Immunotherapy with immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) patients only achieves response rates of 25%-30%, indicating the necessity of new therapies for non-responder patients. Since myeloid-related suppressive factors are associated with poor responses to ICI in a subgroup of HCC patients, modulation of these targets may improve response rates. Our aim was to characterize the expression of the efferocytosis receptor MERTK in HCC and to analyze its potential as a new therapeutic target. In HCC patients, MERTK was expressed by myeloid cells and was associated with poorer survival. In a murine HCC model with progressive myeloid cell infiltration, MERTK was detected in dendritic cells and macrophages with an activated phenotype, which overexpressed the checkpoint ligand PD-L1. Concomitant expression of PD-1 in tumor T-cells suggested the pertinence of combined PD-1/PD-L1 and MERTK blockade. In vivo experiments in mice showed that inhibition of MERTK improved the therapeutic effect promoted by anti-PD-1 or by ICI combinations currently approved for HCC. This effect was associated with enhanced tumor infiltration and superior activity of antigen presenting cells and effector lymphocytes. Our results indicate that MERTK may behave as a relevant target for immunotherapeutic combinations in those HCC patients with tumors enriched in a myeloid component.

Breast cancer is a highly heterogeneous disease, characterized by tumor and nontumor cells at various cell states. Ecotyper is an innovative machine learning framework that quantifies the tumor microenvironment and delineates the tumor ecosystem, demonstrating clinical significance. However, further validation is needed in breast cancer.

Ecotyper was applied to identify multiple cellular states and tumor ecotypes using large-scale breast cancer bulk sequencing data, followed by a detailed analysis of their associations with clinical classification, molecular subtypes, survival prognosis, and immunotherapy response. Identified subtypes were further characterized using single-cell and spatial data sets to reveal molecular profiles.

In a comprehensive analysis of 6578 breast cancer samples from four data sets, Ecotyper identified 69 cellular states and 10 tumor ecotypes. Of these, 37 cellular states significantly correlated with overall survival. Notably, specific states within epithelial cells, macrophages/monocytes, and fibroblasts were linked to a worse prognosis. CE2 abundance was identified as the most significant marker indicating unfavorable prognosis and was further validated in an additional data set of 116 HER2-negative patients. These biomarkers also indicated the efficacy of neoadjuvant immunotherapy in breast cancer. CE2-high cancers were characterized by an abundance of basal-like epithelial cells, scant lymphocytic infiltration, and activation of hypoxia signaling. Single-cell analysis showed that CE2-high areas were rich in SPP1-positive tumor-associated macrophages(TAM), basal-like epithelial cells, and hypoxic cancer-associated fibroblasts(CAF). Spatially, these regions were often peripheral in triple-negative breast cancer, adjacent to fibrotic/necrotic zones. Multiplex immunofluorescence confirmed the enrichment of SPP1+CD68+TAM and HIF1A+SMA+CAF in hypoxic triple-negative breast cancer (TNBC) regions.

Ecotyper identified novel biomarkers for breast cancer prognosis and treatment prediction. The CE2-high region may represent a hypoxic immune-suppressive niche.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, characterized by a complex molecular landscape. EGF Domain Specific O-linked β-N-acetylglucosamine transferase (EOGT) functions as an O-GlcNAc transferase with specific activity towards proteins containing epidermal growth factor (EGF) repeats. Although it is known to potentially play an oncogenic role in HCC, the exact mechanisms remain unclear. Induction of ferroptosis is a primary mechanism by which anticancer drugs such as sorafenib treat HCC. This study aimed to elucidate the expression profile of EOGT in HCC and its relationship with ferroptosis, as well as to investigate the underlying molecular mechanisms.

Utilizing bioinformatics resources, we explored the potential role of EOGT in HCC. The effects of EOGT on HCC cell behavior were examined using cell models and subcutaneous xenograft models in nude mice. Further insights into the molecular mechanisms were obtained through RNA-seq in cell models, hydrodynamic modeling in mice, Western blotting, chromatin immunoprecipitation (ChIP) sequencing, and dual-luciferase reporter assays to analyze the interaction between HEY1 and SLC7A11. Multiple validation steps were employed to thoroughly investigate the roles of these factors in the regulation of ferroptosis in HCC.

Our findings revealed that EOGT is upregulated in HCC and correlates with poor prognosis and drug resistance. Knockdown of EOGT inhibited HCC cell proliferation and enhanced sensitivity to ferroptosis by downregulating SLC7A11, a process mediated by HEY1. These results were confirmed by cell viability assays, quantitative real-time PCR (qPCR), Western blotting, and dual-luciferase reporter gene assays.

EOGT promotes HCC proliferation and inhibits ferroptosis by modulating the HEY1-SLC7A11 axis, suggesting a potential therapeutic target for HCC treatment.

The heterogeneity in prognostic survival and treatment response of hepatocellular carcinoma (HCC) limits the accurate assessment of HCC-specific mortality. This study aimed to identify potential HCC subtypes through latent class analysis (LCA) to improve HCC-specific mortality prediction and optimize treatment recommendations. We analyzed data from 7746 HCC patients in the Surveillance, Epidemiology, and End Results (SEER) databases, incorporating demographic and clinicopathological information and applying LCA to identify HCC subtypes. Prognostic survival and treatment response across different HCC subtypes were evaluated utilizing Cox proportional hazards regression and competing risks models. The classification was externally validated with data from 6791 patients. Four HCC subtypes (LCAC1-LCAC4) were determined. Compared with LCAC1, both LCAC2 (HR = 1.887, p < .001) and LCAC4 (HR = 1.317, p < .001) were associated with significantly shorter overall survival. LCAC2 had the highest HCC-specific mortality (HR: 2.395, p < .001), followed by LCAC4 (HR: 1.531, p < .001), and LCAC3 (HR: 1.424, p < .001). LCAC3 was associated with the lowest risk of non-HCC-specific mortality (HR: 0.613, p < .001). Surgical treatment, particularly preoperative systemic therapy, significantly improved survival across all HCC subtypes, whereas chemotherapy and radiotherapy had limited efficacy in LCAC1 and LCAC3 patients. External validation corroborated these findings. This study provides a classification system that differentiates HCC-specific mortality, facilitating accurate survival stratification and treatment recommendations, and provides valuable insight for clinical decision-making.

Tumor-associated macrophages (TAMs) are closely associated with tumor development and patient outcomes due to their plasticity and polarization capacity. Several distinct TAMs have been proposed, but a complete understanding of heterogeneity and differentiation spectrum of macrophage in human primary liver cancer remains elusive.

Deep single-cell RNA sequencing (scRNA-seq) data from 19 primary liver cancer patients were used to profile the transcriptomes of TAMs in liver cancer. Ingenuity pathway analysis (IPA) and in vitro experiments were used to explore possible mechanisms responsible for related signaling pathways altered at the transcriptional level. Finally, we analyzed the relationship between the abundance of the TAMs and the survival outcomes of the 428 patients in the Cancer Genome Atlas (TCGA).

Transcriptional profiles allowed us to identify four distinct TAMs cell subsets based on molecular and functional properties and to reconstruct their developmental trajectory. Specifically, TAM_c4 was preferentially enriched and potentially expanded in the advanced-stage patients or those receiving immune checkpoint blockade therapy (ICT). Gene pathway analysis revealed aberrant TGFB1 activation in TAM_c4, which was experimentally confirmed to drive TAM phenotypic transitions via autophagy signaling. High abundance of TAM_c4 is found to be related to a short survival time and low abundance of CD8+ T cells in primary liver cancers.

This integrated transcriptome compendium and experimental validation offer both mechanistic insights and a resource for understanding TAM heterogeneity in primary liver cancers.

Immunotherapy has revolutionized cancer treatment, but its effectiveness is limited due to the complexity of the tumor immune microenvironment. Identifying reliable biomarkers that can predict immunotherapy response is essential for enhancing treatment strategies. This study evaluated the potential of Neurogranin (NRGN) as a biomarker for prognosis and immunotherapy response across multiple cancers. Through pan-cancer bioinformatics analyses, coupled with in vitro and in vivo experiments, we explored NRGN's differential expression across various cancer types and its role in the immune microenvironment. Our approach involved database mining, immune genomic feature correlation analyses, and functional validation through NRGN knockdown and overexpression studies. The results revealed differential NRGN expression across cancers, particularly hepatocellular carcinoma (HCC), where elevated levels correlated with immune evasion, poor prognosis, and upregulation of checkpoint genes like TGFB1. NRGN modulated T cell activity and macrophage polarization by regulating the TGF-β pathway through interaction with TCF4 and promoting its nuclear localization, driving tumor progression. Targeting TGF-β with anti-TGF-β and anti-PD-1 antibodies additively inhibited HCC in an Nrgn-dependent manner in mice. These findings indicate that NRGN may serve as a promising immunotherapeutic target, as its overexpression predicts poor prognosis and immune evasion, thereby offering insights for improving immunotherapy and developing new treatments.

The incidence of thyroid cancer (TC) increases year by year. It is necessary to construct a prognostic model for risk stratification and management of TC patients. Glutamine metabolism is essential for tumor progression and the tumor microenvironment. The present study aimed to develop a predictive model for TC using a glutamine metabolism gene set. Differentially expressed genes in cells with high glutamine metabolism levels from single cell RNA‑sequencing data were compared with genes differentially expressed between normal and TC tissues from The Cancer Genome Atlas Program data. Through Boruta feature selection methods and multivariate Cox regression, six crucial genes were identified for a risk‑scoring system to develop a prognostic model. The role of each gene was verified in TC cells in vitro. A risk‑scoring system was developed according to the glutamine gene set to forecast the overall survival of TC patients. This risk score could stratify TC patients and minimize unnecessary surgeries and invasive treatments. In addition, signal induced proliferation associated 1 like 2 (SIPA1L2), an important gene in the prognostic model, knockdown in TPC‑1 and BCPAP cell lines enhanced TC cell proliferation, migration and invasion. A risk model was developed based on a glutamine metabolism gene set. The model has reference values for TC stratification.

Hypoxia promotes M2 polarization of macrophages and the formation of the immunosuppressive tumor microenvironment (TME) in hepatocellular carcinoma (HCC). Oleanolic acid (OA) has shown great potential in the treatment of HCC. However, the mechanisms of macrophage M2 polarization in hypoxic tumor TME and the regulating effect of OA is still unclear.

To investigate the mechanisms of macrophage M2 polarization induced by hypoxic HCC cells-derived exosomes and examine the efficacy of OA in remedying the immunosuppressive TME and the anti-PD1 therapy potential.

Hypoxic and normoxic HCC-derived exosomes (H-Exo and N-Exo) were collected by centrifugation. The microRNAs (miRNA) carried by the exosomes were sequenced and then screened to identify the functional miRNA. THP-1-induced macrophages were treated with exosomes or miRNAs to induce the M2 polarization of macrophages. Real-time RT-PCR and Western blotting were used to identify the direct target of miR-130b-3p and its downstream molecules. Hepa1-6 hepatoma-bearing mice were subjected to determine the efficacy of OA in regulating the TME and the anti-PD1 therapy potential.

H-Exo promotes macrophage M2 polarization, and thereby accelerates the migration and epithelial-mesenchymal transition (EMT) of HCC cells. Exosomal miRNA sequencing and subsequent functional validation showed that miR-130b-3p was the mediator of H-Exo-induced macrophage M2 polarization. PTEN was identified as the target of miR-130b-3p, and downregulation of PTEN by miR-130b-3p led to the activation of PI3K/Akt signaling and macrophage M2 polarization. In addition, miR-130b-3p also enhanced the glycolysis. OA suppressed H-Exo and miR-130b-3p-induced macrophage M2 polarization, also inhibited miR-130b-3p-induced glycolysis. In vivo, OA treatment enhanced the efficacy of anti-PD1 antibody by decreasing the number of M2 macrophages and increasing the number of CD8+ T cells.

Our findings uncover a new mechanism of hypoxic HCC cells-induced M2 polarization of macrophages through exosomal miR-130b-3p-PTEN-PI3K-Akt signaling. The combination therapy of OA with anti-PD1 antibody may lead to substantial improvements of the immunotherapy efficacy and expand the beneficiaries.

Regulatory T cells (Tregs), an immunosuppressive subpopulation of CD4+ T cells, are prevalent in tumor tissues, where they impede effective antitumor immune responses and represent potential targets for immunotherapy. However, targeting tumor-infiltrating Treg cells (TiTregs) remains challenging. In this study, we identified CD177 as a biomarker specifically expressed in TiTregs but not in adjacent or peripheral Treg cells through single-cell transcriptome sequencing combined with a stringent screening strategy. These CD177+ TiTregs exhibited distinct transcriptional profiles characterized by enhanced immunosuppressive capabilities and were correlated with poor patient prognosis. Mechanistically, the apoptosis-related transcription factor REL drove the differentiation of CD177+ TiTregs, accompanied by apoptosis and enhanced immunosuppression. Furthermore, using a CD177 Treg conditional knockout mouse model, we demonstrated that inhibiting CD177 in Tregs significantly impaired their immunosuppressive function and inhibited the progression of hepatocellular carcinoma (HCC) in vitro. Our results underscore the critical role of CD177+ TiTregs in cancer immunology and highlight their potential as novel therapeutic targets in HCC.

Epigenetic alteration leads to the aberrant transcriptional programmes that faciliate cancer onset and progression. In-depth understanding of the epigenetic alteration of cancers is critical for crucial in developing meaningful cancer treatment that may provide a meaningful improvement in overall survival. Based on the data in The Cancer Genome Atlas (TCGA), we performed a comprehensive and systematic genomic study of epigenetic genes. We defined the epigenetic score to reveal the functional roles of epigenetic genes. We found that epigenetic score was higher in tumors than in normal tissues in most cancers and was associated with poorer prognosis, especially in hepatocellular carcinoma (HCC).Our study also found that epigenetic score is significantly related to immune evasion in HCC. To guide efficient pharmalogical intervention of unfolded protein response to help patients, we performed virtual screening and found some compounds targeting UHRF1 could become a good pharmaceutical therapeutic candidate in unique or adjuvant therapeutic approaches toward HCC.

Adenosine signaling pathway is a kind of signal regulation hub widely existing in human body, which is involved in a series of physiological processes such as energy supply of body cells. CD73 is a highly concerned signaling protein in purine adenosine pathway, and its role in tumor development and prognosis has been paid more and more attention in recent years, especially in hepatocellular carcinoma (HCC). In this paper, the specific mechanism by which CD73-adenosine signaling regulates tumor microenvironment (TME) of liver cancer tumors was analyzed in detail, highlighting the importance of this pathway as a therapeutic target to combat tumor immunosuppression and enhance the anti-tumor immune response to prevent and treat hepatocellular carcinoma (HCC). In addition, a variety of current targeted therapeutic strategies for adenosine metabolic pathways are summarized, including the development of new drugs in the stage of preclinical research and clinical trials, and the mechanism of action, implementation possibility, and clinical effects of these therapies are discussed. By summarizing the latest scientific research results, in this review, we attempt to paint a panorama of the mechanism of adenosine action in tumor immunotherapy, with the aim to provide a solid theoretical basis and practical guidance for subsequent research and clinical application, ultimately promoting the development of more accurate and efficient tumor immunotherapy.

Cancer stem cells (CSCs) are strongly associated with the refractory characteristics of Hepatocellular carcinoma (HCC). However, the complex interaction between CSCs and the tumor microenvironment remains incompletely understood. In this study, we identified a novel long non-coding RNA (lncRNA) NEAT1 in cancer-associated fibroblast (CAFs)-derived extracellular vesicles (EVs) that play a critical role in the induction of CSCs and HCC tumorigenesis. NEAT1 was significantly overexpressed in human HCC tissues. Furthermore, high expression of lncRNA NEAT1 in EVs was found to be associated with poor prognosis. Knockdown of NEAT1 in CAFs inhibited invasion, migration, and tumor growth. Mechanistically, NEAT1 promoted cancer cell stemness, including 3D spheroid formation, by facilitating the liquid-liquid phase separation (LLPS) of the transcription factor YAP. Specifically, NEAT1 is directly bound to the intrinsic disordered region in the YAP protein, promoting the formation of LLPS biomolecular condensates. Additionally, a positive correlation between NEAT1 and Nanog was observed in clinical HCC tissues. In conclusion, our findings reveal that NEAT1 promotes HCC carcinogenesis and CSC induction by facilitating the LLPS of the YAP protein.

The liver is a central metabolic organ, but is also hosting a unique immune microenvironment to sustain homeostasis and proper defense measures against injury threats in healthy individuals. Liver macrophages, mostly represented by the tissue-resident Kupffer cells and bone marrow- or monocyte-derived macrophages, are intricately involved in various aspects of liver homeostasis and disease, including tissue injury, inflammation, fibrogenesis and repair mechanisms.

We review recent findings on defining the liver macrophage landscape and their functions in liver diseases with the aim of highlighting potential targets for therapeutic interventions. A comprehensive literature search in PubMed and Google Scholar was conducted to identify relevant literature up to date.

Liver macrophages orchestrate key homeostatic and pathogenic processes in the liver. Thus, targeting liver macrophages represents an attractive strategy for drug development, e.g. to ameliorate liver inflammation, steatohepatitis or fibrosis. However, translation from fundamental research to therapies remains challenging due to the versatile nature of the liver macrophage compartment. Recent and major technical advances such as single-cell and spatially-resolved omics approaches deepened our understanding of macrophage biology at a molecular level. Yet, further studies are needed to identify suitable, etiology- and stage-dependent strategies for the treatment of liver diseases.

Despite the significant advances in the development of immune checkpoint inhibitors (ICI), primary and acquired ICI resistance remains the primary impediment to effective cancer immunotherapy. Residing in the tumor microenvironment (TME), tumor-associated macrophages (TAMs) play a pivotal role in tumor progression by regulating diverse signaling pathways. Notably, accumulating evidence has confirmed that TAMs interplay with various cellular components within the TME directly or indirectly to maintain the dynamic balance of the M1/M2 ratio and shape an immunosuppressive TME, consequently conferring immune evasion and immunotherapy tolerance. Detailed investigation of the communication network around TAMs could provide potential molecular targets and optimize ICI therapies. In this review, we systematically summarize the latest advances in understanding the origin and functional plasticity of TAMs, with a focus on the key signaling pathways driving macrophage polarization and the diverse stimuli that regulate this dynamic process. Moreover, we elaborate on the intricate interplay between TAMs and other cellular constituents within the TME, that is driving tumor initiation, progression and immune evasion, exploring novel targets for cancer immunotherapy. We further discuss current challenges and future research directions, emphasizing the need to decode TAM-TME interactions and translate preclinical findings into clinical breakthroughs. In conclusion, while TAM-targeted therapies hold significant promise for enhancing immunotherapy outcomes, addressing key challenges-such as TAM heterogeneity, context-dependent plasticity, and therapeutic resistance-remains critical to achieving optimal clinical efficacy.

Neoadjuvant anti-PD-1 immunotherapy combined with chemotherapy has shown promising pathologic responses in various cancers, including oral squamous cell carcinoma (OSCC). However, the pathologic response of lymph node (LN) metastases remains poorly understood. This study aims to systematically evaluate the pathologic response rates (pRR) of LN metastases in patients with OSCC and identify potential targets to improve therapeutic outcomes.

We assessed the pRRs of LN metastases and matched primary tumors (PT) in patients with OSCC enrolled in a randomized, two-arm, phase II clinical trial (NCT04649476). Single-cell and spatial transcriptomics and multiplex IHC were performed to analyze the tumor microenvironment and identify potential therapeutic targets in LN metastases. A neoadjuvant orthotopic OSCC mouse model was established to evaluate the therapeutic potential of these targets.

We observed significant heterogeneity in pathologic regression of LN metastases, with lower pRRs compared with PTs. pRRs in LN metastases were correlated with overall and disease-free survival in patients with OSCC. We identified an abundance of macrophages in LN metastases exhibiting an unfolded protein response and activated protein kinase RNA-like endoplasmic reticulum kinase (PERK) signaling. These macrophages contributed to an extracellular matrix-enriched microenvironment through interactions with fibroblasts, which hindered T cell-mediated cytotoxicity. Pharmacologic inhibition of the PERK pathway significantly enhanced anti-PD-1 therapy in LN metastases and PTs in the mouse model.

Our study confirms that the pathologic response of LN metastases in patients with OSCC undergoing neoadjuvant immunotherapy or immunochemotherapy is inferior to that of PTs. It suggests that targeting the PERK pathway in macrophages could be a potential strategy to enhance treatment outcomes.

Glioblastoma multiforme (GBM) is a pervasive and aggressive malignant brain tumor. In the tumor immune microenvironment, CD8 + TIM3 + CD101 + T cells (CCT cells) play a pivotal role in tumor progression and immune evasion. This study aimed to characterize differentially expressed genes (DEGs) in CCT cells, establish a prognostic model for GBM, and explore clinical implications.

Analysis of data from TCGA, CGGA, and GEO databases included whole-genome expression profiles, clinical data, single nucleotide mutations, and single-cell RNA sequencing. DEGs were identified, and cell trajectories were constructed using Seurat, Monocle 2, and CellChat packages. Functional enrichment analysis was conducted with clusterProfiler, and a prognostic model was developed. Immune infiltration and drug sensitivity analyses were performed to evaluate therapeutic implications.

Eight distinct cell types were distinguished, encompassing T cells, macrophages, neurons, mural cells, endothelial cells, oligodendrocytes, fibroblasts, and B cells. Comparative analysis revealed differences in these cell types between GBM samples with new adjuvant therapy and initial diagnosis controls. Pseudotime analysis indicated CD8 + TIM3 + CD101-T cells as precursors to CCT cells, unveiling unique gene expression patterns during this transition. The prognostic model, incorporating 22 gene features via LASSO regression, demonstrated strong predictive ability through Receiver Operating Characteristic (ROC) curves. Analysis of 28 immune cell types revealed differences between high-risk and low-risk groups, providing insights into GBM's immune evasion mechanisms. Drug sensitivity analysis proposed potential therapeutic strategies for high-risk patients.

This study offers an in-depth understanding of CCT cells in GBM, introducing a novel prognostic model and suggesting promising therapeutic approaches.

The heterogeneity of cancer-associated fibroblasts (CAFs) could affect the response to immune checkpoint inhibitor (ICI) therapy. However, limited studies have investigated the role of inflammatory CAFs (iCAFs) in ICI therapy using pan-cancer single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics sequencing (ST-seq) analysis. We performed pan-cancer scRNA-seq and ST-seq analyses to identify the subtype of GSN+ iCAFs, exploring its spatial distribution characteristics in the context of ICI therapy. The pan-cancer scRNA-seq and bulk RNA-seq data are incorporated to develop the Caf.Sig model, which predicts ICI response based on CAF gene signatures and machine learning approaches. Comprehensive scRNA-seq analysis, along with in vivo and in vitro experiments, investigates the mechanisms by which GSN+ iCAFs influence ICI efficacy. The Caf.Sig model demonstrates well performances in predicting ICI therapy response in pan-cancer patients. A higher proportion of GSN+ iCAFs is observed in ICI non-responders compared to responders in the pan-cancer landscape and clear cell renal cell carcinoma (ccRCC). Using real-world immunotherapy data, the Caf.Sig model accurately predicts ICI response in pan-cancer, potentially linked to interactions between GSN+ iCAFs and CD8+ Tex cells. ST-seq analysis confirms that interactions and cellular distances between GSN+ iCAFs and CD8+ exhausted T (Tex) cells impact ICI efficacy. In a co-culture system of primary CAFs, primary tumour cells and CD8+ T cells, downregulation of GSN on CAFs drives CD8+ T cells towards a dysfunctional state in ccRCC. In a subcutaneously tumour-grafted mouse model, combining GSN overexpression with ICI treatment achieves optimal efficacy in ccRCC. Our study provides the Caf.Sig model as an outperforming approach for patient selection of ICI therapy, and advances our understanding of CAF biology and suggests potential therapeutic strategies for upregulating GSN in CAFs in cancer immunotherapy.

Immunotherapy has transformed the neoadjuvant treatment landscape for patients with resectable locally advanced non-small cell lung cancer (NSCLC). However, a population of patients cannot obtain major pathologic response (MPR) and thus benefit less from neoadjuvant immunotherapy, highlighting the need to uncover the underlying mechanisms driving resistance to immunotherapy.

Two published single-cell RNA sequencing (scRNA-seq) datasets were used to analyze the subsets of cancer-associated fibroblasts (CAFs) and T cells and functional alterations after neoadjuvant immunotherapy. The stromal signature predicting ICI response was identified and validated using our local cohort with stage III NSCLC receiving neoadjuvant immunotherapy and other 4 public ICI transcriptomic cohorts.

Non-MPR tumors showed higher enrichment of CAFs and increased extracellular matrix deposition than MPR tumors, as suggested by bioinformatic analysis. Further, CAF-mediated immune suppression may involve reciprocal interactions with T cells in addition to a physical barrier mechanism. In contrast, MPR tumors demonstrated therapy-induced activation of memory CD8+ T cells into an effector phenotype. Additionally, neoadjuvant immunotherapy resulted in expansion of precursor exhausted T (Texp) cells, which were remodeled into an anti-tumor phenotype. Notably, we identified metabolic heterogeneity within distinct T cell clusters during immunotherapy. Methionine recycling emerged as a predictive factor for T-cell differentiation and a favorable pathological response. The stromal signature was associated with ICI response, and this association was validated in five independent ICI transcriptomic cohorts.

These discoveries underscore the distinct tumor microenvironments in MPR and non-MPR patients and may elucidate resistance mechanisms to immunotherapy in NSCLC.

Chimeric antigen receptor (CAR)-T-cell therapy achieves considerable success in the treatment of malignant tumors, but clinical relapse due to the tumor microenvironment (TME) is very common. The TME of solid tumors is characterized by weak acidity, hypoxia, and elevated reactive oxygen species (ROS) levels, which collectively impair the function and persistence of infiltrating CAR-T cells. In this study, acid-sensitive responsive CaMnCO3 nanoparticles (CMC NPs), are developed that simultaneously mitigate TME acidosis and hypoxia. IL-21 is encapsulated within CMC NPs (denoted as CMC-21), which are then surface-conjugated to CAR-T cells as functional 'vitality backpacks' to enhance cellular activity. The CMC-21 backpack enables sustained release of IL-21, persistently enhancing CAR-T cell antitumor immunity across both low- and high-dose infusion regimens. Furthermore, CMC NPs exert dual modulatory effects on the TME by: 1) consuming protons to neutralize acidic conditions, and 2) catalytically converting endogenous H2O2 to O2 to relieve hypoxia. This multimodal remodeling of the immunosuppressive TME significantly enhances the infiltration and activity of adoptively transferred CAR-T cells while simultaneously boosting endogenous T cell and NK cell recruitment in vivo. These findings establish a novel CAR-T cell enhancement strategy through sustained IL-21 release from CMC-21 backpacks, offering new possibilities for solid tumor immunotherapy.

Increasing evidence highlights the pivotal role of RNA methylation and miRNAs in hepatocellular carcinoma (HCC). However, the risk associated with RNA methylation-related miRNAs (RMRMs) in the HCC immune microenvironment remains largely unknown. Here, we predicted the correlation between RMRM risk and immune cell infiltration in HCC using machine learning.

MiRNA sequencing data was used to identify RMRMs. A risk score model of HCC was developed utilizing four RMRMs, including miR-551a, miR-4739, miR-326, and miR-210-3p.

Patients with high-risk scores exhibited poorer prognoses. Single-cell RNA sequencing (scRNA-seq) analysis revealed the high-risk group exhibited increased infiltration levels of several immune cell subtypes, including myeloid-derived suppressor cell (MDSC), macrophage, and T cells. The data integration of scRNA-seq and bulk RNA-seq showed the decreased TIDE score in the high-risk patients and the elevated levels of Macro-secreted phosphoprotein 1 (SPP1), MDSC-meiotic nuclear divisions 1 (MND1), γδ T cells, and Macro-complement C1q C chain (C1QC) predicted adverse prognosis. ScRNA-seq and spatial transcriptomics data integration unveiled the spatial distribution of RMRMs risk scores and their correlation with immune cell subtype localization. Risk model-based clustering of HCC samples revealed that cluster 2, characterized by a higher risk score, correlated with a poorer prognosis and reduced immune and stromal scores. In vitro, the overexpression of miR-4739 in Huh-7 cells significantly induced SPP1+ macrophages, and the culture medium derived from SPP1+ macrophages further promoted the proliferation and migration of Huh-7 cells. Furthermore, miR-4739 reduced m1A methylation by inhibiting tRNA methyltransferase 61A (TRMT61A) expression.

Our study reveals that the RMRM risk model could effectively predict the prognosis of HCC, and SPP1+ macrophages regulated by miR-4739-RNA methylation promote the proliferation and migration of HCC cells. These results highlight the potential of RMRMs in predicting the prognosis of HCC.

Immune cells at the maternal-fetal interface (MFI) undergo dynamic changes to facilitate fetal growth and development during pregnancy. In contrast to the adaptive immune system, where effector T cells, Tregs, and suppressor T cells play key roles in maintaining immune tolerance toward the semi-allogeneic fetus, the innate immune system-comprising decidual nature killer (dNK) cells, macrophages, and dendritic cells (DCs)-makes up a significant portion of the decidual leukocyte population. These innate immune cells are crucial in modulating trophoblast invasion, spiral artery remodeling, and apoptotic cell phagocytosis. Dysregulation of the innate immune system has been linked to impaired uterine vessel remodeling and defective trophoblast invasion, which can lead to complications such as spontaneous abortion, preeclampsia (PE), and preterm. This review focuses on recent advancements in understanding the innate immune defenses at the maternal-fetal interface and their connections to pregnancy-related diseases, with particular emphasis on the role of macrophages.

We identified a subset of patients with colorectal cancer (CRC) enriched with "collagen-TAMs," designated the CM class, using large integrated colon cancer transcriptome and single-cell transcriptome datasets. This classification system could be used as an extension of the traditional CMS classification system for CRC to guide more accurate classification and treatment.We also screened CAF-derived THBS2 as a potential biomarker for CM and found that it plays an important role in CRC disease models in vitro and in vivo, promoting tumor development and metastasis as well as TAM recruitment. Targeting THBS2 combined with PD-1 therapy effectively improved the therapeutic effect of immunotherapy in vivo. The CM classification provides a new perspective for CRC treatment, and THBS2, which is highly expressed in CM cases, can be used as a new potential combined target for immunotherapy.

Although the treatment landscape for advanced hepatocellular carcinoma (HCC) has seen significant advancements in the past decade with the introduction of immune checkpoint inhibitors and antiangiogenic drugs, progress has fallen short of expectations. Recently, a novel engineered oncolytic virus (OHSV2) that secretes dual-specific T-cell engagers (DSTEs) targeting the fibroblast activation protein (FAP) was developed and combined with GPC3-targeting CAR-T cells and immunotoxins to exert a synergistic antitumor effect.

OHSV2-DSTEFAP5/CD3 was initially generated by transducing the DSTEs engaging FAP5 on fibroblasts into the backbone of our oncolytic virus OHSV2. An innovative high-order combination was devised in a xenograft mouse model to conceptually explore whether enhanced anti-tumor effects could be achieved. Additionally, the underlying mechanisms of synergistic effects and safety profiles were preliminarily investigated.

OHSV2-DSTEFAP5/CD3 effectively targeted and eliminated fibroblasts in vitro while maintaining cytotoxicity and inducing immune activation compared to parental OHSV2. In vivo, dose-adjusted combination therapy resulted in a remarkable antitumor effect compared to control treatments, leading to tumor regression in 40% of mice without significant toxicity to major organs. Mechanistically, rather than directly depleting fibroblasts, OHSV2-DSTEFAP5/CD3 played an essential role in priming T-cell proliferation, infiltration, and activation, and inhibiting the supportive interaction between cancer cells and fibroblasts.

This high-order combination represents a novel multiple-wave immunotherapeutic approach for HCC. Despite being a conceptual exploration, this strategy has demonstrated promising therapeutic efficacy and acceptable safety profiles.

This study investigates key microscopic regions involved in colorectal cancer liver metastasis (CRLM), focusing on the crucial role of cancer-associated fibroblasts (CAFs) in promoting tumor progression and providing molecular- and metabolism-level insights for its diagnosis and treatment using multi-omics. We followed 12 fresh surgical samples from 2 untreated CRLM patients. Among these, 4 samples were used for spatial transcriptomics (ST), 4 for spatial metabolomics, and 4 for single-cell RNA sequencing (scRNA-seq). Additionally, 92 frozen tissue samples from 40 patients were collected. Seven patients were used for immunofluorescence and RT-qPCR, while 33 patients were used for untargeted metabolomics. ST revealed that the spatial regions of CRLM consists of 7 major components, with fibroblast-dominated regions being the most prominent. These regions are characterized by diverse cell-cell interactions, and immunosuppressive and tumor growth-promoting environments. scRNA-seq identified that SPP1+ fibroblasts interact with CD44+ tumor cells, as confirmed through immunofluorescence. Spatial metabolomics revealed suberic acid and tetraethylene glycol as specific metabolic components of this structure, which was further validated by untargeted metabolomics. In conclusion, an SPP1+ fibroblast-rich spatial region with metabolic reprogramming capabilities and immunosuppressive properties was identified in CRLM, which potentially facilitates metastatic outgrowth through interactions with tumor cells.

Progesterone and adipose Q receptor 5 (PAQR5), a membrane receptor characterized by seven transmembrane domains, has been indirectly implicated in pro-carcinogenic activities, though its specific role in hepatocellular carcinoma (HCC) remains to be defined.

This study aimed to elucidate the molecular mechanisms by which PAQR5 facilitates HCC progression and contributes to the immunosuppressive microenvironment through an integrative approach combining multi-omics analysis and experimental validation. Utilizing data from bulk, single-cell, and spatial transcriptomics cohorts, this study systematically assessed the expression patterns, immune landscape, and functional characteristics of PAQR5 across different levels of resolution in HCC.

PAQR5 expression was significantly upregulated in tumor tissues and correlated with poor clinical outcomes. Enrichment analysis revealed that PAQR5 activated the NF-κB signaling pathway in HCC. Single-cell transcriptomics identified PAQR5 as predominantly localized within malignant cell clusters, with significant association with NF-κB pathway activation. Spatial transcriptomics further corroborated the alignment of PAQR5 expression with tumor cell distribution. In vitro assays showed elevated PAQR5 levels in HCC cell lines, and silencing PAQR5 significantly suppressed cell proliferation, invasion, epithelial-mesenchymal transition (EMT), and prevented the formation of immunosuppressive microenvironment. In vivo studies demonstrated that targeting PAQR5 attenuated tumorigenic potential, disrupted the invasion-metastasis cascade and inhibited the tumor immune escape. Mechanistically, PAQR5 was found to activate NF-κB signaling by inducing ERK phosphorylation, thereby driving proliferation, invasion, EMT, and immune escape in HCC through the pathway.

Hepatocellular carcinoma (HCC) is a lethal malignancy, and predicting patient prognosis remains a significant challenge in clinical treatment. T cells play a crucial role in the tumor microenvironment, influencing tumorigenesis and progression. In this study, we constructed a T cell-related prognostic model for HCC. Using single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database, we identified 6,281 T cells from 10 HCC patients and subsequently identified 855 T cell-related genes. Comprehensive analyses were conducted on T cells and their associated genes, including enrichment analysis, cell-cell communication, trajectory analysis, and transcription factor analysis. By integrating scRNA-seq and bulk RNA-seq data with prognostic information from The Cancer Genome Atlas (TCGA), we identified T cell-related prognostic genes and constructed a model using LASSO regression. The model, incorporating PTTG1, LMNB1, SLC38A1, and BATF, was externally validated using the International Cancer Genome Consortium (ICGC) database. It effectively stratified patients into high- and low-risk groups based on risk scores, revealing significant differences in immune cell infiltration between these groups. Differential expression levels of PTTG1 and BATF between HCC and adjacent non-tumor tissues were further validated by immunohistochemistry (IHC) in 25 patient tissue samples. Moreover, a Cox regression analysis was performed to integrate risk scores with clinical features, resulting in a nomogram capable of predicting patient survival probabilities. This study introduces a novel prognostic risk model for HCC patients, aimed at stratifying patients by risk, enhancing personalized treatment strategies, and offering new insights into the role of T cell-related genes in HCC progression.

The gut microbiota crucially regulates the efficacy of immune checkpoint inhibitor (ICI) based immunotherapy, but the underlying mechanisms remain unclear at the single-cell resolution. Using single-cell RNA sequencing and subsequent validations, we investigate gut microbiota-ICI synergy by profiling the tumor microenvironment (TME) and elucidating critical cellular interactions in mouse models. Our findings reveal that intact gut microbiota combined with ICIs may synergistically increase the proportions of CD8+, CD4+, and γδ T cells, reduce glycolysis metabolism, and reverse exhausted CD8+ T cells into memory/effector CD8+ T cells, enhancing antitumor response. This synergistic effect also induces macrophage reprogramming from M2 protumor Spp1+ tumor-associated macrophages (TAMs) to Cd74+ TAMs, which act as antigen-presenting cells (APCs). These macrophage subtypes show a negative correlation within tumors, particularly during fecal microbiota transplantation. Depleting Spp1+ TAMs in Spp1 conditional knockout mice boosts ICI efficacy and T cell infiltration, regardless of gut microbiota status, suggesting a potential upstream role of the gut microbiota and highlighting the crucial negative impact of Spp1+ TAMs during macrophage reprogramming on immunotherapy outcomes. Mechanistically, we propose a γδ T cell-APC-CD8+ T cell axis, where gut microbiota and ICIs enhance Cd40lg expression on γδ T cells, activating Cd40 overexpressing APCs (e.g., Cd74+ TAMs) through CD40-CD40L-related NF-κB signaling and boosting CD8+ T cell responses via CD86-CD28 interactions. These findings highlight the potential importance of γδ T cells and SPP1-related macrophage reprogramming in activating CD8+ T cells, as well as the synergistic effect of gut microbiota and ICIs in immunotherapy through modulating the TME.

Alveolar echinococcosis (AE) is caused by the chronic infection of E. multilocularis, whose tumor-like growth can lead to high fatality if improperly treated. The early diagnosis of infection and the treatment of advanced AE remain challenging. Herein, bulk RNA-seq, scRNA-seq, and spatial transcriptomics technologies are integrated, to reveal the host immune response mechanism against E. multilocularis both spatially and chronologically, collecting mouse liver samples at multiple timepoints up to 15 months post infection. These results unveil an unprecedented high-resolution spatial atlas of the E. multilocularis infection foci and the functional roles of neutrophils, Spp1+ macrophages, and fibroblasts during disease progression. The heterogeneity of neutrophil and macrophage subpopulations are critical in both parasite-killing and the occurrence of immunosuppression during AE progression. These findings indicate the transition of parasite control strategy from "active killing" to "negative segregation" by the host, providing instructive insights into the treatment strategy for echinococcosis.

Osteopontin (OPN) is a multifunctional secretory protein which can be expressed and secreted by a variety of tumor cells and immune cells. Tumor microenvironment remodeling provides favorable conditions for tumor progression, immune escape and therapy resistance. As a bridge molecule in crosstalk between tumor cells and tumor microenvironment, OPN can not only come from tumor cells to regulate the functions of various immune cells, promoting the formation of immunosuppressive environment, but also can be secreted by immune cells to act on tumor cells, leading to tumor progression, thus constructing a positive feedback regulatory network. Here, we summarize the molecular structure, source and receptor of OPN, and clarify the mechanism of OPN on tumor-associated macrophages, dendritic cells, myeloid-derived suppressor cells, tumor progression and therapy resistance to comprehensively understand the great potential of OPN as a tumor biomarker and therapeutic target.

Hepatocellular carcinoma (HCC) is a malignant tumor characterized by rapid progression. To explore the regulatory mechanism of rapid tumor growth and metastasis, we conducted proteomic and scRNA-Seq analyses on advanced HCC tissues and identified a significant molecule, guanine monophosphate synthase (GMPS), closely associated with the immune evasion in HCC. We analyzed the immune microenvironment characteristics remodeled by GMPS using scRNA-Seq and found GMPS induced tumor immune evasion in HCC by impairing the tumor-killing function of CD8 + T cells. Further investigation revealed that GMPS increased PD-L1 expression by regulating its ubiquitination and glycosylation modification. Mechanistically, GMPS enhanced the bond between PD-L1 and the catalytic subunit STT3A of oligosaccharyltransferase (OST) by acting as an additional module connecting the Sec61 channel complex and STT3A, which aided in the translocation and modification of nascent peptides. Increased PD-L1 impaired the tumor-killing function of CD8 + T cells, leading to the immune evasion. Importantly, targeting GMPS with angustmycin A, an inhibitor of GMPS activity, significantly suppressed PD-L1 expression and tumor growth in HCC, which also increased the sensitivity to anti-CTLA-4 immunotherapy. These findings suggested the potential of targeting GMPS as a promising therapeutic approach for HCC.