Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution

Manganese-coordinated nanoparticles loaded with CHK1 inhibitor dually activate cGAS-STING pathway and enhance efficacy of immune checkpoint therapy

Notable advancements have been made in utilizing immune checkpoint blockade (ICB) for the treatment of various cancers. However, the overall response rates and therapeutic effectiveness remain unsatisfactory. One cause is the inadequate immune environment characterized by poor T cell infiltration in tumors. To address these limitations, enhancing immune infiltration is crucial for optimizing the therapeutic efficacy of ICB. Activating the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway is essential for initiating immune response and has become a potential target for developing combination therapies with ICB. In this study, we designed and fabricated manganese-containing nanoparticles loaded with the CHK1 inhibitor PF477736, which were subsequently encapsulated with macrophage membrane (PF/MMSN@MPM). This innovative design achieved excellent tumor targeting and demonstrated potent antitumor effects. The combination therapy dually amplified the cGAS-STING pathway, causing a cascade of enhanced therapeutic effects against tumors. Furthermore, single-cell mass cytometry (CyTOF) analysis revealed that PF/MMSN@MPM enhanced the activation and infiltration of immune cells. Moreover, the combination of PF/MMSN@MPM with anti-PD-1 (αPD-1) exhibited a stronger therapeutic effect compared to αPD-1 alone. PF/MMSN@MPM precisely and synergistically activated the cGAS-STING pathway, significantly improving therapeutic efficacy of ICB, and offering promising potential for tumor therapy.

Updates on Treatments and Management of Nasopharyngeal Carcinoma

Nasopharyngeal carcinoma (NPC) is a unique head and neck cancer, where the endemic subtype is strongly associated with Epstein-Barr virus (EBV) infection, whereas emerging data suggest that a subset of nonendemic NPC may be associated with human papillomavirus (HPV) infection. Nonetheless, treatment advances have been driven by clinical trials conducted in endemic NPC, investigating optimal sequencing of chemotherapy and immune checkpoint inhibitors with radiotherapy for locoregionally advanced disease. The preference for induction chemotherapy (IC) in these patients has also led to evolution in the concept of radiotherapy target delineation. Because of its association with EBV, plasma EBV DNA is an archetypal biomarker for endemic NPC, and it is being explored for precise stratification and treatment individualization in several ongoing trials. In the space of recurrent or metastatic-NPC, with the advent of platinum-doublet chemotherapy and anti-PD-1 antibody as the new standard of care, several trials are investigating new immunotherapeutic combinations, bispecific antibodies, and antibody-drug conjugates that have demonstrated promise in early phase trials. An important advance for NPC in 2025 is the update of the 9th version of the TNM staging system, which has introduced several key changes, including downgrading of the TNM stage groupings for localized disease, and splitting of metastatic NPC into IVA and IVB based on the number of metastatic lesions. These revisions would have implications for the treatment and design of future trials. These advances are also relevant to nonendemic NPC, where evidence is inconclusive whether this disease responds differently to current treatments compared with endemic NPC.

Mitochondrial function changes in T cell subsets during radiotherapy for patients with nasopharyngeal carcinoma

Mitochondrial dysfunction-mediated T cell exhaustion is associated with the efficacy of tumor therapy; however, the effect of radiotherapy (RT) on the mitochondrial function of peripheral blood immune cells remains still unclear. Therefore, the current study aimed to determine mitochondrial function indicators in immune cells, in particular mitochondrial mass (MM) and mitochondrial membrane potential (MMP), to assess the dynamic changes of immune status in patients with nasopharyngeal carcinoma (NPC) during RT. Peripheral venous blood was collected from patients with locally advanced NPC at day 1 pre-RT, at the 10th fraction of RT and within 2 days after RT. Based on a novel immunofluorescence technique, flow cytometry was used to assess the proportion of lymphocytes and their subsets in peripheral blood and the mitochondrial indexes, MM and low MMP (MMPlow). Univariate and multivariate logistic regression analyses were performed to evaluate the clinical factors associated with the efficacy of RT. A total of 27 patients were enrolled. After RT, lymphocyte count (P<0.05) and the proportion of CD4+ T cells (P<0.05) demonstrated a downward trend. In addition, the proportion of CD4+ memory-effector T (Tem; P<0.05) cells and CD8+ Tem cells (P=0.005) significantly increased during RT. No significant changes were demonstrated for MM in CD4+ effector T (Te) cells, whilst MMPlow was significantly reduced (P=0.047). However, the mitochondrial function of CD8+ T cells did not significantly change. Multivariate logistic regression analysis revealed that lymphocyte count [odds ratio (OR), 47.317; 95% confidence interval (CI), 1.240-1806.065] and MMPlow in CD4+ Te cells (OR, 0.889; 95% CI, 0.792-0.997) were independent factors that could affect clinical efficacy. Receiver operating characteristic curve analysis demonstrated that the area under the curve values for MMPlow in CD4+ T cells, lymphocyte count and their combination were 0.72 (P=0.13), 0.69 (P=0.19) and 0.89 (P=0.0073), respectively. These findings suggest that RT could inhibit immune cells in peripheral blood. However, this treatment approach could activate the memory cell subsets of immune cells and enhance the MMP of effector CD4+ T cells. Therefore, the evaluation of mitochondrial function in lymphocytes could be used as a predictor of RT efficacy in patients with locally advanced NPC.

Integrating bulk RNA-seq and scRNA-seq analyses with machine learning to predict platinum response and prognosis in ovarian cancer

Platinum-based therapy is an integral part of the standard treatment for ovarian cancer. However, despite extensive research spanning several decades, the identification of dependable predictive biomarkers for platinum response in clinical practice has proven to be a formidable challenge. Recently, the development of single-cell technology has enabled more precise investigations into the heterogeneity of cancer. In this study, we isolated cancer cells from the single-cell transcriptomic data of platinum-sensitive and platinum-resistant patients with ovarian cancer. Differential gene analysis of platinum-sensitive and platinum-resistant cancer cells revealed that several of the differentially expressed genes had previously been reported in other studies to be associated with platinum resistant. Gene set enrichment analysis revealed the up-regulation of pathways involved in processes such as autophagy, cell cycle regulation, and DNA damage repair, which are known to promote platinum resistance in ovarian cancer. Based on these findings, we hypothesized that these differentially expressed genes could be used to predict the response of ovarian cancer patients to platinum-based chemotherapy. To validate this hypothesis, we explored 7 different machine learning models for predicting platinum chemotherapy response at varying feature gene counts. Ultimately, the random forest model performed the best, with 5 genes (PAX2, TFPI2, APOA1, ADIRF and CRISP3) and achieve an AUC of 0.993 in test cohort and 0.989 in GSE63885 independent validation cohorts. We named this model GPPS (Genes to Predict Platinum response Signature). Furthermore, we discovered that the GPPS model can also predict patient prognosis.

Tumor-infiltrated double-negative regulatory T cells predict outcome of T cell-based immunotherapy in nasopharyngeal carcinoma

Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TILs) has demonstrated clinical success in solid tumors. We analyze 47 TIL infusion products and 62 pretreatment tumor microenvironments (TMEs) from a randomized phase 2 clinical study of concurrent chemoradiotherapy plus TIL-ACT (NCT02421640). Using single-cell and bulk RNA sequencing along with flow cytometry, we identify 14 CD3+ T cell clusters within 26 TIL infusion products: 11 CD3+CD8+ TILs, 2 CD3+CD4+ TILs, and 1 CD3+CD8-CD4- double-negative (DN) TIL. (DN) TILs, significantly associated with poor TIL-ACT outcomes, exhibit an activated regulatory T cell-like phenotype and include two CD56+ and four CD56- subsets. Among them, CD56-KZF2+ (DN) TILs are predominantly suppressive. (DN) TILs inhibit CD8+ TIL expansion via Fas-FasL, transforming growth factor β (TGF-β), and interleukin (IL)-10 signaling. Distinct CD8+ T subsets differentially impact on TIL-ACT outcomes, while 9 baseline TME gene signatures and 14 intracellular T cell genes hold prognostic value. Our findings identify predictive TIL subsets and biomarkers for TIL-ACT outcomes.

Intratumoral CD8+ tumor-infiltrating lymphocytes as prognostic predictors in radio-chemoradiotherapy-treated nasopharyngeal carcinoma

Background

The prognostic value of tumor-infiltrating lymphocytes (TILs) in nasopharyngeal carcinoma (NPC) has been established. However, the prognostic significance of CD4+ and CD8+ TIL subtypes in NPC remains unclear.

Methods

We collected 214 tissue samples diagnosed with NPC for immunohistochemical staining. The density of CD4+ and CD8+ TILs was evaluated in intratumoral (within tumor cell nests) and stromal (the surrounding stroma of tumor cell nests) areas. Correlations between TIL density and progression-free survival (PFS) and overall survival (OS) were analyzed.

Results

High levels of intratumoral CD8+ TILs were significantly associated with reduced risk of disease progression (HR 0.382; 95% CI, 0.178-0.819, P = 0.013) and death (HR 0.265; 95% CI, 0.104-0.675, P = 0.005). Although high stromal CD8+ TIL levels were linked to higher PFS and OS, these differences did not reach statistical significance (P = 0.114 and P = 0.079, respectively). CD4+ TILs showed no significant correlation with PFS or OS. In multivariate analysis, intratumoral CD8+ TILs remained an independent prognostic factor for PFS and OS. Subgroup analysis revealed that in patients with locally advanced disease, high intratumoral CD8+ TILs were significantly associated with improved PFS (HR 0.329; 95% CI, 0.129-0.843, P = 0.021) and OS (HR 0.209; 95% CI, 0.064-0.681, P = 0.009). Conversely, in early-stage patients, neither CD8+ nor CD4+ TILs were significantly associated with PFS or OS.

Conclusion

Our findings suggest that intratumoral CD8+ TILs serve as a reliable prognostic biomarker for NPC, with their prognostic value particularly pronounced in patients with locally advanced disease.

AI-Driven Drug Target Screening Platform Identified Oncogene CACNA2D1 Activated by Enhancer Infestation in Epstein-Barr Virus-Associated Nasopharyngeal Carcinoma

The management of nasopharyngeal cancer (NPC) is rapidly evolving, with immune checkpoint inhibitors emerging as a prominent treatment approach. However, drug development targeting specific molecular and cellular abnormalities in NPC has slowed. Recent advancements in artificial intelligence (AI) and bioinformatics, particularly those integrating multi-omics data, offer a more effective alternative to traditional in vitro screening methods for identifying clinically actionable targets in NPC. Through a combination of multi-omics analyses and AI-driven screening, we identified CACNA2D1 as a novel cancer-cell-specific therapeutic target in NPC. Our research indicates that exploiting Epstein-Barr virus (EBV) tethering increases H3K27 acetylation near the CACNA2D1 promoter. Analysis of clinical specimens revealed significant upregulation of CACNA2D1 at both the transcriptional and translational levels (p-value < 0.01). Functional studies demonstrated that the mouse tumour size shrank by one-third upon the depletion of CACNA2D1, and there was an 85% reduction in cancer cell growth through the blockage of enhancers, while the presence of CACNA2D1 conferred a survival advantage during NPC tumour development. These findings highlight the potential of CACNA2D1 as a promising target for therapeutic intervention in NPC.

Immunosequencing identifies signatures of T cell responses for early detection of nasopharyngeal carcinoma

To identify nasopharyngeal carcinoma (NPC)-relevant T cell receptors (TCRs), we profile the repertoires of peripheral blood TCRβ chains from 228 NPC patients, 241 at-risk controls positive for serum Epstein-Barr virus (EBV) VCA-IgA antibody, and 251 seronegative controls. We develop a TCR-based signature (T-score) based on 208 NPC-enriched CDR3β sequences, which accurately diagnoses NPC in both the original and independent validation cohorts. Notably, a higher T-score, associated with a shorter time interval to NPC diagnosis, effectively identifies early-stage NPC among EBV-seropositive at-risk individuals prior to clinical diagnosis. These NPC-enriched TCRs react against not only EBV-specific antigens but also non-EBV antigens expressed by NPC cells, indicating a broad range of specificities. Moreover, the abundance of NPC-enriched CD8+ T cells in blood correlates with the infiltration of non-exhausted T cell counterparts in tumors and predicts prolonged survival, suggesting that these NPC-enriched T cells have significant potential for disease monitoring and therapeutic applications.

EBV Vaccines in the Prevention and Treatment of Nasopharyngeal Carcinoma

Epstein-Barr virus (EBV), a ubiquitous human herpesvirus, has been robustly linked to the pathogenesis of nasopharyngeal carcinoma (NPC). The mechanism of EBV-induced NPC involves complex interactions between viral proteins and host cell pathways. This review aims to comprehensively outline the mechanism of EBV-induced NPC and the latest advances in targeted EBV vaccines for prophylaxis and treatment. This review explores the intricate molecular mechanisms by which EBV contributes to NPC pathogenesis, highlighting viral latency, genetic and epigenetic alterations, and immune evasion strategies. It emphasizes the pivotal role of key viral proteins, including EBNA1, LMP1, and LMP2A, in carcinogenesis. Subsequently, the discussion shifts towards the development of targeted EBV vaccines, including preventive vaccines aimed at preventing primary EBV infection and therapeutic vaccines aimed at treating diagnosed EBV-related NPC. The review underscores the challenges and future directions in the field, stressing the importance of developing innovative vaccine strategies and combination therapies to improve efficacy. This review synthesizes current insights into the molecular mechanisms of EBV-induced NPC and the development of EBV-targeted vaccines, highlighting the potential use of mRNA vaccines for NPC treatment.

MIST: An interpretable and flexible deep learning framework for single-T cell transcriptome and receptor analysis

Joint analysis of transcriptomic and T cell receptor (TCR) features at single-cell resolution provides a powerful approach for in-depth T cell immune function research. Here, we introduce a deep learning framework for single-T cell transcriptome and receptor analysis, MIST (Multi-insight for T cell). MIST features three latent spaces: gene expression, TCR, and a joint latent space. Through analyses of antigen-specific T cells, and T cell datasets related to lung cancer immunotherapy and COVID19, we demonstrate MIST's interpretability and flexibility. MIST easily and accurately resolves cell function and antigen specificity by vectorizing and integrating transcriptome and TCR data of T cells. In addition, using MIST, we identified the heterogeneity of CXCL13+ subsets in lung cancer infiltrating CD8+ T cells and their association with immunotherapy, providing additional insights into the functional transition of CXCL13+ T cells related to anti-PD-1 therapy that were not reported in the original study.

A rare KLHDC4 variant Glu510Lys is associated with genetic susceptibility and promotes tumor metastasis in nasopharyngeal carcinoma

Various genetic association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with nasopharyngeal carcinoma (NPC) risk. However, these studies have predominantly focused on common variants, leaving the contribution of rare variants to the "missing heritability" largely unexplored. Here, we integrate genotyping data from 3925 NPC cases and 15,048 healthy controls to identify a rare SNP, rs141121474, resulting in a Glu510Lys mutation in KLHDC4 gene linked to increased NPC risk. Subsequent analyses reveal that KLHDC4 is highly expressed in NPC and correlates with poorer prognosis. Functional characterizations demonstrate that KLHDC4 acts as an oncogene in NPC cells, enhancing their migratory and metastatic capabilities, with these effects being further augmented by the Glu510Lys mutation. Mechanistically, the Glu510Lys mutant exhibits increased interaction with Vimentin compared to the wild-type KLHDC4 (KLHDC4-WT), leading to elevated Vimentin protein stability and modulation of the epithelial-mesenchymal transition process, thereby promoting tumor metastasis. Moreover, Vimentin knockdown significantly mitigates the oncogenic effects induced by overexpression of both KLHDC4-WT and the Glu510Lys variant. Collectively, our findings highlight the critical role of the rare KLHDC4 variant rs141121474 in NPC progression and propose its potential as a diagnostic and therapeutic target for NPC patients.

Dendritic cell maturation in cancer

Dendritic cells (DCs) are specialized antigen-presenting cells that are present at low abundance in the circulation and tissues; they serve as crucial immune sentinels by continually sampling their environment, migrating to secondary lymphoid organs and shaping adaptive immune responses through antigen presentation. Owing to their ability to orchestrate tolerogenic or immunogenic responses to a specific antigen, DCs have a pivotal role in antitumour immunity and the response to immune checkpoint blockade and other immunotherapeutic approaches. The multifaceted functions of DCs are acquired through a complex, multistage process called maturation. Although the role of inflammatory triggers in driving DC maturation was established decades ago, less is known about DC maturation in non-inflammatory contexts, such as during homeostasis and in cancer. The advent of single-cell technologies has enabled an unbiased, high-dimensional characterization of various DC states, including mature DCs. This approach has clarified the molecular programmes associated with DC maturation and also revealed how cancers exploit these pathways to subvert immune surveillance. In this Review, we discuss the mechanisms by which cancer disrupts DC maturation and highlight emerging therapeutic opportunities to modulate DC states. These insights could inform the development of DC-centric immunotherapies, expanding the arsenal of strategies to enhance antitumour immunity.

IRF8 and CD2 are potential targets of immunotherapy in non-small cell lung cancer

Background

Immune checkpoint inhibitors (ICIs) are clinically effective in the treatment of non-small cell lung cancer (NSCLC), but the response rate in nonselective NSCLC patients is approximately 20%. It is important to expand the pool of benefits of immunotherapy. However, current solution strategies are limited. Our research is to identify new targets for combined immunotherapy and expand the beneficiary population of immunotherapy.

Methods

Functional enrichment analysis was performed for differentially expressed genes (DEGs) in 175 NSCLC immunotherapy cohorts and 494 non-immunotherapy cohorts, and single-sample gene set enrichment analysis (ssGSEA) was used to quantify the level of infiltration of different immune cell subpopulations. Weighted correlation network analysis (WGCNA), univariate Cox regressions, least absolute shrinkage and selection operator (LASSO) regressions, and gene correlation analysis were applied to identify immune signature genes associated with immune cell infiltration, and a nomogram was constructed to predict the survival rate.

Results

The DEGs were not enriched in the classical antitumour immune response and the dendritic cells (DCs) infiltration level in the tumour microenvironment (TME) was at a low level in the immunotherapy cohort. The high expression of IRF8 and CD2 was positively correlated with the level of DCs infiltration, the core of tumour immune response regulation, and can bring better survival prognosis for patients. Besides, targeted activation of IRF8 and CD2 can improve the efficacy of ICIs.

Conclusions

High expression of IRF8 and CD2 enhances the antitumour immune response, and IRF8 and CD2 may be new prognostic indicators and targets of combined ICIs for lung adenocarcinoma in NSCLC.

Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction

The pervasive occurrence of nasopharyngeal carcinoma (NPC) is intricately linked to Epstein-Barr virus (EBV) infection, making EBV and its associated pathways promising therapeutic targets for NPC and other EBV-related cancers. Lytic induction therapy, an emerging virus-targeted therapeutic strategy, capitalizes on the presence of EBV in tumor cells to specifically induce cytotoxicity against EBV-associated malignancies. Despite the expanding repertoire of compounds developed to induce EBV lytic reactivation, achieving universal induction across all infected cells remains elusive. The inherent heterogeneity of tumor cells likely contributes to this variability. In this study, we used the NPC43 cell line, an EBV-positive NPC in vitro model, and single-cell transcriptomics to characterize the diverse cellular responses to EBV lytic induction. Our longitudinal monitoring revealed a distinctive lytic induction non-responsive cellular state characterized by elevated expression of SOX2 and NTRK2. Cells in this state exhibit phenotypic similarities to cancer stem cells (CSCs), and we verified the roles of SOX2 and NTRK2 in manifesting these phenotypes. Our findings reveal a significant challenge for lytic induction therapy, as not all tumor cells are equally susceptible. These insights highlight the importance of combining lytic induction with therapies targeting CSC-like properties to enhance treatment efficacy for NPC and other EBV-associated cancers.

Epstein-Barr virus hijacks histone demethylase machinery to drive epithelial malignancy progression through KDM5B upregulation

Epstein-Barr virus (EBV) is a significant epigenetic driver in the development of epithelial-origin nasopharyngeal carcinoma (NPC) and gastric cancer (GC), which together represent 80% of EBV-associated malignancies. Despite its known association, the specific mechanisms, particularly those involving EBV-induced histone modifications, remain poorly understood. Through integrative analyses of single-cell and bulk transcriptome data from epithelial tumor tissues and EBV-infected cells, we identified KDM5B as a critical histone-modifying factor consistently upregulated following EBV infection. We demonstrated that EBV stimulates KDM5B expression via interactions of its latent gene EBNA1 with transcription factor CEBPB and through direct binding of its lytic gene BZLF1 to Zta-response elements on the KDM5B promoter. Functional assays revealed that KDM5B acts as an oncogene, correlating with poor survival outcomes in EBV-associated epithelial cancers. Mechanistically, KDM5B inhibited the tumor suppressor gene PLK2 through histone demethylation, thereby activating the PI3K/AKT/mTOR signaling pathway and promoting malignant progression. Furthermore, treatment with the KDM5B inhibitor AS-8351 markedly attenuated this signaling activity and exhibited strong anti-tumor effect in both in vitro and in vivo patient-derived xenograft models from EBV-associated tumors. Together, these findings provide novel insights into how EBV hijacks KDM5B to mediate histone demethylation of PLK2, facilitating tumor progression through the PI3K/AKT/mTOR pathway in epithelial cancers, highlighting promising therapeutic strategies targeting epigenetic alterations in EBV-associated cancers.

Analysis of Head and Neck Cancer scRNA-seq Data Identified PRDM6 Promotes Tumor Progression by Modulating Immune Gene Expression

Head and neck squamous cell carcinoma (HNSCC) is a biologically aggressive and heterogeneous group of cancers with limited treatment options for patients who do not respond to standard therapies. While HPV-related HNSCCs tend to show better therapeutic outcomes, we still had limited understanding of the immune mechanisms underlying these cancers. Immune-responsive genes (IRGs) have emerged as critical factors in regulating both tumor progression and immune response. Recent advances in single-cell RNA sequencing (scRNA-seq) and the development of cell-type specific regulon inference tools, such as IRIS3, have provided new insights into the tumor immune microenvironment. In this study, we leveraged the IRIS3 platform to analyze scRNA-seq data from HNSCC patient samples, identifying novel transcription factor (TF)-IRG networks that contribute to tumor proliferation and immune escape. Specifically, we identified PRDM6, a histone methyltransferase, possesses the previously unknown role in promoting tumor cell proliferation by inducing IRG expression. We further demonstrated that HPV viral oncoproteins (E6/E7) oncoproteins up-regulate the PRDM6 expression, which associates PRDM6 with HPV-positive HNSCC.

Transcriptomic profiling reveals mechanism, therapeutic potential, and prognostic value of cancer stemness characteristic in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) recurrence, distant metastasis, and drug resistance remain significant obstacles in clinical prognosis. Cancer stemness is hypothesized to be a key contributor, though direct evidence is sparse. We utilized bioinformatics and machine learning techniques on single-cell RNA-seq and bulk transcriptomic datasets, complemented by basic experiments, to investigate stemness-based characteristics in NPC. Our analysis identified two potential developmental trajectories of nasopharyngeal cancer cells, each exhibiting varying levels of stemness. We subsequently identified and validated a cancer stemness-related signature (STEM-signature). Single-cell profiling revealed enrichment of LAYN + CD8 + , CTLA4 + CD4 + , CXCL13 + CD4 + T cells, tumor-associated macrophages, and CD14 + monocytes in NPC patients with high stemness. NicheNet analysis suggested these immune cells regulate cancer stemness. Bulk transcriptomic analysis corroborated these findings, indicating a poor therapeutic response in high-stemness NPC. We predicted 13 potential drugs and identified 13 stemness-related miRNAs for NPC with high stemness. A Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression model, based on this miRNA signature, predicted overall survival with an AUC of 0.71 and 0.72 in validation and testing sets, respectively. The miRNA-based stemness signature outperformed previous established signatures. Multivariate Cox regression analysis indicated that our prognostic signature could serve as an independent prognostic factor (p < 0.001). Basic experiments showed that miR-300, miR-361-5p, miR-1246, and miR-1290 enhanced the stemness characteristics of NPC cells, promoting proliferation, invasion, and migration. These findings suggest that these four stemness-related miRNAs could serve as therapeutic targets, potentially improving therapeutic responses by targeting stemness-related genes.

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.

Cell-associated galectin 9 interacts with cytotoxic T cells confers resistance to tumor killing in nasopharyngeal carcinoma through autophagy activation

Immune effector cells, including cytotoxic T lymphocytes (CTLs) play essential roles in eliminating cancer cells. However, their functionality is often compromised, even when they infiltrate the tumor microenvironment (TME) or are transferred to cancer patients adoptively. In this study, we focused on galectin 9 (G9), an inhibitory ligand that we observed to be predominately positioned on the plasma membrane and readily interacts with CD8 + CTL in the TME of nasopharyngeal carcinoma (NPC). We discovered that cell-cell contact between activated effector CTLs and target tumor cells (TarTC) with G9 overexpression led to cellular death defects. Despite the formation of CTL-TarTC conjugates, there is no impact on the cell number nor viability of CTL, and the release of cytolytic content and associated activity were not completely abrogated. Instead, this interaction promoted autophagy and restricted necrosis in the TarTC. Furthermore, reducing G9 expression in tumor cells enhanced the suppressive effect on tumor growth upon adoptive transfer of activated effector CTL. Additionally, inhibiting autophagy effectively controlled tumor growth in cases of G9 overexpression. Therefore, we highlight the contribution of G9 in facilitating the resistance of NPC to CTL-mediated killing by inducing a selection-cell death state in tumor cells, characterized by increased autophagy and decreased necrosis.

Adoptive cell therapy against tumor immune evasion: mechanisms, innovations, and future directions

Tumors employ a range of strategies to evade detection and eradication by the host's immune system. These include downregulating antigen expression, altering antigen presentation processes, and inhibiting immune checkpoint pathways. etc. Adoptive Cell Therapy (ACT) represents a strategy that boosts anti-tumor immunity. This is achieved by amplifying or genetically engineering immune cells, which are either sourced from the patient or a donor, in a laboratory setting. Subsequently, these cells are reintroduced into the patient to bolster their immune response against cancer. ACT has successfully restored anti-tumor immune responses by amplifying the activity of T cells from patients or donors. This review focuses on the mechanisms underlying tumor escape, including alterations in tumor cell antigens, the immunosuppressive tumor microenvironment (TME), and modulation of immune checkpoint pathways. It further explores how ACT can avddress these factors to enhance therapeutic efficacy. Additionally, the review discusses the application of gene-editing technologies (such as CRISPR) in ACT, highlighting their potential to strengthen the anti-tumor capabilities of T cells. Looking forward, the personalized design of ACT, combined with immune checkpoint inhibitors and targeted therapies, is expected to significantly improve treatment outcomes, positioning this approach as a key strategy in the field of cancer immunotherapy.

Single-cell profiling and clinical characteristics analysis of lung squamous carcinoma

Lung squamous carcinoma (LUSC) is a highly heterogeneous disease. However, the tumor microenvironment (TME) landscape and clinical characteristics for LUSC have not yet been elucidated. To map the TME and clinical characteristics of LUSC, we performed single-cell RNA sequencing for 504 LUSC samples on basis of TCGA and Gene Expression Omnibus. We introduced the computational algorithms "ESTIMATE" and "CIBERSORT" to analyze immune cell infiltration and immune-checkpoint-related gene signatures in various LUSC clusters. Weighted gene co-expression network analysis was used to explore the connections between molecular characteristics and clinical traits in LUSC. A prognostic model was constructed by performing multivariate COX. Two gene clusters exhibiting disparate immune and clinical characteristics were identified. Our findings indicate that patients in cluster 2, who have a more favorable prognosis, exhibit immune characteristics such as elevated levels of immunosuppression-associated M2 macrophages, resting memory CD4 T cells, resting dendritic cells (DC), and TNFRSF4, alongside reduced infiltration of activated DC and lower expression of TNFRSF18.Whereafter, the Risk Score model was built on basis of 3-DEGs signature consisted of cystatin C (CST3), transglutaminase type 2 (TGM2), JUN, which were proved by q-PCR and immunofluorescence. Besides, high-Risk Score may be responsible for poor prognosis in LUSC patients. Our study identified that tumor-infiltrating immune cell subtypes and the Risk Score model might shed light on the heterogeneity in LUSC patients. The TME, three DEGs and Risk Score can effectively serve as biomarkers to elucidate the immune landscape and predict prognosis in LUSC patients. They may provide insights to the investigations on therapeutic strategies for LUSC.

Anti-LAG-3 antibody LBL-007 plus anti-PD-1 antibody toripalimab in advanced nasopharyngeal carcinoma and other solid tumors: an open-label, multicenter, phase Ib/II trial

PURPOSE

Open-label phase Ib/II study to investigate the safety and efficacy of LBL-007, an anti-LAG-3 antibody, plus toripalimab, an anti-PD-1 antibody, in patients with previously treated advanced nasopharyngeal carcinoma (NPC) and other solid tumors.

METHODS

Patients with advanced tumors refractory to prior standard therapies were enrolled. In phase Ib, patients received LBL-007 200 mg or 400 mg and toripalimab 240 mg intravenously once every 3 weeks. In phase II, all patients received LBL-007 at the recommended phase II dose (RP2D) and toripalimab 240 mg intravenously once every 3 weeks. The primary end points were safety in phase Ib and objective response rate (ORR) in phase II. The exploratory end point was the predictive capability of LAG-3 and PD-L1 expression for efficacy.

RESULTS

Between November 30, 2021, and December 1, 2023, 80 patients were enrolled, including 30 (37.5%) with NPC and 50 (62.5%) with other tumors. Median follow-up was 26.0 months. In Phase Ib, LBL-007 was administered at 200 mg to four patients and 400 mg to six patients, with no dose-limiting toxicities observed. Therefore, the 400 mg dose of LBL-007 was established as the RP2D and administered to 70 patients in phase II. Nine (11.3%) of 80 patients had grade 3 or 4 treatment-related adverse events, the most common of which included anemia (2.5%), hyponatremia (2.5%), increased alanine aminotransferase (2.5%), increased aspartate aminotransferase (1.3%), and fatigue (1.3%). Eight patients (10.0%) had treatment-related serious adverse events. No treatment-related deaths were reported. In immunotherapy-naive NPC patients (n = 12), ORR was 33.3%, disease control rate (DCR) was 75%, and median progression-free survival (PFS) was 10.8 months (95% CI, 1.3 to not estimated). In IO-treated NPC patients (n = 17), ORR was 11.8%, DCR was 64.7%, and median PFS was 2.7 months (95% CI, 1.4 to 4.9). For other tumors, ORRs were 15.8% in immunotherapy-naive patients and 3.7% in immunotherapy-treated patients. Patients with ≥ 2 + LAG-3 expression had a higher ORR of 28.0%, compared to 7.7% in those with < 2 + LAG-3 expression.

CONCLUSION

LBL-007 plus toripalimab exhibited a manageable safety profile in patients with advanced solid tumors and demonstrated promising antitumor activity in NPC, especially in immunotherapy-naive patients. These findings warrant further validation in future studies.

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age

A comprehensive understanding of the evolution of the immune landscape in humans across the entire lifespan at single-cell transcriptional and protein levels, during development, maturation and senescence is currently lacking. We recruited a total of 220 healthy volunteers from the Shanghai Pudong Cohort (NCT05206643), spanning 13 age groups from 0 to over 90 years, and profiled their peripheral immune cells through single-cell RNA-sequencing coupled with single T cell and B cell receptor sequencing, high-throughput mass cytometry, bulk RNA-sequencing and flow cytometry validation experiments. We revealed that T cells were the most strongly affected by age and experienced the most intensive rewiring in cell-cell interactions during specific age. Different T cell subsets displayed different aging patterns in both transcriptomes and immune repertoires; examples included GNLY+CD8+ effector memory T cells, which exhibited the highest clonal expansion among all T cell subsets and displayed distinct functional signatures in children and the elderly; and CD8+ MAIT cells, which reached their peaks of relative abundance, clonal diversity and antibacterial capability in adolescents and then gradually tapered off. Interestingly, we identified and experimentally verified a previously unrecognized 'cytotoxic' B cell subset that was enriched in children. Finally, an immune age prediction model was developed based on lifecycle-wide single-cell data that can evaluate the immune status of healthy individuals and identify those with disturbed immune functions. Our work provides both valuable insights and resources for further understanding the aging of the immune system across the whole human lifespan.

Exploring the tumor microenvironment of colorectal cancer patients post renal transplantation by single-cell analysis

Patients with colorectal cancer (CRC) following renal transplantation require long-term immunosuppressants to prevent graft rejection. However, the impact of these immunosuppressants on the tumor immune microenvironment and the roles of immune cells within it remain poorly understood. We conducted comprehensive single-cell RNA sequencing on tumor and normal tissues from four CRC patients post renal transplantation and compared these with published data from 23 non-transplant CRC patients. We set four groups for detailed comparative analysis based on the renal transplantation status and tissue origin: non-renal transplantation normal (nRT_Normal), non-renal transplantation tumor (nRT_Tumor), renal transplantation normal (RT_Normal), renal transplantation tumor (RT_Tumor). Our analysis revealed significant tumor immune microenvironment landscape alterations in the transplantation group. CD8+effector T cells of RT_Tumor showed significantly diminished cytotoxicity and tumor neoantigen recognition (p < 0.0001), while CD4+FOXP3 regulatory T cells of RT_Tumor displayed a higher inhibitory score (p < 0.05), indicating preserved immunomodulatory potential compared with non-transplant CRC. Notably, significantly increased CTLA4 expression in T cells of RT_Tumor was found and testified (p < 0.05). Our findings provide novel mechanistic insights for understanding the immune landscape in renal transplant recipients with CRC and pave the way for potential immunotherapeutic strategies that may improve survival and quality of life for this patient population.

CXCL16/CXCR6/TGF-β Feedback Loop Between M-MDSCs and Treg Inhibits Anti-Bacterial Immunity During Biofilm Infection

Staphylococcus aureus (S. aureus) is a leading cause of Periprosthetic  joint  infection (PJI), a severe complication after joint arthroplasty. Immunosuppression is a major factor contributing to the infection chronicity of S. aureus PJI, posing significant treatment challenges. This study investigates the relationship between the immunosuppressive biofilm milieu and S. aureus PJI outcomes in both discovery and validation cohorts. This scRNA-seq analysis of synovium from PJI patients reveals an expansion and heightened activity of monocyte-related myeloid-derived suppressor cells (M-MDSCs) and regulatory T cells (Treg). Importantly, CXCL16 is significantly upregulated in M-MDSCs, with its corresponding CXCR6 receptor also elevated on Treg. M-MDSCs recruit Treg and enhance its activity via CXCL16-CXCR6 interactions, while Treg secretes TGF-β, inducing M-MDSCs proliferation and immunosuppressive activity. Interfering with this cross-talk in vivo using Treg-specific CXCR6 knockout PJI mouse model reduces M-MDSCs/Treg-mediated immunosuppression and alleviates bacterial burden. Immunohistochemistry and recurrence analysis show that PJI patients with CXCR6high synovium have poor prognosis. This findings highlight the critical role of CXCR6 in Treg in orchestrating an immunosuppressive microenvironment and biofilm persistence during PJI, offering potential targets for therapeutic intervention.

Integrative mapping of human CD8+ T cells in inflammation and cancer

CD8+ T cells exhibit remarkable phenotypic diversity in inflammation and cancer. However, a comprehensive understanding of their clonal landscape and dynamics remains elusive. Here we introduce scAtlasVAE, a deep-learning-based model for the integration of large-scale single-cell RNA sequencing data and cross-atlas comparisons. scAtlasVAE has enabled us to construct an extensive human CD8+ T cell atlas, comprising 1,151,678 cells from 961 samples across 68 studies and 42 disease conditions, with paired T cell receptor information. Through incorporating information in T cell receptor clonal expansion and sharing, we have successfully established connections between distinct cell subtypes and shed light on their phenotypic and functional transitions. Notably, our approach characterizes three distinct exhausted T cell subtypes and reveals diverse transcriptome and clonal sharing patterns in autoimmune and immune-related adverse event inflammation. Furthermore, scAtlasVAE facilitates the automatic annotation of CD8+ T cell subtypes in query single-cell RNA sequencing datasets, enabling unbiased and scalable analyses. In conclusion, our work presents a comprehensive single-cell reference and computational framework for CD8+ T cell research.

Pembrolizumab with or without bevacizumab in platinum-resistant recurrent or metastatic nasopharyngeal carcinoma: a randomised, open-label, phase 2 trial

BACKGROUND

Vascular endothelial growth factor (VEGF) is overexpressed in nasopharyngeal carcinoma and suppresses the anti-tumour immune response. Previous studies have shown that adding anti-VEGF treatment to PD-1 inhibition treatment strategies improves tumour response. We aimed to compare the efficacy of pembrolizumab, a PD-1 inhibitor, with or without bevacizumab, a VEGF inhibitor, in nasopharyngeal carcinoma.

METHODS

In this randomised, open-label, phase 2 trial done at two hospitals (National University Cancer Institute and Tan Tock Seng Hospital) in Singapore, patients with platinum-resistant recurrent or metastatic nasophayngeal carcinoma were eligible if they were aged 21 years or older and had an Eastern Cooperative Oncology Group (ECOG) performance status of 0-1. Patients were assigned (1:1; using random permuted blocks with varying sizes of 4 and 6) to receive either intravenous pembrolizumab (200 mg) every 21 days or a combination of pembrolizumab with intravenous bevacizumab (7·5 mg/kg) administered 1 week prior to each dose, until radiographic disease progression, unacceptable toxicity, completion of 32 cycles, or withdrawal of consent. The study was open label, therefore no masking of treatment assignment was implemented. The primary endpoint was objective response rate, assessed using RECIST (version 1.1) by independent radiologists and analysed in the intention-to-treat population (ie, all randomly assigned patients). This trial is registered with ClinicalTrials.gov, NCT03813394, and enrolment has closed.

FINDINGS

Between May 13, 2019, and Dec 6, 2023, we assessed 60 individuals for eligibility, 12 were excluded, and 48 were randomly allocated to pembrolizumab alone (n=24) or a combination of bevacizumab and pembrolizumab (n=24). The median age was 56 years (IQR 48-65), and 40 (83%) of 48 patients were male and eight (17%) were female. The median follow-up was 28·3 months (IQR 15·1-55·9). The objective response rate was significantly higher in the bevacizumab and pembrolizumab group (58·3% [95% CI 36·6-77·9] than in the pembrolizumab group (12·5% [2·7-32·4]; unadjusted RR 4·67 [95% CI 1·54-14·18]; p=0·0010). Grade 3 treatment-related adverse events occurred in two (8%) of 24 patients in the pembrolizumab group and in seven (29%) of 24 patients in the bevacizumab and pembrolizumab group; the most common severe or grade 3-4 treatment-related adverse events were thrombosis or bleeding (four [17%] of 24 patients in the bevacizumab and pembrolizumab group vs none of 24 patients in the pembrolizumab group), and others were transaminitis (none vs 1 [4%]), colitis (1 [4%] vs none]), cytopenias (none vs 1 [4%]), dermatological toxicities (1 [4%] vs none]), hypertension (1 [4%] vs none]), and proteinuria (1 [4%] vs none]). There were no grade 4 treatment-related adverse events or treatment-related deaths in either group.

INTERPRETATION

Pembrolizumab in combination with bevacizumab was more efficacious than pembrolizumab monotherapy, with manageable toxicities in platinum-resistant nasopharyngeal carcinoma. If validated in a phase 3 trial, the combination therapy could be a new standard of care in this population of patients.

FUNDING

National Medical Research Council of Singapore, National Research Foundation Singapore, Singapore Ministry of Education under its Research Centres of Excellence initiatives, and Merck Sharp & Dohme.

Herpesviruses mimic zygotic genome activation to promote viral replication

Zygotic genome activation (ZGA) is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In humans, ZGA is induced by DUX4, a pioneer factor that drives expression of downstream germline-specific genes and retroelements. Here we show that herpesviruses from all subfamilies, papillomaviruses and Merkel cell polyomavirus actively induce DUX4 expression to promote viral transcription and replication. Analysis of single-cell sequencing data sets from patients shows that viral DUX4 activation is of relevance in vivo. Herpes-simplex virus 1 (HSV-1) immediate early proteins directly induce expression of DUX4 and its target genes, which mimics zygotic genome activation. Upon HSV-1 infection, DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for infection, since genetic depletion by CRISPR/Cas9 as well as degradation of DUX4 by nanobody constructs abrogates HSV-1 replication. Our results show that DNA viruses including herpesviruses mimic an embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

Unveiling immune resistance mechanisms in nasopharyngeal carcinoma and emerging targets for antitumor immune response: tertiary lymphoid structures

Nasopharyngeal carcinoma (NPC) is a prevalent malignancy in China, commonly associated with undifferentiated cell types and Epstein-Barr virus (EBV) infection. The presence of intense lymphocytic infiltration and elevated expression of programmed cell death ligand 1(PD-L1) in NPC highlights its potential for immunotherapy, yet current treatment outcomes remain suboptimal. In this review, we explore the tumor microenvironment of NPC to better understand the mechanisms of resistance to immunotherapy, evaluate current therapeutic strategies, and pinpoint emerging targets, such as tertiary lymphoid structures (TLSs), that could enhance treatment outcomes and prognostic accuracy. TLSs have demonstrated positive prognostic value in NPC, making them a promising target for future therapies. This review summarizes the key characteristics of TLSs and latest research in the context of NPC. We are optimistic that targeting TLSs could improve immunotherapy outcomes for NPC patients, ultimately leading to more effective treatment strategies and better patient survival.

Single-cell transcriptome atlas of peripheral immune features to Omicron breakthrough infection under booster vaccination strategies

Introduction

The high percentage of Omicron breakthrough infection in vaccinees is an emerging problem, of which we have a limited understanding of the phenomenon.

Methods

We performed single-cell transcriptome coupled with T-cell/B-cell receptor (TCR/BCR) sequencing in 15 peripheral blood mononuclear cell (PBMC) samples from Omicron infection and naïve with booster vaccination.

Results

We found that after breakthrough infection, multiple cell clusters showed activation of the type I IFN pathway and widespread expression of Interferon-stimulated genes (ISGs); T and B lymphocytes exhibited antiviral and proinflammatory-related differentiation features with pseudo-time trajectories; and large TCR clonal expansions were concentrated in effector CD8 T cells, and clonal expansions of BCRs showed a preference for IGHV3. In addition, myeloid cells in the BA.5.2 breakthrough infection with the fourth dose of aerosolized Ad5-nCoV were characterized by enhanced proliferation, chemotactic migration, and antigen presentation.

Discussion

Collectively, our study informs the comprehensive understandings of immune characterization for Omicron breakthrough infection, revealing the positive antiviral potential induced by booster doses of vaccine and the possible "trained immunity" phenomenon in the fourth dose of aerosolized Ad5-nCoV, providing a basis for the selection of vaccination strategies.

Spatial and single-cell transcriptomics reveal cellular heterogeneity and a novel cancer-promoting Treg cell subset in human clear-cell renal cell carcinoma

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) is the most common histologic type of RCC. However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.

METHODS

To further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue. On the basis, the findings were investigated in vitro using tissue and blood samples from 15 patients with ccRCC and validated in the broader samples on tissue microarrays.

RESULTS

In this study, we revealed previously unreported subsets of both stromal and immune cells, as well as mapped their spatial location at finer resolution. In addition, we validated the clusters of tumor cells after removing batch effects according to six characterized gene sets, including epithelial-mesenchymal transitionhigh clusters, metastatic clusters and proximal tubulehigh clusters. Importantly, we identified a special regulatory T (Treg) cell subpopulation that has the molecular characteristics of terminal effector Treg cells but expresses multiple cytokines, such as interleukin (IL)-1β and IL-18. This group of Treg cells has stronger immunosuppressive function and was associated with a worse prognosis in ccRCC cohorts. They were colocalized with MRC1 + FOLR2 + tumor-associated macrophages (TAMs) at the tumor-normal interface to form a positive feedback loop, maintaining a synergistic procarcinogenic effect. In addition, we traced the origin of IL-1β+ Treg cells and revealed that IL-18 can induce the expression of IL-1β in Treg cells via the ERK/NF-κB pathway.

CONCLUSIONS

We demonstrated a novel cancer-promoting Treg cell subset and its interactions with MRC1 + FOLR2 +TAMs, which provides new insight into Treg cell heterogeneity and potential therapeutic targets for ccRCC.

Specifically blocking αvβ8-mediated TGF-β signaling to reverse immunosuppression by modulating macrophage polarization

BACKGROUND

Targeting the TGF-β pathway in tumor therapy has proven challenging due to the highly context-dependent functions of TGF-β. Integrin αvβ8, a pivotal activator of TGF-β, has been implicated in TGF-β signaling within tumors, as demonstrated by the significant anti-tumor effects of anti-αvβ8 antibodies. Nevertheless, the expression profile of αvβ8 remains a subject of debate, and the precise mechanisms underlying the anti-tumor effects of anti-αvβ8 antibodies are not yet fully elucidated.

METHODS

We utilized single-cell RNA sequencing to assess αvβ8 expression across various human tumors. An anti-αvβ8 antibody was developed and characterized for its binding and blocking properties in vitro. Cryo-EM single-particle analysis was employed to study the detailed interaction between αvβ8 and the antibody Fab fragment. The anti-tumor efficacy of the antibody was evaluated in syngeneic mouse models with varying levels of αvβ8 expression, both as a monotherapy and in combination with PD-1 antibodies. Human PBMCs were isolated to investigate αvβ8 expression in myeloid cells, and macrophages were exposed to the antibody to study its impact on macrophage polarization. Pharmacokinetic studies of the αvβ8 antibody were conducted in cynomolgus monkeys.

RESULTS

Integrin αvβ8 is notably expressed in certain tumor types and tumor-infiltrating macrophages. The specific αvβ8 antibody 130H2 demonstrated high affinity, specificity, and blocking potency in vitro. Cryo-EM analysis further revealed that 130H2 interacts exclusively with the β8 subunit, without binding to the αv subunit. In vivo studies showed that this antibody significantly inhibited tumor growth and alleviated immunosuppression by promoting immune cell infiltration. Furthermore, combining the antibody with PD-1 inhibition produced a synergistic anti-tumor effect. In human PBMCs, monocytes exhibited high αvβ8 expression, and the antibody directly modulated macrophage polarization. Tumors with elevated αvβ8 expression were particularly responsive to 130H2 treatment. Additionally, favorable pharmacokinetic properties were observed in cynomolgus monkeys.

CONCLUSIONS

In summary, integrin αvβ8 is highly expressed in certain tumors and tumor-infiltrating macrophages. Targeting αvβ8 with a blocking antibody significantly inhibits tumor growth by modulating macrophage polarization and enhancing immune cell infiltration. Combining αvβ8 targeting with PD-1 treatment markedly increases the sensitivity of immune-excluded tumors. These results support further clinical evaluation of αvβ8 antibodies.

Whole-exome sequencing association study reveals genetic effects on tumor microenvironment components in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) presents a substantial clinical challenge due to the limited understanding of its genetic underpinnings. Here we conduct the largest scale whole-exome sequencing association study of NPC to date, encompassing 6,969 NPC cases and 7,100 controls. We unveil 3 germline genetic variants linked to NPC susceptibility: a common rs2276868 in RPL14, a rare rs5361 in SELE, and a common rs1050462 in HLA-B. We also underscore the critical impact of rare genetic variants on NPC heritability and introduce a refined composite polygenic risk score (rcPRS), which outperforms existing models in predicting NPC risk. Importantly, we reveal that the polygenic risk for NPC is mediated by EBV infection status. Utilizing a comprehensive multiomics approach that integrates both bulk-transcriptomic (n = 356) and single-cell RNA sequencing (n = 56) data with experimental validations, we demonstrate that the RPL14 variant modulates the EBV life cycle and NPC pathogenesis. Furthermore, our data indicate that the SELE variant contributes to modifying endothelial cell function, thereby facilitating NPC progression. Collectively, our study provides crucial insights into the intricate genetic architecture of NPC, spotlighting the vital interplay between genetic variations and tumor microenvironment components, including EBV and endothelial cells, in predisposing to NPC. This study opens new avenues for advancements in personalized risk assessments, early diagnosis, and targeted therapies for NPC.

Multi-omics analysis unveils the role of inflammatory cancer-associated fibroblasts in chordoma progression

Cancer-associated fibroblasts (CAFs) constitute the primary cellular component of the stroma in chordomas, characterized by an abundance of mucinous stromal elements, potentially facilitating their initiation and progression; however, this inference has yet to be fully confirmed. In this study, single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), bulk RNA-seq, multiplexed quantitative immunofluorescence (QIF), and in vivo and in vitro experiments were performed to determine the heterogeneity, spatial distribution, and clinical significance of CAFs in chordoma. ScRNA-seq was performed on 87,693 single cells derived from seven tumor samples and four control nucleus pulposus samples. A distinct CAF cluster distinguished by the upregulated expression of inflammatory genes and enriched functionality in activating inflammation-associated cells was identified. Pseudotime trajectory and cell communication analyses suggested that this inflammatory CAF (iCAF) subset originated from normal fibroblasts and interacted extensively with tumors and various other cell types. By integrating the scRNA-seq results with ST, the presence of iCAF in chordoma tissue was further confirmed, indicating their positioning at a distance from the tumor cells. Bulk RNA-seq data analysis from 126 patients revealed a correlation between iCAF signature scores, chordoma invasiveness, and poor prognosis. QIF validation involving an additional 116 patients found that although iCAFs were not in close proximity to tumor cells compared with other CAF subsets, their density correlated with malignant tumor phenotypes and adverse outcomes. In vivo and in vitro experiments further confirmed that iCAFs accelerate the malignant progression of chordomas. These findings could provide insights into the development of novel therapeutic strategies. © 2024 The Pathological Society of Great Britain and Ireland.

Fatty acid metabolism: A new target for nasopharyngeal carcinoma therapy

Lipid metabolic reprogramming is considered one of the most prominent metabolic abnormalities in cancer, and fatty acid metabolism is a key aspect of lipid metabolism. Recent studies have shown that fatty acid metabolism and its related lipid metabolic pathways play important roles in the malignant progression of nasopharyngeal carcinoma (NPC). NPC cells adapt to harsh environments by enhancing biological processes such as fatty acid metabolism, uptake, production, and oxidation, thereby accelerating their growth. In addition, the reprogramming of fatty acid metabolism plays a central role in the tumor microenvironment (TME) of NPC, and the phenotypic transformation of immune cells is closely related to fatty acid metabolism. Moreover, the reprogramming of fatty acid metabolism in NPC contributes to immune escape, which significantly affects disease treatment, progression, recurrence, and metastasis. This review explores recent advances in fatty acid metabolism in NPC and focuses on the interconnections among metabolic reprogramming, tumor immunity, and corresponding therapies. In conclusion, fatty acid metabolism represents a potential target for NPC treatment, and further exploration is needed to develop strategies that target the interaction between fatty acid metabolic reprogramming and immunotherapy.

Epstein-Barr Virus BRRF1 Induces Butyrophilin 2A1 in Nasopharyngeal Carcinoma NPC43 Cells via the IL-22/JAK3-STAT3 Pathway

Epstein-Barr virus is highly associated with nasopharyngeal carcinoma (NPC) with genes expressed for tumor transformation or maintenance of viral latency, but there are certain genes that can modulate immune molecules. Butyrophilin 2A1 (BTN2A1) is an important activating protein for presenting phosphoantigens for recognition by Vγ9Vδ2 T cells to achieve antitumor activities. We have previously shown that Vγ9Vδ2 T cells achieve efficacy against NPC when BTN2A1 and BTN3A1 are upregulated by stimulating EBV gene expression, particularly LMP1. While BTN3A1 can be induced by the LMP1-mediated IFN-γ/JNK/NLRC5 pathway, the viral gene that can regulate BTN2A1 remains elusive. We showed that BTN2A1 expression is directly mediated by EBV BRRF1, which can trigger the BTN2A1 promoter and downstream JAK3-STAT3 pathway in NPC43 cells, as shown by RNA-seq data and verified via inhibitor experiments. Furthermore, BRRF1 downregulated IL-22 binding protein (IL-22RA2) to complement the EBNA1-targeting probe (P4)-induced IL-22 expression. Therefore, this study elucidated a new mechanism of stimulating BTN2A1 expression in NPC cells via the EBV gene BRRF1. The JAK3-STAT3 pathway could act in concordance with IL-22 to enhance the expression of BTN2A1, which likely leads to increased tumor cell killing by Vγ9Vδ2 T cells for enhanced potential as immunotherapy against the cancer.

Unveiling KLHL23 as a key immune regulator in hepatocellular carcinoma through integrated analysis

Age-related cancers are characterized by impaired protein homeostasis, where Kelch protein superfamily members have showed accumulating clues as critical regulators. In this paper, the cancerous role of Kelch-like family member 23 (KLHL23) was comprehensively analyzed with TCGA and single cell GEO database across overall 33 cancer types. By multi-omics analysis upon the transcriptomic, genomic, and methylation data, the current study explored the association of KLHL23 with patient survival, gene ontology, tumor-infiltrating lymphocytes, and drug responses. The correlation of copy number variations and methylation with dysregulated expression of KLHL23 were also addressed. Notably, KLHL23 levels correlated with survival in cancers such as hepatocellular carcinoma and low-grade glioma. The study also highlighted how reduced KLHL23 expression is linked to increased immune activity and sensitivity to chemotherapy, suggesting its potential as a biomarker for cancer prognosis and treatment responsiveness.

CX3CL1 (Fractalkine): An important cytokine in physiological and pathological pregnancies

C-X3-C motif chemokine ligand 1 (CX3CL1), commonly known as Fractalkine, is an important chemokine with dual functions of chemotaxis and adhesion. It plays a pivotal role in a variety of physiological processes and pathological conditions, particularly in conjunction with its receptor, C-X3-C motif chemokine receptor 1 (CX3CR1). This review focuses on the expression and intricate regulatory mechanisms of CX3CL1 at the maternal-fetal interface, emphasizing its multifaceted role during pregnancy. CX3CL1 was detected in the trophoblast and decidua tissues, playing a crucial role in recruitment of immune cells, enhancing endometrial receptivity, and modulating trophoblast cell activities. Abnormal expression of CX3CL1 has been correlated with adverse pregnancy outcomes such as spontaneous abortion, gestational diabetes, preeclampsia, and preterm births. By elucidating the complex interplay of CX3CL1 at the maternal-fetal interface, this review aims to shed light on its potential roles in pregnancy-related complications.

Single-cell transcriptomic landscape deciphers olfactory neuroblastoma subtypes and intra-tumoral heterogeneity

Olfactory neuroblastoma (ONB) is a rare malignancy known to originate from the olfactory epithelium. The complex tumor ecosystem of this pathology remains unclear. Here, we explored the cellular components within ten ONB tumors and one olfactory mucosa sample based on single-cell RNA profiles. We showed the intra-tumoral heterogeneity by identifying five unique expression programs among malignant epithelial cells. A distinct three-classification system (neural, basal, mesenchymal) for ONB was established according to the distinguished gene expression patterns. Biomarkers for categorizing bulk tumors into uncharacterized subtypes were elucidated. Different responses towards certain chemotherapy regimens could be cautiously inferred according to the molecular features representing the three tumor types, thus helping with precision chemotherapy. We also analyzed subclusters of the tumor microenvironment (TME) and the interactions among different cell types within the TME. The relative abundance of immunosuppressive tumor-associated macrophages suggests potential benefits of immunotherapies targeting macrophages.

Micropeptide MPM regulates cardiomyocyte proliferation and heart growth via the AKT pathway

The role of micropeptide in cardiomyocyte proliferation remains unknown. We found that MPM (micropeptide in mitochondria) was highly expressed in cardiomyocytes. Compared to MPM+/+ mice, MPM knockout (MPM-/-) mice exhibited reduction in left ventricular (LV) mass, myocardial thickness and LV fractional shortening. RNA-sequencing analysis in H9c2, a rat cardiomyocyte cell line, identified downregulation of cell cycle-promoting genes as the most significant alteration in MPM-silencing cells. Consistently, gain- and loss-of-function analyses in H9c2 cells revealed that cardiomyocyte proliferation was repressed by silencing MPM but was promoted by overexpressing MPM. Moreover, the cardiomyocytes in the hearts of MPM-/- mice displayed reduced proliferation rates. Mechanism investigations disclosed that MPM is crucial for AKT activation in cardiomyocytes. We also identified an interaction between MPM and PTPMT1, and found that silencing PTPMT1 attenuated the effect of MPM in activating the AKT pathway, whereas inhibition of the AKT pathway abrogated the role of MPM in promoting cardiomyocyte proliferation. Collectively, these results indicate that MPM may promote cardiomyocyte proliferation and thus heart growth by interacting with PTPMT1 to activate the AKT pathway. Our findings identify the novel function and regulatory network of MPM and highlight the importance of micropeptides in cardiomyocyte proliferation and heart growth.

CX3CR1+CD8+ T cells: Key players in antitumor immunity

CX3CR1 functions as the specific receptor for the chemokine CX3CL1, demonstrating expression across a broad spectrum of immune cells. This underscores its pivotal role in communication and response mechanisms within the immune system. Upon engagement with CX3CL1, CX3CR1 initiates a cascade of downstream signaling pathways that regulate various biological functions. In the context of tumor progression, the intricate and inhibitory nature of the tumor microenvironment presents a significant challenge to current clinical treatment techniques. This review aims to comprehensively explore the tumor-destructive potential shown by CX3CR1+CD8+ T cells. Simultaneously, it investigates the promising prospects of utilizing CX3CR1 in future tumor immunotherapies.

Guiding induction chemotherapy of locoregionally advanced nasopharyngeal carcinoma with ternary classification of predicted individual treatment effect

BACKGROUND AND PURPOSE

Induction chemotherapy (IC) before concurrent chemoradiotherapy does not universally improve long-term overall survival (OS) in locoregionally advanced nasopharyngeal carcinoma (LANPC). Conventional risk stratification often yields suboptimal IC decisions. Our study introduces a ternary classification of predicted individual treatment effect (PITE) to guide personalized IC decisions.

MATERIALS AND METHODS

A two-center retrospective analysis of 1,213 patients with LANPC was conducted to develop and validate prognostic models integrating magnetic resonance imaging and clinical data to estimate individual 5-year OS probabilities for IC and non-IC treatments. Differences in these probabilities defined PITE, facilitating patient stratification into three IC recommendation categories. Model effectiveness was validated using Kaplan-Meier estimators, decision curve-like analysis, and evaluations of variable importance and distribution.

RESULTS

The models exhibited strong predictive performance in both treatments across training and cross-validation sets, enabling accurate PITE calculations and patient classification. Compared with non-IC treatment, IC markedly improved OS in the IC-preferred group (HR = 0.62, p = 0.02), had no effect in the IC-neutral group (HR = 1.00, p = 0.70), and worsened OS in the IC-opposed group (HR = 2.00, p = 0.03). The ternary PITE classification effectively identified 41.7 % of high-risk patients not benefiting from IC, and yielded a 2.68 % higher mean 5-year OS probability over risk-based decisions. Significantly increasing distributions of key prognostic indicators, such as metastatic lymph node number and plasma Epstein-Barr virus DNA level from IC-opposed to IC-preferred groups, further validated the clinical relevance of PITE classification.

CONCLUSION

The ternary PITE classification offers an accurate and clinically advantageous approach to guide personalized IC decision-making in patients with LANPC.

FOXA1 enhances antitumor immunity via repressing interferon-induced PD-L1 expression in nasopharyngeal carcinoma

BACKGROUND

Nasopharyngeal carcinoma (NPC) is a distinct subtype of head and neck cancer which is prevalent in south of China and southeastern of Asia. Consistent activation of interferon (IFN) signaling, and impairment of T cell mediated antitumor immunity is frequent in NPC. Forkhead box A1 (FOXA1) is one of the earliest discovered pioneer factors, which can open up compact chromatin structures to facilitate the binding of other proteins to chromatin.

METHODS

By using RNA sequencing, it was discovered that FOXA1 suppresses the activation of the interferon signaling pathway and the expression of the related interferon-responsive genes in NPC cells. The effect of FOXA1 on programmed death-ligand 1 (PD-L1) expression in C666-1 and HK1 cells under conditions with or without IFN-γ was detected through quantitative PCR (qPCR), western blot, and flow cytometry. After co-culturing T cells with IFN-γ-treated NPC cells in vitro, apoptosis of CD8+ T cells and the expression of cytotoxic cytokines were assessed by flow cytometry. The cytotoxic effects of T cells on tumor cells in nude mice were measured by tumorigenesis in nude mice and adoptive T cell therapy. The effects of IFN-γ on the expression and nuclear localization of STAT1, as well as the colocalization of FOXA1 with STAT1 were detected by immunofluorescence, qPCR, western blot, and co-immunoprecipitation experiments.

RESULTS

In this study, we reported that loss of FOXA1, a pioneer factor downregulated in NPC, results in activation of IFN signaling in NPC cells. Repression of FOXA1 facilitates IFN-γ induced PD-L1 expression, whereas overexpression of FOXA1 exerts the opposite effect. Mechanistically, FOXA1 interacts with STAT1 and inhibits IRF1 expression and binding to PD-L1 promoter on IFN-γ treatment. Co-culture with FOXA1-silenced NPC cells promotes apoptosis of in vitro activated tumor-specific CD8+T cells and reduces the expression of cytotoxic effector molecules. Furthermore, overexpression of FOXA1 increases the therapeutic efficacy of PD-L1 antibody (atezolizumab) against NPC in nude mice receiving adoptive T-cell therapy.

CONCLUSIONS

We demonstrated that FOXA1 prevents tumor immune evasion by inhibiting IFN-γ induced PD-L1 expression in NPC cells. Our research findings provide new insights into the immunotherapeutic biomarkers and targets for NPC, which is important for the clinical application of programmed cell death protein-1/PD-L1 antibodies in NPC.

Integrated analysis of single-cell, spatial and bulk RNA-sequencing identifies a cell-death signature for predicting the outcomes of head and neck cancer

Background

Cell death plays an essential role in carcinogenesis, but its function in the recurrence and postoperative prognosis of head and neck cancer (HNC), which ranks as the 7th most common malignancy globally, remains unclear.

Methods

Data from five main subtypes of HNC related single-cell RNA sequencing (scRNA-seq) were recruited to establish a single-cell atlas, and the distribution of cell death models (CDMs) across different tissues as well as cell subtypes were analyzed. Bulk RNA-seq from the Cancer Genome Atlas Program (TCGA) dataset was subjected to a machine learning-based integrative procedure for constructing a consensus cell death-related signature risk score (CDRscore) model and validated by external data. The biofunctions including different expression analysis, immune cell infiltration, genomic mutations, enrichment analysis as well as cellchat analysis were compared between the high- and low- risk score groups categorized by this CDRscore model. Finally, samples from laryngeal squamous cell cancer (LSCC) were conducted by spatial transcriptomics (ST) to further validate the results of CDRscore model.

Results

T cells from HNC patients manifested the highest levels of cell death while HPV infection attenuates malignant cell death based on single-cell atlas. CDMs are positively correlated with the tumor-cell stemness, immune-related score and T cells are infiltrated. A CDRscore model was established based on the transcription of ten cell death prognostic genes (MRPL10, DDX19A, NDFIP1, PCMT1, HPRT1, SLC2A3, EFNB2, HK1, BTG3 and MAP2K7). It functions as an independent prognostic factor for overall survival in HNC and displays stable and powerful performance validated by GSE41613 and GSE65858 datasets. Patients in high CDRscore manifested worse overall survival, more active of epithelial mesenchymal transition, TGF-β-related pathways and hypoxia, higher transcription of T cell exhausted markers, and stronger TP53 mutation. ST from LSCC showed that spots with high-risk scores were colocalized with TGF-β and the proliferating malignant cells, additionally, the risk scores have a negative correlation with TCR signaling but positive association with LAG3 transcription.

Conclusion

The CDRscore model could be utilized as a powerful prognostic indicator for HNC.

Hepatic stellate cells promote hepatocellular carcinoma development by regulating histone lactylation: Novel insights from single-cell RNA sequencing and spatial transcriptomics analyses

This study evaluated the cellular heterogeneity and molecular mechanisms of hepatocellular carcinoma (HCC). Single cell RNA sequencing (scRNA-seq), transcriptomic data, histone lactylation-related genes were collected from public databases. Cell-cell interaction, trajectory, pathway, and spatial transcriptome analyses were executed. Differential expression and survival analyses were conducted. Western blot, Real-time reverse transcription PCR (qRT-PCR), and Cell Counting Kit 8 (CCK8) assay were used to detect the expression of αSMA, AKR1B10 and its target genes, and verify the roles of AKR1B10 in HCC cells. Hepatic stellate cell (HSC) subgroups strongly interacted with tumor cell subgroups, and their spatial distribution was heterogeneous. Two candidate prognostic genes (AKR1B10 and RMRP) were obtained. LONP1, NPIPB3, and ZSWIM6 were determined as AKR1B10 targets. Besides, the expression levels of AKR1B10 and αSMA were significantly increased in LX-2 + HepG2 and LX-2 + HuH7 groups compared to those in LX-2 group, respectively. sh-AKR1B10 significantly inhibited the HCC cell proliferation and change the expression of AKR1B10 target genes, Bcl-2, Bax, Pan Kla, and H3K18la at protein levels. Our findings unveil the pivotal role of HSCs in HCC pathogenesis through regulating histone lactylation.

SPP1+ TAM Regulates the Metastatic Colonization of CXCR4+ Metastasis-Associated Tumor Cells by Remodeling the Lymph Node Microenvironment

Lymph node metastasis, the initial step in distant metastasis, represents a primary contributor to mortality in patients diagnosed with oral squamous cell carcinoma (OSCC). However, the underlying mechanisms of lymph node metastasis in OSCC remain incompletely understood. Here, the transcriptomes of 56 383 single cells derived from paired tissues of six OSCC patients are analyzed. This study founds that CXCR4+ epithelial cells, identified as highly malignant disseminated tumor cells (DTCs), exhibited a propensity for lymph node metastasis. Importantly, a distinct subset of tumor-associated macrophages (TAMs) characterized by exclusive expression of phosphoprotein 1 (SPP1) is discovered. These TAMs may remodel the metastatic lymph node microenvironment by potentially activating fibroblasts and promoting T cell exhaustion through SPP1-CD44 and CD155-CD226 ligand-receptor interactions, thereby facilitating colonization and proliferation of disseminated tumor cells. The research advanced the mechanistic understanding of metastatic tumor microenvironment (TME) and provided a foundation for the development of personalized treatments for OSCC patients with metastasis.

Systemic longitudinal immune profiling identifies proliferating Treg cells as predictors of immunotherapy benefit: biomarker analysis from the phase 3 CONTINUUM and DIPPER trials

The identification of predictors for immunotherapy is often hampered by the absence of control groups in many studies, making it difficult to distinguish between prognostic and predictive biomarkers. This study presents biomarker analyses from the phase 3 CONTINUUM trial (NCT03700476), the first to show that adding anti-PD-1 (aPD1) to chemoradiotherapy (CRT) improves event-free survival (EFS) in patients with locoregionally advanced nasopharyngeal carcinoma. A dynamic single-cell atlas was profiled using mass cytometry on peripheral blood mononuclear cell samples from 12 pairs of matched relapsing and non-relapsing patients in the aPD1-CRT arm. Using a supervised representation learning algorithm, we identified a Ki67+ proliferating regulatory T cells (Tregs) population expressing high levels of activated and immunosuppressive molecules including FOXP3, CD38, HLA-DR, CD39, and PD-1, whose abundance correlated with treatment outcome. The frequency of these Ki67+ Tregs was significantly higher at baseline and increased during treatment in patients who relapsed compared to non-relapsers. Further validation through flow cytometry (n = 120) confirmed the predictive value of this Treg subset. Multiplex immunohistochemistry (n = 249) demonstrated that Ki67+ Tregs in tumors could predict immunotherapy benefit, with aPD1 improving EFS only in patients with low baseline levels of Ki67+ Tregs. These findings were further validated in the multicenter phase 3 DIPPER trial (n = 262, NCT03427827) and the phase 3 OAK trial of anti-PD-L1 immunotherapy in NSCLC, underscoring the predictive value of Ki67+ Treg frequency in identifying the beneficiaries of immunotherapy and potentially guiding personalized treatment strategies.

Stiff Hydrogel Encapsulation Retains Mesenchymal Stem Cell Stemness for Regenerative Medicine

Mesenchymal stem cell (MSC) stands as a prominent choice in regenerative medicine, yet their therapeutic potential remains controversial due to challenges in maintaining lineage and viability. As directly injected MSCs are quickly cleared by the host immune system, entrapping viable cells in a 3D semi-permeable hydrogel matrix extends cell retention, showing great promise in enhancing therapeutic effect. However, the effects of hydrogel encapsulation on MSC subpopulations are not fully understood. Here, we fabricate thin-shell alginate hydrogel microcapsules using droplet microfluidics, controlling the shell mechanical properties by adjusting alginate molecular weight. We find that a stiffer shell increases the proliferation and supports the residence of MSCs in vivo than a softer shell. The stiff 3D hydrogel also promotes the maintenance of stemness, as confirmed by single-cell RNA sequencing. Our work demonstrates the potential of hydrogel-encapsulated stem cells for long-term therapeutic applications, offering insight into modulating MSC subpopulations for specific function.

Single-cell sequencing analysis reveals the dynamic tumour ecosystems of primary and metastatic lymph nodes in nasopharyngeal carcinoma

Lymph node metastasis contributed to the leading cause and treatment failure in nasopharyngeal carcinoma (NPC). The microenvironment and the cellular communications of lymph node metastasized tumours determine the tumour progression and therapeutic effect, but the ecosystems about the lymph node metastasis (LNM) for NPC patients remain poorly characterized. Here, we integrated the transcriptomes of 47,618 single cells from eight samples related to NPC LNM. The dynamic immune ecosystems and immunosuppressive microenvironment including T cells, myeloid cells and B cells were observed in the lymph node metastatic samples compared with primary tumours. Additionally, the heterogeneity of epithelial cells was also revealed, and several clusters with expression programs that were associated with the progression-free survival of NPC patients were identified. Additionally, our data revealed the complex intercellular communications from primary to lymph node metastasis. The rewiring of CCL signalling which plays an important role in tumour metastasis was further identified. Altogether, we systematically characterized the ecosystem of NPC primary and lymph node metastasized tumours, which may shed light on the development of a therapeutic strategy to improve clinical outcomes of NPC patients with lymph node metastasis.

Unravelling the Complexity of HNSCC Using Single-Cell Transcriptomics

BACKGROUND/OBJECTIVES

Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous and the most common form of head and neck cancer, posing significant challenges for disease management. The objective of this review is to assess the utility of single-cell RNA sequencing (scRNAseq) in addressing these challenges by enabling a detailed characterization of the tumor microenvironment (TME) at the cellular level.

METHODS

This review compiles and analyzes current strategies that utilize scRNAseq and other single-cell technologies in HNSCC research.

RESULTS

For HNSCC etiology, scRNAseq allows for the construction of cellular atlases, characterization of different cell types, and investigation of genes and processes involved in cancer initiation, development, and progression within the TME. In terms of HNSCC diagnosis and prognosis, the resolution offered by scRNAseq enables the identification of cell type-specific signatures, enhancing prognostic models and disease stratifiers for patient outcome assessments. Regarding HNSCC treatment, scRNAseq provides insights into cellular responses to various treatments, including radiotherapy, chemotherapy, and immunotherapy, contributing to a better understanding of treatment efficacy and patient outcomes.

CONCLUSIONS

This review highlights the contributions of scRNAseq to HNSCC research, addressing its cellular and biological complexity, and emphasizes its potential for advancing research and clinical practice in other cancer types.