2023, to July 1, 2024, yielded 41 patients with progressive stage IV non-small cell lung cancer. Tumor response was evaluated by RECIST 1.1 criteria. A propensity matched cohort of 50 patients with advanced NSCLC undergoing systemic therapy was identified. Statistical analyses, including Kaplan-Meier survival estimates and Hazard ratios, were conducted. RESULTS The PEF-treated cohort exhibited a 1-year PFS of 63.2 % and OS of 74.3 %. In contrast, the matched cohort demonstrated a 1-year PFS of 11.8 % and OS of 33 %. The hazard ratio for PFS in the PEF group was 3.66 (p < 0.0001) and for OS was 3.5 (p = 0.0007), indicating a significant survival advantage for patients receiving PEF. CONCLUSION This study suggests that PEF therapy may be associated with significantly improved PFS and OS in patients with progressive stage IV non-small cell lung cancer compared to the matched cohort. Prospective controlled studies are required to confirm these preliminary findings, to better understand the mechanism of action of PEF, and to identify which patient populations would best benefit from this therapy.
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Affiliation(s)
- William H Moore
- NYU Grossman School of Medicine, Department of Radiology, United States.
| | - Mikhail Silk
- NYU Grossman School of Medicine, Department of Radiology, United States
| | | | - Bradley B Pua
- Weill Cornell Medicine, Department of Radiology, United States
| | | | - Daniel H Sterman
- NYU Grossman School of Medicine, Department of Medicine, United States
| | - Abraham Chachoua
- NYU Grossman School of Medicine, Department of Medicine, United States
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6
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Li H, Zhang MJ, Zhang B, Lin WP, Li SJ, Xiong D, Wang Q, Wang WD, Yang QC, Huang CF, Deng WW, Sun ZJ. Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4 + T cells in head and neck cancer. Nat Commun 2025; 16:4228. [PMID: 40335494 PMCID: PMC12059173 DOI: 10.1038/s41467-025-59341-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 04/18/2025] [Indexed: 05/09/2025] Open
Abstract
Tumor tertiary lymphoid structures (TLS), especially mature TLS (mTLS), have been associated with better prognosis and improved responses to immune checkpoint blockade (ICB), but the underlying mechanisms remain incompletely understood. Here, by performing single-cell RNA, antigen receptor sequencing and spatial transcriptomics on tumor tissue from head and neck squamous cell carcinoma (HNSCC) patients with different statuses of TLS, we observe that mTLS are enriched with stem-like T cells, and B cells at various maturation stages. Notably, progenitor exhausted CD4+ T cells, with features resembling follicular helper T cells, support these responses, by activating B cells to produce plasma cells in the germinal center, and interacting with DC-LAMP+ dendritic cells to support CD8+ T cell activation. Conversely, non-mTLS tumors do not promote local anti-tumor immunity which is abundant of immunosuppressive cells or a lack of stem-like B and T cells. Furthermore, patients with mTLS manifest improved overall survival and response to ICB compared to those with non-mTLS. Overall, our study provides insights into mechanisms underlying mTLS-mediated intra-tumoral immunity events against cancer.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Meng-Jie Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Boxin Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wen-Ping Lin
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shu-Jin Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Dian Xiong
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Qing Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wen-Da Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Qi-Chao Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Cong-Fa Huang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wei-Wei Deng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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7
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Gorvel L, Panouillot M, Rouvière MS, Billon E, Fattori S, Sonongbua J, Boucherit N, Ben Amara A, Quilichini O, Granjeaud S, Degos C, Nunès JA, Carcopino X, Lambaudie E, Chrétien AS, Sabatier R, Dieu-Nosjean MC, Olive D. Tertiary Lymphoid Structures Are Associated with Enhanced Macrophage Activation and Immune Checkpoint Expression and Predict Outcome in Cervical Cancer. Cancer Immunol Res 2025; 13:712-728. [PMID: 39888676 DOI: 10.1158/2326-6066.cir-24-0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 12/23/2024] [Accepted: 01/31/2025] [Indexed: 02/02/2025]
Abstract
Cervical tumors are usually treated using surgery, chemotherapy, and radiotherapy and would benefit from immunotherapies. However, the immune microenvironment in cervical cancer remains poorly described. Tertiary lymphoid structures (TLS) were recently described as markers for better immunotherapy response and overall better prognosis in patients with cancer. We evaluated the cervical tumor immune microenvironment, specifically focusing on TLS, using combined high-throughput phenotyping, soluble factor concentration dosage in the tumor microenvironment, and spatial interaction analyses. We found that TLS presence was associated with a more inflammatory soluble microenvironment, with the presence of B cells as well as more activated macrophages and dendritic cells (DC). Furthermore, this myeloid cell activation was associated with the expression of immune checkpoints, such as PD-L1 and CD40, and the proximity of activated conventional type 2 DCs to CD8+ T cells, indicating better immune interactions and tumor control. Finally, we associated TLS presence, greater B-cell density, and activated DC density with improved progression-free survival, substantiating TLS presence as a potential prognostic marker. Our results provide evidence that TLS presence denotes cell activation and immunotherapy target expression.
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Affiliation(s)
- Laurent Gorvel
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Marylou Panouillot
- UMRS1135 Sorbonne University, INSERM U1135, Centre of Immunology and Microbial Infections (Cimi), Immune Microenvironment and Immunotherapy Team, Paris, France
| | - Marie-Sarah Rouvière
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Emilien Billon
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Stéphane Fattori
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Jumaporn Sonongbua
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Nicolas Boucherit
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Amira Ben Amara
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Olivia Quilichini
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Clara Degos
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Jacques A Nunès
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Xavier Carcopino
- Department of Obstetrics and Gynecology, Hôpital Nord, APHM, Aix-Marseille University (AMU), CNRS, IRD, IMBE UMR 7263, 13397, Marseille, France
| | - Eric Lambaudie
- Department of Surgical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Anne-Sophie Chrétien
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
| | - Renaud Sabatier
- Predictive Oncology Laboratory, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Marie-Caroline Dieu-Nosjean
- UMRS1135 Sorbonne University, INSERM U1135, Centre of Immunology and Microbial Infections (Cimi), Immune Microenvironment and Immunotherapy Team, Paris, France
| | - Daniel Olive
- Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
- Immunomonitoring Platform, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France
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8
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Hugaboom MB, Wirth LV, Street K, Ruthen N, Jegede OA, Schindler NR, Shah V, Zaemes JP, Ahmar NE, Matar S, Savla V, Choueiri TK, Denize T, West DJ, McDermott DF, Plimack ER, Sosman JA, Haas NB, Stein MN, Alter R, Bilen MA, Hurwitz ME, Hammers H, Signoretti S, Atkins MB, Wu CJ, Braun DA. Presence of Tertiary Lymphoid Structures and Exhausted Tissue-Resident T Cells Determines Clinical Response to PD-1 Blockade in Renal Cell Carcinoma. Cancer Discov 2025; 15:948-968. [PMID: 39992403 PMCID: PMC12048281 DOI: 10.1158/2159-8290.cd-24-0991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 01/08/2025] [Accepted: 02/21/2025] [Indexed: 02/25/2025]
Abstract
SIGNIFICANCE We describe a paradigm wherein combined high TLS and low tissue-resident exhausted CD8+ T cells are required for optimal response to PD-1 blockade in RCC. This analysis identifies key determinants of response to PD-1 blockade in advanced RCC and suggests avenues for future immune modulation through rational combination therapy strategies.
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Affiliation(s)
- Miya B. Hugaboom
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Lena V. Wirth
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Street
- Division of Biostatistics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Neil Ruthen
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Opeyemi A. Jegede
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Valisha Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P. Zaemes
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Nourhan El Ahmar
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sayed Matar
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Varunika Savla
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Destiny J. West
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - David F. McDermott
- Division of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Jeffrey A. Sosman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Naomi B. Haas
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark N. Stein
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Robert Alter
- Hackensack University Medical Center, Hackensack, NJ, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Michael E. Hurwitz
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Hans Hammers
- Department of Internal Medicine, Division of Hematology and Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Michael B. Atkins
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A. Braun
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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9
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Lai Z, Kong D, Li Q, Wang Y, Li K, Duan X, Shao J, Xie Y, Chen J, Zhang T, Feng Y, Deng H, Wang J, Wang C, Shu K, Zhao H, Du H, Jia C, Dai H, Xie L, Liu J, Luo X, Wang L, Xu L, Zhu Z, Lei X, Wang Y, Yang Y, Liu Y, Liang Y, Yang Y, Xie J, Liu B, Deng Z, Liu X. Single-cell spatial transcriptomics of tertiary lymphoid organ-like structures in human atherosclerotic plaques. NATURE CARDIOVASCULAR RESEARCH 2025; 4:547-566. [PMID: 40295810 DOI: 10.1038/s44161-025-00639-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/20/2025] [Indexed: 04/30/2025]
Abstract
Tertiary lymphoid organs have been identified in the arterial adventitia in both mouse models of atherosclerosis and patients with atherosclerosis, yet their role in the disease remains insufficiently explored. Here we present a spatially resolved single-cell transcriptome atlas of human atherosclerotic plaques, identifying 14 distinct cell types and providing evidence of plaque tertiary lymphoid organs (PTLOs). The development of PTLOs was associated with the expression of lymphangiogenic chemokine genes and the adhesion molecule gene in fibroblast-like smooth muscle cells. PTLOs harbor abundant B cells with expanded and diversified B cell receptors, suggesting substantial immune involvement. We also observed that B cells may be exchanged between PTLOs and perivascular adipose tissues. The presence of PTLO-like structures correlates with cerebrovascular events, which may be mediated by PTLO-derived IgG antibodies enhancing macrophage functional activity. Our findings suggest the existence and characteristics of PTLOs in human atherosclerosis, elucidating their cellular functions and clinical implications and offering avenues for understanding, diagnosing and treating this condition.
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Affiliation(s)
- Zhichao Lai
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Deqiang Kong
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Yue Wang
- BGI Research, Beijing, China
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Kang Li
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaohan Duan
- BGI Research, Beijing, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Shao
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yiyun Xie
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Junye Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Pathophysiology, Peking Union Medical College, Beijing, China
| | - Tianjing Zhang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuyao Feng
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | - Jiaxian Wang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Chaonan Wang
- Department of Hemangiomas and Vascular Malformations, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Keqiang Shu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hongmei Zhao
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hanze Du
- Department of Endocrinology, Key Laboratory of Endocrinology of National Health Commission, Translation Medicine Centre, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Congwei Jia
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Huanyu Dai
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lizhi Xie
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Lin Wang
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Leyin Xu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhan Zhu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangling Lei
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuru Wang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yixuan Yang
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yanan Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Jun Xie
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | | | - Xin Liu
- BGI Research, Beijing, China.
- Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan, China.
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10
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Gao L, Liu Y, Zou J, Deng F, Liu Z, Zhang Z, Zhao X, Chen L, Tong HHY, Ji Y, Le H, Zou X, Hao J. Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data. Brief Bioinform 2025; 26:bbaf160. [PMID: 40315434 PMCID: PMC12047704 DOI: 10.1093/bib/bbaf160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 02/28/2025] [Accepted: 03/19/2025] [Indexed: 05/04/2025] Open
Abstract
Single-cell sequencing has advanced our understanding of cellular heterogeneity and disease pathology, offering insights into cellular behavior and immune mechanisms. However, extracting meaningful phenotype-related features is challenging due to noise, batch effects, and irrelevant biological signals. To address this, we introduce Deep scSTAR (DscSTAR), a deep learning-based tool designed to enhance phenotype-associated features. DscSTAR identified HSP+ FKBP4+ T cells in CD8+ T cells, which linked to immune dysfunction and resistance to immune checkpoint blockade in non-small cell lung cancer. It has also enhanced spatial transcriptomics analysis of renal cell carcinoma, revealing interactions between cancer cells, CD8+ T cells, and tumor-associated macrophages that may promote immune suppression and affect outcomes. In hepatocellular carcinoma, it highlighted the role of S100A12+ neutrophils and cancer-associated fibroblasts in forming tumor immune barriers and potentially contributing to immunotherapy resistance. These findings demonstrate DscSTAR's capacity to model and extract phenotype-specific information, advancing our understanding of disease mechanisms and therapy resistance.
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Affiliation(s)
- Lianchong Gao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, 800# Dong Chuan Road, Minhang District, Shanghai 200240, China
| | - Yujun Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Jiawei Zou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Fulan Deng
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| | - Zheqi Liu
- Department of Oral and Maxillofacial Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhen Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Ninth People’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Xinran Zhao
- Department of Oral and Maxillofacial-Head and Neck Oncology, Ninth People’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Lei Chen
- Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Henry H Y Tong
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| | - Yuan Ji
- Molecular Pathology Center, Dept. Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Huangying Le
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, 800# Dong Chuan Road, Minhang District, Shanghai 200240, China
| | - Xin Zou
- Digital Diagnosis and Treatment Innovation Center for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, 800# Dong Chuan Road, Shanghai 200240, China
| | - Jie Hao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Chen Hua Road, Songjiang District, Shanghai 201602, China
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai 200032, China
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11
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Guo CK, Xia CR, Peng G, Cao ZJ, Gao G. Learning Phenotype Associated Signature in Spatial Transcriptomics with PASSAGE. SMALL METHODS 2025; 9:e2401451. [PMID: 39905872 DOI: 10.1002/smtd.202401451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/31/2024] [Indexed: 02/06/2025]
Abstract
Spatially resolved transcriptomics (SRT) is poised to advance the understanding of cellular organization within complex tissues under various physiological and pathological conditions at unprecedented resolution. Despite the development of numerous computational tools that facilitate the automatic identification of statistically significant intra-/inter-slice patterns (like spatial domains), these methods typically operate in an unsupervised manner, without leveraging sample characteristics like physiological/pathological states. Here PASSAGE (Phenotype Associated Spatial Signature Analysis with Graph-based Embedding), a rationally-designed deep learning framework is presented for characterizing phenotype-associated signatures across multiple heterogeneous spatial slices effectively. In addition to its outstanding performance in systematic benchmarks, PASSAGE's unique capability in calling sophisticated signatures has been demonstrated in multiple real-world cases. The full package of PASSAGE is available at https://github.com/gao-lab/PASSAGE.
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Affiliation(s)
- Chen-Kai Guo
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen-Rui Xia
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing, 100871, China
- Changping Laboratory, Beijing, 102206, China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Jie Cao
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing, 100871, China
- Changping Laboratory, Beijing, 102206, China
| | - Ge Gao
- State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing, 100871, China
- Changping Laboratory, Beijing, 102206, China
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12
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De Domenico P, Gagliardi F, Roncelli F, Snider S, Mortini P. Tumor-infiltrating and circulating B cells mediate local and systemic immunomodulatory mechanisms in Glioblastoma. J Neurooncol 2025; 172:527-548. [PMID: 40080248 DOI: 10.1007/s11060-025-04989-z] [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: 01/13/2025] [Accepted: 02/24/2025] [Indexed: 03/15/2025]
Abstract
BACKGROUND Glioblastoma (GBM) demonstrates extensive immunomodulatory mechanisms that challenge effective therapeutic interventions. These phenomena extend well beyond the tumor microenvironment (TME) and are reflected in the circulating immunophenotype. B lymphocytes (B cells) have received limited attention in GBM studies despite their emerging importance in mediating both local and systemic immune responses. Recent findings highlight the complex regulatory interactions between B cells and other immune cell populations, including tumor-infiltrating macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), and other infiltrating lymphocytes (TILs). B cells are believed to hinder the efficacy of modern immunotherapy strategies focusing on T cells. METHODS This is a focused review of available evidence regarding B cells in GBM through January 2025. RESULTS Peripheral blood reflects a systemically dampened immune response, with sustained lymphopenia, increased plasma cells, and dysfunctional memory B cells. The tumor immune landscape is enriched in cells of B-lineage. Subsets of poorly characterized B regulatory cells (Bregs) populate the TME, developing their phenotype due to their proximity to MDSCs, TAMs, and tumoral cells. The Bregs inhibit CD8+ T activity and may have potential prognostic significance. CONCLUSION Understanding the role of B cells, how they are recruited, and their differentiation shifted towards an immunomodulatory role could inform better therapeutic strategies and unleash their full antitumoral potential in GBM.
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Affiliation(s)
- Pierfrancesco De Domenico
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Via Olgettina 60, 20132, Milan, Italy.
| | - Filippo Gagliardi
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Via Olgettina 60, 20132, Milan, Italy
| | - Francesca Roncelli
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Via Olgettina 60, 20132, Milan, Italy
| | - Silvia Snider
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Via Olgettina 60, 20132, Milan, Italy
| | - Pietro Mortini
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Via Olgettina 60, 20132, Milan, Italy
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13
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Yochum ZA, Braun DA. Immunotherapy for Renal Cell Carcinoma-What More is to Come? Target Oncol 2025; 20:467-483. [PMID: 40208564 DOI: 10.1007/s11523-025-01143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2025] [Indexed: 04/11/2025]
Abstract
The treatment of renal cell carcinoma (RCC), a malignancy that is typically chemoresistant, has drastically evolved with the introduction of vascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR TKIs) and immune checkpoint inhibitors (ICIs). The introduction of ICI-based regimens has significantly improved outcomes for patients with metastatic RCC. Currently, first-line therapy for patients with metastatic RCC involves multiple ICI-based regimens, either dual ICIs (with anti-cytotoxic T-lymphocyte-associated protein 4 (anti-CTLA- 4) and anti-programmed cell death- 1 (PD- 1) therapies) or anti-PD- 1 therapy in combination with VEGFR TKIs. Despite improving patient outcomes with ICI-based regimens, durable responses remain uncommon, highlighting the need for innovative treatment strategies. In this review, we highlight the current standard of care ICI-based regimens followed by ongoing clinical trials with novel combinations of existing FDA-approved agents and targets. We also discuss novel immunotherapies currently in clinical trials, which aim to improve antitumor T cell immunity either by improving T cell activation or T cell navigation to the tumor microenvironment. The incorporation of these novel therapies offers the potential to improve RCC patient outcomes, particularly by enhancing the durability of treatment responses.
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Affiliation(s)
- Zachary A Yochum
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, New Haven, CT, USA
| | - David A Braun
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.
- Center of Molecular and Cellular Oncology, Yale Cancer Center, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Department of Urology, Yale School of Medicine, New Haven, CT, USA.
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14
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Chen Z, Hu B, Cai K, Gao H, Xian Z, Zhang S, Fang Z, Zhou Q, Ren D, Zou Q. Dynamics of tertiary lymphoid structures and immune cross talk in early versus advanced colorectal cancer: potential implications for immunotherapy. Cancer Immunol Immunother 2025; 74:185. [PMID: 40287532 PMCID: PMC12033131 DOI: 10.1007/s00262-025-04027-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 03/19/2025] [Indexed: 04/29/2025]
Abstract
BACKGROUND Irrespective of microsatellite status, immune checkpoint inhibitor therapy shows superior efficacy in early-stage colorectal cancer (CRC) compared to advanced cases. The distinctions of the tumor microenvironment (TME) and tertiary lymphoid structure (TLS) between early- and advanced-stage CRC may represent a critical factor, yet remain incompletely elucidated. METHODS We comprehensively analyzed single-cell RNA sequencing data, bulk RNA transcription data and pathological tissue data to investigate the dynamic changes in the TME. The features of TLS in early- and advanced-stage tumors and their potential impact on immunotherapy were explored using three in-house cohorts. RESULTS We provided single-cell fine maps of the immune landscape in early and advanced CRC. Significant functional differences were identified in CD4 + Tfh and BGC cells between early and advanced CRC. We revealed CXCL13 expression on CD8 + Tex cells, along with CD40-CD40L interactions between CD4 + Tfh and BGC cells, could be key regulators of TLS functionality and subsequently affect the response to immunotherapy. CONCLUSIONS Our research shed light on the multilayered immune dysfunction in advanced CRC and elucidates the alterations in the TLS during the progression of CRC, providing insights for functional studies and the exploration of potential target in advanced CRC.
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Affiliation(s)
- Zixu Chen
- School of Basic Medical Sciences, Shandong Provincial Hospital, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Bang Hu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Keyu Cai
- Department of Gastrointestinal Surgery, Shenshan Medical Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Shanwei, 516600, People's Republic of China
| | - Han Gao
- Department of Emergency Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Zhenyu Xian
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Shuang Zhang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Zhen Fang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250000, Shandong, People's Republic of China
| | - Qian Zhou
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Donglin Ren
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, People's Republic of China
| | - Qi Zou
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250000, Shandong, People's Republic of China.
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15
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Pei G, Min J, Rajapakshe KI, Branchi V, Liu Y, Selvanesan BC, Thege F, Sadeghian D, Zhang D, Cho KS, Chu Y, Dai E, Han G, Li M, Yee C, Takahashi K, Garg B, Tiriac H, Bernard V, Semaan A, Grem JL, Caffrey TC, Burks JK, Lowy AM, Aguirre AJ, Grandgenett PM, Hollingsworth MA, Guerrero PA, Wang L, Maitra A. Spatial mapping of transcriptomic plasticity in metastatic pancreatic cancer. Nature 2025:10.1038/s41586-025-08927-x. [PMID: 40269162 DOI: 10.1038/s41586-025-08927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/20/2025] [Indexed: 04/25/2025]
Abstract
Patients with treatment-refractory pancreatic cancer often succumb to systemic metastases1-3; however, the transcriptomic heterogeneity that underlies therapeutic recalcitrance remains understudied, particularly in a spatial context. Here we construct high-resolution maps of lineage states, clonal architecture and the tumour microenvironment (TME) using spatially resolved transcriptomics from 55 samples of primary tumour and metastases (liver, lung and peritoneum) collected from rapid autopsies of 13 people. We observe discernible transcriptomic shifts in cancer-cell lineage states as tumours transition from primary sites to organ-specific metastases, with the most pronounced intra-patient distinctions between liver and lung. Phylogenetic trees constructed from inferred copy number variations in primary and metastatic loci in each patient highlight diverse patient-specific evolutionary trajectories and clonal dissemination. We show that multiple tumour lineage states co-exist in each tissue, including concurrent metastatic foci in the same organ. Agnostic to tissue site, lineage states correlate with distinct TME features, such as the spatial proximity of TGFB1-expressing myofibroblastic cancer-associated fibroblasts (myCAFs) to aggressive 'basal-like' cancer cells, but not to cells in the 'classical' or 'intermediate' states. These findings were validated through orthogonal and cross-species analyses using mouse tissues and patient-derived organoids. Notably, basal-like cancer cells aligned with myCAFs correlate with plasma-cell exclusion from the tumour milieu, and neighbouring cell analyses suggest that CXCR4-CXCL12 signalling is the underlying basis for observed immune exclusion. Collectively, our findings underscore the profound transcriptomic heterogeneity and microenvironmental dynamics that characterize treatment-refractory pancreatic cancer.
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Affiliation(s)
- Guangsheng Pei
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jimin Min
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimal I Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vittorio Branchi
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benson Chellakkan Selvanesan
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fredrik Thege
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dorsay Sadeghian
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kyung Serk Cho
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kazuki Takahashi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bharti Garg
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Herve Tiriac
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Vincent Bernard
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Semaan
- Department of Surgery, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jean L Grem
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Thomas C Caffrey
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jared K Burks
- Department of Leukemia and Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew M Lowy
- Department of Surgery, Division of Surgical Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paola A Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
- James P. Allison Institute, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Institute for Data Science in Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Lee Y, Lee M, Shin Y, Kim K, Kim T. Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications. Int J Mol Sci 2025; 26:3949. [PMID: 40362187 PMCID: PMC12071594 DOI: 10.3390/ijms26093949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 04/17/2025] [Accepted: 04/17/2025] [Indexed: 05/15/2025] Open
Abstract
Spatial omics integrates molecular profiling with spatial tissue context, enabling high-resolution analysis of gene expression, protein interactions, and epigenetic modifications. This approach provides critical insights into disease mechanisms and therapeutic responses, with applications in cancer, neurology, and immunology. Spatial omics technologies, including spatial transcriptomics, proteomics, and epigenomics, facilitate the study of cellular heterogeneity, tissue organization, and cell-cell interactions within their native environments. Despite challenges in data complexity and integration, advancements in multi-omics pipelines and computational tools are enhancing data accuracy and biological interpretation. This review provides a comprehensive overview of key spatial omics technologies, their analytical methods, validation strategies, and clinical applications. By integrating spatially resolved molecular data with traditional omics, spatial omics is transforming precision medicine, biomarker discovery, and personalized therapy. Future research should focus on improving standardization, reproducibility, and multimodal data integration to fully realize the potential of spatial omics in clinical and translational research.
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Affiliation(s)
- Yoonji Lee
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (Y.L.); (M.L.); (Y.S.)
| | - Mingyu Lee
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (Y.L.); (M.L.); (Y.S.)
| | - Yoojin Shin
- College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea; (Y.L.); (M.L.); (Y.S.)
| | - Kyuri Kim
- College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul 07804, Republic of Korea;
| | - Taejung Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Republic of Korea
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17
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Huang R, Kee L, Gont A, Meens J, Ferens FG, Irwin MS, Ailles L, Yuzwa SA, Robinson CM, Ohh M. Comparative single-cell transcriptomic profiling of patient-derived renal carcinoma cells in cellular and animal models of kidney cancer. FEBS Open Bio 2025. [PMID: 40241258 DOI: 10.1002/2211-5463.70022] [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: 09/05/2024] [Revised: 02/26/2025] [Accepted: 03/06/2025] [Indexed: 04/18/2025] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer that often displays resistance to conventional cancer therapies, including chemotherapy and radiation therapy. Targeted treatments, including immunotherapies and small molecular inhibitors, have been associated with improved outcomes. However, variations in the patient response and the development of resistance suggest that more models that better recapitulate the pathogenesis and metastatic mechanisms of ccRCC are required to improve our understanding and disease management. Here, we examined the transcriptional landscapes of in vitro cell culture as well as in vivo orthotopic and metastatic NOD/SCID-γ mouse models of ccRCC using a single patient-derived RCC243 cell line to allow unambiguous comparison between models. In our mouse model assays, RCC243 cells formed metastatic tumors, and all tumors retained clear cell morphology irrespective of model type. Notably, gene expression profiles differed markedly between the RCC243 tumor models-cell culture, orthotopic tumors, and metastatic tumors-suggesting an impact of the experimental model system and whether the tumor was orthotopic or metastatic. Furthermore, we found conserved prognostic markers between RCC243 tumor models and human ccRCC patient datasets, and genes upregulated in metastatic RCC243 were associated with worse patient outcomes.
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Affiliation(s)
- Richard Huang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
| | - Lynn Kee
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Alexander Gont
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Fraser G Ferens
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
| | - Meredith S Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Canada
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
| | - Laurie Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Canada
| | - Scott A Yuzwa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
| | - Claire M Robinson
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
- Department of Biochemistry, University of Toronto, Canada
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18
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Yu J, Fu L, Wu R, Che L, Liu G, Ran Q, Xia Z, Liang X, Zhao G. Immunocytes in the tumor microenvironment: recent updates and interconnections. Front Immunol 2025; 16:1517959. [PMID: 40297580 PMCID: PMC12034658 DOI: 10.3389/fimmu.2025.1517959] [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: 10/27/2024] [Accepted: 03/11/2025] [Indexed: 04/30/2025] Open
Abstract
The tumor microenvironment (TME) is a complex, dynamic ecosystem where tumor cells interact with diverse immune and stromal cell types. This review provides an overview of the TME's evolving composition, emphasizing its transition from an early pro-inflammatory, immune-promoting state to a later immunosuppressive milieu characterized by metabolic reprogramming and hypoxia. It highlights the dual roles of key immunocytes-including T lymphocytes, natural killer cells, macrophages, dendritic cells, and myeloid-derived suppressor cells-which can either inhibit or support tumor progression based on their phenotypic polarization and local metabolic conditions. The article further elucidates mechanisms of immune cell plasticity, such as the M1/M2 macrophage switch and the balance between effector T cells and regulatory T cells, underscoring their impact on tumor growth and metastasis. Additionally, emerging therapeutic strategies, including checkpoint inhibitors and chimeric antigen receptor (CAR) T and NK cell therapies, as well as approaches targeting metabolic pathways, are discussed as promising avenues to reinvigorate antitumor immunity. By integrating recent molecular insights and clinical advancements, the review underscores the importance of deciphering the interplay between immunocytes and the TME to develop more effective cancer immunotherapies.
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Affiliation(s)
- Jiyao Yu
- Department of Ultrasound, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Li Fu
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Department of Gastroenterology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Rui Wu
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Department of Neurosurgery, Jiangyou People’s Hospital, Mianyang, China
| | - Linyi Che
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guodong Liu
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Qinwen Ran
- General Practice Department, Wufu Town Hospital, Chongqing, China
| | - Zhiwei Xia
- Department of Neurology, Hunan Aerospace Hospital, Hunan Normal University, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Guanjian Zhao
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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19
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Cui X, Liu S, Song H, Xu J, Sun Y. Single-cell and spatial transcriptomic analyses revealing tumor microenvironment remodeling after neoadjuvant chemoimmunotherapy in non-small cell lung cancer. Mol Cancer 2025; 24:111. [PMID: 40205583 PMCID: PMC11980172 DOI: 10.1186/s12943-025-02287-w] [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: 10/04/2024] [Accepted: 02/28/2025] [Indexed: 04/11/2025] Open
Abstract
Non-small cell lung cancer (NSCLC) represents the most common pathological type of lung cancer, and the combination of neoadjuvant immunotherapy with chemotherapy has emerged as the first-line treatment for NSCLC. Nevertheless, the efficacy of this therapeutic approach remains variable. The present study aims to examine the impact of chemoimmunotherapy in NSCLC patients, with a view to identifying key molecules, critical cell subpopulations, communication patterns and spatial distributions that potentially correlate with therapeutic sensitivity. A total of 16 lung cancer tissue samples were collected from a cohort of 12 NSCLC patients and subjected to single-cell RNA and spatial transcriptome sequencing. Our data demonstrated that the distribution of CD4 + Treg T cells and mCAFs indicated an immunosuppressive tumor microenvironment, while the accumulation of CD4 + Th17 T cells and iCAFs could act as a positive marker for the sensitivity to chemoimmunotherapy. Furthermore, a significant high level of SELENOP-macrophages was observed in tissues from positive responders, and a strong co-localization between SELENOP-macrophages and antigen-presenting cancer associated fibroblasts (CAFs) in the tumor boundaries was identified, indicating the cooperative roles of these two cell types in response to combined therapy. Moreover, SELENOP-macrophages were observed to be accumulated in tertiary lymphoid structures, which further suggested its critical role in recruiting lymphocytes. Furthermore, analysis of cell-cell communication, based on spatial transcriptomics, suggests that the interactions between SELENOP-macrophages, apCAFs, CD4 + and CD8 + T cells were significantly enhanced in responders. In addition, SELENOP-macrophages recruited CD4 + Naïve, Helper and CD8 + Naïve T cells through pathways such as the cholesterol, interleukin, chemokine and HLA when responding to combined therapy. The present study further unveils the dynamic spatial and transcriptional changes in the tumor microenvironment of non-small cell lung cancer in response to combination therapy.
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Affiliation(s)
- Xiaolu Cui
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - Siyuan Liu
- Department of Thoracic Surgery, First Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - He Song
- Department of Gastrointestinal Surgery, First Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China.
| | - Jingjing Xu
- Department of Rheumatology and Immunology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province , 110004, China.
| | - Yanbin Sun
- Department of Thoracic Surgery, First Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China.
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20
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Su X, Kang D, Wang J, Li L, Huang R, Zou Z. Tertiary lymphoid structures associated with improved survival and enhanced antitumor immunity in acral melanoma. NPJ Precis Oncol 2025; 9:103. [PMID: 40200106 PMCID: PMC11978811 DOI: 10.1038/s41698-025-00891-z] [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: 09/25/2024] [Accepted: 03/31/2025] [Indexed: 04/10/2025] Open
Abstract
Understanding the impact of tertiary lymphoid structures (TLSs) on acral melanoma (AM) and the tumor microenvironment (TME) is critical. We analyzed TLS features in primary AM lesions from 46 patients and identified intratumoral TLSs (intra-TLSs) in 25 patients. Intra-TLS presence was significantly associated with improved overall survival. Hematoxylin and eosin staining and multiplex immunofluorescence revealed increased T-cell and CD8+ T-cell infiltration and fewer tumor-associated macrophages in the TME of intra-TLS patients. Transcriptomic analysis identified a TLS-associated Th1/B-cell gene set as a predictor of survival and immunotherapy response. These findings highlight the prognostic value of intra-TLSs in AMs and suggest that targeting TLS formation could enhance immunotherapy efficacy.
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Affiliation(s)
- Xinyu Su
- Department of the Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Donglin Kang
- Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Jiayu Wang
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lin Li
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Rong Huang
- Department of the Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Zhengyun Zou
- Department of the Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Cancer Center, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China.
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China.
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21
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Lv Z, Jiao J, Xue W, Shi X, Wang R, Wu J. Activation-induced cytidine deaminase in tertiary lymphoid structures: dual roles and implications in cancer prognosis. Front Oncol 2025; 15:1555491. [PMID: 40270606 PMCID: PMC12014437 DOI: 10.3389/fonc.2025.1555491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Accepted: 03/25/2025] [Indexed: 04/25/2025] Open
Abstract
Activation-induced cytidine deaminase (AID) serves as a critical molecular orchestrator in the germinal center (GC) reaction within secondary lymphoid organs (SLOs), driving the production of high-affinity antibodies through somatic hypermutation. While its pathological implications are well-documented - including ectopic expression in non-B cell populations and transcriptional dysregulation linked to hematological malignancies and solid tumorigenesis - the cellular provenance of AID in solid tumors remains an unresolved paradox. This review advances two principal hypotheses: (1) AID may derive from tertiary lymphoid structures (TLSs), ectopic immune niches mirroring SLO organization, and (2) exhibits context-dependent transcriptional duality, capable of both potentiating and suppressing gene expression based on microenvironmental cues. Through systematic analysis of AID/GC involvement across cancer subtypes, we delineate mechanistic connections between lymphoid neogenesis and tumor progression. Our examination extends to TLS architecture, revealing three critical dimensions: (i) structural organization and cellular heterogeneity, (ii) developmental trajectories, and (iii) bidirectional interactions with tumor microenvironments. Crucially, we establish functional parallels between tumor-infiltrating B cells (TIL-Bs) in SLOs versus TLSs, while elucidating the differential roles of AID in canonical GC versus TLS-associated GC formation. This synthesis ultimately proposes that AID's functional dichotomy - acting as both oncogenic collaborator and tumor suppressor - underlies the paradoxical prognostic associations observed with TLS presence across malignancies. The review thereby provides a conceptual framework reconciling AID's dual functionality with the context-dependent immunobiology of tumor-associated lymphoid structures.
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Affiliation(s)
- Zhuangwei Lv
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, China
| | - Junna Jiao
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
- Xinxiang Engineering Technology Research Center of Immune Checkpoint Drug for Liver-Intestinal Tumors, Xinxiang Medical University, Xinxiang, China
| | - Wuyang Xue
- Department of Laboratory Medicine, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaoyu Shi
- School of Junji College, Xinxiang Medical University, Xinxiang, Henan, China
| | - Ruihan Wang
- School of Junji College, Xinxiang Medical University, Xinxiang, Henan, China
| | - Jinhua Wu
- School of Junji College, Xinxiang Medical University, Xinxiang, Henan, China
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22
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Kalemoglu E, Jani Y, Canaslan K, Bilen MA. The role of immunotherapy in targeting tumor microenvironment in genitourinary cancers. Front Immunol 2025; 16:1506278. [PMID: 40260236 PMCID: PMC12009843 DOI: 10.3389/fimmu.2025.1506278] [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: 10/04/2024] [Accepted: 03/19/2025] [Indexed: 04/23/2025] Open
Abstract
Genitourinary (GU) cancers, including renal cell carcinoma, prostate cancer, bladder cancer, and testicular cancer, represent a significant health burden and are among the leading causes of cancer-related mortality worldwide. Despite advancements in traditional treatment modalities such as chemotherapy, radiotherapy, and surgery, the complex interplay within the tumor microenvironment (TME) poses substantial hurdles to achieving durable remission and cure. The TME, characterized by its dynamic and multifaceted nature, comprises various cell types, signaling molecules, and the extracellular matrix, all of which are instrumental in cancer progression, metastasis, and therapy resistance. Recent breakthroughs in immunotherapy (IO) have opened a new era in the management of GU cancers, offering renewed hope by leveraging the body's immune system to combat cancer more selectively and effectively. This approach, distinct from conventional therapies, aims to disrupt cancer's ability to evade immune detection through mechanisms such as checkpoint inhibition, therapeutic vaccines, and adoptive cell transfer therapies. These strategies highlight the shift towards personalized medicine, emphasizing the importance of understanding the intricate dynamics within the TME for the development of targeted treatments. This article provides an in-depth overview of the current landscape of treatment strategies for GU cancers, with a focus on IO targeting the specific cell types of TME. By exploring the roles of various cell types within the TME and their impact on cancer progression, this review aims to underscore the transformative potential of IO strategies in TME targeting, offering more effective and personalized treatment options for patients with GU cancers, thereby improving outcomes and quality of life.
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Affiliation(s)
- Ecem Kalemoglu
- Department of Internal Medicine, Rutgers-Jersey City Medical Center, Jersey City, NJ, United States
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Türkiye
| | - Yash Jani
- Medical College of Georgia, Augusta, GA, United States
| | - Kubra Canaslan
- Department of Medical Oncology, Dokuz Eylul University, Izmir, Türkiye
| | - Mehmet Asim Bilen
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, United States
- Department of Urology, Emory University School of Medicine, Atlanta, GA, United States
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23
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Cui M, Zhou M, Zhou L, Zhou G, Liu Y. Tertiary lymphoid structures achieve 'cold' to 'hot' transition by remodeling the cold tumor microenvironment. Biochim Biophys Acta Rev Cancer 2025; 1880:189312. [PMID: 40189114 DOI: 10.1016/j.bbcan.2025.189312] [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: 06/11/2024] [Revised: 03/30/2025] [Accepted: 03/31/2025] [Indexed: 04/10/2025]
Abstract
Immune checkpoint blockade (ICB) therapies have demonstrated significant clinical efficacy in immune-infiltrated tumors such as melanoma and non-small cell lung cancer. However, "cold tumors"-including ovarian cancer, pancreatic cancer, and gliomas-exhibit insufficient immune infiltration, leading to poor therapeutic responses to ICBs and limited improvement in patient prognosis. Recent studies have shown that tumor-associated tertiary lymphoid structures (TLSs) can induce strong local immune responses within the tumor microenvironment (TME), serving as important biological markers for predicting ICB therapy efficacy. Notably, preclinical and clinical studies on cold tumors have confirmed that TLSs can potently enhance ICB efficacy through TME remodeling-a breakthrough that has attracted considerable attention. Here, we systematically examine the immunological profile of cold tumors and decipher the mechanistic basis for their impaired immune cell infiltration. We further delineate the distinctive features of tumor-associated TLSs in generating antitumor immunity and establish criteria for their identification. Significantly, we emphasize the unique capability of TLSs to reprogram the immunosuppressive tumor microenvironment characteristic of cold tumors. Based on these insights, we evaluate clinical evidence supporting TLS-mediated enhancement of ICB efficacy and discuss emerging strategies for exogenous TLSs induction.
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Affiliation(s)
- Mengke Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road Changsha, 410008, PR China; National Laboratory of Medical Genetics, Central South University, Changsha 410078, PR China
| | - Mengfan Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road Changsha, 410008, PR China; National Laboratory of Medical Genetics, Central South University, Changsha 410078, PR China
| | - Lu Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road Changsha, 410008, PR China; National Laboratory of Medical Genetics, Central South University, Changsha 410078, PR China
| | - Gan Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road Changsha, 410008, PR China; National Laboratory of Medical Genetics, Central South University, Changsha 410078, PR China; National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, 110 Xiangya Road, Changsha, Hunan 410008, PR China.
| | - Yingzi Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road Changsha, 410008, PR China; National Laboratory of Medical Genetics, Central South University, Changsha 410078, PR China.
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24
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McKinnon MB, Rini BI, Haake SM. Biomarker-informed care for patients with renal cell carcinoma. NATURE CANCER 2025; 6:573-583. [PMID: 40240621 DOI: 10.1038/s43018-025-00942-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 03/06/2025] [Indexed: 04/18/2025]
Abstract
Kidney cancer is a commonly diagnosed cancer in adults, and clear cell renal cell carcinoma (ccRCC) is the most common histological subtype. Immune checkpoint inhibitors have revolutionized care for patients with ccRCC, either as adjuvant therapy or combined with other agents in advanced disease. However, biomarkers to predict therapeutic benefits are lacking. Here, we explore biomarkers that predict therapeutic response in other tumor types and discuss the reasons for their ineffectiveness in ccRCC. We also review emerging predictive and prognostic biomarkers to prioritize in ccRCC, including gene expression signatures.
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Affiliation(s)
- Mackenzie B McKinnon
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian I Rini
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Scott M Haake
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
- Department of Veterans Affairs, Nashville, TN, USA.
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25
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Poudel K, Ji Z, Njauw CN, Rajadurai A, Bhayana B, Sullivan RJ, Kim JO, Tsao H. Fabrication and functional validation of a hybrid biomimetic nanovaccine (HBNV) against Kit K641E -mutant melanoma. Bioact Mater 2025; 46:347-364. [PMID: 39834347 PMCID: PMC11742834 DOI: 10.1016/j.bioactmat.2024.12.023] [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: 09/10/2024] [Revised: 12/03/2024] [Accepted: 12/20/2024] [Indexed: 01/22/2025] Open
Abstract
Cancer nanovaccines hold the promise for personalization, precision, and pliability by integrating all the elements essential for effective immune stimulation. An effective immune response requires communication and interplay between antigen-presenting cells (APCs), tumor cells, and immune cells to stimulate, extend, and differentiate antigen-specific and non-specific anti-tumor immune cells. The versatility of nanomedicine can be adapted to deliver both immunoadjuvant payloads and antigens from the key players in immunity (i.e., APCs and tumor cells). The imperative for novel cancer medicine is particularly pressing for less common but more devastating KIT-mutated acral and mucosal melanomas that are resistant to small molecule c-kit and immune checkpoint inhibitors. To overcome this challenge, we successfully engineered nanotechnology-enabled hybrid biomimetic nanovaccine (HBNV) comprised of membrane proteins (antigens to activate immunity and homing/targeting ligand to tumor microenvironment (TME) and lymphoid organs) from fused cells (of APCs and tumor cells) and immunoadjuvant. These HBNVs are efficiently internalized to the target cells, assisted in the maturation of APCs via antigens and adjuvant, activated the release of anti-tumor cytokines/inhibited the release of immunosuppressive cytokine, showed a homotypic effect on TME and lymph nodes, activated the anti-tumor immune cells/downregulated the immunosuppressive immune cells, reprogram the tumor microenvironment, and showed successful anti-tumor therapeutic and prophylactic effects.
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Affiliation(s)
- Kishwor Poudel
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhenyu Ji
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ching-Ni Njauw
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anpuchchelvi Rajadurai
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brijesh Bhayana
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ryan J. Sullivan
- Mass General Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jong Oh Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Hensin Tsao
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Mass General Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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26
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Tang Z, Bai Y, Fang Q, Yuan Y, Zeng Q, Chen S, Xu T, Chen J, Tan L, Wang C, Li Q, Lin J, Yang Z, Wu X, Shi G, Wang J, Yin C, Guo J, Liu S, Peng S, Kuang M. Spatial transcriptomics reveals tryptophan metabolism restricting maturation of intratumoral tertiary lymphoid structures. Cancer Cell 2025:S1535-6108(25)00112-6. [PMID: 40185093 DOI: 10.1016/j.ccell.2025.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 01/22/2025] [Accepted: 03/10/2025] [Indexed: 04/07/2025]
Abstract
Tertiary lymphoid structures (TLSs) are ectopic lymphoid aggregates found in numerous cancers, often linked to enhanced immunotherapy responses and better clinical outcomes. However, the factors driving TLS maturation are not fully understood. Using near single-cell spatial transcriptomic mapping, we comprehensively profile TLSs under various maturation stages and their microenvironment in hepatocellular carcinoma (HCC). Based on their developmental trajectories, we classify immature TLSs into two groups: conforming and deviating TLSs. Our findings indicate that conforming TLSs, similar to mature TLSs, possess a niche function for immunotherapy responses, while deviating TLSs do not. We discover that the tryptophan-enriched metabolic microenvironment shaped by malignant cells contributes to the deviation of TLS maturation. Inhibiting tryptophan metabolism promotes intratumoral TLS maturation and enhances tumor control, synergizing with anti-PD-1 treatments. Therefore, promoting TLS maturation represents a potential strategy to improve antitumor responses and immunotherapy outcomes.
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Affiliation(s)
- Zhonghui Tang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yinqi Bai
- BGI Research, Sanya 572025, China; BGI Research, Hangzhou 310030, China
| | - Qi Fang
- BGI Research, Hangzhou 310030, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Qianwen Zeng
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuling Chen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Diagnostic and Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Tianyi Xu
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianyu Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Li Tan
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Chunqing Wang
- BGI Research, Chongqing 401329, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Li
- BGI Research, Sanya 572025, China; BGI Research, Hangzhou 310030, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinpei Lin
- BGI Research, Sanya 572025, China; BGI Research, Hangzhou 310030, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Zhuoxuan Yang
- BGI Research, Sanya 572025, China; BGI Research, Hangzhou 310030, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Ji Wang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Changjun Yin
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute for Cardiovascular Prevention, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Jianping Guo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China; Shenzhen Bay Laboratory, Shenzhen 518000, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, China; The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangzhou 510000, China.
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Clinical Trial Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
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27
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Cui X, Gu X, Li D, Wu P, Sun N, Zhang C, He J. Tertiary lymphoid structures as a biomarker in immunotherapy and beyond: Advancing towards clinical application. Cancer Lett 2025; 613:217491. [PMID: 39862919 DOI: 10.1016/j.canlet.2025.217491] [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: 10/13/2024] [Revised: 01/19/2025] [Accepted: 01/20/2025] [Indexed: 01/27/2025]
Abstract
Tertiary lymphoid structures (TLSs) are ectopic immune cell clusters formed in nonlymphoid tissues affected by persistent inflammation, such as in cancer and prolonged infections. They have features of the structure and function of secondary lymphoid organs, featuring central CD20+ B cells, surrounded by CD3+ T cells, CD21+ follicular dendritic cells, and CD68+ macrophages, with a complex vascular system. TLS formation is governed by lymphotoxin-α1β2, TNF, and chemokines like CCL19, CCL21, and CXCL13, differing from secondary lymphoid organ development in developing later in life at sites of chronic inflammation. Their role in enhancing immune responses, particularly in the context of cancer, makes them a focal point in immunotherapy. This review discusses recent advances in TLS assessment that involves complex gene expression signatures, histological analysis, artificial intelligence, and spatial omics. The presence and maturity of TLS are associated with better outcomes in various cancers, acting as a biomarker for immunotherapy effectiveness. This review explores the structure, formation, and role of TLS in disease prognosis, including their roles in immunotherapy and non-immunotherapy treatments, highlighting a need to develop novel techniques for precise characterization of TLS as well as their significance as predictive biomarkers beyond traditional biomarkers.
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Affiliation(s)
- Xinyu Cui
- 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, 100021, China; 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Xuanyu Gu
- 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, 100021, China; 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Dongyu 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, 100021, China; 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Peng Wu
- 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, 100021, China.
| | - Nan Sun
- 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, 100021, China.
| | - Chaoqi 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, 100021, China.
| | - Jie He
- 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, 100021, China.
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28
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Wang H, Li J, Jing S, Lin P, Qiu Y, Yan X, Yuan J, Tang Z, Li Y, Zhang H, Chen Y, Wang Z, Li H. SOAPy: a Python package to dissect spatial architecture, dynamics, and communication. Genome Biol 2025; 26:80. [PMID: 40158115 PMCID: PMC11954224 DOI: 10.1186/s13059-025-03550-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/18/2025] [Indexed: 04/01/2025] Open
Abstract
Advances in spatial omics enable deeper insights into tissue microenvironments while posing computational challenges. Therefore, we developed SOAPy, a comprehensive tool for analyzing spatial omics data, which offers methods for spatial domain identification, spatial expression tendency, spatiotemporal expression pattern, cellular co-localization, multi-cellular niches, cell-cell communication, and so on. SOAPy can be applied to diverse spatial omics technologies and multiple areas in physiological and pathological contexts, such as tumor biology and developmental biology. Its versatility and robust performance make it a universal platform for spatial omics analysis, providing diverse insights into the dynamics and architecture of tissue microenvironments.
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Affiliation(s)
- Heqi Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiarong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Siyu Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ping Lin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiling Qiu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xi Yan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jiao Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - ZhiXuan Tang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haibing Zhang
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yujie Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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29
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Yu Q, Li YY, Chen Y. scMalignantFinder distinguishes malignant cells in single-cell and spatial transcriptomics by leveraging cancer signatures. Commun Biol 2025; 8:504. [PMID: 40148533 PMCID: PMC11950360 DOI: 10.1038/s42003-025-07942-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 03/17/2025] [Indexed: 03/29/2025] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for characterizing tumor heterogeneity, yet accurately identifying malignant cells remains challenging. Here, we propose scMalignantFinder, a machine learning tool specifically designed to distinguish malignant cells from their normal counterparts using a data- and knowledge-driven strategy. To develop the tool, multiple cancer datasets were collected, and the initially annotated malignant cells were calibrated using nine carefully curated pan-cancer gene signatures, resulting in over 400,000 single-cell transcriptomes for training. The union of differentially expressed genes across datasets was taken as the features for model construction to comprehensively capture tumor transcriptional diversity. scMalignantFinder outperformed existing automated methods across two gold-standard and eleven patient-derived scRNA-seq datasets. The capability to predict malignancy probability empowers scMalignantFinder to capture dynamic characteristics during tumor progression. Furthermore, scMalignantFinder holds the potential to annotate malignant regions in tumor spatial transcriptomics. Overall, we provide an efficient tool for detecting heterogeneous malignant cell populations.
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Affiliation(s)
- Qiaoni Yu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai Genbase Biotechnology Co., Ltd, Shanghai, China
| | - Yuan-Yuan Li
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Yunqin Chen
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
- Shanghai Genbase Biotechnology Co., Ltd, Shanghai, China.
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30
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Andreev G, Vollmer T, Zirngibl M, Werner M, Grabbert M, Schilling O, Rogg M, Schell C. Spatial Correlation of the Extracellular Matrix to Immune Cell Phenotypes in the Tumor Boundary of Clear Cell Renal Cell Carcinoma Revealed by Cyclic Immunohistochemistry. J Transl Med 2025; 105:104130. [PMID: 40120686 DOI: 10.1016/j.labinv.2025.104130] [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: 10/30/2024] [Revised: 02/17/2025] [Accepted: 03/04/2025] [Indexed: 03/25/2025] Open
Abstract
The significance of the tumor microenvironment (TME) in predicting immunotherapy efficacy is increasingly acknowledged. However, the complexity of the TME necessitates novel technological approaches for the precise characterization of individual cell types, functional phenotypes, and heterocellular spatial interactions. This study utilizes a streamlined multiplex cyclic immunohistochemistry (cycIHC) protocol for detailed TME annotation. Unlike proprietary methods, cycIHC relies on iterative cycles of conventional immunohistochemistry, using off-the-shelf antibodies and reagents, followed by digitalization, chromogen removal, and antibody stripping. The method was combined with open-source tools for the coregistration of individual staining cycles. Using clear cell renal cell carcinoma (ccRCC) as a model, the protocol was applied for granular annotation of cellular and acellular structures in the tumor boundary zone. Our results demonstrate that the tumor periphery, particularly the pseudocapsule of ccRCC, is homogeneously organized across the 3D scale, yet exhibits distinct cellular distribution gradients of T and B cells. These patterns correspond to deposited extracellular matrix proteins, especially collagen types I and VI. Our findings indicate an instructive impact of extracellular matrix proteins on defining the spatial organization of immune cells in the TME of ccRCC. The developed cycIHC method facilitates detailed characterization of the TME and may enhance the understanding of tumor-immune cell interactions.
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Affiliation(s)
- Grigor Andreev
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Tino Vollmer
- Department of Internal Medicine, Oncology and Hemato-Oncology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Max Zirngibl
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Department of Urology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Markus Grabbert
- Department of Urology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Manuel Rogg
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Christoph Schell
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany.
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31
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Walker SL, Leete P, Boldison J. Tissue Resident and Infiltrating Immune Cells: Their Influence on the Demise of Beta Cells in Type 1 Diabetes. Biomolecules 2025; 15:441. [PMID: 40149976 PMCID: PMC11939886 DOI: 10.3390/biom15030441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 03/11/2025] [Accepted: 03/17/2025] [Indexed: 03/29/2025] Open
Abstract
Type 1 diabetes (T1D) is an organ-specific autoimmune disease that results in the selective loss of pancreatic beta cells and an eventual deficit in insulin production to maintain glucose homeostasis. It is now increasingly accepted that this dynamic disease process is multifactorial; involves a variety of immune cells which contribute to an inflamed pancreatic microenvironment; and that the condition is heterogenous, resulting in variable rates of subsequent beta cell damage. In this review, we will explore the current understanding of the cellular interactions between both resident and infiltrating immune cells within the pancreatic environment, highlighting key mechanisms which may promote the beta cell destruction and islet damage associated with T1D.
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Affiliation(s)
| | | | - Joanne Boldison
- Department of Clinical and Biomedical Sciences, University of Exeter, RILD Building (Level 4), Barrack Road, Exeter EX2 5DW, UK; (S.L.W.); (P.L.)
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32
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Xiao Z, Puré E. The fibroinflammatory response in cancer. Nat Rev Cancer 2025:10.1038/s41568-025-00798-8. [PMID: 40097577 DOI: 10.1038/s41568-025-00798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/06/2025] [Indexed: 03/19/2025]
Abstract
Fibroinflammation refers to the highly integrated fibrogenic and inflammatory responses mediated by the concerted function of fibroblasts and innate immune cells in response to tissue perturbation. This process underlies the desmoplastic remodelling of the tumour microenvironment and thus plays an important role in tumour initiation, growth and metastasis. More specifically, fibroinflammation alters the biochemical and biomechanical signalling in malignant cells to promote their proliferation and survival and further supports an immunosuppressive microenvironment by polarizing the immune status of tumours. Additionally, the presence of fibroinflammation is often associated with therapeutic resistance. As such, there is increasing interest in targeting this process to normalize the tumour microenvironment and thus enhance the treatment of solid tumours. Herein, we review advances made in unravelling the complexity of cancer-associated fibroinflammation that can inform the rational design of therapies targeting this.
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Affiliation(s)
- Zebin Xiao
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Ellen Puré
- Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, PA, USA.
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Jing SY, Wang HQ, Lin P, Yuan J, Tang ZX, Li H. Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments. NPJ Precis Oncol 2025; 9:68. [PMID: 40069556 PMCID: PMC11897387 DOI: 10.1038/s41698-025-00857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 02/25/2025] [Indexed: 03/15/2025] Open
Abstract
The tumor microenvironment (TME) plays a crucial role in orchestrating tumor cell behavior and cancer progression. Recent advances in spatial profiling technologies have uncovered novel spatial signatures, including univariate distribution patterns, bivariate spatial relationships, and higher-order structures. These signatures have the potential to revolutionize tumor mechanism and treatment. In this review, we summarize the current state of spatial signature research, highlighting computational methods to uncover spatially relevant biological significance. We discuss the impact of these advances on fundamental cancer biology and translational research, address current challenges and future research directions.
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Affiliation(s)
- Si-Yu Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - He-Qi Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Ping Lin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jiao Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Xuan Tang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Hong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.
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Li Z, Liu S, Liu D, Yang K, Xiong J, Fang Z. Multiple mechanisms and applications of tertiary lymphoid structures and immune checkpoint blockade. J Exp Clin Cancer Res 2025; 44:84. [PMID: 40038799 PMCID: PMC11881293 DOI: 10.1186/s13046-025-03318-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 02/05/2025] [Indexed: 03/06/2025] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) inhibits tumor immune escape and has significantly advanced tumor therapy. However, ICB benefits only a minority of patients treated and may lead to many immune-related adverse events. Therefore, identifying factors that can predict treatment outcomes, enhance synergy with ICB, and mitigate immune-related adverse events is urgently needed. MAIN TEXT Tertiary lymphoid structures (TLS) are ectopic lymphoid tissues that arise from the tumor periphery. They have been found to be associated with better prognosis and improved clinical outcomes after ICB therapy. TLS may help address the problems associated with ICB. The multiple mechanisms of action between TLS and ICB remain unknown. This paper described potential mechanisms of interaction between the two and explored their potential applications.
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Affiliation(s)
- Zelin Li
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Shuhan Liu
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Deyu Liu
- Department of Clinical Medicine, Queen Mary School of Nanchang University, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Kangping Yang
- The 2st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jing Xiong
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
- Department of General Practice, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
| | - Ziling Fang
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
- Department of Oncology, The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
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35
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Lehmann J, Thelen M, Kreer C, Schran S, Garcia-Marquez MA, Cisic I, Siepmann K, Hagen EM, Eckel HNC, Lohneis P, Kruger S, Boeck S, Ormanns S, Rudelius M, Werner J, Popp F, Klein F, von Bergwelt-Baildon MS, Bruns CJ, Quaas A, Wennhold K, Schlößer HA. Tertiary Lymphoid Structures in Pancreatic Cancer are Structurally Homologous, Share Gene Expression Patterns and B-cell Clones with Secondary Lymphoid Organs, but Show Increased T-cell Activation. Cancer Immunol Res 2025; 13:323-336. [PMID: 39661055 DOI: 10.1158/2326-6066.cir-24-0299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/02/2024] [Accepted: 12/06/2024] [Indexed: 12/12/2024]
Abstract
Tertiary lymphoid structures (TLS) in cancer are considered ectopic hotspots for immune activation that are similar to lymphoid follicles in secondary lymphoid organs (SLO). This study elucidates shared and TLS/SLO-specific features in pancreatic ductal adenocarcinoma (PDAC). TLS abundance was related to superior survival and T-cell abundance in 110 treatment-naïve PDAC samples, underlining their clinical relevance. Immunofluorescence microscopy identified structural homologies between TLSs and SLOs. In RNA expression analyses of laser-microdissected TLSs and paired SLOs, we observed largely overlapping expression patterns of immune-related gene clusters but distinct expression patterns of T-cell and complement-associated genes. Immune cells in TLS expressed essential markers of germinal center formation. Increased activation of tumor-draining lymph nodes in patients with high numbers of TLSs highlights the relevance of these tumor-related structures to systemic immune response. In line with this, we identified an overlap of expanded B-cell receptor clonotypes in TLSs and SLOs, which suggests a vivid cross-talk between the two compartments. We conclude that combined therapeutic approaches exploiting TLS-mediated antitumor immune responses may improve susceptibility of PDAC to immunotherapy.
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Affiliation(s)
- Jonas Lehmann
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Thelen
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Faculty of Medicine and University Hospital Cologne, Institute of Virology, University of Cologne Cologne, Germany
| | - Simon Schran
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Maria A Garcia-Marquez
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Igor Cisic
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Klara Siepmann
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Elena M Hagen
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Hans Nikolaus Caspar Eckel
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne, Germany
| | - Philipp Lohneis
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stephan Kruger
- Department of Internal Medicine III, University Hospital, Ludwig Maximilians University, Munich, Germany
| | - Stefan Boeck
- Department of Internal Medicine III, University Hospital, Ludwig Maximilians University, Munich, Germany
- Department of Hematology and Oncology, München Klinik Neuperlach, Munich, Germany
| | - Steffen Ormanns
- Faculty of Medicine, Institute of Pathology, Ludwig Maximilians University, Munich, Germany
- Innpath Institute of Pathology, Tirol Kliniken, Innsbruck, Austria
| | - Martina Rudelius
- Faculty of Medicine, Institute of Pathology, Ludwig Maximilians University, Munich, Germany
| | - Jens Werner
- Department of General, Visceral and Transplant Surgery, University Hospital, Ludwig Maximilians University, Munich, Germany
| | - Felix Popp
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Florian Klein
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Laboratory of Experimental Immunology, Faculty of Medicine and University Hospital Cologne, Institute of Virology, University of Cologne Cologne, Germany
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Michael S von Bergwelt-Baildon
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of Internal Medicine III, University Hospital, Ludwig Maximilians University, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christiane J Bruns
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Kerstin Wennhold
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Hans A Schlößer
- Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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Lee CYC, McCaffrey J, McGovern D, Clatworthy MR. Profiling immune cell tissue niches in the spatial -omics era. J Allergy Clin Immunol 2025; 155:663-677. [PMID: 39522655 DOI: 10.1016/j.jaci.2024.11.001] [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: 07/15/2024] [Revised: 10/29/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
Abstract
Immune responses require complex, spatially coordinated interactions between immune cells and their tissue environment. For decades, we have imaged tissue sections to visualize a limited number of immune-related macromolecules in situ, functioning as surrogates for cell types or processes of interest. However, this inevitably provides a limited snapshot of the tissue's immune landscape. Recent developments in high-throughput spatial -omics technologies, particularly spatial transcriptomics, and its application to human samples has facilitated a more comprehensive understanding of tissue immunity by mapping fine-grained immune cell states to their precise tissue location while providing contextual information about their immediate cellular and tissue environment. These data provide opportunities to investigate mechanisms underlying the spatial distribution of immune cells and its functional implications, including the identification of immune niches, although the criteria used to define this term have been inconsistent. Here, we review recent technological and analytic advances in multiparameter spatial profiling, focusing on how these methods have generated new insights in translational immunology. We propose a 3-step framework for the definition and characterization of immune niches, which is powerfully facilitated by new spatial profiling methodologies. Finally, we summarize current approaches to analyze adaptive immune repertoires and lymphocyte clonal expansion in a spatially resolved manner.
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Affiliation(s)
- Colin Y C Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Cellular Genetics, the Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - James McCaffrey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Cellular Genetics, the Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Dominic McGovern
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Cellular Genetics, the Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Cellular Genetics, the Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.
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Rugh KM, Ashton LV, Schaffer PA, Olver CS. Lymphoid Aggregates in Canine Cutaneous and Subcutaneous Sarcomas: Immunohistochemical and Gene Expression Evidence for Tertiary Lymphoid Structures. Vet Comp Oncol 2025; 23:10-19. [PMID: 39462771 PMCID: PMC11830466 DOI: 10.1111/vco.13020] [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: 02/16/2024] [Revised: 10/03/2024] [Accepted: 10/04/2024] [Indexed: 10/29/2024]
Abstract
Canine cutaneous/subcutaneous soft-tissue sarcomas (STS) are diversely derived mesenchymal neoplasms with a risk of recurrence and/or metastasis depending on the extent of surgical excision and histologic grade. Lymphoid aggregates (LAs) are often described in these tumours but not characterised. In humans, LA characterised as tertiary lymphoid structures (TLSs) improve the prognosis of many tumours, including sarcomas. We sought to determine if LA meeting a size criterion (> 700 cells) in canine sarcomas met the criteria of TLS and the overall prevalence of LA of any size. RNA expression in large LAs versus aggregate-adjacent sarcoma tissue (AAS) was measured in laser capture microdissected tissue and compared to curl-derived RNA from aggregate-free sarcomas and lymph nodes. CD3, CD20, MUM-1 and PNAd expressions were measured using immunohistochemistry. CD20 and CD3 mRNA were more highly expressed in LA versus AAS (13.8 fold, p = 0.0003 and 2.3 fold, p = 0.043). This was supported by the IHC findings. The large LAs were also enriched in chemokine RNA expression characteristic of TLS (CXCR5 5.8 fold, p < 00001, CCL19 3.68 fold, p = 0.0209, CCL21 6.87 fold, p = 0.0209 and CXCL13 2.68 fold, p = 0.0924). Plasma cells and high endothelial venules were identified in LA containing tumours but not in control tissue. Large LAs were present in 12% of tumours, and LA of any size in 30%. We conclude that large LAs in canine STS are consistent with TLS.
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38
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Martinis E, Tonon S, Colamatteo A, La Cava A, Matarese G, Pucillo CEM. B cell immunometabolism in health and disease. Nat Immunol 2025; 26:366-377. [PMID: 39984733 DOI: 10.1038/s41590-025-02102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 01/15/2025] [Indexed: 02/23/2025]
Abstract
B cells have crucial roles in the initiation and progression of many pathological conditions, and several therapeutic strategies have targeted the function of these cells. The advent of immunometabolism has provided compelling evidence that the metabolic reprogramming of immune cells can dramatically alter physiopathological immune activities. A better knowledge of the metabolic profiles of B cells can provide valuable means for developing therapies tuning defined cell pathways. Here we review the cellular and molecular mechanisms by which immunometabolism controls the physiology and pathophysiology of B cells and discuss the experimental evidence linking B cell metabolism to health, autoimmunity, and cancer. Considering that several metabolic pathways in B cells are involved differently, or even in opposite ways, in health and disease, we discuss how targeted modulation of B cell immunometabolism could be exploited mechanistically to rebalance abnormal B cell functions that have become altered in disease states.
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Affiliation(s)
| | - Silvia Tonon
- Department of Medicine, University of Udine, Udine, Italy
| | - Alessandra Colamatteo
- Treg Cell Lab, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II', Napoli, Italy
| | - Antonio La Cava
- Treg Cell Lab, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II', Napoli, Italy
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Giuseppe Matarese
- Treg Cell Lab, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II', Napoli, Italy.
- Laboratorio di Immunologia, Istituto per l'Endocrinologia e l'Oncologia Sperimentale 'G. Salvatore' - Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli, Italy.
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39
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Li C, Ke F, Mao S, Montemayor Z, Traore MDM, Balsa AD, Djibo M, Karekar N, Hu H, Wen H, Gao W, Sun D. SARS-CoV-2 B Epitope-Guided Neoantigen NanoVaccines Enhance Tumor-Specific CD4/CD8 T Cell Immunity through B Cell Antigen Presentation. ACS NANO 2025; 19:7038-7054. [PMID: 39943808 DOI: 10.1021/acsnano.4c15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
Current neoantigen cancer vaccines activate T cell immunity through dendritic cell/macrophage-mediated antigen presentation. It is unclear whether incorporating B cell-mediated antigen presentation into current neoantigen vaccines could enhance CD4/CD8 T cell immunity to improve their anticancer efficacy. We developed SARS-CoV-2 B cell epitope-guided neoantigen peptide/mRNA cancer nanovaccines (BSARSTNeoAgVax) to improve anticancer efficacy by enhancing tumor-specific CD4/CD8 T cell antitumor immunity through B cell-mediated antigen presentation. BSARSTNeoAgVax cross-linked with B cell receptor, promoted SARS-CoV-2 B cell-mediated antigen presentation to tumor-specific CD4 T cells, increased tumor-specific follicular/nonfollicular CD4 T cells, and enhanced B cell-dependent tumor-specific CD8 T cell immunity. BSARSTNeoAgVax achieved superior efficacy in melanoma, pancreatic, and breast cancer models compared with the current neoantigen vaccines. Our study provides a universal platform, SARS-CoV-2 B epitope-guided neoantigen nanovaccines, to improve anticancer efficacy against various cancer types by enhancing CD4/CD8 T cell antitumor immunity through viral-specific B cell-mediated antigen presentation.
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Affiliation(s)
- Chengyi Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fang Ke
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuai Mao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zera Montemayor
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mohamed Dit Mady Traore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alejandra Duran Balsa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mahamadou Djibo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Neha Karekar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hongxiang Hu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hanning Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Gao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology and Pharmaceutical Science, College of Pharmacy, The University of Houston, Houston, Texas 77204, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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Sibai M, Cervilla S, Grases D, Musulen E, Lazcano R, Mo CK, Davalos V, Fortian A, Bernat A, Romeo M, Tokheim C, Barretina J, Lazar AJ, Ding L, Grande E, Real FX, Esteller M, Bailey MH, Porta-Pardo E. The spatial landscape of cancer hallmarks reveals patterns of tumor ecological dynamics and drug sensitivity. Cell Rep 2025; 44:115229. [PMID: 39864059 DOI: 10.1016/j.celrep.2024.115229] [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: 08/15/2024] [Accepted: 12/31/2024] [Indexed: 01/28/2025] Open
Abstract
Tumors are complex ecosystems of interacting cell types. The concept of cancer hallmarks distills this complexity into underlying principles that govern tumor growth. Here, we explore the spatial distribution of cancer hallmarks across 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. We show that hallmark activity is spatially organized, with the cancer compartment contributing to the activity of seven out of 13 hallmarks, while the tumor microenvironment (TME) contributes to the activity of the rest. Additionally, we discover that genomic distance between tumor subclones correlates with differences in hallmark activity, even leading to clone-hallmark specialization. Finally, we demonstrate interdependent relationships between hallmarks at the junctions of TME and cancer compartments and how they relate to sensitivity to different neoadjuvant treatments in 33 bladder cancer patients from the DUTRENEO trial. In conclusion, our findings may improve our understanding of tumor ecology and help identify new drug biomarkers.
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Affiliation(s)
- Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Sergi Cervilla
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Daniela Grases
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Eva Musulen
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Department of Pathology, Hospital Universitari General de Catalunya Grupo-QuirónSalud, Sant Cugat del Vallès, Spain
| | - Rossana Lazcano
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chia-Kuei Mo
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Arola Fortian
- Institut de Recerca Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Adrià Bernat
- Institut de Recerca Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Margarita Romeo
- Institut de Recerca Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jordi Barretina
- Institut de Recerca Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Alexander J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Enrique Grande
- Medical Oncology Department. MD Anderson Cancer Center Madrid, Madrid, Spain
| | - Francisco X Real
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain; Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Matthew H Bailey
- Department of Biology and Simmons Center for Cancer Research, Brigham Young University, Provo, UT, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Barcelona Supercomputing Center (BSC), Barcelona, Spain.
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41
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Shi H, Wang W, Luo J, Song G, Han R. POU2F2 + B cells enhance antitumor immunity and predict better survival in non small cell lung cancer. Sci Rep 2025; 15:6549. [PMID: 39994401 PMCID: PMC11850725 DOI: 10.1038/s41598-025-90817-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 02/17/2025] [Indexed: 02/26/2025] Open
Abstract
Immune checkpoint inhibitors are an effective adjuvant therapy for non-small cell lung cancer (NSCLC). Recent studies have highlighted the critical role of tumor-infiltrating B cells in tumor immunity. However, research specifically focusing on B cells in NSCLC is limited. This study aims to elucidate the role of POU2F2+ B cells in patient survival and immune cell infiltration in NSCLC. Pseudotime analysis was performed to identify B cell pseudotime-related gene sets from two single-cell RNA sequencing (scRNA-seq) datasets of NSCLC. Differentially expressed genes (DEGs) were identified from two NSCLC immunotherapy-related bulk RNA sequencing datasets. A Venn diagram was used to determine core genes shared between these datasets. Kaplan-Meier survival curves were utilized to analyze overall survival (OS). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed based on the differential genes between POU2F2+ and POU2F2- B cells. CIBERSORT analysis was conducted to compare the proportions of immune cell subpopulations between groups. Multiplex immunohistochemistry (mIHC) was used to localize POU2F2+ cells and measure distances between different immune cells. Three hallmark genes, POU2F2, CD2, and CST7, were identified as being associated with B cell maturation and immunotherapy efficacy in NSCLC. High expression of POU2F2 was associated with poorer OS in both LUAD and LUSC. However, the POU2F2+ B cell score specifically correlated with the OS of LUAD but not with LUSC. Further analysis using scRNA-seq and mIHC methods revealed that POU2F2 is predominantly expressed in B cells. In LUAD tumor tissues, POU2F2+ CD20+ B cells were spatially further from PD-1+ CD8+ T cells and CD206+ CD68+ macrophages compared to POU2F2- CD20+ B cells. In LUSC tumor tissues, POU2F2+ CD20+ B cells were spatially further from CD206+ CD68+ macrophages but showed no significant spatial difference from PD-1+ CD8+ T cells compared to POU2F2- CD20+ B cells. In patients with high POU2F2+ B cell scores, LUAD tissues showed an increased proportion of CD8+ T cells and M1 macrophages, and a decreased proportion of M2 macrophages. In contrast, in LUSC tissues, a high POU2F2+ B cell score was associated only with an increased proportion of M1 macrophages, with no significant differences in the proportions of CD8+ T cells or M2 macrophages between groups. This study elucidates the significant role of POU2F2+ B cells in influencing survival and immune cell infiltration in NSCLC. Our findings highlight POU2F2 as a novel target for NSCLC immunotherapy. Targeting POU2F2 may modulate the tumor immune microenvironment, enhance the infiltration and activity of critical immune cells, and ultimately improve patient survival.
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Affiliation(s)
- Hengchuan Shi
- Department of Laboratory Medicine, Jiangsu Province Geriatric Hospital, Geriatric Hospital of Nanjing Medical University, Nanjing, 210009, Jiangsu, China
| | - Wenqing Wang
- Department of Laboratory Medicine, Jiangsu Province Geriatric Hospital, Geriatric Hospital of Nanjing Medical University, Nanjing, 210009, Jiangsu, China
| | - Jun Luo
- Department of Central Laboratory, Jiangsu Health Vocational College, Nanjing, 210009, Jiangsu, China
| | - Guoxin Song
- Department of Pathology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210009, Jiangsu, China.
| | - Rongbo Han
- Department of Oncology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, Jiangsu, China.
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Wang D, Lu R, Yan F, Lin Y, Wang H, Xiong H. Analysis of thyroid carcinoma composition and spatial architecture in the progression of dedifferentiation, lymphatic metastasis, and gastric metastasis. J Transl Med 2025; 23:213. [PMID: 39984992 PMCID: PMC11844095 DOI: 10.1186/s12967-025-06252-5] [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: 08/04/2024] [Accepted: 02/11/2025] [Indexed: 02/23/2025] Open
Abstract
BACKGROUND Gastrointestinal metastases are rare in patients with thyroid carcinoma (TC), and their underlying mechanisms remain unclear. Thus, in this study, we aimed to explore the spatial distribution characteristics of TCs and associated gastrointestinal metastatic cells. METHODS We used spatial transcriptomics to generate an atlas that captures spatial gene expression patterns in papillary thyroid cancer (PTC), anaplastic thyroid carcinoma (ATC), ATC-associated lymphatic metastasis (ATC-LM), and rare ATC-associated gastric metastasis (ATC-GM). RESULTS We demonstrated that tumor-specific myeloid cells with high SFRP4 expression were correlated with TC dedifferentiation and poor prognosis. Moreover, we validated their close localization to CD44+ tissue stem cells using immunofluorescence staining and spatial transcriptomics. We also demonstrated that ATC-LM and ATC-GM tissues exhibited high levels of CD44+PKHD1L1+ cells, which could serve as markers for these two pathological types. CONCLUSIONS These findings highlight the dynamic changes in cell composition, intercellular communication, and potential markers associated with TC dedifferentiation and distant metastasis. Further research based on our findings may contribute to improving diagnostic and therapeutic strategies for patients with TC.
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Affiliation(s)
- Di Wang
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, 272067, China
| | - Ruichun Lu
- Department of Cadre Healthcare/Geriatrics, Qingdao Hospital, University of Health Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, 266017, China
| | - Fenglian Yan
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, 272067, China
| | - Yansong Lin
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Hao Wang
- Department of Radiotherapy, Qingdao Hospital, University of Health Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, 266071, China.
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, 272067, China.
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Zhang P, Gao C, Zhang Z, Yuan Z, Zhang Q, Zhang P, Du S, Zhou W, Li Y, Li S. Systematic inference of super-resolution cell spatial profiles from histology images. Nat Commun 2025; 16:1838. [PMID: 39984438 PMCID: PMC11845739 DOI: 10.1038/s41467-025-57072-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 02/07/2025] [Indexed: 02/23/2025] Open
Abstract
Inferring cell spatial profiles from histology images is critical for cancer diagnosis and treatment in clinical settings. In this study, we report a weakly-supervised deep-learning method, HistoCell, to directly infer super-resolution cell spatial profiles consisting of cell types, cell states and their spatial network from histology images at the single-nucleus-level. Benchmark analysis demonstrates that HistoCell robustly achieves state-of-the-art performance in terms of cell type/states prediction solely from histology images across multiple cancer tissues. HistoCell can significantly enhance the deconvolution accuracy for the spatial transcriptomics data and enable accurate annotation of subtle cancer tissue architectures. Moreover, HistoCell is applied to de novo discovery of clinically relevant spatial organization indicators, including prognosis and drug response biomarkers, across diverse cancer types. HistoCell also enable image-based screening of cell populations that drives phenotype of interest, and is applied to discover the cell population and corresponding spatial organization indicators associated with gastric malignant transformation risk. Overall, HistoCell emerges as a powerful and versatile tool for cancer studies in histology image-only cohorts.
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Affiliation(s)
- Peng Zhang
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, China
| | - Chaofei Gao
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, China
| | - Zhuoyu Zhang
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, China
| | - Zhiyuan Yuan
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Qian Zhang
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, China
| | - Ping Zhang
- Department of Pathology, Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shiyu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Weixun Zhou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Li
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Shao Li
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing, China.
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Zhang Y, Yu Y, Gu X, Li Z, Zhou Y, Xiang J. Exosomes derived from colorectal cancer cells suppress B-cell mediated anti-tumor immunity. Int Immunopharmacol 2025; 148:114176. [PMID: 39884085 DOI: 10.1016/j.intimp.2025.114176] [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: 11/16/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 02/01/2025]
Abstract
Exosomes derived from cancer cells significantly influence the tumor immune microenvironment and can limit the efficacy of immunotherapy. However, the impact of exosomes on B cell-dependent anti-tumor immunity remains poorly understood. Here, we demonstrate that exosomes secreted by MC38 (MC38-Exos), a murine colorectal cancer cell line, induce B cells to adopt immunosuppressive phenotypes. MC38-Exos inhibits B cell proliferation and survival. Additionally, MC38-Exos induce B cells to acquire characteristics of regulatory B cells, including the upregulation of IL-10 and TGF-β. Finally, B cells treated with MC38-Exos impair the functional efficacy of CD8+ T cells. Transcriptome analysis reveals that MC38-Exos markedly suppresses gene pathways associated with B cell receptor (BCR) signaling, as well as antigen processing and presentation in B cells, but up-regulates genes involving apoptosis pathway. Mechanistically, NF-κB pathway was enriched in KEGG analysis, and was validated by western blot. Finally, inhibition of MC38-Exo in vivo activates B-cell mediated anti-tumor immunity. Thus, MC38-Exo has a profound effect of transcriptome of B cells and attenuates B cell-dependent anti-tumor immunity, supporting the rationale for targeted exosome therapy in human colorectal cancer.
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Affiliation(s)
- Yukun Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China
| | - Yeping Yu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China
| | - Xiaodong Gu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China
| | - Zhenyang Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China
| | - Yiming Zhou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China
| | - Jianbin Xiang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040 China.
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Ruffin AT, Casey AN, Kunning SR, MacFawn IP, Liu Z, Arora C, Rohatgi A, Kemp F, Lampenfeld C, Somasundaram A, Rappocciolo G, Kirkwood JM, Duvvuri U, Seethala R, Bao R, Huang Y, Cillo AR, Ferris RL, Bruno TC. Dysfunctional CD11c -CD21 - extrafollicular memory B cells are enriched in the periphery and tumors of patients with cancer. Sci Transl Med 2025; 17:eadh1315. [PMID: 39970232 DOI: 10.1126/scitranslmed.adh1315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 02/07/2024] [Accepted: 01/16/2025] [Indexed: 02/21/2025]
Abstract
Many patients with recurrent and metastatic cancer fail to produce a durable response to immunotherapy, highlighting the need for additional therapeutic targets to improve the immune landscape in tumors. Recent studies have highlighted the importance of B cells in the antitumor response, with memory B cells (MBCs) being prognostic in a variety of solid tumors. MBCs are a heterogenous B cell subset and can be generated through both germinal center reactions and extrafollicular (EF) responses. EF-derived MBCs have been recently linked to poor prognosis and treatment resistance in solid tumors and thus may represent candidate biomarkers or immunotherapy targets. EF-derived MBCs, termed "double-negative" (DN) MBCs may be further classified on the basis of surface expression of CD11c and CD21 into DN1, DN2, and DN3 MBCs. CD11c-CD21+ DN1 MBCs and CD11c+CD21- DN2 MBCs have been well studied across inflammatory diseases; however, the biology and clinical relevance of CD11c-CD21- DN3 MBCs remain unknown. Here, we report an accumulation of DN3 MBCs in the blood and tumors of patients with head and neck squamous cell carcinoma (HNSCC) and an increase in DN3 MBCs in locally advanced HNSCC tumors. Circulating and intratumoral DN3 MBCs were hyporesponsive to antigen stimulation, had low antibody production, and failed to differentiate into antibody-secreting cells. Moreover, DN3 MBCs accumulated selectively outside of tertiary lymphoid structures. Last, circulating DN3 MBCs correlated with poor therapeutic response, advanced disease, and worse outcomes in patients with HNSCC and melanoma, supporting further assessment of EF-derived MBCs as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Ayana T Ruffin
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Allison N Casey
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- Molecular Genetics and Developmental Biology Graduate Program, Pittsburgh, PA 15213, USA
| | - Sheryl R Kunning
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Ian P MacFawn
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Zhentao Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Charu Arora
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Anjali Rohatgi
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Felicia Kemp
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Caleb Lampenfeld
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Ashwin Somasundaram
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | | | - John M Kirkwood
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Umamaheswar Duvvuri
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Raja Seethala
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Riyue Bao
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yufei Huang
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmaceutical Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Robert L Ferris
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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Xu S, Han C, Zhou J, Yang D, Dong H, Zhang Y, Zhao T, Tian Y, Wu Y. Distinct maturity and spatial distribution of tertiary lymphoid structures in head and neck squamous cell carcinoma: implications for tumor immunity and clinical outcomes. Cancer Immunol Immunother 2025; 74:107. [PMID: 39932546 PMCID: PMC11813844 DOI: 10.1007/s00262-025-03952-1] [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: 10/15/2024] [Accepted: 01/20/2025] [Indexed: 02/14/2025]
Abstract
The influence of tertiary lymphoid structures (TLSs) on disease progression and the response to immunotherapy in head and neck squamous cell carcinoma (HNSCC) is well established, yet the heterogeneity among these structures remains largely unexplored. We utilized digital spatial profiling technology to perform in situ transcriptomic sequencing of TLSs across varying levels of maturation and distinct tumor regions within HNSCC. We assessed the prognostic significance of TLS maturation and spatial distribution in 260 patients with HNSCC through hematoxylin and eosin staining and multiplex immunohistochemistry. Furthermore, we established a TLS scoring system to predict survival in patients with HNSCC. Our study revealed that mature TLSs in the intratumor region (Intra-TLSs) of HNSCC, enriched with memory B cells, plasma cells, and CD4+ T cells, presented increased B-cell activity gene expression. Conversely, early TLSs (E-TLSs), abundant in endothelial cells, fibroblasts, and regulatory T cells, express epithelial‒mesenchymal transition (EMT)-related genes, potentially fostering tumor growth. Compared with mature TLSs within the peritumoral region (Peri-TLSs), mature Intra-TLSs have greater memory B-cell and macrophage densities and upregulate genes involved in B-cell receptor signaling and immune effector processes. Mature Peri-TLSs, characterized by endothelial cell enrichment and EMT receptor interaction genes, may contribute to tumor progression and immune evasion. Patients with mature Intra-TLSs or invasive margin TLSs (Invas-TLSs) have improved 5-year survival, whereas those with mature Peri-TLSs have poorer prognoses. By integrating TLS maturity and distribution in HNSCC, we developed a TLS scoring system to guide personalized treatments, which is crucial for predicting outcomes.
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Affiliation(s)
- Shuai Xu
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
- Department of Head and Neck Surgery, The Second Affiliated Hospital, Third Military Medical University (Army Medical University), Chongqing, 400037, People's Republic of China
| | - Chao Han
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Jian Zhou
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Di Yang
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Hui Dong
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Yiwei Zhang
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China
| | - Tingting Zhao
- Chongqing International Institute for Immunology, Chongqing, 400030, People's Republic of China
| | - Yi Tian
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China.
| | - Yuzhang Wu
- Institute of Immunology, Third Military Medical University (Army Medical University), Chongqing, 400038, People's Republic of China.
- Chongqing International Institute for Immunology, Chongqing, 400030, People's Republic of China.
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Verona F, Di Bella S, Schirano R, Manfredi C, Angeloro F, Bozzari G, Todaro M, Giannini G, Stassi G, Veschi V. Cancer stem cells and tumor-associated macrophages as mates in tumor progression: mechanisms of crosstalk and advanced bioinformatic tools to dissect their phenotypes and interaction. Front Immunol 2025; 16:1529847. [PMID: 39981232 PMCID: PMC11839637 DOI: 10.3389/fimmu.2025.1529847] [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: 11/17/2024] [Accepted: 01/17/2025] [Indexed: 02/22/2025] Open
Abstract
Cancer stem cells (CSCs) are a small subset within the tumor mass significantly contributing to cancer progression through dysregulation of various oncogenic pathways, driving tumor growth, chemoresistance and metastasis formation. The aggressive behavior of CSCs is guided by several intracellular signaling pathways such as WNT, NF-kappa-B, NOTCH, Hedgehog, JAK-STAT, PI3K/AKT1/MTOR, TGF/SMAD, PPAR and MAPK kinases, as well as extracellular vesicles such as exosomes, and extracellular signaling molecules such as cytokines, chemokines, pro-angiogenetic and growth factors, which finely regulate CSC phenotype. In this scenario, tumor microenvironment (TME) is a key player in the establishment of a permissive tumor niche, where CSCs engage in intricate communications with diverse immune cells. The "oncogenic" immune cells are mainly represented by B and T lymphocytes, NK cells, and dendritic cells. Among immune cells, macrophages exhibit a more plastic and adaptable phenotype due to their different subpopulations, which are characterized by both immunosuppressive and inflammatory phenotypes. Specifically, tumor-associated macrophages (TAMs) create an immunosuppressive milieu through the production of a plethora of paracrine factors (IL-6, IL-12, TNF-alpha, TGF-beta, CCL1, CCL18) promoting the acquisition by CSCs of a stem-like, invasive and metastatic phenotype. TAMs have demonstrated the ability to communicate with CSCs via direct ligand/receptor (such as CD90/CD11b, LSECtin/BTN3A3, EPHA4/Ephrin) interaction. On the other hand, CSCs exhibited their capacity to influence immune cells, creating a favorable microenvironment for cancer progression. Interestingly, the bidirectional influence of CSCs and TME leads to an epigenetic reprogramming which sustains malignant transformation. Nowadays, the integration of biological and computational data obtained by cutting-edge technologies (single-cell RNA sequencing, spatial transcriptomics, trajectory analysis) has significantly improved the comprehension of the biunivocal multicellular dialogue, providing a comprehensive view of the heterogeneity and dynamics of CSCs, and uncovering alternative mechanisms of immune evasion and therapeutic resistance. Moreover, the combination of biology and computational data will lead to the development of innovative target therapies dampening CSC-TME interaction. Here, we aim to elucidate the most recent insights on CSCs biology and their complex interactions with TME immune cells, specifically TAMs, tracing an exhaustive scenario from the primary tumor to metastasis formation.
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Affiliation(s)
- Francesco Verona
- Department of Precision Medicine in Medical, Surgical and Critical Care, University of Palermo, Palermo, Italy
| | - Sebastiano Di Bella
- Department of Precision Medicine in Medical, Surgical and Critical Care, University of Palermo, Palermo, Italy
| | - Roberto Schirano
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Camilla Manfredi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Francesca Angeloro
- Department of Health Promotion Sciences, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Giulia Bozzari
- Department of Precision Medicine in Medical, Surgical and Critical Care, University of Palermo, Palermo, Italy
| | - Matilde Todaro
- Department of Health Promotion Sciences, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
- Azienda Ospedaliera Universitaria Policlinico “Paolo Giaccone” (AOUP), Palermo, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
- Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Giorgio Stassi
- Department of Precision Medicine in Medical, Surgical and Critical Care, University of Palermo, Palermo, Italy
| | - Veronica Veschi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
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Jiang S, Mantri M, Maymi V, Leddon SA, Schweitzer P, Bhandari S, Holdener C, Ntekas I, Vollmers C, Flyak AI, Fowell DJ, Rudd BD, De Vlaminck I. A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.31.635509. [PMID: 39975238 PMCID: PMC11838507 DOI: 10.1101/2025.01.31.635509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-γ) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.
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Affiliation(s)
- Shaowen Jiang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Madhav Mantri
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Viviana Maymi
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Scott A Leddon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Peter Schweitzer
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Subash Bhandari
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Chase Holdener
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrew I Flyak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Deborah J Fowell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Samiea A, Celis G, Yadav R, Rodda LB, Moreau JM. B cells in non-lymphoid tissues. Nat Rev Immunol 2025:10.1038/s41577-025-01137-6. [PMID: 39910240 DOI: 10.1038/s41577-025-01137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2025] [Indexed: 02/07/2025]
Abstract
B cells have long been understood to be drivers of both humoral and cellular immunity. Recent advances underscore this importance but also indicate that in infection, inflammatory disease and cancer, B cells function directly at sites of inflammation and form tissue-resident memory populations. The spatial organization and cellular niches of tissue B cells have profound effects on their function and on disease outcome, as well as on patient response to therapy. Here we review the role of B cells in peripheral tissues in homeostasis and disease, and discuss the newly identified cellular and molecular signals that are involved in regulating their activity. We integrate emerging data from multi-omic human studies with experimental models to propose a framework for B cell function in tissue inflammation and homeostasis.
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Affiliation(s)
- Abrar Samiea
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA
| | - George Celis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Rashi Yadav
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Lauren B Rodda
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA.
| | - Joshua M Moreau
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
- Department of Dermatology, Oregon Health & Science University, Portland, OR, USA.
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA.
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50
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Lau D, Elliott T. Imaging antigen processing and presentation in cancer. IMMUNOTHERAPY ADVANCES 2025; 5:ltaf002. [PMID: 40265075 PMCID: PMC12012451 DOI: 10.1093/immadv/ltaf002] [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: 09/17/2024] [Accepted: 02/04/2025] [Indexed: 04/24/2025] Open
Abstract
Introduction Antigen processing and presentation are vital processes of the adaptive immunity. These processes involve a series of intracellular and extracellular events, including the enzymology within cells during antigen processing, the loading and presentation of antigenic peptides on major histocompatibility complexes, the recruitment of T cells, their interaction with antigen-presenting cells, and the expression of adhesion, co-stimulatory and co-inhibitory molecules at the T cell immunological synapse. These events collectively fine-tune and sustain antigen recognition and T cell function. Dysregulation of this machinery can profoundly impact the efficacy of cancer immunotherapy. Imaging technologies have emerged as powerful tools for elucidating the mechanisms underlying antigen processing and presentation. By providing complementary perspectives into the cellular and molecular interactions at play, imaging has significantly enhanced our understanding of these complex immunological events in cancer. Such insights can improve the monitoring of immunotherapy responses, facilitate the identification of effective treatments, and aid in predicting patient outcomes. Methods This review explores the role of imaging in studying antigen processing and presentation in the context of cancer. Conclusion It highlights key considerations for developing imaging tools and biomarkers to detect components of these pathways. Additionally, it examines the strengths and limitations of various imaging approaches and discusses their potential for clinical translation.
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Affiliation(s)
- Doreen Lau
- Centre for Inflammation Research and Translational Medicine, Department of Life Sciences, Division of Biosciences, Brunel University London, London, United Kingdom
- Department of Radiology, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tim Elliott
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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