Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy

MERTK inhibition improves therapeutic efficacy of immune checkpoint inhibitors in hepatocellular carcinoma

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.

Latent class analysis-derived classification for cancer-specific death stratification of hepatocellular carcinoma

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.

TGF-β1 induces autophagy and mediates the effect on macrophages differentiation in primary liver cancer

BACKGROUND

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.

METHODS

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).

RESULTS

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.

CONCLUSIONS

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

RNA‑seq analysis of predictive markers associated with glutamine metabolism in thyroid cancer

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.

Oleanolic acid inhibits M2 macrophage polarization and potentiates anti-PD-1 therapy in hepatocellular carcinoma by targeting miR-130b-3p-PTEN-PI3K-Akt signaling and glycolysis

BACKGROUND

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.

OBJECTIVE

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.

METHODS

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.

RESULTS

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.

CONCLUSION

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.

Integrated single-cell and spatial transcriptomic profiling reveals that CD177+ Tregs enhance immunosuppression through apoptosis and resistance to immunotherapy in hepatocellular carcinoma

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.

Reviewing the function of macrophages in liver disease

INTRODUCTION

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.

AREAS COVERED

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.

EXPERT OPINION

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.

Tumor-associated macrophages remodel the suppressive tumor immune microenvironment and targeted therapy for immunotherapy

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.

PERK+ Macrophages Drive Immunotherapy Resistance in Lymph Node Metastases of Oral Squamous Cell Carcinoma

PURPOSE

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.

PATIENTS AND METHODS

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.

RESULTS

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.

CONCLUSIONS

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.

Characterization and prognostic of CD8 + TIM3 + CD101 + T cells in glioblastoma multiforme

BACKGROUND

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.

METHODS

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.

RESULTS

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.

CONCLUSION

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

Deciphering the Immunomodulatory Function of GSN+ Inflammatory Cancer-Associated Fibroblasts in Renal Cell Carcinoma Immunotherapy: Insights From Pan-Cancer Single-Cell Landscape and Spatial Transcriptomics Analysis

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.

Cancer-associated fibroblasts and metabolic reprogramming predict pathologic response to neoadjuvant PD-1 blockade in resected non-small cell lung cancer

PURPOSE

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.

METHODS

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.

RESULTS

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.

CONCLUSION

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

IL-21 Loading CaMnCO3 Vitality Backpacks Boost CAR-T Cell Synergistic Immunotherapy

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.

Macrophage at maternal-fetal Interface: Perspective on pregnancy and related disorders

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.

Identification of the "Collagen-Macrophage" sub-category of patients with colorectal cancer as an extension of the CMS4 subtype with THBS2 as a therapeutic target

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.

Spatial multi-omics reveals the potential involvement of SPP1+ fibroblasts in determining metabolic heterogeneity and promoting metastatic growth of colorectal cancer liver metastasis

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.

PAQR5 drives the malignant progression and shapes the immunosuppressive microenvironment of hepatocellular carcinoma by activating the NF-κB signaling

BACKGROUND

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.

METHODS

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.

RESULTS

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.

Integration of single-cell and bulk RNA sequencing identifies and validates T cell-related prognostic model in hepatocellular carcinoma

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.

Single-cell transcriptomic analysis reveals gut microbiota-immunotherapy synergy through modulating tumor microenvironment

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.

Spatiotemporal Transcriptomic Profiling Reveals the Dynamic Immunological Landscape of Alveolar Echinococcosis

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 promotes tumor microenvironment remodeling and therapy resistance

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.

A STT3A-dependent PD-L1 glycosylation modification mediated by GMPS drives tumor immune evasion in hepatocellular carcinoma

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.

Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data

Single-cell sequencing has advanced our understanding of cellular heterogeneity and disease pathology, offering insights into cellular behavior and immune mechanisms. However, extracting meaningful phenotype-related features is challenging due to noise, batch effects, and irrelevant biological signals. To address this, we introduce Deep scSTAR (DscSTAR), a deep learning-based tool designed to enhance phenotype-associated features. DscSTAR identified HSP+ FKBP4+ T cells in CD8+ T cells, which linked to immune dysfunction and resistance to immune checkpoint blockade in non-small cell lung cancer. It has also enhanced spatial transcriptomics analysis of renal cell carcinoma, revealing interactions between cancer cells, CD8+ T cells, and tumor-associated macrophages that may promote immune suppression and affect outcomes. In hepatocellular carcinoma, it highlighted the role of S100A12+ neutrophils and cancer-associated fibroblasts in forming tumor immune barriers and potentially contributing to immunotherapy resistance. These findings demonstrate DscSTAR's capacity to model and extract phenotype-specific information, advancing our understanding of disease mechanisms and therapy resistance.

Integrative multi-omics and Mendelian randomization analysis reveal SPP1+ tumor-associated macrophage-driven prognostic signature for hepatocellular carcinoma

Background

The SPP1+ tumor-associated macrophages (TAMs) have been implicated in tumor metastasis and immune evasion. However, the prognostic significance of SPP1+ TAMs in hepatocellular carcinoma (HCC) remains largely unexplored. This study aimed to identify SPP1+ TAMs-related genes and construct a model to predict overall survival (OS) in HCC patients.

Methods

Single-cell RNA sequencing (scRNA-seq) datasets from HCC patients were analyzed to identify SPP1+ TAMs. SPP1+ TAMs-related risk score (STRS) was developed using Mendelian randomization (MR) analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression. HCC patients from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts were stratified into high- and low-STRS groups based on STRS. Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve analysis, and functional enrichment analysis were performed to assess the prognostic value of STRS.

Results

SPP1+ TAMs exhibited strong associations with immunosuppressive functions. 16 SPP1+ TAMs-related genes were used to construct STRS. Patients in the high-STRS group had significantly worse OS than those in the low-STRS group (p < 0.001). ROC analysis demonstrated robust predictive power, with AUC values ranging from 0.685 to 0.748 for 1-year OS, 0.717 to 0.739 for 2-year OS, and 0.719 to 0.738 for 3-year OS. The STRS model also exhibited strong predictive capability for the distinction of drug resistance.

Conclusion

This study identified SPP1+ TAMs-related genes as key prognostic indicators in HCC. The STRS model provides an effective tool for predicting patient survival and may facilitate personalized treatment strategies for HCC. These findings enhance the understanding of TAMs-driven immune modulation in HCC and highlight potential therapeutic targets for improving patient outcomes.

Single-cell sequencing combined with bulk RNA seq reveals the roles of natural killer cell in prognosis and immunotherapy of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a type of highly heterogeneous tumor characterized by a high mortality rate and poor prognosis. Natural Killer cells (NK cells) are important immune cells that play an important role in anti-tumor activities, antiviral responses, and immune regulation. The relationship between NK cells and HCC remains unclear. It would be valuable to identify a NK-related prognostic signature for HCC. WGCNA and single-cell sequencing RNA were performed to identify NK cell related genes. Gene Enrichment Analysis were used to identify the potential signal pathway. After combing genes from WGCNA and scRNA, Unicox, LASSO + StepCox and Multicox analysis were used to filter prognostic-related gene and construct a prognostic model. Then we performed Proposed time analysis to identify the developmental trajectories of NK cells. Finally, ssGSEA and estimate methods were used to evaluate the immune microenvironment and sensitivity drugs. Using the scRNA-seq data, we identified 1396 genes with high NK cell scores. Based on the results of scRNA-seq, 250 NK-related genes were identified from WGCNA. We identified 223 intersecting genes between the scRNA-seq and WGCNA. After integrating clinical data with the bulk RNA-seq data of these intersecting genes, we constructed a prognostic model to accurately predict the prognosis of HCC patients. Eventually, we found that high-risk HCC patients exhibited worse survival outcomes and lower sensitivity to immunotherapy. We constructed a risk model based on NK cell-related genes that can predict the prognosis of HCC patients accurately. This model can also predict the immunotherapy response of HCC effectively.

Neurogranin facilitates maintaining the immunosuppressive state of hepatocellular carcinoma by promoting TGF-β1 secretion

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.

Tumor-resident Malassezia can promote hepatocellular carcinoma development by downregulating bile acid synthesis and modulating tumor microenvironment

Bacterial dysbiosis coincides with the carcinogenesis in malignancies such as lung and colon cancer, and has recently been suggested to involve in the pathogenesis of hepatocellular carcinoma (HCC). However, the mycobiome has not yet been definitively linked to liver tumorigenesis. Here we showed that the microbiota composition of HCC tumors was distinct from that of the normal adjacent to tumor (NAT) on the basis of richness and beta-diversity indices. Specifically, the fungal community that infiltrated HCC tumors was markedly enriched for Malassezia spp. and genus Malassezia in tumors was substantially more abundant than that in NAT. We also discovered that the relative abundance of genus Malassezia was strongly correlated with the tumor microenvironment (TME) signatures, including stromal and immune components. In addition, tumor-resident Malassezia could inhibit bile acid synthesis by downregulating the expression level of CYP7 A1 and CYP27 A1. To improve clinical usability, we developed a set of Malassezia-related genes, called Malassezia.Sig, which could accurately predict patient survival. Collectively, our work shows that tumor-resident Malasseiza may promote HCC progression by downregulating bile acid synthesis and modulating the TME, although more studies are needed.

Nanoparticle-mediated dual targeting of stromal and immune components to overcome fibrotic and immunosuppressive barriers in hepatocellular carcinoma

Cancer-associated fibroblasts (CAFs) are key drivers of hepatocellular carcinoma (HCC) through their promotion of fibrosis and immune suppression activity. To overcome this stroma-immune barrier, we developed D/F@MRL, a stroma-immune co-targeting nanoplatform that enables the spatiotemporal coordination of CAF reprogramming and immune activation. In D/F@MRL, MMP-2-responsive hybrid liposomes (MRL) was employed to co-load digoxin (Dig) and PD-L1-degrading nanofibers (NFs). Upon encountering the MMP-2-enriched HCC stroma, D/F@MRL undergoes enzymatic cleavage, thereby enabling the targeted release of Dig and NFs within the HCC microenvironment. Mechanistically, Dig inhibits the phosphorylation of SMAD3 in CAFs, while PD-L1 degradation destabilizes the TGFβ receptor, synergistically silencing TGF-β/Smad signaling to reprogram CAFs. This combination not only disrupts the fibrotic barrier but also creates a feed-forward loop that further enhances drug penetration, while reinforcing the immune activation driven by Dig-induced immunogenic cell death (ICD) and PD-L1 degradation. In the humanized immune PDX model, D/F@MRL successfully reprogrammed CAFs and robustly remodeled the stromal and immune microenvironments without causing systemic toxicity, highlighting its promising potential for clinical translation. By integrating CAF reprogramming with ICD and immune checkpoint inhibition, this strategy overcame the limitations of single-target therapies, induced robust immune activation, further provided a clinic-transformative approach for fibrotic malignancies.

Lactate drives senescence-resistant lineages in hepatocellular carcinoma via histone H2B lactylation of NDRG1

Hepatocellular carcinoma (HCC) treatment options remain limited despite advances in targeted therapies for molecularly-defined cancers. To address tumor heterogeneity, we reconstructed HCC clonal evolution through single-cell RNA sequencing trajectory analysis, identifying 902 signature genes across seven cellular states. Weighted gene co-expression network analysis of public HCC datasets revealed tumor-grade-associated modules and established a 14-gene prognostic model linked to clonal evolution. Central to this model is the LDHA-NDRG1 axis - two hypoxia-responsive regulators showing coordinated spatiotemporal expression patterns during cancer progression. Dual-expressing cell lineages correlated with poor prognosis and senescence resistance through LDHA-mediated lactylation of histone H2B at K58 on NDRG1, an epigenetic mechanism connecting metabolic reprogramming to senescence evasion. Therapeutically, dual inhibition of this axis extended survival in metastatic HCC murine models. Our findings reveal that lactate-driven epigenetic modification via the LDHA-NDRG1 axis creates a molecularly distinct subpopulation enabling senescence resistance, providing mechanistic insights into HCC heterogeneity. This work proposes a precision medicine strategy targeting lactylation-mediated epigenetic regulation, with implications for developing combination therapies and patient stratification based on clonal evolution patterns.

Macrophage-derived exosomes in cancer: a double-edged sword with therapeutic potential

Solid cancer contains a complicated communication network between cancer cells and components in the tumor microenvironment (TME), significantly influencing the progression of cancer. Exosomes function as key carriers of signaling molecules in these communications, including the intricate signalings of tumor-associated macrophages (TAMs) on cancer cells and the TME. With their natural lipid bilayer structures and biological activity that relates to their original cell, exosomes have emerged as efficient carriers in studies on cancer therapy. Intrigued by the heterogeneity and plasticity of both macrophages and exosomes, we regard macrophage-derived exosomes in cancer as a double-edged sword. For instance, TAM-derived exosomes, educated by the TME, can promote resistance to cancer therapies, while macrophage-derived exosomes generated in vitro have shown favorable potential in cancer therapy. Here, we depict the reasons for the heterogeneity of TAM-derived exosomes, as well as the manifold roles of TAM-derived exosomes in cancer progression, metastasis, and resistance to cancer therapy. In particular, we emphasize the recent advancements of modified macrophage-derived exosomes in diverse cancer therapies, arguing that these modified exosomes are endowed with unique advantages by their macrophage origin. We outline the challenges in translating these scientific discoveries into clinical cancer therapy, aiming to provide patients with safe and effective treatments.

Solute carrier family 2 member 2 (glucose transporter 2): a common factor of hepatocyte and hepatocellular carcinoma differentiation

GLUT2 (SLC2A2), a vital glucose transporter in liver, pancreas, and kidney tissues, regulates blood glucose levels and energy metabolism. Beyond its metabolic role, SLC2A2 contributes to cell differentiation and metabolic adaptation during embryogenesis and tissue regeneration. Despite its significance, the role of SLC2A2 in liver differentiation and hepatocellular carcinoma (HCC) remains underexplored. This study investigated SLC2A2's role in liver differentiation using in silico, in vitro, and in vivo approaches. Analysis of GEO datasets (GSE132606, GSE25417, GSE67848) and TCGA HCC data revealed that while SLC2A2 expression decreases with HCC progression, stemness-associated genes, including SOX2 and POU5F1, are upregulated. Zebrafish embryos injected with SLC2A2-targeting morpholino exhibited reduced expression of the liver differentiation marker fabp10a without significantly altering the hepatoblast marker hhex. In HepG2 cells, SLC2A2 knockdown increased stemness and IGF1R pathway markers, indicating a shift toward less differentiated states. These findings suggest that SLC2A2 supports liver differentiation by regulating glucose metabolism and suppressing pathways associated with stemness and malignancy. Targeting SLC2A2 may serve as a promising therapeutic strategy for liver-related diseases, particularly HCC, by addressing its dual role in differentiation and tumor progression. Further mechanistic studies are warranted to fully elucidate these processes.

Long non-coding RNA in the regulation of cell death in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the predominant form of primary liver cancer, accounting for 90% of all cases. Currently, early diagnosis of HCC can be achieved through serum alpha-fetoprotein detection, B-ultrasound, and computed tomography scanning; however, their specificity and sensitivity are suboptimal. Despite significant advancements in HCC biomarker detection, the prognosis for patients with HCC remains unfavorable due to tumor heterogeneity and limited understanding of its pathogenesis. Therefore, it is crucial to explore more sensitive HCC biomarkers for improved diagnosis, monitoring, and management of the disease. Long non-coding RNA (lncRNA) serves as an auxiliary carrier of genetic information and also plays diverse intricate regulatory roles that greatly contribute to genome complexity. Moreover, investigating gene expression regulation networks from the perspective of lncRNA may provide insights into the diagnosis and prognosis of HCC. We searched the PubMed database for literature, comprehensively classified regulated cell death mechanisms and systematically reviewed research progress on lncRNA-mediated cell death pathways in HCC cells. Furthermore, we prospectively summarize its potential implications in diagnosing and treating HCC.

Prognostic impact of extracellular volume fraction derived from equilibrium contrast-enhanced CT in HCC patients receiving immune checkpoint inhibitors

This study aimed to investigate whether extracellular volume (ECV) fraction derived from equilibration contrast-enhanced computed tomography (CECT) affects prognosis in HCC patients receiving ICIs. This retrospective study ultimately included 211 HCC patients undergoing ICIs, of whom 60 were included in an internal validation to assess the reproducibility of the results. Baseline unenhanced and equilibrated CECT were used to measure CT values of the tumor, liver and aorta, which were combined with hematocrit to calculate the ECV fraction. Correlation analysis was used to investigate the association between tumor ECV and liver ECV fractions. The effects of clinical variables and ECV fraction on progression-free survival (PFS) and overall survival (OS) were evaluated using Cox proportional hazards models and Kaplan-Meier curves. Of these 151 patients, tumor ECV fraction positively correlated with liver ECV fraction. In the Lower tumor ECV group, PFS (5.6 vs. 7.6 months) and OS (10.5 vs. 15.5 months) were notably shorter than in the Higher tumor ECV group, while no significant differences were found between the Higher and Lower liver ECV groups. Furthermore, the multivariable Cox regression model demonstrated that higher tumor ECV fraction level was an independent protective factor for PFS and OS (all P < 0.001). Internal validation cohort preliminary demonstrated reproducibility of results. The tumor ECV fraction is expected to become a routine indicator before ICIs therapy for HCC patients in contrast to liver ECV fraction, contributing to their subsequent management.

A spatially resolved transcriptome landscape during thyroid cancer progression

Tumor microenvironment (TME) remodeling plays a pivotal role in thyroid cancer progression, yet its spatial dynamics remain unclear. In this study, we integrate spatial transcriptomics and single-cell RNA sequencing to map the TME architecture across para-tumor thyroid (PT) tissue, papillary thyroid cancer (PTC), locally advanced PTC (LPTC), and anaplastic thyroid carcinoma (ATC). Our integrative analysis reveals extensive molecular and cellular heterogeneity during thyroid cancer progression, enabling the identification of three distinct thyrocyte meta-clusters, including TG+IYG+ subpopulation in PT, HLA-DRB1+HLA-DRA+ subpopulation in early cancerous stages, and APOE+APOC1+ subpopulation in late-stage progression. We reveal stage-specific tumor leading edge remodeling and establish high-confidence cell-cell interactions, such as COL8A1-ITHB1 in PTC, LAMB2-ITGB4 in LPTC, and SERPINE1-PLAUR in ATC. Notably, both SERPINE1 expression level and SERPINE1+ fibroblast abundance correlate with malignant progression and prognosis. These findings provide a spatially resolved framework of TME remodeling, offering insights for thyroid cancer diagnosis and treatment.

Biological mechanisms and immunotherapy of brain metastases in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related mortality worldwide, with Brain Metastases serving as a significant adverse prognostic factor. The blood-brain barrier poses a substantial challenge in the treatment of brain metastases, as it restricts the penetration of many anticancer agents. Novel immunotherapy, such as immune checkpoint inhibitors (ICIs) have emerged as promising treatment for NSCLC and its associated brain metastases. This review summarizes the biological mechanism underlying NSCLC brain metastases and provides an overview of the current landscape of immunotherapy, exploring the mechanism of action and clinical applications of these advanced treatments.

Tumor-Derived CD109 Orchestrates Reprogramming of Tumor-Associated Macrophages to Dampen Immune Response

BACKGROUND & AIMS

Despite remarkable advancements in immunotherapy, poor responsiveness in intrahepatic cholangiocarcinoma (iCCA) remains a persistent challenge. Here, we explored the immunosuppressive-related secreted proteins derived from iCCA and the underlying regulatory mechanisms in tumor immune microenvironment (TIME) remodeling, with the aim of developing new targets to inhibit tumor growth and improve the efficacy of immunotherapy.

METHODS

Proteomic analysis, single-cell transcriptomics, CyTOF, RNA sequencing, and mass spectrometry were conducted to identify the key secreted protein involved in immune suppression and elucidate the underlying biological mechanisms.

RESULTS

We revealed that tumor-derived soluble CD109 (sCD109) is associated with the immunosuppressive TIME, where elevated sCD109 promotes the enrichment of CD73+ TAMs, hindering T cell immune response. Mechanistically, sCD109 upregulates CD73 mRNA transcription by activating the FcγRI/SYK/NFκB signaling pathway. Meanwhile, sCD109 is internalized into the cytoplasm of macrophages and inhibit the degradation of CD73 protein by binding to the E3 ligase TRIM21, competing with CD73 for its binding site. Dual blockade of CD109 and PD-L1 can improve the infiltration and function of lymphocyte, significantly prolonging the anti-tumor response.

CONCLUSIONS

Our findings reveal sCD109 as a 'secreted immune checkpoint' that reprograms the TIME and suggest that CD109 inhibition is a valuable strategy to sensitize the effectiveness of iCCA immunotherapy.

IMPACT AND IMPLICATIONS

Poor response to tumor immunotherapy in patients with intrahepatic cholangiocarcinoma (iCCA) has long been a challenge for clinicians. In this study, we used multiomics approaches to elucidate that tumor cells secrete soluble CD109, which reprograms macrophages, leading to the accumulation of CD73+ macrophages in the tumor immune microenvironment (TIME). This effect significantly inhibits T cell proliferation and the immune response of CD8+ T cells, thereby impairing the efficacy of immunotherapy. In preclinical studies, we demonstrated that targeting CD109 in mice can markedly improve the immunosuppressive TIME, sensitizing iCCA cells to anti-PD-L1 immunotherapy. These findings represent a crucial step toward developing more effective therapies for iCCA and have significant implications for clinicians, scientists, and drug developers in the field.

Research status and frontiers in liver cancer immunotherapy: a bibliometric perspective on highly cited literature

Background

Liver cancer is one of the major causes of cancer-related death in the world. As a breakthrough therapy, immunotherapy had significantly improved the prognosis of patients. However, the current research status and research hotspots in the field of liver cancer immunotherapy still lack systematic review. Based on the bibliometric analysis of highly cited papers, this study intended to reveal the current research status, research hotspots and future research trends in this field.

Objective

The purpose of this study was to analyze the national/regional contributions, authors and institutions cooperation network, keywords clustering and keywords burst analysis of highly cited papers on liver cancer immunotherapy through bibliometrics, so as to clarify the research frontier and development direction, and provide objective data support for future research direction and clinical practice.

Methods

The highly cited papers on liver cancer immunotherapy from the Web of Science core collection up to February 23, 2025 were retrieved, and 232 studies were included. CiteSpace was used to build a knowledge map, analyze the distribution of years, countries, authors, institutions and cooperation networks, and identify research hotspots and emerging trends through keyword clustering and burst detection.

Results

The number of highly cited papers continued to increase from 2014 and reached a peak in 2022. China and the United States had the highest number of publications and the centrality of cooperation networks. The author with the highest number of papers was Llovet, Josep M, whose research direction mainly focused on immune checkpoint inhibitor combination therapy and molecular typing. The author with the highest cooperation network centrality was Duda, Dan G, whose research team focused on tumor microenvironment regulation. Harvard University and the University of Barcelona played an important central role in the institutional collaboration. Keywords analysis showed that immune checkpoint inhibitors, tumor microenvironment and combination therapy were the core of liver cancer immunotherapy. Burst keywords such as cell lung cancer, pembrolizumab, advanced melanoma, blockade, lymphocytes, etc. had revealed the research frontier of liver cancer immunotherapy research.

Conclusion

The research on liver cancer immunotherapy had made multi-dimensional progress, with China and the United States leading the global cooperation. The main research directions were the combination strategy of immunization, the regulation of tumor microenvironment and the exploration of novel targets. In the future, it is necessary to optimize treatment resistance solutions, integrate interdisciplinary resources, and promote the development of precision and personalized treatment.

Epigenetic-modification associated hnRNPA3 acts as a prognostic biomarker and promotes malignant progression of HCC

OBJECTIVE

hnRNPA3 is highly expressed in numerous malignancies, including hepatocellular carcinoma (HCC), but its function and mechanism has not been elucidated. In this study, we performed a comprehensive bioinformatics analysis of hnRNPA3 in the TCGA-LIHC dataset and several experiments in vitro to investigate the function and potential mechanisms of hnRNPA3 in HCC.

METHODS

Pan-cancer expression including hnRNPA3 levels as well as DNA methylation, associated ceRNA, immune infiltration, and immune checkpoint genes of hnRNPA3 in TCGA-LIHC dataset were assessed. Logistic regression, receiver operating characteristic curve (ROC), Kaplan-Meier analysis, and nomogram modeling were used to evaluate prognostic values of hnRNPA3 in HCC. hnRNPA3 level in cell subtypes in HCC tumor microenvironment was analysed through spatial transcriptomic. "pRRophetic" package was used to predict potential chemotherapeutic drugs sensitivity. hnRNPA3 level in HCC patients and cell lines were detected by qRT-PCR or WB. hnRNPA3's impact on proliferation, migration were studied in SNU449 and HuH7 cell lines. RNA-seq showed hnRNPA3 controled different important singaling passways in HCC.

RESULTS

hnRNPA3 was significantly elevated in HCC tumors compared to controls. hnRNPA3 levels correlated with Age, HCC stage, histologic grade, and tumor status, and may independently predict the overall and disease-specific survival. Significant associations were found between hnRNPA3 levels and DNA methylation. hsa-miR-22-3p may act as a regulatory factor for hnRNPA3 and form a ceRNA network with multiple lncRNAs.Analysis of immune infiltration and immune checkpoint genes revealed a correlation between hnRNPA3 expression and macrophages. The similar conclusion also occurred in the spatial transcriptomic detection. 5-Fluorouracil, Doxorubicin, Etoposide, et al., may be potential sensitive drugs in therapy of high-hnRNPA3 HCC patients. Silencing hnRNPA3 expression in SNU449 and HuH7 cells resulted in reducing proliferation and migration. RNA-seq showed hnRNPA3 played an important regulatory role in the malignant progression of HCC.

CONCLUSION

hnRNPA3 was found to represent a promising biomarker within HCC diagnosis and prognosis and maybe a potential drug-target in HCC therapy.

Mapping immunotherapy potential: spatial transcriptomics in the unraveling of tumor-immune microenvironments in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) often exhibits poor response rates to immune checkpoint inhibitor (ICI) therapies, largely owing to the intricate composition and spatial organization of immune cells within the tumor-immune microenvironment (TIME). The diversity of immune cell populations, their spatial relationships, and dynamic interactions significantly influence the immunosuppressive nature of the TIME, thereby limiting the efficacy of immunotherapy. To address these challenges and enhance the therapeutic potential of ICIs in HNSCC, a comprehensive analysis of the TIME is essential. Spatial transcriptomics (ST), a cutting-edge technology, enables high-resolution mapping of gene expression within the spatial context of the tumor, providing critical insights into the functional roles and interactions of immune cells in the TIME. This review highlights the importance of ST in uncovering the complexities of the TIME in HNSCC and proposes strategies for leveraging these insights to develop more effective immunotherapeutic approaches. By integrating spatial and molecular information, this review aims to pave the way for personalized and precision-based treatments in HNSCC, ultimately improving patient outcomes.

CCR8 antagonist suppresses liver cancer progression via turning tumor-infiltrating Tregs into less immunosuppressive phenotype

BACKGROUND

Regulatory T cells (Tregs) are the main immunosuppressive cells in tumor immune microenvironment (TIME). However, systemic Treg depletion is not favored due to the crucial role of Tregs in the maintenance of immune homeostasis and prevention of autoimmunity. Recently, CCR8 has been identified as a key chemokine receptor expressed on tumor-infiltrating Tregs and targeted blockade of CCR8 exerts anticancer effect in several cancer types, but whether this pathway is involved in the progression of hepatocellular carcinoma (HCC) remains unclear.

METHODS

We determined the involvement of CCR8+ Tregs in HCC using human HCC tissues and TCGA database, and examined the anticancer effect and the underlying molecular mechanisms of the CCR8 antagonist, IPG0521m, which was developed in house, in murine liver cancer model with flow cytometry, bulk and single-cell RNA sequencing and Real-Time PCR.

RESULTS

Remarkable increase in CCR8+ Tregs was observed in human HCC tissues. Treatment of syngeneic liver cancer model with IPG0521m resulted in dramatic inhibition of tumor growth, associated with increased CD8+ T cells in tumor tissues. Bulk RNA sequencing analysis indicated that IPG0521m treatment resulted in remarkable increase in antitumor immunity. Furthermore, single-cell RNA sequencing analysis demonstrated that IPG0521m treatment resulted in a switch of Tregs from high immunosuppression to low immunosuppression phenotype, associated with elevated CD8+ T and NK cell proliferation and cytotoxicity, and decreased myeloid-derived suppressor cells and tumor-associated macrophages in the tumor tissues.

CONCLUSIONS

IPG0521m inhibited liver cancer growth via reducing the immunosuppressive function of Tregs, thereby boosting anti-cancer immunity. Our study paves the way for the clinical study of CCR8 antagonist in HCC and other cancers.

Predicting treatment response and prognosis of immune checkpoint inhibitors-based combination therapy in advanced hepatocellular carcinoma using a longitudinal CT-based radiomics model: a multicenter study

BACKGROUND

Identifying effective predictive strategies to assess the response of immune checkpoint inhibitors (ICIs)-based combination therapy in advanced hepatocellular carcinoma (HCC) is crucial. This study presents a new longitudinal CT-based radiomics model to predict treatment response and prognosis in advanced HCC patients undergoing ICIs-based combination therapy.

METHODS

Longitudinal CT images were collected before and during the treatment for HCC patients across three institutions from January 2019 to April 2022. A total of 1316 radiomic features were extracted from arterial and portal venous phase abdominal CT images for each patient. A model called Longitudinal Whole-liver CT-based Radiomics (LWCTR) was developed to categorize patients into responders or non-responders using radiomic features and clinical information through support vector machine (SVM) classifiers. The area under the curve (AUC) was used as the performance metric and subsequently applied for risk stratification and prognostic assessment. The Shapley Additive explanations (SHAP) method was used to calculate the Shapley value, which explains the contribution of each feature in the SVM model to the prediction.

RESULTS

This study included 395 eligible participants, with a median age of 57 years (IQR 51-66), comprising 344 males and 51 females. The LWCTR model performed well in predicting treatment response, achieving an AUC of 0.883 (95% confidence interval [CI] 0.881-0.888) in the training cohort, 0.876 (0.858-0.895) in the internal validation cohort, and 0.875 (0.860-0.887) in the external test cohort. The Rad-Nomo model, integrating the LWCTR model's prediction score (Rad-score) with the modified Response Evaluation Criteria in Solid Tumors (mRECIST), demonstrated strong prognostic performance. It achieved time-dependent AUC values of 0.902, 0.823, and 0.850 at 1, 2, and 3 years in the internal validation cohort and 0.893, 0.848, and 0.762 at the same intervals in the external test cohort.

CONCLUSION

The proposed LWCTR model performs well in predicting treatment response and prognosis in patients with HCC receiving ICIs-based combination therapy, potentially contributing to personalized and timely treatment decisions.

Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

SIGNIFICANCE

Integration of spatial transcriptomic (GeoMx Digital Spatial Profiler) and single-cell RNA sequencing data from multiple gastric cancers identifies spatially resolved expression-based intratumoral heterogeneity, associated with distinct immune microenvironments. We uncovered two separate evolutionary trajectories associated with specific molecular subtypes, clinical prognoses, stromal neighborhoods, and genetic drivers. Tumor-stroma interfaces emerged as a unique state of tumor ecology.

FABP5+ lipid-loaded macrophages process tumour-derived unsaturated fatty acid signal to suppress T-cell antitumour immunity

BACKGROUND & AIMS

Tumour-associated macrophages (TAMs) contribute to hepatocellular carcinoma (HCC) progression. However, while the pro-tumour and immunosuppressive roles of lipid-loaded macrophages are well established, the mechanisms by which lipid metabolism enhances the tumour-promoting effects of TAMs remain unclear.

METHODS

Single-cell RNA sequencing was performed on mouse and human HCC tumour samples to elucidate the landscape of HCC TAMs. Macrophages were stimulated with various long-chain unsaturated fatty acids (UFAs) to assess immunosuppressive molecule expression in vitro. Additionally, in vivo and in vitro studies were conducted using mice with macrophage-specific deficiencies in fatty acid-binding protein 5 (FABP5) or peroxisome proliferator-activated receptor γ (PPARγ).

RESULTS

Single-cell RNA sequencing identified a subpopulation of FABP5+ lipid-loaded TAMs characterized by enhanced immune checkpoint blocker ligands and immunosuppressive molecules in an oncogene-mutant HCC mouse model and human HCC tumours. Mechanistically, long-chain UFAs released by tumour cells activate PPARγ via FABP5, resulting in immunosuppressive properties in TAMs. FABP5 deficiency in macrophages decreases immunosuppressive molecule expression, enhances T cell-dependent antitumour immunity, diminishes HCC growth, and improves immunotherapy efficacy.

CONCLUSIONS

This study demonstrates that UFAs promote tumourigenesis by enhancing the immunosuppressive tumour microenvironment via FABP5-PPARγ signalling and provides a proof-of-concept for targeting this pathway to improve the efficacy of tumour immunotherapy.

IMPACT AND IMPLICATIONS

Despite the role of tumour-associated macrophages (TAMs) in promoting tumour progression being well established, the mechanisms by which lipid metabolism enhances the tumour-promoting effects of TAMs remain unclear. Our study reveals that FABP5-mediated unsaturated fatty acid metabolism in TAMs is crucial for modulating antitumour T-cell immunity and influencing the efficacy of immunotherapy. This finding provides novel insights into the immunomodulatory roles of FABP5+ lipid-loaded TAMs in hepatocellular carcinoma and suggests that targeting FABP5 could offer a new approach to liver cancer treatment.

Cancer-associated fibroblasts in hepatocellular carcinoma: heterogeneity, mechanisms and therapeutic targets

Hepatocellular carcinoma (HCC) is one of the common malignant cancers worldwide. Although immunotherapy has improved the treatment outcome in HCC, a significant percentage of patients with advanced HCC still cannot benefit from immunotherapy. Therefore, developing new targets or combination therapeutic strategies to improve the efficacy of immunotherapy is urgently needed. A deeper understanding of the mechanisms underlying immune regulation may help in this regard. The tumor microenvironment (TME) consists of a diverse set of components modulating the efficacy of immunotherapy. Cancer-associated fibroblasts (CAFs) are critical components of the TME and can regulate both tumor and immune cells through secreted cytokines and exosomes that impact various signaling pathways in target cells. CAF-derived cytokines can also participate in extracellular matrix (ECM) remodeling, thereby impacting cancer progression and tumor responsiveness to immunotherapy among other effects. A thorough understanding of the phenotypic and functional profile dynamism of CAFs may lead the way for new treatment strategies and/or better treatment outcomes in HCC patients. In this review, we outline the biomarkers and functional heterogeneity of CAFs in HCC and elaborate on molecular mechanisms of CAFs, including anti-programmed cell death protein 1 (PD-1)/PD-ligand 1 (PD-L1) immunotherapy. We also examine current clinical implications of CAFs-related targets as potential therapeutic candidates in HCC.

Angiogenesis Is Associated With Aggressive Biology That Counterbalances With Tumor Immunogenicity in Hepatocellular Carcinoma

Background

Hepatocellular carcinoma (HCC) is an arterialized tumor; thus, anti-angiogenesis targeted therapy is in clinical practice. Herein, we hypothesized that HCC with high angiogenesis is biologically aggressive with worse survival.

Methods

Angiogenesis score (AS) was derived from the Molecular Signatures Database (MSigDB) Hallmark Angiogenesis Gene Set, and median was used to divide high versus low groups. Transcriptome of HCC patients of The Cancer Genome Atlas (TCGA, n = 386) and GSE76427 (n = 115) cohorts were analyzed.

Results

High AS correlated with angiogenesis-related gene expressions. Both microvascular and lymphatic endothelial cell infiltrations were higher in high angiogenesis HCC. Surprisingly, no survival difference was seen with varying levels of angiogenesis. High angiogenesis significantly enriched tumor aggravating signaling pathways: glycolysis, Notch, Hedgehog, KRAS, epithelial mesenchymal transition, and transforming growth factor-beta (TGF-β) in Gene Set Enrichment Analysis (GSEA), but also infiltrated less CD8+ T cells and T-helper 1 cells, and higher M1 macrophages and conventional dendritic cells (cDCs) with elevated cytolytic activity score in both cohorts. In agreement, immune response-related gene sets: inflammatory response, tumor necrosis factor-alpha (TNF-α) signaling, allograft rejection, interferon-alpha, and interferon-gamma were all enriched to high angiogenesis HCC. Programmed cell death protein 1 (PD1), programmed death ligand 1 (PD-L1), programmed death ligand 2 (PD-L2), and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) were higher in high angiogenesis HCC in TCGA, but not in GSE76427 cohort.

Conclusions

Angiogenesis quantified using transcriptome of HCC patients demonstrated that it is associated with aggressive biology but also with tumor immunogenicity and immune response that counterbalance and did not reflect in survival. Given high expression of immune checkpoint molecules, we cannot help but speculate that immunotherapy may be useful for high angiogenesis HCC patients.

Unraveling the immune-activated tumor microenvironment correlated with clinical response to atezolizumab plus bevacizumab in advanced HCC

Background & Aims

Despite atezolizumab plus bevacizumab being a standard treatment for advanced hepatocellular carcinoma (HCC), a significant proportion of patients do not achieve durable benefit. This study aimed to identify predictive biomarkers for this therapy by investigating the role of immune activation within the tumor microenvironment (TME).

Methods

We characterized the intratumoral TME of patients with advanced HCC treated with atezolizumab plus bevacizumab using single cell transcriptomics on pretreatment tumor biopsies from 12 patients. To complement and support these findings, we integrated our single cell data with publicly available bulk RNA-sequencing data from independent clinical trial cohorts.

Results

Patients who responded to combination therapy with atezolizumab plus bevacizumab demonstrated an immune-activated TME, marked by enhanced cytotoxicity and a tumor-specific T cell response. These patients also exhibited an increased proportion of inflammatory cytokine-enriched tumor-associated macrophage clusters with stronger interactions with T cells, an increased population of conventional dendritic cells, and activated antigen-presenting function in tumor endothelial cells. When publicly available bulk RNA-sequencing data from independent clinical trial cohorts were analyzed, these immune activation features were associated with improved progression-free survival (median 10.8 months, 95% CI: 7.3-not reached versus 5.5 months, 95% CI: 4.0-6.7; p <0.001).

Conclusions

These findings suggest that the existence of an activated immune TME before treatment is crucial for a favorable clinical response in patients with HCC treated with atezolizumab plus bevacizumab.

Impact and implications

Only a subset of patients with HCC benefit from combination therapy with atezolizumab plus bevacizumab, limiting its clinical utility. In this study, we used single cell RNA analysis to identify TME features associated with a clinical response to this therapy. Our findings suggest that a pre-existing immune-activated TME is crucial for predicting the response to atezolizumab plus bevacizumab. Specifically, features such as enhanced T cell cytotoxicity, inflammatory cytokine-enriched macrophage clusters, active antigen presentation in endothelial cells, and an increased presence of dendritic cells may aid patient selection and inform therapeutic strategies.

Dynamic single-cell transcriptomic reveals the cellular heterogeneity and a novel fibroblast subpopulation in laryngotracheal stenosis

BACKGROUND

Laryngotracheal stenosis (LTS), a pathological narrowing of the upper airway caused by excessive extracellular matrix (ECM) deposition, often leads to dyspnea and even respiratory failure. However, systematic studies addressing the specific subpopulations and their contribution to LTS development still remain underexplored.

RESULTS

We collected laryngotracheal tissue at multiple time points of LTS rat model, established by injuring their laryngotracheal lining, and performed dynamic single-cell RNA sequencing (scRNA-seq) to elucidate the transcriptomic atlas of LTS development. The results showed, from the inflammatory state to the repair/fibrotic state, infiltration of immune cells such as monocyte macrophages decreased and fibroblast increased. We delineated the markers and functional status of different fibroblasts subsets and identified that fibrotic fibroblasts may originate from multiple fibroblast subpopulations, including a new subpopulation characterized by the expression of chondrogenic markers such as Ucma and Col2a1, we designated this subcluster as chondrocyte injury-related fibroblasts (CIRF). Furthermore, we categorized monocytes/macrophages into several subtypes and identified that SPP1 high macrophages represented the largest macrophage subpopulation in LTS, providing evidence to clarify the importance of SPP1 macrophages in fibrosis disease. Our findings also revealed the interactions among these cells to explore the molecular mechanism associated with LTS pathogenesis.

CONCLUSIONS

Our study, for the first time, conducted dynamic scRNA-seq on LTS, revealing the cellular heterogeneity and providing a valuable resource for exploring the intricate molecular landscape of LTS. We propose CIRF may represent a tissue-specific fibroblast lineage in LTS and potentially originate from cells in the perichondrium of the trachea and transform into fibrotic fibroblasts. Integration of our study with those of other respiratory fibrotic diseases will allow for a comprehensive understanding of airway remodeling in respiratory diseases and exploring potential new therapeutic targets for their treatment.

PPY-Induced iCAFs Cultivate an Immunosuppressive Microenvironment in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by cancer cells surrounded by affluent stromal components, which may underlie their limited response to various therapeutic interventions, including immunotherapy. Inflammatory cancer-associated fibroblasts (iCAFs), a crucial subset of CAFs within the PDAC microenvironment, play a pivotal role in shaping an immunosuppressive microenvironment. In this study, single-cell RNA sequencing analysis is performed to screen for cancer cells-secreted proteins associated with iCAF induction, and PPY (pancreatic polypeptide) is validated as a potent inducer. Unlike previously reported iCAF inducers, PPY is a gastrointestinal hormone predominantly expressed in the pancreas, suggesting that targeting it may have minimal systemic effects. Multiplex immunohistochemistry (mIHC) on human PDAC tissue microarrays, orthotopic allograft mouse models, and co-culture experiments are utilized to validate the crucial role of PPY in iCAF induction. Mechanistic studies integrating mRNA sequencing, immunoprecipitation-mass spectrometry, and molecular docking reveal that PPY induces iCAFs by activating the non-canonical NF-κB pathway through EGFR. Importantly, targeting PPY enhanced the efficacy of anti-PD-1 immunotherapy in KPC (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre) mice, as evidenced by reduced tumor burden on PET-CT imaging and improved survival. This research is expected to provide a novel strategy for improving immunotherapy in PDAC by targeting a key inducer of iCAFs.

Phase separation of EEF1E1 promotes tumor stemness via PTEN/AKT-mediated DNA repair in hepatocellular carcinoma

This study aimed to investigate the associations of liquid-liquid phase separation (LLPS) and tumor stemness in hepatocellular carcinomas (HCC). LLPS-related genes were extracted from DrLLPS, LLPSDB and PhaSepDB databases. Stemness index (mRNAsi) was calculated based on the data from TCGA and Progenitor Cell Biology Consortium. Through some series of bioinformatics methods, we first found that stemness index mRNAsi was associated with worse survival outcomes, immune infiltration and therapy sensitivity in HCC. G2M checkpoint and DNA repair pathways were significantly activated with high mRNAsi. Totally, 71 differentially expressed LLPS genes in HCC were correlated with mRNAsi, and a mRNAsi-associated LLPS gene signature (KPNA2, EEF1E1 and ATIC) was identified to predict prognosis for HCC patients. mRNAsi-associated LLPS genes contributed to cluster HCC patients into four molecular clusters that markedly differed on survival, immune infiltration and therapy sensitivity. Further in vivo and in vitro experiments showed that EEF1E1 was highly expressed in HepG2 and HCCLM3 cells, and EEF1E1 silencing observably inhibited tumor cell growth, liver cancer stem cells (CSCs) markers (CD133, EpCAM and SOX2) expression, enhanced DNA damage marker γH2AX expression by activating PTEN/AKT pathway. EEF1E1 could undergo LLPS condensates, and roles of EEF1E1 on tumor cells were partly reversed after inhibiting LLPS using 1, 6-hexanediol. In conclusion, EEF1E1 was identified as a phase separation protein and involves in tumor stemness and DNA damage repair in HCC. EEF1E1 and its LLPS condensate may be novel targets to elaborate the underlying mechanisms of CSCs propagation in HCC.

The dual role of CXCL9/SPP1 polarized tumor-associated macrophages in modulating anti-tumor immunity in hepatocellular carcinoma

Introduction

The main challenge for cancer therapy lies in immuno-suppressive tumor micro-environment. Reprogramming tumor-associated macrophages (TAMs) into an anti-tumor phenotype is a promising strategy.

Methods

A comprehensive analysis by combing multi-regional single-cell, bulk and spatial transcriptome profiling with radiomics characterization was conducted to dissect the heterogeneity of TAMs and resolve the landscape of the CXCL9:SPP1 (CS) macrophage polarity in HCC.

Results

TAMs were particularly increased in HCC. SPP1+ TAMs and CXCL9+ TAMs were identified as the dominant subtypes with different evolutionary trajectories. SPP1+ TAMs, located in the tumor core, co-localized with cancer-associated fibroblasts to promote tumor growth and further contributed to worse prognosis. In contrast, CXCL9+ TAMs, located in the peritumoral region, synergized with CD8+ T cells to create an immunostimulatory micro-environment. For the first time, we explored the applicability of CS polarity in HCC tumors and revealed several key transcription factors involved in shaping this polarity. Moreover, CS polarity could serve as a potential indicator of prognostic and micro-environmental status for HCC patients. Based on medical imaging data, we developed a radiomics tool, RCSP (Radiogenomics-based CXCL9/SPP1 Polarity), to assist in non-invasively predicting the CS polarity in HCC patients.

Conclusion

Our research sheds light on the regulatory roles of SPP1+ TAMs and CXCL9+ TAMs in the micro-environment and provides new therapeutic targets or insights for the reprogramming of targeted macrophages in HCC.