Clinical characterization and immunosuppressive regulation of CD161 (KLRB1) in glioma through 916 samples

Insights of immune cell heterogeneity, tumor-initiated subtype transformation, drug resistance, treatment and detecting technologies in glioma microenvironment

BACKGROUND

With the gradual understanding of glioma development and the immune microenvironment, many immune cells have been discovered. Despite the growing comprehension of immune cell functions and the clinical application of immunotherapy, the precise roles and characteristics of immune cell subtypes, how glioma induces subtype transformation of immune cells and its impact on glioma progression have yet to be understood.

AIM OF THE REVIEW

In this review, we comprehensively center on the four major immune cells within the glioma microenvironment, particularly neutrophils, macrophages, lymphocytes, myeloid-derived suppressor cells (MDSCs), and other significant immune cells. We discuss (1) immune cell subtype markers, (2) glioma-induced immune cell subtype transformation, (3) the mechanisms of each subtype influencing chemotherapy resistance, (4) therapies targeting immune cells, and (5) immune cell-associated single-cell sequencing. Eventually, we identified the characteristics of immune cell subtypes in glioma, comprehensively summarized the exact mechanism of glioma-induced immune cell subtype transformation, and concluded the progress of single-cell sequencing in exploring immune cell subtypes in glioma.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In conclusion, we have analyzed the mechanism of chemotherapy resistance detailly, and have discovered prospective immunotherapy targets, excavating the potential of novel immunotherapies approach that synergistically combines radiotherapy, chemotherapy, and surgery, thereby paving the way for improved immunotherapeutic strategies against glioma and enhanced patient outcomes.

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

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

CD161, a promising prognostic biomarker in hepatocellular carcinoma, correlates with immune infiltration

Background

CD161, encoded by the killer cell lectin-like receptor B1 (KLRB1) gene, exhibits varied roles among different tumors. This study aimed to explore both the potential value of CD161 as a prognostic biomarker for hepatocellular carcinoma (HCC) and its association with immune cell infiltration.

Methods

A total of 109 HCC patients who underwent surgery were retrospectively analyzed. Immunohistochemistry, bioinformatic analyses, and statistical measurements were used to investigate the associations between CD161 expression, immune cell infiltration, and clinical outcomes in both public databases and in-house cohorts.

Results

CD161 was highly expressed at both protein and mRNA levels in adjacent normal tissues compared to tumor tissues of HCC patients. Meanwhile, CD161 was enriched in HCC cases characterized by smaller tumor sizes (≤5 cm) and the absence of portal vein tumor thrombus. Individuals with high CD161 expression showed extended overall survival (OS) and relapse free survival (RFS) compared to those with lower CD161 levels. CD161 was identified as an independent prognostic indicator for both OS and RFS. In addition, the enrichment analysis indicated a close correlation between CD161 and immune response, as well as between CD161 and the signaling pathways of cytokines and chemokines, implying its role in immune regulation during cancer development. Specifically, CD161 expression was positively associated with immunomodulators and tumor-infiltrating immune cells, especially CD8+T cells, CD4+T cells, and dendritic cells. Multiple public databases showed that patients with high CD161 expression were more likely to derive benefits from immunotherapy.

Conclusion

CD161 was identified as a promising prognostic biomarker for HCC, as its expression indicates a favorable prognosis. Additionally, CD161 is closely linked to high infiltration of immune cells, participates in the regulation of the tumor immune microenvironment, and holds promise as a potential biomarker for predicting the efficacy of immunotherapy.

Predictive circulating biomarkers of the response to anti-PD-1 immunotherapy in advanced HER2 negative breast cancer

BACKGROUND

Immunotherapy shows promise for treating advanced breast cancer, but only a few patients could respond. Predictive biomarkers from peripheral blood are urgently needed.

METHODS

We designed a comprehensive 42-marker mass cytometry panel to profile the peripheral blood samples from 57 patients diagnosed with advanced HER2-negative breast cancer receiving anti-PD-1 combination therapy. Patients were categorized as responders and non-responders according to 6-month progression-free survival (PFS), followed by phenotypic and functional comparations to identify candidate predictive biomarkers. Longitudinal analysis of paired samples further revealed dynamic changes in these specific subpopulations.

RESULTS

Non-responders exhibited significantly higher frequencies of CD39+ Tregs (adjusted p = .031) in the T-cell milieu at baseline, which exhibited a positive correlation with PD-1+ T cells in the NR group. Longitudinal assessment indicated a significant decrease of PD-1+ T cells and an increase of CD39+ Tregs following anti-PD-1 treatment, suggesting their potential role in immunotherapy resistance. In the myeloid compartment, responders showed significantly higher CCR2+ monocyte-derived dendritic cell frequencies than non-responders (adjusted p = .037). These cells were positively correlated with other dendritic cells in responders but negatively with naïve T cells in non-responders. Based on these two efficacy-related biomarkers, we developed an immunotherapy prognostic prediction model and confirmed its superiority in distinguishing patient PFS (p < .001).

CONCLUSION

Peripheral CD39+ Tregs and monocyte-derived dendritic cells are correlated with immunotherapy response, serving as potential biomarkers to guide therapeutic choices in immunotherapy.

KEY POINTS

CD39+ Tregs in peripheral blood are associated with poor response to anti-PD-1 immunotherapy in advanced breast cancer. Higher frequencies of CCR2+ monocyte-derived dendritic cells correlate with better immunotherapy outcomes. A predictive model based on CD39+ Tregs and monocyte-derived dendritic cells effectively distinguishes patient progression-free survival. Peripheral blood biomarkers offer a non-invasive approach to guide immunotherapy choices.

Electric field-induced conformational dynamics of CA9: a potential biomarker for glioblastoma multiforme

GBM, a malignant brain tumor prevalent in adults, can be treated using Electric field (EF) therapy. However, the underlying mechanism of EF-based GBM therapy is not well understood. In this study, we used bioinformatics and MD analysis to explore CA9 in EF therapy for GBM. CA9 was identified as a differentially expressed gene (DEG) sensitive to EF stimulation in GBM using GEO and TCGA for integrated analysis. Elevated CA9 expression was associated with reduced overall survival in GBM patients, indicating that CA9 was an adverse prognostic factor. Single-cell data demonstrated that CA9 expression was significantly higher in GBM cells than in normal cells, suggesting that CA9 could be an EF-sensitive biomarker for GBM. GSVA analysis suggested that CA9 was related to hypoxia and glucose metabolism in glioblastoma. MD simulations were employed to examine the impact of EF (0 V/nm ≤ E ≤ 0.5 V/nm) on the conformation of the CA9 protein, including RMSF, RMSD, Rg, secondary structure, and dipole moment. The CA9 protein structure was altered with different EF intensities, affecting the motion of protein atoms in an EF intensity-dependent manner. The number of hydrogen bonds was significantly reduced as the EF intensity increased, indicating that EF disrupted the hydrogen bonds. Additionally, the EF intensity affected the dipole moment and characteristic time. Besides, the CA9 gene family analysis suggested that this gene family was highly conserved. Overall, CA9 showed potential as a GBM biomarker sensitive to EF, presenting a prospective target for therapeutic interventions in EF-mediated GBM treatment.

Identification of key immune-related genes and potential therapeutic targets in immune checkpoint inhibitor-associated myocarditis

BACKGROUND

Immune checkpoint inhibitors (ICIs) are widely used in cancer treatment; however, the emergence of ICI-associated myocarditis (ICI-MC) presents a severe and potentially fatal complication with poorly understood pathophysiological mechanisms. This study aimed to identify crucial immune-related genes in ICI-MC and uncover potential therapeutic targets using bioinformatics.

METHODS

Using the GSE180045 dataset, which includes three groups-Group A: ICI patients without immune adverse events, Group B: ICI patients with non-myocarditis immune adverse events, and Group C: ICI patients with myocarditis-we analyzed differentially expressed genes (DEGs) between ICI-MC samples (Group C) and non-myocarditis controls (Groups A and B). These DEGs were then cross-referenced with 1796 immune-related genes from the immPort database to identify immune-related DEGs. We conducted functional enrichment analyses (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis), constructed a protein-protein interaction network, and identified hub genes. Validation using the GSE4172 dataset led to the identification of optimal feature genes from the overlap between hub genes and DEGs. Predictions of target MicroRNAs (miRNAs) were made, and a competing endogenous RNA (ceRNA) network was constructed. Target drugs for hub genes were predicted using the Connectivity Map database.

RESULTS

We identified 58 DEGs between ICI-MC and controls, which led to the identification of 32 immune-related DEGs after intersection with 1796 immune-related genes. Functional analyses revealed enrichment in cell lysis, CD8+ T-cell receptor, natural killer cell-mediated cytotoxicity, and RAGE signaling. Notably upregulated hub genes included IL7R, PRF1, GNLY, CD3G, NKG7, GZMH, GZMB, KLRB1, KLRK1, and CD247. In the validation dataset, 407 DEGs were uncovered, resulting in the identification of 3 optimal feature genes (KLRB1, NKG7, GZMH). The predicted target miRNAs, lincRNAs, and circRNAs constituted a comprehensive ceRNA network. Among the top 10 drugs with elevated connectivity scores was acetohydroxamic acid, indicating a need for caution in ICI treatment.

CONCLUSION

KG7, GZMH, and KLRB1 were identified as pivotal immune-related genes in ICI-MC. Biological enrichments included pathways involved in cell lysis, the CD8+ T-cell receptor pathway, natural killer cell-mediated cytotoxicity, RAGE signaling, and proinflammatory responses. The ceRNA network illuminated the role of critical molecules and underscored the importance of avoiding drugs such as acetohydroxamic acid in ICI treatment. Key message What is already known on this topic  Myocarditis is recognized as a serious ICI-associated toxicity, seemingly infrequent yet often fulminant and lethal. The underlying mechanisms of ICI-associated myocarditis remain not fully understood. Although the significance of T cells and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is evident, the inciting antigens, the reasons for their recognition, and the mechanisms causing cardiac cell injury are not well characterized. An improved understanding of ICI-associated myocarditis will provide insights into the equilibrium between the immune and cardiovascular systems. What this study adds  Our study further validates the significance of T cells and CTLA-4 in ICI-associated myocarditis. More importantly, we identified three genes-NKG7, GZMH, and KLRB1-essential for the development of ICI-MC and proposed ceRNA networks involving these three key genes. How this study might affect research, practice or policy  The newly discovered key genes and their intricate molecular interactions offer a comprehensive perspective on the mechanisms underlying ICI-MC. Furthermore, our findings advise caution regarding the use of drugs like acetohydroxamic acid during ICI treatment. As our understanding of these regulatory networks deepens, our study provides valuable insights that could inform future therapeutic strategies for ICI-MC.

Innovative treatment of age-related hearing loss using MSCs and EVs with Apelin

Utilizing single-cell transcriptome sequencing (scRNA-seq) technology, this study explores the viability of employing mesenchymal stem cells (MSCs) as a therapeutic approach for age-related hearing loss (ARHL). The research demonstrates MSCs' ability to differentiate into inner ear cell subpopulations, particularly hair cells, delivering Apelin via extracellular vesicles (EVs) to promote M2 macrophage polarization. In vitro experiments show reduced inflammation and preservation of hair cell health. In elderly mice, MSCs transplantation leads to hair cell regeneration, restoring auditory function. These findings highlight the regenerative capabilities of MSCs and EV-mediated therapeutic approaches for ARHL.

Super-enhancer-driven SLCO4A1-AS1 is a new biomarker and a promising therapeutic target in glioblastoma

Glioblastoma (GBM) is the most common intracranial malignancy, but current treatment options are limited. Super-enhancers (SEs) have been found to drive the expression of key oncogenes in GBM. However, the role of SE-associated long non-coding RNAs (lncRNAs) in GBM remains poorly understood. Here, we screened for an up-regulated lncRNA-SLCO4A1-AS1 expressed in GBM by analyzing data from GSE54791, GSE4536 and TCGA. We systematically analyzed its relationship with clinical characteristics, prognosis, epigenetics, tumor microenvironment (TME), biological functions, and transcription factors. We found that SE-driven SLCO4A1-AS1 was significantly upregulated in GBM and correlated with poor prognosis. Knockdown of SLCO4A1-AS1 decreased glioma cell proliferation, invasive ability, self-renewal ability, and increased apoptosis. Epigenetic analysis revealed that SOX2 and SE could drive SLCO4A1-AS1 expression. In vitro experiments further demonstrated that GBM cells with high SLCO4A1-AS1 expression were more sensitive to VX-11e, and overexpression of SLCO4A1-AS1 could reverse the inhibitory effect of VX-11e on GBM cells. In conclusion, this study revealed that SE-driven SLCO4A1-AS1 may be a potential therapeutic target in GBM.

RBM47 is a novel immunotherapeutic target and prognostic biomarker in gliomas

The role of RBM47, an RNA-binding protein, in shaping the immune landscape of gliomas and tumor immune responses is yet to be fully studied. Therefore, a comprehensive investigation into the immunomodulatory roles of RBM47 in gliomas was conducted, leveraging gene expression data from multi-omic datasets. The prognosis of patients with gliomas considering RBM47 was elucidated using bioinformatics methods and clinical data, with results validated using immunohistochemistry and immunofluorescence analyses. The expression of RBM47 in gliomas was higher than that in normal tissues and was positively correlated with the World Health Organization tumor grade. Increased RBM47 expression is associated with poor prognosis in patients with glioma, serving as an independent predictor of overall survival. The nomogram combining RBM47 expression levels with clinical prognostic factors demonstrated strong predictive accuracy, achieving a C-index of up to 0.863 in both TCGA training and CGGA validation groups. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Variation Analysis indicated that RBM47 is closely related to immunity and inflammation. Single-cell sequencing and immunofluorescence assays confirmed the enrichment of RBM47 in CD163 + macrophages. Therefore, RBM47 plays a vital role in the immune microenvironment of gliomas and may be a potential immunotherapy target.

IGF2BP2 orchestrates global expression and alternative splicing profiles associated with glioblastoma development in U251 cells

Glioblastoma (GBM) is a highly invasive and malignant central nervous system tumor with a median survival duration of 15 months despite multimodal therapy. The insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) has been implicated in various cancers and is known to regulate RNA metabolism and alternative splicing (AS). However, its role in GBM remains unclear. Overexpression of IGF2BP2 led to significant alterations in gene expression, with 472 genes upregulated and 99 downregulated. Gene ontology (GO) analysis indicated enrichment in immune-related biological processes. Notably, IGF2BP2 was found to regulate AS events, with 1372 regulated AS genes (RASGs) and 2096 significantly distinct ASEs identified. Furthermore, IGF2BP2 selectively bound to 3' and 5' untranslated regions (UTRs) via GG[AU]C motifs, and IFIH1 was identified as a direct binding partner and upregulated gene upon IGF2BP2 overexpression. Functional enrichment analysis suggested that IGF2BP2 influences pathways related to RNA splicing and immune responses. Our findings demonstrate that IGF2BP2 plays a crucial role in GBM by modulating the transcriptome and AS events. The upregulation of immune-related genes and the regulation of AS by IGF2BP2 highlight its potential as a therapeutic target in GBM, particularly for immunotherapy. The study provides a foundation for further investigation into the molecular mechanisms of IGF2BP2 in GBM and its implications for cancer treatment.

Intrahepatic CD161hiCD8+T Cell Recruitment Has a Pathogenetic Potential in Chronic HBV Infection

BACKGROUNDS AND AIMS

CD8+T cells are crucially associated with the fight against hepatitis B virus (HBV) infection. CD161 has been shown to express remarkably on HCV-specific CD8+T cells. However, the accurate function of CD161+CD8+T cells in HBV immunity or pathogenesis remains undetermined.

METHODS

Blood samples were collected from 25 chronic hepatitis B (CHB) patients. Peripheral blood levels of CD161+CD8+T cells and their correlation with serum ALT levels were analyzed in CHB patients. To analyze the in vivo CD161+CD8+T cell's number, function, and intrahepatic recruitment characteristics, HBV replication mouse models were established. The expression of CD161 on HBV-specific CD8+T cells was also detected by analyzing CD161+CD8+T cell functions during infection.

RESULTS

Patients with CHB infection had a markedly lower peripheral blood frequency of CD161+CD8+T cells than did healthy controls and negatively correlated with serum ALT level. Furthermore, compared to the control mice, the frequency of CD161+CD8+T cells was significantly decreased in the blood of acute and chronic HBV-replicating mice. Moreover, CHB-replicating mice had significantly increased hepatic levels of CD161+CD8+T cells, which was not observed in the acute group of mice. Additionally, the CD161+CD8+T cells were categorized into CD161hi and CD161intCD8+T cells and it was revealed that in the liver of CHB-replicating mice the primary recruited cells were CD161hiCD8+T. Intrahepatic CD161hiCD8+T cells demonstrated increased CXCR6 expression, enhanced production of cytokine IL-17 and TNF-ɑ, and reduced IFN-γ secretion. Accordingly, the CXCL16 mRNA expression in the liver tissue of CHB-replication mice was markedly higher than in acute HBV-replicating and control mice. The study also revealed that HBV-specific CD8+T cells were mainly CD161-CD8+T cells.

CONCLUSION

During HBV infection, the intrahepatic recruitment of CD161+CD8+T cells was mainly CD161hiCD8+T cell subpopulation, which has a weak antiviral response, but increased pro-inflammatory effect, suggesting that CD161 may serve as a potential marker of liver-damaging T cells.

SOCS1: A potential diagnostic and prognostic marker for aggressive gliomas and a new target for immunotherapy

Gliomas, the most common and deadly cancers of the central nervous system, present a unique immunological barrier that severely undermines the effectiveness of immunotherapies. Suppressor of cytokine signaling 1 (SOCS1), belonging to the SOCS protein family and playing a pivotal role in various cancer treatment strategies and is abundant in high-grade gliomas. This study conducted a comparative analysis of SOCS1 and glioma immune checkpoints. It underscores the feasibility of leveraging SOCS1 as a promising diagnostic and prognostic marker for aggressive gliomas, thus offering novel targets for glioma immunotherapy. Comprehensive gene expression analyses and clinical data validations were performed across multiple databases. The expression and biological functions of SOCS1 were examined through an array of techniques including pan-cancer analysis, functional enrichment, gene set variation analysis, and immune microenvironment examination. This was done alongside a comparison of the similarities between SOCS1 and various glioma immune checkpoints. Utilizing clinical information from patients, a bespoke predictive model was developed to further corroborate the prognostic capabilities of SOCS1. The investigation revealed considerable similarities between SOCS1 and several immune checkpoints such as CTLA4, demonstrating SOCS1's role as an independent prognostic factor positively influencing glioma patient outcomes. The inclusion of SOCS1 in the developed predictive model significantly enhanced its precision. Our findings highlight SOCS1's potential as an innovative target for glioma immunotherapy, providing a novel strategy to overcome the immunological barriers posed by gliomas. Furthermore, identifying SOCS1 as a viable diagnostic marker for aggressive gliomas improves the accuracy of prognostic predictions for affected patients.

Current research status of Raman spectroscopy in glioma detection

Glioma is the most common primary tumor of the nervous system. Conventional diagnostic methods for glioma often involve time-consuming or reliance on externally introduced materials. Consequently, there is an urgent need for rapid and reliable diagnostic techniques. Raman spectroscopy has emerged as a promising tool, offering rapid, accurate, and label-free analysis with high sensitivity and specificity in biomedical applications. In this review, the fundamental principles of Raman spectroscopy have been introduced, and then the progress of applying Raman spectroscopy in biomedical studies has been summarized, including the identification and typing of glioma. The challenges encountered in the clinical application of Raman spectroscopy for glioma have been discussed, and the prospects have also been envisioned.

Expression of senescence-related CD161 promotes extranodal NK/T cell lymphoma by affecting T cell phenotype and cell cycle

PURPOSE

The intention of this work is to probe the role of senescence-related gene CD161 in extranodal NK/T cell lymphoma (ENKTL).

METHODS

This study used H2O2 to establish three distinct in vitro oxidative stress aging models (NKL, SNT-8, and YT). Western blotting was employed to assess the levels of two iconic aging proteins, MMP1 and P53, and flow cytometry was utilized to investigate cell cycle and the expressions of CD4, CD8, and CD161. Cell viability was evaluated via the CCK-8 assay. The transcriptome analysis assessed the differential gene expression between the control and aging group of NKL. In vivo, we established a BALB/c mice aging tumor model. After 15 days, the mice were euthanized to harvest tumors. ELISA was employed to measure aging indicators in the mouse tissues. Flow cytometry was utilized to assess the levels of CD4, CD8, and CD161 in tumor samples. Hematoxylin-eosin (HE) staining was performed to evaluate the structure and cellular morphology of the tumor tissue.

RESULTS

In the NKL, SNT-8 and YT aging models, the levels of MMP1 and P53 proteins were significantly increased. Flow cytometry results indicated that all three cell types exhibited marked arrest in the G1 phase. Compared with the control group, the expressions of CD4 and CD161 in the aging group were significantly increased, while the expression of CD8 was decreased. Transcriptome analysis revealed 2,843 differentially expressed genes (DEGs) between the control and aging groups, with 2,060 up-regulated and 783 down-regulated genes identified. Following CD161 knockdown, cell viability of three cell types in the aging group was significantly reduced compared to the control group. The G1 phase of the cells was significantly interrupted. The expressions of CD4 and CD161 were significantly increased, and the expression of CD8 was decreased. However, in the aging + si-CD161 group, a partial alleviation of oxidative stress was observed with a reduction in CD161 expression levels. Animal experiments demonstrated that knockout of CD161 can inhibit tumor progression and partially mitigate oxidative stress.

CONCLUSIONS

CD161 may inhibit ENKTL tumor development by regulating cell cycle and T-cell phenotype.

Detailed pathological role of non-coding RNAs (ncRNAs) in regulating drug resistance of glioblastoma, and update

Glioma is a kind of brain tumor that develops in the central nervous system and is classified based on its histology and molecular genetic features. The lifespan of patients does not exceed 22 months. One of the motives for the low effectiveness of glioma treatment is its radioresistance and chemoresistance. Noncoding RNAs (ncRNAs) are a diverse set of transcripts that do not undergo translation to become proteins in glioma. The ncRNAs have been identified as significant regulators of several biological processes in different cell types and tissues, and their abnormal function has been linked to glioma. They are known to impact important occurrences, including carcinogenesis, progression, and enhanced treatment resistance in glioma cells. The ncRNAs control cell proliferation, migration, epithelial-to-mesenchymal transition (EMT), invasion, and drug resistance in glioma cells. The main focus of this study is to inspect the involvement of ncRNAs in the drug resistance of glioma.

Comprehensive analysis of clinical features, mRNA splicing, and immunological role of REEP5 in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is a prevalent malignancy within the digestive system, characterized by high incidence and mortality rates. The biological role of REEP5 in ESCC progression remains poorly understood, despite its associations with various diseases, potentially accelerating tumor malignancy. We retrieved RNA-seq data and clinical information from 179 ESCC patients from the Gene Expression Omnibus (GEO) and 93 patients from The Cancer Genome Atlas (TCGA) databases. Bioinformatics analyses were conducted to explore the biological functions of REEP5 in ESCC, its role in the tumor microenvironment, and its prognostic value. Additionally, utilizing single-cell RNA-seq (scRNA-seq) data from 3 ESCC patients in the GEO database, we performed cluster analyses to investigate cell-specific expression differences of REEP5 between cancerous and adjacent non-cancerous tissues. Molecular biology experiments were also conducted to validate REEP5 expression disparities between tumor and non-tumor tissues. Compared to normal tissues, REEP5 was significantly enriched in ESCC tissues. High REEP5 expression was closely associated with poor prognosis in ESCC patients. Gene Ontology (GO) analysis revealed strong correlations between REEP5 and processes such as mRNA splicing and protein stabilization. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) indicated positive correlations between REEP5 and mRNA spliceosome assembly and disassembly. Pearson correlation analysis demonstrated positive associations between REEP5 and cancer-inhibitory immune checkpoints CTLA-4, TIM-3, and HVEM. Single-cell clustering and CIBERSORT analysis showed that REEP5 expression was closely related to T-cell infiltration in ESCC, with significant enrichment effects observed in CD8+ T-cell infiltration. REEP5 expression is closely correlated with the pathological and molecular pathology of ESCC, potentially playing a crucial role in Mast cell or T-cell-mediated immune responses in ESCC. Therefore, REEP5 holds promise as a novel therapeutic target for ESCC.

Expression and prognostic impact of VDAC3 in colorectal adenocarcinoma

Background

Colorectal adenocarcinoma (COAD) is a malignant tumor with high mortality and low 5-year survival rate. Voltage-dependent anion channel 3 (VDAC3) is the least understood isoform of voltage-dependent anion-selective channels in the mitochondrial outer membrane. In this thesis, we aimed to investigate the prognostic value of VDAC3 and provide new insights into colon adenocarcinoma.

Methods

We utilized The Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) database, Human Protein Atlas online database, and the University of ALabama at Birmingham CANcer data analysis Portal (UALCAN) database to analyze VDAC3 expression in COAD and assess patient survival rates. Univariate and multivariate Cox regression analyses were employed to evaluate VDAC3's prognostic significance for COAD. Gene set variation analysis (GSVA) was utilized to explore COAD-related signaling pathways associated with VDAC3. Additionally, we predicted the relationship between VDAC3 expression and anticancer drug sensitivity using the CellMiner database.

Results

In the TCGA database, VDAC3 demonstrated elevated expression levels in COAD, which was further validated by findings from the GEO database. Survival analysis conducted using Kaplan-Meier (K-M) curves highlighted that the patients with decreased VDAC3 expression exhibited significantly shorter overall survival durations. VDAC3 expression demonstrated correlation with COAD pathological stage. VDAC3 gene mutation was linked to COAD outcomes. Cox regression analysis showed that VDAC3 was an independent predictor. In addition, GSVA analysis showed that VDAC3 was closely related to mitochondria-related biological processes and involved in the occurrence and development of mitochondria-related diseases. Finally, analysis of the CellMiner database predicted that VDAC3 expression was positively correlated with chelerythrine and cladribine, but negatively correlated with Ergenyl.

Conclusions

Our study suggests that VDAC3 may be a potential biomarker for early diagnosis, prognosis, and treatment of COAD.

Integration of Bioinformatics and Machine Learning to Identify CD8+ T Cell-Related Prognostic Signature to Predict Clinical Outcomes and Treatment Response in Breast Cancer Patients

The incidence of breast cancer (BC) continues to rise steadily, posing a significant burden on the public health systems of various countries worldwide. As a member of the tumor microenvironment (TME), CD8+ T cells inhibit cancer progression through their protective role. This study aims to investigate the role of CD8+ T cell-related genes (CTRGs) in breast cancer patients.

METHODS

We assessed the abundance of CD8+ T cells in the TCGA and METABRIC datasets and obtained CTRGs through WGCNA. Subsequently, a prognostic signature (CTR score) was constructed from CTRGs screened by seven machine learning algorithms, and the relationship between the CTR score and TME, immunotherapy, and drug sensitivity was analyzed. Additionally, CTRGs' expression in different cells within TME was identified through single-cell analysis and spatial transcriptomics. Finally, the expression of CTRGs in clinical tissues was verified via RT-PCR.

RESULTS

The CD8+ T cell-related prognostic signature consists of two CTRGs. In the TCGA and METABRIC datasets, the CTR score appeared to be negatively linked to the abundance of CD8+ T cells, and BC patients with higher risk score show a worse prognosis. The low CTR score group exhibits higher immune infiltration levels, closely associated with inhibiting the tumor microenvironment. Compared with the high CTR score group, the low CTR score group shows better responses to chemotherapy and immune checkpoint therapy. Single-cell analysis and spatial transcriptomics reveal the heterogeneity of two CTRGs in different cells. Compared with the adjacent tissues, CD163L1 and KLRB1 mRNA are downregulated in tumor tissues.

CONCLUSIONS

This study establishes a robust CD8+ T cell-related prognostic signature, providing new insights for predicting the clinical outcomes and treatment responses of breast cancer patients.

High expression of SIGLEC7 may promote M2-type macrophage polarization leading to adverse prognosis in glioma patients

Introduction

Gliomas are the most common primary intracranial tumors, known for their high invasiveness and destructiveness. Sialic acid-binding immunoglobulin-like lectin 7 (SIGLEC7) is present in various immune cells, especially macrophages, and significantly affects immune homeostasis and cancer cell response. However, research on the role and prognostic impact of SIGLEC7 in glioma patients is currently limited.

Methods

We utilized transcriptomic data from 702 glioma patients in The Cancer Genome Atlas (TCGA) and 693 glioma patients in the Chinese Glioma Genome Atlas (CGGA), along with clinical samples we collected, to comprehensively investigate the impact of SIGLEC7 on glioma expression patterns, biological functions, and prognostic value. We focused on its role in glioma-related immune responses and immune cell infiltration and analyzed its expression at the single-cell level. Finally, we validated the role of SIGLEC7 in gliomas through tissue and cell experiments.

Results

SIGLEC7 expression was significantly increased in glioma patients with malignant characteristics. Survival analysis indicated that glioma patients with high SIGLEC7 expression had significantly lower survival rates. Gene function analysis revealed that SIGLEC7 is primarily involved in immune and inflammatory responses and is strongly negatively correlated with tumor-associated immune regulation. Additionally, the expression of most immune checkpoints was positively correlated with SIGLEC7, and immune cell infiltration analysis clearly demonstrated a significant positive correlation between SIGLEC7 expression and M2 macrophage infiltration levels. Single-cell analysis, along with tissue and cell experiments, confirmed that SIGLEC7 enhances macrophage polarization towards the M2 phenotype, thereby promoting glioma invasiveness through the immunosuppressive effects of M2 macrophages. Cox regression analysis and the establishment of survival prediction models indicated that high SIGLEC7 expression is an unfavorable prognostic factor for glioma patients.

Discussion

High SIGLEC7 expression predicts poor prognosis in glioma patients and is closely associated with M2 macrophages in the tumor environment. In the future, SIGLEC7 may become a promising target for glioma immunotherapy.

Research progress and challenges of stem cell therapy for ischemic stroke

Ischemic stroke is a significant global cause of death and disability. Currently, treatment options for acute ischemic stroke are limited to intravenous thrombolysis and mechanical recanalization. Therefore, novel neuroprotective strategies are imperative. Stem cell transplantation possesses the capabilities of differentiation, proliferation, neuronal replacement, nerve pathway reconstruction, secretion of nerve growth factors, and enhancement of the microenvironment; thus, it is a potential therapeutic approach for ischemic stroke. In addition, the immunomodulatory function of stem cells and the combined treatment of stem cells and exosomes exhibit a favorable protective effect on brain injury and neurological dysfunction following stroke. Meanwhile, the theory of microbiota-gut-brain axis provides us with a novel perspective for comprehending and managing neurological diseases. Lastly, stem cell transplantation has demonstrated promising outcomes not only in treating ischemic stroke but also in dealing with other neurological disorders, such as brain tumors. Furthermore, challenges related to the tissue source, delivery method, immune response, and timing of transplantation still need to be addressed to optimize the treatment.

Breaking the barrier: Nanoparticle-enhanced radiotherapy as the new vanguard in brain tumor treatment

The pursuit of effective treatments for brain tumors has increasingly focused on the promising area of nanoparticle-enhanced radiotherapy (NERT). This review elucidates the context and significance of NERT, with a particular emphasis on its application in brain tumor therapy-a field where traditional treatments often encounter obstacles due to the blood-brain barrier (BBB) and tumor cells' inherent resistance. The aims of this review include synthesizing recent advancements, analyzing action mechanisms, and assessing the clinical potential and challenges associated with nanoparticle (NP) use in radiotherapy enhancement. Preliminary preclinical studies have established a foundation for NERT, demonstrating that nanoparticles (NPs) can serve as radiosensitizers, thereby intensifying radiotherapy's efficacy. Investigations into various NP types, such as metallic, magnetic, and polymeric, have each unveiled distinct interactions with ionizing radiation, leading to an augmented destruction of tumor cells. These interactions, encompassing physical dose enhancement and biological and chemical radio sensitization, are crucial to the NERT strategy. Although clinical studies are in their early phases, initial trials have shown promising results in terms of tumor response rates and survival, albeit with mindful consideration of toxicity profiles. This review examines pivotal studies affirming NERT's efficacy and safety. NPs have the potential to revolutionize radiotherapy by overcoming challenges in targeted delivery, reducing off-target effects, and harmonizing with other modalities. Future directions include refining NP formulations, personalizing therapies, and navigating regulatory pathways. NERT holds promise to transform brain tumor treatment and provide hope for patients.

Immune mechanisms and predictive biomarkers related to neoadjuvant immunotherapy response in stage III melanoma

The treatment for stage III melanoma has advanced significantly, nevertheless, a substantial proportion of patients experience relapse. Neoadjuvant immune checkpoint blockade has emerged as a promising approach, allowing early micrometastatic disease treatment, reduction of tumor burden before surgery, and enhanced tumor-specific T-cell responses. However, not all patients respond to treatment, highlighting the need for understanding immune mechanisms behind failure and identification of predictive markers. Here we performed a robust evaluation of systemic and tumoral immune profiles in a well-defined cohort of advanced melanoma patients treated with immune checkpoint inhibitors. Elevated CTACK and CXCL9 chemokines pre-treatment suggested their potential as predictive tools for treatment response. Furthermore, CD95 expression in CD8+ T lymphocytes surfaced as a favorable prognostic indicator, while PD-1, CD161, and PD-L2 exhibited correlations with worst outcomes. These findings shed light on the intricate interplay between immune markers and melanoma response to neoadjuvant immune checkpoint therapy, offering insights into personalized treatment strategies.

Deciphering the role of KLRB1: a novel prognostic indicator in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) represents a significant global health challenge with high incidence and mortality rates. T cells and natural killer (NK) cells are pivotal in this context, yet HCC can evade immune surveillance. CD161 (KLRB1), a C-type lectin receptor, modulates immune responses and is expressed on NK cells and a subset of T cells. Its relevance in HCC remains poorly understood, with conflicting findings regarding its impact on patient prognosis.

METHODS

Utilizing TCGA data and single-cell analysis, we investigated the biological functions of KLRB1 in HCC. Peripheral blood samples from 126 HCC patients were collected to assess KLRB1 expression on NK and T cells. The diagnostic performance of KLRB1 on NK and CD8 + T cells was evaluated using receiver operating characteristic curve (ROC) analysis, while its prognostic significance was assessed using Kaplan-Meier analysis and COX regression models.

RESULTS

Analysis of TCGA data revealed a significant correlation between KLRB1 expression and immune activation, particularly T cell activation. Single-cell data further demonstrated elevated KLRB1 expression in tissue-resident NK and T cells within HCC, which co-expressed markers of immune activation. Clinical data showed downregulated KLRB1 expression on NK and T cells in HCC patients compared to health individuals, with lower expression levels correlating with poorer prognosis.

CONCLUSION

KLRB1 emerges as a promising biomarker in HCC, with its downregulation on peripheral blood NK and T cells suggesting potential prognostic value. Further elucidation of KLRB1's role in HCC may pave the way for the development of targeted immunotherapies and the improvement of patient outcomes.

The predictive value of E2F7 in immunotherapy efficacy for lung adenocarcinoma: An observational study

Lung adenocarcinoma (LUAD) is the most common pathological type of lung cancer. In recent years, immunotherapy has greatly changed the treatment pattern of advanced LUAD. However, only a small proportion of LUAD patients benefitted from immune checkpoint inhibitor therapy. There is an urgent need to develop a biomarker to predict immune therapy response. E2F7 has been shown to be closely related to immune cell infiltration and immune checkpoint expression in tumors. However, it is unclear whether the E2F7 expression is related to the immunotherapy efficacy in LUAD. Therefore, we conducted this study to investigate the clinical characteristics, function, and immunotherapy responsiveness of E2F7 expression, and to explore the potential of E2F7 as an immunotherapy response biomarker in LUAD. We analyzed the clinical characteristics and biological function of E2F7 expression based on data from the Cancer Genome Atlas and Gene Expression Omnibus database. In addition, we used single-cell sequencing data to analyze the immune regulatory effects of E2F7 in LUAD. Furthermore, we analyzed the immunotherapy response prediction ability of E2F7 expression based on the immunotherapy database. Compared to normal lung tissue, E2F7 was specifically overexpressed in LUAD, and its expression was associated with higher malignancy and poor efficacy. E2F7 high expression was an independent risk factor affecting the prognosis of LUAD. E2F7 was enriched in cell division and cell cycle functions. In addition, the expressions of immune checkpoints were correlated with the E2F7 expression. E2F7 was highly expressed in myeloid cells, and E2F7 highly expressed myeloid cells were associated with immune and inflammatory responses. Moreover, the expression level of E2F7 can effectively distinguish different immune therapy responses in LUAD patients. E2F7 was upregulated in LUAD, and high expression of E2F7 was associated with higher malignancy and poor efficacy. E2F7 high expression was an independent risk factor affecting the prognosis of LUAD. Moreover, E2F7 may exert its immunosuppressive effect by affecting the function of myeloid cells. These results indicated the potential role of E2F7 as a biomarker for predicting LUAD immunotherapy responses.

Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes

BACKGROUND

Oropharyngeal squamous cell carcinoma (OPSCC) induced by human papillomavirus (HPV-positive) is associated with better clinical outcomes than HPV-negative OPSCC. However, the clinical benefits of immunotherapy in patients with HPV-positive OPSCC remain unclear.

METHODS

To identify the cellular and molecular factors that limited the benefits associated with HPV in OPSCC immunotherapy, we performed single-cell RNA (n=20) and T-cell receptor sequencing (n=10) analyses of tonsil or base of tongue tumor biopsies prior to immunotherapy. Primary findings from our single-cell analysis were confirmed through immunofluorescence experiments, and secondary validation analysis were performed via publicly available transcriptomics data sets.

RESULTS

We found significantly higher transcriptional diversity of malignant cells among non-responders to immunotherapy, regardless of HPV infection status. We also observed a significantly larger proportion of CD4+ follicular helper T cells (Tfh) in HPV-positive tumors, potentially due to enhanced Tfh differentiation. Most importantly, CD8+ resident memory T cells (Trm) with elevated KLRB1 (encoding CD161) expression showed an association with dampened antitumor activity in patients with HPV-positive OPSCC, which may explain their heterogeneous clinical outcomes. Notably, all HPV-positive patients, whose Trm presented elevated KLRB1 levels, showed low expression of CLEC2D (encoding the CD161 ligand) in B cells, which may reduce tertiary lymphoid structure activity. Immunofluorescence of HPV-positive tumors treated with immune checkpoint blockade showed an inverse correlation between the density of CD161+ Trm and changes in tumor size.

CONCLUSIONS

We found that CD161+ Trm counteracts clinical benefits associated with HPV in OPSCC immunotherapy. This suggests that targeted inhibition of CD161 in Trm could enhance the efficacy of immunotherapy in HPV-positive oropharyngeal cancers.

TRIAL REGISTRATION NUMBER

NCT03737968.

REEP4 as Potential Biomarker Associated with Predictive Prognosis and Immune Response in Kidney Clear Cell Carcinoma

Kidney clear cell carcinoma (KIRC) commonly presents with metastases upon diagnosis, highlighting the critical need to identify more precise biomarkers for early detection, intervention, and personalized treatment. Although The REEP family has been investigated in cancer development, the specific relationship between REEP4 and cancer remains unclear. In our study, we employed bioinformatics analysis and conducted fundamental experiments to evaluate the potential of REEP4 as a biomarker for predicting the prognosis and therapeutic efficacy of KIRC. Comparing KIRC tumor tissues to normal tissues, we observed a significant upregulation in REEP4 expression, with higher levels of REEP4 correlating positively with tumor malignancy. Further COX regression analysis, as well as single and multifactorial analyses, confirmed that high REEP4 expression indicated lower survival rates in KIRC. Gene function analysis also identified associations between REEP4 and critical pathways such as the cell cycle, along with its involvement in protein binding. Furthermore, our investigation of the immune response suggests that a favorable immunotherapeutic response is linked to a reduction in REEP4 expression. Subsequently, we conducted in vitro experiments to confirm the overexpression of REEP4 in KIRC tumor tissues and renal cancer cells. In summary, our study revealed a close association between REEP4 expression and KIRC, emphasizing its correlation with prognosis and the immune response. These findings suggest that REEP4 is a potential biomarker for KIRC.

Down-regulation of KLRB1 is associated with increased cell growth, metastasis, poor prognosis, as well as a dysfunctional immune microenvironment in LUAD

Killer cell lectin-like receptor B1 (KLRB1) is implicated in cancer progression and immunity. In this study, we aimed to evaluate the expression levels of KLRB1 in lung adenocarcinoma (LUAD) and analyze the relationship between KLRB1 expression levels, LUAD progression, and the tumor immune microenvironment. KLRB1 levels in LUAD were analyzed using data from the TCGA and XENA databases. Additionally, the diagnostic values of KLRB1 were analyzed in patients with LUAD. Survival and meta-analyses were employed to investigate the relationship between KLRB1 levels and other prognostic factors in patients with LUAD. Bioinformatics and cellular experiments were used to understand the functions and mechanisms of KLRB1. In addition, correlation analysis was used to investigate the relationship between KLRB1 levels and the immune microenvironment in LUAD. Reduced KLRB1 expression in LUAD was found to positively correlate with tumor size, distant metastasis, pathological stage, age, overall survival, diagnostic value, and disease-specific survival in patients with LUAD (P < 0.05). Conversely, increased KLRB1 expression was found to positively correlate with the overall survival and disease-specific survival in patients with LUAD (P < 0.05). We also found that the overexpression of KLRB1 can inhibit the proliferation, migration, and invasion of LUAD cells and promote apoptosis. KLRB1 was involved in immune cell differentiation, NF-kB, PD-L1, and PD-1 checkpoint pathways and others. Additionally, KLRB1 expression was linked to tumor purity, stromal, immune, and estimate scores, the levels of immune cells including B cells, CD8+ T cells, and CD4+ T cells, and immune cell markers in LUAD. Reduced KLRB1 expression has a significant positive correlation with diagnosis, poor prognosis, and immunity to cancer in patients with LUAD. KLRB1 inhibited cell proliferation and migration in patients with LUAD. These results suggest that KLRB1 may serve as a potential therapeutic target in patients with LUAD.

Basic Transcription Factor 3 Like 4 Enhances Malignant Phenotypes through Modulating Tumor Cell Function and Immune Microenvironment in Glioma

Recent investigations into the tumor microenvironment have provided insights into the limited response of glioma progression to immunotherapy. However, the specific involvement of basic transcription factor 3 like 4 (BTF3L4) in glioma progression and its correlation with immune cell infiltration remain areas of uncertainty that require further exploration. In the current study, BTF3L4 expression was delineated by using gene expression profiling/interactive analysis and multiplex-immunohistologic staining of tissue microarrays. The prognostic value of BTF3L4 was then assessed by using Cox regression models and Kaplan-Meier methods, and in vitro experiments were conducted to investigate how BTF3L4 protein affects the proliferation, migration, and invasion capabilities of glioma cells. Furthermore, the CIBERSORT and ESTIMATE methods were used to quantify immune cells that correlate to BTF3L4 expression, and multiplex-immunohistologic staining was applied to investigate its correlation with infiltrated immune cells in glioma tissues. These findings revealed higher BTF3L4 expression in glioma tissues compared with non-tumor brain tissues, which correlated with clinical characteristics and worse patient prognosis. Furthermore, the down-regulation of BTF3L4 protein in the glioma cell line had a detrimental effect on cell migration, invasion, and proliferation. In addition, the association between BTF3L4 and key immune molecules in glioma, particularly with the infiltration of CD66B+ neutrophils and programmed death ligand 1 expression, was identified. These results highlight the prognostic significance of BTF3L4 and propose BTF3L4 as a potential target for glioma immune therapy.

Machine learning unveils immune-related signature in multicenter glioma studies

In glioma molecular subtyping, existing biomarkers are limited, prompting the development of new ones. We present a multicenter study-derived consensus immune-related and prognostic gene signature (CIPS) using an optimal risk score model and 101 algorithms. CIPS, an independent risk factor, showed stable and powerful predictive performance for overall and progression-free survival, surpassing traditional clinical variables. The risk score correlated significantly with the immune microenvironment, indicating potential sensitivity to immunotherapy. High-risk groups exhibited distinct chemotherapy drug sensitivity. Seven signature genes, including IGFBP2 and TNFRSF12A, were validated by qRT-PCR, with higher expression in tumors and prognostic relevance. TNFRSF12A, upregulated in GBM, demonstrated inhibitory effects on glioma cell proliferation, migration, and invasion. CIPS emerges as a robust tool for enhancing individual glioma patient outcomes, while IGFBP2 and TNFRSF12A pose as promising tumor markers and therapeutic targets.

A comprehensive analysis of the KLRB1 expression and its clinical implication in testicular germ cell tumors: A review

Testicular germ cell tumors (TGCT) are the most common testicular malignancies. KLRB1 is considered to influence the development and progression of a number of cancers. However, it is unclear how the KLRB1 gene functions in TGCT. First, it was determined the expression level of KLRB1 in TGCT using The Cancer Genome Atlas (TCGA) (The Cancer Genome Atlas) dataset and GTEx (Genotype-Tissue Expression) dataset. The clinical significance and biological functions of KLRB1 were explored using the TCGA dataset, and we analyzed the correlation of the KLRB1 gene with tumor immunity and infiltrating immune cells using gene set variation analysis and the TIMER database. We found that the expression level of KLRB1 was upregulated in TGCT malignant tissues with the corresponding normal tissues as controls, and KLRB1 expression correlated with clinicopathologic features of TGCT. Functional enrichment analysis suggested that KLRB1 might be involved in immune response and inflammatory response. KLRB1 was highly positively correlated with natural killer cell activation in immune response and positively correlated with tumor-infiltrating immune cells. This study demonstrated for the first time the role of KLRB1 in TGCT, which may serve as a new biomarker associated with immune infiltration and provide a potential therapeutic target for the treatment of TGCT.

Klotho exerts protection in chronic kidney disease associated with regulating inflammatory response and lipid metabolism

BACKGROUND

The anti-aging protein Klotho plays a protective role in kidney disease, but its potential as a biomarker for chronic kidney disease (CKD) is controversial. Additionally, the main pathways through which Klotho exerts its effects on CKD remain unclear. Therefore, we used bioinformatics and clinical data analysis to determine its role in CKD.

RESULTS

We analyzed the transcriptomic and clinical data from the Nephroseq v5 database and found that the Klotho gene was mainly expressed in the tubulointerstitium, and its expression was significantly positively correlated with estimated glomerular filtration rate (eGFR) and negatively correlated with blood urea nitrogen (BUN) in CKD. We further found that Klotho gene expression was mainly negatively associated with inflammatory response and positively associated with lipid metabolism in CKD tubulointerstitium by analyzing two large sample-size CKD tubulointerstitial transcriptome datasets. By analyzing 10-year clinical data from the National Health and Nutrition Examination Survey (NHANES) 2007-2016, we also found that Klotho negatively correlated with inflammatory biomarkers and triglyceride and positively correlated with eGFR in the CKD population. Mediation analysis showed that Klotho could improve renal function in the general population by modulating the inflammatory response and lipid metabolism, while in the CKD population, it primarily manifested by mediating the inflammatory response. Restricted cubic spline (RCS) analysis showed that the optimal concentration range for Klotho to exert its biological function was around 1000 pg/ml. Kaplan-Meier curves showed that lower cumulative hazards of all-cause mortality in participants with higher levels of Klotho. We also demonstrated that Klotho could reduce cellular inflammatory response and improve cellular lipid metabolism by establishing an in vitro model similar to CKD.

CONCLUSIONS

Our results suggest that Klotho exerts protection in CKD, which may be mainly related to the regulation of inflammatory response and lipid metabolism, and it can serve as a potential biomarker for CKD.

Low expression of KLRB1 predicts poor survival outcomes and is associated with immune infiltration in breast cancer

Background

KLRB1 is downregulated in various cancer types. Nevertheless, the specific involvement of KLRB1 in the context of breast cancer (BRCA) has not been fully elucidated. This research aimed to explore its clinical value in BRCA.

Methods

A dataset comprising 1,109 BRCA samples and 113 healthy samples was retrieved from The Cancer Genome Atlas (TCGA) database to establish the association between KLRB1 expression and pan-cancer. Subsequently, an analysis was executed to explore the link between KLRB1 and BRCA. T-tests and Chi-squared tests were conducted to assess the expression of KLRB1 and its clinical implications in BRCA. The prognosis-predictive value of KLRB1 in BRCA was assessed using the Kaplan-Meier method and Cox regression analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses screened biological pathways to analyze the association between the immune infiltration level and KLRB1 expression in BRCA. Lastly, the conclusion was validated through quantitative polymerase chain reaction (qPCR), immunohistochemistry (IHC), and Cell Counting Kit-8 (CCK8) assays.

Results

KLRB1 exhibited low expression in patients with BRCA. Furthermore, KLRB1 demonstrated strong diagnostic potential, as indicated by an area under curve (AUC) of 0.712. Kaplan-Meier survival and Cox regression analyses indicated that attenuated expression of KLRB1 was independently linked to unfavorable clinical outcomes. GO and KEGG enrichment analyses were performed on the top 10 genes that exhibited positive and negative correlations with KLRB1. Analysis of genes positively correlated with KLRB1 revealed associations with signaling receptor activator activity, lymphocyte proliferation, mononuclear cell proliferation, leukocyte proliferation, receptor-ligand activity, immunoglobulin binding, and hematopoietic cell lineage signaling pathway. KLRB1 expression exhibited significant correlations with all immune cells. Furthermore, qPCR and IHC outcomes demonstrated that KLRB1 was significantly downregulated in BRCA tissues. CCK8 findings showed a decrease in the proliferation of BRCA MCF7 cells upon knockout of KLRB1.

Conclusions

This research investigated the mechanism and potential therapeutic target of the KLRB1 gene in BRCA. By analyzing the expression and function of the KLRB1 gene, the study aims to find its significant role in the onset and progression of BRCA. This research endeavors to offer novel strategies and approaches for treating BRCA.

Necroptosis-related KLRB1 was a potent tumor suppressor and immunotherapy determinant in breast cancer

Breast cancer is a multifaceted and diverse illness that impacts millions of people globally. Identifying the underlying causes of BRCA and creating efficient treatment plans are urgent. Necroptosis is widely involved in cancer development. However, the specific roles of necroptosis in cancer immunotherapy of breast cancer have not been explored. In this study, we aim to establish the connection between necroptosis and immunotherapy in BRCA. TCGA, METABRIC, GSE103091, GSE159956, and GSE96058 were included for bioinformatics analysis. NMF and CoxBoost algorithms were used to develop the necroptosis-related patterns and model, respectively. A necroptosis-related model was developed and determined KLRB1 as a critical tumor suppressor by in vitro validation. The mutation characteristics, immune characteristics, and molecular functions of KLRB1 were explored. We further examined how necroptosis-related KLRB1 functions in BRCA as a powerful tumor suppressor and regulates the activity of macrophages by in vitro validation, including CCK8, EdU, and Transwell assays. KLRB1 was also revealed to be an immunotherapy determinant.

Identification of SRSF10 as a promising prognostic biomarker with functional significance among SRSFs for glioma

AIMS

The serine/arginine-rich splicing factor (SRSF) protein family members are essential mediators of the alternative splicing (AS) regulatory network, which is tightly implicated in cancer progression. However, the expression, clinical correlation, immune infiltration, and prognostic value of SRSFs in gliomas remain unclear.

MATERIALS AND METHODS

Glioma samples were extracted from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) datasets. Several databases, such as HPA, DAVID, UALCAN were used to comprehensively explore the roles of SRSFs. In addition, experimental validation of SRSF10 was also conducted.

KEY FINDINGS

Here, we found the expression alterations of the SRSF family in glioma samples using data from the TCGA and CGGA_325 datasets. Among the 12 genes, most were found to be closely associated with glioma clinical features, which linked to poor prognosis in glioma patients. Interestingly, survival analysis identified only SRSF10 as a potential independent risk prognostic biomarker for glioma patients. Immune analysis indicated that glioma patients with high SRSF10 expression may respond well to immunotherapies targeting immune checkpoint (ICP) genes. Finally, knocking down SRSF10 reduced glioma cell viability, induced G1 cell cycle arrest, and induced the exclusion of bcl-2-associated transcription factor 1 (BCLAF1) exon 5a.

SIGNIFICANCE

Overall, this study uncovers the oncogenic roles of most SRSF family members in glioma, with the exception of SRSF5, while highlighting SRSF10 as a potential novel independent prognostic biomarker for glioma.

CTSC promoted the migration and invasion of glioma cells via activation of STAT3/SERPINA3 axis

Cathepsin C (CTSC) has been reported to be upregulated in several cancers, however, there are still many missing links about the role of CTSC in glioma. To address this knowledge gap, the present study employed bioinformatics analysis, Transwell assay, RT-qPCR and Western blot assays to investigate the expression level of CTSC in glioma tissues, its relationship with survival period, and its effect on the migration and invasion ability of glioma cells. The findings revealed that CTSC was upregulated in glioma and was associated with poor prognosis. Moreover, CTSC was found to promote cell migration and invasion abilities as well as epithelial-mesenchymal transition (EMT). A further study found that CTSC induced SERPINA3 and STAT3 expression in glioma cells. Additionally, we demonstrated that STAT3 signaling mediated upregulation of SERPINA3 expression by CTSC. In sum, our findings suggest that CTSC activates the STAT3/SERPINA3 axis to promote migration and invasion of glioma cells, which may lead to new potential therapeutic approaches for humans with cancer.

KLRB1 is a novel prognostic biomarker in endometrial cancer and is associated with immune infiltration

Background

Endometrial cancer (EC) has the characteristics of high mortality and poor prognosis in the advanced stage, which seriously threatens women's health. Killer cell lectin-like receptor B1 (KLRB1) is a promising immune checkpoint of which the expression level can regulate the killing effect on tumor cells of the immune system, thereby affecting the survival and prognosis of tumor patients. However, it is still unclear whether KLRB1 is associated with survival and prognosis in patients with EC. Therefore, our study focused on the relationship between KLRB1 and immune cells to explore the role of KLRB1 on the immune microenvironment, and to further explore its feasibility as a prognostic marker in EC.

Methods

In this study, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the messenger RNA (mRNA) expression level of KLRB1 in normal endometrial and EC tissues. The University of Alabama at Birmingham Cancer data analysis Portal (UALCAN) database was used to determine the correlation between KLRB1 mRNA expression and clinical features among the EC patients. KLRB1 expression levels were investigated in the Tumor IMmune Estimation Resource (TIMER) database to reveal its relationship with immune cell infiltration of EC. Finally, using the R package clusterProfiler, enrichment analysis was performed on KLRB1 to study its potential function.

Results

The results suggested that KLRB1 expression varied in different tumor tissues, and the EC group had lower mRNA expression levels than did the control group. It was also found that patients with high expression of KLRB1 had a better prognosis. According to further enrichment and immune infiltration analyses, KLRB1 expression had a closed relationship with the level of infiltration of some immune cell types, such as B cells memory, eosinophils, and Tregs, among others.

Conclusions

KLRB1 expression is associated with the infiltration of immune cells and can be used as a prognostic biomarker in EC.

Cellular Components of the Tumor Environment in Gliomas-What Do We Know Today?

A generation ago, the molecular properties of tumor cells were the focus of scientific interest in oncology research. Since then, it has become increasingly apparent that the tumor environment (TEM), whose major components are non-neoplastic cell types, is also of utmost importance for our understanding of tumor growth, maintenance and resistance. In this review, we present the current knowledge concerning all cellular components within the TEM in gliomas, focusing on their molecular properties, expression patterns and influence on the biological behavior of gliomas. Insight into the TEM of gliomas has expanded considerably in recent years, including many aspects that previously received only marginal attention, such as the phenomenon of phagocytosis of glioma cells by macrophages and the role of the thyroid-stimulating hormone on glioma growth. We also discuss other topics such as the migration of lymphocytes into the tumor, phenotypic similarities between chemoresistant glioma cells and stem cells, and new clinical approaches with immunotherapies involving the cells of TEM.

The mitotic cell cycle-associated nomogram predicts overall survival in lung adenocarcinoma

BACKGROUND

This study aimed to develop a prognostic model for lung adenocarcinoma (LUAD) associated with mitotic cell cycle. The model will predict the probability of survival at different time points and serve as a reference tool to evaluate the effectiveness of LUAD treatment.

METHODS

A cohort of 442 patients with LUAD from the gene expression omnibus (GEO) database was randomly divided into a training group (n = 299) and a validation group (n = 99). The least absolute shrinkage and selection operator (LASSO)-COX algorithm was used to reduce the number of predictors based on the clinicopathological and RNA sequencing data to establish mutant characteristics that could predict patient survival. Additionally, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set variation analysis (GSVA), and gene set enrichment analysis (GSEA) analyses were conducted on the mutant characteristics. The performance of the developed nomogram was evaluated using calibration curves and the C-index.

RESULTS

The mutant characteristics had prognostic value for LUAD and acted as an independent prognostic factor. The mutant characteristics profile derived from the LASSO-COX algorithm demonstrated a significant association with overall survival in patients with LUAD. Functional annotation based on the mutant score, its involvement in the phase transition of the mitotic cell cycle, and its regulatory processes. The nomogram, which combined the mutant score with clinical factors associated with prognosis, showed robust accuracy in both the training and validation groups.

CONCLUSION

This study presents the first individualized model that establishes a mutant score for predicting survival in LUAD. This model can be used as a predictive tool for determining 1-, 2-, 3-, and 5-year survival probabilities in patients with LUAD.

TTC7B is a new prognostic biomarker in head and neck squamous cell carcinoma linked to immune infiltration and ferroptosis

OBJECTIVE

To investigate the expression of TTC7B and its prognostic significance, biological roles, and impact on the immune system in patients with head and neck squamous cell carcinoma (HNSCC).

MATERIALS AND METHODS

Clinical and genomic data were obtained from TCGA (The Cancer Genome Atlas), GEO (Gene Expression Omnibus), GEPIA2 (Gene Expression Profiling Interactive Analysis 2.0), and TIMER2.0 (Tumor Immune Estimation Resource 2.0) databases. R software was utilized to process the retrieved data. qPCR and immunohistochemical assays were performed to validate the findings obtained from the databases.

RESULTS

High expression of TTC7B was observed in HNSCC, and this heightened expression is significantly associated with reduced overall survival (OS) in patients, making it an independent risk factor impacting OS. TTC7B is correlated with focal adhesions and cell migration pathways based on functional enrichment analysis. CIBERSORT analysis and TIMER2.0 show a positive link between TTC7B and multiple immune cells, particularly macrophages. Pearson's analysis reveals a significant correlation between TTC7B and ferroptosis-related genes.

CONCLUSION

In all, TTC7B could serve as a promising prognostic indicator of HNSCC, and is closely associated with focal adhesions, immune infiltration, and ferroptosis.

Inhibiting KLRB1 expression is associated with impairing cancer immunity and leading to cancer progression and poor prognosis in breast invasive carcinoma patients

BACKGROUND

The association between Killer cell lectin like receptor B1 (KLRB1) and cancer has been reported, but the roles of KLRB1 in breast invasive carcinoma (BRCA) has not been fully revealed.

METHODS

Our study utilized the Cancer Genome Atlas (TCGA), Kaplan-Meier (K-M) Plotter, and TIMER databases to investigate the expression and clinical relevance of KLRB1 in BRCA and to explore its roles and mechanism in BRCA progression using gene set enrichment analysis, CCK-8, migration, apoptosis, and western blotting. We examined the relationship between KLRB1 expression and the BRCA immune microenvironment, using data from TCGA, and Gene Expression Profiling Interactive Analysis (GEPIA) databases and validated these findings in K-M Plotter databases.

RESULTS

A significant decrease of KLRB1 expression was observed in BRCA patients. BRCA patients with low KLRB1 levels were associated with older age, advanced disease stage, HER2-positivity, poor prognosis, and a decreased survival probability compared to the high-expression group. Increased KLRB1 expression levels were correlated with inhibition of breast cancer cell proliferation, migration, and invasion, as well as promotion of cell apoptosis, possible through regulation of the NF-κB, PI3K/AKT, and TNF signaling pathways. Moreover, the study also indicated that decreased KLRB1 expression correlated with tumor purity, immune score, and immune cell infiltration (B cells, CD8+ T cells, CD4+ T cells, neutrophils, dendritic cells, among others), cell markers, and immunotherapy.

CONCLUSION

Decreased KLRB1 expression in BRCA is associated with poor prognosis and immune microenvironment. This study also highlights KLRB1 as a potential molecular marker for poor prognosis in BRCA patients, and therefore, it may provide clinical implications for the management of patients with BRCA.

Drug resistance in glioblastoma: from chemo- to immunotherapy

As the most common and aggressive type of primary brain tumor in adults, glioblastoma is estimated to end over 10,000 lives each year in the United States alone. Stand treatment for glioblastoma, including surgery followed by radiotherapy and chemotherapy (i.e., Temozolomide), has been largely unchanged since early 2000. Cancer immunotherapy has significantly shifted the paradigm of cancer management in the past decade with various degrees of success in treating many hematopoietic cancers and some solid tumors, such as melanoma and non-small cell lung cancer (NSCLC). However, little progress has been made in the field of neuro-oncology, especially in the application of immunotherapy to glioblastoma treatment. In this review, we attempted to summarize the common drug resistance mechanisms in glioblastoma from Temozolomide to immunotherapy. Our intent is not to repeat the well-known difficulty in the area of neuro-oncology, such as the blood-brain barrier, but to provide some fresh insights into the molecular mechanisms responsible for resistance by summarizing some of the most recent literature. Through this review, we also hope to share some new ideas for improving the immunotherapy outcome of glioblastoma treatment.

S100A6 is a potential diagnostic and prognostic biomarker for human glioma

S100 calcium-binding protein A6 (S100A6) is a protein that belongs to the S100 family. The present study aimed to investigate the function of S100A6 in the diagnosis and survival prediction of glioma and elucidated the potential processes affecting glioma development. The Cancer Genome Atlas database was searched to identify the relationship among S100A6 expression, immune cell infiltration, clinicopathological parameters and glioma prognosis. Several clinical cases were used to verify these findings. S100A6 gene expression was high in glioma tissues, suggesting its diagnostic significance. In particular, S100A6 upregulation in glioma tissues exhibited a significant and positive correlation with the World Health Organization (WHO) grade, histological type, age, sex, primary treatment outcomes, 1p/19q codeletion, isocitrate dehydrogenase (IDH) status, overall survival (OS), progression-free interval and disease-specific survival. Kaplan-Meier and Cox regression analyses revealed that S100A6 gene expression can independently function as a risk factor affecting the prognosis of patients with glioma. Furthermore, Gene Ontology functional enrichment analysis revealed that S100A6 is implicated in immune responses and that the expression profiles of S100A6 are linked to the immune microenvironment. Furthermore, immunohistochemistry revealed that increased S100A6 protein levels are correlated with age, 1p/19q codeletion, IDH status, WHO grade and OS. The present findings suggest that increased S100A6 expression is an indicator of the dismal prognosis of patients with glioma and that it can be used as a potential diagnostic biomarker for this condition.

The DEAD-box RNA helicase, DDX60, Suppresses immunotherapy and promotes malignant progression of pancreatic cancer

Excessive proliferation, invasion, metastasis, and immune resistance in pancreatic cancer (PC) makes it one of the most lethal malignant tumors. Recently, DDX60 was found to be involved in the development of various tumors and in immunotherapy. Therefore, we aimed to investigate whether DDX60 is a new factor involved in PC immunotherapy. The DDX60 mRNA was screened using transcriptome sequencing (RNA-seq). The Cox and survival analysis of DDX60 was performed using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. In addition, clinical and immune infiltration data in the databases were analyzed and plotted using the R language. Clinical samples and in vitro experiments were used to determine the molecular evolution of DDX60 during PC progression. We found that DDX60 was upregulated in PC tissues (P value = 0.0083) and was associated with poor prognosis and short survival time of patients with PC. Results of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set variation analyses showed that viral defense, tumor, and immune-related pathways were significantly enriched in samples with high DDX60 expression. The Pearson correlation test demonstrated that DDX60 expression correlated strongly with immune checkpoint and immune system-related metagene clusters. Our results indicated that DDX60 promoted cell proliferation, migration, and invasion and was related to poor prognosis and immune resistance. Therefore, DDX60 may be a promising novel target for PC immunotherapy.

Molecular Mechanisms of Tumor Cell Stemness Modulation during Formation of Spheroids

Cancer stem cells (CSCs), their properties and interaction with microenvironment are of interest in modern medicine and biology. There are many studies on the emergence of CSCs and their involvement in tumor pathogenesis. The most important property inherent to CSCs is their stemness. Stemness combines ability of the cell to maintain its pluripotency, give rise to differentiated cells, and interact with environment to maintain a balance between dormancy, proliferation, and regeneration. While adult stem cells exhibit these properties by participating in tissue homeostasis, CSCs behave as their malignant equivalents. High tumor resistance to therapy, ability to differentiate, activate angiogenesis and metastasis arise precisely due to the stemness of CSCs. These cells can be used as a target for therapy of different types of cancer. Laboratory models are needed to study cancer biology and find new therapeutic strategies. A promising direction is three-dimensional tumor models or spheroids. Such models exhibit properties resembling stemness in a natural tumor. By modifying spheroids, it becomes possible to investigate the effect of therapy on CSCs, thus contributing to the development of anti-tumor drug test systems. The review examines the niche of CSCs, the possibility of their study using three-dimensional spheroids, and existing markers for assessing stemness of CSCs.

Machine learning immune-related gene based on KLRB1 model for predicting the prognosis and immune cell infiltration of breast cancer

Objective

Breast cancer is a prevalent malignancy that predominantly affects women. The development and progression of this disease are strongly influenced by the tumor microenvironment and immune infiltration. Therefore, investigating immune-related genes associated with breast cancer prognosis is a crucial approach to enhance the diagnosis and treatment of breast cancer.

Methods

We analyzed data from the TCGA database to determine the proportion of invasive immune cells, immune components, and matrix components in breast cancer patients. Using this data, we constructed a risk prediction model to predict breast cancer prognosis and evaluated the correlation between KLRB1 expression and clinicopathological features and immune invasion. Additionally, we investigated the role of KLRB1 in breast cancer using various experimental techniques including real-time quantitative PCR, MTT assays, Transwell assays, Wound healing assays, EdU assays, and flow cytometry.

Results

The functional enrichment analysis of immune and stromal components in breast cancer revealed that T cell activation, differentiation, and regulation, as well as lymphocyte differentiation and regulation, play critical roles in determining the status of the tumor microenvironment. These DEGs are therefore considered key factors affecting TME status. Additionally, immune-related gene risk models were constructed and found to be effective predictors of breast cancer prognosis. Further analysis through KM survival analysis and univariate and multivariate Cox regression analysis demonstrated that KLRB1 is an independent prognostic factor for breast cancer. KLRB1 is closely associated with immunoinfiltrating cells. Finally, in vitro experiments confirmed that overexpression of KLRB1 inhibits breast cancer cell proliferation, migration, invasion, and DNA replication ability. KLRB1 was also found to inhibit the proliferation of breast cancer cells by blocking cell division in the G1/M phase.

Conclusion

KLRB1 may be a potential prognostic marker and therapeutic target associated with the microenzymic environment of breast cancer tumors, providing a new direction for breast cancer treatment.

The strange Microenvironment of Glioblastoma

Glioblastoma (GB) is the most common and aggressive primary brain tumor, with poor patient survival and lack of effective therapies. Late advances trying to decipher the composition of the GB tumor microenvironment (TME) emphasized its role in tumor progression and potentialized it as a therapeutic target. Many components participate critically to tumor development and expansion such as blood vessels, immune cells or components of the nervous system. Dysmorphic tumor vasculature brings challenges to optimal delivery of cytotoxic agents currently used in clinics. Also, massive infiltration of immunosuppressive myeloid cells and limited recruitment of T cells limits the success of conventional immunotherapies. Neuronal input seems also be required for tumor expansion. In this review, we provide a comprehensive report of vascular and immune component of the GB TME and their cross talk during GB progression.

Distinct single-cell immune ecosystems distinguish true and de novo HBV-related hepatocellular carcinoma recurrences

OBJECTIVE

Revealing the single-cell immune ecosystems in true versus de novo hepatocellular carcinoma (HCC) recurrences could help the optimal development of immunotherapies.

DESIGN

We performed 5'and VDJ single-cell RNA-sequencing on 34 samples from 20 recurrent HCC patients. Bulk RNA-sequencing, flow cytometry, multiplexed immunofluorescence, and in vitro functional analyses were performed on samples from two validation cohorts.

RESULTS

Analyses of mutational profiles and evolutionary trajectories in paired primary and recurrent HCC samples using whole-exome sequencing identified de novo versus true recurrences, some of which occurred before clinical diagnosis. The tumour immune microenvironment (TIME) of truly recurrent HCCs was characterised by an increased abundance in KLRB1+CD8+ T cells with memory phenotype and low cytotoxicity. In contrast, we found an enrichment in cytotoxic and exhausted CD8+ T cells in the TIME of de novo recurrent HCCs. Transcriptomic and interaction analyses showed elevated GDF15 expression on HCC cells in proximity to dendritic cells, which may have dampened antigen presentation and inhibited antitumour immunity in truly recurrent lesions. In contrast, myeloid cells' cross talk with T cells-mediated T cell exhaustion and immunosuppression in the TIME of de novo recurrent HCCs. Consistent with these findings, a phase 2 trial of neoadjuvant anti-PD-1 immunotherapy showed more responses in de novo recurrent HCC patients.

CONCLUSION

True and de novo HCC recurrences occur early, have distinct TIME and may require different immunotherapy strategies. Our study provides a source for genomic diagnosis and immune profiling for guiding immunotherapy based on the type of HCC recurrence and the specific TIME.

Tumor Microenvironment in Gliomas: A Treatment Hurdle or an Opportunity to Grab?

Gliomas are the most frequent central nervous system (CNS) primary tumors. The prognosis and clinical outcomes of these malignancies strongly diverge according to their molecular alterations and range from a few months to decades. The tumor-associated microenvironment involves all cells and connective tissues surrounding tumor cells. The composition of the microenvironment as well as the interactions with associated neoplastic mass, are both variables assuming an increasing interest in these last years. This is mainly because the microenvironment can mediate progression, invasion, dedifferentiation, resistance to treatment, and relapse of primary gliomas. In particular, the tumor microenvironment strongly diverges from isocitrate dehydrogenase (IDH) mutated and wild-type (wt) tumors. Indeed, IDH mutated gliomas often show a lower infiltration of immune cells with reduced angiogenesis as compared to IDH wt gliomas. On the other hand, IDH wt tumors exhibit a strong immune infiltration mediated by several cytokines and chemokines, including CCL2, CCL7, GDNF, CSF-1, GM-CSF, etc. The presence of several factors, including Sox2, Oct4, PD-L1, FAS-L, and TGF β2, also mediate an immune switch toward a regulatory inhibited immune system. Other important interactions are described between IDH wt glioblastoma cells and astrocytes, neurons, and stem cells, while these interactions are less elucidated in IDH-mutated tumors. The possibility of targeting the microenvironment is an intriguing perspective in terms of therapeutic drug development. In this review, we summarized available evidence related to the glioma microenvironment, focusing on differences within different glioma subtypes and on possible therapeutic development.

Development and validation of an inflammatory response-related prognostic model and immune infiltration analysis in glioblastoma

Background

Despite receiving standard treatment, the prognosis of glioblastoma (GBM) patients is still poor. Considering the heterogeneity of each patient, it is imperative to identify reliable risk model that can effectively predict the prognosis of each GBM patient to guide the personalized treatment.

Methods

Transcriptomic gene expression profiles and corresponding clinical data of GBM patients were downloaded from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Inflammatory response-related genes were extracted from Gene Set Enrichment Analysis (GSEA) website. Univariate Cox regression analysis was used for prognosis-related inflammatory genes (P<0.05). A polygenic prognostic risk model was constructed using least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Validation was performed through CGGA cohort. Overall survival (OS) was compared by Kaplan-Meier analysis. A nomogram was plotted to accurately predict the prognosis for each patient. GSEA was used for the pathway enrichment analysis. The single sample GSEA (ssGSEA) algorithm was implemented to conduct the immune infiltration analysis. The potential role of oncostatin M receptor (OSMR) in GBM was investigated through the in vitro experiment.

Results

A prognostic risk model consisting of 4 genes (PTPRN, OSMR, MYD88, and EFEMP2) was developed. GBM patients in the high-risk group had worse OS. The time-dependent ROC curves showed an area under the curve (AUC) of 0.782, 0.765, and 0.784 for 1-, 2-, and 3-year survival in TCGA cohort, while the AUC in the CGGA cohort was 0.589, 0.684, and 0.785 at 1, 2, and 3 years, respectively. The risk score, primary-recurrent-secondary (PRS) type, and isocitrate dehydrogenase (IDH) mutation could predict the prognosis of GBM patients well. The nomogram accurately predicted the 1-, 2-, and 3-year OS for each patient. Immune cell infiltration was associated with the risk score and the model could predict immunotherapy responsiveness. The expression of the prognostic gene was correlated with the sensitivity to antitumor drugs. Interference of OSMR inhibited proliferation and migration and promoted apoptosis of GBM cells.

Conclusions

The prognostic model based on 4 inflammatory response-related genes had reliable predictive power to effectively predict clinical outcome in GBM patients and provided the guide for the personalized treatment.

Comprehensive Bioinformatics Analysis Reveals PTPN1 (PTP1B) Is a Promising Immunotherapy Target Associated with T Cell Function for Liver Cancer

Recently, PTP1B was identified as a novel immune checkpoint whose removal can unleash T cell responses. However, research on the influence of PTP1B as an immune regulator on liver cancer is limited. This study aimed to investigate the immunological correlation and function of PTP1B in liver cancer. The expression profiles and corresponding clinical information of liver cancer patients were obtained from the TCGA and ICGC databases. GSE146115 and GSE98638 retrieved from the GEO database were used for the single-cell RNA-seq analysis. The mRNA expression of PTP1B (PTPN1) was increased in patients with most malignancies (all p < 0.05), including liver cancer (p < 0.001). Furthermore, up-regulated PTPN1 was connected to advanced tumor stage (p < 0.05) and worse prognosis (p < 0.01) in liver cancer. Through Cox regression analysis, PTPN1 was considered as an independent prognosis factor of overall survival (p < 0.05) and acted as a high-risk factor (hazard ratio > 1). Gene function and pathway analysis suggested PTPN1 was involved in T cell-related immune responses. Moreover, a close relationship was also found between PTPN1 expression and immune checkpoints as well as immune cells, especially with T cell-related checkpoints (all p < 0.001) and T cells (all p < 0.001). Single-cell RNA-seq analysis further illustrated that the enrichment of PTPN1 in the T cell population may be linked to its exhaustion in the liver cancer microenvironment. Overall, PTPN1 (PTP1B) closely related to T cell may function as an immunotherapy target for liver cancer.