Intratumoral CXCL13+CD8+T cell infiltration determines poor clinical outcomes and immunoevasive contexture in patients with clear cell renal cell carcinoma

Cell simulation as cell segmentation

Single-cell spatial transcriptomics promises a highly detailed view of a cell's transcriptional state and microenvironment, yet inaccurate cell segmentation can render these data murky by misattributing large numbers of transcripts to nearby cells or conjuring nonexistent cells. We adopt methods from ab initio cell simulation, in a method called Proseg (probabilistic segmentation), to rapidly infer morphologically plausible cell boundaries. Benchmarking applied to datasets generated by three commercial platforms shows superior performance and computational efficiency of Proseg when compared to existing methods. We show that improved accuracy in cell segmentation aids greatly in detection of difficult-to-segment tumor-infiltrating immune cells such as neutrophils and T cells. Last, through improvements in our ability to delineate subsets of tumor-infiltrating T cells, we show that CXCL13-expressing CD8+ T cells tend to be more closely associated with tumor cells than their CXCL13-negative counterparts in data generated from samples from patients with renal cell carcinoma.

TERT promoter methylation predicts overall survival, immune cell infiltration and response to immunotherapy in clear cell renal cell carcinoma

PURPOSE

Telomerase reverse transcriptase (TERT) is one of the most well-established oncogenes in tumor development and progression. It is widely known that TERT promoter hypermethylation is associated with its transcription activation. Despite its canonical role in maintaining telomere length in cancer cells, TERT is also involved in various oncogenic processes independent of its enzymatic activity. However, the role of TERT in the tumor immune microenvironment has been largely unexplored. Hence, we assessed the associations between TERT promoter methylation and its expression, clinicopathological features, overall survival, immune cell infiltration, and response to immune checkpoint inhibitor therapy in clear cell renal cell carcinoma.

METHODS

A single-sample gene-set enrichment analysis algorithm was used to quantify the relative abundance of each type of immune cell infiltration in the tumor microenvironment (TME) of the TCGA KIRC cohort. We used Spearman's rank correlation to calculate the correlation coefficients between TERT promoter methylation and immune cell infiltration. The relative methylation of cg11625005 in our validation cohort was detected by pyrosequencing and the relative infiltration of CD4 + and CD8 + T cells infiltration in the TME was measured by immunohistochemistry.

RESULTS

The TERT promoter was significantly hypermethylated in clear cell renal cell tumor tissues, which was related to the transcriptional activation of TERT. TERT promoter hypermethylation was significantly correlated with aggressive phenotypes and poor survival in clear cell renal cell carcinoma patients. Furthermore, TERT promoter methylation was significantly positively correlated with CD4 + /CD8 + T cells infiltration and immune checkpoint molecule (CTLA-4, TIGIT, PD-1 and LAG3) expression. And TERT promoter methylation was correlated with the therapeutic response to anti-PD1 immunotherapy.

CONCLUSION

TERT promoter methylation is a promising predictive biomarker of immune cell infiltration, overall survival, clinicopathological characteristics and response to anti-PD1 immunotherapy treatment in clear cell renal cell carcinoma patients.

Integrating machine learning and multi-omics analysis to unveil key programmed cell death patterns and immunotherapy targets in kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC), a cancer characterized by substantial immune infiltration, exhibits limited sensitivity to conventional radiochemotherapy. Although immunotherapy has shown efficacy in some patients, its applicability is not universally effective. Studies have indicated that programmed cell death (PCD) can modulate the activity of immune cells and participate in the regulation of antitumor immune responses. However, systematic research on how various PCD patterns in KIRC affect the responsiveness to immunotherapy is lacking and requires in-depth investigation. We utilized a combination of 101 machine learning algorithms to analyze the TCGA-KIRC cohort and the GSE22541 KIRC patients, screening for cell death patterns closely associated with prognosis from 18 potential modes. Integrating multi-omics analysis, including immune cell infiltration, phenotyping, functional analysis, immune checkpoint exploration, and gene set enrichment analysis (GSEA), we explored the relationship between key cell death patterns and patients' responses to immunotherapy. Finally, potential drug targets were identified through drug sensitivity screening and molecular docking techniques. Our sophisticated risk assessment model successfully identified two PCD patterns, Anoikis and lysosome-dependent cell death (LDCD), closely associated with the prognosis of KIRC patients, with the high-risk group exhibiting poor outcomes. Immune cell analysis revealed upregulated expression of T follicular helper (Tfh) cells in both PCD patterns. Analysis of immune checkpoints disclosed enhanced expression of human leukocyte antigen E (HLA-E) across both patterns. Frequent mutations in the TTN and MUC16 genes were observed in the Anoikis pattern, whereas in the LDCD pattern, although the high-risk group had a higher mutation rate, there was no significant difference in tumor mutational burden. GSEA analysis indicated significant enrichment of the primary immunodeficiency pathway in the Anoikis high-risk group and significant enrichment of the spliceosomal tri-snrnp complex assembly pathway in the LDCD high-risk group. Drug sensitivity analysis showed notable sensitivity to SB505124 in both PCD patterns. HMOX1 and PIK3CG were identified as common genes in the two key PCD patterns, and molecular docking analysis confirmed stable binding affinity between Carnosol and HMOX1, and between PROTAC and PIK3CG. Our study identifies Anoikis and LDCD as prognostic PCD patterns in KIRC, with key immune cells, genetic mutations, and drug sensitivity profiles. HMOX1 and PIK3CG are common genes with stable binding to Carnosol and PROTAC, respectively, while SB505124 shows significant sensitivity to both PCD modes, suggesting potential therapeutic targets.

The role of programmed cell death in renal cancer: a bibliometric perspective (1998-2024)

OBJECTIVE

This bibliometric study aimed to map the global research landscape of programmed cell death (PCD) in renal cancer, delineating publication trends, influential authors, contributing regions, and thematic shifts between 1998 and 2023 year.

METHODS

We retrieved 5, 134 records from the Web of Science Core Collection (1998-2023) using comprehensive keywords encompassing "renal cancer," "programmed cell death," and related synonyms. After applying inclusion and exclusion criteria, we conducted co-citation, keyword, and cluster analyses with CiteSpace (v.6.3.R2) and VOSviewer (v.1.6.20) to identify major research fronts, collaboration networks, and thematic clusters.

RESULTS

Findings revealed a progressive increase in publications, notably accelerating after 2010 in tandem with the rise of immunotherapeutic strategies and targeted molecular interventions. China and the United States emerged as leading contributors, while journals such as Cancer Research and Clinical Cancer Research dominated in both publication frequency and citation impact. Authors including Kwon Taeg Kyu and Dahiya Rajvir significantly shaped foundational apoptosis research. Keyword and cluster analyses demonstrated a shift from earlier apoptosis- and angiogenesis-focused studies toward intersections of metabolic reprogramming, immune infiltration, and newer cell death modalities (e.g., ferroptosis, pyroptosis). High-impact papers underscored immunotherapy's pivotal role in modulating cell death pathways and informing novel combination regimens.

CONCLUSION

PCD research in renal cancer has evolved into a dynamic, interdisciplinary domain integrating immunology, molecular targeting, and multi-omic profiling. Future development of the field aimed at refining precision therapies that exploit diverse cell death mechanisms and thereby improve clinical outcomes.

Tertiary lymphoid structures in gliomas: impact on tumour immunity and progression

Tertiary lymphoid structures (TLSs) are ectopic lymphoid formations that develop in chronically inflamed tissues, including various solid tumours. In the context of gliomas, the presence of TLSs has recently attracted considerable attention because of their potential implications in tumour immunology and therapy. The tumour immune microenvironment (TIME) plays a crucial role in cancer progression, and tumour-infiltrating immune cells (TILs) are key players in this environment. These immune cell aggregates, known as TLSs, display distinct characteristics across different solid tumours. However, central nervous system (CNS) tumours are highly heterogeneous, and the immune environment within these tumours is often more deficient than that of peripheral tissue tumours. This leads to differences in the formation and function of TLSs in CNS tumours. These variations are particularly relevant in the context of glioma immunotherapy and could have important implications for treatment strategies. This review focuses on the composition and function of TLSs, examines the complexity of the glioblastoma (GBM) immune microenvironment, and highlights the unique characteristics of TLSs in GBM, providing new theoretical insights and practical foundations for targeting TLSs in glioma immunotherapy.

Retrospective study on the correlation between CXCL13, immune infiltration, and tertiary lymphoid structures in cutaneous squamous cell carcinoma

Background

C-X-C motif chemokine ligand 13 (CXCL13) is a crucial chemokine for the recruitment of immune cells and the formation of tertiary lymphoid structure (TLS) in the tumor microenvironment. However, the relationship between CXCL13 and immune infiltration in cutaneous squamous cell carcinoma (cSCC) remains unclear.

Objective

We aimed to investigate the expression of CXCL13 and explore its association with immune activation and TLS in cSCC.

Methods

A total of 63 cSCC patients were involved in the present study. Hematoxylin and eosin staining was used for pathological examination of cSCC. Bioinformatics analyses and immunohistochemical staining were employed to access the expression of CXCL13 and TLS states. Public single cell RNA-sequencing atlas of skin disorders and multiplex immunofluorescence were used to explore CXCL13-producing cells.

Results

Utilizing the public database and our clinical cohort, we observed robust CXCL13 expression in cSCC tissues and a significant correlation with immune activation. Higher expression levels of CXCL13 were associated with lower histopathological grades and increased TLS formation. Furthermore, we confirmed that T cells and fibroblasts were the predominant cell types of CXCL13 secretion in cSCC.

Conclusions

CXCL13 is up-regulated in cSCC, which shows a significant positive correlation with immune infiltration and TLS formation. Our results underscore the role of CXCL13 in shaping the cSCC microenvironment, highlighting its potential as a therapeutic target.

A prognostic microRNA-based signature for localized clear cell renal cell carcinoma: the Bio-miR study

BACKGROUND

Two thirds of renal cell carcinoma (RCC) patients have localized disease at diagnosis. A significant proportion of these patients will relapse. There is a need for prognostic biomarkers to improve risk-stratification and specific treatments for patients that relapse. The objective of this study is to determine the clinical utility of microRNA signatures as prognostic biomarkers in localized clear cell RCC (ccRCC) and propose new therapeutic targets in patients with a high-risk of relapse.

PATIENTS AND METHODS

The microRNA profiles from a discovery cohort of 71 T1-T2 ccRCC patients (n = 88) were analyzed using microarrays. MicroRNAs prognostic value was established, and a microRNAs signature predicting relapse for T1b-T3 disease was defined. Independent validation was carried out by qPCR in cohorts from UK (n = 75) and Spain (n = 180), and the TCGA cohort (n = 175). In the Spanish validation cohort, proteomics experiments were done. Proteins were extracted from FFPE tissue and analyzed using by data-independent acquisition mass spectrometry. Additionally, ccRCC TCGA RNA-seq data was also analyzed. Both protein and RNA-seq data was analyzed using Significance Analysis of Micorarrays (SAM) and probabilistic graphical models, which allow the identification of relevant biological processes between low and high-risk tumors.

RESULTS

A 9-microRNAs signature, Bio-miR, classified patients into low- and high-risk with disease-free survival (DFS) at 5 years of 87.12 vs. 54.17% respectively (p = 0.0086, HR = 3.58, 95%CI: 1.37-8.3). Results were confirmed in the validation cohorts with 5-year DFS rates of 94% vs. 62% in the UK cohort (HR = 7.14, p = 0.001), 82.9% vs. 58.7% in the Spanish cohort (HR = 2.46, p = 0.0013), and 5-year overall survival rates of 72.7% vs. 44.5% in the TCGA cohort (HR = 2.43, p = 0.0012). Among low-risk patients according to adjuvant immunotherapy clinical trial criteria, Bio-miR identified a high-risk group. Maybe those patients ought to be considered to receive adjuvant therapy. Proteins overexpressed in the high-risk group were mainly related to focal adhesion, serine and inositol metabolism, and angiogenesis. Probabilistic graphical models defined eight functional nodes related to specific biological processes. Differences between low- and high-risk tumors were detected in complement activation and translation functional nodes. In ccRCC TCGA cohort, 676 genes were differentially expressed between low and high-risk patients, mainly related to complement activation, adhesion, and chemokine and cytokine cascades. In this case, probabilistic graphical models defined ten functional nodes. Calcium binding, membrane, adhesion, extracellular matrix, blood microparticle, inflammatory response and immune response had higher functional node activity, and metabolism node, containing genes related to retinol and xenobiotic and CYP450 metabolism, had lower activity in the high-risk group.

CONCLUSIONS

Bio-miR dichotomizes ccRCC patients with non-metastatic disease into those with low- and high-risk of relapse. This has implications for treatment and follow-up, identifying patients most likely to benefit from adjuvant treatment in clinical trials, preventing unnecessary exposure to side-effects, and providing health economics benefits. Additionally, promising therapeutic targets, as angiogenesis, immune response, metabolism, or complement activation, were found deregulated in high-risk ccRCC patients defined by Bio-miR. These findings may be useful to select patients for tailored, molecularly-driven clinical trials. Identifying which patients with kidney cancer are most at risk of their cancer coming back after surgery is critical, so that they can be prioritized for early treatment. We have identified a combination of biomarkers present in the cancer tissue (called BiomiR) which can help to do this.

CXCL9 and CXCL13 shape endometrial cancer immune-activated microenvironment via tertiary lymphoid structure formation

Immune checkpoint inhibitor (ICI) therapy has been successfully applied to various cancers; however, not all patients respond to ICI therapy. Tumors with an immune-activated environment are highly responsive to ICIs. To identify the cells and molecules essential to the formation of an immune-activated cancer microenvironment, we focused on the tertiary lymphoid structure (TLS) and performed histological and genomic analyses using endometrial cancer material. In the high immunogenic group, numerous TLSs were observed, and CXCL9 and CXCL13 expression was markedly increased. CXCL9-positive antigen-presenting and CXCL13-positive follicular dendritic cells were distributed in the T- and B-cell zones of TLSs, respectively. A group of molecules whose expression was upregulated along with CXCL9 and CXCL13 expression was strongly associated with cellular immunity. These results suggest that CXCL9-expressing antigen-presenting cells and CXCL13-expressing follicular dendritic cells coordinately shape the immune-activated microenvironment through TLS formation. The current findings will contribute to a better understanding of the mechanisms underlying the activated cancer immune microenvironment, thereby advancing the field of precision cancer medicine.

Smad4 loss identifies aggressive subtype with immunotherapy and anti-HER-2 treatment resistance in gastric cancer

BACKGROUND

SMAD4 mutation and homozygous deletion represent the most prevalent genomic events driving aggressive biological behavior in gastric cancer (GC). However, clinical outcome and therapeutic response in GC patients with Smad4-loss remains obscure.

METHODS

This study included 990 GC patients from four independent clinical centers including the Zhongshan Hospital (ZSHS) cohort, the Cancer Genomic Atlas (TCGA) cohort, the Samsung Medical Center (SMC) cohort and the Memorial Sloan Kettering Cancer Center (MSKCC) cohort.

RESULTS

In ZSHS cohort, 60/454 GC patients harbored Smad4-loss are characterized by lower pN stage, well histology differentiation, lower EBV infection, null p53 staining and lower tumor proliferation. Smad4-loss GC patients exhibit miserable overall survival across ZSHS cohort and TCGA cohort. Moreover, Smad4-loss GC patients yield no impact on adjuvant chemotherapy, poor outcome upon anti-PD-1 immunotherapy or anti-HER-2 therapy. Interestingly, Smad4-loss GC show more well and intermediate differentiation and lower Ki67 staining. Furthermore, Smad4-loss GC exhibit tumor immunosuppressive contexture characterized with enriched CXCL13+CD8+T cells, reduced IFN-γ+ cells and GZMB+ cells infiltration.

CONCLUSIONS

Smad4 loss yields poor clinical outcome, immunotherapy and anti-HER-2 treatment resistance and tumor immunosuppressive contexture in GC patients. Our findings provide clues for further detailed biological investigation and aggressive clinical management in Smad4-loss GC patients.

LPCAT3 regulates the immune infiltration and prognosis of ccRCC patients by mediating ferroptosis and endoplasmic reticulum stress

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) accounts for 70% of renal cell carcinoma (RCC) cases. Although surgery remains the mainstay treatment, renal injury and high metastasis rates after nephrectomy dramatically reduce patient quality of life. Drugs that stimulate the immune system by targeting checkpoint pathways improve overall survival in patients with RCC. Here, we investigated the applicability of lysophosphatidylcholine acyltransferase 3 (LPCAT3) as a target for immunotherapy.

METHODS

In the present study, high LPCAT3 expression in ccRCC was identified using The Cancer Genome Atlas (TCGA) data and validated in two external cohorts from the Gene Expression Omnibus (GEO) database. qRT-PCR was performed to identify the mRNA level of LPCAT3 in tumors and adjacent normal tissues. And immunohistochemistry was used to evaluate the protein level of LPCAT3 between two groups of samples. Furthermore, gene set enrichment analysis was performed to explore the biological processes and pathways related to LPCAT3 expression. Key gene expression and correlation analyses were performed to determine the crosstalk among LPCAT3 expression, ferroptosis, and endoplasmic reticulum stress (ERS). Subsequently, CIBERSORT was used to analyze the immune infiltration status of patients with high and low LPCAT3 expression.

RESULTS

TCGA and GEO data revealed that LPCAT3 expression in ccRCC tumor tissues was higher than that in adjacent normal tissues; moreover, patients with high LPCAT3 expression had better survival outcomes. qRT-PCR and immunohistochemistry verified the high LPCAT3 expression in tumor tissue. Pathways related to ferroptosis and ERS were upregulated in patients with high LPCAT3 expression. Univariate and multivariate regression analyses revealed that low LPCAT3 levels represent an independent risk factor for ccRCC. LPCAT3 expression was positively correlated with M2 macrophage infiltration levels but negatively correlated with the memory B cell, CD8+ T cell, follicular helper T cell, regulatory T cell, activated natural killer cell, and activated memory CD4+ T cell infiltration levels.

CONCLUSIONS

LPCAT3was identified as a ccRCC biomarker and may regulate immune infiltration and prognosis in ccRCC by mediating ferroptosis and ERS. Thus, it has potential for exploitation as a prognostic and immune therapeutic target for patients with ccRCC.

Deciphering immune predictors of immunotherapy response: A multiomics approach at the pan-cancer level

Immune checkpoint blockade (ICB) therapy has transformed cancer treatment, yet many patients fail to respond. Employing single-cell multiomics, we unveil T cell dynamics influencing ICB response across 480 pan-cancer and 27 normal tissue samples. We identify four immunotherapy response-associated T cells (IRATs) linked to responsiveness or resistance and analyze their pseudotemporal patterns, regulatory mechanisms, and T cell receptor clonal expansion profiles specific to each response. Notably, transforming growth factor β1 (TGF-β1)+ CD4+ and Temra CD8+ T cells negatively correlate with therapy response, in stark contrast to the positive response associated with CXCL13+ CD4+ and CD8+ T cells. Validation with a cohort of 23 colorectal cancer (CRC) samples confirms the significant impact of TGF-β1+ CD4+ and CXCL13+ CD4+ and CD8+ T cells on ICB efficacy. Our study highlights the effectiveness of single-cell multiomics in pinpointing immune markers predictive of immunotherapy outcomes, providing an important resource for crafting targeted immunotherapies for successful ICB treatment across cancers.

FOXP3/TLS; a prognostic marker in patients with bladder carcinoma without muscle invasion

OBJECTIVE

Bladder carcinoma (BC) is a common type of cancer. Approximately 20% of BC patients have non-muscle invasive bladder cancer (NMIBC). Despite adequate BCG treatment, recurrence occurs in approximately 40% of the patients. There is no adequate prognostic marker for recurrence in a group of patients. Forkhead box P3 (FOXP3) is a regulatory T cell marker that sometimes exhibits anti-tumoral effects and can be used as a tumor marker. T-cell immunoglobulin and mucin domain 3 (TIM-3) is an immune checkpoint inhibitor of T cells. Tertiary lymphoid structures (TLS) increase malignancy and inflammation in non-lymphoid organs. Therefore, we aimed to evaluate the prognostic value of FOXP3, TIM-3, and TLS in patients with NMIBC.

METHODS

Patients with pathologically confirmed NMIBC were included in this study. Stromal and intraepithelial cells were evaluated separately using immunohistochemistry, and FOXP3, TIM-3, TLS, FOXP3/TLS, and TIM-3/TLS were calculated and noted. The cutoff value was determined using ROC analysis. Recurrence-free survival (RFS) and overall survival (OS) were evaluated using univariate and multivariate Cox proportional hazard analyses.

RESULTS

The study included ninety-six patients. FOXP3/TLS high group had a better RFS than FOXP3/TLS low group (P = 0.001; HR, 0.079; 95% CI, 0.019-0.337). This was also significant in the multivariate analysis (P = 0.018; HR, 0.125; 95% CI, 0.022-0.705). In the group receiving BCG, FOXP3/TLS, FOXP3-TLS, TIM-3-TLS and TIM-3/TLS elevation were lower in patients with relapse than in patients without relapse and were statistically significant. Combined TIM-3 and FOXP3 elevation was found to be good prognostic regardless of whether it was found in intraepithelial, stromal or TLS.

CONCLUSION

FOXP3/TLS elevation is a good prognostic and predictive marker in all non-muscle invasive bladder cancer cases and in the subgroup receiving BCG. Elevation of FOXP3-TLS, TIM-3-TLS, and TIM-3/TLS is associated with longer RFS in patients receiving BCG. Combined TIM-3 and FOXP3 elevation is indicative of a low recurrence rate in NMIBC.

Unveiling the key mechanisms of FOLR2+ macrophage-mediated antitumor immunity in breast cancer using integrated single-cell RNA sequencing and bulk RNA sequencing

Breast cancer (BRCA) is a common malignant tumor, and its immune microenvironment plays a crucial role in disease progression. In this research, we utilized single-cell RNA sequencing and bulk RNA sequencing technologies, combined with in vivo and in vitro experiments, to thoroughly investigate the immunological functions and mechanisms of FOLR2+ macrophages in BRCA. Our findings demonstrate a significant enhancement in the interaction between FOLR2+ macrophages and CD8+ T cells within the tumor tissues of BRCA patients. FOLR2 is closely associated with T cell infiltration in the tumor microenvironment of BRCA patients, particularly with CD8+ T cells. By secreting CXCL9 and engaging with CXCR3, FOLR2+ macrophages can activate the functionality of CD8+ T cells, thereby promoting cancer cell apoptosis. Further animal experiments confirm that FOLR2+ macrophages activate CD8+ T cells through the CXCL9-CXCR3 axis, exhibiting an antitumor immunity effect in BRCA. FOLR2+ macrophages play a crucial role in antitumor immunity in BRCA through the CXCL9-CXCR3 axis.

Astragalus polysaccharide enhances the therapeutic efficacy of cisplatin in triple-negative breast cancer through multiple mechanisms

Background

Cisplatin (DDP) has been used in the treatment of various human cancers. However, DDP alone lacks efficacy in treating triple-negative breast cancer (TNBC), and its clinical application is often hampered by side effects. Astragalus polysaccharide (APS) is one of the active components extracted from Astragalus membranaceus and has gained attention for its various biological properties. This research is aimed to evaluate the effectiveness of a combination of APS and DDP on TNBC and explore the potential mechanisms.

Methods

The efficacy and mechanisms of single or combined treatment were evaluated using Cell Counting Kit-8 (CCK8) assay, Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) staining, wound healing assay, trans-well invasion/migration assay, hematoxylin-eosin (HE) staining, immunohistochemical (IHC) staining, Western Blot (WB) analysis, and fluorescence-activated cell sorting (FACS). An orthotopic model of TNBC was used to assess the in vivo treatment efficacy of single or combination treatment.

Results

APS significantly enhanced the anti-proliferative, anti-migratory, and anti-invasive effects of DDP on TNBC cells. The combination of APS and DDP downregulated anti-apoptotic genes (Bcl2 and Bcl-xL) while upregulating pro-apoptotic genes (Puma, Cle-Caspase3, Cle-PARP), leading to enhanced apoptosis. This combination treatment increased E-cadherin levels, decreased Vimentin, Snail, Slug, and Twist levels, and effectively suppressed epithelial-mesenchymal transition (EMT)-associated cell invasion. In the orthotopic model of TNBC, a synergistic reduction in tumor growth was observed in mice treated with APS and DDP. Additionally, the combination of APS and DDP induced the infiltration of CD8+ T lymphocytes into the tumor immune microenvironment.

Conclusion

The combination of APS and DDP exhibits more potent tumor inhibition and anti-tumor immunity than either agent alone, representing a novel approach to enhance therapeutic efficacy without increasing the side effects of DDP.

Significant association between systemic inflammation response index and prognosis in patients with urological malignancies

Background

The systemic inflammation response index (SIRI) as an immune marker, is associated with prognosis of urological malignancies(UM). However, the conclusion remains controversial. Therefore, the objective of this study was to conduct a meta-analysis to comprehensively evaluate the predictive value of SIRI in patients with UM.

Methods

A comprehensive search of PubMed, Web of Science, and EMBASE databases was performed for articles investigating the association between SIRI and UM. The search deadline was August 28, 2024. Survival outcome such as overall survival (OS), disease-free survival (DFS), progression-free survival (PFS), and recurrence-free survival (RFS) were analyzed.

Results

15 studies from 13 articles involving 4985 patients were included in the meta-analysis. The results showed that increased SIRI was associated with poorer OS (HR: 2.16, 95% CI: 1.61-2.89) and DFS/PFS/RFS (HR: 3.56, 95% CI: 1.41-8.99). Subgroup analysis further confirmed the prognostic value of SIRI in urinary system cancer.

Multi-omics perspective: mechanisms of gastrointestinal injury repair

In this review, we examine the significance of multi-omics technologies in understanding the plethora of intricate processes that activate gastrointestinal (GI) injury repair. Multi-omics, which includes genomics, transcriptomics, proteomics, and metabolomics, allows intricate mapping of cellular responses and molecular pathways involved in GI repair. We highlight the potential of multi-omics to discover previously unknown therapeutic targets or elucidate the molecular basis of the pathogenesis of GI. Furthermore, we explore the possibilities of integrating omics data to improve prediction models, and summarize the state-of-the-art technological developments and persisting obstacles that hinder the translation of multi-omics into clinical practice. Finally, innovative multi-omics approaches that can improve patient outcomes and advance therapeutic strategies in GI medicine are discussed.

CASP5 associated with PANoptosis promotes tumorigenesis and progression of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a globally severe cancer with an unfavorable prognosis. PANoptosis, a form of cell death regulated by PANoptosomes, plays a role in numerous cancer types. However, the specific roles of genes associated with PANoptosis in the development and advancement of ccRCC remain unclear. Our study developed a risk model utilizing three PANoptosis-associated genes (Caspase 4 (CASP4), TLR3, and CASP5). This model demonstrated a high degree of precision in predicting the prognosis for patients with ccRCC. ccRCC patients in the high-risk group had the strongest immune cell activity, experiencing immune evasion, and might potentially derive advantages from treatment involving combined immune checkpoint inhibitors. CASP5 was highly expressed in ccRCC tissues by RT-qPCR, western blotting, and immunofluorescence. Stable CASP5 knockdown cell lines were constructed by lentivirus in vitro transfection technique. Reducing CASP5 level suppressed the growth, migration, and invasion of ccRCC cells, while encouraging cell apoptosis. In addition, the results of in vivo tumorigenesis experiments showed that down-regulating CASP5 expression inhibited the tumorigenic ability of 786-O cells. Together, the innovative risk model using PANoptosis-associated genes effectively forecasts the tumor microenvironment and survival rates for ccRCC, offering a novel approach to the early, precise diagnosis of ccRCC and the advancement of personalized treatment strategies.

The protein circPETH-147aa regulates metabolic reprogramming in hepatocellular carcinoma cells to remodel immunosuppressive microenvironment

Metabolic reprogramming fuels cancer cell metastasis and remodels the immunosuppressive tumor microenvironment (TME). We report here that circPETH, a circular RNA (circRNA) transported via extracellular vesicles (EVs) from tumor-associated macrophages (TAMs) to hepatocellular carcinoma (HCC) cells, facilitates glycolysis and metastasis in recipient HCC cells. Mechanistically, circPETH-147aa, encoded by circPETH in an m6A-driven manner, promotes PKM2-catalyzed ALDOA-S36 phosphorylation via the MEG pocket. Furthermore, circPETH-147aa impairs anti-HCC immunity by increasing HuR-dependent SLC43A2 mRNA stability and driving methionine and leucine deficiency in cytotoxic CD8+ T cells. Importantly, through virtual and experimental screening, we find that a small molecule, Norathyriol, is an effective inhibitor that targets the MEG pocket on the circPETH-147aa surface. Norathyriol reverses circPETH-147aa-facilitated acquisition of metabolic and metastatic phenotypes by HCC cells, increases anti-PD1 efficacy, and enhances cytotoxic CD8+ T-cell function. Here we show that Norathyriol is a promising anti-HCC agent that contributes to attenuating the resistance of advanced HCC to immune checkpoint blocker (ICB) therapies.

Novel biomarkers: the RUNX family as prognostic predictors in colorectal cancer

While biomarkers have been shown to enhance the prognosis of patients with colorectal cancer (CRC) compared to conventional treatments, there is a pressing need to discover novel biomarkers that can assist in assessing the prognostic impact of immunotherapy and in formulating individualized treatment plans. The RUNX family, consisting of RUNX1, RUNX2, and RUNX3, has been recognized as crucial regulators in developmental processes, with dysregulation of these genes also being implicated in tumorigenesis and cancer progression. In our present study, we demonstrated a crucial regulatory role of RUNX in CD8+T and CD103+CD8+T cell-mediated anti-tumor response within the tumor microenvironment (TME) of human CRC. Specifically, RUNXs were significantly differentially expressed between tumor and normal tissues in CRC. Patients with a greater proportion of infiltrating CD8+RUNX1+, CD103+CD8+RUNX1+, CD8+RUNX2+, CD103+CD8+RUNX2+, CD8+RUNX3+, or CD103+CD8+RUNX3+ T cells demonstrated improved outcomes compared to those with lower proportions. Additionally, the proportions of infiltrating CD8+RUNX1+T and CD8+RUNX3+T cells may serve as valuable prognostic predictors for CRC patients, independent of other clinicopathological factors. Moreover, further bioinformatic analysis conducted utilizing the TISIDB and TIMER platforms demonstrated significant associations between the members of the RUNX family and immune-infiltrating cells, specifically diverse subpopulations of CD8+TILs. Our study of human colorectal cancer tissue microarray (TMA) also revealed positive and statistically significant correlations between the expressions of RUNX1, RUNX2, and RUNX3 in both CD8+T cells and CD103+CD8+T cells. Our study comprehensively revealed the varied expressions and prognostic importance of the RUNX family in human colorectal cancer tissues. It underscored their potential as vital biomarkers for prognostic evaluation in colorectal cancer patients and as promising targets for immunotherapy in treating this disease.

Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions

T cell receptors (TCR) and gene expression provide two complementary and essential aspects in T cell understanding, yet their diversity presents challenges in integrative analysis. We introduce TCRclub, a novel method integrating single-cell RNA sequencing data and single-cell TCR sequencing data using local harmony to identify functionally similar T cell groups, termed 'clubs'. We applied TCRclub to 298,106 T cells across seven datasets encompassing various diseases. First, TCRclub outperforms the state-of-the-art methods in clustering T cells on a dataset with over 400 verified peptide-major histocompatibility complex categories. Second, TCRclub reveals a transition from activated to exhausted T cells in cholangiocarcinoma patients. Third, TCRclub discovered the pathways that could intervene in response to anti-PD-1 therapy for patients with basal cell carcinoma by analyzing the pre-treatment and post-treatment samples. Furthermore, TCRclub unveiled different T-cell responses and gene patterns at different severity levels in patients with COVID-19. Hence, TCRclub aids in developing more effective immunotherapeutic strategies for cancer and infectious diseases.

Roles of cathepsin S expression levels on the prognosis and tumour microenvironment in clear cell renal cell carcinoma

BACKGROUND

Increasing evidence suggests a link between the enzyme cathepsin S (CTSS) and tumour development. However, the potential involvement and molecular functions of CTSS in clear cell renal cell carcinoma (ccRCC) remain unclear.

METHODS

We downloaded original data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and integrated them using R. Kaplan-Meier plots of integrated expression scores were used to analyse survival outcomes. Additionally, we investigated mRNA expression, clinicopathological features, immune infiltrates, and single-cell sequencing analysis of CTSS in ccRCC. In vitro experiments were conducted with qRT-PCR and IHC staining.

RESULTS

CTSS transcriptomic and proteomic levels were higher in ccRCC than in para-cancerous tissues. Low CTSS expression was correlated with poor prognosis in patients with ccRCC. Our data demonstrated that the expression of CTSS was strongly correlated with immune cell infiltration levels and gene markers of immune cells, chemokines, and receptors. Single-cell sequencing analysis demonstrated that CTSS expression was detectable in monocytes/macrophages. Finally, certain chemicals were confirmed to affect CTSS expression.

CONCLUSION

Our findings indicate that CTSS offers promise as a prognostic biomarker and novel immune-related therapeutic target for ccRCC.

Study on correlation between CXCL13 and prognosis and immune characteristics of ovarian cancer

Ovarian cancer (OC) has a limited immunotherapeutic response; hence, this study aimed to investigate the relationship between CXC-chemokine ligand 13 (CXCL13) expression and overall survival (OS) rate, key immune pathways, degree of immune cell infiltration, and progressive disease (PD)-1 checkpoint blockade. A total of 703 differentially expressed genes were obtained from "The Cancer Genome Atlas" (TCGA) database based on the immune and stromal scores of 379 OC patients for getting the targeted gene CXCL13. The association between CXCL13 and OS in OC patients, biological function annotation of CXCL13, and its correlation with immune components were assessed. The results indicated that upregulated CXCL13 expression was positively correlated with better OC patient prognosis. CXCL13 expression was associated with 6 immune-related pathways, 10 immune cells, and PD-1 expression of OC micro-environment. Moreover, high expression of CXCL13 was related to a better tumor response and more extended tumor-stable stage after PD-1 blocking therapy in IMvigor210. The study concluded that CXCL13 could be a prognostic marker and a potential immunotherapy target for OC patients, especially PD-1 checkpoint blockade.

Comprehensive assessment of the association between tumor-infiltrating immune cells and the prognosis of renal cell carcinoma

BACKGROUND

According to current statistics, renal cancer accounts for 3% of all cancers worldwide. Renal cell carcinoma (RCC) is the most common solid lesion in the kidney and accounts for approximately 90% of all renal malignancies. Increasing evidence has shown an association between immune infiltration in RCC and clinical outcomes. To discover possible targets for the immune system, we investigated the link between tumor-infiltrating immune cells (TIICs) and the prognosis of RCC.

AIM

To investigate the effects of 22 TIICs on the prognosis of RCC patients and identify potential therapeutic targets for RCC immunotherapy.

METHODS

The CIBERSORT algorithm partitioned the 22 TIICs from the Cancer Genome Atlas cohort into proportions. Cox regression analysis was employed to evaluate the impact of 22 TIICs on the probability of developing RCC. A predictive model for immunological risk was developed by analyzing the statistical relationship between the subpopulations of TIICs and survival outcomes. Furthermore, multivariate Cox regression analysis was used to investigate independent factors for the prognostic prediction of RCC. A value of P < 0.05 was regarded as statistically significant.

RESULTS

Compared to normal tissues, RCC tissues exhibited a distinct infiltration of immune cells. An immune risk score model was established and univariate Cox regression analysis revealed a significant association between four immune cell types and the survival risk connected to RCC. High-risk individuals were correlated to poorer outcomes according to the Kaplan-Meier survival curve (P = 1^E−05). The immunological risk score model was demonstrated to be a dependable predictor of survival risk (area under the curve = 0.747) via the receiver operating characteristic curve. According to multivariate Cox regression analysis, the immune risk score model independently predicted RCC patients' prognosis (hazard ratio = 1.550, 95%CI: 1.342–1.791; P < 0.001). Finally, we established a nomogram that accurately and comprehensively forecast the survival of patients with RCC.

CONCLUSION

TIICs play various roles in RCC prognosis. The immunological risk score is an independent predictor of poor survival in kidney cancer cases.

VHL missense mutation delineate aggressive clear cell renal cell carcinoma subtype with favorable immunotherapeutic response

BACKGROUND

von Hippel-Lindau (VHL) harbors the highest mutational frequency in clear cell renal cell carcinoma (ccRCC). Although VHL mutational subtypes exert diverse impacts on the functionality of the VHL protein, the clinical significance of VHL mutational heterogeneity remains largely obscure.

METHODS

This study included a total of 1331 patients with ccRCC from localized data sets, including our localized Zhongshan Hospital (ZSHS) cohort (n=1270) and Zhongshan immune checkpoint blockade cohort (n=61), as well as 525 patients with ccRCC from two publicly available data sets with matched clinical annotation and multidimensional data. According to the putative biological effect, we subclassified VHL mutation into VHL Trunc and VHL Miss. The association of VHL status with clinical outcomes, genomic, oncogenic and immunologic characteristics was further depicted.

RESULTS

VHL Miss ccRCC was associated with reduced survival in the localized ZSHS and The Cancer Genome Atlas cohorts. Clinical benefit from immunotherapy was observed in VHL Miss patients in all immunotherapy cohorts. VHL Miss ccRCC exhibited hyper-activated cell cycle and nuclear factor kappa B (NF-κB) instead of canonical hypoxia inducible factor pathways, which might contribute to its proliferative morphology. Meanwhile, VHL Miss ccRCC featured an inflamed microenvironment with enriched tertiary lymphoid structures.

CONCLUSIONS

VHL Miss mutations delineate an aggressive ccRCC subtype with distinct clinical outcomes, likely attributed to its specific oncogenic, morphologic and immunologic features.

CXCL9, CXCL10, and CCL19 synergistically recruit T lymphocytes to skin in lichen planus

Lichen planus (LP) is a chronic, debilitating, inflammatory disease of the skin and mucous membranes that affects 1%-2% of Americans. Its molecular pathogenesis remains poorly understood, and there are no FDA-approved treatments. We performed single-cell RNA sequencing on paired blood and skin samples (lesional and nonlesional tissue) from 7 patients with LP. We discovered that LP keratinocytes and fibroblasts specifically secrete a combination of CXCL9, CXCL10, and CCL19 cytokines. Using an in vitro migration assay with primary human T cells, we demonstrated that CCL19 in combination with either of the other 2 cytokines synergistically enhanced recruitment of CD8+ T cells more than any individual cytokine. Moreover, exhausted T cells in lesional LP skin secreted CXCL13, which, along with CCL19, also enhanced recruitment of T cells, suggesting a feed-forward loop in LP. Finally, LP blood revealed decreased circulating naive CD8+ T cells compared with that in healthy volunteers, consistent with recruitment to skin. Molecular analysis of LP skin and blood samples increased our understanding of disease pathogenesis and identified CCL19 as a new therapeutic target for treatment.

Tertiary Lymphoid Structures in Microorganism-Related Cancer

Tertiary lymphoid structures (TLSs) are ectopic lymphoid tissues formed by the accumulation of lymphocytes and other components outside lymphoid organs. They have been shown to be widespread in cancers and have predictive effects on prognosis and immunotherapy efficacy; however, there is no standardized measurement guide. This paper provides a reference for future research. Moreover, the induction strategy for the formation mechanism of TLSs is a new direction for future cancer treatment, such as cancer vaccines for microorganisms. The effects of microorganisms on cancer are dual. The role of microorganisms, including bacteria, parasites, viruses, and fungi, in promoting cancer has been widely confirmed. However, the specific mechanism of their tumor suppressor effect, particularly the promotion of TLS formation, is currently unknown. In this review, we summarize the role of TLSs in cancer related to microbial infection and provide new ideas for further understanding their mechanisms of action in cancer.

Pilot study: Understanding canine transmissible venereal tumor through its transcriptional profile

Canine transmissible venereal tumor (CTVT) is transmitted through the implantation of tumor cells. CTVT was the first tumor described with contagious characteristics and remains one of the few tumors with this capability. This study aimed to map the transcriptomic profile of CTVT to elucidate the potential mechanisms through which this tumor implants and evades host immune surveillance. For this study, 11 dogs aged ≥ 2 years diagnosed with CTVT were selected. Tumor biopsies were performed, RNA was extracted and converted into complementary DNA, followed by RT-qPCR analysis. The transcriptomic profile of CTVT revealed a wide array of differentially expressed genes. However, only the most relevant genes from an oncological perspective were discussed. IL-8, CXCL13, NCAM1, RNASEL, COROA1, and CBLB demonstrated potential associations with immune system evasion and transmission via implantation. Therefore, studying these genes may contribute to the development of targeted therapies that prevent contagion and immune evasion.

Blood-based circulating biomarkers for prediction of immune-checkpoint inhibitors efficacy in renal cell carcinoma

Immune checkpoint inhibitors (ICI)-based combinations have become the standard first-line treatment for advanced clear cell renal cell carcinoma (ccRCC). Despite significant improvements in survival and the achievement of sustained long-term responses, a subset of patients remains refractory to ICI, and most will eventually develop resistance. Thus, identifying predictive biomarkers for ICI efficacy and resistance is essential for optimizing therapeutic strategies. Up to now, tissue-based biomarkers have not been successful as predictive biomarkers in RCC. Circulating blood-based biomarkers offer a promising alternative. These biomarkers, including circulating immune cells, soluble factors, tumor-derived markers, and those based on metabolomics, are less invasive, offer reproducibility over time, and provide a comprehensive assessment of tumor biology and patient immune status, as well as allow dynamic monitoring during treatment. This review aims to evaluate the current evidence on the different candidate circulating biomarkers being investigated for their potential to predict ICI efficacy in RCC patients.

The molecular landscape of T cell exhaustion in the tumor microenvironment and reinvigoration strategies

Immunotherapy has emerged as a promising therapeutic approach for cancer treatment by harnessing the immune system to target cancer cells. However, the efficacy of immunotherapy is hindered by the tumor microenvironment (TME), comprising regulatory T cells (Tregs), macrophages, myeloid-derived suppressor cells (MDSCs), neutrophils, soluble factors (TGF-β, IL-35, IL-10), and hypoxia. These components interact with inhibitory receptors (IRs) on T cells, leading to alterations in T cell transcriptomes, epigenomes, and metabolism, ultimately resulting in T cell exhaustion and compromising the effectiveness of immunotherapy. T cell exhaustion occurs in two phases: pre-exhaustion and exhaustion. Pre-exhausted T cells exhibit reversibility and distinct molecular properties compared to terminally exhausted T cells. Understanding these differences is crucial for designing effective interventions. This comprehensive review summarizes the characteristics of pre-exhausted and exhausted T cells and elucidates the influence of TME components on T cell activity, transcriptomes, epigenomes, and metabolism, ultimately driving T cell exhaustion in cancer. Additionally, potential intervention strategies for reversing exhaustion are discussed. By gaining insights into the mechanisms underlying T cell exhaustion and the impact of the TME, this review aims to inform the development of innovative approaches for combating T cell exhaustion and enhancing the efficacy of immunotherapy in cancer treatment.

Phenotypic and spatial heterogeneity of CD8+ tumour infiltrating lymphocytes

CD8+ T cells are the workhorses executing adaptive anti-tumour response, and targets of various cancer immunotherapies. Latest advances have unearthed the sheer heterogeneity of CD8+ tumour infiltrating lymphocytes, and made it increasingly clear that the bulk of the endogenous and therapeutically induced tumour-suppressive momentum hinges on a particular selection of CD8+ T cells with advantageous attributes, namely the memory and stem-like exhausted subsets. A scrutiny of the contemporary perception of CD8+ T cells in cancer and the subgroups of interest along with the factors arbitrating their infiltration contextures, presented herein, may serve as the groundwork for future endeavours to probe further into the regulatory networks underlying their differentiation and migration, and optimise T cell-based immunotherapies accordingly.

Single-cell analysis reveals the disparities in immune profiles between younger and elder patients

PURPOSE

The immune profiles of elder patients with non-small cell lung cancer (NSCLC) differ significantly from those of younger patients. The tumor microenvironment (TME) is a crucial factor in cancer progression and therapeutic responses. The present study aims to decipher the difference in TME between younger and elderly patients with lung cancers.

METHODS

We downloaded single-cell RNA data from public databases. The algorithm of uniform manifold approximation and projection (UMAP) was applied to cluster and visualize single-cell sequencing data. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) analysis were performed to evaluate the physiological functional characteristics in sub-group cells. CellPhoneDB was used to identify cell-cell interactions between immune cells within TME.

RESULTS

We conducted single-cell RNA sequencing on 96,491 cells from elderly patients and 169,207 cells from younger patients, respectively. We observed that epithelial cells were the predominant component of the TME in younger patients, whereas T/NK cells were the predominant cell type in the TME of elderly patients. We also found that there was a higher proportion of Tregs and a lower proportion of NK, effector CD8+T and γδT cells in elder patients compared with younger patients. In addition, a comparative GSEA analysis of NK cells between older and younger patients revealed that the pathways of Parkinson's disease, Alzheimer's disease, mismatch repair, and base excision repair were up-regulated in NK cells from elderly patients, while the pathways related to natural killer cell-mediated cytotoxicity and allograft rejection were downregulated. Furthermore, we identified tumor-associated neutrophils (TANs) in elder patients, and GSVA analysis demonstrated that the pathway of angiogenesis was upregulated, and the pathway of interferon_γ_response, inflammatory_response, TNFα_signaling_via_NFκB pathways were downregulated. Importantly, the pro-inflammatory response scores of complement C1q C chain positive (C1QC+) macrophages, tissue-resident macrophages (TRM), non-classical monocytes (NCM), secreted phosphoprotein 1 positive (SPP1+) macrophages, and classical monocytes (CM) in elder patients were significantly lower compared to those in younger patients. Finally, cell-to-cell communication analyses unveiled the disparities in regulatory patterns between elder and younger patients, namely the pairs of CXCL13-ACKR4 and CSF1-SIRPA in elder patients and the pairs of CTLA4-CD86 and TIGIT-NECTIN2 in younger patients.

CONCLUSION

This study reveals the distinct immune profiles between younger and elder NSCLC patients, and the elder patients were likely to exhibit a more immunosuppressive TME and attenuated tumor-killing capability compared with younger patients.

Identification and Validation of Cytotoxicity-Related Features to Predict Prognostic and Immunotherapy Response in Patients with Clear Cell Renal Cell Carcinoma

Background

Clear cell renal cell carcinoma (ccRCC) is a renal cortical malignancy with a complex pathogenesis. Identifying ideal biomarkers to establish more accurate promising prognostic models is crucial for the survival of kidney cancer patients.

Methods

Seurat R package was used for single-cell RNA-sequencing (scRNA-seq) data filtering, dimensionality reduction, clustering, and differentially expressed genes analysis. Gene coexpression network analysis (WGCNA) was performed to identify the cytotoxicity-related module. The independent cytotoxicity-related risk model was established by the survival R package, and Kaplan-Meier (KM) survival analysis and timeROC with area under the curve (AUC) were employed to confirm the prognosis and effectiveness of the risk model. The risk and prognosis in patients suffering from ccRCC were predicted by establishing a nomogram. A comparison of the level of immune infiltration in different risk groups and subtypes using the CIBERSORT, MCP-counter, and TIMER methods, as well as assessment of drug sensitivity to conventional chemotherapeutic agents in risk groups using the pRRophetic package, was made.

Results

Eleven ccRCC subpopulations were identified by single-cell sequencing data from the GSE224630 dataset. The identified cytotoxicity-related T-cell cluster and module genes defined three cytotoxicity-related molecular subtypes. Six key genes (SOWAHB, SLC16A12, IL20RB, SLC12A8, PLG, and HHLA2) affecting prognosis risk genes were selected for developing a risk model. A nomogram containing the RiskScore and stage revealed that the RiskScore contributed the most and exhibited excellent predicted performance for prognosis in the calibration plots and decision curve analysis (DCA). Notably, high-risk patients with ccRCC demonstrate a poorer prognosis with higher immune infiltration characteristics and TIDE scores, whereas low-risk patients are more likely to benefit from immunotherapy.

Conclusions

A ccRCC survival prognostic model was produced based on the cytotoxicity-related signature, which had important clinical significance and may provide guidance for ccRCC treatment.

Tertiary lymphoid structures in diseases: immune mechanisms and therapeutic advances

Tertiary lymphoid structures (TLSs) are defined as lymphoid aggregates formed in non-hematopoietic organs under pathological conditions. Similar to secondary lymphoid organs (SLOs), the formation of TLSs relies on the interaction between lymphoid tissue inducer (LTi) cells and lymphoid tissue organizer (LTo) cells, involving multiple cytokines. Heterogeneity is a distinguishing feature of TLSs, which may lead to differences in their functions. Growing evidence suggests that TLSs are associated with various diseases, such as cancers, autoimmune diseases, transplant rejection, chronic inflammation, infection, and even ageing. However, the detailed mechanisms behind these clinical associations are not yet fully understood. The mechanisms by which TLS maturation and localization affect immune function are also unclear. Therefore, it is necessary to enhance the understanding of TLS development and function at the cellular and molecular level, which may allow us to utilize them to improve the immune microenvironment. In this review, we delve into the composition, formation mechanism, associations with diseases, and potential therapeutic applications of TLSs. Furthermore, we discuss the therapeutic implications of TLSs, such as their role as markers of therapeutic response and prognosis. Finally, we summarize various methods for detecting and targeting TLSs. Overall, we provide a comprehensive understanding of TLSs and aim to develop more effective therapeutic strategies.

Tertiary lymphoid structure-related immune infiltrates in NSCLC tumor lesions correlate with low tumor-reactivity of TIL products

Adoptive transfer of tumor infiltrating lymphocytes (TIL therapy) has proven highly effective for treating solid cancers, including non-small cell lung cancer (NSCLC). However, not all patients benefit from this therapy for yet unknown reasons. Defining markers that correlate with high tumor-reactivity of the autologous TIL products is thus key for achieving better tailored immunotherapies. We questioned whether the composition of immune cell infiltrates correlated with the tumor-reactivity of expanded TIL products. Unbiased flow cytometry analysis of immune cell infiltrates of 26 early-stage and 20 late-stage NSCLC tumor lesions was used for correlations with the T cell differentiation and activation status, and with the expansion rate and anti-tumor response of generated TIL products. The composition of tumor immune infiltrates was highly variable between patients. Spearman's Rank Correlation revealed that high B cell infiltration negatively correlated with the tumor-reactivity of the patient's expanded TIL products, as defined by cytokine production upon exposure to autologous tumor digest. In-depth analysis revealed that tumor lesions with high B cell infiltrates contained tertiary lymphoid structure (TLS)-related immune infiltrates, including BCL6+ antibody-secreting B cells, IgD+BCL6+ B cells and CXCR5+BLC6+ CD4+ T cells, and higher percentages of naïve CD8+ T cells. In conclusion, the composition of immune cell infiltrates in NSCLC tumors associates with the functionality of the expanded TIL product. Our findings may thus help improve patient selection for TIL therapy.

The roles of tertiary lymphoid structures in genitourinary cancers: molecular mechanisms, therapeutic strategies, and clinical applications

The presence of tertiary lymphoid structures (TLSs) associated with distinct treatment efficacy and clinical prognosis has been identified in various cancer types. However, the mechanistic roles and clinical implications of TLSs in genitourinary (GU) cancers remain incompletely explored. Despite their potential role as predictive markers described in numerous studies, it is essential to comprehensively evaluate the characteristics of TLSs, including drivers of formation, structural foundation, cellular compositions, maturation stages, molecular features, and specific functionality to maximize their positive impacts on tumor-specific immunity. The unique contributions of these structures to cancer progression and biology have fueled interest in these structures as mediators of antitumor immunity. Emerging data are trying to explore the effects of therapeutic interventions targeting TLSs. Therefore, a better understanding of the molecular and phenotypic heterogeneity of TLSs may facilitate the development of TLSs-targeting therapeutic strategies to obtain optimal clinical benefits for GU cancers in the setting of immunotherapy. In this review, the authors focus on the phenotypic and functional heterogeneity of TLSs in cancer progression, current therapeutic interventions targeting TLSs and the clinical implications and therapeutic potential of TLSs in GU cancers.

Dysfunction of CD8+ T cells around tumor cells leads to occult lymph node metastasis in NSCLC patients

Occult lymph node metastasis (OLNM) is one of the main causes of regional recurrence in inoperable N0 non-small cell lung cancer (NSCLC) patients following stereotactic ablation body radiotherapy (SABR) treatment. The integration of immunotherapy and SABR (I-SABR) has shown preliminary efficiency in mitigating this recurrence. Therefore, it is necessary to explore the functional dynamics of critical immune effectors, particularly CD8+ T cells in the development of OLNM. In this study, tissue microarrays (TMAs) and multiplex immunofluorescence (mIF) were used to identify CD8+ T cells and functional subsets (cytotoxic CD8+ T cells/predysfunctional CD8+ T cells (CD8+ Tpredys)/dysfunctional CD8+ T cells (CD8+ Tdys)/other CD8+ T cells) among the no lymph node metastasis, OLNM, and clinically evident lymph node metastasis (CLNM) groups. As the degree of lymph node metastasis escalated, the density of total CD8+ T cells and CD8+ Tdys cells, as well as their proximity to tumor cells, increased progressively and remarkably in the invasive margin (IM). In the tumor center (TC), both the density and proximity of CD8+ Tpredys cells to tumor cells notably decreased in the OLNM group compared with the group without metastasis. Furthermore, positive correlations were found between the dysfunction of CD8+ T cells and HIF-1α+CD8 and cancer microvessels (CMVs). In conclusion, the deterioration in CD8+ T cell function and interactive dynamics between CD8+ T cells and tumor cells play a vital role in the development of OLNM in NSCLC. Strategies aimed at improving hypoxia or targeting CMVs could potentially enhance the efficacy of I-SABR.

Comprehensive analysis of signaling lymphocyte activation molecule family as a prognostic biomarker and correlation with immune infiltration in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a common type of kidney cancer and accounts for 2-3% of all cancer cases. Furthermore, a growing number of immunotherapy approaches are being used in antitumor treatment. Signaling lymphocyte activation molecule family (SLAMF) members have been well studied in several cancers, whereas their roles in ccRCC have not been investigated. The present study comprehensively assessed the molecular mechanisms of SLAMF members in ccRCC, performed using The Cancer Genome Atlas database, with analysis of gene transcription, prognosis, biological function, clinical features, tumor-associated immune cells and the correlation with programmed cell death protein 1/programmed death-ligand 1 immune checkpoints. Simultaneously, the Tumor Immune Dysfunction and Exclusion algorithm was used to predict the efficacy of immune checkpoint blockade (ICB) therapy in patients with high and low SLAMF expression levels. The results demonstrated that all SLAMF members were highly expressed in ccRCC, and patients with high expression levels of SLAMF1, 4, 7 and 8 had a worse prognosis that those with low expression. SLAMF members were not only highly associated with immune activation but also with immunosuppressive agents. The level of immune cell infiltration was associated with the prognosis of patients with ccRCC with high SLAMF expression. Moreover, high ICB response rates were observed in patients with high expression levels of SMALF1 and 4. In summary, SLAMF members may serve as future potential biomarkers for predicting the prognosis of ccRCC and emerge as a novel immunotherapy target.

SOX11 as a prognostic biomarker linked to m6A modification and immune infiltration in renal clear cell carcinoma

Background

The prognosis for patients with kidney renal clear cell carcinoma (KIRC) remains unfavorable, and the understanding of SRY-box transcription factor 11 (SOX11) in KIRC is still limited. The purpose of this paper is to explore the role of SOX11 in the prognosis of KIRC.

Methods

We analyzed SOX11 expression in KIRC and adjacent normal tissues using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Our study aims to establish a correlation between SOX11 expression and clinical pathological features. Differentially expressed genes (DEGs) were assessed using R software. Furthermore, we conducted Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and gene set enrichment analysis (GSEA). Integration of data from the Tumor Immune Estimation Resource (TIMER) and TCGA databases allowed us to assess the association between SOX11 expression and immune infiltration in KIRC. Additionally, we analyzed the association between SOX11 gene expression and N6-methyladenosine (m6A) modification in KIRC using TCGA and GEO data.

Results

Our findings revealed high SOX11 expression in KIRC, which showed a significant correlation with tumor staging and prognosis. GO/KEGG and GSEA analyses indicated that SOX11 was closely associated with sodium ion transport, synaptic vesicle circulation, and oxidative phosphorylation. Analysis of the TIMER and TCGA databases demonstrated correlations of SOX11 expression levels with the presence of CD8+ T lymphocytes, neutrophils, CD4+ T cells, as well as B cells. Moreover, both the TCGA and GEO datasets showed a substantial association between SOX11 and m6A modification-related genes, namely ZC3H13, FTO, METTL14, YTHDC1, IGF2BP1, and IGF2BP2.

Conclusions

SOX11 exhibits a correlation with m6A modification and immune infiltration, suggesting its potential as a prognostic biomarker for KIRC.

A Multi-Omics Analysis of an Exhausted T Cells' Molecular Signature in Pan-Cancer

T cells are essential tumor suppressors in cancer immunology, but their dysfunction induced by cancer cells can result in T cell exhaustion. Exhausted T cells (Tex) significantly influence the tumor immune environment, and thus, there is a need for their thorough investigation across different types of cancer. Here, we address the role of Tex cells in pan-cancer, focusing on the expression, mutations, methylation, immune infiltration, and drug sensitivity of a molecular signature comprising of the genes HAVCR2, CXCL13, LAG3, LAYN, TIGIT, and PDCD1across multiple cancer types, using bioinformatics analysis of TCGA data. Our analysis revealed that the Tex signature genes are differentially expressed across 14 cancer types, being correlated with patient survival outcomes, with distinct survival trends. Pathway analysis indicated that the Tex genes influence key cancer-related pathways, such as apoptosis, EMT, and DNA damage pathways. Immune infiltration analysis highlighted a positive correlation between Tex gene expression and immune cell infiltration in bladder cancer, while mutations in these genes were associated with specific immune cell enrichments in UCEC and SKCM. CNVs in Tex genes were widespread across cancers. We also highlight high LAYN methylation in most tumors and a negative correlation between methylation levels and immune cell infiltration in various cancers. Drug sensitivity analysis identified numerous correlations, with CXCL13 and HAVCR2 expressions influencing sensitivity to several drugs, including Apitolisib, Belinostat, and Docetaxel. Overall, these findings highlight the importance of reviving exhausted T cells to enhance the treatment efficacy to significantly boost anti-tumor immunity and achieve better clinical outcomes.

PD1/PD-L1 blockade in clear cell renal cell carcinoma: mechanistic insights, clinical efficacy, and future perspectives

The advent of PD1/PD-L1 inhibitors has significantly transformed the therapeutic landscape for clear cell renal cell carcinoma (ccRCC). This review provides an in-depth analysis of the biological functions and regulatory mechanisms of PD1 and PD-L1 in ccRCC, emphasizing their role in tumor immune evasion. We comprehensively evaluate the clinical efficacy and safety profiles of PD1/PD-L1 inhibitors, such as Nivolumab and Pembrolizumab, through a critical examination of recent clinical trial data. Furthermore, we discuss the challenges posed by resistance mechanisms to these therapies and potential strategies to overcome them. We also explores the synergistic potential of combination therapies, integrating PD1/PD-L1 inhibitors with other immunotherapies, targeted therapies, and conventional modalities such as chemotherapy and radiotherapy. In addition, we examine emerging predictive biomarkers for response to PD1/PD-L1 blockade and biomarkers indicative of resistance, providing a foundation for personalized therapeutic approaches. Finally, we outline future research directions, highlighting the need for novel therapeutic strategies, deeper mechanistic insights, and the development of individualized treatment regimens. Our work summarizes the latest knowledge and progress in this field, aiming to provide a valuable reference for improving clinical efficacy and guiding future research on the application of PD1/PD-L1 inhibitors in ccRCC.

Changes in the Expression of Genes Regulating the Response to Hypoxia, Inflammation, Cell Cycle, Apoptosis, and Epithelial Barrier Functioning during Colitis-Associated Colorectal Cancer Depend on Individual Hypoxia Tolerance

One of the factors contributing to colorectal cancer (CRC) development is inflammation, which is mostly hypoxia-associated. This study aimed to characterize the morphological and molecular biological features of colon tumors in mice that were tolerant and susceptible to hypoxia based on colitis-associated CRC (CAC). Hypoxia tolerance was assessed through a gasping time evaluation in a decompression chamber. One month later, the animals were experimentally modeled for colitis-associated CRC by intraperitoneal azoxymethane administration and three dextran sulfate sodium consumption cycles. The incidence of tumor development in the distal colon in the susceptible to hypoxia mice was two times higher and all tumors (100%) were represented by adenocarcinomas, while in the tolerant mice, only 14% were adenocarcinomas and 86% were glandular intraepithelial neoplasia. The tumor area assessed on serially stepped sections was statistically significantly higher in the susceptible animals. The number of macrophages, CD3-CD19+, CD3+CD4+, and NK cells in tumors did not differ between animals; however, the number of CD3+CD8+ and vimentin+ cells was higher in the susceptible mice. Changes in the expression of genes regulating the response to hypoxia, inflammation, cell cycle, apoptosis, and epithelial barrier functioning in tumors and the peritumoral area depended on the initial mouse's hypoxia tolerance, which should be taken into account for new CAC diagnostics and treatment approaches development.

Lymphocyte homing and recirculation with tumor tertiary lymphoid structure formation: predictions for successful cancer immunotherapy

The capacity of lymphocytes continuously home to lymphoid structures is remarkable for cancer immunosurveillance and immunotherapy. Lymphocyte homing and recirculation within the tumor microenvironment (TME) are now understood to be adaptive processes that are regulated by specialized cytokines and adhesion molecule signaling cascades. Restricted lymphocyte infiltration and recirculation have emerged as key mechanisms contributing to poor responses in cancer immunotherapies like chimeric antigen receptor (CAR)-T cell therapy and immune checkpoint blockades (ICBs). Uncovering the kinetics of lymphocytes in tumor infiltration and circulation is crucial for improving immunotherapies. In this review, we discuss the current insights into the adhesive and migrative molecules involved in lymphocyte homing and transmigration. The potential mechanisms within the TME that restrain lymphocyte infiltration are also summarized. Advanced on these, we outline the determinates for tertiary lymphoid structures (TLSs) formation within tumors, placing high expectations on the prognostic values of TLSs as therapeutic targets in malignancies.

Cell Simulation as Cell Segmentation

Single-cell spatial transcriptomics promises a highly detailed view of a cell's transcriptional state and microenvironment, yet inaccurate cell segmentation can render this data murky by misattributing large numbers of transcripts to nearby cells or conjuring nonexistent cells. We adopt methods from ab initio cell simulation to rapidly infer morphologically plausible cell boundaries that preserve cell type heterogeneity. Benchmarking applied to datasets generated by three commercial platforms show superior performance and computational efficiency of this approach compared with existing methods. We show that improved accuracy in cell segmentation aids greatly in detection of difficult to accurately segment tumor infiltrating immune cells such as neutrophils and T cells. Lastly, through improvements in our ability to delineate subsets of tumor infiltrating T cells, we show that CXCL13-expressing CD8+ T cells tend to be more closely associated with tumor cells than their CXCL13-negative counterparts in data generated from renal cell carcinoma patient samples.

Assessment of AURKA expression and prognosis prediction in lung adenocarcinoma using machine learning-based pathomics signature

Objective

This study aimed to develop quantitative feature-based models from histopathological images to assess aurora kinase A (AURKA) expression and predict the prognosis of patients with lung adenocarcinoma (LUAD).

Methods

A dataset of patients with LUAD was derived from the cancer genome atlas (TCGA) with information on clinical characteristics, RNA sequencing and histopathological images. The TCGA-LUAD cohort was randomly divided into training (n = 229) and testing (n = 98) sets. We extracted quantitative image features from histopathological slides of patients with LUAD using computational approaches, constructed a predictive model for AURKA expression in the training set, and estimated their predictive performance in the test set. A Cox proportional hazards model was used to assess whether the pathomic scores (PS) generated by the model independently predicted LUAD survival.

Results

High AURKA expression was an independent risk factor for overall survival (OS) in patients with LUAD (hazard ratio = 1.816, 95 % confidence intervals = 1.257-2.623, P = 0.001). The model based on histopathological image features had significant predictive value for AURKA expression: the area under the curve of the receiver operating characteristic curve in the training set and validation set was 0.809 and 0.739, respectively. Decision curve analysis showed that the model had clinical utility. Patients with high PS and low PS had different survival rates (P = 0.019). Multivariate analysis suggested that PS was an independent prognostic factor for LUAD (hazard ratio = 1.615, 95 % confidence intervals = 1.071-2.438, P = 0.022).

Conclusion

Pathomics models based on machine learning can accurately predict AURKA expression and the PS generated by the model can predict LUAD prognosis.

Integrated analysis of tertiary lymphoid structures and immune infiltration in ccRCC microenvironment revealed their clinical significances: a multicenter cohort study

BACKGROUND

Tertiary lymphoid structures (TLSs) serve as organized lymphoid aggregates that influence immune responses within the tumor microenvironment. This study aims to investigate the characteristics and clinical significance of TLSs and tumor-infiltrating lymphocytes (TILs) in clear cell renal cell carcinoma (ccRCC).

METHODS

TLSs and TILs were analyzed comprehensively in 754 ccRCC patients from 6 academic centers and 532 patients from The Cancer Genome Atlas. Integrated analysis was performed based on single-cell RNA-sequencing datasets from 21 ccRCC patients to investigate TLS heterogeneity in ccRCC. Immunohistochemistry and multiplex immunofluorescence were applied. Cox regression and Kaplan-Meier analyses were used to reveal the prognostic significance.

RESULTS

The study demonstrated the existence of TLSs and TILs heterogeneities in the ccRCC microenvironment. TLSs were identified in 16% of the tumor tissues in 113 patients. High density (>0.6/mm2) and maturation of TLSs predicted good overall survival (OS) (p<0.01) in ccRCC patients. However, high infiltration (>151) of scattered TILs was an independent risk factor of poor ccRCC prognosis (HR=14.818, p<0.001). The presence of TLSs was correlated with improved progression-free survival (p=0.002) and responsiveness to therapy (p<0.001). Interestingly, the combination of age and TLSs abundance had an impact on OS (p<0.001). Higher senescence scores were detected in individuals with immature TLSs (p=0.003).

CONCLUSIONS

The study revealed the contradictory features of intratumoral TLSs and TILs in the ccRCC microenvironment and their impact on clinical prognosis, suggesting that abundant and mature intratumoral TLSs were associated with decreased risks of postoperative ccRCC relapse and death as well as favorable therapeutic response. Distinct spatial distributions of immune infiltration could reflect effective antitumor or protumor immunity in ccRCC.

TCL1A-expressing B cells are critical for tertiary lymphoid structure formation and the prognosis of oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) is a malignant tumor with a poor prognosis. Traditional treatments have limited effectiveness. Regulation of the immune response represents a promising new approach for OSCC treatment. B cells are among the most abundant immune cells in OSCC. However, the role of B cells in OSCC treatment has not been fully elucidated.

METHODS

Single-cell RNA sequencing analysis of 13 tissues and 8 adjacent normal tissues from OSCC patients was performed to explore differences in B-cell gene expression between OSCC tissues and normal tissues. We further investigated the relationship between differentially expressed genes and the immune response to OSCC. We utilized tissue microarray data for 146 OSCC clinical samples and RNA sequencing data of 359 OSCC samples from The Cancer Genome Atlas (TCGA) to investigate the role of T-cell leukemia 1 A (TCL1A) in OSCC prognosis. Multiplex immunohistochemistry (mIHC) was employed to investigate the spatial distribution of TCL1A in OSCC tissues. We then investigated the effect of TCL1A on B-cell proliferation and trogocytosis. Finally, lentiviral transduction was performed to induce TCL1A overexpression in B lymphoblastoid cell lines (BLCLs) to verify the function of TCL1A.

RESULTS

Our findings revealed that TCL1A was predominantly expressed in B cells and was associated with a better prognosis in OSCC patients. Additionally, we found that TCL1A-expressing B cells are located at the periphery of lymphatic follicles and are associated with tertiary lymphoid structures (TLS) formation in OSCC. Mechanistically, upregulation of TCL1A promoted the trogocytosis of B cells on dendritic cells by mediating the upregulation of CR2, thereby improving antigen-presenting ability. Moreover, the upregulation of TCL1A expression promoted the proliferation of B cells.

CONCLUSION

This study revealed the role of B-cell TCL1A expression in TLS formation and its effect on OSCC prognosis. These findings highlight TCL1A as a novel target for OSCC immunotherapy.

Immune Cell Migration to Cancer

Immune cell migration is required for the development of an effective and robust immune response. This elegant process is regulated by both cellular and environmental factors, with variables such as immune cell state, anatomical location, and disease state that govern differences in migration patterns. In all cases, a major factor is the expression of cell surface receptors and their cognate ligands. Rapid adaptation to environmental conditions partly depends on intrinsic cellular immune factors that affect a cell's ability to adjust to new environment. In this review, we discuss both myeloid and lymphoid cells and outline key determinants that govern immune cell migration, including molecules required for immune cell adhesion, modes of migration, chemotaxis, and specific chemokine signaling. Furthermore, we summarize tumor-specific elements that contribute to immune cell trafficking to cancer, while also exploring microenvironment factors that can alter these cellular dynamics within the tumor in both a pro and antitumor fashion. Specifically, we highlight the importance of the secretome in these later aspects. This review considers a myriad of factors that impact immune cell trajectory in cancer. We aim to highlight the immunotherapeutic targets that can be harnessed to achieve controlled immune trafficking to and within tumors.

Interaction of immune cells with renal cancer development: Mendelian randomization (MR) study

BACKGROUND

Renal cell carcinoma (RCC) is a prevalent and extensively immune-infiltrated malignancy of the urinary system. Immune cells play a crucial role in both the progression and therapeutic interventions targeting RCC. Nevertheless, the interplay between RCC and immune cells remains understudied, lacking substantial evidence supporting their causal relationship.

METHODS

For the purpose of investigating the causal connection between RCC and immune cell characteristics, a two-way two-sample Mendelian randomization (MR) analysis was carried out in this study. The aim was to determine whether specific immune cell traits have a causal impact on the risk of RCC. In order to achieve this, publicly accessible genetic data was utilized to examine and establish the potential relationship between 731 immune cell characteristics and the likelihood of developing RCC. Additionally, various techniques were applied to verify the reliability, variability, and presence of horizontal pleiotropy in the outcomes.

RESULTS

We found a bidirectional causal relationship between RCC and immune cells according to the MR analysis results. It should be noted that CD4-CD8-T cells (OR = 1.61, 95%CI = 1.02-2.55, P = 4.07 × 10-2) pose a risk for RCC, whereas BAFF-R (OR = 0.69, 95%CI = 0.53-0.89, P = 5.74 × 10-3) and CD19 (OR = 0.59, 95%CI = 1.02-2.55, P = 4.07 × 10-2) on B cells act as protective factors. Furthermore, the presence of RCC reduces the levels of B cells (OR = 1.05, 95%CI = 1.01-1.09, P = 1.19 × 10-2) and CD8 + T cells (OR = 1.04, 95%CI = 1.00-1.08, P = 2.83 × 10-2).

CONCLUSIONS

Our research illustrates the intricate correlation between immune cells and RCC, presenting novel insights for the prospective safeguarding against RCC risk and the exploration of fresh therapeutic targets.

Integrating transcriptomics and machine learning for immunotherapy assessment in colorectal cancer

Colorectal cancer (CRC) is a highly prevalent and lethal malignancy worldwide. Although immunotherapy has substantially improved CRC outcomes, intolerance remains a major concern among most patients. Considering the pivotal role of the tumor microenvironment (TME) in tumor progression and treatment outcomes, profiling the TME at the transcriptomic level can provide novel insights for developing CRC treatment strategies. Seventy-seven TME-associated signatures were acquired from previous studies. To elucidate variations in prognosis, clinical features, genomic alterations, and responses to immunotherapy in CRC, we employed a non-negative matrix factorization algorithm to categorize 2595 CRC samples of 27 microarrays from the Gene Expression Omnibus database. Three machine learning techniques were employed to identify a signature specific to immunotherapy. Subsequently, the mechanisms by which this signature interacts with TME subtypes and immunotherapy were investigated. Our findings revealed five distinct TME subtypes (TMESs; TMES1-TMES5) in CRC, each exhibiting a unique pattern of immunotherapy response. TMES1, TMES4, and TMES5 had relatively inferior outcomes, TMES2 was associated with the poorest prognosis, and TMES3 had a superior outcome. Subsequent investigations revealed that activated dendritic cells could enhance the immunotherapy response rate, with their augmentation effect closely associated with the activation of CD8+T cells. We successfully classified CRC into five TMESs, each demonstrating varying response rates to immunotherapy. Notably, the application of machine learning to identify activated dendritic cells helped elucidate the underlying mechanisms contributing to these differences. We posit that these TMESs hold promising clinical implications for prognostic evaluation and guidance of immunotherapy strategies, thereby providing valuable insights to inform clinical decision-making.

Identification of Treg-related prognostic molecular subtypes and individualized characteristics in clear cell renal cell carcinoma through single-cell transcriptomes and bulk RNA sequencing

BACKGROUND

In clear cell renal cell carcinoma (ccRCC), the role of Regulatory T cells (Treg cells) as prognostic and immunotherapy response predictors is not fully explored.

METHODS

Analyzing renal clear cell carcinoma datasets from TISCH, TCGA, and GEO, we focused on 8 prognostic Treg genes to study patient subtypes in ccRCC. We assessed Treg subtypes in relation to patient prognosis, tumor microenvironment, metabolism. Using Cox regression and principal component analysis, we devised Treg scores for individual patient characterization and explored the molecular role of C1QL1, a critical gene in the Treg model, through in vivo and in vitro studies.

RESULTS

Eight Treg-associated prognostic genes were identified, classifying ccRCC patients into cluster A and B. Cluster A patients showed poorer prognosis with distinct clinical and molecular profiles, potentially benefiting more from immunotherapy. Low Treg scores correlated with worse outcomes and clinical progression. Low scores also suggested that patients might respond better to immunotherapy and targeted therapies. In ccRCC, C1QL1 knockdown reduced tumor proliferation and invasion via NF-kb-EMT pathways and decreased Treg cell infiltration, enhancing immune efficacy.

CONCLUSIONS

The molecular subtype and Treg score in ccRCC, based on Treg cell marker genes, are crucial in personalizing ccRCC treatment and underscore C1QL1's potential as a tumor biomarker and target for immunotherapy.