Inflamed Yet Immune-Evasive? A Transcriptomic Meta-Analysis Identifies Conserved Inflammatory, Developmental, and Neuronal Signatures Associated with Polyploid Giant Cancer Cells

Single-cell profiling identifies STAT3/NF-κB regulatory hubs and cytokine crosstalk in the tumor microenvironment

Integrative single-cell RNA sequencing analysis of publicly available datasets from non-small cell lung cancer and breast cancer is performed to systematically map transcriptional heterogeneity and regulatory networks within the TME, providing a systems-level framework of TME organization.

Epigenetic silencing of innate and adaptive immunity genes underlies the immune evasion cancer hallmark in Theileria-infected B-cells.

Cancer hallmarks are characterized by wide-scale changes in gene expression programs. Pioneering studies showed how viral oncogenes target regulatory pathways, but little is known about tumorigenic mechanisms of non-viral pathogens. Theileria annulata is an intracellular parasite (related to apicomplexa parasites causing malaria) which remarkably transforms bovine leukocytes, hijacking host signaling pathways to induce cancer phenotypes, akin to human leukemias. While some host genes contribute to the proliferative or invasive hallmark phenotypes, there is still limited comprehensive understanding of the impact of Theileria infection on host transcription and transformation. We performed a multi-omics meta-analysis to investigate the effect of Theileria infection on cancer hallmarks in bovine B lymphocytes. Combining transcriptomic, proteomic and epigenomic analysis across multiple datasets, we show that Theileria infection suppresses host immune pathways. Specifically, genes encoding innate and adaptive immune mediators are repressed in T. annulata-infected B cells (and in T. parva infected T cells), including downregulation of genes for Toll-like receptors (TLR), inflammasome components of the guanylate binding protein (GBP) family and major histocompatibility complex class (MHC) II genes. Treatment with distinct theilericidal drugs could partially rescue immune gene expression. Mechanistically, we describe alterations in the host epigenome, including loss of activating histone modifications (e.g., H3K18ac, H3K4me3, H3K27ac) on the promoters of repressed immune genes, and enrichment of silencing marks (H3K27me3) on promoters of the BOLA genes and the gene encoding CIITA, the master transcriptional regulator of MHC class II gene expression. Our results suggest that intracellular T. annulata and T. parva parasites could drive an immune evasion cancer hallmark in host lymphocytes by epigenetic silencing of genes for innate and adaptive immunity.

Integrative multi-omics reveals the POSTN+ CAF–APOE+ macrophage axis drives immunosuppression and progression in prostate cancer

Background The progression of prostate cancer to lethal castration-resistant (CRPC) and metastatic (mCRPC) stages is driven by a profoundly remodeled tumor microenvironment (TME). However, the identity of key stromal cell populations, their developmental dynamics, and their precise crosstalk with immune cells remain incompletely understood, limiting our ability to target the TME therapeutically. Methods We integrated single-cell RNA sequencing (scRNA-seq) data from 222,529 cells across 10 studies, encompassing normal prostate, primary tumors, CRPC, and mCRPC. Fibroblast heterogeneity was resolved using unsupervised clustering, trajectory inference (Monocle2), and regulon analysis (pySCENIC). Intercellular communication was deciphered using CellChat. Spatial transcriptomic data were integrated via CellTrek and SpaGene for validation. Clinical associations were evaluated in multiple bulk transcriptomic cohorts (e.g., TCGA-PRAD, IMvigor210) and extended to a pan-cancer atlas of 11 tumor types. Results We identified a distinct POSTN+ CAF subset that was progressively enriched in advanced disease. Trajectory analysis positioned POSTN+ CAFs as a progenitor-like state potentially transitioning toward inflammatory or contractile subtypes, with STAT1-centered regulon activity associated with this process. POSTN+ CAFs created an extracellular matrix (ECM)-remodeled, immune-excluded niche, correlated with elevated T-cell exclusion scores. We further uncovered a predicted communication axis where POSTN+ CAFs are computationally inferred to interact with M2-like, immunoregulatory APOE+ macrophages via the MDK-NCL ligand-receptor pair. The co-occurrence of POSTN+ cancer-associated fibroblasts and APOE+ macrophages correlated with worse patient outcomes. In the IMvigor210 urothelial carcinoma cohort (as indirect cross-cancer evidence), high co-infiltration was associated with diminished anti-PD-L1 response, although this finding requires validation in prostate cancer-specific cohorts. Exploratory pan-cancer analysis suggested conserved enrichment and adverse prognostic impact of this stromal-immune axis across diverse tumor types, though tissue-specific context should be considered. Conclusions Our integrated single-cell atlas defines a critical POSTN+ CAF–APOE+ macrophage unit that is associated with a fibrotic and immunosuppressive TME in advanced prostate cancer. If functionally validated, targeting this stromal-immune crosstalk axis could represent a promising therapeutic strategy to remodel the TME and overcome treatment resistance, although this remains speculative at present.

Single-cell multiomics reveals exosome-mediated reprogramming and clonotypic remodeling of T cells in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive and immunogenic subtype lacking targeted therapies. While tumor-derived exosomes are known to modulate immune function, their direct impact on human T cell plasticity and antigen specificity remains poorly defined. Here, we conducted a comprehensive single-cell multiomic analysis of primary human T cells exposed to exosomes derived from 17 genomically diverse TNBC cell lines and 35 patient samples. Integrating single-cell RNA-seq, V(D)J sequencing, non-coding RNA profiling, bulk and single-cell cytokine analyses, we uncovered conserved and subtype-specific immunomodulatory programs induced by TNBC exosomes. Exosome-treated T cells displayed skewing toward regulatory and dysfunctional phenotypes, including Th17-like, Treg, and PD-1⁺/PD-L1⁺ Tfh cells. Functional profiling revealed suppression of early activation markers and cytokine responses, alongside selective preservation of cytotoxic features in γδ T and NKT subsets. Transcriptomic and miRNA network analyses demonstrated widespread downregulation of immune effector genes (e.g., HBEGF and TNFSF9) mediated by exosome-delivered regulatory miRNAs (has-miR-98-5p). Notably, exosome-stimulated T cells displayed distinct clonotypic expansions, characterized by the emergence of five tumor-specific γδ TCR clonotypes and 30 unique αβ TCR CDR3 sequences that were absent in mock-treated controls, underscoring the role of exosomes in shaping TCR repertoire dynamics.

Proteomics of human cancer-associated T cells identifies regulators of T cell functionality

CD8⁺ T cells in solid cancers progressively lose anti-tumor activity, yet the cell-intrinsic mechanisms driving this loss of function remain incompletely defined. Here, we performed matched proteomic and transcriptomic profiling of dysfunctional and bystander CD8⁺ tumor-infiltrating T cells isolated from primary tumors of treatment-naïve non-small cell lung cancer patients. Proteomic analysis revealed widespread discordance with mRNA expression, with 8% of all quantified proteins displaying differential expression exclusively at the protein level. Genetic perturbation of such differentially expressed proteins identified the chromatin remodeler CHD4 and fatty acid synthase (FASN) as cell-intrinsic regulators of T cell function. CHD4 deletion resulted in altered gene-regulatory networks that promoted effector differentiation and enhanced cytokine production. In contrast, FASN deletion preserved mitochondrial fitness and sustained T cell functionality under chronic T cell receptor stimulation. Together, these findings demonstrate that proteomic profiling uncovers regulators of T cell functionality that are not apparent from transcriptomic analyses alone, highlighting an additional layer of regulatory control. One Sentence Summary Integrated multi-omic profiling of human tumor-infiltrating T cells reveals cell-intrinsic regulators of T cell dysfunction that are missed by transcriptomic analyses alone.

Comprehensive transcriptomic profiling uncovers an inflammatory maturation program conserved in human and mouse dendritic cells