Biology Direct最新文献

Background: RNAs fold into complex structures that critically influence gene expression. A prominent class of regulatory elements resides in the 5' untranslated region (5' UTR), where internal ribosome entry sites (IRESs) promote cap-independent translation by directly engaging the ribosome. First discovered in viral genomes, IRESs have been classified into four types according to their structural compactness and factor requirements. While viral IRESs are well studied, cellular IRESs remain poorly understood: they display limited sequence conservation, reduced structural compactness, and variable dependence on auxiliary RNA-binding proteins known as IRES trans-acting factors (ITAFs). Whether their activity relies mainly on RNA structure or protein assistance remains unresolved. Here, we present a computational framework that combines in silico mutagenesis and RNA-protein interaction profiling to investigate IRES mechanisms and guide the design of synthetic elements.

Results: Using the Hepatitis C Virus (HCV) IRES as a benchmark, we performed systematic single-nucleotide mutagenesis coupled with structural predictions. Mutations were classified as synonymous or non-synonymous based on their effect on the secondary structure. The HCV IRES showed overall robustness, but the domain interacting with eIF3 was particularly sensitive, consistent with its essential role in translation initiation. Extending this approach to other viral IRES families revealed distinct profiles of resilience: Aphthoviruses retained structural integrity despite extensive sequence variation, whereas Cripaviruses displayed higher variability. We then applied the same analysis to cellular IRESs, which proved to be more structurally sensitive, suggesting stronger reliance on cofactor support. To probe this connection, we used the catRAPID approach to predict interactions with translation-related proteins. The method distinguished IRESs with known ITAF binding, such as PTBP1, and highlighted stability-promoting mutations that increased the predicted affinity for translation factors.

Conclusions: Our in silico analysis indicates that mutational tolerance mirrors IRES cofactor dependence: compact viral IRESs are structurally robust, whereas non-viral IRESs are more reliant on protein interactions. By linking structure prediction with interaction profiling, we identify variants that both stabilize IRESs and improve binding to ITAFs or translation factors. This framework provides mechanistic insight into sequence-structure-function relationships and supports the rational design of synthetic IRES elements for therapeutic and biotechnological applications.

Autophagy - the cell's built-in recycling and quality-control programme - touches every layer of cutaneous biology. In keratinocytes it sculpts the cornified envelope; in melanocytes it balances pigment synthesis and oxidative stress; in immune and appendageal cells it fine-tunes defence, repair and hair-follicle cycling. When this choreography falters, skin disorders emerge. This review journeys from basic mechanisms (ULK1 signalling, Beclin-1/VPS34 nucleation, LC3B lipidation, selective mitophagy) to their fingerprints in health and disease. We dissect how autophagy malfunctions drive psoriasis hyper-proliferation, atopic-dermatitis barrier leakiness, vitiligo depigmentation and the metabolic rewiring of melanoma. Non-melanoma cancers, infectious dermatoses, wound repair, ageing and photo-damage are mapped onto the same autophagic atlas. Therapeutically, the pathway is a double-edged sword. mTOR or caloric-restriction mimetics jump-start a protective flux; chloroquine derivatives and ULK1 blockers clip tumour survival circuits; cannabinoids, photodynamic therapy and immune-checkpoint combinations exploit context-specific toggling between induction and brake. Emerging biomarkers (LC3B-II, p62, AMBRA1) promise patient-stratified interventions. By weaving together molecular detail, pre-clinical insight and clinical translation, we show why autophagy is no longer a backstage process but a star player in dermatology - and how targeting its switches could reshape future treatment algorithms.

Background: Peripheral artery disease (PAD), caused by atherosclerosis resulting in reduced blood flow in the lower extremities, impairs both skeletal muscle mass and function in humans, and its molecular mechanism is not clear. Recent studies have demonstrated that Nicotinamide phosphoribosyl transferase (NAMPT) influences skeletal muscle mass and function by modulating NAD⁺ levels and cellular Ca²⁺ homeostasis. However, its role in muscle fiber type transition remains to be elucidated.

Results: NAMPT is downregulated in ischemic skeletal muscle and CoCl₂-treated C2C12 myotubes. NAMPT enhances the functional performance of ischemic limbs, reduces apoptosis, increases the formation of oxidative muscle fibers, and improves mitochondrial function. The cGMP‒PKG pathway is activated by NAMPT in ischemic limbs. Exogenous inhibition of cGMP-PKG signaling inhibits the formation of oxidative muscle fibers induced by NAMPT.

Conclusions: NAMPT protects against ischemic limb injury via the cGMP‒PKG signaling pathway, suggesting that it is a promising therapeutic and predictive target for myopathy associated with PAD.

Clinical trial number: Not applicable.

Background: Disruption of circadian rhythm (DCR) has been connected with breast cancer (BC) susceptibility; whereas it is unclear whether status of key clock genes could be used in predicting BC prognosis, tumor immune microenvironment, and immunotherapy responses.

Results: Circadian clock genes demonstrate significant dysregulation in BC, where elevated CLOCK expression emerges as an independent prognostic factor strongly correlated with adverse clinical outcomes. CLOCK-overexpressing BC cells exhibit enhanced proliferative ability and strong resistance to chemotherapy drugs doxorubicin and gemcitabine. High CLOCK expression correlates with reduced CD8⁺ T cell infiltration and increased M2 macrophage polarization, consistent with increased immune checkpoint molecule PD-L1 expression in the TCGA BC dataset. Additionally, patients with high CLOCK expression display lower Tumor Immune Dysfunction and Exclusion (TIDE) score. Mechanistically, RNA-sequencing identified suppressed NF-κB, TNF, MAPK pathways, and PD-L1 expression in sh-CLOCK MCF-7 cells. Subsequent in vitro validation demonstrated that CLOCK mediates NF-κB p65 acetylation at K56 site, potentiating its transcriptional activation of PD-L1, thereby facilitating immune evasion in BC.

Conclusions: CLOCK functions as a critical prognostic biomarker in BC by promoting tumor proliferation, chemoresistance, and immune evasion. Mechanistically, CLOCK mediates NF-κB p65 acetylation to enhance PD-L1 transcription, promoting immune evasion in BC.

Ca²⁺ signaling is essential for neuronal development, migration, synaptic activity, spine plasticity, neurotransmitter release, membrane excitability, and long-term synaptic plasticity, as well as for the coupling between membrane depolarization and downstream signaling. Traditionally, Plasma Membrane Ca²⁺ ATPases (PMCAs) were considered high-affinity, low-capacity calcium extruders. However, recent evidence reveals that the PMCA-Neuroplastin complex facilitates ultrafast Ca²⁺ clearance at kilohertz frequencies, reshaping our understanding of calcium regulation, in particular in neurons. For bulk Ca²⁺ clearance, they are overshadowed by more powerful low-affinity/high-capacity systems on the plasma membrane. This raises key questions: what is the specific physiological and pathological role of PMCAs? Why do cells require a high-affinity/low-capacity, ATP-dependent extrusion mechanism? What is the functional meaning of the diversity of isoforms (four) and splice variants (over thirty)? And why do neurons localize distinct PMCA pumps to pre- and postsynaptic sites? The prevailing hypothesis is that PMCAs fine-tune Ca²⁺ microdomains through local regulation and interactions with specific protein partners. Finally, understanding their role in Purkinje cells (PCs) is particularly relevant, as alterations in PMCA function have been implicated in cerebellar pathology and ataxia.