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supplementary information 12916_2025_3889_moesm1_esm springer nature data availability abbreviations gc single-cell rna data discussion funding underwent anti-pd-1/pd-l1 therapy state privacy rights cxcl13+cd103+cd8+ tissue-resident memory additional information publisher single-cell sequencing cohort compromising biological information single-cell copy-number variation performed spatial transcriptomics conclusions high-resolution cell-mapping techniques single-cell transcriptomic atlas spatial transcriptomics rna-seq data original author rights strong anti-tumour effect single-cell transcriptomic analysis tertiary lymphoid structures gzma-f2r/f2rl3 axis 500-µm-wide zone centred comprehensive information information flow immune-related progression-free survival external t-cell zone ten-fold cross-validation freeze-thaw lysis based analytical methods methods patients intratumoral lymphoid structures sharing jak2/stat1 signal suppression cd4+ctla-4−foxp3−pd-l1− restore anti-tumor immunity single-cell data kaplan–meier curve showing single-cell resolution bonferroni-corrected p-adjusted cancer-related deaths worldwide content ethics committee pre-optimised antibody concentration information pro-inflammatory macrophage polarisation

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         headline:Immune microenvironment spatial landscapes of tertiary lymphoid structures in gastric cancer
         description:Tertiary lymphoid structures (TLS) correlate with tumour prognosis and immunotherapy responses in gastric cancer (GC) studies. However, understanding the complex and diverse immune microenvironment within TLS requires comprehensive analysis. We examined the prognostic impact of TLS within the tumour core (TC) of 59 GC patients undergoing immunotherapy. Multispectral fluorescence imaging was employed to evaluate variations in immune cell infiltration across different TLS sites among 110 GC patients, by quantifying immune cell density and spatial characteristics. We also generated a single-cell transcriptomic atlas of TLS-positive (n = 4) and TLS-negative (n = 8) microenvironments and performed spatial transcriptomics (ST) analysis on two samples. TLS presence in the TC significantly correlated with improved immune-related overall survival (P = 0.049). CD8+LAG-3−PD-1+TIM-3−, CD4+PD-L1+, and CD4+FoxP3− T cell densities were significantly higher in the TLS within TC compared to tumour and stromal regions. Immune cells within TLS exhibited closer intercellular proximity than those outside TLS. Five key density and spatial characteristics of immune cells within TLS in the TC were selected to develop the Density and Spatial Score risk model. Single-cell RNA sequencing revealed strong intercellular interactions in the presence of TLS within the microenvironment. However, TLS-absent environment facilitated tumour cell interactions with immune cells through MIF- and galectin-dependent pathways, recruiting immunosuppressive cells. ST analysis confirmed that T and B cells co-localise within TLS, enhancing immune response activation compared to cancer nests and exerting a strong anti-tumour effect. TLS presence facilitates frequent cell-to-cell communication, forming an active immune microenvironment, highlighting the prognostic value of TLS.
         datePublished:2025-02-04T00:00:00Z
         dateModified:2025-02-04T00:00:00Z
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            Gastric cancer
            Tertiary lymphoid structures
            Tumour microenvironment
            Immunotherapy
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      headline:Immune microenvironment spatial landscapes of tertiary lymphoid structures in gastric cancer
      description:Tertiary lymphoid structures (TLS) correlate with tumour prognosis and immunotherapy responses in gastric cancer (GC) studies. However, understanding the complex and diverse immune microenvironment within TLS requires comprehensive analysis. We examined the prognostic impact of TLS within the tumour core (TC) of 59 GC patients undergoing immunotherapy. Multispectral fluorescence imaging was employed to evaluate variations in immune cell infiltration across different TLS sites among 110 GC patients, by quantifying immune cell density and spatial characteristics. We also generated a single-cell transcriptomic atlas of TLS-positive (n = 4) and TLS-negative (n = 8) microenvironments and performed spatial transcriptomics (ST) analysis on two samples. TLS presence in the TC significantly correlated with improved immune-related overall survival (P = 0.049). CD8+LAG-3−PD-1+TIM-3−, CD4+PD-L1+, and CD4+FoxP3− T cell densities were significantly higher in the TLS within TC compared to tumour and stromal regions. Immune cells within TLS exhibited closer intercellular proximity than those outside TLS. Five key density and spatial characteristics of immune cells within TLS in the TC were selected to develop the Density and Spatial Score risk model. Single-cell RNA sequencing revealed strong intercellular interactions in the presence of TLS within the microenvironment. However, TLS-absent environment facilitated tumour cell interactions with immune cells through MIF- and galectin-dependent pathways, recruiting immunosuppressive cells. ST analysis confirmed that T and B cells co-localise within TLS, enhancing immune response activation compared to cancer nests and exerting a strong anti-tumour effect. TLS presence facilitates frequent cell-to-cell communication, forming an active immune microenvironment, highlighting the prognostic value of TLS.
      datePublished:2025-02-04T00:00:00Z
      dateModified:2025-02-04T00:00:00Z
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         Gastric cancer
         Tertiary lymphoid structures
         Tumour microenvironment
         Immunotherapy
         Prognostic model
         Single-cell RNA sequencing
         Spatial transcriptomics
         Medicine/Public Health
         general
         Biomedicine
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      name:Yu Sun
      affiliation:
            name:Peking University Cancer Hospital and Institute
            address:
               name:Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Lin Shen
      affiliation:
            name:Peking University Cancer Hospital and Institute
            address:
               name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Yang Chen
      affiliation:
            name:Peking University Cancer Hospital and Institute
            address:
               name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
               type:PostalAddress
            type:Organization
            name:Beijing GoBroad Hospital
            address:
               name:Department of Gastrointestinal Cancer, Beijing GoBroad Hospital, Beijing, China
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
      name:Department of Gastrointestinal Cancer, Beijing GoBroad Hospital, Beijing, China

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