Search Results (274)

Background: Human cell lines underpin modern biomedical research, offering reproducibility, standardisation, and unrestricted access to biological material. Among the 1206 human lines documented in the Human Protein Atlas, in vitro systems overcome the ethical and technical constraints of primary tissues. The liver is an organ of intricate structure, diverse physiological roles, and limited in vitro viability. Liver-derived cell lines are increasingly used to address the growing burden of liver disease and to accelerate pharmaceutical development, yet their capacity to replicate native hepatic functions remains uncertain. The mutational profiles and expression patterns of hepatocyte-characteristic genes provide critical benchmarks for their suitability for pharmacology and toxicology. Methods: Here, we systematically compare ten widely used hepatic cell lines (HepG2, Huh7, Hep3B, LX-2, HepaRG, HLF, HLE, MHCC97H, SK-Hep1, PLC/PRF/5) with primary hepatocytes and liver tissue, focusing on drug-metabolizing enzyme (DME) gene expression. Beyond literature synthesis, we analysed pre-processed RNA-seq expression data. Results: Overall, among the models examined, the HepaRG cell line shows the greatest similarity to liver and primary hepatocytes, most faithfully reproducing the expression patterns of DME genes. HepG2, Hep3B, and Huh7 form a cluster that retains only a subset of hepatic characteristics. Other models display more pronounced deviations from the reference profile and are generally used for specialized applications. Thus, no universal cell line exists that can fully substitute for the liver. Each model has its own limitations and biases in the expression profile of DME genes, which must be carefully considered when selecting an appropriate system for specific research objectives. Full article

Background: The search for reliable aging biomarkers using proteomic databases and large-scale proteomic studies presents a significant challenge in biogerontology. Existing proteomic databases and studies contain valuable information; however, there is inconsistency in approaches to biomarker selection and data integration. This creates barriers to translating existing knowledge into clinical practice and use in biomedical research. This work analyzed experimental proteomic studies, the content of proteomic databases, and proposed recommendations for optimization and improvement of proteomic database formation and enrichment. Methods: The study utilized publications devoted to proteomic data acquisition methods, proteomic databases, and experimental studies. Results: Methods for obtaining proteomic data were analyzed (Protein Pathway Array (PPA), Tissue Microarray (TMA), Luminex (Bead Array), MSD (Meso Scale Discovery), Simoa (Quanterix), SOMAscan (SomaLogic), Olink (PEA), Alamar NULISA (PEA+), and Oxford Nanopore. A total of 16 proteomic databases were investigated (HAGR, KEGG, STRING, Aging Atlas, HALL, Human Protein Atlas, UniProt, AgeAnnoMO, AgeFactDB, AgingBank, iProX, jMorp, jPOSTrepo, MassIVE, MetaboAge DB, PRIDE Archive). Additionally, 22 proteomic studies devoted to aging and age-associated diseases were analyzed. Conclusions: Proteomic databases and experimental studies individually contain valuable information about aging biomarkers. Using data from different sources within biomedical research poses challenges for improving and optimizing methodological solutions for publication selection, database formation, and marker development. Full article

Background: Ovarian cancer (OC) is the second most common gynecologic malignancy in the United States and remains the leading cause of death among cancers of the female reproductive system. Alarmingly, mortality rates have risen disproportionately among women of African ancestry compared to those of European or Asian descent. Identifying microRNA (miRNA) signatures that contribute to these disparities may enhance prognostic accuracy and inform personalized therapeutic strategies. Methods: In this study, we identified prognostic markers of overall survival in serous ovarian cancer (SOC) using data from The Cancer Genome Atlas (TCGA) and the Human Protein Atlas. Integrative bioinformatic analyses revealed three key prognostic genes—TIMP3 (Tissue Inhibitor of Metalloproteinases-3), BRAF (v-raf murine sarcoma viral oncogene homolog B), and ITGB1 (Integrin Beta-1)—as critical molecular determinants associated with survival in patients with SOC. Candidate miRNAs regulating these genes were predicted using TargetScanHuman v8.0, identifying a core regulatory set comprising miR-192, miR-30d, miR-16-5p, miR-143-3p, and miR-20a-5p. To validate their clinical relevance, formalin-fixed, paraffin-embedded (FFPE) and fresh SOC tumor samples were obtained from African American and Caucasian patients who underwent surgery at Loma Linda University (LLU) between 2010 and 2023. Results and Discussion: Among all these, ITGB1 (p = 0.00033), TIMP3 (p = 0.0035), and BRAF (p = 0.026) emerged as statistically significant predictors. Following total RNA extraction, cDNA synthesis, and quantitative reverse transcription PCR (qRT-PCR), the expression levels of these miRNAs and their target genes were quantified. In the LLU cohort, ITGB1 and TIMP3 were significantly upregulated in African American patients compared to Caucasian patients (p < 0.01 and p < 0.02, respectively). Among the miRNAs, miR-192-5p was particularly noteworthy, showing marginally differential expression in LLU samples (p = 0.0712) but strong statistical significance in the TCGA cohort (p = 0.00013), where elevated expression correlated with poorer overall survival (p = 0.021). Pathway enrichment and gene ontology analyses (miRTargetLink2.0, Enrichr) revealed interconnected regulatory networks linking miR-192, miR-16-5p, miR-143-3p, and miR-20a-5p to ITGB1; miR-143-3p/miR-145-5p to BRAF; and miR-16-5p and miR-30c/d to TIMP3. Conclusions: Collectively, these findings identify distinct miRNA–mRNA regulatory signatures—particularly the miR-192-5p–ITGB1/TIMP3 axis—as potential clinically relevant biomarkers that may contribute to racial disparities and disease progression in ovarian cancer. Full article

Hepatocellular carcinoma (HCC), the most common primary liver malignancy worldwide, is strongly associated with chronic Hepatitis B Virus (HBV) infection, a significant risk factor. The ubiquitin–proteasome system, central to protein degradation, cellular homeostasis, and cell cycle regulation, has been implicated in the pathogenesis of several cancers, including HCC. Despite this, the specific expression patterns of proteasomal subunits during HBV infection and HBV-induced HCC, as well as the association between mRNA expression of proteasomal subunits and proteasomal activity, remain poorly defined. To address this critical knowledge gap, we analyzed mRNA expression profiles of proteasomal subunits in HBV-infected humanized mouse models to uncover HBV-specific molecular alterations. Our findings revealed that the chymotrypsin-like activity (β5) subunit of the proteasome (PSMB5) is consistently overexpressed following HBV infection. Functional studies demonstrated that β5 deficiency decreases MHC I levels on the cell surface and leads to the accumulation of ubiquitinated proteins, establishing a direct link between β5 overexpression and increased proteasomal activity. Concordantly, HBV-infected patient livers—regardless of HCC status—displayed elevated β5 mRNA/protein levels and enhanced chymotrypsin-like activity. Additionally, analysis of Protein Atlas data revealed that elevated β5 mRNA expression correlates with poor clinical prognosis in HCC patients. In summary, this study highlights how HBV infection induces significant alterations in proteasome function by elevating β5 expression and activity in human and mouse livers. These findings underscore the critical role of proteasomal dysregulation in HBV-associated liver pathology and provide new insights into its involvement in HCC development. Understanding the interplay between HBV infection and proteasome dynamics offers a valuable avenue for the identification of novel therapeutic targets and biomarkers in HCC. Full article

Periodontitis (PD) is a multifactorial, progressive inflammatory disease affecting the teeth-supporting tissues, characterized by an imbalance of the oral microbiota and the presence of bacterial biofilms leading to host response. Nowadays, reliable biochemical markers for early and objective diagnosis, and for predicting disease progression, are still lacking. Our previous proteomic investigations revealed the significant overexpression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in periodontal pocket tissue, gingival crevicular fluid (GCF), and tooth-surface-collected material (TSCM) from PD patients in comparison to periodontally healthy controls, proposing it as a possible biomarker of PD. This study aimed to evaluate the expression of GAPDH in saliva, a more accessible, non-invasive, and clinically relevant oral sample. The whole saliva was analyzed by a preliminary mass spectrometry-based proteomic approach, identifying significantly increased levels of GAPDH also in salivary samples from periodontal-affected subjects. These data were further validated by enzyme-linked-immunosorbent assay (ELISA). Additionally, protein–protein interaction networks were generated through the Human Protein Atlas database, using different datasets (OpenCell, IntAct, and BioGRID). Bioinformatic analysis provided noteworthy GAPDH-associated networks potentially relevant to periodontal pathology. The scientific significance of this study lies in the detection of salivary GAPDH as a novel strategy to advance periodontal clinical diagnostics from the perspective of a non-invasive screening test. In correlation with other protein markers, salivary GAPDH could constitute a promising set of distinctive and predictive targets to enhance early diagnosis of PD, disease monitoring, and treatment planning in periodontology. Full article

The heparan sulfate proteoglycan syndecan-3 (SDC3) is a critical regulator of cell–matrix interactions. While other syndecan family members contribute to the progression of multiple cancers, SDC3’s functional contributions to tumor biology remain largely unexplored. This study investigates the potential role of SDC3 in the pathogenesis of breast cancer. By conducting an in-silico analysis of publicly available datasets, including TNM-plot, The Human Protein Atlas, and Kaplan–Meier Plotter, we observed that SDC3 is upregulated in breast cancer tissue. Notably, high SDC3 expression correlates with improved relapse-free survival in breast cancer patients. In vitro experiments revealed that SDC3 depletion significantly impairs cell viability, cell-cycle progression, cell migration, and 3D-spheroid-formation in MDA-MB-231 and MCF-7 breast cancer cells. Furthermore, SDC3 depletion results in upregulated gene expression of matrix metalloproteinases (MMP1, MMP9), downregulation of E-cadherin (CDH1), and altered levels of vascular endothelial growth factor A (VEGFA). Activation of proto-oncogene tyrosine-protein kinase Src was inhibited when SDC3 depletion was combined with tissue factor pathway inhibitor treatment. These findings demonstrate that breast cancer cell-derived SDC3 plays a pivotal role in tumor progression. Full article

Background/Objectives: Galectin-3 (Gal-3), encoded by LGALS3, is a β-galactoside-binding lectin involved in diverse tumor-associated processes, including immune modulation, cell cycle regulation, and stress adaptation. Despite its known roles in cancer biology, the full extent of its molecular functions and prognostic relevance across tumor types remains incompletely understood. This study aimed to systematically investigate the transcriptomic impact of LGALS3 deletion and assess its clinical significance in cancer. Methods: We analyzed CRISPR-Cas9 knockout transcriptomic data from the SigCom LINCS database to characterize the consensus gene signature associated with LGALS3 loss using functional enrichment analyses. Pan-cancer survival analyses were conducted using TIMER2.0. Differential Gal-3 protein levels in ductal adenocarcinoma and normal pancreatic tissues were evaluated using the Human Protein Atlas. Finally, functional analyses were performed in pancreatic ductal adenocarcinoma (PDAC). Results: LGALS3 deletion across multiple cancer cell lines led to transcriptomic changes involving mitotic progression, stress responses, and axonal guidance pathways. High LGALS3 expression was significantly associated with worse overall survival in lower-grade glioma, PDAC, uveal melanoma, and kidney renal papillary cell carcinoma. LGALS3 knockout in YAPC cells recapitulated the pan-cancer findings, linking LGALS3 to cell morphogenesis and proliferation. Conclusions: These findings identify Galectin-3 as a key regulator of oncogenic programs and a potential prognostic biomarker in PDAC and other malignancies, with implications for therapeutic targeting. Full article

Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease caused by mutations in the DMD gene, leading to muscle degeneration and shortened life expectancy. Beyond motor symptoms, DMD patients frequently exhibit brain co-morbidities, linked to loss of brain-expressed dystrophin isoforms: most frequently Dp427 and Dp140, and occasionally Dp71 and Dp40. DMD mouse models, including mdx^5cv and mdx52, replicate key aspects of the human cognitive phenotype and recapitulate the main genotypic categories of brain phenotype. However, the spatio-temporal expression of brain dystrophin in mice remains poorly defined, limiting insights into how its deficiency disrupts brain development and function. We systematically mapped RNA and protein expression of brain dystrophin isoforms (Dp427 variants, Dp140, Dp71, and Dp40) across brain regions and developmental stages in wild-type mice. Dp427 isoforms were differentially expressed in the adult brain, with Dp427c enriched in the cortex, Dp427p1/p2 in the cerebellum, and Dp427m was also detected across specific brain regions. Dp140 was expressed at lower levels than Dp427; Dp71 was the most abundant isoform in adulthood. Dp140 and Dp71 displayed dynamic developmental changes, from E15 to P60, suggesting stage-specific roles. We also analysed mdx^5cv mice lacking Dp427 and mdx52 mice lacking both Dp427 and Dp140. Both models had minimal Dp427 transcript levels, likely due to the nonsense-mediated decay, and neither expressed Dp427 protein. As expected, mdx52 mice lacked Dp140, confirming their genotypic relevance to human DMD. Our study provides the first atlas of dystrophin expression in the wild-type mouse brain, aiding understanding of the anatomical basis of behavioural and cognitive comorbidities in DMD. Full article

(1) Background: Somatostatin receptor 2 (SSTR2), a G protein-coupled receptor, is overexpressed in multiple malignancies, including hepatocellular carcinoma (HCC). While SSTR2 has traditionally been viewed as an inhibitory receptor involved in suppressing hormone secretion and cell proliferation, emerging evidence suggests a more complex role in cancer biology. However, the functional implications of SSTR2 expression in HCC remain poorly understood. This study aimed to systematically investigate the molecular landscape associated with SSTR2 expression in HCC and evaluate its potential as a therapeutic target. (2) Methods: SSTR2 expression patterns across 22 tumor types were assessed using TNMplot, and its expression in HCC was further validated through The Human Protein Atlas. Integrative analysis of transcriptomic profiles, protein expression data, and somatic copy number alterations was performed using data from The Cancer Genome Atlas (TCGA) to stratify HCC patients by SSTR2 expression levels. Gene Ontology (GO) enrichment analysis was conducted via SRplot to uncover biological processes and signaling pathways associated with SSTR2. Kaplan–Meier survival analyses were performed using GEO datasets to determine the prognostic significance of SSTR2 expression. (3) Results: SSTR2 is moderately expressed in the majority of HCC tumors. Elevated SSTR2 expression correlates with significantly poorer overall and disease-specific survival. High SSTR2 levels are associated with activation of oncogenic signaling cascades related to cell proliferation, epithelial-to-mesenchymal transition (EMT), angiogenesis, and metastasis. Additionally, SSTR2 expression is positively correlated with several receptor tyrosine kinases and oncogenes implicated in HCC progression. (4) Conclusions: Our findings suggest that SSTR2 is not merely a passive biomarker but may contribute to HCC pathogenesis through modulation of oncogenic pathways. These data support the rationale for further development of SSTR2-directed therapeutic strategies to inhibit tumor growth and invasion in HCC patients. Full article

Proteasome subunit beta type-9 (PSMB9), a member of the proteasome beta subunit family, encodes the pivotal β1i component of the immunoproteasome. PSMB9 plays a crucial role in antigen processing and presentation; however, its comprehensive role in orchestrating a tumor-immune landscape and regulating the anti-tumor immune responses remains unexplored. Here we investigated the context-dependent functions of PSMB9 by integrating multi-omics data from The Cancer Genome Atlas, Genotype-Tissue Expression database, Human Protein Atlas, Tumor Immunotherapy Gene Expression Resource, and multiple other databases. Moreover, we explored the predictive value of PSMB9 in multiple immunotherapy cohorts and investigated its functional relevance in CAR-T therapy using genome-scale CRISPR/Cas9 screening, gene knockout cell line in vitro, and clinical cohort validation. We found widespread dysregulation in PSMB9 across cancers, predominantly upregulated in most malignancies and associated with advanced pathological stages in specific contexts. PSMB9 was also broadly and negatively correlated with tumor stemness indices. Crucially, PSMB9 expression was robustly linked to anti-tumor immunity by being significantly correlated with immune-pathway activation (e.g., IFN response, cytokine signaling), immune regulatory and immune checkpoint gene expression, and enhanced infiltration of T cells across nearly all tumor types. Consequently, elevated PSMB9 predicted superior response to immune checkpoint inhibitors in multiple cohorts, showing comparable predictive power to established predictive signatures. Furthermore, CRISPR/Cas9 screening identified PSMB9 loss as a novel mechanism of resistance to CD19 CAR T cell therapy, with PSMB9-deficient tumor cells exhibiting a survival advantage under CAR-T pressure, supported by trends in clinical CAR-T outcomes. Our study uncovers PSMB9 as a previously unrecognized critical regulator of the tumor immune landscape in a pan-cancer scope, whose expression orchestrates key immune processes within the tumor microenvironment and serves as a potent biomarker for patient prognosis. Critically, we first established PSMB9 as a novel prognostic indicator for both checkpoint blockade and CAR-T cell therapies, highlighting its dual role as a crucial immune modulator and a promising biomarker for guiding T cell-based immunotherapy strategies across diverse human cancers. Full article

Circular RNAs (circRNAs) are increasingly recognized as regulators of gene expression, although their roles in hematopoietic differentiation remain relatively understudied. This study compares circRNA expression profiles between erythroblasts derived from human fetal liver and bone marrow CD34⁺ hematopoietic stem cells using publicly available RNA-seq datasets (GEO: GSE90878). Twelve samples from each developmental source were analyzed. Differential expression analysis was performed, and circAtlas 3.0 was employed to predict interactions between circRNAs, microRNAs (miRNAs), and RNA-binding proteins. Differentially expressed miRNAs were curated from miRNA-seq data (GEO: GSE110936) profiling the same cell types. Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R² = 0.065). One circRNA, circALS2(4).1, was significantly upregulated in bone marrow-derived erythroblasts (adjusted p < 0.05), and ten additional circRNAs showed suggestive evidence for differential expression (adjusted p < 0.1). The resulting interaction networks reveal distinct circRNA landscapes and suggest regulatory circuits that may contribute to developmental differences in human erythropoiesis, indicating that the functions of circRNAs in hematopoietic development remain to be further elucidated. Full article

Background/Objectives: Human endogenous retroviruses (ERVs) are genomic sequences integrated into the human genome from ancestral exogenous retroviruses and are epigenetically silenced under normal conditions. Growing evidence has shown that they can be reactivated in human diseases such as cancers and autoimmune diseases. However, their clinical implications in colon cancer are yet to be explored. Methods: RNA-seq data were downloaded from RNA Atlas and TCGA for cell lines and tissue samples, respectively. After alignment, ERV expression was quantified against comprehensively compiled ERVs (3220). ERV expression profiles were compared between sequencing protocols, cancer and normal cells, and matched tumor and normal tissue pairs. Unsupervised clustering was used to identify ERV-defined tumor subtypes and their associations with clinical and other molecular features. ERV association with disease-specific survival (DSS) was performed using the Cox regression model. Results: PolyA and total RNA protocols were comparable in ERV expression detection. Cancer cells had significantly increased ERV expression and reactivation. Upregulated ERVs were significantly enriched in viral protein interactions with cytokine and cytokine receptors. ERV expression-defined tumor classes were significantly associated with tumor mutation burden and immuno-phenotypes such as antigen processing and presenting machinery and tumor immune infiltration score. Survival analysis identified 152 ERVs to be independently associated with DSS. Conclusions: ERV abnormal expression is common in colon cancer. The ERV-defined subtypes are associated with tumor immunity, and some ERVs are independently associated with patient outcomes. Full article

Cancer is a multifaceted and life-threatening disease characterized by the unregulated proliferation of malignant cells. Developing new therapies and diagnostic methods for cancer remains a critical focus of research. Proteins involved in cancer progression are being targeted to facilitate the discovery of effective biological treatments. Among these, the ART1 protein plays a critical role in promoting cancer progression, establishing it as a key target for drug therapy. Actinomycetes, known for their anticancer activity, were explored in this study for their potential to inhibit ART1. One hundred bioactive secondary metabolites derived from actinomycetes were subjected to in silico screening to evaluate their potential anticancer activity through inhibition of ART1. The three-dimensional structure of ART1 was generated using the SWISS-MODEL tool and validated through the Save server 6.0 and ProSa web. The structural stability of the ART1 protein was evaluated through molecular dynamics analysis using the iMod server. The potential active sites within the ART1 structure were mapped using the Computed Atlas of Surface Topography of Proteins (CASTp). Molecular docking and protein–ligand interaction studies were performed using AutoDock Vina. Additionally, pharmacophore modeling was conducted using the Pharmit server to identify promising compounds. Toxicity predictions and in silico drug-likeness assessments were carried out using Swiss-ADME and ADMET Lab which evaluate Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. Molecular dynamics simulations results for the ART1 protein demonstrated high stability over time. Additionally, resistomycin, borrelidin, tetracycline, and oxytetracycline were identified as the top-ranking ligands, exhibiting binding energies between −8.9 kcal/mol and −9.3 kcal/mol. These ligands exhibited favorable pharmacophore profiles, drug-likeness, and ADMET properties, indicating their potential safety and efficacy in humans. In conclusion, the selected actinomycete-derived ligands show promise for further research and development as potential anticancer agents targeting ART1. Full article

The search for the biomarkers of Alzheimer’s disease (AD) may prove essential in the diagnosis and prognosis of the pathology, and the differential expression of key proteins may assist in identifying new therapeutic targets. In this proof-of-concept (POC) study, a new approach of data mining and matching combined with the biochemical analysis of proteins was applied to AD investigation. Three influential online open databases (UniProt, AlzGene, and Allen Human Brain Atlas) were explored to identify the genes and encoded proteins involved in AD linked to mitochondrial and iron dysmetabolism. The databases were searched using specific keywords to collect information about protein composition, and function, and meta-analysis data about their correlation with AD. The extracted datasets were matched to yield a list of relevant proteins in AD. The biochemical analysis of their amino acid content suggested a defective synthesis of these proteins in poorly oxygenated brain tissue, supporting their relevance in AD progression. The result of our POC study revealed several potential new markers of AD that deserve further molecular and clinical investigation. This novel database search approach can be a valuable strategy for biomarker search that can be exploited in many diseases. Full article

Leishmaniasis, caused by protozoan parasites of the genus Leishmania, is one of the most neglected human diseases, affecting millions worldwide. A detailed understanding of the molecular mechanisms that govern the outcome of macrophage–Leishmania interactions is crucial for a comprehensive understanding of leishmaniasis; however, our current knowledge of these mechanisms remains limited. It is clear that Leishmania has co-evolved to engage several clever strategies to regulate the cell biology of host macrophages to survive and multiply in phagolysosomes of these cells. In this review, we discuss how Leishmania exploits the macrophage Yin-Yang 1 protein as a critical proxy virulence factor to promote its survival. Additionally, we discuss an atlas of YY1-dependent proteins in human macrophages, which could serve as a valuable resource for researchers studying the role of YY1 in macrophage cell biology. Full article