Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts

This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.

The prognostic value of AST-lymphocyte ratio index in liver cancer patients treated with TACE: a systematic review and single-center retrospective study

BACKGROUND AND AIMS

AST-lymphocyte ratio index (ALRI) has been proposed as a potentially prognostic indicator of liver cancer patients underwent transcatheter arterial chemoembolization (TACE) in studies, but the numbers were small and the results were controversial. In this study, we systematically assessed the prognostic value of ALRI in liver cancer patients treated with TACE by integrating meta-analysis with single-center clinical analysis.

METHODS

We conducted a systematic literature search across multiple databases and evaluated the quality of included studies using the Newcastle-Ottawa Scale. We employed a fixed-effect model to calculate the pooled hazard ratio (HR) and 95% confidence interval (CI). Publication bias were evaluated using funnel plot, Begg's and Egger's tests. Concurrently, we integrated clinical data from 127 HCC patients treated with TACE at our center, employed X-tile software to ascertain the optimal cutoff value for ALRI, and analyzed the relationship between ALRI and clinical characteristics as well as overall survival (OS), using chi-square tests, Kaplan-Meier survival curves, and Cox proportional hazards models.

RESULTS

The meta-analysis included 7 studies, and the pooled hazard ratio (HR) indicated that elevated ALRI was significantly associated with poorer OS in liver cancer patients underwent TACE (HR = 1.75, 95% CI: 1.46-2.1, P<0.01), with no significant heterogeneity (P = 0.542, I2 = 0.00%). Clinical analysis of 127 patients further supported this finding, with patients in the high ALRI group showed significantly lower OS compared to those in the low ALRI group (1-year OS rate: 96.7% vs. 87.9%, 2-year OS rate: 61.5% vs. 42.7%; C2 = 28.006, P<0.01). Multivariate Cox regression analysis revealed that number of tumors, tumor size and ALRI were all independent prognostic factors for OS (ALRI HR = 6.456, 95%CI: 2.247-18.55, P < 0.01).

CONCLUSIONS

An increase in ALRI may serve as an independent prognostic indicator of poor outcomes in liver cancer patients undergoing TACE. While it offers benefits such as being non-invasive and cost-effective, further large-scale, multicenter, prospective studies are essential to validate the efficacy of ALRI and establish standardized cutoff values for clinical application.

An elevated percentage of CD4⁺CD25⁺CD127low regulatory T cells in peripheral blood indicates a poorer prognosis in hepatocellular carcinoma after curative hepatectomy

BACKGROUND

Previous studies suggest the percentage of CD4⁺CD25⁺CD127low regulatory T cells (Tregs) in peripheral blood of patients with hepatocellular carcinoma (HCC) was significantly higher than that in healthy, which may be a significant predictor of HCC clinical outcome, and we examined the utility of Tregs in predicting prognosis in HCC after curative hepatectomy.

METHODS

77 diagnosed HCC patients from August 2018 to March 2023 were selected as research objects, we retrospectively analyzed whether the preoperative percentage of CD4⁺CD25⁺CD127low Tregs in peripheral blood predicts prognosis after curative hepatectomy in HCC patients. The percentage of CD4⁺CD25⁺CD127low Tregs was detected by flow cytometry.

RESULTS

The percentage of CD4⁺CD25⁺CD127low Tregs was significantly elevated in patients who developed recurrence and death (p < 0.050). X-tile software was used to calculate optimal cut-off value of Treg percentage (5.85%), and patients were divided into two groups with high and low Treg percentage. Patients with higher preoperative Treg percentage had a significantly poorer prognosis (p < 0.050). Cox regression demonstrated the percentage of CD4⁺CD25⁺CD127low Tregs was an independent indicator for poor prognosis after hepatectomy. The Recurrence-free survival (RFS) (the log-rank test, p < 0.001) and Overall survival (OS) (the log-rank test, p = 0.008) in patients with higher Treg percentage were significantly lower than that in patients with lower Treg percentage. The results were confirmed by the subgroup analysis.

CONCLUSION

The percentage of CD4⁺CD25⁺ CD127low Tregs in peripheral blood is associated with poor prognosis in HCC patients. It can be suggested as a potential prognostic indicator for HCC patients after hepatectomy and complement existing risk stratification tools. Measuring the percentage of CD4⁺CD25⁺ CD127low Tregs may contribute to the formulation of treatment strategies and the improvement of the prognosis for HCC patients.

SPP1 + macrophages cause exhaustion of tumor-specific T cells in liver metastases

Functional tumor-specific CD8+ T cells are essential for effective anti-tumor immune response and immune checkpoint inhibitor therapy. Here we show that, compared to other organ sites, primary, metastatic liver tumors in murine models contain a higher number of tumor-specific CD8+ T cells which are also dysfunctional. High-dimensional, multi-omic analysis of patient samples reveals a higher frequency of exhausted tumor-reactive CD8+ T cells and enriched interactions between these cells and SPP1+ macrophages in profibrotic, alpha-SMA rich regions specifically in the liver. Differential pseudotime trajectory inference analysis reveals that extrahepatic signaling promotes an intermediate cell (IC) population in the liver, characterized by co-expression of VISG4, CSF1R, CD163, TGF-βR, IL-6R, and SPP1. Analysis of premetastatic adenocarcinoma patient samples reveals enrichment of this population may predict liver metastasis. These findings suggest a mechanism by which extrahepatic tumors drive liver metastasis by promoting an IC population that inhibits tumor-reactive CD8+ T cell function.

Characterizing the immune landscape of tumor-infiltrating lymphocytes in non-small cell lung cancer

Tumor-Infiltrating Lymphocytes (TILs) immunotherapy is a highly promising treatment for Non-small Cell Lung Cancer (NSCLC), which is responsible for 18% of all cancer-related deaths. The heterogeneity of TILs remains poorly understood. Here, we utilized combined single-cell RNA (scRNA)/T cell receptor sequencing (scTCR-seq) data from lung adenocarcinoma (LUAD) patients. Naïve CD4+ and effector memory CD8+ T cells were increased in tumor tissue compared with circulating blood samples. Activated signaling pathways were detected, and GZMA was identified as a potential novel diagnostic biomarker. During the transitional phase, macrophages (FTL) and dendritic (AIF1) cells transported the most CD3 TCR clones to T cells, while cytotoxicity CD8+ T (NKG7) cells transported to terminal exhausted CD8+ T cells. In both transition and expansion phases, T helper cells (CXCL13) are transported to regulatory T cells (Tregs). Additionally, we investigated the expression profiles of key cytokines, checkpoint receptors, and their ligands. Cytotoxicity CD8+ T cells (CCL5 and IFNG), T helper cells (FTL, TNFRSF4, and TIGIT), and regulatory T cells (CTLA4, TIGIT and FTL) exhibited functional roles in both primary and metastatic tumor stages. Taken together, our study provides a single-cell resolution of the TIL immune landscape and suggests potential treatment strategies to overcome drug resistance.

Peripheral T lymphocyte immune characteristics dictate response to transarterial chemoembolization in unresectable hepatocellular carcinoma

Background

Although transcatheter arterial chemoembolization (TACE) is one of the first-line treatments for unresectable HCC (uHCC) patients, its overall efficacy varies significantly. Therefore, the identification of reliable biomarkers capable of effectively distinguishing TACE-responsive populations is clinically critical.

Objectives

Our research aims to investigate T-lymphocyte subpopulations and associated pathways in peripheral blood that contribute to TACE refractoriness, as well as to develop effective methods for predicting TACE efficacy.

Design

This is an observational study.

Methods

A total of 50 patients who underwent standard TACE-based therapy between January 2020 and December 2022 were included in this study. TACE response was evaluated within 1-3 months following two consecutive TACE sessions. Patients with TACE failure were assigned to the Non-Response group, whereas the remaining were categorized into the Response group. Blood samples were collected prior to treatment and subsequently analyzed using flow cytometry and RNA sequencing. Predictors were analyzed using univariate and multivariate analyses within the bivariate logistic regression models. Pathway enrichment analysis was performed using gene set enrichment analysis (GSEA).

Results

A total of 24 of 50 (48%) exhibited TACE failure (Non-Response). Baseline peripheral T-lymphocyte analysis revealed that the Non-Response group had a higher abundance of senescent phenotype (TSenescence, CD27-CD28-) in both CD4/CD8+ T cells (p < 0.0001), but a lower proportion of memory stem cell (TSCM) subpopulation (CD4+ TSCM: p = 0.0411; CD8+ TSCM: p < 0.0001). Furthermore, in CD8+ T cells, they exhibited higher expression of exhaustion marks (PD-1: p = 0.0005; LAG-3: p = 0.0026; TIGIT: p = 0.0014) and significantly lower production of effector molecules (TNF-α: p < 0.0001; IFN-γ: p = 0.0018; GZMB: p < 0.0001). Transcriptomics revealed that the Response group was enriched in pathways associated with energy and drug metabolism. Univariate and multivariate analyses demonstrated that the baseline CD8+ TSCM and CD8+ TSenescence subpopulations were significant predictive factors for TACE efficacy.

Conclusion

Our study demonstrated significant differences in the immune characteristics of peripheral T lymphocytes between the Non-Response and Response groups. The CD8+ TSCM and CD8+ TSenescence subsets are potential predictors of TACE efficacy and long-term survival. These insights into peripheral blood T lymphocytes offer valuable evidence to help clinicians more effectively identify potential TACE-responsive populations, predict survival, and develop personalized treatment regimens for patients with uHCC.

Pathogenesis and Systemic Treatment of Hepatocellular Carcinoma: Current Status and Prospects

Hepatocellular carcinoma (HCC) remains one of the major threats to human health worldwide. The emergence of systemic therapeutic options has greatly improved the prognosis of patients with HCC, particularly those with advanced stages of the disease. In this review, we discussed the pathogenesis of HCC, genetic alterations associated with the development of HCC, and alterations in the tumor immune microenvironment. Then, important indicators and emerging technologies related to the diagnosis of HCC are summarized. Also, we reviewed the major advances in treatments for HCC, offering insights into future prospects for next-generation managements.

Integrated transcriptomics profile reveals the role of Gal-1 and miR-21 in intrahepatic cholangiocarcinoma progression

Intrahepatic cholangiocarcinoma (ICC) is a highly invasive liver tumor with a poor prognosis, arises from the intrahepatic bile ducts. It is the second most common type of liver cancer. Understanding the mechanisms driving ICC progression is crucial for identification of biomarkers and therapeutic targets. Galectin-1 (Gal-1), encoded by the LGALS1 gene, is known to be upregulated in various malignancies and plays a significant role in cancer progression. However, its underlying mechanisms in ICC have yet to be fully elucidated. The study employed RNA-seq analysis, western blot, cell migration, colony forming, EdU assay, qRT-PCR, luciferase assay and mIHC to investigate the expression pattern of Gal-1 in ICC and its role in the progression of the disease. Our findings revealed a significant upregulation of Gal-1 in ICC tissues. Notably, downregulation of Gal-1inhibited ICC cell proliferation and migration. Further, Gal-1 appears to promote ICC progression through miR-21/STAT3-related pathways, playing a critical role to the tumor microenvironment. These results suggest that Gal-1 may serve as a promising molecular diagnostic marker and therapeutic target for ICC.

Cholinergic T cells revitalize the tumor immune microenvironment: TIME to ChAT

Crosstalk between the nervous system and the immune system shapes the tumor microenvironment. Cholinergic T cells, a unique population of T cell antigen receptor-induced acetylcholine-producing T cells, have emerged as an integrative interface between these two fundamental body systems. Here we review the distinct characteristics and functions of cholinergic T cells in cancer settings. We first outline the expression of choline acetyltransferase and the cholinergic machinery in T cells. We then describe the dysfunctional state of choline acetyltransferase-expressing T cells in cancer and delve into their modulatory effects on T cells, cancer cells and the tumor microenvironment, including its populations of immune cells, its vasculature and its nerves. We also discuss the clinical implications of harnessing the potential of cholinergic T cells and future directions for increasing our understanding of their importance and possible exploitation.

Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer

Head and neck cancer (HNC) is the sixth most common disease in the world. The recurrence rate of patients is relatively high, and the heterogeneity of tumor immune microenvironment (TIME) cells may be an important reason for this. Single-cell sequencing (SCS) is currently the most promising and mature application in cancer research. It can identify unique genes expressed in cells and study tumor heterogeneity. According to current research, the heterogeneity of immune cells has become an important factor affecting the occurrence and development of HNC. SCSs can provide effective therapeutic targets and prognostic factors for HNC patients through analyses of gene expression levels and cell heterogeneity. Therefore, this study analyzes the basic theory of HNC and the development of SCS technology, elaborating on the application of SCS technology in HNC and its potential value in identifying HNC therapeutic targets and biomarkers.

Dissecting the Single-Cell Diversity and Heterogeneity Underlying Cervical Precancerous Lesions and Cancer Tissues

The underlying cellular diversity and heterogeneity from cervix precancerous lesions to cervical squamous cell carcinoma (CSCC) is investigated. Four single-cell datasets including normal tissues, normal adjacent tissues, precancerous lesions, and cervical tumors were integrated to perform disease stage analysis. Single-cell compositional data analysis (scCODA) was utilized to reveal the compositional changes of each cell type. Differentially expressed genes (DEGs) among cell types were annotated using BioCarta. An assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis was performed to correlate epigenetic alterations with gene expression profiles. Lastly, a logistic regression model was used to assess the similarity between the original and new cohort data (HRA001742). After global annotation, seven distinct cell types were categorized. Eight consensus-upregulated DEGs were identified in B cells among different disease statuses, which could be utilized to predict the overall survival of CSCC patients. Inferred copy number variation (CNV) analysis of epithelial cells guided disease progression classification. Trajectory and ATAC-seq integration analysis identified 95 key transcription factors (TF) and one immunohistochemistry (IHC) testified key-node TF (YY1) involved in epithelial cells from CSCC initiation to progression. The consistency of epithelial cell subpopulation markers was revealed with single-cell sequencing, bulk sequencing, and RT-qPCR detection. KRT8 and KRT15, markers of Epi6, showed progressively higher expression with disease progression as revealed by IHC detection. The logistic regression model testified the robustness of the resemblance of clusters among the various datasets utilized in this study. Valuable insights into CSCC cellular diversity and heterogeneity provide a foundation for future targeted therapy.

Comprehensive single-cell analysis deciphered the immunoregulatory mechanism of TPPU in alleviating sepsis-related acute liver injury

INTRODUCTION

Sepsis-related acute liver injury involves complex immune dysfunctions. Epoxyeicosatrienoic acids (EETs), bioactive molecules derived from arachidonic acid (AA) via cytochrome P450 (CYP450) and rapidly hydrolyzed by soluble epoxide hydrolase (sEH), possess anti-inflammatory properties. Nevertheless, the impact of the sEH inhibitor TPPU on sepsis-related acute liver injury remains uncertain.

OBJECTIVES

This study utilized comprehensive single-cell analysis to investigate the immunoregulatory mechanism of TPPU in alleviating sepsis-related acute liver injury.

METHODS

Hepatic bulk RNA sequencing and proteomics analyses were employed to investigate the mechanisms underlying sepsis-related acute liver injury induced by cecal ligation and puncture in mice. Cytometry by time-of-flight and single-cell RNA sequencing were conducted to thoroughly examine the immunoregulatory role of TPPU at single-cell resolution.

RESULTS

Downregulation of AA metabolism and the CYP450 pathway was observed during sepsis-related acute liver injury, and TPPU treatment reduced inflammatory cytokine production and mitigated sepsis-related hepatic inflammatory injury. Comprehensive single-cell analysis revealed that TPPU promotes the expansion of anti-inflammatory CD206+CD73+ M2-like macrophages and PDL1-CD39-CCR2+ neutrophils, reprogramming liver neutrophils to an anti-inflammatory CAMP+NGP+CD177+ phenotype. Additionally, TPPU inhibits the CCL6-CCR1 signaling mediated by M2-like macrophages and CAMP+NGP+CD177+ neutrophils, altering intercellular communication within the septic liver immune microenvironment.

CONCLUSION

This study demonstrated TPPU's protective efficacy against sepsis-related acute liver injury, underscoring its vital role in modulating liver macrophages and neutrophils and enhancing prospects for personalized immunomodulatory therapy.

Single-cell RNA sequencing dissects the immunosuppressive signatures in Helicobacter pylori-infected human gastric ecosystem

Helicobacter pylori (H. pylori) manipulates the host immune system to establish a persistent colonization, posing a serious threat to human health, but the mechanisms remain poorly understood. Here we integrate single-cell RNA sequencing and TCR profiling for analyzing 187,192 cells from 11 H. pylori-negative and 12 H. pylori-positive individuals to describe the human gastric ecosystem reprogrammed by H. pylori infection, as manifested by impaired antigen presentation and phagocytosis function. We further delineate a monocyte-to-C1QC+ macrophage differentiation trajectory driven by H. pylori infection, while T cell responses exhibit broad functional impairment and hyporesponsiveness with restricted clonal expansion capacity. We also identify an HLA-DRs- and CTLA4-expressing T cell population residing in H. pylori-inhabited stomach that potentially contribute to immune evasion. Together, our findings provide single-cell resolution information into the immunosuppressive microenvironment shaped by H. pylori infection, offering critical insights for developing novel therapeutic approaches to eliminate this globally prevalent pathogen.

The dynamic immune behavior of primary and metastatic ovarian carcinoma

Patients with high-grade serous ovarian carcinoma (HGSC) are usually diagnosed with advanced-stage disease, and the tumors often have immunosuppressive characteristics. Together, these factors are important for disease progression, drug resistance, and mortality. In this study, we used a combination of single-cell sequencing and spatial transcriptomics to identify the molecular mechanisms that lead to immunosuppression in HGSC. Primary tumors consistently showed a more active immune microenvironment than did omental tumors. In addition, we found that untreated primary tumors were mostly populated by dysfunctional CD4 and CD8 T cells in later stages of differentiation; this, in turn, was correlated with expression changes in the interferon α and γ pathways in epithelial cells, showing that cross-communication between the epithelial and immune compartments is important for immune suppression in HGSC. These findings could have implications for the design of clinical trials with immune-modulating drugs.

Spinal Cord Organoids from Human Amniotic Fluid iPSC Recapitulate the Diversity of Cell Phenotypes During Fetal Neural Tube Morphogenesis

Myelomeningocele (MMC) is a severe form of spina bifida associated with substantial neurologic morbidity. In vitro modeling systems of human spinal cord development may help to elucidate the underlying pathophysiology of the MMC spinal cord. To that end, we developed spinal cord organoids (SCO), defined as self-organized, three-dimensional clusters of spinal tissue, that were derived from human amniotic fluid-induced pluripotent stem cells. Here, we used a variety of analyses, including immunofluorescent and single-cell transcriptomic approaches, to characterize SCOs from healthy and MMC fetuses. Organoids contained a diverse range of neural and mesodermal phenotypes when cultured for up to 130 days in vitro. Multielectrode arrays revealed functional activity with evidence of emerging neuronal networks. Fetal spina bifida environment modeling was successfully established by culturing SCOs in second- and third-trimester amniotic fluid for 3 weeks. Taken together, we show that functional SCOs can recapitulate the cellular identity of the fetal spinal cord and represent a novel research platform to study the interplay between cellular, biochemical, and mechanical cues during human MMC neural tube morphogenesis.

Discovery of Genomic Targets and Therapeutic Candidates for Liver Cancer Using Single-Cell RNA Sequencing and Molecular Docking

Liver cancer is one of the most common malignancies and the second leading cause of cancer-related deaths worldwide, particularly in developing countries, where it poses a significant financial burden. Early detection and timely treatment remain challenging due to the complex mechanisms underlying the initiation and progression of liver cancer. This study aims to uncover key genomic features, analyze their functional roles, and propose potential therapeutic drugs identified through molecular docking, utilizing single-cell RNA sequencing (scRNA-seq) data from liver cancer studies. We applied two advanced hybrid methods known for their robust identification of differentially expressed genes (DEGs) regardless of sample size, along with four top-performing individual methods. These approaches were used to analyze four scRNA-seq datasets, leading to the identification of essential DEGs. Through a protein-protein-interaction (PPI) network, we identified 25 hub-of-hub genes (hHubGs) and 20 additional hHubGs from two naturally occurring gene clusters, ultimately validating a total of 36 hHubGs. Functional, pathway, and survival analyses revealed that these hHubGs are strongly linked to liver cancer. Based on molecular docking and binding-affinity scores with 36 receptor proteins, we proposed 10 potential therapeutic drugs, which we selected from a pool of 300 cancer meta-drugs. The choice of these drugs was further validated using 14 top-ranked published receptor proteins from a set of 42. The proposed candidates include Adozelesin, Tivozanib, NVP-BHG712, Nilotinib, Entrectinib, Irinotecan, Ponatinib, and YM201636. This study provides critical insights into the genomic landscape of liver cancer and identifies promising therapeutic candidates, serving as a valuable resource for advancing liver cancer research and treatment strategies.

The crosstalk between broad epigenetic modification and T cell metabolism within tumor microenvironment

T cells play an important role in adaptive immune responses, providing antigen specificity for pathogen and tumor recognition. Recent studies have elucidated the complex interplay between T cell metabolism and broad epigenetic modifications in response to tumors, occurring at transcriptional, post-transcriptional, and post-translational levels. At the transcriptional level, gene expression is regulated through mechanisms such as DNA methylation, chromatin remodeling, and transcription factor activity. Post-transcriptionally, gene expression is further modulated by non-coding RNAs and RNA modifications, an area of increasing research interest. In addition, histone proteins are primarily regulated by well-established post-translational modifications (PTMs), including acetylation and methylation. Novel PTMs such as succinylation, glycosylation, glutamylation, and lactylation add complexity to the regulation and warrant further investigation. At present, the interaction between CD8+ T cell metabolism and epigenetic modifications in response to malignancies has been reported extensively. However, the interplay in CD4+ T cells remains less understood. In this review, we introduce the differentiation trajectories of T cells and critically evaluate existing interplay between metabolic activity and epigenetic modifications influences the functional dynamics in both CD8+ and CD4+ T cells, offering promising avenues for the development of novel cancer immunotherapies.

Safety and Therapeutic Outcomes of Adjuvant Immunotherapy With Autologous Cytokine-induced Killer Cells for Patients With Hepatocellular Carcinoma Beyond Milan Criteria After Liver Transplantation

BACKGROUND

Adjuvant immunotherapy with autologous cytokine-induced killer (CIK) cells for hepatocellular carcinoma (HCC) remains understudied in liver transplant patients because of potential risks of acute rejection and diminished efficacy by immunosuppression.

METHODS

This study examined the safety and effectiveness of CIK therapy in patients with HCC exceeding the Milan criteria, treated at 2 Korean hospitals between 2019 and 2021. We analyzed clinical outcomes of 16 patients who underwent CIK therapy compared with 44 propensity-matched controls who did not receive CIK therapy. CIK cells were administered in 6 escalating doses, either 3 or 6 times over the course of weeks 4, 5, 6, 8, 10, and 12 posttransplantation.

RESULTS

CIK therapy was well-tolerated without significant treatment-related adverse reactions. Maximal tolerated dose of CIK cells was 10 × 109, which had been repeated 6 times. The CIK group exhibited higher 2-y HCC recurrence-free (87.5% versus 62.9%, P = 0.027) and patient survival (100% versus 81.5%, P = 0.002) rates, with no significant difference in rejection-free survival rates (92.9% versus 95.0%, P = 0.926) compared with the no-CIK group. Subgroup analysis showed that the CIK group in patients with high retreat scores, elevated R3-α-fetoprotein scores, and those beyond the University of California San Francisco criteria had improved HCC recurrence-free survival. Immunological evaluation showed elevated CD8+ T cells and polymorphonuclear myeloid-derived suppressor cells with transient increases in granzyme B and tumor necrosis factor-α levels in the CIK group.

CONCLUSIONS

These findings advocate CIK therapy as a safe and effective, potential adjuvant treatment for HCC beyond Milan criteria after transplantation, supporting further validation trials.

Monitoring Immune Responses to Vaccination: A Focus on Single-Cell Analysis and Associated Challenges

Monitoring the immune response to vaccination encompasses both significant challenges and promising opportunities for scientific advancement. The primary challenge lies in the inherent complexity and interindividual variability of immune responses, influenced by factors including age, genetic background, and prior immunological history. This variability necessitates the development of sophisticated, highly sensitive assays capable of accurately quantifying immune parameters such as antibody titers, T-cell responses, and cytokine profiles. Furthermore, the temporal dynamics of the immune response require comprehensive longitudinal studies to elucidate the durability and quality of vaccine-induced immunity. Challenges of this magnitude pave the way for immunological research advancements and diagnostic methodologies. Cutting-edge monitoring techniques, such as high-throughput sequencing and advanced flow cytometry, enable deeper insights into the mechanistic underpinnings of vaccine efficacy and contribute to the iterative design of more effective vaccines. Additionally, the integration of analytical tools holds the potential to predict immune responses and tailor personalized vaccination strategies. This will be addressed in this review to provide insight for enhancing public health outcomes and fortifying preparedness against future infectious disease threats.

The effect of TIGIT and PD1 expression on T cell function and prognosis in adult patients with acute myeloid leukemia at diagnosis

T cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT) is a recently-identified immune checkpoint molecule, and no study ever explores the prognostic significance of TIGIT on bone marrow T cells of newly-diagnosed acute myeloid leukemia (AML) patients. We collected fresh marrow samples from 71 adult AML patients at diagnosis and 31 healthy donors (HDs) to test for TIGIT and PD1 expression in T cells by flow cytometry. Fifteen newly-diagnosed AML patients and six HDs were performed T cell activation in vitro and tested intracellular TNF-α and INF-γ production. Three bone marrow samples of AML patients were performed single cell RNA-sequencing (scRNA-seq). AML patients had significantly higher frequency of TIGIT + cells in CD4 + T cells but similar frequency in CD8 + T cells compared with HDs (p = 0.0006 and 0.77). High percentage of TIGIT + PD1 + in CD8 + T cells independently predicted poor relapse-free survival (RFS) (p = 0.029). Differing from HDs, AML patients had lower level of intracellular TNF-α and INF-γ in TIGIT + cells compared with their TIGIT- counterparts in both CD4 + T and CD8 + T cells. TIGIT + PD1 + CD8 + T cells of patients exhibited significantly lower level of intracellular TNF-α compared with those of HDs (p = 0.024). scRNA-seq data showed that TIGIT + PDCD1 + CD8 + T cells had significantly higher exhaustion score than TIGIT + and PD1 + CD8 + T cells and lower cytotoxic score than TIGIT + CD8 + T cells (p = 0.0016, 0.012 and 0.0014). Therefore, CD8 + T cells with TIGIT and PD1 co-expression exhibited high degree of exhaustion and dysfunctional cytotoxicity, and high percentage of bone marrow TIGIT + PD1 + in CD8 + T cells at diagnosis predicted poor outcome in AML.

Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that potentiate stratification of patients with extrahepatic cholangiocarcinoma

BACKGROUND

Extrahepatic cholangiocarcinoma (eCCA) is a rare but refractory cancer with dense desmoplasia. Prognosis-associated stromal cells in eCCA remain poorly characterized. Here, we profiled the tumor cellular composition and identified prognosis-related stromal signatures by single-cell RNA sequencing (scRNA-seq) in eCCA. ECCA patients were further stratified into different categories based on identified stromal signatures.

METHODS

Using scRNA-seq, we profiled the transcriptomes of 37,498 individual cells from eight eCCA biopsies, including five tumor tissues and three paired adjacent normal tissues. Bulk RNA sequencing (bRNA-seq) was also performed on 43 eCCA tumor tissues. Stromal cell composition and heterogeneity were examined through differential gene expression and gene set enrichment analyses. By assessing the expression levels of marker genes in bRNA-seq data, the correlation of stromal cell clusters with survival was explored. The GSVA scores of the cell-specific signature genes of the prognosis-related stromal cell subtypes were calculated and used to stratify eCCA patients.

RESULTS

The results revealed that tumor stroma in eCCA were composed of hematopoietic progenitor-like cells (HPLCs), fibroblasts (Fb), Schwann cells (Sch), endothelial cells and immune cells. Prognosis-associated stromal cell subpopulations included MKI67 + HPLC, TMEM158 + C3-Fb, FOXP3 + regulatory T cells (Treg), SLIT2 + Sch, TPSD1 + C2-mast cells (MC) and CTSG + C3-MC. Based on these stromal signatures, the eCCA tumors were categorized into three classes: proliferative Group 1 with enrichment of MKI67 + HPLC, inflammatory and fibrotic Group 2 with enrichment of TPSD1 + C2- MC, FOXP3 + Treg and TMEM158 + C3-Fb, and neuronal Group 3 with enrichment of SLIT2 + Sch and CTSG + C3-MC. ECCA patients in Group 3 had a better prognosis when compared to Group 1 and 2, reflecting different impact of stromal subtypes on tumor progression.

CONCLUSION

Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that potentiate the stratification of eCCA into proliferative, inflammatory and fibrotic, and neuronal phenotypes, which has important implications on molecular classification and exploring therapeutic targets in eCCA.

HBx/WDR5 enhances IGF-1 transcription in hepatocellular carcinoma cells and promotes recruitment, infiltration, and activity of Treg cells

HBV X protein (HBx), the smallest open reading frame in the hepatitis B virus (HBV) genome, can promote hepatocellular carcinoma (HCC) tumorigenesis by activating the expression of multiple oncogenes through inducing epigenetic alterations and interacting with the underlying transcriptional machinery. HBV non-infected HepG2 and Huh7 cells were transfected with HBx expression plasmids. The transcriptional, protein expression, and secretion levels of IGF-1 were detected by RT-qPCR, western blot, and ELISA, respectively. ChIP-qPCR was used to analyze the binding proteins on the IGF-1 gene. A co-culture system of HCC and Treg cells was designed using Transwell chambers. IGF-1 mRNA, protein, and secretion levels were increased in HepG2 and Huh7 cells exogenously expressing HBx. HBx was able to enter the nucleus and interact with the enhancer region of the IGF-1 gene. Levels of WDR5 and H3K4me1, which bind to the enhancer region of the IGF-1 gene, were also increased in HepG2 and Huh7 cells ectopically expressing HBx. Knockdown of WDR5 counteracted the upregulation of IGF-1 mRNA and protein levels by HBx. In the cell co-culture system, HBx/IGF-1 signaling in HCC cells promoted Treg cells expansion, IL-10 secretion, and infiltration, which was blocked by the IGF-1R inhibitor picropodophyllin. HBx/WDR5 promoted IGF-1 transcription in HCC cells through enhancers. HBx could promote Treg cell recruitment, infiltration, and activity by enhancing IGF-1 expression. IGF-1/IGF-1R signaling plays an important role in the communication between HCC cells and Treg cells. Targeting WDR or IGF-1/IGF-1R would be beneficial for the treatment of HCC.

Regulatory T cells converted from Th1 cells in tumors suppress cancer immunity via CD39

Regulatory T (Treg) cells are known to impede antitumor immunity, yet the regulatory mechanisms and functional roles of these cells remain poorly understood. In this study, through the characterization of multiple cancer models, we identified a substantial presence of peripherally induced Treg cells in the tumor microenvironment (TME). Depletion of these cells triggered antitumor responses and provided potent therapeutic effects by increasing functional CD8+ T cells. Fate-mapping and transfer experiments revealed that IFN-γ-expressing T helper (Th) 1 cells differentiated into Treg cells in response to TGF-β signaling in tumors. Pseudotime trajectory analysis further revealed the terminal differentiation of Th1-like Treg cells from Th1 cells in the TME. Tumor-resident Treg cells highly expressed T-bet, which was essential for their functions in the TME. Additionally, CD39 was highly expressed by T-bet+ Treg cells in both mouse and human tumors, and was necessary for Treg cell-mediated suppression of CD8+ T cell responses. Our study elucidated the developmental pathway of intratumoral Treg cells and highlighted novel strategies for targeting them in cancer patients.

A bibliometric and visual analysis based on immune checkpoint inhibitors for hepatocellular carcinoma: 2014 - 2024

Background

Immune checkpoint inhibitors (ICIs) have changed the treatment landscape of hepatocellular carcinoma (HCC), especially those with unresectable advanced stages. The field has progressed rapidly, and the research hotspots have significantly changed compared to previous years. The study aims to comprehensively review and analyze the development history, knowledge structure, current research focus, and emerging trends in ICIs for HCC.

Materials and methods

Reviews and articles published in English from The Web of Science Core Collection (WoSCC) database from 2014 to 2024 were systemically retrieved. Citespace, VOSviewer, and Bibliometrix R package were used for further bibliometric analysis and visualization for countries, institutions, authors, references, and keywords.

Results

2,941 records were included for analysis. The literature on ICIs for HCC has continued to grow steadily over the past decade. Three major research centers have emerged: North America, Europe, and East Asia. The Chinese institution has the highest publication volume, but Kudo Masatoshi from Japan has the highest number of publications. At the same time, Richard S. Finn from the United States leads in citations and co-citations. The most prolific journal is "Cancers". The clustering and Timeline view of critical literature and keywords indicated that research on ICIs for HCC is rapidly advancing toward a more evidence-based, personalized, and multimodal approach. Immune evasion mechanisms, predictive biomarkers, and high-quality clinical trials focusing on Novel combination, conversion, and perioperative therapies, including ICIs, are emerging hotspots.

Conclusion

This study highlights the groundbreaking advancements of ICIs in treating HCC and shows a trend rapidly advancing towards a more evidence-based, personalized, and multimodal approach. The study updated the current understanding of ICIs in hepatocellular carcinoma and identified vital future directions for research, such as the exploration of mechanisms of immune evasion, developing predictive biomarkers, and combining therapy strategies.

VDAC2 loss elicits tumour destruction and inflammation for cancer therapy

Tumour cells often evade immune pressure exerted by CD8+ T cells or immunotherapies through mechanisms that are largely unclear1,2. Here, using complementary in vivo and in vitro CRISPR-Cas9 genetic screens to target metabolic factors, we established voltage-dependent anion channel 2 (VDAC2) as an immune signal-dependent checkpoint that curtails interferon-γ (IFNγ)-mediated tumour destruction and inflammatory reprogramming of the tumour microenvironment. Targeting VDAC2 in tumour cells enabled IFNγ-induced cell death and cGAS-STING activation, and markedly improved anti-tumour effects and immunotherapeutic responses. Using a genome-scale genetic interaction screen, we identified BAK as the mediator of VDAC2-deficiency-induced effects. Mechanistically, IFNγ stimulation increased BIM, BID and BAK expression, with VDAC2 deficiency eliciting uncontrolled IFNγ-induced BAK activation and mitochondrial damage. Consequently, mitochondrial DNA was aberrantly released into the cytosol and triggered robust activation of cGAS-STING signalling and type I IFN response. Importantly, co-deletion of STING signalling components dampened the therapeutic effects of VDAC2 depletion in tumour cells, suggesting that targeting VDAC2 integrates CD8+ T cell- and IFNγ-mediated adaptive immunity with a tumour-intrinsic innate immune-like response. Together, our findings reveal VDAC2 as a dual-action target to overcome tumour immune evasion and establish the importance of coordinately destructing and inflaming tumours to enable efficacious cancer immunotherapy.

Landscape of T Cells in Tuberculous Pleural Effusion

The distribution and the function of T lymphocyte subsets in pleural effusion (PE) and peripheral blood (PB) in tuberculous pleural effusion (TPE) patients remain unclear. In this study, we aimed to explore the expression patterns, regulatory mechanisms, and functions of T lymphocyte subsets in TPE patients, especially the distribution of T lymphocyte subsets at the single cell level. The CD3+ T cells were isolated from PE and PB of four TPE patients for single-cell RNA sequencing (scRNA-seq) to screen T cell subsets. T-SNE projection, Gene Set Variation Analysis (GSVA), and pseudotime analysis were performed to analyze the composition, molecular and functional properties, and developmental trajectories of T cell subsets. Finally, ELISA was carried out to identify the cytokines secreted by PE and PB. We found that CD4+CD8- T lymphocytes (Th1, Th2, and FOXP3+ Treg cells) were preferentially enriched in PE. The proportion of exhausted CD4-CD8+ cells in PE was higher than that in PB, while the proportion of initial and effector CD4-CD8+ cells was quite the reverse. We also found a large number of unexpected double positive (DP) cells in PE and PB, among which the proportion of CD4+CD8+-C10-CCL3 cells was the most different between PE and PB. Meanwhile, CD4+CD8+-C10-CCL3 was the group with the largest number of interactions with other groups. CD4-CD8- cells were mainly found in PE and may be involved in the immunomodulatory effect of PE. Furthermore, the concentrations of cytokines secreted by Th1, Th2, and Treg in PE were higher than those in PB. Our study is helpful to understand the distribution pattern and dynamic changes of T cells in PE and PB of TPE patients and further understand that the functional status and regulation of T cells will be crucial for the successful development of TPE immunotherapy.

Development and Functions of MAIT Cells

Mucosal-associated invariant T (MAIT) cells are evolutionarily conserved T cells that recognize microbial metabolites. They are abundant in humans and conserved during mammalian evolution, which suggests that they have important nonredundant functions. In this article, we discuss the evolutionary conservation of MAIT cells and describe their original developmental process. MAIT cells exert a wide variety of effector functions, from killing infected cells and promoting inflammation to repairing tissues. We provide insights into these functions and discuss how they result from the context of stimulation encountered by MAIT cells in different tissues and pathological settings. We describe how MAIT cell numbers and features are modified in disease states, focusing mainly on in vivo models. Lastly, we discuss emerging strategies to manipulate MAIT cells for therapeutic purposes.

Deciphering T-cell exhaustion in the tumor microenvironment: paving the way for innovative solid tumor therapies

In solid tumors, the tumor microenvironment (TME) is a complex mix of tumor, immune, stromal cells, fibroblasts, and the extracellular matrix. Cytotoxic T lymphocytes (CTLs) constitute a fraction of immune cells that may infiltrate into the TME. The primary function of these T-cells is to detect and eliminate tumor cells. However, due to the immunosuppressive factors present in the TME primarily mediated by Myeloid-Derived Suppressor Cells (MDSCs), Tumor associated macrophages (TAMs), Cancer Associated Fibroblasts (CAFs) as well as the tumor cells themselves, T-cells fail to differentiate into effector cells or become dysfunctional and are unable to eliminate the tumor. In addition, chronic antigen stimulation within the TME also leads to a phenomenon, first identified in chronic lymphocytic choriomeningitis virus (LCMV) infection in mice, where the T-cells become exhausted and lose their effector functions. Exhausted T-cells (Tex) are characterized by the presence of remarkably conserved inhibitory receptors, transcription and signaling factors and the downregulation of key effector molecules. Tex cells have been identified in various malignancies, including melanoma, colorectal and hepatocellular cancers. Recent studies have indicated novel strategies to reverse T-cell exhaustion. These include checkpoint inhibitor blockade targeting programmed cell death protein 1 (PD-1), T-cell immunoglobulin and mucin-domain containing-3 (Tim-3), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), or combinations of different immune checkpoint therapies (ICTs) or combination of ICTs with cytokine co-stimulation. In this review, we discuss aspects of T-cell dysfunction within the TME with a focus on T-cell exhaustion. We believe that gaining insight into the mechanisms of T-cell exhaustion within the TME of human solid tumors will pave the way for developing therapeutic strategies to target and potentially re-invigorate exhausted T-cells in cancer.

Therapeutic potential of tocotrienols as chemosensitizers in cancer therapy

Chemoresistance is the adaptation of cancer cells against therapeutic agents. When exhibited by cancer cells, chemoresistance helps them to avoid apoptosis, cause relapse, and metastasize, making it challenging for chemotherapeutic agents to treat cancer. Various strategies like dosage modification of drugs, nanoparticle-based delivery of chemotherapeutics, antibody-drug conjugates, and so on are being used to target and reverse chemoresistance, one among such is combination therapy. It uses the combination of two or more therapeutic agents to reverse multidrug resistance and improve the effects of chemotherapy. Phytochemicals are known to exhibit chemosensitizing properties and are found to be effective against various cancers. Tocotrienols (T3) and tocopherols (T) are natural bioactive analogs of vitamin E, which exhibit important medicinal value and potential curative properties apart from serving as an antioxidant and nutrient supplement. Notably, T3 exhibits a variety of pharmacological activities like anticancer, anti-inflammatory, antiproliferative, and so on. The chemosensitizing property of tocotrienol is exhibited by modulating several signaling pathways and molecular targets involved in cancer cell survival, proliferation, invasion, migration, and metastasis like NF-κB, STATs, Akt/mTOR, Bax/Bcl-2, Wnt/β-catenin, and many more. T3 sensitizes cancer cells to chemotherapeutic drugs including cisplatin, doxorubicin, and paclitaxel increasing drug concentration and cytotoxicity. Discussed herewith are the chemosensitizing properties of tocotrienols on various cancer cell types when combined with various drugs and biological molecules.

DNA Origami Scaffold-Based Peptide-Major Histocompatibility Complex Multimers for Spatial Imaging of T Cells

Visualizing the spatial distribution of antigen-specific T cells is essential for understanding immune responses and improving therapeutic strategies. However, detecting low-affinity antigen-specific T cells and enhancing signals from low-abundance populations remain challenging due to limitations in sensitivity. Here, we report DNA origami scaffold-based peptide-major histocompatibility complex multimers (DOS-pMHCs) with precise spatial organization of pMHC and signaling molecules on the nanoscale for enhanced in situ visualization of antigen-specific T cells. The two-dimensional triangular DNA origami precisely organizes pMHCs and signaling molecules with high valency, significantly improving binding to antigen-specific T cells and signal amplification. These DOS-pMHCs facilitate enhanced visualization of antigen-specific T cells in lymphoid tissues compared to traditional tetramers. Moreover, we show that DOS-pMHCs enable the in situ detection of autoimmune T cells with lower affinity T cell receptors (TCRs), which are difficult to identify using traditional tetramers. This in situ detection strategy provides a powerful tool for mapping the spatial distribution of antigen-specific T cells, thus holding great potential for advancing our understanding of immune responses and guiding personalized immunotherapy.

Unveiling the role of PPIF and macrophage subtypes in LSCC progression via single-cell and exosome RNA sequencing

Laryngeal squamous cell carcinoma (LSCC) is a highly aggressive malignancy with a rising incidence over time. The tumor microenvironment (TME) plays a crucial role in LSCC development, yet the precise cellular characteristics of laryngeal cancer and its TME remain unclear. Here, we employed single-cell RNA sequencing analysis to uncover the heterogeneous populations of tumor and immune cells and investigate the role of the TME in LSCC. This analysis revealed significant heterogeneity among malignant cells, T cells, and macrophages. Notably, regulatory T cells were markedly increased at tumor sites, and macrophage analysis identified an increased presence of the Macrophage-C1-C1QC subset with up-regulated PPIF expression. Bulk RNA-seq further confirmed PPIF up-regulation in exosomes derived from LSCC tissues. Consistently, survival analysis indicated that high PPIF expression was associated with poor prognosis in LSCC. Further analyses suggested that PPIF up-regulation in Macrophage-C1-C1QC cells was associated with the enhancement of their anti-inflammatory phenotype and the promotion of F11R-F11R signaling with malignant cells, allowing LSCC cells to evade macrophage-mediated cytotoxicity. Our study provides new insights into the cellular dynamics of LSCC and highlights the critical role of Macrophage-C1-C1QC and PPIF in LSCC progression, offering potential therapeutic targets for treatment.

T lymphocyte-based immune response and therapy in hepatocellular carcinoma: focus on TILs and CAR-T cells

Hepatocellular carcinoma (HCC) is among the leading causes of cancer-related death worldwide. The primary therapies for HCC are liver transplantation, hepatic tumor excision, radiofrequency ablation, and molecular-targeted medicines. An unfavorable prognosis marks HCC and has limited pharmacological response in therapeutic studies. The tumor immune microenvironment (TME) imposes significant selection pressure on HCC, resulting in its evolution and recurrence after various treatments. As the principal cellular constituents of tumor-infiltrating lymphocytes (TILs), T cells have shown both anti-tumor and protumor actions in HCC. T cell-mediated immune responses are pivotal in cancer monitoring and elimination. TILs are recognized for their critical involvement in the progression, prognosis, and immunotherapeutic management of HCC. Foxp3 + , CD8 + , CD3 + , and CD4 + T cells are the extensively researched subtypes of TILs. This article examines the functions and processes of several subtypes of TILs in HCC. Emerging T cell-based therapies, including TILs and chimeric antigen receptor (CAR)-T cell therapy, have shown tumor regression in several clinical and preclinical studies. Herein, it also delves into the existing T cell-based immunotherapies in HCC, with emphasis on TILs and CAR-T cells.

An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution

T cells have various subtypes and states with different functions. However, a reference list and automated annotation tool for T cell subtypes and states are lacking, which is critical for analyzing and comparing T cells under various conditions. We constructed the largest human T cell reference, containing 1,348,268 T cells from 35 conditions and 16 tissues. We classified T cells into 33 subtypes and further stratified them into 68 categories according to subtype and state. Based on this reference, we developed a tool named STCAT to automatically annotate T cells from scRNA-seq data by hierarchical models and marker correction. The accuracy of STCAT was 28% higher than that of existing tools validated on six independent datasets, including cancer and healthy samples. Using STCAT, we consistently discovered that CD4+ Th17 cells were enriched in late-stage lung cancer patients in multiple datasets, whereas MAIT cells were prevalent in milder-stage COVID-19 patients. We also confirmed a decrease in Treg cytotoxicity in post-treatment ovarian cancer. Systematic landscape analyses of CD4+ and CD8+ T cell references revealed that CD4+ Treg cells were enriched in tumor samples and that CD8+ naive-related cells were abundant in healthy individuals. Finally, we deposited all the T cell references and annotations into a TCellAtlas (https://guolab.wchscu.cn/TCellAtlas) database, which allows users to browse T cell expression profiles and analyze customized scRNA-seq data by STCAT. In conclusion, comprehensive human T cell subtypes and states reference, automated annotation tool, and database will greatly facilitate research on T cell immunity and tumor immunology.

Deciphering the Premetastatic Lymphatic Niche of Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most prevalent types of malignancies in the oral cavity, with a high incidence of lymph node (LN) metastasis. While previous studies have explored the mechanisms of lymphatic metastasis, little is known about the cellular architecture within the premetastatic niche of LNs. In this study, we established mouse models of premetastatic LNs, which demonstrated an immunosuppressive premetastatic environment in tumor-draining LNs prior to metastasis. We performed single-cell RNA sequencing on LNs from patients with OSCC, including premetastatic tumor-draining LNs and paired contralateral LNs. Our analysis identified a subset of CD4+ T cells that exclusively expressed MIR155HG, characterized by a preexhausted state and active immune exhaustion signaling with myeloid cells (henceforth, CD4+ Tex-pre cells). In silico analyses and in vivo experiments revealed a higher abundance of CD4+ Tex-pre cells in tumor-draining premetastatic LNs when compared with contralateral LNs, with their numbers increasing as LN metastasis progressed. Moreover, adoptive transfer of CD4+ Tex-pre cells aggravated immune suppression in tumor-draining premetastatic LNs and promoted LN metastasis. The presence of CD4+ Tex-pre cells was further validated by integrating external data sets and conducting in situ RNAscope staining. Finally, using bulk RNA sequencing data sets, we found that CD4+ Tex-pre infiltration was associated with lymphatic metastasis and that CD4+ Tex-pre scores could inform treatment decisions for low-grade cases without clinical nodal involvement. Overall, our study provides a comprehensive view of the single-cell landscape in the premetastatic niche of OSCC LNs and highlights the role of CD4+ Tex-pre cells in shaping the premetastatic niche.

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.

Heterogeneous cellular responses to hyperthermia support combined intraperitoneal hyperthermic immunotherapy for ovarian cancer mouse models

The benefit of hyperthermic intraperitoneal chemotherapy (HIPEC) in ovarian cancer remains controversial, hindering the development of rational combination therapies based on hyperthermia (HT). This study reports the preliminary results of the neoadjuvant HIPEC (NHIPEC) trial (ChiCTR2000038173), demonstrating enhanced tumor response in high-grade serous ovarian cancer with NHIPEC. Through single-cell RNA sequencing analysis, we identified both homogeneous and heterogeneous cellular responses to HT within the tumor and microenvironment. Epithelial-mesenchymal transition-activated tumor cells and matrix metallopeptidase 11 (MMP-11)+ cancer-associated fibroblasts (CAFs) exhibited greater reductions and higher sensitivity to HT. CUT&Tag and RNA sequencing integration unveiled the differential binding programs and transcriptional regulatory mechanisms of HSF1 under normothermia (NT) and HT in tumor cells and CAFs. Furthermore, HT ameliorated the immunosuppressive tumor microenvironment, and in vivo mouse models confirmed the combined antitumor effects of HT and programmed cell death ligand 1 blockade. These findings provide an innovative strategy for rational combination therapy with HT in ovarian cancer.

Distinct cellular mechanisms underlie chemotherapies and PD-L1 blockade combinations in triple-negative breast cancer

Combining immune checkpoint blockade (ICB) with chemotherapy shows promise for treating triple-negative breast cancer (TNBC), though the mechanisms remain incompletely understood. Here, we integrate published and new single-cell RNA sequencing (scRNA-seq) data to investigate the tumor immune microenvironment (TIME) in TNBC patients treated with paclitaxel (PTX), nab-paclitaxel (Nab-PTX), and their combinations with the anti-PD-L1 antibody atezolizumab (ATZ). Compared to ATZ plus PTX, ATZ plus Nab-PTX rewires TCF7+ stem-like effector memory CD8+ T cells (Tsem) and CD4+ T follicular helper (Tfh) cells. Nab-paclitaxel, unlike PTX, also reshapes the myeloid compartment, expanding mast cells and pro-inflammatory macrophages. Our analyses in human TNBC and murine models underscore the crucial role of mast cells in orchestrating anti-tumor immune responses, likely by promoting the recruitment and activation of T and B cells. In vivo experiments demonstrate that activating mast cells alongside PD-L1 blockade attenuates TNBC progression, suggesting mast cells as a promising adjunct for enhancing ICB therapy efficacy.

Progressive T cell exhaustion and predominance of aging tissue associated macrophages with advancing disease stage in penile squamous cell carcinoma

Penile squamous cell carcinoma (PSCC) is a rare malignancy with limited understanding of the tumor immune microenvironment (TIME). The interplay between PSCC and the immune system across disease progression and HPV infection status remains poorly characterized. This study aims to assess the TIME changes from localized to advanced disease and between HPV-positive versus negative tumors to identify potential immune evasion mechanisms in advanced PSCC. scRNA-seq was performed on ten PSCC tissue samples from penile, lymph node and distant metastatic sites with four matched penile and lymph node samples to understand the cellular heterogeneity within PSCC tumors. Analysis of immune cell populations and transcriptional hallmarks were performed stratified by localized (pT1-3, N0) versus advanced (N1-3, M0 or any N, M1) disease states and HPV infection status. We observed significant differences in immune cell infiltration between localized and advanced PSCC disease states and by HPV status. Advanced disease states demonstrated an exhausted immune phenotype, characterized by terminally exhausted CD8+ T cells, M2-like macrophages and hypoxic signature, while localized disease states demonstrated an active innate immune system characterized by increased DCs. HPV-negative tumors displayed low immune cell infiltration while HPV-positive tumors demonstrated an immune exhausted phenotype. These findings offer valuable insights into the evolving PSCC immune landscape, paving the way for the development of potential therapeutic approaches for advanced PSCC.

Cordycepin mediates pyroptosis in HCC through the upregulation of TXNIP and synergizes with anti-PD-L1 immunotherapy

BACKGROUND

Immune checkpoint inhibitors are effective treatments for HCC; however, their therapeutic efficacy is often limited by the development of drug resistance. Therefore, investigating new combination therapeutics involving immune checkpoint inhibitors is critical to improving patient prognosis. In this study, we investigated the therapeutic effect of cordycepin (COR) in HCC and its synergistic effect with anti-programmed cell death ligand 1 (anti-PD-L1) immunotherapy.

METHODS

We selected 2 HCC cell lines to investigate the effects of COR on HCC growth using in vivo and in vitro experiments. We performed RNA sequencing of the MHCC97H cell line treated with or without COR to understand the underlying mechanism and identify the key regulatory genes. Through in vivo and in vitro experiments on gene knockdown cells, we identified thioredoxin-interacting protein as a key molecule involved in the role of COR. Next, we used mouse subcutaneous and orthotopic tumor models to evaluate the therapeutic effects of COR, atezolizumab (a programmed death-ligand 1 [PD-L1] inhibitor), or their combination. Multiple immunofluorescence staining revealed that the combination of atezolizumab and COR therapy greatly increased the number of tumor-infiltrating CD8+ T cells and PD-L1 expression in HCC compared to monotherapy.

RESULTS

Our study revealed that COR significantly inhibited HCC growth both in vitro and in vivo. Mechanistically, we showed that COR induces endoplasmic reticulum stress, which upregulates thioredoxin-interacting protein expression and leads to HCC cell pyroptosis. In addition, the combination treatment with COR and PD-L1 inhibitors profoundly inhibited HCC.

CONCLUSIONS

Overall, our study successfully established a combined therapeutic strategy using COR and PD-L1 inhibitors. This strategy has significant synergistic effects on cancer cells, highlighting its importance in cancer therapy.

Analyze the Diversity and Function of Immune Cells in the Tumor Microenvironment From the Perspective of Single-Cell RNA Sequencing

BACKGROUND

Cancer development is closely associated with complex alterations in the tumor microenvironment (TME). Among these, immune cells within the TME play a huge role in personalized tumor diagnosis and treatment.

OBJECTIVES

This review aims to summarize the diversity of immune cells in the TME, their impact on patient prognosis and treatment response, and the contributions of single-cell RNA sequencing (scRNA-seq) in understanding their functional heterogeneity.

METHODS

We analyzed recent studies utilizing scRNA-seq to investigate immune cell populations in the TME, focusing on their interactions and regulatory mechanisms.

RESULTS

ScRNA-seq reveals the functional heterogeneity of immune cells, enhances our understanding of their role in tumor antibody responses, and facilitates the construction of immune cell interaction networks. These insights provide guidance for the development of cancer immunotherapies and personalized treatment approaches.

CONCLUSION

Applying scRNA-seq to immune cell analysis in the TME offers a novel pathway for personalized cancer treatment. Despite its promise, several challenges remain, highlighting the need for further advancements to fully integrate scRNA-seq into clinical applications.

Generation of allogeneic CAR-NKT cells from hematopoietic stem and progenitor cells using a clinically guided culture method

Cancer immunotherapy with autologous chimeric antigen receptor (CAR) T cells faces challenges in manufacturing and patient selection that could be avoided by using 'off-the-shelf' products, such as allogeneic CAR natural killer T (AlloCAR-NKT) cells. Previously, we reported a system for differentiating human hematopoietic stem and progenitor cells into AlloCAR-NKT cells, but the use of three-dimensional culture and xenogeneic feeders precluded its clinical application. Here we describe a clinically guided method to differentiate and expand IL-15-enhanced AlloCAR-NKT cells with high yield and purity. We generated AlloCAR-NKT cells targeting seven cancers and, in a multiple myeloma model, demonstrated their antitumor efficacy, expansion and persistence. The cells also selectively depleted immunosuppressive cells in the tumor microenviroment and antagonized tumor immune evasion via triple targeting of CAR, TCR and NK receptors. They exhibited a stable hypoimmunogenic phenotype associated with epigenetic and signaling regulation and did not induce detectable graft versus host disease or cytokine release syndrome. These properties of AlloCAR-NKT cells support their potential for clinical translation.

Machine Learning-Based Pathomics Model Predicts Angiopoietin-2 Expression and Prognosis in Hepatocellular Carcinoma

Angiopoietin-2 (ANGPT2) shows promise as prognostic marker and therapeutic target in hepatocellular carcinoma (HCC). However, assessing ANGPT2 expression and prognostic potential using histopathology images viewed with naked eye is challenging. Herein, machine learning was employed to develop a pathomics model for analyzing histopathology images to predict ANGPT2 status. HCC cases obtained from The Cancer Genome Atlas (TCGA-HCC; n = 267) were randomly assigned to the training or testing set, and cases from a single center were employed as a validation set (n = 91). In the TCGA-HCC cohort, the group with high ANGPT2 expression had a significantly lower overall survival compared with the group with low ANGPT2. Histopathologic features in the training set were extracted, screened, and incorporated into a gradient-boosting machine model that generated a pathomics score, which successfully predicted ANGPT2 expression in the three data sets and showed remarkable risk stratification for overall survival in both the TCGA-HCC (P < 0.0001) and single-center cohorts (P = 0.001). Multivariate analysis suggested that the pathomics score could serve as a predictor of prognosis (P < 0.001). Bioinformatics analysis illustrated a distinction in tumor growth and development related gene-enriched pathways, vascular endothelial growth factor-related gene expression, and immune cell infiltration between high and low pathomics scores. This study indicates that the use of histopathology image features can enhance the prediction of molecular status and prognosis in HCC. The integration of image features with machine learning may improve prognosis prediction in HCC.

Biological functions and therapeutic applications of human mucosal-associated invariant T cells

Mucosal-associated invariant T (MAIT) cells are a unique subset of innate-like T lymphocytes that bridge innate and adaptive immunity. Characterized by their semi-invariant T cell receptor (TCR) and abundant localization in mucosal tissues, MAIT cells recognize microbial metabolites, primarily derived from the riboflavin biosynthesis pathway, presented by the major histocompatibility complex (MHC)-related protein 1 (MR1). This interaction, along with co-stimulatory signals, triggers rapid immune responses, including cytokine secretion and cytotoxic activity, highlighting their importance in maintaining immune homeostasis and combating infections. This review provides an in-depth overview of MAIT cell biology, including development, activation pathways, and functional diversity, highlighting their protective roles in immunity, contributions to diseases like cancer and inflammatory bowel disease (IBD), and context-dependent dual functions in health and pathology. This review also highlights the emerging therapeutic potential of MAIT cells in immunotherapy. Their unique TCR specificity, abundance, and tissue-homing properties make them ideal candidates for engineering novel therapies, such as chimeric antigen receptor (CAR)-MAIT cells, targeting infections, cancers, and autoimmune diseases. Challenges like antigen escape, T cell exhaustion, and CAR design optimization must be addressed to enhance clinical efficacy. In summary, MAIT cells are integral to immune function, and their therapeutic potential presents exciting opportunities for the treatment of a wide range of diseases. Further research is essential to unlock the full potential of these versatile immune cells.

HBV-associated hepatocellular carcinomas inhibit antitumor CD8+ T cell via the long noncoding RNA HDAC2-AS2

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Extracellular vesicles (EV) are critical mediators of intercellular communication within the tumor microenvironment, and cancer-cell-secreted EVs often facilitate cancer progression. Here we show that in HBV-associated HCC, tumor-cell-derived EVs contain a TGFβ-inducible long noncoding RNA, termed HDAC2-AS2. EVs enriched with HDAC2-AS2 facilitate cancer progression by suppressing cytotoxicity of intra-tumor CD8+ T cells. Mechanistically, in activated cytotoxic CD8+ T cells, translocation of the transcription factor cyclin-dependent kinase 9 (CDK9), to the cytoplasm is critical for functional integrity. HDAC2-AS2 targets and blocks cytosolic CDK9, and this results in exhaustion of PD-1+CD8+ T cells and suppression of IFN-γ+CD8+ T cell cytotoxicity. Notably, we demonstrate that low CDK9 and high HDAC2-AS2 expressions are associated with poor survival of HCC, which can be rescued by anti-PD-1 therapy. These findings emphasize the significance of tumor-derived EVs in suppressing antitumor CD8+ T cell immunity to promote tumorigenesis, and highlight extracellular HDAC2-AS2 as a promising biomarker and therapeutic target for HCC.

Uncovering immune cell heterogeneity in hepatocellular carcinoma by combining single-cell RNA sequencing with T-cell receptor sequencing

BACKGROUND

Understanding the status and function of tumor-infiltrating immune cells is essential for improving immunotherapeutic effects and predicting the clinical response in human patients with carcinoma. However, little is known about tumor-infiltrating immune cells, and the corresponding research results in hepatocellular carcinoma (HCC) are limited.

AIM

To investigate potential biomarker genes that are important for the development of HCC and to understand how immune cell subsets react throughout this process.

METHODS

Using single-cell RNA sequencing and T-cell receptor sequencing, the heterogeneity and potential functions of immune cell subpopulations from HCC tissue and normal tissue adjacent to carcinoma, as well as their possible interactions, were analyzed.

RESULTS

Eight T-cell clusters from patients were analyzed and identified using bioinformatics, including six typical major T-cell clusters and two newly identified T-cell clusters, among which Fc epsilon receptor 1G+ T cells were characterized by the upregulation of Fc epsilon receptor 1G, tyrosine kinase binding protein, and T cell receptor delta constant, whereas metallothionein 1E+ T cells proliferated significantly in tumors. Differentially expressed genes, such as regulator of cell cycle, cysteine and serine rich nuclear protein 1, SMAD7 and metallothionein 1E, were identified as significantly upregulated in tumors and have potential as biomarkers. In association with T-cell receptor analysis, we inferred the clonal expansion characteristics of each T-cell cluster in HCC patients.

CONCLUSION

We identified lymphocyte subpopulations and potential biomarker genes critical for HCC development and revealed the clonal amplification of infiltrating T cells. These data provide valuable resources for understanding the response of immune cell subsets in HCC.

Integration of single-cell and bulk RNA sequencing to identify a distinct tumor stem cells and construct a novel prognostic signature for evaluating prognosis and immunotherapy in LUAD

BACKGROUND

Cancer stem cells (CSCs) are crucial for lung adenocarcinoma (LUAD). This study investigates tumor stem cell gene signatures in LUAD using single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq), aiming to develop a prognostic tumor stem cell marker signature (TSCMS) model.

METHODS

LUAD scRNA-seq and RNA-seq data were analyzed. CytoTRACE software quantified the stemness score of tumor-derived epithelial cell clusters. Gene Set Variation Analysis (GSVA) identified potential biological functions in different clusters. The TSCMS model was constructed using Lasso-Cox regression, and its prognostic value was assessed through Kaplan-Meier, Cox regression, and receiver-operating characteristic (ROC) curve analyses. Immune infiltration was evaluated using the Cibersortx algorithm, and drug response prediction was performed using the pRRophetic package. TAF10 functional investigations in LUAD cells involved bioinformatics analysis, qRT-PCR, Western blot, immunohistochemistry, and assays for cell proliferation.

RESULTS

Seven distinct cell clusters were identified by CytoTRACE, with epithelial cell cluster 1 (Epi_C1) showing the highest stemness potential. The TSCMS model included 49 tumor stemness-related genes; high-risk patients exhibited lower immune and ESTIMATE scores and increased tumor purity. Significant differences in immune landscapes and chemotherapy sensitivity were observed between risk groups. TAF10 positively correlated with RNA expression-based stemness scores in various tumors, including LUAD. It was over-expressed in LUAD cell lines and clinical tumor tissues, with high expression linked to poor prognosis. Silencing TAF10 inhibited LUAD cell proliferation and tumor sphere formation.

CONCLUSIONS

This study demonstrates the TSCMS model's prognostic value in LUAD, reveals insights into immune infiltration and therapeutic response, and identifies TAF10 as a potential therapeutic target.

Tumor-derived colorectal cancer organoids induce a unique Treg cell population by directing CD4+ T cell differentiation

In colorectal cancer (CRC), increased numbers of tumor-infiltrating CD4+ regulatory T (Treg) cells correlate with tumor development, immunotherapy failure, and poor prognosis. To assess how CRC tumors directly modulate Treg cell differentiation, we developed an in vitro co-culture system using CD4+ T cells from Foxp3eGFP mice and CRC tumor-derived organoids. Co-culture resulted in a significant increase in Treg cell numbers. RNA-sequencing identified a distinct transcriptional profile of CRC organoid-induced Treg cells, with upregulation of genes associated with CRC Treg cells in vivo. High expression of genes upregulated in CRC organoid-induced Treg cells correlates with shorter progression-free intervals and overall survival in CRC patients. Human CRC organoids similarly induced Treg cells with enhanced suppressive capacity and upregulated genes linked to CRC Treg cells in vivo. This model provides insights into how CRC tumors modulate CD4+ T cell differentiation and can identify approaches to disrupt Treg cells and stimulate anti-tumor immunity.

Therapeutic implications of endoplasmic reticulum stress gene CCL3 in cervical squamous cell carcinoma

This study investigated ERS-related gene expressions in CESC, identifying two molecular subtypes, P1 and P2, and constructing a precise prognostic model based on these subtypes. TCGA's whole-genome expression profiles were used to recognize these subtypes through the ConsensusClusterPlus method, further refining prognostic models with univariate and Lasso Cox regression analyses validated by the GSE39001 dataset. The study analyzed the expression distribution of ERS marker genes within T cell subgroups using scRNA-seq data (GSE168652), highlighting T cell diversity. The critical role of the CCL3 gene in prognostic models was examined explicitly in CD8 + T cells from healthy individuals and CESC patients. Elevated CCL3 levels were observed in patients' CD8 + T cells compared to healthy controls. Functional experiments involving CCL3 knockdown and overexpression in HeLa and SiHa CESC cell lines were conducted to investigate its impact on cell proliferation, migration, and invasion. These findings were subsequently validated in a nude mouse model. The results demonstrated that suppressing CCL3 inhibited cell proliferation, migration, and invasion significantly, while its overexpression promoted these processes. In the mouse model, CCL3 silencing reduced tumor growth and decreased Ki-67 labeling within the tumor tissues, indicating the therapeutic potential of targeting CCL3 in CESC treatment, possibly through CD8 + T cell regulation. This study contributes new prognostic assessment tools and personalized treatment options for CESC patients, paving the way for more targeted therapies in CESC by discovering the CCL3 gene, presenting significant clinical implications.

AWT020: a novel fusion protein harnessing PD-1 blockade and selective IL-2 Cis-activation for enhanced anti-tumor immunity and diminished toxicity

Background

The clinical success of the immune checkpoint inhibitor (ICI) targeting programmed cell death protein 1 (PD-1) has revolutionized cancer treatment. However, the full potential of PD-1 blockade therapy remains unrealized, as response rates are still low across many cancer types. Interleukin-2 (IL-2)-based immunotherapies hold promise, as they can stimulate robust T cell expansion and enhance effector function - activities that could synergize potently with PD-1 blockade. Yet, IL-2 therapies also carry a significant drawback: they can trigger severe systemic toxicities and induce immune suppression by expanding regulatory T cells.

Methods

To overcome the challenges of PD-1 blockade and IL-2 therapies while enhancing safety and efficacy, we have engineered a novel fusion protein, AWT020, combining a humanized anti-PD-1 nanobody and an engineered IL-2 mutein (IL-2c). The IL-2c component of AWT020 has been engineered to exhibit no binding to the IL-2 receptor alpha (IL-2Rα) subunit and attenuated affinity for the IL-2 receptor beta and gamma (IL-2Rβγ) complex, aiming to reduce systemic immune cell activation, thereby mitigating the severe toxicity often associated with IL-2 therapies. The anti-PD-1 antibody portion of AWT020 serves a dual purpose: it precisely delivers the IL-2c payload to tumor-infiltrating T cells while blocking the immune-inhibitory signals mediated by the PD-1 pathway.

Results

AWT020 showed significantly enhanced pSTAT5 signaling in PD-1 expressing cells and promoted the proliferation of activated T cells over natural killer (NK) cells. In preclinical studies using both anti-PD-1-sensitive and -resistant mouse tumor models, the mouse surrogate of AWT020 (mAWT020) demonstrated markedly enhanced anti-tumor efficacy compared to an anti-PD-1 antibody, IL-2, or the combination of an anti-PD-1 antibody and IL-2. In addition, the mAWT020 treatment was well-tolerated, with minimal signs of toxicity. Immune profiling revealed that mAWT020 preferentially expands CD8+ T cells within tumors, sparing peripheral T and NK cells. Notably, this selective tumoral T-cell stimulation enables potent tumor-specific T-cell responses, underscoring the molecule's enhanced efficacy and safety.

Conclusion

The AWT020 fusion protein offers a promising novel immunotherapeutic strategy by integrating PD-1 blockade and IL-2 signaling, conferring enhanced anti-tumor activity with reduced toxicity.

Role of CD4+ T cells in cancer immunity: a single-cell sequencing exploration of tumor microenvironment

Recent oncological research has intensely focused on the tumor immune microenvironment (TME), particularly the functions of CD4 + T lymphocytes. CD4+ T lymphocytes have been implicated in antigen presentation, cytokine release, and cytotoxicity, suggesting their contribution to the dynamics of the TME. Furthermore, the application of single-cell sequencing has yielded profound insights into the phenotypic diversity and functional specificity of CD4+ T cells in the TME. In this review, we discuss the current findings from single-cell analyses, emphasizing the heterogeneity of CD4+ T cell subsets and their implications in tumor immunology. In addition, we review the critical signaling pathways and molecular networks underpinning CD4+ T cell activities, thereby offering novel perspectives on therapeutic targets and strategies for cancer treatment and prognosis.