Single-cell and bulk RNA sequencing analysis reveals CENPA as a potential biomarker and therapeutic target in cancers

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(1), P. e0314745 - e0314745

Published: Jan. 16, 2025

Cancer remains one of the most significant public health challenges worldwide. A widely recognized hallmark cancer is ability to sustain proliferative signaling, which closely tied various cell cycle processes. Centromere Protein (CENPA), a variant standard histone H3, crucial for selective chromosome segregation during cycle. Despite its importance, comprehensive pan-cancer bioinformatic analysis CENPA has not yet been conducted. Data on genomes, transcriptomes, and clinical information were retrieved from publicly accessible databases. We analyzed CENPA's genetic alterations, mRNA expression, functional enrichment, association with stemness, mutations, expression across populations cellular locations, link cycle, impact survival, relationship immune microenvironment. Additionally, prognostic model glioma patients was developed demonstrate potential as biomarker. Furthermore, drugs targeting in cells identified predicted using drug sensitivity correlations protein-ligand docking. exhibited low levels gene mutation cancers. It found be overexpressed nearly all types TCGA, relative normal controls, predominantly located nucleus malignant cells. showed strong particularly biomarker G2 phase. also emerged valuable diagnostic multiple types. In glioma, demonstrated reliable when used alongside other factors. linked Drugs such CD-437, 3-Cl-AHPC, Trametinib, BI-2536, GSK461364 target serves cancers, offering both value.

Language: Английский

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Uridine-cytidine kinase 2 is correlated with immune, DNA damage repair and promotion of cancer stemness in pan-cancer

Frontiers in Oncology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 27, 2025

Background UCK2 (Uridine-Cytidine Kinase 2) is a promising prognostic marker for malignant tumors, but its association with immune infiltration and cancer stemness in pan-cancer remains to be fully understood. we find that gene closed related RNA scores (RNAss) DNA (DNAss), which measured the tumor stemness. We also discover an between expression cells by CIBERSORT algorithm, ESTIMATE algorithm ssGSEA especially, T cell, monocytes, mast cells, macrophages. This study aims shed light on role possible mechanism of pan-cancer. Methods used R programming language bulk sequencing data analysis, were obtained from University California, Santa Cruz (UCSC) datasets. UCSC database very useful explore TCGA other genomics datasets, The explored at transcriptome level came database. differential normal samples. Immunohistochemistry (IHC) was utilized validate different types cancers using tissue chips. correlations prognosis, genetic instability, repair, stem cell characteristics, investigated. Furthermore, single-cell acquired Gene Expression Omnibus (GEO) database, relationship cells. GEO famous public supporting freely disseminates microarray data. Finally, analyzed correlation drug sensitivity. Results observed high most remarkably prognosis pan-cancers. found increased associated higher instability. Additionally, positive relationships mismatch repair genes, homologous recombination across types. There significant Moreover, as expected, checkpoint human leucocyte antigen (HLA) negatively UCK2. Similarly, have negative major histocompatibility complex (MHC) genes. noted had sensitivity various anti-cancer drug. Conclusion plays pivotal roles immunity, it exhibits strong checkpoints HLA. highlights potential impact

Language: Английский

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Protein Kinases in Phagocytosis: Promising Genetic Biomarkers for Cancer

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 11, 2024

Abstract Cancer is a complex disease characterized by genetic and molecular diversity, often involving dysregulation of critical cellular pathways. Recent advances in pan-cancer research have highlighted the importance shared oncogenic mechanisms across different cancer types, providing new avenues for therapeutic exploration. Protein kinases, particularly those involved phagocytosis, play pivotal roles homeostasis immune response. This study systematically examines alterations expression profiles protein kinases associated with phagocytosis various using data from The Genome Atlas (TCGA) other publicly available resources. We analyzed single nucleotide variations (SNVs), copy number (CNVs), methylation patterns, mRNA to identify recurring their associations survival outcomes. Our findings reveal that MET MERTK are most frequently mutated genes, missense mutations dominating cancers. CNV analysis shows significant correlations cancers like UCEC, KIRP, KIRC, while indicates cancer-specific regulatory patterns affecting gene expression. Differential highlights distinct cancer-type-specific profiles, genes BTK displaying variation. Crosstalk pathway further reveals involvement these key cancer-related pathways, such as epithelial-mesenchymal transition (EMT) apoptosis. Drug sensitivity identifies potential targets, correlating significantly cell line responsiveness specific compounds. These underscore phagocytotic kinome biology suggest strategies targeting enhance response improve treatment

Language: Английский

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Bladder cancer biomarkers: current approaches and future directions

Frontiers in Oncology, Journal Year: 2024, Volume and Issue: 14

Published: Nov. 29, 2024

Bladder cancer is a significant health concern worldwide, necessitating effective diagnostic and monitoring strategies. Biomarkers play crucial role in the early detection, prognosis, treatment of this disease. This review explores current landscape bladder biomarkers, including FDA-approved molecular biomarkers emerging ones. such as BTA stat, TRAK, NMP22, have been instrumental diagnosing cancer. These are derived from urinary samples particularly useful due to their sensitivity specificity. As we move forward, should continue seek ways optimize our processes outcomes, these markers remain seriously challenged detection limited For instance, sensitivities stat tumor varied between 40-72%, while its specificities vary 29-96%. In same way, 70% 80% specificity recorded for 11-85.7% 77-100% documented NMP22 BladderChek. The given variations, especially low diagnosis at an stage call invention better systems. Moreover, different sample collection handling procedures applied laboratories further contribute inconsistent results obtained. Extracellular vesicles (EVs) exosomes, which carry vast number proteins, being considered potential biomarkers. Although show promise, challenges non-standardized isolation techniques lack reproducibility across studies. discovery new ongoing. UBC

Language: Английский

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Epstein-Barr Virus and <i>Helicobacter pylori</i> as Two Main Risk Factors in Gastric Cancer

OBM Genetics, Journal Year: 2024, Volume and Issue: 08(04), P. 1 - 25

Published: Nov. 20, 2024

Microbial and viral pathogens have emerged as pivotal agents in oncogenesis. Research conducted the last twenty years has significantly enhanced our comprehension of cancer-causing capabilities infectious agents. An illustrative instance is gastric cancer (GC), which closely associated with Helicobacter pylori (H. pylori) Epstein-Barr virus (EBV) infections. Despite concerted endeavors, GC remains a serious clinical challenge ranking fifth most commonly diagnosed worldwide. In 2020, an estimated 768,793 people died from world. The pathogenicity island (PAI), cagA protein, VacA other virulence factors H. several latency such EBNA-1, LMP-1 LMP2A well pattern gene methylation EBV co-infection are shown main causes pathogen-related GC. unique molecular characteristics GC, highlight importance further understanding their respective roles development progression. This knowledge may inform future preventive therapeutic strategies targeting these context review aims to elucidate mechanisms underpinning pylori-induced carcinogenesis

Language: Английский

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