bims-spamet Biomed News
on Spatial metabolomics of T cells
Issue of 2026–11–01
thirteen papers selected by
Peio Azcoaga, Katholieke Universiteit te Leuven
  1. The Y chromosome gene KDM5D restrains CD8+ T cell antitumor immunity through TCR and cholesterol-exhaustion programs.
  2. Beyond Exhaustion: The RNA Regulatory Layer of Tissue-Instructed T Cell Dysfunction.
  3. From Dysfunction to Differentiation: A New Paradigm of T Cell Exhaustion.
  4. The fate of cysteine's sulfur in CD8+ T cell function.
  5. Hypoxic conditioning of neuroblastoma cells promotes CD8+ T-cell dysfunction through the HIF-1α/PD-L1 axis.
  6. A Double-Edged Sword: The Dichotomous Roles of Dendritic Cell Subsets in Shaping CD8+ T Cell Immunity and Tolerance Within the Tumor Microenvironment.
  7. Spatial Lineage Tracing Reveals Tumor-Microenvironment Coevolution.
  8. Time-Encoded Ligand Presentation via a Magnetically Actuated Hydrogel Mitigates T Cell Exhaustion.
  9. Preparation of Melanoma Tissue for Multiplex Immunofluorescence Histology Analysis of Immune Infiltration and Spatial Organization.
  10. Glucose restriction induced by intermittent fasting promotes alternative metabolic fluxes leading to memory CD8+ T cell development.
  11. Single-cell multi-omics reveals archetypal regulatory programs shared across T cell subsets.
  12. Comprehensive Approach to Heterogenous Tumor Cell Dynamics Analysis for Intravital Microscopy.
  13. VISTA as a tumour-microenvironment checkpoint: spatial, metabolic and cellular control of antitumour immunity.
  1. bioRxiv. 2026 Sep 01. pii: 2026.07.23.740424. [Epub ahead of print]
    The Y chromosome gene KDM5D restrains CD8+ T cell antitumor immunity through TCR and cholesterol-exhaustion programs.
    Jiexi Li, Chi Yin Ching, Aviad Ben-Shmuel, Paulino Tallón de Lara, Jingjing Liu, Jiang Shan, Chaohao Li, Ziyuan Zhang, William Huaiyang Wu, Max Slotnik, Xiaotian Wang, Raul Caballero Montes, Abhinav K Jain, Nicholas Hornstein, Fadl Zeineddine, Mohammad Zeineddine, Scott Eric Woodman, Natividad Roberto Fuentes, Denise J Spring, John Paul Shen, Scott Kopetz, Ronald A DePinho.
      Sex differences in immunity shape cancer risk, autoimmunity, and responses to immunotherapy, yet the sex-chromosome genes that regulate antitumor T cell function remain incompletely defined. Here, we identify the Y chromosome-encoded KDM5D histone demethylase as a male-specific suppressor of CD8+ T cell antitumor immunity. In murine colorectal cancer (CRC) models, male CD8+ T cells displayed reduced cytokine production, proliferation, cytotoxicity, TCRβ abundance, and proximal TCR signaling relative to female CD8+ T cells. CRISPR-RNP-mediated KDM5D depletion in male CD8+ T cells enhanced effector function, increased TCRβ expression, augmented TCR signaling, and improved tumor control after adoptive transfer. Transcriptomic and functional analyses further linked KDM5D to cholesterol biosynthesis and exhaustion-associated programs, with KDM5D depletion reducing SREBP2/XBP1-associated cholesterol and exhaustion signatures. Correspondingly, human CRC single-cell analyses supported the clinical relevance of this axis, showing enrichment of exhausted and cholesterol-associated CD8+ T cell states in male tumors. Pharmacologic inhibition of cholesterol biosynthesis with lovastatin partially attenuated select exhaustion-associated markers in male CD8+ T cells and delayed tumor growth in vivo. Together, these findings define KDM5D as a sex chromosome-encoded regulator of male CD8+ T cell dysfunction and point to cholesterol-exhaustion programs as a potential therapeutic vulnerability in male CRC.
    DOI:  https://doi.org/10.64898/2026.07.23.740424
  2. Eur J Immunol. 2026 Oct;pii: e70286. [Epub ahead of print]56(10):
    Beyond Exhaustion: The RNA Regulatory Layer of Tissue-Instructed T Cell Dysfunction.
    Francesco Andreata, Federica Marasca, Beatrice Bodega, Matteo Iannacone.
      CD8+ T cell exhaustion is a differentiation program driven by persistent antigen stimulation and stabilized through multiple regulatory layers, including transcription factor networks and chromatin. Beyond these established frameworks, an RNA regulatory layer, encompassing noncoding RNAs, RNA-binding proteins, alternative splicing isoforms, and epitranscriptomic modifications, is emerging as a further determinant of exhausted T cell identity. Retrotransposon-derived transcripts remain largely underexplored in this context, with the exception of LINE1-containing transcripts, which are causally linked to exhaustion and directly therapeutically addressable. Yet, whether this RNA layer is a generalizable feature of exhaustion or is instead instructed by the tissue in which antigen priming occurs remains unknown. Most of the current understanding derives from settings in which naïve CD8+ T cells are primed by professional antigen-presenting cells in secondary lymphoid organs. In the liver, however, hepatocytes can prime naïve CD8+ T cells directly, generating a hypofunctional state that is transcriptionally and pharmacologically distinct from canonical exhaustion, refractory to checkpoint blockade yet reversible by 4-1BB agonism. We propose that the RNA regulatory layer is a plausible substrate through which tissue-derived signals are encoded, and that the liver offers a powerful model to define and therapeutically target tissue-instructed T cell dysfunction.
    Keywords:  CD8+ T cell exhaustion; LINE1 retrotransposons; Liver immunology; RNA therapeutics; Regulatory RNAs
    DOI:  https://doi.org/10.1002/eji.70286
  3. Acta Naturae. 2026 Jul-Sep;18(3):18(3): 4-18
    From Dysfunction to Differentiation: A New Paradigm of T Cell Exhaustion.
    V M Stepanova, A S Logvinov, E A Emelyanov, N A Katin, Yu P Rubtsov.
      CD8+ T cell exhaustion is the loss of certain functions typical of cytotoxic lymphocytes. CD8+ cytotoxic T cells originate from naive CD8+ T cells upon antigen exposure. Chronic or excessive antigen exposure during certain infections and cancers triggers inhibitory mechanisms that lead to functional exhaustion - a loss of the ability to secrete IFN-γ and other cytokines, as well as to produce granzyme- and perforin-containing lytic granules in response to stimulation. Functional exhaustion also affects CD4+ helper T cells, which further reduces CD8+ T cell cytotoxicity. This leads to the loss of the CD8+ T cell's ability to kill target cells, which negatively impacts immunity and reduces the efficacy of therapeutic T cells. Currently, T cell exhaustion is considered as a multistage, partially reversible differentiation program. Heterogeneous subsets of stem-like progenitor exhausted T cells (Tex-prog) and terminally exhausted T cells (Tex-term) have been identified. These cells differ in their degrees of dysfunction and, thus, in their potential to restore lost functions. The transcriptional exhaustion program is controlled by key transcription factors, such as TCF1, TOX, T-bet, EOMES, BATF, IRF4, etc. Understanding the dynamic changes taking place in the transcriptional profile and cellular phenotype is critical for effective immunotherapy, in particular in immune checkpoint blockade (ICB) and CAR-T cell therapy, because its success depends entirely on the T cell state. In this review, we discuss current concepts on the molecular and cellular mechanisms of T cell exhaustion, various exhaustion-associated phenotypic and functional changes, and opportunities for preventing T cell exhaustion to optimize anti-tumor immunotherapy strategies.
    Keywords:  CD8+ T cells; T cells; cellular immunotherapy; functional exhaustion; immune checkpoint blockade; negative co-stimulation; transcription factors
    DOI:  https://doi.org/10.32607/actanaturae.27873
  4. Trends Endocrinol Metab. 2026 Oct 27. pii: S1043-2760(26)00274-2. [Epub ahead of print]
    The fate of cysteine's sulfur in CD8+ T cell function.
    Beth Kelly, Erika L Pearce.
      CD8+ T cells modulate their metabolism to support activation, proliferation, and effector function. The sulfur-containing amino acid cysteine is essential for these processes, but beyond its role in protein synthesis, cysteine is metabolized into multiple products that differentially regulate T cell immunity. Here, we review recent advances in understanding how intracellular cysteine routing controls CD8+ T cell function. Cysteine-derived glutathione, iron-sulfur clusters, coenzyme A, hydrogen sulfide, and taurine each have distinct effects on T cell activation, mitochondrial metabolism, and antitumor immunity. Additionally, cysteine-dependent post-translational modifications-including sulfenylation and persulfidation-modulate signaling and gene expression. Understanding how cells balance competing cysteine fates may reveal new therapeutic strategies to enhance T cell responses in cancer and other diseases.
    Keywords:  CD8(+) T cell; Fe–S cluster; cysteine; glutathione; immunometabolism; sulfur
    DOI:  https://doi.org/10.1016/j.tem.2026.10.002
  5. Front Pediatr. 2026 ;14 1923893
    Hypoxic conditioning of neuroblastoma cells promotes CD8+ T-cell dysfunction through the HIF-1α/PD-L1 axis.
    Yujin Chao, Guili Zheng.
       Objective: To investigate whether hypoxic conditioning of neuroblastoma (NB) cells induces CD8+ T cell dysfunction/exhaustion-like phenotype via the HIF-1α/PD-L1 axis and whether targeting this axis reverses immune suppression.
    Methods: Human NB cell lines SK-N-SH, SK-N-BE(2), and SK-N-AS were exposed to 1% O₂ hypoxia. HIF-1α and PD-L1 expression were assessed by Western blot, qRT-PCR, and flow cytometry. ChIP-qPCR and dual-luciferase assays were used to verify HIF-1α binding and transcriptional activation of the PD-L1 promoter. SK-N-SH cells pre-conditioned under normoxia or hypoxia were co-cultured with primary human CD8+ T cells. CD8+ T cell dysfunction/exhaustion-like phenotype (PD-1+TIM-3+), apoptosis, IFN-γ, Granzyme B, CD107a, and specific cytotoxicity were evaluated. HIF-1α siRNA, YC-1, and PD-L1 neutralizing antibody were applied. The direct effect of YC-1 on T cells was also assessed.
    Results: Hypoxia increased HIF-1α and PD-L1 expression in a time-dependent manner and also upregulated PD-L1 in additional NB cell lines. ChIP-qPCR and dual-luciferase assays confirmed direct HIF-1α binding to the HRE (5'-AGGTGC-3') and transcriptional activation. PD-L1 elevation declined after reoxygenation. Hypoxia-preconditioned NB cells increased PD-1+TIM-3+ CD8+ T cells (5.49%-32.24%) and apoptosis (10.61%-26.89%), while reducing IFN-γ +, Granzyme B+, CD107a+ cells and specific cytotoxicity (79.94%-38.40%). HIF-1α knockdown or PD-L1 blockade alleviated these effects. YC-1 at 25 μM did not significantly affect T cell viability or IFN-γ secretion.
    Conclusion: Hypoxic conditioning of NB cells stabilizes HIF-1α, enhances its binding to the PD-L1 promoter HRE, upregulates PD-L1, and induces CD8+ T cell dysfunction/exhaustion-like phenotype and impaired antitumor function. Targeting HIF-1α or PD-L1 partially restores T cell function in this co-culture model. The hypoxia-driven HIF-1α/PD-L1 axis contributes to immune suppression in NB and may be a potential therapeutic target.
    Keywords:  HIF-1α; PD-l1; T cell dysfunction; exhaustion-like phenotype; hypoxia; neuroblastoma
    DOI:  https://doi.org/10.3389/fped.2026.1923893
  6. Int J Mol Sci. 2026 Oct 13. pii: 9064. [Epub ahead of print]27(20):
    A Double-Edged Sword: The Dichotomous Roles of Dendritic Cell Subsets in Shaping CD8+ T Cell Immunity and Tolerance Within the Tumor Microenvironment.
    Guoyao Gao, Ke Chen.
      Dendritic cells (DCs) function as a double-edged sword in tumor immunity, capable of both activating and tolerizing CD8+ cytotoxic T lymphocytes (CTLs). While conventional type 1 dendritic cells (cDC1s) are well-established mediators of cross-presentation for initiating anti-tumor CTL responses, existing reviews-largely overlook the tolerogenic potential of cDC1s and the context-dependent immunostimulatory capacity of cDC2s, monocyte-derived DCs (moDCs), and plasmacytoid DCs (pDCs). Furthermore, no prior synthesis has systematically reconciled the divergent functions of DC subsets across steady-state versus inflammatory conditions, migratory versus resident phenotypes, and human versus mouse model systems. The tumor microenvironment (TME) and tumor-derived exosomes further drive DCs toward an immunosuppressive phenotype, facilitating immune escape. Here, we establish a multi-dimensional framework that dissects the dichotomous roles of diverse DC subsets in regulating CTL immunity and tolerance, resolving key biological contradictions-including recent in vivo evidence that cDC2s can cross-present immune-complexed antigens via a WDFY4-dependent pathway shared with cDC1s-an activity that complements, but does not replace, the cDC1-restricted cross-presentation of cell-associated antigens. We also provide a hierarchical analysis of strategies to restore DC-mediated anti-tumor activity, extending the DC-CTL regulatory paradigm to autoimmunity and solid organ transplantation. A comprehensive summary table categorizes DC-based therapeutic approaches by clinical development stage. By elucidating this dynamic balancing mechanism, we offer refined insights for optimizing cancer immunotherapy design and cross-disciplinary therapeutic applications.
    Keywords:  CD8+ T lymphocytes; DC-based vaccines; antitumor immunity; autoimmunity; dendritic cells (DCs); immune tolerance; solid organ transplantation; tumor microenvironment
    DOI:  https://doi.org/10.3390/ijms27209064
  7. Cancer Discov. 2026 Oct 27. OF1
    Spatial Lineage Tracing Reveals Tumor-Microenvironment Coevolution.
      
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2026-095
  8. Adv Mater. 2026 Oct 26. pii: e75515. [Epub ahead of print]
    Time-Encoded Ligand Presentation via a Magnetically Actuated Hydrogel Mitigates T Cell Exhaustion.
    Xuemei Wang, Runyao Wang, Guangli Xiang, Xueyou Zhang, Luyang Wang, Wai Ki Wong, Yingrui Deng, Yongkang Yang, Jiwon Oh, Xian Xie, Zhinan Yang, Nathanael Chun Him Lai, Bohan Yin, Kunyu Zhang, Liming Bian, Siu Hong Dexter Wong.
      Adoptive T cell therapy (ACT) requires ex vivo expansion of tumor-reactive CD8+ T cells, yet prolonged antigenic stimulation frequently induces exhaustion, limiting persistence and therapeutic efficacy. Here, we present a magnetically actuated, extracellular matrix-mimetic hydrogel that enables reversible control of T cell receptor (TCR) stimulation timing. By embedding αCD3ε/αCD28-functionalized magnetic nanoparticles within a soft hyaluronic acid matrix, external magnetic fields dynamically expose or conceal stimulatory ligands, allowing programmable alternation between activation and rest. Continuous ligand presentation sustains TCR signaling and drives inhibitory receptor expression and functional exhaustion. In contrast, alternating activation-rest cycles periodically attenuate proximal TCR signaling, reduce exhaustion-associated marker expression, and bias differentiation toward central memory-like states while preserving cytokine production and recall capacity. T cells expanded under intermittent stimulation exhibit enhanced antigen-specific cytotoxicity, reduced dependence on PD-1 blockade, and superior tumor control in vivo, together with increased CD8+ T cell abundance across analyzed tissues. These results identify temporal control of mechanochemical signaling as a materials-encoded regulator of T cell fate and provide a non-genetic strategy for generating functionally competent T cell products with reduced exhaustion-associated dysfunction and improved antitumor activity.
    Keywords:  T cell exhaustion; adoptive cell therapy; dynamic ligand presentation; immuno‐materials engineering; magnetically actuated hydrogel; time‐encoded signaling
    DOI:  https://doi.org/10.1002/adma.75515
  9. Methods Mol Biol. 2027 ;3089 349-361
    Preparation of Melanoma Tissue for Multiplex Immunofluorescence Histology Analysis of Immune Infiltration and Spatial Organization.
    Victoria Ann Remley, Marya Dunlap-Brown, Kelly T Smith, Sheri Vanhoose, Sara J Adair, Todd W Bauer, Ileana S Mauldin.
      Immunotherapies extend survival in melanoma patients by increasing the immune system's capacity to detect tumors and mediate tumor cell death. Understanding mechanisms of antitumor immunity requires evaluating changes in immune infiltrate composition, activation, and spatial distribution within the tumor microenvironment (TME). Despite this need, relatively few methods allow for detailed analysis of both the structural organization and immunological characteristics of tumor-infiltrating immune cells in preclinical cancer models. In this chapter, we present a multiplex immunofluorescence staining approach for identifying, characterizing, and quantifying tumor-infiltrating immune cells in murine melanoma, allowing evaluation of how therapies influence immune infiltration in preclinical models.
    Keywords:  IHC; Immune infiltration; Melanoma; Multiplex immunofluorescence Histology
    DOI:  https://doi.org/10.1007/978-1-0716-5619-8_24
  10. Sci Adv. 2026 Oct 30. 12(44): eaeg0361
    Glucose restriction induced by intermittent fasting promotes alternative metabolic fluxes leading to memory CD8+ T cell development.
    Da-Jeong Park, Young-Jun Ju, Young Jin Pyung, Cheol Gyun Kim, Narae Kim, MinJi Lim, Hyungseok Seo, Seung Hyun Han, Jae-Ho Cho, Cheol-Heui Yun.
      Dietary restrictions are increasingly recognized as modulators of immune cell function. However, how they shape CD8+ T cell fate decisions remains incompletely understood. Here, we investigated the impact of intermittent fasting (IF) on differentiation of heterogeneous effector T cell subsets and the formation of a long-lived homeostatic memory pool. We found that IF skewed CD8+ T cell differentiation toward memory precursor effector cells (MPECs) and enhanced the central memory CD8+ T cell development and functions. Mechanistically, glucose restriction induced by IF promotes alternative metabolic fluxes leading to fatty acid oxidation. This metabolic shift enhanced mitochondrial fitness and supported MPEC differentiation via metabolic-epigenetic cross-talk, culminating in durable and functionally robust memory CD8+ T cell responses. Applying this strategy in adoptive transfer therapy, intratumoral defects could be circumvented by imprinting a memory phenotype under IF-mimicking conditions, resulting in improved and long-lasting antitumor activity. Collectively, these findings underscore the importance of IF in orchestrating metabolic-epigenetic cross-talk to enhance memory formation and antitumor immunity.
    DOI:  https://doi.org/10.1126/sciadv.aeg0361
  11. Cell Rep. 2026 Oct 26. pii: S2211-1247(26)01235-0. [Epub ahead of print]45(11): 118156
    Single-cell multi-omics reveals archetypal regulatory programs shared across T cell subsets.
    Sarah K Walker, Joris van der Veeken, Alexander Y Rudensky, Yuri Pritykin.
      T cells differentiate into functionally distinct subsets in response to pathogens, yet essential immune functions such as self-renewal, expansion, cytokine production, and cytotoxicity are common to multiple subsets and therefore must be programmed via shared regulatory mechanisms. To uncover these "archetypal" epigenomic programs, we integrated a single-cell multiomic (scATAC+RNA-seq) dataset of CD4 and CD8 T cells responding to acute and chronic viral infection with a comprehensive bulk ATAC-seq compendium. Our analysis reveals a modular architecture governing T cell identity, implicating distinct transcription factors in reusing regulatory programs across subsets and lineages. Notably, translationally important progenitor CD8 T cells, critical for sustained immunity and present in both acute and chronic infection, exhibit a composite regulatory state, combining a CD8 exhaustion program with a follicular helper CD4 T cell program. In sum, this resource and generalizable computational framework will aid the mechanistic dissection of adaptive immunity and immunotherapy design.
    Keywords:  CP: genomics; CP: immunology; LCMV; T cell exhaustion; Tfh; Tpex; follicular helper T cells; gene regulation; progenitor exhausted CD8 T cells; scATAC-seq; scRNA-seq; single-cell multi-omics
    DOI:  https://doi.org/10.1016/j.celrep.2026.118156
  12. Methods Mol Biol. 2027 ;3085 257-273
    Comprehensive Approach to Heterogenous Tumor Cell Dynamics Analysis for Intravital Microscopy.
    Emilio Rios-Jimenez, Sandra F Archidona, Maria Alieva.
      Intravital microscopy (IVM) enables observation of single-cell behaviors in live animal models, allowing detailed analysis of cancer cell dynamics within native 3D environments. However, comprehensively analyzing the extensive and complex data generated by IVM requires robust tools that exceed conventional approaches. This chapter presents a protocol for profiling heterogeneous cancer cell behavior within IVM movies, facilitating the study of cellular movement patterns and their associations with microenvironmental cues. The protocol allows researchers to systematically quantify single-cell (morpho)dynamics, providing unbiased analysis of cellular heterogeneity without requiring advanced computational expertise. The framework is adaptable to various tumor and non-tumor models, supporting insights into processes such as invasion, migration, and spatial relationships with distinct cell types, offering an accessible approach to studying heterogeneous cell behavior within its microenvironment.
    Keywords:  3D image analysis; Cell dynamics; Cellular invasion; Motility patterns; Tumor heterogeneity; Unsupervised learning
    DOI:  https://doi.org/10.1007/978-1-0716-5591-7_16
  13. Front Immunol. 2026 ;17 1901272
    VISTA as a tumour-microenvironment checkpoint: spatial, metabolic and cellular control of antitumour immunity.
    Kexun Li, Zilong Qian, Jianzhe Zhang, Jie Mao, Tengfei Ke.
      V-domain immunoglobulin suppressor of T-cell activation (VISTA; also termed VSIR, PD-1H or B7-H5) is increasingly recognised as an immune checkpoint whose biological and clinical significance depends less on total expression than on the tumour microenvironment (TME) in which it operates. Rather than acting as a linear T-cell exhaustion receptor, VISTA integrates tumour chemistry, stromal architecture, innate and adaptive immune states, and therapy-induced feedback inhibition. It is expressed by tumour cells and multiple immune populations, including macrophages, myeloid-derived suppressor cells, dendritic cells, neutrophils, regulatory T cells and activated or quiescent T cells. VISTA can also function through pH-dependent and pH-independent ligand-receptor interactions. This review reframes VISTA as a TME-gated regulatory system. Low pH, hypoxia, transforming growth factor beta (TGF-β), histamine, aldehyde metabolism, Yes-associated protein (YAP)/TEA domain (TEAD) signalling, macrophage polarity, antigen-presenting-cell fitness and spatial immune exclusion can jointly determine whether VISTA marks immune resistance, immune activation under feedback restraint or tumour-cell-intrinsic evasion. This context helps explain the divergent prognostic associations of VISTA across pancreatic, gastric, colorectal, lung, breast, bladder, gynaecological, skin, brain, mesothelial and haematological malignancies. Therapeutically, VISTA should therefore not be treated as another universal immune-checkpoint target. More plausible strategies include pH-selective antibodies, ligand-axis disruption, local or nanoparticle delivery, targeted degradation, tumour-cell-intrinsic pathway inhibition and combinations that convert suppressive TME niches into antigen-presenting and cytotoxic niches. A TME-centred framework can make VISTA biology clinically interpretable and guide biomarker development, trial design and rational combination immunotherapy.
    Keywords:  VISTA; cancer immunotherapy; immune checkpoint resistance; metabolic immune regulation; spatial immunology; tumour microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2026.1901272
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