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Biomedicines

Biomedicines is an international, peer-reviewed, open access journal on biomedicines published monthly online by MDPI.

Indexed in PubMed | Quartile Ranking JCR - Q1 (Pharmacology and Pharmacy)

All Articles (15,308)

Background: Clear cell renal cell carcinoma (ccRCC) is a prevalent urological malignancy, accounting for approximately 1.6% of all cancer-related deaths in 2022. While endocrine-disrupting chemicals (EDCs) have been implicated as risk factors for ccRCC, the toxicological profiles and immune mechanisms underlying Bisphenol A (BPA) exposure in ccRCC progression remain inadequately understood. Materials and Methods: Protein–protein interaction (PPI) analysis and visualization were performed on overlapping genes between ccRCC and BPA exposure. This was followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to elucidate potential underlying mechanisms. Subsequently, 108 distinct machine learning algorithm combinations were evaluated to identify the optimal predictive model. An integrated CoxBoost and Ridge regression model was constructed to develop a prognostic signature, the performance of which was rigorously validated across two independent external datasets. Finally, molecular docking analyses were employed to investigate interactions between key genes and BPA. Results: A total of 114 overlapping targets associated with both ccRCC and BPA were identified. GO and KEGG analyses revealed enrichment in cancer-related pathways, including pathways in cancer, endocrine resistance, PD-L1 expression and PD-1 checkpoint signaling, T-cell receptor signaling, endocrine function, and immune responses. Machine learning algorithm selection identified the combined CoxBoost-Ridge approach as the optimal predictive model (achieving a training set concordance index (C-index) of 0.77). This model identified eight key genes (CHRM3, GABBR1, CCR4, KCNN4, PRKCE, CYP2C9, HPGD, FASN), which were the top-ranked by coefficient magnitude in the prognostic model. The prognostic signature demonstrated robust predictive performance in two independent external validation cohorts (C-index = 0.74 in cBioPortal; C-index = 0.81 in E-MTAB-1980). Furthermore, molecular docking analyses predicted strong binding affinities between BPA and these key targets (Vina scores all <−6.5 kcal/mol), suggesting a potential mechanism through which BPA may modulate their activity to promote renal carcinogenesis. Collectively, These findings suggested potential molecular mechanisms that may underpin BPA-induced ccRCC progression, generating hypotheses for future experimental validation. Conclusions: These findings enhance our understanding of the molecular mechanisms by which BPA induces ccRCC and highlight potential targets for therapeutic intervention, particularly in endocrine and immune-related pathways. This underscores the need for collaborative efforts to mitigate the impact of environmental toxins like BPA on public health.

13 November 2025

Venn diagram of the targets of BPA and ccRCC. The Venn diagram illustrates the intersection between BPA-related targets (blue) and renal cell carcinoma disease targets (yellow). The blue circle represents 192 BPA-related targets, which intersect with 5954 ccRCC-related targets, identifying 114 potential toxicity targets (grey region) that may mediate BPA-induced ccRCC progression.

Long noncoding RNAs and microRNAs in Endometriosis

  • Edi Muhaxhiri,
  • Maruša Debeljak and
  • Katarina Trebušak Podkrajšek
  • + 1 author

Endometriosis represents a prevalent gynaecological disorder, impacting around 10% of the female population and affecting as many as 50% of women who are facing challenges with infertility. The pathogenesis of the disease encompasses intricate processes such as the formation of adhesions, degradation of the extracellular matrix, angiogenesis, increased cell proliferation, impaired apoptosis, and dysregulation of the immune response. Although endometriosis is common, its precise etiology remains unidentified, despite various hypotheses being suggested. Recent findings underscore the significance of non-coding RNAs, specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), which have been identified as important regulators in the development of endometriosis. This literature review integrates findings from various transcriptomic and molecular studies to distinguish between lncRNAs and miRNAs that are associated with direct pathogenic roles and those that simply represent altered gene expression profiles in endometriosis. Particular long non-coding RNAs, such as H19, MALAT1, and LINC01116, are associated with chromatin remodeling, functioning as competitive endogenous RNAs, and influencing critical signaling pathways. Concurrently, specific microRNAs, including the miR-200 family, miR-145, and let-7b, seem to govern processes like epithelial-to-mesenchymal transition, angiogenesis, and cell adhesion. The findings highlight the significant potential of non-coding RNAs to serve as biomarkers for diagnostic purposes and as innovative therapeutic targets. Subsequent research endeavours ought to focus on corroborating these findings and elucidating the specific pathogenic roles of these non-coding RNAs in the context of endometriosis.

13 November 2025

Over the past decade, interest has grown in understanding the morphofunctional changes that mesenchymal stem cells (MSCs) undergo due to age-associated senescence—a process particularly relevant given that adults and elderly individuals are the primary candidates for regenerative therapies. This study addresses this knowledge gap by systematically analyzing the influence of age-related senescence on the morphofunctional properties of MSCs derived from the oral cavity. A scoping review was conducted following the PRISMA-ScR guidelines. The databases searched were MEDLINE, SCOPUS, and Web of Science. In vitro studies were included if their primary objective was to investigate oral cavity mesenchymal stromal cells and age-related senescence. A total of 455 studies were identified, of which 17 were selected. Studies on MSCs from the oral cavity have shown that age-related senescence, starting around 35 years, reduces proliferation, viability, clonogenic capacity, and differentiation potential—particularly toward osteogenic and chondrogenic lineages—with higher values observed in younger individuals. However, MSC surface markers remain stably expressed and show no association with aging. Some studies also report no significant differences in proliferation rate or cell doubling time at early passages, and MSCs retain some plasticity at these stages. Despite age-related limitations, oral MSCs from elderly donors remain a promising therapeutic source, especially at early in vitro passages. Further research is needed to explore innovative strategies to enhance the regenerative potential of oral MSCs from older donors.

13 November 2025

The Kidney in the Shadow of Cirrhosis: A Critical Review of Renal Failure

  • Livia-Mirela Popa,
  • Paula Anderco and
  • Oana Stoia
  • + 2 authors

Hepatorenal syndrome (HRS) is a high-mortality, potentially reversible form of kidney failure that arises from a tight hemodynamic–inflammatory coupling in cirrhosis. Contemporary redefinitions prioritize creatinine kinetics over static thresholds and recognize non-acute kidney injury (AKI) functional phenotypes, enabling earlier recognition but heightening the need for precise etiologic triage. This narrative synthesis integrates current concepts across pathophysiology, diagnosis and management. Portal hypertension, bacterial translocation and inflammatory mediators amplify splanchnic vasodilation and effective arterial underfilling. Compensatory neurohumoral activation precipitates renal vasoconstriction, intrarenal microcirculatory dysfunction and sodium–water retention. The pivotal diagnostic fork remains HRS–AKI versus acute tubular necrosis. A pragmatic, tiered strategy, structured volume assessment, filtration markers and a parsimonious tubular-injury panel offer actionable discrimination, whereas fractional excretion indices serve as adjuncts only. Initial therapy should be bundled and time-sensitive: remove nephrotoxins, treat infection and initiate albumin plus a vasoconstrictor. The transplant strategy should default to isolated liver transplantation unless end-stage renal disease is established. Future priorities include validated biomarker cut-offs, ultrasound-guided volume algorithms and pathway-based trials to reduce diagnostic delay and improve survival.

13 November 2025

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Biomedicines - ISSN 2227-9059