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PTPRN Serves as a Prognostic Biomarker and Correlated with Immune Infiltrates in Low Grade Glioma.
BACKGROUND: Glioma is one of the most common malignant tumors of the central nervous system. Immune infiltration of tumor microenvironment was associated with overall survival in low grade glioma (LGG). However, effects of Tyrosine phosphatase receptor type N (PTPRN) on the progress of LGG and its correlation with tumor infiltration are unclear. METHODS: Here, datasets of LGG were from The Cancer Genome Atlas (TCGA) and normal samples were from GTEx dataset. Gepia website and Human Protein Atlas (HPA) Database were used to analyze the mRNA and protein expression of PTPRN. We evaluated the influence of PTPRN on survival of LGG patients. MethSurv was used to explore the expression and prognostic patterns of single CpG methylation of PTPRN gene in LGG. The correlations between the clinical information and PTPRN expression were analyzed using logistic regression and Multivariate Cox regression. We also explored the correlation between PTPRN expression and cancer immune infiltration by TIMER. Gene set enrichment analysis (GSEA) was formed using TCGA RNA-seq datasets. RESULTS: PTPRN mRNA and protein expression decreased in LGG compared to normal brain tissue in TCGA and HPA database. Kaplan-Meier analysis showed that the high expression level of PTPRN correlated with a good overall survival (OS) of patients with LGG. The Multivariate Cox analysis demonstrated that PTPRN expression and other clinical-pathological factors (age, WHO grade, IDH status, and primary therapy outcome) significantly correlated with OS of LGG patients. The DNA methylation pattern of PTPRN with significant prognostic value were confirmed, including cg00672332, cg06971096, cg01382864, cg03970036, cg10140638, cg16166796, cg03545227, and cg25569248. Interestingly, PTPRN expression level significantly negatively correlated with infiltrating level of B cell, CD4+ T cells, Macrophages, Neutrophils, and DCs in LGG. Finally, GSEA showed that signaling pathways, mainly associated with tumor microenvironment and immune cells, were significantly enriched in PTPRN high expression. CONCLUSION: PTPRN is a potential biomarker and correlates with tumor immune infiltration in LGG.
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The value of EYA1/3/4 in clear cell renal cell carcinoma: a study from multiple databases.
There is evidence from multiple studies that dysregulation of the Eyes Absent (EYA) protein plays multiple roles in many cancers. Despite this, little is known about the prognostic significance of the EYAs family in clear cell renal cell carcinoma (ccRCC). We systematically analyzed the value of EYAs in Clear Cell Renal Cell Carcinoma. Our analysis included examining transcriptional levels, mutations, methylated modifications, co-expression, protein-protein interactions (PPIs), immune infiltration, single-cell sequencing, drug sensitivity, and prognostic values. We based our analysis on data from several databases, including the Cancer Genome Atlas database (TCGA), the Gene Expression Omnibus database (GEO), UALCAN, TIMER, Gene Expression Profiling Interactive Analysis (GEPIA), STRING, cBioPortal and GSCALite. In patients with ccRCC, the EYA1 gene was significantly highly expressed, while the expression of EYA2/3/4 genes showed the opposite trend. The level of expression of the EYA1/3/4 gene was significantly correlated with the prognosis and clinicopathological parameters of ccRCC patients. Univariate and multifactorial Cox regression analyses revealed EYA1/3 as an independent prognostic factor for ccRCC, establishing nomogram line plots with good predictive power. Meanwhile, the number of mutations in EYAs was also significantly correlated with poor overall survival (OS) and progression-free survival (PFS) of patients with ccRCC. Mechanistically, EYAs genes play an essential role in a wide range of biological processes such as DNA metabolism and double-strand break repair in ccRCC. The majority of EYAs members were related to the infiltration of immune cells, drug sensitivity, and methylation levels. Furthermore, our experiment confirmed that EYA1 gene expression was upregulated, and EYA2/3/4 showed low expression in ccRCC. The increased expression of EYA1 might play an important role in ccRCC oncogenesis, and the decreased expression of EYA3/4 could function as a tumor suppressor, suggesting EYA1/3/4 might serve as valuable prognostic markers and potential new therapeutic targets for ccRCC.
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Targeting PSMB5-induced PANoptosis in bladder cancer: multi-omics insights and TCM candidate discovery.
BACKGROUND: Bladder cancer (BLCA) is among the most common malignancies worldwide, with significant mortality rates. The function of PANoptosis in BLCA, as a controlled process of programmed cell death, remains largely unelucidated. The study aimed to elucidate the role of PANoptosis-related genes in BLCA and investigate their molecular mechanisms, prognostic significance, and therapeutic potential. METHODS: By analyzing differentially expressed genes in BLCA from The Cancer Genome Atlas (TCGA) and PANoptosis-associated genes, we discovered 98 genes associated with PANoptosis. Functional enrichment and consensus clustering identified molecular subtypes linked to these genes. A prognostic model was developed via LASSO regression based on these genes. Subsequent analyses assessed clinical significance, characteristics of the immunological milieu, and treatment responsiveness. Systematic screening with machine learning (ML) identified PSMB5 as a pivotal gene, with its functional importance further clarified using single-cell sequencing and Mendelian randomization analysis (MR). In vitro research confirmed the biological activities of PSMB5 in BLCA. Molecular docking demonstrated PSMB5's binding affinity with traditional Chinese medicines (TCMs). RESULTS: Clustering of 98 PANoptosis-associated genes revealed molecular subgroups A and B. A prognostic approach identified high-risk and low-risk cohorts, revealing considerable disparities in clinical characteristics and immunological landscapes across the groups. ML and MR identified PSMB5 as a risk factor in BLCA. Single-cell sequencing revealed that PSMB5 expression is predominantly associated with three cell lines linked to lymph node metastases. In vitro findings demonstrated that PSMB5 knockdown inhibited the proliferation and migration of BLCA cells while promoting apoptosis, whereas overexpression has the opposite effect. Molecular docking revealed a robust binding affinity between PSMB5 and five TCMs. CONCLUSIONS: A prognostic model incorporating PANoptosis-related genes was developed for stratifying BLCA risk and assessing the immune microenvironment. PSMB5 has been recognized as a crucial therapeutic target, exhibiting dual importance in the molecular etiology of BLCA and traditional Chinese medicine intervention.
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Hepatocellular carcinoma resistance to tyrosine kinase inhibitors: Current status and perspectives.
The study conducted by Wang et al, focuses on the role of Rho GTPase activating protein 12 (ARHGAP12), in hepatocellular carcinoma (HCC). This research reveals that ARHGAP12 expression, markedly elevated in malignant cells of HCC, correlates strongly with adverse outcomes for patients. Furthermore, the study illustrates that ARHGAP12 enhances the ability of HCC cells to invade and contributes to their resistance to tyrosine kinase inhibitors (TKIs) through modulation of the focal adhesion pathway. To comprehensively investigate the relationship between ARHGAP12 and TKI resistance, this study integrates single-cell and bulk RNA sequencing methodologies along with data from tumor immune single-cell hub 2, Gene Expression Omnibus, The Cancer Genome Atlas, CellMiner, Genomics of Drug Sensitivity in Cancer 2, as well as immunohistochemical staining and proteomic analyses. Statistical analyses, including the Wilcoxon rank-sum test and receiver operating characteristic curve analysis, were employed to evaluate the correlation between ARHGAP12 expression levels and clinical parameters, as well as drug sensitivity. It is evident that a more profound exploration of the molecular dynamics of HCC, especially those related to resistance against TKIs, is essential.
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T cell receptor-centric perspective to multimodal single-cell data analysis.
The T cell receptor (TCR), despite its importance, is underutilized in single-cell analysis, with gene expression features solely driving current strategies. Here, we argue for a TCR-first approach, more suited toward T cell repertoires. To this end, we curated a large T cell atlas from 12 prominent human studies, containing in total 500,000 T cells spanning multiple diseases, including melanoma, head and neck cancer, blood cancer, and lung transplantation. Here, we identified severe limitations in cell-type annotation using unsupervised approaches and propose a more robust standard using a semi-supervised method or the TCR arrangement. We showcase the utility of a TCR-first approach through application of the STEGO.R tool for the identification of treatment-related dynamics and previously unknown public T cell clusters with potential antigen-specific properties. Thus, the paradigm shift to a TCR-first can highlight overlooked key T cell features that have the potential for improvements in immunotherapy and diagnostics.
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Galectin-9/TIM-3 as a Key Regulator of Immune Response in Gliomas With Chromosome 1p/19q Codeletion.
Gliomas with chromosome 1p/19q codeletion were considered a specific tumor entity. This study was designed to reveal the biological function alterations tightly associated with 1p/19q codeletion in gliomas. Clinicopathological and RNA sequencing data from glioma patients were obtained from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases. Gene set variation analysis was performed to explore the differences in biological functions between glioma subgroups stratified by 1p/19q codeletion status. The abundance of immune cells in each sample was detected using the CIBERSORT analytical tool. Single-cell sequencing data from public databases were analyzed using the t-distributed stochastic neighbor embedding (t-SNE) algorithm, and the findings were verified by in vitro and in vivo experiments and patient samples.We found that the activation of immune and inflammatory responses was tightly associated with 1p/19q codeletion in gliomas. As the most important transcriptional regulator of Galectin-9 in gliomas, the expression level of CCAAT enhancer-binding protein alpha in samples with 1p/19q codeletion was significantly decreased, which led to the downregulation of the immune checkpoints Galectin-9 and TIM-3. These results were validated in three independent datasets. The t-SNE analysis showed that the loss of chromosome 19q was the main reason for the promotion of the antitumor immune response. IHC protein staining, in vitro and in vivo experiments verified the results of bioinformatics analysis. In gliomas, 1p/19q codeletion can promote the antitumor immune response by downregulating the expression levels of the immune checkpoint TIM-3 and its ligand Galectin-9.
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High-resolution transcriptome atlas of bladder cancer highlights the functional myeloid subsets in modulating immune microenvironment.
BACKGROUND: Despite the recent advancements in characterizing the heterogeneity of the tumour microenvironment (TME), the immunological understanding of myeloid subsets in bladder cancer (BC) remains restricted. A more comprehensive exploration of myeloid cells in BC may uncover critical immune-modulating features. METHODS: We employed density gradient centrifugation to enrich the population of immune cells and collected paired tumour and normal bladder tissues from 11 patients with bladder cancer for single-cell transcriptome analysis. Additionally, in vitro cultures and mouse tumour models were further used to validate our findings. FINDINGS: We revealed the metabolic alterations in TREM2+ macrophages and CMA1+ mast cells within BC tissues, and further demonstrated that knockout of Trem2 significantly reprogrammed the TME and upregulated PD-L1 expression on dendritic cells (DCs). Our deconvolution analysis elucidated the prognostic value of CMA1+ mast cells, CD1C+ DCs and LAMP3+ DCs in BC, as well as delineated four distinct immune cellular modules to investigate their cellular associations. Furthermore, our exploration of the interactome landscapes highlighted the anti-tumour effect of App knockdown in remodelling the TME, as well as the pivotal roles of ANNEXIN and GALECTIN pathways in BC pathogenesis. INTERPRETATION: Our findings provide a high-resolution resource for BC, elucidating the functional myeloid cell states, including TREM2+ macrophages, CMA1+ mast cells, and CD1C+ DCs. Furthermore, our study demonstrates that TREM2 and APP function as immune-modulating molecules, with potential therapeutic implications in the context of bladder cancer. FUNDING: National Natural Science Foundation of China (31991174); the National Key Research and Development Program of China (2021YFA1301603 and 2023YFC2507000); the National Basic Science Center Program of China (82388101); the National Key Research and Development Program of China (2019YFA0508502 and 2022YFC2505001).
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MAX deficiency impairs human endometrial decidualization through down-regulating OSR2 in women with recurrent spontaneous abortion.
Human uterine stromal cell undergoes decidualization for pregnancy establishment and maintenance, which involved extensive proliferation and differentiation. Increasing studies have suggested that recurrent spontaneous abortion (RSA) may result from defective endometrial stromal decidualization. However, the critical molecular mechanisms underlying impaired decidualization during RSA are still elusive. By using our recently published single-cell RNA sequencing (scRNA-seq) atlas, we found that MYC-associated factor X (MAX) was significantly downregulated in the stromal cells derived from decidual tissues of women with RSA, followed by verification with immunohistochemistry (IHC) and quantitative real-time polymerase chain reaction (qRT-PCR). MAX knockdown significantly impairs human endometrial stromal cells (HESCs) proliferation as determined by MTS assay and Ki67 immunostaining, and decidualization determined by F-actin, and decidualization markers. RNA-seq together with chromatin immunoprecipitation sequencing (ChIP-seq) and cleavage under targets and release using nuclease sequencing (CUT&RUN-seq) analysis were applied to explore the molecular mechanisms of MAX in regulation of decidualization, followed by dual-luciferase reporter assay to verify that MAX targets to (odd-skipped related transcription factor 2) OSR2 directly. Reduced expression of OSR2 was also confirmed in decidual tissues in women with RSA by IHC and qRT-PCR. OSR2 knockdown also significantly impairs HESCs decidualization. OSR2-overexpression could at least partly rescue the downregulated insulin-like growth factor binding protein 1 (IGFBP1) expression level in response to MAX knockdown. Collectively, MAX deficiency observed in RSA stromal cells not only attenuates HESCs proliferation but also impairs HESCs decidualization by downregulating OSR2 expression at transcriptional level directly.
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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.
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The Comprehensive Analysis of Weighted Gene Co-Expression Network Analysis and Machine Learning Revealed Diagnostic Biomarkers for Breast Implant Illness Complicated with Breast Cancer.
PURPOSE: An increasing number of breast cancer (BC) patients choose prosthesis implantation after mastectomy, and the occurrence of breast implant illness (BII) has received increasing attention and the underlying molecular mechanisms have not been clearly elucidated. This study aimed to identify the crosstalk genes between BII and BC and explored their clinical value and molecular mechanism initially. METHODS: We retrieved the data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), and identified the differentially expressed genes (DEG) as well as module genes using Limma and weighted gene co-expression network analysis (WGCNA). Enrichment analysis, the protein-protein interaction network (PPI), and machine learning algorithms were performed to explore the hub genes. We employed a nomogram and receiver operating characteristic curve to evaluate the diagnostic accuracy. Single-cell analysis disclosed variations in the expression of key genes across distinct cellular populations. The expression levels of the key genes were further confirmed in BC cell lines. Immunohistochemical analysis was utilized to examine protein levels from 25 patients with breast cancer undergoing prosthetic implant surgery. Ultimately, we deployed single-sample Gene Set Enrichment Analysis (ssGSEA) to scrutinize the immunological profiles between the normal and BC cohorts, as well as between the non-BII and BII groups. RESULTS: WGCNA identified 1137 common genes, whereas DEG analysis found 541 overlapping genes in BII and BC. After constructing the PPI network, 17 key genes were selected, and three potential hub genes include KRT14, KIT, ALB were chosen for nomogram creation and diagnostic assessment through machine learning. The validation of these results was conducted by examining gene expression patterns in the validation dataset, breast cancer cell lines, and BII-BC patients. However, ssGSEA uncovered different immune cell infiltration patterns in BII and BC. CONCLUSION: We pinpointed shared three central genes include KRT14, KIT, ALB and molecular pathways common to BII and BC. Shedding light on the complex mechanisms underlying these conditions and suggesting potential targets for diagnostic and therapeutic strategies.