bims-spamet 2026-05-31 papers

bims-spamet

Biomed News

on Spatial metabolomics of T cells

Issue of 2026–05–31
seven papers selected by
Peio Azcoaga, Katholieke Universiteit te Leuven

CLEC2B-KLRB1 axis acts as an immune checkpoint, governing the exhaustion of CD8+ T cells and their resistance to immune checkpoint blockade.
ZBP1 Drives CD8+ T cell-mediated anti-tumor immunity in head and neck squamous cell carcinoma.
Early Recurrence of HCC Is Driven by Inflammation-Related HIF-1α Independent Angiogenesis Rather than Hypoxia-Induced Immune Escape.
PI3Kδ inhibition alters CD8 T cell differentiation and reprograms the tumor microenvironment following adoptive immunotherapy.
Development and validation of an interpretable prediction model using spatial patterns of tumor-infiltrating lymphocytes in H&E-stained whole-slide images for immune subtyping of lung adenocarcinoma.
High-throughput time-lapse imaging of B16 target cell killing by ovalbumin-specific CD8+ T cells.
Spatiotemporal mapping of CD112 unveils its dichotomous role in T-cell exhaustion and ferroptosis crosstalk in cervical cancer.

J Immunother Cancer. 2026 May 28. pii: e013637. [Epub ahead of print]14(5):

CLEC2B-KLRB1 axis acts as an immune checkpoint, governing the exhaustion of CD8+ T cells and their resistance to immune checkpoint blockade.

Jie Cheng, Jiahua Lu, Zhaoya Gao, Yifeng Xiao, Pengju Chen, Mengting Zhou, Dandan Huang, Zihao Zhao, Xiaohui Zhang, Yuan Zhao, Ming Li, Jin Gu.

   BACKGROUND: Many patients with cancer benefit little from immune checkpoint blockade (ICB), a major obstacle to immunotherapy for decades. Finding alternative immune checkpoints that control CD8+ T-cell exhaustion is urgent if we are to improve the efficacy of immunotherapies, particularly in microsatellite stable (MSS) colorectal cancer (CRC) that is resistant to ICB.
METHODS: Spatial proximity is essential for suppressive ligand-receptor signaling. Here, we mapped the spatial tumor microenvironment of patients with MSS CRC at single-cell resolution and analyzed the cells interacting with exhausted CD8+ T cells to identify immune checkpoint ligand-receptor pairs. To investigate the function of this previously unrecognized immune checkpoint, we performed validation studies spanning cellular experiments, mouse models, and clinical patient samples.
RESULTS: We found that a subset of MSS CRC exhibits substantial CD8+ T-cell infiltration, but their function is suppressed. We identified CLEC2B (ligand)-KLRB1 (receptor) as a novel inhibiting ligand-receptor pair for CD8+ T cells. KLRB1 acts as an immune checkpoint receptor, increasing CD8+ T-cell exhaustion and facilitating immune escape in various human cancers. Binding of CLEC2B to KLRB1 initiates immunosuppressive signaling in CD8+ T cells. Clinically, CLEC2B-KLRB1 expression correlates positively with cancer progression and poor response to ICB, demonstrating that KLRB1+ CD8+ T cells are a key marker of the poorly responsive ICB subtype. Furthermore, blocking CLEC2B-KLRB1 signaling with antibodies enhances the antitumor function of CD8+ T cells, providing a potential immunotherapy target for ICB non-responders.
CONCLUSIONS: Our study revealed CLEC2B-KLRB1 as a previously unrecognized immune checkpoint axis that drives T-cell exhaustion specifically in ICB poor responsive MSS CRC. Blockade of KLRB1 with a therapeutic antibody reinvigorated CD8+ T-cell antitumor immunity, positioning this axis as a promising target for enhancing immunotherapy efficiency in malignancies, including CRC and other ICB-resistant cancers.

Keywords:  Colorectal Cancer; Immune Checkpoint Inhibitor; T cell

DOI:  https://doi.org/10.1136/jitc-2025-013637
PLoS Genet. 2026 May 26. 22(5): e1012107

ZBP1 Drives CD8+ T cell-mediated anti-tumor immunity in head and neck squamous cell carcinoma.

Yu Min, Ge Song, Lianlian Yang, Ling He, Shihong Xu, Kun Gao, Zheran Liu, Xingchen Peng, Lei Dai.

Head and neck squamous cell carcinoma (HNSCC) frequently resists PD-1 blockade due to an immunologically "cold" tumor microenvironment (TME). Here, we identify Z-DNA binding protein 1 (ZBP1) as a key immunoregulator that reprograms immune-suppressive TMEs. Integrated TCGA/SangerBox analyses revealed ZBP1 as a hub gene strongly correlated with cytotoxic CD8+ T cells (r = 0.48, p < 0.0001) and M1 macrophages (r = 0.39, p < 0.0001). Multi-model validation in 92 HNSCC specimens revealed elevated ZBP1 expression versus normal tissues (p < 0.01), co-localized with infiltrating CD8+/CD4+ T cells and CD68+ macrophages through multiplex immunofluorescence. Clinically, high ZBP1 predicted improved survival (HR = 0.61 for overall survival; HR = 0.45 for disease specific survival; p < 0.0001) and early-stage presentation (p = 0.004). Mechanistically, ZBP1 overexpression in SCC-7/MOC2 models suppressed tumor growth while enhancing IFN-γ+ CD8+ T cell activation and reducing M2 polarization (CD206+: 16.91% vs 38.19% in ZBP1-high vs control, p < 0.001). Single-cell transcriptomics uncovered ZBP1-driven TME remodeling through chemokine signaling networks and expanded effector T cell compartments, validated by 1.49-fold increased CD8+ T cell infiltration via flow cytometry. Spatial analysis revealed ZBP1 overexpression amplified immune cell crosstalk (1.65-fold interaction increase, p < 0.001), upregulating CD8+ T cell chemotaxis (CXCR3/CCR5-CCL5 axis) and effector functions (p < 0.0001). Concurrently, it suppressed immunosuppressive pathways (ARG1 ↓ /IDO1↓) through metabolic reprogramming, establishing ZBP1 as a dual regulator synchronizing lymphocyte recruitment and myeloid suppression. Our integrative approach bridges computational biology with functional validation, demonstrating ZBP1's capacity to convert "cold" tumors into immunologically active niches. This work positions ZBP1 as both a stratification biomarker for checkpoint inhibitor response and a therapeutic target for TME reprogramming in HNSCC.

DOI: https://doi.org/10.1371/journal.pgen.1012107
Biomolecules. 2026 May 14. pii: 723. [Epub ahead of print]16(5):

Early Recurrence of HCC Is Driven by Inflammation-Related HIF-1α Independent Angiogenesis Rather than Hypoxia-Induced Immune Escape.

Lianda Siregar, Rino Alvani Gani, Toar J M Lalisang, Irsan Hasan, Suhendro, Heriawan Soejono, Siti Boedina Kresno, Nurjati Chairani Siregar, Muhammad Begawan Bestari.

   BACKGROUND: Hepatocellular carcinoma (HCC) shows a high rate of early recurrence after curative resection, indicating a critical contribution of tumor microenvironment-driven molecular mechanisms. Early recurrence of hepatocellular carcinoma is defined as recurrence within 6 months after curative resection, with a prevalence exceeding 30%. Hypoxia signaling and immune dysregulation have been implicated, yet their compartment-specific relevance remains unclear.
METHODS: This multicenter nested case-control study included 49 HCC patients to evaluate associations between hypoxia-inducible factor-1 alpha (HIF-1α), vascular endothelial growth factor (VEGF), tumor-infiltrating lymphocytes (TILs), CD4+ T cells, CD8+ T cells, regulatory T cells (Tregs), programmed cell death protein 1 (PD-1), and programmed death-ligand 1 (PD-L1) and early recurrence after resection. TIL density was assessed using hematoxylin and eosin staining, while immunohistochemistry was performed to quantify intratumoral and peritumoral expression of the studied markers. Receiver operating characteristic (ROC) curve analysis was used to evaluate the predictive performance. Recurrence-free survival (RFS) was analyzed using the Kaplan-Meier, and independent predictors were identified using multivariate Cox proportional hazards regression.
RESULTS: Early recurrence occurred in 11 of 49 patients (22.4%) of Child-Pugh A patients. Recurrent tumors were characterized by elevated VEGF expression despite absent HIF-1α, alongside significant depletion of intratumoral TILs (HR 5.02; 95% CI 1.09-23.26), CD4+ (HR 7.68; 95% CI 1.66-35.60) and CD8+ cells (HR 6.68; 95% CI 1.77-25.23) and reduced peritumoral CD8+ infiltration (HR 4.20; 95% CI 1.11-15.91). Multivariable analysis identified low intratumoral CD4+ (HR 7.98; 95% CI 1.63-39.07) and reduced peritumoral CD8+ expression (HR 4.98; 95% CI 1.14-21.70) as independent predictors, whereas HIF-1α, VEGF, Treg, PD-1, and PD-L1 were not significantly associated.
CONCLUSIONS: Early HCC recurrence shows HIF-1α-independent angiogenesis alongside spatial immune depletion, supporting integrated immune profiling over single angiogenic markers.

Keywords:  CD4; CD8; PD-1; PDL1; T regulation; VEGF; angiogenesis; early recurrence; hepatocellular carcinoma; hypoxia

DOI:  https://doi.org/10.3390/biom16050723
J Immunol. 2026 May 14. pii: vkag108. [Epub ahead of print]215(5):

PI3Kδ inhibition alters CD8 T cell differentiation and reprograms the tumor microenvironment following adoptive immunotherapy.

Alexandrea Turnquist, Azka Javaid, Owen M Wilkins, Fred Kolling Iv, Patricia A Pioli, Chrystal M Paulos, Hildreth Robert Frost, Edward J Usherwood.

  T cell exhaustion remains a significant barrier to effective adoptive cell therapy in solid tumors. Here, we demonstrate that in vitro treatment with the PI3Kδ inhibitor CAL-101 generates T cells with enhanced stemness and metabolic fitness. These cells show increased mitochondrial dependence and spare respiratory capacity while maintaining normal basal metabolism. Under chronic antigen stimulation, CAL-101-treated T cells, including human T cells, resist terminal exhaustion and maintain stem-like properties. Using single-cell RNA sequencing and spatial transcriptomics of B16 melanoma tumors, we found that CAL-101-treated T cells preferentially differentiate into progenitor exhausted T cells within the tumor microenvironment. These cells demonstrate enhanced tumor infiltration and upregulate the Cxcl10/Cxcr3 signaling axis. The tumor microenvironment of tumors containing CAL-101-treated T cells show reduced glycolysis, oxidative phosphorylation, and proliferation, while exhibiting increased proinflammatory signaling and decreased presence of immunosuppressive tumor-associated macrophages. Single-cell analysis reveals that the CAL-10-treated T cells concurrently increase oxidative phosphorylation, proliferation, and immune signaling pathways. Mechanistically, CAL-101-treated T cells maintain high expression of stemness-associated genes (Tcf7, Slamf6) while resisting expression of genes associated with terminal exhaustion (Tim3, Mt1/2). These findings reveal the mechanisms behind how PI3Kδ inhibition generates T cells capable of establishing and maintaining an antitumor immune response, suggesting a promising strategy for improving adoptive cell therapy outcomes in solid tumors.

Keywords:  T cells; cancer; cytotoxic; memory; tumor immunity

DOI:  https://doi.org/10.1093/jimmun/vkag108
Front Immunol. 2026 ;17 1773927

Development and validation of an interpretable prediction model using spatial patterns of tumor-infiltrating lymphocytes in H&E-stained whole-slide images for immune subtyping of lung adenocarcinoma.

Xia Li, Hai-Zhen Qin, Jing-Yu Wei, Kang-Lai Wei, Zhao-Quan Huang.

   Objective: To develop an interpretable prediction model for lung adenocarcinoma immune subtyping by quantifying spatial distribution patterns of tumor-infiltrating lymphocytes in H&E whole-slide images, providing a computational tool for tumor immune microenvironment evaluation.
Methods: Immune subtyping was performed on the TCGA lung adenocarcinoma cohort using ssGSEA to quantify immune gene set activity, followed by hierarchical clustering and t-SNE visualization to stratify patients into high- and low-immunity subgroups. Immune cell infiltration was assessed using CIBERSORT, while tumor mutation burden and somatic mutation profiles were analyzed with maftools. Differential expression and functional enrichment analyses were conducted using GO and KEGG databases. In pathological image analysis, an automated annotation model optimized with study-specific data was employed to process whole-slide images. Immune subtype prediction criteria were established by quantifying spatial distribution features of tumor-infiltrating lymphocytes. The model's predictive performance was validated in both internal and external cohorts.
Results: Transcriptomic analysis stratified 503 LUAD patients into high- and low-immunity subgroups. The high-immunity group exhibited elevated infiltration of CD8+T cells and M1 macrophages, higher tumor mutation burden, and enriched T cell activation pathways. The low-immunity group showed predominant resting immune cells. The automated annotation model, achieved a 95.09% Dice score for tissue contour segmentation, 91.53% for tumor parenchyma segmentation, and a 79.51% F1-score with an mAP@0.5 of 82.13% for TIL identification. Quantitative TIL spatial distribution analysis with a 0.2 high-attention threshold enabled development of an immune subtyping model using a 0.05 classification cutoff, which achieved an AUC of 0.839 for immune subtype classification in the internal validation cohort. In the external validation cohort, the model achieved an AUC of 0.927, and immunohistochemical analysis confirmed significantly higher densities of CD3+, CD8+, CD20+, and CD68+ cells in predicted high-immunity samples.
Conclusion: This study establishes an interpretable immune subtype prediction model for LUAD based on TIL spatial distribution in H&E-stained sections. Through a modular design that integrates deep learning-based annotation with statistical classification, the model links morphological phenotypes to molecular immune subtypes while maintaining transparency and verifiability throughout the analytical workflow. This cost-effective and scalable tool offers potential value for assessing tumor immune status and guiding immunotherapy decision-making.

Keywords:  computational pathology; immune subtyping; interpretable model; lung adenocarcinoma; tumor-infiltrating lymphocytes

DOI:  https://doi.org/10.3389/fimmu.2026.1773927
Methods Cell Biol. 2026 ;pii: S0091-679X(26)00094-4. [Epub ahead of print]207 119-138

High-throughput time-lapse imaging of B16 target cell killing by ovalbumin-specific CD8+ T cells.

Beatriz Chaves, Nicolas Socquet-Juglard, Loïc Dupré, Hélène Daniels-Treffandier.

  Cytotoxic T Lymphocytes (CTLs) mediate tumor clearance and anti-tumoral responses through the elimination of target cancerous cells upon antigen recognition and TCR engagement. The killing of cancerous cells mediated by CTLs can be modulated by the strength of the TCR engagement, notably through the antigen affinity to the TCR, the quality of the immune synapse, the time of contact between CTLs and targets, among other parameters. Unveiling the mechanisms, kinetics and factors influencing cancer cell elimination by CTLs is essential for the amelioration of lymphocyte-based immunotherapies, such as CAR-T cells, and the understanding of tumoral clearance in vivo. Here, we provide a method to precisely monitor the cytotoxic capacity of murine CTLs in an antigen-specific manner, using ovalbumin (OVA) specific CTLs expressing the modified OT1 TCR and four different tumoral B16-F10 cell lines expressing OVA peptides with variable affinity for the OT1 TCR. We present step-by-step the implementation of a high throughput image-based pipeline allowing, on one hand, the time-lapse monitoring of CTL-mediated cytotoxicity and, on the other hand, the measurement of morphological parameters of CTLs and target cells based on fluorescent labeling. This method is suitable for ex-vivo exploration of lymphocyte cytotoxicity and related parameters, and can be adapted for mechanistic studies or screening approaches.

Keywords:  Antigen-specific killing; Cytotoxic T cells; High content cell imaging; Variable affinity

DOI:  https://doi.org/10.1016/bs.mcb.2026.03.001
Cell Death Dis. 2026 May 27.

Spatiotemporal mapping of CD112 unveils its dichotomous role in T-cell exhaustion and ferroptosis crosstalk in cervical cancer.

Lihua Chen, Wenyu Lin, Yuxuan Huang, Chen Li, Ming Du, Yang Liu, Weidi Wang, Duancheng Tian, Pengming Sun, Yang Xiang.

CD112 emerges as a novel immune checkpoint (IC) in various malignancies, its spatial biology and dual mechanisms in cervical cancer (CC) progression are unexplored. This study systematically analyzes the dual-functions of CD112 in immune evasion and metabolic adaptation in CC. Proteomics and immune checkpoint analysis were performed on 10 CC and normal tissues to explore key targets. Multiplex immunofluorescence (mIHC) on 318 CC tissue microarrays analyzed CD112/CD112R spatial distribution and prognosis. Tumor cell and T cell co-culture models and immunocompetent murine models were used to validate effects of anti-CD112 mAb±anti-PD-1 treatment. CD112 expression in the infiltrated and margine areas correlated with PD-1+CD8+ T cells density (r = 0.545, P < 0.001), predicting unfavorable prognosis. Functional studies show that CD112 on tumor cells interacts with CD112R on CD8+ T cells, promoting abnormal numbers and functions of CD8+T cells, while CD112 antibodies can reverse CD8+ T cell exhaustion and enhance the anti-tumor effects by synergized with PD-1 inhibitors. Mechanistically, the transcription factor Sp1 drives the overexpression of CD112 in CC cells. Additionally, CD112 confers resistance to ferroptosis in CC through the SLC7A11/GPX4 pathway. CD112 acts as a "dual-target" mediating immune suppression and ferroptosis resistance. Combining CD112 and PD-1 inhibition may enhance CC immunotherapy.

DOI: https://doi.org/10.1038/s41419-026-08902-y