Pan-cancer Biomarker Research Articles

ZNF165: A Pan-Cancer Biomarker with Prognostic and Therapeutic Potential.

The role of ZNF165 in only a few tumors has been reported. ZNF165 plays an important role in liver cancer, gastric cancer, and breast cancer, especially in regulating the immune microenvironment, promoting tumor cell proliferation and migration, and serving as a potential target for immunotherapy. This study aimed to enhance an understanding of how the ZNF165 gene functions and influences cancer development. Using a suite of online resources, including TIMER, TCGA, GTEx, GEPIA2, cBioPortal, TIMER2, STRING, DAVID, RNAactDrug, CancerSEA, and UCSC, along with comprehensive statistical analyses, we conducted a thorough investigation of the pan-cancer landscape of ZNF165. This study encompassed an assessment of ZNF165 levels, their associations with patient outcomes, and clinical correlates. We examined the interplay between ZNF165 and key cancer biomarkers, such as Microsatellite Instability (MSI), Tumor Mutational Burden (TMB), immune cell infiltration, and the expression of immune checkpoint genes. We delved into the genetic variations of ZNF165, its biological roles across various cancer types, and its potential links to drug responsiveness. We analyzed single-cell expression patterns of ZNF165 and their implications for the functional dynamics of cancer. We employed quantitative Reverse Transcription PCR (qRT-PCR) to measure ZNF165 levels in Ovarian Cancer (OC) cell lines. ZNF165 expression displayed aberrations across a diverse range of human cancers and exhibited correlations with clinical stages. High ZNF165 expression in KIRC, KIRP, STAD, and UCEC was significantly associated with poor overall survival. ZNF165 has encouraging diagnostic value in specific tumor types, with gene amplification identified as the predominant genetic alteration. Our analysis further uncovered significant associations between ZNF165 levels and MSI across three distinct cancer types, as well as with TMB in six different malignancies. We detected substantial correlations between ZNF165 levels and immune cell infiltration, as well as the expression of immune checkpoint genes. ZNF165 was found to be involved in several prevalent signaling pathways across various cancer types. ZNF165 may potentially contribute to chemotherapy and chemoresistance, and was observed to be involved in cancer progression. A ceRNA regulatory network involving AFDN-DT, miR-191-5p, and ZNF165 was constructed for OC, revealing significantly elevated ZNF165 levels in OC cell lines. Dysregulated ZNF165 expression across a spectrum of malignancies might play a role in cancer initiation and advancement via multiple biological pathways. ZNF165 may serve as a promising therapeutic target for the treatment of cancer in human patients.

The thyroid hormone activating enzyme, DIO2, is a potential pan-cancer biomarker and immunotherapy target.

Type 2 deiodinase (D2), encoded by DIO2 gene, catalyzes the activation of the prohormone thyroxine (T4) into the bioactive hormone triiodothyronine (T3) in peripheral tissues, thereby regulating the intracellular Thyroid Hormone (TH) availability. Recently, several studies have demonstrated that a drastic increase in the peripheral activation of TH, via D2, fosters tumor progression, metastasis, and immunity. To further prove the clinical relevance of D2 in human cancer, based on public Database of The Cancer Genome Atlas (TCGA), we conducted a pan-cancer analysis of DIO2 expression in various cancer types and investigated the association of DIO2 expression with the tumor microenvironment (TME) components and immune cell infiltration, along with the DIO2 genetic alteration types. Although with different expression levels between the various cancer types, the pan-cancer analysis showed that DIO2 was highly expressed in most tumors and related to the progression of some tumor types. Furthermore, DIO2 expression was also significantly correlated with TME components, immune cell infiltration, and immunoinhibitory and immunostimulatory gene subsets. The relevance of this study is that it adds a clinical relevance to the recent demonstrations that D2 accelerates tumor invasion in animal models and poses DIO2 gene as a potential prognostic marker in various human cancers.

N7-methyladenosine-induced SLC7A7 serves as a prognostic biomarker in pan-cancer and promotes CRC progression in colorectal cancer

Solute transport family 7A member 7 (SLC7A7) mutations contribute to lysinuric protein intolerance (LPI), which is the mechanism of action that has been extensively studied. In colorectal cancer (CRC), SLC7A7 appears to play a role, but the features and mechanisms are not yet well understood. Survival was analyzed using the Kaplan–Meier analysis. Enrichment analysis was performed to characterize, immune infiltration, methylation, genetic instability, and crucial pathways of SLC7A7. Afterward, functional experiments were conducted in vitro to investigate how SLC7A7 affects tumor metastasis. Mechanistically, quantitative real-time PCR (qRT-PCR), western blot (WB), and methylated RNA immunoprecipitation (me-RIP) were carried out to confirm the methylation modification of SLC7A7 and related functions. High levels of expression of SLC7A7 are predictive of a worse prognosis for CRC patients. Enrichment analysis showed that SLC7A7 was significantly enriched during EMT and could be enriched in the Wnt/β-catenin signaling pathway, immune infiltration analysis of pan-cancer showed that SLC7A7 was significantly enriched in macrophages, and methylation analysis showed that SLC7A7 methylation modification affected the prognosis of specific cancers. SLC7A7 was indicated to promote the migration and invasion of CRC cells in in vitro functional experiments. Mechanistically, SLC7A7 was observed to potentially interact with the Wnt/β-catenin signaling pathway, possibly by influencing adenomatous polyposis coli (APC) expression. Furthermore, we identified that SLC7A7 undergoes N7-methylguanosine (m7G) modification, which may regulate SLC7A7 mRNA stability, with Quaking (QKI) potentially playing a role in this process by recognizing the m7G modification. Our results indicate that SLC7A7 may promote CRC metastasis through the SLC7A7/APC/Wnt/β-catenin signaling pathway. Moreover, m7G modification might be involved in regulating SLC7A7 mRNA stability, highlighting a novel layer of regulation.

Systematic pan-cancer analysis identifies ZBTB11 as a potential pan-cancer biomarker and immunotherapy target in multiple tumor types

Systematic pan-cancer analysis identifies ZBTB11 as a potential pan-cancer biomarker and immunotherapy target in multiple tumor types

BIRC5 as a prognostic and diagnostic biomarker in pan-cancer: an integrated analysis of expression, immune subtypes, and functional networks.

BIRC5 (Survivin) is a crucial anti-apoptotic protein overexpressed in various cancers, promoting tumor growth and treatment resistance. This study investigates its expression across 33 cancer types and explores its diagnostic, prognostic, and immune-related significance. We analyzed RNA-seq data from TCGA and protein expression data from the Human Protein Atlas. Expression levels were compared between tumor and normal tissues. Correlations with molecular and immune subtypes were explored using TISIDB. Prognostic significance was evaluated through survival analysis, Cox regression, and ROC curve analysis. The PPI network was constructed using STRING. BIRC5 was significantly overexpressed in tumor tissues across 33 cancer types, with higher expression levels observed in tumors compared to normal tissues. The protein expression analysis revealed a similar trend. BIRC5 expression was significantly correlated with various molecular and immune subtypes in multiple cancer types. Survival analysis indicated that high BIRC5 expression was associated with poor prognosis across multiple cancers, including lung adenocarcinoma (LUAD) and kidney renal clear cell carcinoma (KIRC). ROC analysis showed that BIRC5 exhibited strong diagnostic potential, with high AUC values (>0.9) in several cancers. The PPI network analysis identified key interacting proteins involved in the cell cycle and tumor progression, further supporting BIRC5's role in cancer biology. Functional experiments in lung adenocarcinoma (LUAD) revealed that BIRC5 upregulation enhances cell proliferation, migration, and invasion, while its knockdown suppresses these activities. BIRC5 is a promising diagnostic and prognostic biomarker in multiple cancers. Its association with immune subtypes suggests a potential role in the tumor immune microenvironment. These findings support BIRC5 as a therapeutic target for cancer treatment.

Immunotherapy for metastatic gastric cancer

This editorial discusses the article written by Chen et al that was published in the latest edition of the World Journal of Gastrointestinal Surgery . The current study found that programmed cell death 1 ligand 1 (PD-L1) expression is considered as one of the pan-cancer biomarkers of immune checkpoint inhibitors (ICIs) treatment response. Four molecular subtypes are widely used to guide and evaluate the prognosis and diagnosis and treatment of gastric cancer (GC) patients. Clinical trials of ICI treatment including Nivolumab, Pembrolizumab, Avelumab have been conducted for metastatic GC (mGC). The effects of various single agent ICIs on mGC therapy varied. ICIs combined with chemotherapy can indeed bring survival benefits to patients with mGC. Combining ICIs with chemotherapy can give more patients the chance of surgery in the treatment of GC transformation. However, not all PD-L1 positive patients can benefit from it. It is urgent to find better biomarkers to predict the response of ICIs for more precise clinical treatment.

Pan-Cancer Analysis Reveals the Potential of PLOD1 as a Prognostic and Immune Biomarker for Human Cancer.

Background/Objectives: Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) is known as an enhancer of collagen fiber deposition and cross-linking stability. However, there is limited information on its function in tumors. In this study, we aimed to elucidate the function and potential mechanism of action of PLOD1 across cancers. Methods: We assessed the pan-cancer expression, mutation, methylation and prognostic value of PLOD1 through multiple online databases. In addition, we performed correlation analyses of its immunological features, as well as functional assessment analyses of PLOD1. Finally, we assessed the effect of PLOD1 knockdown on bladder tumor cells using in vitro experiments. Results: Our findings suggest that PLOD1 is aberrantly expressed in multiple cancer types, accompanied by a poor prognosis. Epigenetic alterations in PLOD1 are highly heterogeneous across a wide range of tumors, and aberrant methylation and copy number variants correlate with a poor prognosis. In the tumor microenvironment, PLOD1 expression correlated positively with the infiltration level of various immunosuppressive cells (e.g., monocytes, macrophages and tumor-associated fibroblasts) and negatively with immune-killing cells (e.g., CD8+ T cells, B cells and CD4+ T cells). In addition, PLOD1 expression was associated with immune checkpoints and immunomodulatory genes. Finally, in vitro experiments demonstrated that knockdown of PLOD1 reduced the proliferation, migration and antiapoptotic abilities of T24 cells. Conclusions: The results of this study demonstrate that PLOD1 is a potential oncogene and prognostic biomarker in pan-cancer; tumor tissues with high PLOD1 expression reveal a relatively immunosuppressive tumor microenvironment.

Immuno-PET/CT Imaging of Trop2 with [18F]AlF-RESCA-T4 Differentiates Lung Cancer from Inflammation.

Immuno-PET/CT imaging, a branch of molecular imaging, can noninvasively and specifically visualize biomarker expression across the body. Trophoblast cell surface antigen 2 (Trop2) is a pan-cancer biomarker and plays a crucial role in tumorigenesis through multiple signaling pathways. The study aims to develop and translate novel Trop2 single-domain antibody (sdAb) tracers for clinical use. Methods: Two sdAbs (i.e., His-tagged T4 and His-tag-free RT4) are recombinantly expressed in Chinese hamster ovary cells. The purities and binding kinetics are determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis, high-performance liquid chromatography, and surface plasmon resonance assays. The AlF restrained complexing agent (RESCA) method is applied to develop 18F-labeled sdAb tracers ([18F]AlF-RESCA-T4 and [18F]AlF-RESCA-RT4), followed by thorough preclinical imaging and blocking studies on tumor-bearing mice and a pilot clinical trial evaluating the clinical imaging safety and feasibility of [18F]AlF-RESCA-T4 immuno-PET/CT. Results: [18F]AlF-RESCA-T4 and [18F]AlF-RESCA-RT4 possess high radiochemical purities. Preclinical imaging in the T3M-4 tumor model revealed prominent uptake (percentage injected dose/g) of [18F]AlF-RESCA-T4 (11.13 ± 1.53, n = 4) and [18F]AlF-RESCA-RT4 (8.83 ± 1.22, n = 4), which were significantly reduced by coinjection of unlabeled T4 and RT4 in blocking studies. The His-tag removal strategy further optimized the probe's invivo pharmacokinetics and reduced renal radioactivity accumulation without significantly decreasing tumor uptake. In a pilot clinical trial, [18F]AlF-RESCA-T4 immuno-PET/CT showed promising potency in annotating Trop2 expression and differentiating tumors from inflammatory diseases such as tuberculosis. Conclusion: [18F]AlF-RESCA-T4 and [18F]AlF-RESCA-RT4 can specifically annotate Trop2 expression. Clinical [18F]AlF-RESCA-T4 immuno-PET/CT imaging can screen patients for Trop2-targeted therapies and differentiate lung inflammation from cancer.

Magnesium-related gene ITGAL: a key immunotherapy predictor and prognostic biomarker in pan-cancer.

Integrin subunit alpha L (ITGAL) is crucial for activating CD8+ T cells through magnesium-mediated immune synapse formation and specific cytotoxicity. ITGAL might exert an important function in the growth and transformation of cancer. Our study comprehensively analyzed ITGAL expression across various cancers, validated by Immunochemistry (IHC) in the laboratory. ITGAL showed prognostic significance in pan-cancer patients, correlated with clinical features, and associated with specific signaling pathways. We also observed a relationship between ITGAL and immune cell infiltration. In HNSCC, ITGAL demonstrated prognostic value and potential implications for immunotherapy response and novel drug targets. ITGAL expression linked to tumor prognosis across 27 cancers. Elevated ITGAL correlated with good prognosis in CESC, LUAD, SARC, HNSCC, and SKCM. ITGAL involved in immune regulation pathways and showed positive correlation with immune cell infiltration. ITGAL associated with CD8+ T cell infiltration. And high ITGAL expression in CD8+ T cells and NK cells. In HNSCC, ITGAL linked to favorable prognosis and sensitivity to immunotherapy. Predicted potential drugs for HNSCC. ITGAL is remarkably associated with CD8+T cells and crucial in the tumor immune microenvironment of pan-cancer. Furthermore, our findings may provide a targeted anti-tumor strategy for ITGAL by influencing the tumor immune microenvironment.

NEK2 is a potential pan-cancer biomarker and immunotherapy target

BackgroundNEK2 is a member of the NEKs family and plays an important role in cell mitosis. Increasing evidence suggests that NEK2 is associated with the development of multiple tumors, but systematic studies of NEK2 in cancer are still lacking. Therefore, we evaluated the prognostic value of NEK2 in 33 cancers to elucidate the potential function of NEK2 in pan-cancers.MethodsWe investigated the role of NEK2 in pan-cancers utilizing The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. Additionally, we analyzed the association between NEK2 gene expression across various cancers, protein expression, the tumor microenvironment (TME), and drug sensitivity using several software and web platforms.The potential oncogenic role of NEK2 was initially explored using bioinformatics methods. Furthermore, we conducted in vitro experiments to preliminarily validate the function of NEK2 in cervical cancer.ResultsNEK2 is overexpressed in almost all tumors, and mutation of NEK2 are associated with a poorer tumor prognosis. In addition, the correlation between NEK2 and immune features such as immune cell infiltration, immune checkpoint genes, tumor mutational burden (TMB), Microsatellite instability(MSI) etc. suggest that NEK2 could potentially be applied in the immunotherapy of tumors.ConclusionNEK2 may be a potential pan-cancer biomarker and immunotherapeutic target for improving the efficacy of tumor therapy.

Study on MKNK2 as a potential prognostic and immunological biomarker in pan-cancer.

This study aimed to investigate the expression levels of the MKNK2 gene in pan-cancer, its prognostic significance, and its relationship with the tumor immune microenvironment, as well as to assess its potential as an immunological and prognostic biomarker. The research utilized data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE), including clinical and mutational information. Bioinformatic tools were employed to analyze the association of MKNK2 with carcinogenesis, including its links to prognosis, immune cell infiltration, tumor immune microenvironment, gene mutation, and the stemness of various tumor cells. A variety of statistical software and analytical tools were applied, including R software, SPSS 27.0, TIMER, CIBERSORT algorithm, and EPIC algorithm. The study found that MKNK2 is abnormally expressed in pan-cancer and is associated with a poor prognosis. The levels of MKNK2 are highly related to immune cell infiltration and tumor stemness. Notably, in liver hepatocellular carcinoma, glioblastoma multiforme, low-grade gliomas, and acute myeloid leukemia, MKNK2 expression shows a strong correlation with clinical outcomes and immune infiltration. Furthermore, the expression of MKNK2 shows significant correlations with immune cell infiltration, immune checkpoints, tumor mutational burden (TMB), microsatellite instability (MSI), and stemness scores across various cancers. The abnormal expression of MKNK2 is associated with tumor progression, immune checkpoint genes, immune cell infiltration, microsatellite instability (MSI), tumor mutational burden (TMB), and stemness in a variety of tumors, especially in glioblastoma multiforme low-grade gliomas (GBMLGG). Therefore, MKNK2 may serve as a potent prognostic physiological marker and provide new avenues for the development of tumor mechanisms and therapeutic strategies targeting MKNK2 to enhance the efficacy of immunotherapy.

SPECC1 as a pan-cancer biomarker: unraveling its role in drug sensitivity and resistance mechanisms

Previous studies have shown a relationship between SPECC1 and the prognosis of breast cancer, indicating a potential function for SPECC1 in the initiation and progression of cancer. However, the role played by SPECC1 in other tumors is not yet known. Therefore, we used bioinformatics techniques to conduct a thorough investigation into the possible mechanism of SPECC1 in pan-cancer, analyzing data reported in the literature as well as databases such as GTEx and CCLE, cBioportal, TCGA, and UCSC XENA. Comparing the results with matching normal tissues, the majority of cancers, including pancreatic adenocarcinoma (PAAD) and breast invasive carcinoma (BRCA), exhibited higher levels of SPECC1, while hepatocellular carcinoma (HCC) showed lower expression levels. SPECC1 was also found to be genetically mutated in endometrial cancer, sarcoma, and esophageal cancer. The prognosis of lung adenocarcinoma, kidney papillary cell carcinoma, and breast cancer is highly correlated with dysregulation of SPECC1 expression. This work helps guide clinical therapy by highlighting the sensitivity of tumor-treating medicines and the prognostic importance of SPECC1 in various malignancies. KEGG pathway enrichment analysis revealed focused adhesion, collagen-containing extracellular matrix (collagen), and the primary enrichment domains for SPECC1-related genes. These findings were obtained through gene annotation (GO) examination of SPECC1 expression. Primary mediators of the cytokine-cytokine receptor interaction include PICOC1-associated genes, cell-substrate junction genes, and extracellular matrix containing collagen. PICOC1-associated genes primarily mediate the PI3K-AKT signaling pathway. Drug sensitivity assay showed that SPECC1 high-expressing cell lines were more sensitive to docetaxel, doxorubicin, etc. In conclusion, the current study shows how SPECC1 is expressed in different cancers and how this expression relates to the prognosis of the tumor. It also revealed the mutations and copy number variations of SPECC1 in various tumors and its potential involvement in cellular pathway regulatory networks and cytological processes. This study examines the relationship between immune genes, cellular infiltration, and immunological scores in the tumor microenvironment, which explain the severity of the disease. This study looks at the response of SPEC1 expression to anticancer therapy. Explains the prognostic significance and drug response of SPECC-1.

EBNA1BP2 identified as potential prognostic biomarker for multiple tumor types in pan-cancer analysis

BackgroundEpstein-Barr virus (EBV) infection has been closely linked to the development of various types of cancer. EB nuclear antigen 1 binding protein 2 (EBNA1BP2) is a crucial molecule for stable isolation of EBV in latent infection. However, the role of EBNA1BP2 in multiple tumor types is remains unclear. In this study, we comprehensively analyzed the functional characteristics of EBNA1BP2 and investigate its potential as a prognostic biomarker in pan-cancer.MethodsWe utilized data from TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) databases and employed various bioinformatics analysis tools, including TIMER2.0, HPA, GEPIA2.0, PrognoScan, cBioPortal, CancerSEA, and BioGRID to explore the expression pattern, prognostic value, immune infiltration, and methylation level of EBNA1BP2 in pan-cancer. Additionally, we conducted enrichment analysis of genes associated with EBNA1BP2 to identify potential biological functions and pathways.ResultsOur analysis revealed that EBNA1BP2 expression was significantly higher in tumor tissues compared to tumor-adjacent tissues. We observed that lower expression of EBNA1BP2 in adrenocortical carcinoma (ACC), brain lower grade glioma (LGG), sarcoma (SARC), and uterine carcinosarcoma (UCS) was significantly associated with improved overall survival (OS) and disease-free survival (DFS). Furthermore, the promoter methylation level of EBNA1BP2 was downregulated in the majority of cancer types. At the single-cell level, EBNA1BP2 was found to be positively correlated with cell cycle and DNA repair processes, while negatively correlated with hypoxia. Additionally, EBNA1BP2 was associated with the infiltration of immune cells such as B cells, cancer-associated fibroblast cells, and CD8+ T cells. Gene enrichment analysis indicated that EBNA1BP2 was mainly involved in nucleoplasm and RNA binding pathways.ConclusionOur findings suggest that EBNA1BP2 may serve as a potential prognostic biomarker for survival in pan-cancer. Further experimental studies are needed to validate these findings and explore the underlying mechanisms by which EBNA1BP2 contributes to tumorigenesis.

CISD3 is a prognostic biomarker and therapeutic target in pan-cancer.

Recent studies indicate that CISD3 is crucial in mitochondrial function and tumorigenesis. Using various databases, we systematically analyzed its expression, prognostic value, and immune activity. Our findings show CISD3 is mainly expressed in tumor cells across cancers, with higher mRNA but lower protein levels, degraded post-translationally via the lysosomal pathway. In certain cancers, CISD3 expression is positively correlated with tumor-infiltrating immune cells. Prognostic analysis suggests dual roles as both protective and risk factors, notably an independent prognostic predictor in renal cell carcinoma (RCC). CISD3 copy number variations are linked to homologous recombination defects and tumor-specific neoantigens, negatively correlated with methylation levels. Pathway analysis reveals CISD3 involvement in oncogenic processes, such as proliferation inhibition and epithelial-mesenchymal transition. Protein interactions underline its role in mitochondrial metabolism and redox balance. Experiments confirm low CISD3 expression in cancers, with overexpression reducing proliferation, migration, invasion, and tumor growth in mice. Mechanistic studies indicate CISD3 overexpression disrupts mitochondrial function, increases ROS levels, decreases GSH/GSSG ratios and mitochondrial membrane potential, inhibiting antioxidant activity and promoting cell damage and ferroptosis, thus impeding cancer progression. This study highlights CISD3's potential as a prognostic biomarker and therapeutic target.

Multi-omics analysis identifies BCAT2 as a potential pan-cancer biomarker for tumor progression and immune microenvironment modulation.

Branched-chain amino acid transaminase 2 (BCAT2) encodes a crucial protein involved in the initial catalysis of branched-chain amino acid (BCAA) catabolism, with emerging evidence suggesting its association with tumor progression. This study explores BCAT2 in a pan-cancer multi-omics context and evaluates its prognostic significance. We utilized a multi-database approach, analyzing cBioPortal for genetic alterations, RNA-Seq data from TCGA and GTEx for expression patterns, and RSEM for transcript analysis. Protein expression and interaction networks were assessed using the Human Protein Atlas, UniProt, and STRING. Prognostic value was determined through Cox regression analysis of TCGA clinical survival data, while immune cell infiltration across various cancers was examined using TCGA data and the TIMER2 platform. Our results revealed that BCAT2 alterations are primarily amplifications and is upregulated in various tumors, correlating with poor survival rates in several tumor types, including GBMLGG, LGG, and UVM. Elevated BCAT2 protein levels were common in pan-cancer, interacting with a range of metabolic enzymes. Additionally, BCAT2 expression significantly influenced CD4+ T cells, CD8+ T cells, and Treg cells infiltration, with varied correlations across cancer types. These findings indicate BCAT2 as a potential biomarker for cancer diagnosis and therapy, potentially regulating key metabolic and immune factors to mediate tumor progression and the microenvironment.

Multi-omics landscape of Interferon-stimulated gene OASL reveals a potential biomarker in pan-cancer: from prognosis to tumor microenvironment.

OASL (Oligoadenylate Synthetase-Like), an interferon-induced protein in the OAS family, plays a significant role in anti-viral response. Studies have demonstrated its association with prognosis of certain tumors. However, the mechanism through which OASL affects tumors is unclear. A systemic pan-cancer study of OASL needs to be illustrated. Analysis of OASL expression across 33 tumors was conducted utilizing TCGA, GTEx and CPTAC databases. COX and Log-Rank regressions were employed to calculate the prognosis. We validated the impact of OASL on apoptosis, migration, and invasion in pancreatic cancer cell lines. Moreover, we employed seven algorithms in bulk data to investigate the association of OASL expression and immune cell infiltration within tumor immune microenvironment (TIME) and ultimately validated at single-cell transcriptome level. We discovered elevated expression of OASL and its genetic heterogeneity in certain tumors, which link closely to prognosis. Validation experiments were conducted in PAAD and confirmed these findings. Additionally, OASL regulates immune checkpoint ligand such as programmed death ligand 1 (PD-L1), through IFN-γ/STAT1 and IL-6/JAK/STAT3 pathways in tumor cells. Meanwhile, OASL affects macrophages infiltration in TIME. By these mechanisms OASL could cause dysfunction of cytotoxic T lymphocytes (CTLs) in tumors. Multi-omics analysis reveals OASL as a prognostic and immunological biomarker in pan-cancer.

Cell Polarity-related Gene PTK7, a Potential Diagnostic Biomarker in Pan-cancer.

PTK7 (Protein Tyrosine Kinase 7), a member of the receptor protein tyrosine kinase family, was originally discovered in colon cancer cells. It plays a pivotal role in numerous developmental and physiological processes, particularly in the regulation of cell polarity. Despite accumulating evidence of PTK7's significant influence on tumor development, a comprehensive pan-cancer analysis of PTK7 has yet to be conducted. We conducted a comprehensive analysis of PTK7's expression, prognostic value, and mutational patterns across various tumor types. We further explored the correlations between PTK7 expression and tumor stemness, immune-related genes, immune scores, and immune cell infiltration. Enrichment analysis revealed PTK7's critical involvement in pan-cancer functions and processes, including the WNT pathway, Epithelial-Mesenchymal Transition (EMT), and cell polarity regulation. Additionally, we validated PTK7's expression in gastric cancer via immunohistochemistry. Our study indicates that PTK7 holds promise as an ideal pan-cancer biomarker due to its involvement in tumor progression and tumor immunity.

Intratumoral microbiome of adenoid cystic carcinomas and comparison with other head and neck cancers

Adenoid cystic carcinoma (ACC) is a rare, usually slow-growing yet aggressive head and neck malignancy. Despite its clinical significance, our understanding of the cellular evolution and microenvironment in ACC remains limited. We investigated the intratumoral microbiomes of 50 ACC tumor tissues and 33 adjacent normal tissues using 16S rRNA gene sequencing. This allowed us to characterize the bacterial communities within the ACC and explore potential associations between the bacterial community structure, patient clinical characteristics, and tumor molecular features obtained through RNA sequencing. The bacterial composition in the ACC was significantly different from that in adjacent normal salivary tissue, and the ACC exhibited diverse levels of species richness. We identified two main microbial subtypes within the ACC: oral-like and gut-like. Oral-like microbiomes, characterized by increased diversity and abundance of Neisseria, Leptotrichia, Actinomyces, Streptococcus, Rothia, and Veillonella (commonly found in healthy oral cavities), were associated with a less aggressive ACC-II molecular subtype and improved patient outcomes. Notably, we identified the same oral genera in oral cancer and head and neck squamous cell carcinomas. In both cancers, they were part of shared oral communities associated with a more diverse microbiome, less aggressive tumor phenotype, and better survival that reveal the genera as potential pancancer biomarkers for favorable microbiomes in ACC and other head and neck cancers. Conversely, gut-like intratumoral microbiomes, which feature low diversity and colonization by gut mucus layer-degrading species, such as Bacteroides, Akkermansia, Blautia, Bifidobacterium, and Enterococcus, were associated with poorer outcomes. Elevated levels of Bacteroides thetaiotaomicron were independently associated with significantly worse survival and positively correlated with tumor cell biosynthesis of glycan-based cell membrane components.

HTERT Epigenetics Provides New Perspectives for Diagnosis and Evidence-Based Guidance of Chemotherapy in Cancer.

Strong epigenetic pan-cancer biomarkers are required to meet several current, urgent clinical needs and to further improve the present chemotherapeutic standard. We have concentrated on the investigation of epigenetic alteration of the hTERT gene, which is frequently epigenetically dysregulated in a number of cancers in specific developmental stages. Distinct DNA methylation profiles were identified in our data on early urothelial cancer. An efficient EpihTERT assay could be developed utilizing suitable combinations with sequence-dependent thermodynamic parameters to distinguish between differentially methylated states. We infer from this data set, the epigenetic context, and the related literature that a CpG-rich, 2800 bp region, a prominent CpG island, surrounding the transcription start of the hTERT gene is the crucial epigenetic zone for the development of a potent biomarker. In order to accurately describe this region, we have named it "Acheron" (Ἀχέρων). In Greek mythology, this is the river of woe and misery and the path to the underworld. Exploitation of the DNA methylation profiles focused on this region, e.g., idiolocal normalized Methylation Specific PCR (IDLN-MSP), opens up a wide range of new possibilities for diagnosis, determination of prognosis, follow-up, and detection of residual disease. It may also have broad implications for the choice of chemotherapy.

RPN1: a pan-cancer biomarker and disulfidptosis regulator.

Elevated expression of SLC7A11, in conjunction with glucose deprivation, has revealed disulfidptosis as an emerging cell death modality. However, the prevalence of disulfidptosis across tumor cell lines, irrespective of SLC7A11 levels, remains uncertain. Additionally, deletion of the ribophorin I (RPN1) gene imparts resistance to disulfidptosis, yet the precise mechanism linking RPN1 to disulfidptosis remains elusive. The aim of this study is to determine the mechanism of RPN1-induced disulfidptosis and to determine the possibility of RPN1 as a pan-cancer marker. We hypothesized the widespread occurrence of disulfidptosis in various tumor cells, and proposed that RPN1-mediated disulfidptosis may be executed through cell skeleton breakdown. Experimental validation was conducted via flow cytometry, immunofluorescence, and western blot techniques. Furthermore, given RPN1's status as an emerging cell death marker, we utilized bioinformatics to analyze its expression in tumor tissues, clinical relevance, mechanisms within the tumor microenvironment, and potential for immunotherapy. Conducting experiments on breast cancer (MDA-MB-231) and lung cancer (A549) cell lines under glucose-starved conditions, we found that RPN1 primarily induces cell skeleton breakdown to facilitate disulfidptosis. RPN1 demonstrated robust messenger RNA (mRNA) expression across 16 solid tumors, validated by data from 12 tumor types in the Gene Expression Omnibus (GEO). Across 12 cancer types, RPN1 exhibited significant diagnostic potential, particularly excelling in accuracy for glioblastoma (GBM). Elevated RPN1 expression in tumor tissues was found to correlate with improved overall survival (OS) in certain cancers [diffuse large B-cell lymphoma (DLBC) and thymoma (THYM)] but poorer prognosis in others [adrenocortical carcinoma (ACC), kidney chromophobe (KICH), brain lower grade glioma (LGG), liver hepatocellular carcinoma (LIHC), and pancreatic adenocarcinoma (PAAD)]. RPN1 is enriched in immune-related pathways and correlates with immune scores in tumor tissues. In urothelial carcinoma (UCC), RPN1 demonstrates potential in predicting the efficacy of anti-programmed cell death ligand 1 (PD-L1) immune therapy. This study underscores RPN1's role in facilitating disulfidptosis, its broad relevance as a pan-cancer biomarker, and its association with the efficacy of anti-PD-L1 immune therapy.