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

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.

Spatial multi-omics analysis of tumor-stroma boundary cell features for predicting breast cancer progression and therapy response

Background

The tumor boundary of breast cancer represents a highly heterogeneous region. In this area, the interactions between malignant and non-malignant cells influence tumor progression, immune evasion, and drug resistance. However, the spatial transcriptional profile of the tumor boundary and its role in the prognosis and treatment response of breast cancer remain unclear.

Method

Utilizing the Cottrazm algorithm, we reconstructed the intricate boundaries and identified differentially expressed genes (DEGs) associated with these regions. Cell-cell co-positioning analysis was conducted using SpaCET, which revealed key interactions between tumor-associated macrophage (TAMs) and cancer-associated fibroblasts (CAFs). Additionally, Lasso regression analysis was employed to develop a malignant body signature (MBS), which was subsequently validated using the TCGA dataset for prognosis prediction and treatment response assessment.

Results

Our research indicates that the tumor boundary is characterized by a rich reconstruction of the extracellular matrix (ECM), immunomodulatory regulation, and the epithelial-to-mesenchymal transition (EMT), underscoring its significance in tumor progression. Spatial colocalization analysis reveals a significant interaction between CAFs and M2-like tumor-associated macrophage (TAM), which contributes to immune exclusion and drug resistance. The MBS score effectively stratifies patients into high-risk groups, with survival outcomes for patients exhibiting high MBS scores being significantly poorer. Furthermore, drug sensitivity analysis demonstrates that high-MB tumors had poor response to chemotherapy strategies, highlighting the role of the tumor boundary in modulating therapeutic efficacy.

Conclusion

Collectively, we investigate the spatial transcription group and bulk data to elucidate the characteristics of tumor boundary molecules in breast cancer. The CAF-M2 phenotype emerges as a critical determinant of immunosuppression and drug resistance, suggesting that targeting this interaction may improve treatment responses. Furthermore, the MBS serves as a novel prognostic tool and offers potential strategies for guiding personalized treatment approaches in breast cancer.

Myeloid cell path to malignancy: insights into liver cancer

Clinically approved treatments for advanced liver cancer often lack potency because of the heterogeneous characteristics of hepatocellular carcinoma (HCC). This complexity is largely driven by context-dependent inflammatory responses brought on by diverse etiologies, such as metabolic dysfunction-associated steatohepatitis (MASH), the genetic makeup of cancer cells, and the versatile adaptability of immune cells, such as myeloid cells. In this review, we discuss the evolutionary dynamics of the immune landscape, particularly that of liver-resident Kupffer cells (KCs), TREM2+, and SPP1+ macrophages with an active role during liver disease progression, which eventually fuels hepatocarcinogenesis. We highlight exploitable immunomodulatory avenues amenable to mitigate both the inherent pathological characteristics of liver cancers and the associated external factors that favor malignancy, paving a roadmap toward improving the management and therapeutic outcome for patients with HCC.

Migrasome Marker Epidermal Growth Factor Domain-Specific O-GlcNAc Transferase: Pan-Cancer Angiogenesis Biomarker and the Potential Role of circ_0058189/miR-130a-3p/EOGT Axis in Hepatocellular Carcinoma Progression and Sorafenib Resistance

Background: The EGF domain-specific O-GlcNAc transferase (EOGT), a migrasome marker, plays emerging roles in cancer biology through O-GlcNAcylation modifications, yet its pan-cancer functions and therapeutic implications remain underexplored. This study aimed to systematically characterize EOGT's oncogenic mechanisms across malignancies, with particular focus on hepatocellular carcinoma (HCC) progression and sorafenib resistance. Methods: Multi-omics analysis integrated TCGA/GTEx data from 33 cancer types with spatial/single-cell transcriptomics and 10 HCC cohorts. Functional validation employed Huh7 cell models with EOGT modulation, RNA sequencing, and ceRNA network construction. Drug sensitivity analysis leveraged GDSC/CTRP/PRISM databases, while immune microenvironment assessment utilized ESTIMATE/TIMER algorithms. Results: EOGT showed cancer-specific dysregulation, marked by significant upregulation in HCC correlating with advanced stages and poor survival. Pan-cancer analysis revealed EOGT's association with genomic instability, tumor stemness, and angiogenesis. Experimental validation demonstrated EOGT's promotion of HCC proliferation and migration. A novel exosomal circ_0058189/miR-130a-3p/EOGT axis was identified, showing that circ_0058189 was upregulated in HCC tissues, plasma samples and exosomes of sorafenib-resistant cells. Conclusion: This study establishes EOGT as a pan-cancer angiogenesis biomarker, while elucidating its role in therapeutic resistance via exosomal circRNA-mediated regulation, providing mechanistic insights for targeted intervention strategies.

Intratumoral microbiota-aided fusion radiomics model for predicting tumor response to neoadjuvant chemoimmunotherapy in triple-negative breast cancer

BACKGROUND

Neoadjuvant chemoimmunotherapy (NACI) has emerged as the standard treatment for early-stage triple-negative breast cancer (TNBC). However, reliable biomarkers for identifying patients who are likely to benefit from NACI are lacking. This study aims to develop an intratumoral microbiota-aided radiomics model for predicting pathological complete response (pCR) in patients with TNBC.

METHODS

Intratumoral microbiota are characterized by 16S rDNA sequencing and quantified through experimental assays. Single-cell RNA sequencing is performed to analyze the tumor microenvironment of tumors with various responses to NACI. Radiomics features are extracted from tumor regions on longitudinal magnetic resonance images (MRIs) scanned before and after NACI in the training set. On the basis of treatment response (pCR or non-pCR) and intratumoral microbiota scoring, we select key radiomics features and construct a fusion model integrating multi-timepoint (pre-NACI and post-NACI) MRI to predict the efficacy of immunotherapy, followed by independent external validation.

RESULTS

A total of 124 patients are enrolled, with 88 in the training set and 36 in the validation set. Tumors from patients who achieves pCR present a significantly greater intratumoral microbiota load than tumors from patients who achieve non-pCR (p < 0.05). Additionally, tumors in non-pCR group exhibit greater infiltration of tumor-associated SPP1+ macrophages, which is negatively correlated with the microbiota load. On the basis of intratumoral microbiota scoring, we select 17 radiomics features and use them to construct the fusion radiomics model. The fusion model achieves the highest AUC of 0.945 in the training set, outperforming pre-NACI (AUC = 0.875) and post-NACI (AUC = 0.917) models. In the validation set, this model maintains a superior AUC of 0.873, surpassing those of pre-NACI (AUC = 0.769) and post-NACI (AUC = 0.802) models. Clinically, the fusion model distinguishes patients who achieve pCR from those who do not with an accuracy of 77.8%. Decision curve analysis demonstrates the superior net clinical benefit of this model across varying risk thresholds.

CONCLUSIONS

Our intratumoral microbiota-aided radiomics model could serve as a powerful and noninvasive tool for predicting the response of patients with early-stage TNBC to NACI.

Novel immune drug combination induces tumour microenvironment remodelling and reduces the dosage of anti-PD-1 antibody

Immune checkpoint inhibitors (ICIs) are effective in clinical settings; however, they present immune-related adverse effects and financial burden. Although dose reduction of ICIs may mitigate these limitations, it could compromise therapeutic efficacy. Using two adjuvants (poly(I:C) and LAG-3-Ig) combined with three neoantigen peptides (Comb), we examined whether Comb could enhance the efficacy of reduced dose of αPD-1 monoclonal antibody (RD-αPD-1 mAb), which has limited efficacy. In a murine colorectal cancer model using an MC38 cell line, Comb addition to RD-αPD-1 mAb enhanced treatment efficacy. Analysis of the tumour microenvironment (TME) in mice treated with Comb using flow cytometry and single-cell RNA sequencing revealed decreased macrophages with highly expressing immunosuppressive genes and increased plasmacytoid dendritic cells with highly expressing antigen-presenting genes. A potent infiltration of CD8+ tumour-infiltrating lymphocytes (TILs) with an effector profile was only observed in RD-αPD-1 mAb with Comb. Additionally, single-cell T cell receptor repertoire analysis underscored an oligoclonal expansion of CD8+ TILs following treatment with RD-αPD-1 mAb with Comb. This novel immune drug combination may be a promising strategy for reducing αPD-1 mAb dosage while preserving antitumour efficacy through modulating the TME.

Identification of Genomic Instability-Associated LncRNAs as Potential Therapeutic Targets in Lung Adenocarcinoma

BACKGROUND/OBJECTIVES

Non-small cell lung cancer (NSCLC) is the most common type of cancer, with lung adenocarcinoma (LUAD) as the predominant subtype. Despite advancements in targeted therapies, many NSCLC patients still experience poor outcomes due to treatment resistance and disease progression. Genomic instability (GI), a hallmark of cancer, defined as the increased tendency of DNA mutations and alterations, is closely linked to cancer initiation, progression, and resistance to therapy. Emerging evidence suggests that long non-coding RNAs (lncRNAs)-molecules longer than 200 nucleotides that do not encode proteins but regulate gene expression-play critical roles in cancer biology and are associated with GI. However, the relationship between GI and lncRNA expression in LUAD remains poorly understood.

METHODS

In this study, we analyzed the transcript profiles of lncRNAs and mRNAs from LUAD samples in The Cancer Genome Atlas (TCGA) database and classified them based on their Homologous Recombination Deficiency (HRD) score. The HRD score is an unweighted sum of three independent DNA-based measures of genomic instability: loss of heterozygosity, telomeric allelic imbalance, and large-scale transitions. We then performed a differential gene expression analysis to identify lncRNAs and mRNAs that were either upregulated or downregulated in samples with high HRD scores compared to those with low HRD scores. Following this, we conducted a correlation analysis to assess the significance of the association between HRD scores and the expression of both lncRNAs and mRNAs.

RESULTS

We identified 30 differentially expressed lncRNAs and 200 mRNAs associated with genomic instability. Using an RNA interactome database from sequencing experiments, we found evidence of interactions between GI-associated lncRNAs (GI-lncRNAs) and GI-associated mRNAs (GI-mRNAs). Further investigation showed that some GI-lncRNAs play regulatory and functional roles in LUAD and other diseases. We also found that GI-lncRNAs have potential as prognostic biomarkers, particularly when integrated with HRD stratification. The expression of specific GI-lncRNAs was associated with primary therapy response and immune infiltration in LUAD. Additionally, we identified existing drugs that could modulate GI-lncRNAs, offering potential therapeutic strategies to address GI in LUAD.

CONCLUSIONS

Our findings suggest that GI-associated lncRNAs could serve as valuable biomarkers for LUAD prognosis and therapeutic response. Furthermore, modulating these lncRNAs presents potential treatment avenues to address genomic instability in LUAD.

Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer

Spatial cellular context is crucial in shaping intratumor heterogeneity. However, understanding how each tumor establishes its unique spatial landscape and what factors drive the landscape for tumor fitness remains significantly challenging. Here, we analyzed over 2 million cells from 50 tumor biospecimens using spatial single-cell imaging and single-cell RNA sequencing. We developed a deep learning-based strategy to spatially map tumor cell states and the architecture surrounding them, which we referred to as Spatial Dynamics Network (SDN). We found that different tumor cell states may be organized into distinct clusters, or 'villages', each supported by unique SDNs. Notably, tumor cell villages exhibited village-specific molecular co-dependencies between tumor cells and their microenvironment and were associated with patient outcomes. Perturbation of molecular co-dependencies via random spatial shuffling of the microenvironment resulted in destabilization of the corresponding villages. This study provides new insights into understanding tumor spatial landscape and its impact on tumor aggressiveness.

Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments

The tumor microenvironment (TME) plays a crucial role in orchestrating tumor cell behavior and cancer progression. Recent advances in spatial profiling technologies have uncovered novel spatial signatures, including univariate distribution patterns, bivariate spatial relationships, and higher-order structures. These signatures have the potential to revolutionize tumor mechanism and treatment. In this review, we summarize the current state of spatial signature research, highlighting computational methods to uncover spatially relevant biological significance. We discuss the impact of these advances on fundamental cancer biology and translational research, address current challenges and future research directions.

Single-cell multi-stage spatial evolutional map of esophageal carcinogenesis

Cancer development involves the co-evolution of cancer cells and their surrounding microenvironment, yet the dynamics of this interaction within the physical architecture remains poorly understood. Here, we present a spatial transcriptomic map at single-cell resolution, encompassing 127 multi-stage fields of view from 43 patients, to chart the evolutionary trajectories of human esophageal squamous cell carcinoma (ESCC). By analyzing 6.4 million cells, we reveal that ESCC progression is driven by a proliferative epithelial cell subpopulation that acquires dedifferentiated and invasive characteristics. At the late precancerous stage, these cells disrupt the epithelial-stromal interface and recruit normal fibroblasts via JAG1-NOTCH1 signaling, transforming them into cancer-associated fibroblasts (CAFs). This interaction leads to the formation of a "CAF-Epi" (CAF and epithelial cell) niche at the tumor edge that shields the tumor from immune surveillance. The CAF-Epi niche formation is a key indicator of progression in ESCC and other squamous cell carcinomas and patient outcomes.

Identification and validation of prognostic biomarkers related to tumor immune invasion in pancreatic cancer

Background

The diagnosis and treatment of pancreatic adenocarcinoma (PAAD) remain clinically challenging, and new molecular markers for prognostic assessment and targeted therapy are urgently needed. The tumor microenvironment (TME) and immune invasion play an important role in pancreatic cancer development and progression. Therefore, immunotherapeutic strategies based on the TME and immune invasion may have important clinical value.

Methods

In this study, we extracted transcriptome and clinicopathological data for 179 PAAD samples from the TCGA database and evaluated the immune composition, stromal composition, and infiltrating immune cell landscape in the tumor samples. Then, we identified relevant differentially expressed genes (DEGs) and performed functional annotation and prognostic correlation analysis to identify prognostic biomarkers for pancreatic cancer, the correlation between biomarkers and tumor immune invasion was analyzed to reveal the molecular immune mechanism of pancreatic cancer. Finally, GEO databases (GES71729), GEPIA, TISIDB, TIMER databases and RT-PCR were used for further analysis.

Results

CXCL10 and CXCL11 were highly expressed in pancreatic cancer and associated with poor prognosis of patients through cell adhesion molecules chemokine signaling, cytokine-cytokine receptor interaction, natural killer cell-mediated cytotoxicity, and Toll-like receptor signaling pathways. Finally, the correlation between CXCL10 and CXCL11 and tumor immune invasion was analyzed. The results confirmed that the expression levels of CXCL10 and CXCL11 were positively correlated with the contents of CD8+ T cells. Activated memory CD4+ T cells, M1 macrophages and resting mast cells. The levels of CXCL10 and CXCL11 were related to but negatively correlated with the contents of memory B cells, Tregs and M0 macrophages.

Conclusion

Our study demonstrates that CXCL10 and CXCL11 are novel biomarkers of TME and immune cell infiltration in pancreatic cancer by affecting the distribution of immune cells. CXCL10 and CXCL11 may be new targets for molecular targeted therapy and immunotherapy of pancreatic cancer.

Antigen-presenting cancer associated fibroblasts enhance antitumor immunity and predict immunotherapy response

Cancer-associated fibroblasts (CAF) play a crucial role in tumor progression and immune regulation. However, the functional heterogeneity of CAFs remains unclear. Here, we identify antigen-presenting CAFs (apCAF), characterized by high MHC II expression, in gastric cancer (GC) tumors and find that apCAFs are preferentially located near tertiary lymphoid structures. Both in vivo and in vitro experiments demonstrate that apCAFs promote T cell activation and enhances its cytotoxic and proliferative capacities, thereby strengthening T cell-mediated anti-tumor immunity. Additionally, apCAFs facilitate the polarization of macrophages toward a pro-inflammatory phenotype. These polarized macrophages, in turn, promote the formation of apCAFs, creating a positive feedback loop that amplifies anti-tumor immune responses. Notably, baseline tumors in immunotherapy responders across various cancer types exhibit higher levels of apCAFs infiltration. This study advances the understanding of CAFs heterogeneity in GC and highlights apCAFs as a potential biomarker for predicting immunotherapy response in pan-cancer.

Combining Radioembolization and Immune Checkpoint Inhibitors for the Treatment of Hepatocellular Carcinoma: The Quest for Synergy

Hepatocellular carcinoma is a leading and increasing contributor to cancer-related death worldwide. Recent advancements in both liver-directed therapies in the form of yttrium-90 (90Y) radioembolization (RE) and systemic therapy in the form of immune checkpoint inhibitors (ICI) have expanded treatment options for patients with an otherwise poor prognosis. Despite these gains, ICIs and 90Y-RE each have key limitations with low objective response rates and persistent hazard of out-of-field recurrence, respectively, and overall survival remains low. However, each therapy's strength may mitigate the other's weakness, making them potentially ideal partners for combination treatment strategies. This review discusses the scientific and clinical rationale for combining 90Y-RE with ICIs, highlights early clinical trial data on its safety and effectiveness, and proposes key issues to be addressed in this emerging field. With optimal strategies, combination therapies can potentially result in increasing likelihood of durable and curative outcomes in later stage patients.

High-dimensional deconstruction of HNSC reveals clinically distinct cellular states and ecosystems that are associated with prognosis and therapy response

BACKGROUND

Characterizing the variety of cell types in the tumor microenvironment (TME) and their organization into cellular communities is vital for elucidating the biological diversity of cancer and informing therapeutic strategies.

METHODS

Here, we employed a machine learning-based algorithm framework, EcoTyper, to analyze single-cell transcriptomes from 139 patients with head and neck squamous cell carcinoma (HNSC)and gene expression profiles from 983 additional HNSC patients, aiming to delineate the fundamental cell states and ecosystems integral to HNSC.

RESULTS

A diverse landscape of 66 cell states and 9 ecosystems within the HNSC microenvironment was identified, revealing classical cell types while also expanding upon previous immune classifications. Survival analysis revealed that specific cell states and ecotypes (ecosystems) are associated with patient prognosis, underscoring their potential as indicators of clinical outcomes. Moreover, distinct cell states and ecotypes exhibited varying responses to immunotherapy and chemotherapy, with several showing promise as predictive biomarkers for treatment efficacy.

CONCLUSION

Our large-scale integrative transcriptome analysis provides high-resolution insights into the cellular states and ecosystems of HNSC, facilitating the discovery of novel biomarkers and supporting the development of precision therapies.

Spermine synthase engages in macrophages M2 polarization to sabotage antitumor immunity in hepatocellular carcinoma

Disturbances in tumor cell metabolism reshape the tumor microenvironment (TME) and impair antitumor immunity, but the implicit mechanisms remain elusive. Here, we found that spermine synthase (SMS) was significantly upregulated in tumor cells, which correlated positively with the immunosuppressive microenvironment and predicted poor survival in hepatocellular carcinoma (HCC) patients. Via "subcutaneous" and "orthotopic" HCC syngeneic mouse models and a series of in vitro coculture experiments, we identified elevated SMS levels in HCC cells played a role in immune escape mainly through its metabolic product spermine, which induced M2 polarization of tumor-associated macrophages (TAMs) and subsequently corresponded with a decreased antitumor functionality of CD8+ T cells. Mechanistically, we discovered that spermine reprogrammed TAMs mainly by activating the PI3K-Akt-mTOR-S6K signaling pathway. Spermine inhibition in combination with immune checkpoint blockade effectively diminished tumor burden in vivo. Our results expand the understanding of the critical role of metabolites in regulating cancer progression and antitumor immunity and open new avenues for developing novel therapeutic strategies against HCC.

Hepatic Stellate Cells Functional Heterogeneity in Liver Cancer

Hepatic stellate cells (HSCs) are the liver's pericytes, and play key roles in liver homeostasis, regeneration, fibrosis, and cancer. Upon injury, HSCs activate and are the main origin of myofibroblasts and cancer-associated fibroblasts (CAFs) in liver fibrosis and cancer. Primary liver cancer has a grim prognosis, ranking as the third leading cause of cancer-related deaths worldwide, with hepatocellular carcinoma (HCC) being the predominant type, followed by intrahepatic cholangiocarcinoma (iCCA). Moreover, the liver hosts 35% of all metastatic lesions. The distinct spatial distribution and functional roles of HSCs across these malignancies represent a significant challenge for universal therapeutic strategies, requiring a nuanced and tailored understanding of their contributions. This review examines the heterogeneous roles of HSCs in liver cancer, focusing on their spatial localization, dynamic interactions within the tumor microenvironment (TME), and emerging therapeutic opportunities, including strategies to modulate their activity, and harness their potential as targets for antifibrotic and antitumor interventions.

Galectin-1-Induced Tumor Associated Macrophages Repress Antitumor Immunity in Hepatocellular Carcinoma Through Recruitment of Tregs

Tumor-associated macrophages (TAMs) are commonly considered accomplices in tumorigenesis and tumor development. However, the precise mechanism by which tumor cells prompt TAMs to aid in evading immune surveillance remains to be further investigated. Here, it is elucidated that tumor-secreted galectin-1 (Gal1) conferred immunosuppressive properties to TAMs. Specifically, patient specimens and a public database is first used to analyze the clinical relevance of Gal1 in hepatocellular carcinoma (HCC). Then, it is demonstrated that TAMs functioned as a critical mediator in the Gal1-induced progression of HCC and the establishment of an immunosuppressive tumor microenvironment. Furthermore, RNA-sequencing determined that Gal1 promoted the upregulation of chemokine (C-C motif) ligand 20 (CCL20) in TAMs via activating the PI3K/AKT/NF-κB pathway. Employing an anti-CCL20 neutralizing antibody and Foxp3DTR mice, it is demonstrated that CCR6+Foxp3+ regulatory T cells (Tregs) recruited by Gal1-induced TAMs contributed to reduced infiltration and dysfunctional state of CD8+ T cells, subsequently facilitating tumor progression. Targeting Gal1 dampened the secretion of CCL20 and inhibits the recruitment of Tregs, thereby activating anti-tumor immunity and ameliorating anti-PD-1 resistance. Together, this findings revealed that Gal1-induced TAMs recruited Tregs through the CCL20-CCR6 axis. Inhibition of Gal1 improves the effectiveness of anti-PD1 therapy, shedding important new light on the combination immunotherapy of HCC.

The immune duality of osteopontin and its therapeutic implications for kidney transplantation

Osteopontin (OPN) is a multifunctional glycoprotein with various structural domains that enable it to perform diverse functions in both physiological and pathological states. This review comprehensively examines OPN from multiple perspectives, including its protein structure, interactions with receptors, interactions with immune cells, and roles in kidney diseases and transplantation. This review explores the immunological duality of OPN and its significance and value as a biomarker and therapeutic target in kidney transplantation. In cancer, OPN typically promotes tumor evasion by suppressing the immune system. Conversely, in immune-related kidney diseases, particularly kidney transplantation, OPN activates the immune system by enhancing the migration and activation of immune cells, thereby exacerbating kidney damage. This immunological duality may stem from different OPN splice variants and the exposure, after cleavage, of different structural domains, which play distinct biological roles in cellular interactions. Additionally, OPN has a significant biological impact posttransplantation and on chronic kidney disease and, highlighting its importance as a biomarker and potential therapeutic target. Future research should further explore the specific mechanisms of OPN in kidney transplantation to improve treatment strategies and enhance patient quality of life.

Bibliometric analysis: a study of the microenvironment in cervical cancer (2000-2024)

Objective

The incidence of cervical cancer has increased in recent years. The tumor microenvironment (TME) is the local biological environment involved in tumor occurrence and development. This study aimed to conduct a comprehensive analysis of the global research on the TME in cervical cancer (CC), providing a knowledge framework in this field from a holistic and systematic perspective based on a bibliometric analysis.

Methods

Studies focusing on the TME in cervical cancer were searched using the Web of Science Core Collection database. The annual output, cooperation, hotspots, research status, and development trends in this field were analyzed using bibliometric softwares (VOSviewer and CiteSpace).

Results

A total of 1,057 articles published between 2000 and 2024 were selected. The number of publications and citations has recently increased. Cooperation network analysis indicated that China holds the foremost position in research on the TME in cervical cancer with the highest volume of publications, thus exerting the greatest influence. Fudan University had the highest output. Frontiers in Oncology showed the highest degree of productivity in this field. Rofstad, Einar K. made the most article contributions and was the most co-cited author. Four clusters were obtained after a cluster analysis of the keywords: TME, cervical cancer, immunotherapy, and prognosis. Immunotherapy, human papillomavirus, and biomarkers were relatively recent keywords that attracted increasing attention from researchers.

Discussion

This bibliometric analysis provides a data-based and objective introduction to the TME of cervical cancer, and offers readers a valuable reference for future research.

Conclusions

Comprehensive research in this field was mainly distributed in the TME of cervical cancer through the analysis of keywords and documents. Sufficient evidence supports mechanism research and application exploration. Further research should explore new topics related to the TME of cervical cancer.

Sophisticated roles of tumor microenvironment in resistance to immune checkpoint blockade therapy in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains a serious threat to global health, with rising incidence and mortality rates. Therapeutic options for advanced HCC are quite limited, and the overall prognosis remains poor. Recent advancements in immunotherapy, particularly immune-checkpoint blockade (ICB) targeting anti-PD1/PD-L1 and anti-CTLA4, have facilitated a paradigm shift in cancer treatment, demonstrating substantial survival benefits across various cancer types, including HCC. However, only a subset of HCC patients exhibit a favorable response to ICB therapy, and its efficacy is often hindered by the development of resistance. There are many studies to explore the underlying mechanisms of ICB response. In this review, we compiled the latest progression in immunotherapies for HCC and systematically summarized the sophisticated mechanisms by which components of the tumor microenvironment (TME) regulate resistance to ICB therapy. Additionally, we also outlined some scientific rationale strategies to boost antitumor immunity and enhance the efficacy of ICB in HCC. These insights may serve as a roadmap for future research and help improve outcomes for HCC patients.

Single-cell multi-omics analysis identifies SPP1+ macrophages as key drivers of ferroptosis-mediated fibrosis in ligamentum flavum hypertrophy

BACKGROUND

Ligamentum flavum hypertrophy (LFH) is a primary contributor to lumbar spinal stenosis. However, a thorough understanding of the cellular and molecular mechanisms driving LFH fibrotic progression remains incomplete.

METHODS

Single-cell RNA sequencing (scRNA-seq) was performed to construct the single-cell map of human ligamentum flavum (LF) samples. An integrated multi-omics approach, encompassing scRNA-seq, bulk RNA sequencing (bulk RNA-seq), and Mendelian randomization (MR), was applied to conduct comprehensive functional analysis. Clinical tissue specimens and animal models were employed to further confirm the multi-omics findings.

RESULTS

ScRNA-seq provided a single-cell level view of the fibrotic microenvironment in LF, revealing significantly increased proportions of fibroblasts, myofibroblasts, and macrophages in LFH. Using transmission electron microscopy, single-cell gene set scoring, and MR analysis, ferroptosis was identified as a critical risk factor and pathway within LFH. Subcluster analysis of fibroblasts revealed functional heterogeneity among distinct subpopulations, highlighting the functional characteristics and the metabolic dynamics of fibroblast with a high ferroptosis score (High Ferro-score FB). The quantification of gene expression at single-cell level revealed that ferroptosis increased along with fibrosis in LFH specimens, a finding further validated in both human and mice tissue sections. Consistently, bulk RNA-seq confirmed increased proportions of fibroblasts and macrophages in LFH specimens, underscoring a strong correlation between these cell types through Spearman correlation analysis. Notably, subcluster analysis of the mononuclear phagocytes identified a specific subset of SPP1+ macrophages (SPP1+ Mac) enriched in LFH, which exhibited activation of fibrosis and ferroptosis-related metabolic pathways. Cell-cell communication analysis highlighted that SPP1+ Mac exhibited the strongest outgoing and incoming interactions among mononuclear phagocytes in the LFH microenvironment. Ligand-receptor analysis further revealed that the SPP1-CD44 axis could serve as a key mediator regulating the activity of High Ferro-score FB. Multiplex immunofluorescence confirmed substantial Collagen I deposition and reduced Ferritin Light Chain expression in regions with SPP1-CD44 co-localization in LFH specimens.

CONCLUSIONS

Our findings indicated that SPP1+ Mac may contribute to LFH fibrosis by regulating ferroptosis in High Ferro-score FB through the SPP1-CD44 axis. This study enhances our understanding of the cellular and molecular mechanisms underlying LFH progression, potentially improving early diagnostic strategies and identifying new therapeutic targets.

Targeted delivery of CCL3 reprograms macrophage antigen presentation and enhances the efficacy of immune checkpoint blockade therapy in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related deaths worldwide, especially in advanced stages where limited treatment options result in poor prognosis. The immunosuppressive tumor immune microenvironment (TIME), characterized by low immune cell infiltration and exhaustion, limits immunotherapy efficacy. To address this, our study investigates the role of C-C motif chemokine ligand 3 (CCL3) in modulating the HCC TIME.

METHODS

We analyzed CCL3 expression in human HCC samples from The Cancer Genome Atlas database, focusing on its correlation with inflammatory gene signatures and immune cell infiltration. High-dimensional single-cell RNA sequencing (scRNA-seq), flow cytometry, and multiplex immunofluorescence were used to investigate CCL3's effects on macrophage function and T cell activation. The biological impact of CCL3 on macrophages was assessed using co-culture systems, confocal imaging, metabolite detection, and inhibition assays. Preclinical HCC models and ex vivo tumor fragment assays further explored how CCL3 modulates immune responses and enhances immune checkpoint blockade efficacy.

RESULTS

Our study shows that CCL3 is suppressed in the tumor microenvironment and positively correlates with immune infiltration and inflammatory responses. Targeted liver delivery of rAAV-Ccl3 reprograms the immune microenvironment in HCC, promoting immune cell recruitment and tertiary lymphoid structure formation, thus suppressing tumor growth via immune engagement. Through scRNA-seq, flow cytometry, and multiplex immunofluorescence, we found that CCL3 enhances macrophage antigen uptake and activates cytotoxic T cells. In vivo and in vitro experiments confirmed that CCL3 facilitates T cell infiltration and upregulates MHC II expression on macrophages, enhancing antigen presentation. The CCL3-CCR5 pathway also boosts macrophage metabolism, increasing lysosomal activity and antigen uptake, thereby strengthening adaptive immune responses and increasing sensitivity to immune checkpoint blockade therapies in preclinical models.

CONCLUSIONS

This study highlights the pivotal role of CCL3 in reshaping the TIME and enhancing antitumor immunity in HCC. By promoting immune cell recruitment and enhancing antigen presentation, CCL3 demonstrates significant potential to improve the efficacy of immunotherapy, particularly in combination with immune checkpoint inhibitors. Targeting CCL3 may help to overcome the immunosuppressive TIME in HCC and improve patient outcomes.

Comprehensive multi-omics analyses expose a precision therapy strategy that targets replication stress in hepatocellular carcinoma using WEE1 inhibition

INTRODUCTION

Hepatocellular carcinoma (HCC) is an extremely heterogeneous malignancy with a poor prognosis, highlighting the need to target specific vulnerabilities within the tumor during treatment.

OBJECTIVES

This study employs multi-omics analysis techniques to provide novel insights into personalized therapeutic strategies for HCC patients.

METHODS

We performed proteomic and transcriptomic sequencing on 178 and 94 clinical samples of primary HCC without prior treatment, respectively. We employed an unbiased Kinome CRISPR-Cas9 library screening approach to systematically evaluate and identify novel therapeutic strategies that specifically target replication stress (RS). The synergy between oxaliplatin and adavosertib was verified using in vitro and in vivo models, including hydrodynamic injection, patient-derived organoids, and patient-derived xenografts.

RESULTS

In both proteomic- and transcriptomic-based subtyping analyses, subtypes characterized by hyperproliferative features demonstrated the poorest prognosis and the highest levels of RS. Among all first-line chemotherapeutic agents in these analyses, oxaliplatin accumulated the highest RS levels in HCC, while resistance remained a major challenge. With unbiased Kinome CRISPR loss-of-function gene screening, WEE1 was identified as a synthetic lethal target of oxaliplatin. The synergy between the WEE1 inhibitor adavosertib and oxaliplatin has been demonstrated in multiple in vitro and in vivo models. Mechanistically, adavosertib inhibits oxaliplatin-induced homologous recombination repair and G2/M checkpoint activation, leading to the accumulation of lethal DNA damage. Furthermore, patients with HCC showing high RS levels had poor prognoses and responded well to adavosertib and oxaliplatin combination treatments. This was validated by preclinical models and unsupervised clustering analysis.

CONCLUSIONS

Our findings provide promising insights into the precise therapeutic targeting of RS in HCC at both the proteomic and transcriptomic levels. Furthermore, our study highlights the potential of combining oxaliplatin with adavosertib as a treatment approach for HCC. In this study, we analyzed 178 and 94 pairs of clinical HCC samples using proteomic and transcriptomic sequencing, respectively. We discovered that the subtype characterized by high proliferation had the worst prognosis and highest RS level. Drug screening revealed that oxaliplatin promotes RS accumulation in HCC, but its resistance remains a challenge. Through unbiased CRISPR deletion-gene screening, WEE1 was identified as a lethal target of oxaliplatin. The WEE1 inhibitor adavosertib inhibits oxaliplatin-induced DNA repair, leading to lethal DNA damage accumulation. Furthermore, our clustering analysis based on RS levels demonstrated that HCC patients with high RS levels have poorer prognoses and be more beneficial from adavosertib and oxaliplatin combination therapy. These findings support an individualized treatment approach for HCC targeting RS based on WEE1 Inhibition.

Integration of single-cell and spatial transcriptomics reveals fibroblast subtypes in hepatocellular carcinoma: spatial distribution, differentiation trajectories, and therapeutic potential

BACKGROUND

Cancer-associated fibroblasts (CAFs) are key components of the hepatocellular carcinoma (HCC) tumor microenvironment (TME). regulating tumor proliferation, metastasis, therapy resistance, immune evasion via diverse mechanisms. A deeper understanding of the l diversity of CAFs is essential for predicting patient prognosis and guiding treatment strategies.

METHODS

We examined the diversity of CAFs in HCC by integrating single-cell, bulk, and spatial transcriptome analyses.

RESULTS

Using a training cohort of 88 HCC single-cell RNA sequencing (scRNA-seq) samples and a validation cohort of 94 samples, encompassing over 1.2 million cells, we classified three fibroblast subpopulations in HCC: HLA-DRB1 + CAF, MMP11 + CAF, and VEGFA + CAF based on highly expressed genes of which, which are primarily located in normal tissue, tumor boundaries, and tumor interiors, respectively. Cell trajectory analysis revealed that VEGFA + CAFs are at the terminal stage of differentiation, which, notably, is tumor-specific. VEGFA + CAFs were significantly associated with patient survival, and the hypoxic microenvironment was found to be a major factor inducing VEGFA + CAFs. Through cellular communication with capillary endothelial cells (CapECs), VEGFA + CAFs promoted intra-tumoral angiogenesis, facilitating tumor progression and metastasis. Additionally, a machine learning model developed using high-expression genes from VEGFA + CAFs demonstrated high accuracy in predicting prognosis and sorafenib response in HCC patients.

CONCLUSIONS

We characterized three fibroblast subpopulations in HCC and revealed their distinct spatial distributions within the tumor. VEGFA + CAFs, which was induced by hypoxic TME, were associated with poorer prognosis, as they promote tumor angiogenesis through cellular communication with CapECs. Our findings provide novel insights and pave the way for individualized therapy in HCC patients.

G2M-checkpoint related immune barrier structure and signature for prognosis and immunotherapy response in hepatocellular carcinoma: insights from spatial transcriptome and machine learning

BACKGROUND

Hepatocellular carcinoma (HCC) treatment remains challenging, particularly for immune checkpoint inhibitors (ICIs) non-response patients. Spatial transcriptome (ST) data and machine learning algorithms offer new insights into understanding HCC heterogeneity and ICIs resistance mechanisms.

METHODS

Utilizing ST data from HCC patients on ICIs treatment, we analyzed pathway activity and immune infiltration. We combined 167 machine learning models to develop a G2M-checkpoint related signature (G2MRS) based on differential gene expression. The four cohorts and in-house cohort was used to validate G2MRS, and KPNA2's role was further examined through in vitro experiments in two different liver cancer cell lines.

RESULTS

Our analysis revealed a distinct suppressive immune barrier structure (SIBS) in ICIs non-response patients, associated with upregulated G2M-checkpoint levels. G2MRS, consisting of KPNA2, CENPA, and UCK2, accurately predicted HCC prognosis and ICIs response. Further in vitro experiments demonstrated KPNA2's role in regulating migration, proliferation, and apoptosis in liver cancer.

CONCLUSIONS

This study highlights the importance of spatial heterogeneity and machine learning in refining HCC prognosis and ICIs response prediction. G2MRS and KPNA2 emerge as promising biomarkers for personalized HCC management.

Big lessons from the little Akkermansia muciniphila in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most frequently occurring type of liver tumor and is considered one of the most common primary malignant neoplasms. The prognosis for HCC is dismal because of its complicated etiology and high level of medication resistance. Immunotherapy is presently regarded as one of the most effective therapeutic options for HCC; nevertheless, because of the disturbance of intestinal flora, immunotherapy shows low antitumor efficacy. An increasing body of research indicates that intestinal flora, particularly Akkermansia muciniphila (A. muciniphila), is vital for the treatment of tumors. Studies have demonstrated that the diminished effectiveness of immunotherapy in cancer patients is associated with a reduction in A. muciniphila levels, suggesting that increasing A. muciniphila levels significantly enhance the efficacy of immunotherapy. A. muciniphila functions as a gut probiotic and can treat and prevent a wide range of illnesses, including cancer. Consequently, preserving A. muciniphila abundance is enough to prevent and lower the danger of developing cancer disorders. In this review, we critically evaluate the current body of research on A. muciniphila, with a primary focus on its biological properties and functions. The different illnesses that A. muciniphila treats were then discussed, particularly the way it works with liver cancer. This review aims to give a novel treatment plan for patients with HCC as well as a theoretical foundation for improving HCC immunotherapy.

Interactions between the metabolic reprogramming of liver cancer and tumor microenvironment

Metabolic reprogramming is one of the major biological features of malignant tumors, playing a crucial role in the initiation and progression of cancer. The tumor microenvironment consists of various non-cancer cells, such as hepatic stellate cells, cancer-associated fibroblasts (CAFs), immune cells, as well as extracellular matrix and soluble substances. In liver cancer, metabolic reprogramming not only affects its own growth and survival but also interacts with other non-cancer cells by influencing the expression and release of metabolites and cytokines (such as lactate, PGE2, arginine). This interaction leads to acidification of the microenvironment and restricts the uptake of nutrients by other non-cancer cells, resulting in metabolic competition and symbiosis. At the same time, metabolic reprogramming in neighboring cells during proliferation and differentiation processes also impacts tumor immunity. This article provides a comprehensive overview of the metabolic crosstalk between liver cancer cells and their tumor microenvironment, deepening our understanding of relevant findings and pathways. This contributes to further understanding the regulation of cancer development and immune evasion mechanisms while providing assistance in advancing personalized therapies targeting metabolic pathways for anti-cancer treatment.

Molecular landscape of tumor-associated tissue-resident memory T cells in tumor microenvironment of hepatocellular carcinoma

BACKGROUND

Immunotherapy for liver cancer is used to rejuvenate tumor-infiltrating lymphocytes by modulating the immune microenvironment. Thus, early protective functions of T cell subtypes with tissue-specific residency have been studied in the tumor microenvironment (TME). We identified tumor-associated tissue-resident memory T (TA-TRM) cells in hepatocellular carcinoma (HCC) and characterized their molecular signatures.

METHODS

We obtained single-cell RNA and single-cell TCR sequencing data from five patients with HCC. The heterogeneous characteristics of TRM cell subsets within the TME were then investigated and validated. Risk scores were calculated for survival analysis using significant core marker genes based on data from The Cancer Genome Atlas and the International Cancer Genome Consortium. The signaling pathways, trajectories, and clonal diversity of TA-TRM cells were investigated.

RESULTS

We characterized two TRM clusters (CD69+ and CD103+) that expressed unique signature genes and validated their similar molecular patterns in an independent dataset. Risk scores based on core gene expression in TA-TRM cells were associated with survival in both datasets. Trajectory analysis revealed that the two lineages followed different trajectory paths with distinct marker gene expression across pseudo-time. CD103+ TA-TRM cells showed diverse clonotypes and shared clonotypes with other cell groups. Lower clonal diversity and distinct signaling interactions were observed in the recurrent than in the non-recurrent samples. The CXCL13-CXCR3 interaction between CD103+ TA-TRM and regulatory T cells was observed only in the recurrent samples.

CONCLUSIONS

We identified two subtypes of TA-TRM cells in HCC and demonstrated their unique molecular signatures, relevance to survival, and distinct signaling networks according to recurrence. The study findings provide a better understanding of the molecular characteristics of TA-TRM cells in HCC and potential immunotherapeutic strategies.

Single-cell landscape of dynamic changes in CD8+ T cells, CD4+ T cells and exhausted T cells in hepatocellular carcinoma

Hepatocellular carcinoma has a high incidence and poor prognosis. In this study, we investigated the value of T-cell-related genes in prognosis by single-cell sequencing data in hepatocellular carcinoma. Twelve cases of hepatocellular carcinoma single-cell sequencing were included in the study. The high dimensional weighted gene co-expression network analysis (hdWGCNA) was used to identify gene modules associated with CD4+ T cells, CD8+ T cells and exhausted T cells. Altered signaling pathway activity in exhausted T cells was uncovered by the AUCell algorithm. xCELL, TIMER, QUANTISEQ, CIBERSORT and CIBERSORT-abs were performed to explore immune cell infiltration. Immune checkpoint inhibitor genes and TIDE methods were used to predict immunotherapy response. Finally, immunohistochemistry and real-time PCR were used to verify gene expression. The hdWGCNA algorithm identified 40 genes strongly associated with CD4+ T cells, CD8+ T cells and exhausted T cells. Seven genes were finally selected for transcriptome data modeling. The results of the three independent datasets suggested that the model had strong prognostic value. Model genes were critical factors influencing CD4+ T cell and CD8+ T cell infiltration in patients. The efficacy of PD-1 immunotherapy was higher in patients belonging to the low-risk group. Alterations in signaling pathways' activity within exhausted T cells were crucial factors contributing to the decline in immune function. Differential expression of seven genes in CD8+ T cells, CD4+ T cells and exhausted T cells were key targets for improving immunotherapy response in HCC.

Comprehensive analysis reveals the tumor suppressor role of macrophage signature gene FCER1G in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) progression is closely linked to the role of macrophages. This study utilized single-cell RNA sequencing and genomic analysis to explore the characteristic genes of macrophages in HCC and their impact on patient prognosis. We obtained single-cell se-quencing data from seven HCC samples in the GEO database. Through principal component analysis and t-SNE dimensionality reduction, we identified 2,000 highly variable genes and per-formed clustering and annotation of 17 cell clusters, revealing 482 macrophage-related feature genes. A LASSO regression model based on these genes was developed to predict the prognosis of HCC patients, with validation in the TCGA-LIHC cohort demonstrating model accuracy (AUC = 0.78, 0.72, 0.71 for 1-, 3-, and 5-year survival rates, respectively). Additionally, patients in the high-risk group exhibited elevated tumor stemness scores, although no significant differences were observed in microsatellite instability (MSI) and tumor mutational burden (TMB) scores. Immune-related analyses revealed that FCER1G expression was downregulated in HCC and was associated with key pathways such as apoptosis and ferroptosis. Reduced FCER1G expression significantly affected HCC cell proliferation and migration. Our prognostic model provides new insights into precision and immunotherapy for HCC and holds significant implications for future clinical applications.

Spatial‒temporal heterogeneities of liver cancer and the discovery of the invasive zone

Solid tumours are intricate and highly heterogeneous ecosystems, which grow in and invade normal organs. Their progression is mediated by cancer cells' interaction with different cell types, such as immune cells, stromal cells and endothelial cells, and with the extracellular matrix. Owing to its high incidence, aggressive growth and resistance to local and systemic treatments, liver cancer has particularly high mortality rates worldwide. In recent decades, spatial heterogeneity has garnered significant attention as an unfavourable biological characteristic of the tumour microenvironment, prompting extensive research into its role in liver tumour development. Advances in spatial omics have facilitated the detailed spatial analysis of cell types, states and cell‒cell interactions, allowing a thorough understanding of the spatial and temporal heterogeneities of tumour microenvironment and informing the development of novel therapeutic approaches. This review illustrates the latest discovery of the invasive zone, and systematically introduced specific macroscopic spatial heterogeneities, pathological spatial heterogeneities and tumour microenvironment heterogeneities of liver cancer.

Functionalized biomimetic nanoparticles loaded with salvianolic acid B for synergistic targeted triple-negative breast cancer treatment

The therapeutic effect of immune checkpoint inhibitors (ICIs) in triple-negative breast cancer (TNBC) is unsatisfactory. The immune "cold" microenvironment caused by tumor-associated fibroblasts (TAFs) has an adverse effect on the antitumor response. Therefore, in this study, mixed cell membrane-coated porous magnetic nanoparticles (PMNPs) were constructed to deliver salvianolic acid B (SAB) to induce an antitumor immune response, facilitating the transition from a "cold" to a "hot" tumor and ultimately enhancing the therapeutic efficacy of immune checkpoint inhibitors. PMNP-SAB, which is based on a mixed coating of red blood cell membrane and TAF membrane (named PMNP-SAB@RTM), can simultaneously achieve the dual effects of "immune escape" and "homologous targeting". Under the influence of an external magnetic field (MF), SAB can be targeted and concentrated at the tumor site. The SAB released in tumors can effectively inhibit the production of extracellular matrix (ECM) by TAFs, promote T-cell infiltration, and induce antitumor immune responses. Ultimately, the combination of PMNP-SAB@RTM and BMS-1 (PD-1/PD-L1 inhibitor 1) effectively inhibited tumor growth. Finally, this study presents a precise and effective new strategy for TNBC immunotherapy on the basis of the differentiation of "cold" and "hot" microenvironments.

Single-Nucleus and Spatial Transcriptome Profiling Delineates the Multicellular Ecosystem in Hepatocellular Carcinoma After Hepatic Arterial Infusion Chemotherapy

Hepatic arterial infusion chemotherapy (HAIC) has emerged as a promising treatment strategy for hepatocellular carcinoma (HCC), but a detailed understanding of the multicellular ecosystem after HAIC treatment is lacking. Here, we collected tumor samples from treatment-naïve primary and post-HAIC HCC, and integrated single-nucleus RNA sequencing with spatial transcriptomics to characterize the tumor ecosystem in the post-HAIC HCC. Increased fractions and enhanced cellular communication of CD4+ T, CD20+ B, and dendritic cell subtypes were identified in post-HAIC tumors. Moreover, it is substantiated that HAIC promoted tertiary lymphoid structures (TLS) formation, and addressed the roles of TLSs as spatial niches of cellular communication. Specifically, intermediate exhausted CD8+ T cells expressing Granzyme-K and PD-1 (PD-1+CD8+ Tex-int) expanded following HAIC and exhibited a functionally antitumor phenotype. PD-1+CD8+ Tex-int accumulated in the TLS vicinity and disseminated throughout the tumor microenvironment, demonstrating potential as an effective biomarker for HAIC-based treatment in HCC. This study provides valuable resources and biological insights in the cellular underpinnings of HAIC treatment.

Habitat radiomics based on CT images to predict survival and immune status in hepatocellular carcinoma, a multi-cohort validation study

BACKGROUND AND OBJECTIVE

Though several clinicopathological features are identified as prognostic indicators, potentially prognostic radiomic models are expected to preoperatively and noninvasively predict survival for HCC. Traditional radiomic models are lacking in a consideration for intratumoral regional heterogeneity. The study aimed to establish and validate the predictive power of multiple habitat radiomic models in predicting prognosis of hepatocellular carcinoma (HCC).

METHODS

A total of 232 HCC patients were retrospectively included, including a training/validation cohort and two external testing cohorts from 4 centers. For habitat radiomics, intratumoral habitat partitioning based on CT images was first performed by using Otsu thresholding method. Second, a total of 350 habitat radiomic models were constructed to select the optimal model. Then, both ROC curve analyses and Kaplan-Meier survival curve analyses were applied to assess the predictive performances. Ultimately, an immune status profiling was conducted based on bioinformatic analyses and multiplex immunohistochemistry (mIHC) assays to reveal the potential mechanisms.

RESULTS

A total of 4 habitats were segmented, and the corresponding habitat radiomic models were constructed based on each habitat and an integration of all the four habitats. Generally, habitat radiomic models outperformed traditional radiomic models in stratifying prognosis for HCC. The habitat radiomic model based on the segmented habitat 4 involving decision tree (DT) screening and random forest (RF) classifier was identified as the optimal model with an AUCmean of 0.806. Distinct resting natural killer (NK) cell infiltrations significantly contributed to the prognosis stratification of HCC by the optimal habitat radiomic model.

CONCLUSIONS

The habitat radiomic model based on CT images was potentially predictive of overall survival for HCC, with a superiority over the traditional radiomic model. The prognostic power of the habitat radiomic model was partly attributed to the distinct immune status captured in the CT images.

Advancements in immunotherapy for hepatocellular carcinoma

INTRODUCTION

The advent of immune-based combinations, primarily leveraging immune checkpoint inhibitors, has revolutionized the therapeutic landscape of hepatocellular carcinoma (HCC). The current scenario features multiple therapies that have shown superiority over tyrosine kinase inhibitors; however, the absence of direct comparisons and validated prognostic biomarkers complicates therapeutic decision-making. Additionally, a significant proportion of patients still exhibit primary or secondary resistance to existing immunotherapies, underscoring the ongoing need for novel therapeutic strategies.

AREAS COVERED

This narrative review discusses current strategies aimed at improving the efficacy of immunotherapy for HCC, focusing on the following aspects: available therapeutic options, identification of prognostic biomarkers, approaches to overcoming resistance (including the development of neoantigen vaccines), and the exploration of adjuvant and neoadjuvant strategies.

EXPERT OPINION

The future of systemic therapies for HCC is likely to be driven by advancements in immunotherapy. Key areas of exploration for the coming years include the discovery of novel checkpoint inhibitors or complementary agents to enhance tumor response when combined with existing treatments, a shift toward neoadjuvant/perioperative trials instead of traditional adjuvant approaches, and the development of personalized neoantigen vaccines.

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://lifeome.net/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a novel machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of "variant" cellular states analogy to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the "deviated" states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte "intermediate" states significantly indicate poor prognosis. Besides, we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues.

Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma

Dissecting the spatial heterogeneity of cancer-associated fibroblasts (CAFs) is vital for understanding tumor biology and therapeutic design. By combining pathological image analysis with spatial proteomics, we revealed two stromal archetypes in hepatocellular carcinoma (HCC) with different biological functions and extracellular matrix compositions. Using paired single-cell RNA and epigenomic sequencing with Stereo-seq, we revealed two fibroblast subsets CAF-FAP and CAF-C7, whose spatial enrichment strongly correlated with the two stromal archetypes and opposing patient prognosis. We discovered two functional units, one is the intratumor inflammatory hub featured by CAF-FAP plus CD8_PDCD1 proximity and the other is the marginal wound-healing hub with CAF-C7 plus Macrophage_SPP1 co-localization. Inhibiting CAF-FAP combined with anti-PD-1 in orthotopic HCC models led to improved tumor regression than either monotherapy. Collectively, our findings suggest stroma-targeted strategies for HCC based on defined stromal archetypes, raising the concept that CAFs change their transcriptional program and intercellular crosstalk according to the spatial context.

Phenotypic plasticity and increased infiltration of peripheral blood-derived TREM1+ mono-macrophages following radiotherapy in rectal cancer

In our previously reported phase 2 and phase 3 studies, the combination of short-course radiotherapy and neoadjuvant immunochemotherapy (SIC) is established as effective cancer therapies for locally advanced rectal cancer (LARC). Here, we apply multi-omic analyses to paired pre- and post-treatment LARC specimens undergoing SIC. The peripheral blood-derived TREM1+ mono-macrophage subsets that display a pro-inflammatory phenotype are identified and correlate with complete response to SIC. Mechanically, ionizing radiation (IR) induces peripheral TREM1+ mono-macrophage expansion in tumors. Following IR, the loss of TREM1 in mono-macrophages undermines antitumor immunity by altering mono-macrophage differentiation and inhibiting CD8+ T cell infiltration and activation. The TREM1+ mono-macrophage response may rely on activation of key inflammatory pathways, including nuclear factor κB (NF-κB) signaling and Toll-like receptor pathway. Pharmacological inhibition of TREM1 signaling abolishes IR-induced immunoactivation and reduces combined IR and/or anti-PD-1 treatment. Thus, we establish a crucial role of a mono-macrophage state in mediating effective cancer therapy.

Deciphering SPP1-related macrophage signaling in the pathogenesis of intervertebral disc degeneration

This study delved into the molecular mechanisms underlying mechanical stress-induced intervertebral disc degeneration (msi-IDD) through single-cell and high-throughput transcriptome sequencing in mouse models and patient samples. Results exhibited an upsurge in macrophage presence in msi-IDD intervertebral disc (IVD) tissues, with secreted phosphoprotein 1 (SPP1) identified as a pivotal driver exacerbating degeneration via the protein kinase RNA-like endoplasmic reticulum kinase/ activating transcription factor 4/ interleukin-10 (PERK/ATF4/IL-10) signaling axis. Inhibition of SPP1 demonstrated promising outcomes in mitigating msi-IDD progression in both in vitro and in vivo models. These findings underscore the therapeutic promise associated with the modulation of the PERK signaling pathway in IDD, shedding light on the pathogenesis of msi-IDD and proposing a promising avenue for intervention strategies.

Unraveling the potential mechanism and prognostic value of pentose phosphate pathway in hepatocellular carcinoma: a comprehensive analysis integrating bulk transcriptomics and single-cell sequencing data

Hepatocellular carcinoma (HCC) remains a malignant and life-threatening tumor with an extremely poor prognosis, posing a significant global health challenge. Despite the continuous emergence of novel therapeutic agents, patients exhibit substantial heterogeneity in their responses to anti-tumor drugs and overall prognosis. The pentose phosphate pathway (PPP) is highly activated in various tumor cells and plays a pivotal role in tumor metabolic reprogramming. This study aimed to construct a model based on PPP-related Genes for risk assessment and prognosis prediction in HCC patients. We integrated RNA-seq and microarray data from TCGA, GEO, and ICGC databases, along with single-cell RNA sequencing (scRNA-seq) data obtained from HCC patients via GEO. Based on the "Seurat" R package, we identified distinct gene clusters related to the PPP within the scRNA-seq data. Using a penalized Cox regression model with least absolute shrinkage and selection operator (LASSO) penalties, we constructed a risk prognosis model. The validity of our risk prognosis model was further confirmed in external cohorts. Additionally, we developed a nomogram capable of accurately predicting overall survival in HCC patients. Furthermore, we explored the predictive potential of our risk model within the immune microenvironment and assessed its relevance to biological function, particularly in the context of immunotherapy. Subsequently, we performed in vitro functional validation of the key genes (ATAD2 and SPP1) in our model. A ten-gene signature associated with the PPP was formulated to enhance the prediction of HCC prognosis and anti-tumor treatment response. Following this, the ROC curve, nomogram, and calibration curve outcomes corroborated the model's robust clinical predictive capability. Functional enrichment analysis unveiled the engagement of the immune system and notable variances in the immune infiltration landscape across the high and low-risk groups. Additionally, tumor mutation frequencies were observed to be elevated in the high-risk group. Based on our analyses, the IC50 values of most identified anticancer agents demonstrated a correlation with the RiskScore. Additionally, the high-risk and low-risk groups exhibited differential sensitivity to various drugs. Cytological experiments revealed that silencing ATAD2 or SPP1 suppresses malignant phenotypes, including viability and migration, in liver cancer cells. In this study, a novel gene signature related to the PPP was developed, demonstrating favorable predictive performance. This signature holds significant guiding value for assessing the prognosis of HCC patients and directing individualized treatment strategies.

The role of histone lactylation genes in hepatocellular carcinoma prognostic models and their immune cell infiltration features: a comprehensive analysis of single-cell, spatial transcriptome, Mendelian randomization and experiment

INTRODUCTION

With the increasing impact of hepatocellular carcinoma (HCC) on society, there is an urgent need to propose new HCC diagnostic biomarkers and identification models. Histone lysine lactylation (Kla) affects the prognosis of cancer patients and is an emerging target in cancer treatment. However, the potential of Kla-related genes in HCC is poorly understood.

METHODS

A variety of machine learning methods were used to construct and validate a model of differentially expressed Kla genes with comprehensive evaluations included ROC, Kaplan‒Meier curve, Cox regression, decision curve. Immune infiltration gathered with spatial transcriptome was performed using integrated data from multiple databases. Furthermore, single-cell analysis was used to discover the cell-cell communication and Mendelian randomization was used to study the causal relationships between immune cell and HCC. Lastly, qRT-PCR was used to verify the expression of Kla genes.

RESULTS

We established a model consisting of 12 genes that had well prognostic performance and were identified as independent prognostic factors. Single-cell analysis showed that CD8 T+ cells and conventional dendritic cells were enriched in HCC patients. Spatial transcriptomics analysis indicated that the Kla genes influenced the immune characteristics of HCC. Mendelian randomization results showed that TBNK and monocytes were the main risk factors. qRT-PCR validation results indicated that the expression of multiple genes in Huh7 cells was significantly higher than in LO2 cells.

CONCLUSION

Overall, a Kla-related model was established, which may provide new strategies and insights for the treatment and diagnosis of HCC.

A KIF20A-based thermosensitive hydrogel vaccine effectively potentiates immune checkpoint blockade therapy for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a highly prevalent malignancy with limited treatment efficacy despite advances in immune checkpoint blockade (ICB) therapy. The inherently weak immune responses in HCC necessitate novel strategies to improve anti-tumor immunity and synergize with ICB therapy. Kinesin family member 20A (KIF20A) is a tumor-associated antigen (TAA) overexpressed in HCC, and it could be a promising target for vaccine development. This study confirmed KIF20A as a promising immunogenic antigen through transcriptomic mRNA sequencing analysis in the context of HCC. Therefore, we developed a thermosensitive hydrogel vaccine formulation (K/RLip@Gel) to optimize antigen delivery while enabling sustained in vivo release. The vaccine efficiently elicited robust immune responses by activating DCs and T cells. Moreover, K/RLip@Gel improved the therapeutic efficacy of PD-L1 blockade in subcutaneous and orthotopic cell-derived xenograft (CDX) models, along with immune-humanized patient-derived xenograft (PDX) HCC models, which was evidenced by improved maturation of DCs and elevated infiltration and activation of CD8+ T cells. These findings highlight the potential of KIF20A-based vaccines to synergistically improve ICB therapy outcomes in HCC, providing a promising approach for enhancing anti-tumor immunity and improving clinical outcomes.

Long non-coding RNA MSC-AS1 confers imatinib resistance of gastrointestinal stromal tumor cells by activating FNDC1 and ANLN-mediated PI3K/AKT pathway

Imatinib resistance is a major obstacle to the successful treatment of gastrointestinal stromal tumors (GIST). Long non-coding RNAs (LncRNAs) have been identified as important regulatory factors in chemotherapy resistance. This study aimed to identify key lncRNAs involved in imatinib resistance of GISTs. First, MSC-AS1 was found to be upregulated in imatinib-resistant GIST tissues and imatinib-resistant GIST cells. Cellular experiments demonstrated that MSC-AS1 overexpression decreased imatinib sensitivity of GIST cells, evidenced by increased cell survival, colony formation, migration, and invasion. Moreover, suppression of MSC-AS1 improved the imatinib resistance of imatinib-resistant GIST cells. Furthermore, MSC-AS1 upregulated the expression of FNDC1 and Anillin via sponging miR-200b-3p, activated the phosphatidylinositol-3-kinase-AKT signaling pathway, and thereby driving imatinib resistance in vitro and in vivo. Overall, this study elucidates the crucial role and mechanism of MSC-AS1 in the imatinib resistance of GIST, providing the potential therapeutic strategy for overcoming the imatinib resistance of GIST.

Roles of Cellular Neighborhoods in Hepatocellular Carcinoma Pathogenesis

The development of hepatocellular carcinoma (HCC) involves an intricate interplay among various cell types within the liver. Unraveling the orchestration of these cells, particularly in the context of various etiologies, may hold the key to deciphering the underlying mechanisms of this complex disease. The advancement of single-cell and spatial technologies has revolutionized our ability to determine cellular neighborhoods and understand their crucial roles in disease pathogenesis. In this review, we highlight the current research landscape on cellular neighborhoods in chronic liver disease and HCC, as well as the emerging computational approaches applicable to delineate disease-associated cellular neighborhoods, which may offer insights into the molecular mechanisms underlying HCC pathogenesis and pave the way for effective disease interventions.

HK3: A potential prognostic biomarker with metastasis inhibition capabilities in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) stands as one of the prevalent malignant tumors worldwide. The effectiveness of immunotherapy frequently depends on the intricate dynamics of immunomodulation within the tumor microenvironment (TME). The current study aims to identify prognostically relevant genes and their functional roles in HCC. This is achieved by utilizing immune scores and mutations as the basis, through the application of bioinformatics and molecular biological analysis.

METHODS

Differentially expressed genes (DEGs) analysis was conducted using the "clusterProfiler" package for functional enrichment. Cox regression analysis and LASSO regression analysis were performed for prognostic gene screening. Kaplan-Meier curve were further utilized to verify the prognostic value of these genes. The relationship between selected genes and immune cells was analyzed using ssGSEA algorithm and TIMER. The HK3 expression in HCC cells was tested by Western blot. Additionally, wound healing and transwell assays were utilized to detect the impact of HK3 on HCC metastasis.

RESULTS

Patients who had higher ESTIMATE, stromal, and immune scores exhibited more favorable overall survival rates. There are 17 genes that overlap among the DEGs related to the immune-stromal-ESTIMATE scores, mutated genes, and DEGs in HCC tissues compared to normal tissues. Among the DEGs, three genes (STAB1, COL15A1 and HK3) emerged with the most profound association concerning survival outcomes. Notably, the HK3 genes displayed a pronounced correlation with immune infiltration. Concurrently, diminished expression levels of HK3 were observed in HCC tissues and upregulation of HK3 resulted in a significant reduction in HCC cell metastasis in vitro and in vivo.

CONCLUSIONS

HK3 emerges as a novel prognostic biomarker for HCC, exerting regulatory influence over cellular proliferation, metastasis, and invasiveness. These findings indicate that HK3 holds promise as a potential candidate for treatment and prognosis of HCC.