International Journal of Molecular Sciences

Mitofusin 2 (MFN2), a key outer mitochondrial membrane GTPase, regulates mitochondrial fusion, mitophagy, calcium homeostasis, and cellular bioenergetics. This study investigated the role of MFN2 variants in patients with Dilated Cardiomyopathy (DCM) using whole-exome sequencing (WES) of 5 familial and 10 sporadic DCM cases. A rare de-novo MFN2 variant, c.932A>G (p. N311S), was identified in a DCM patient, which is absent in 100 healthy controls as well as in the 1000 Genomes, IndiGenomes, databases while it shows very low MAF (0.0000081) in gnomAD. Structural modelling predicted the variant to be highly deleterious and revealed marked conformational distortion of the mutant protein (RMSD = 8.95 A). Molecular docking further showed a weakened interaction between MFN2-N311S and PRKN (Parkin), indicating impaired mitophagy and defective mitochondrial quality control. Moreover, functional analysis in stable H9c2 cardiomyoblast cell lines demonstrated significantly reduced MFN2 mutant protein expression, extensive mitochondrial clustering and fragmentation. The mutant protein also indicated significant reduction in mitochondrial membrane potential, ATP production, and oxygen consumption rate (OCR), together with elevated cytosolic Ca2+ and reactive oxygen species (ROS) levels. qRT-PCR analysis further revealed activation of the PI3K/AKT/mTOR signalling pathway and increased expression of hypertrophic markers Myh6, Nppa, Nfatc1, and Nfatc2. The above findings collectively highlight the significant impact of the MFN2 mutation on mitochondrial dynamics and cellular health, suggesting a significant correlation with the pathogenesis of DCM. This finding could further open a door to develop a potential therapeutic target for DCM.

The synthesis of mitochondrial-encoded polypeptides is an essential process, primarily regulated at the posttranscriptional level. In yeast, many regulatory factors have been described as acting in proximity to the mitoribosome to promote efficient translation; however, the precise mechanisms by which these components function remain largely unknown. Here, we expand on findings concerning a previously studied mitoribosome interactor, Mrx9, which is found in large expressosome-like assemblies of mitoribosome clusters. Mrx9 was initially linked to mitochondrial translation and was suggested to be associated with the splicing of COX1 and COB transcripts. Our current data show that Mrx9 is associated with the PHB/m-AAA complex at the polypeptide exit tunnel of the mitoribosome. Overexpression of Mrx9 impairs the proteolytic functions of Yta10 and Yta12 within the prohibitin complex, leading to splicing defects; accumulation of aberrant polypeptides; and a noticeable impairment in the processing of the essential mitoribosomal protein bL32m. These findings support a regulatory role for Mrx9 in the PHB/m-AAA complex by modulating the activities of both Yta10 and Yta12.

Background: Chronic lowgrade inflammation in long standing rheumatoid arthritis (RA) contributes not only to joint damage but also to metabolic dysregulation, endothelial dysfunction, and elevated cardiovascular (CV) risk. Although combination disease modifying anti rheumatic drugs (DMARDs) remain the mainstay of therapy, their long term efficacy in controlling systemic inflammation and preventing metabolic complications appears limited. Phytochemicals such as resveratrol, a polyphenolic compound widely used in traditional and complementary medicine, possess anti inflammatory and immunomodulatory properties. Objectives: To investigate whether resveratrol can complement the immunomodulatory effects of combination DMARDs in long duration RA patients by modulating inflammatory cytokines and the JNK-IRS-Akt insulin signaling axis. Methods: This study enrolled early and late rheumatoid arthritis patients to assess disease activity, vascular markers, and ex vivo PBMC responses. PBMCs were isolated for cytotoxicity testing and resveratrol treatment, followed by ELISA and Western blot analysis. Statistical comparisons evaluated immunomodulatory effects and alterations in inflammatory signaling. Results: Longitudinal follow up of RA patients showed significant first year improvement in disease activity and atherosclerotic markers, correlated with MTX dose. An early versus late RA comparison revealed elevated cytokines and enhanced JNK mediated stress signaling in longstanding disease. Resveratrol maintained PBMC viability, reduced LPS induced TNF&alpha and adipokine levels, and downregulated pJNK and GSK&beta, indicating targeted anti inflammatory modulation independent of Akt activation. Conclusion: Chronic RA showed persistent inflammatory and metabolic dysregulation driven by JNK-NF&kappaB activation. Resveratrol reduced cytokines, corrected adipokine imbalance, and selectively inhibited JNK, suggesting adjunct therapeutic value alongside DMARDs for improving immunometabolic disturbances in long-standing RA.

Individuals carrying a G4C2 repeat expansion in C9orf72 can develop amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD), at various and unpredictable ages. The contribution of the expansion to this extreme clinical variability remained a matter of debate. In this work, we validated the use of optical genome mapping to efficiently size this expansion from blood and applied this method to a cohort of 54 repeat expansion carriers including patients with FTD (n = 23), ALS (n = 22) and presymptomatic individuals (n = 9). Despite the high variability in expansion profiles, distinct groups can be inferred. Although consensus repeat profiles were similar between FTD and ALS patients, relationships between repeat number, indexes of repeat instability, and the age at sampling differed between clinical conditions. An age at sampling-dependent increase of repeat instability in blood was observed in presymptomatic carriers and FTD patients (p = 0.01 and p = 0.04 respectively), in contrast to patients with ALS (p = 0.9). The proportion of shorter repeats ([500-1500 repeats]) increased with the age at sampling in ALS patients but decreased in presymptomatic and FTD cohorts, while the proportion of larger repeats (>2000 G4C2), in particular those exceeding 4000 repeats, increased along with the age at sampling in presymptomatic carriers and FTD cases (p <1.10-e4 and p = 0.006 respectively) conversely to patients with ALS (p = 0.98). In conclusion, this work strongly supports different dynamics of repeat instability of the C9orf72 pathogenic expansion in blood linked to the clinical evolution. These findings provide new insights into the relationship between expansion profiles and clinical variability.

Mutations in p53 and its 12 isoforms can alter its functions. As N-terminally truncated isoforms of p53 (delta40p53, delta133p53, and delta160p53) participate in tetramer formation, they are important regulators of cancer fate. Although delta40p53- and delta133p53-mediated regulation of cancer is well reported, the mechanism underlying delta160p53 production and its functional role remains unclear. We investigated the internal ribosomal entry site (IRES)-mediated translation of {Delta}160p53 and its role in cancer regulation. As differential synthesis of delta160p53 was observed under different stress conditions, IRES-mediated translation of this isoform was demonstrated using bicistronic luciferase constructs. No cryptic promoters or splicing sites were detected in the IRES sequence. Cell death and late apoptosis were significantly decreased, while proliferation, the number of cells in the S phase, and drug resistance were induced by delta160p53. Furthermore, delta160p53 did not induce p53-responsive promoters. RNA sequencing analysis of delta160p53 overexpression showed similar results, along with the inhibition of other tumor suppressor genes. Overall, our results provide insights into IRES-mediated translation of delta160p53, which can be considered a novel target for cancer treatment.

The TMEM16 family of calcium-activated phospholipid scramblases (CaPLSs) and chloride channels (CaCCs) performs diverse physiological functions that include regulation of blood coagulation and apoptotic signaling, through a shared ten-transmembrane-helix (TM) architecture organized around a hydrophilic lipid-translocating groove. Mechanistic studies of TMEM16 family members have been hampered by the absence of a unified positional reference framework that would permit direct comparison of structurally equivalent residues across paralogs with different sequence numbering systems. Here we introduce a generic numbering scheme for TMEM16 scramblases (GNS-TMEM16), modeled on the Ballesteros & Weinstein system established for class A G protein-coupled receptors. A reference alignment (TMEM16-RA) was constructed from twelve human and mouse TMEM16 scramblases (TMEM16C/D/E/F/G/J) using structure-based ClustalW alignment of the ten TM helices. From this alignment, a TM-specific reference residue (TsRR) was identified for each helix by hierarchical application of three criteria: (1) 100% conservation in the core TMEM16-RA; (2) conservation in an augmented reference alignment (TMEM16-ARA) incorporating a group of phylogenetically more distant homologs composed of nhTMEM16, afTMEM16, TMEM16K, TMEM16A, and TMEM16B; and (3) structural and functional considerations, including helix-perturbing character, groove localization, conserved motif membership, and central TM position. The resulting ten TsRRs are Y1.50, W2.50, R3.50, E4.50, F5.50, P6.50, E7.50, D8.50, W9.50, and E10.50, and are illustrated in mTMEM16F. Each residue is assigned the identifier N.m(k), where N is the TM number, m is the position relative to the TsRR (for which m = 50), and k is the absolute sequence number. Loop residues receive dual identifiers referenced to the TsRRs of both flanking helices. Application of the GNS-TMEM16 is illustrated with the comparisons of the groove-opening measurements using pairwise distances between residues identified by their N.m indices to be corresponding across mTMEM16F, afTMEM16, and nhTMEM16. The results bring to light the advantages of corresponding residues identification in different TMEM16 proteins and show that the mammalian scramblase undergoes substantially larger separation at the extracellular groove entrance than either fungal homolog. Comparison of mutagenesis data guided by N.m correspondence shows at the conserved (E3.55,R6.26) salt-bridge locus, Ala substitution reduces activity more than 100-fold in nhTMEM16 but less than 2-fold in afTMEM16, illustrating that the GNS identifies structural equivalence of position without implying functional equivalence of the residue, which is a distinct advantage of GNS in providing mechanistic interpretation across paralogs. Also described is a protocol for extending the GNS-TMEM16 to uncharacterized protein sequences, including AlphaFold-predicted models, using structural superposition to mTMEM16F. Thus, the presented GNS-TMEM16 provides a stable positional reference for the integration and comparative analysis of structural, computational, and functional data across the TMEM16 family, utilizing a construction strategy applicable to yet other polytopic membrane protein families sharing a common transmembrane fold.

Neurodegenerative diseases are a major threat to older adults and represent a growing global health burden as the elderly population continues to expand. The complexity of neurodegenerative diseases and the incomplete understanding of their pathophysiology limit the development of effective therapeutics. To study common neurodegenerative mechanisms and accordingly potential drug targets across Alzheimers, Parkinsons, and Huntingtons diseases, transcriptomic profiles of patients with each disease were analyzed to detect common differentially expressed genes and common enriched pathways. Common differentially expressed genes involved in the shared pathways were identified as key drug targets and validated in silico to study the impact of their dysregulation. Three pathways were enriched and upregulated across the three diseases, along with 274 common differentially expressed genes. Two of the shared pathways were involved in activation of the transcription factor nuclear factor kappa B (NF-{kappa}B), indicating inflammatory signaling. The third pathway involved regulation of BCL2L11 transcription by RUNX3, which contributes to the protective effect of neurodegenerative diseases against cancer. Five key drug targets were identified: NFKBIA, NFKB1, RELA, TRIM4, and SMAD4. They were significantly upregulated across all three diseases and involved in the shared pathways. Drugs that target the expression of these genes and previously approved by Food and Drug Administration were reported for treatment repurposing for the three neurodegenerative diseases. The resultant drug list included the conventional and commonly safe antihyperlipidemics, antihypertensives, antidiabetics, analgesics, diuretics, antiparkinsons, and antipsychotics.

BackgroundThe variants G1 and G2 within the APOL1 gene confer a higher risk of APOL1-mediated kidney disease (AMKD) whilst associated with an evolutionary advantage against trypanosome-mediated sleeping sickness. MethodsIn this study, we analysed transcriptome data of kidney biopsies from FSGS patients with the APOL1 high-risk (HR) and low-risk (LR) variants and compared it to cellular models based on patient-specific podocytes, HEK cells with engineered over-expressing HR variants and HR variant single-cell-RNA-seq data from kidney organoids. ResultsWe identified a signature of up- and down-regulated genes between biopsies from FSGS patients with APOL1 HR and LR variants. The up-regulated genes are functionally annotated to be associated with Calcium and mTOR signaling, whilst the down-regulated genes with inflammatory and immune response pathways. These pathways were confirmed by comparing with cellular models. Analysis of small molecules reverting the IFN-{gamma} stimulated gene expression to the non-stimulated gene expression in genome-edited APOL-G1 kidney organoids revealed several putative candidates such as the mTOR inhibitor AZD-2014. ConclusionWe have unveiled a signature of up- and down-regulated genes between APOL1 HR and LR kidney biopsies which could be assigned as associated with Calcium and mTOR signaling and down-regulated immune response.

Background Intervertebral disc degeneration (IDD) is a leading cause of chronic low back pain and disability worldwide, affecting most individuals over 50 years of age. Despite its prevalence, no disease-modifying therapies exist, and current interventions are limited to reducing pain. Cellular senescence and the associated secretory phenotype (SASP) have been increasingly recognized as major drivers of disc matrix degradation and inflammation. However, the upstream molecular mechanisms that lead to IDD degeneration are still unknown. Connexin 43 (Cx43), a gap junction protein implicated in progression of age-related diseases, has emerged as a key regulator of cellular senescence and inflammatory signalling in musculoskeletal tissues. Methods Human primary cells were isolated from intervertebral disc samples obtained from patients classified into clinically meaningful groups: healthy controls, chronic/mechanical degeneration (DDD, ADJ, ASD), and acute/inflammatory event (herniated nucleus pulposus, HNP). Cx43 expression was assessed by qPCR and Western blotting. Cellular senescence was evaluated through SA-{beta}-gal staining and analysis of p53/p21 expression. SASP factors and EMT-related markers were measured by qPCR. Protein expression was quantified by immunoblotting across different age groups and degeneration grades. Results In this current study Cx43, was identified as the most abundant connexin isoform in human intervertebral discs, showing a progressive increase in expression with age and disc degeneration. Also, high Cx43 expression correlated with increased expression of the senescent markers p53 and p21 and increased SA-{beta}-gal activity. Besides, increased expression of EMT-related and differentiation markers has been correlated with high Cx43 levels in human IDD samples, consistent with fibrotic remodeling processes. Conclusions These findings identify aberrant upregulation of Cx43 signaling as a potential mechanistic link between intervertebral disc cellular senescence and extracellular matrix degradation, with the ensuing inflammatory response, representing a novel potential therapeutic target to modulate senescence-driven pathogenesis and modulate IDD progression.

Abstract Optic Atrophy 1 (OPA1), an important inner mitochondrial membrane GTPase, regulates mitochondrial fusion, maintains cristae structure, calcium buffering, cellular bioenergetics, preserves mtDNA and controls apoptosis. Here we examined the role of OPA1 variants in DCM using whole-exome sequencing (WES) of 5 familial and 10 sporadic DCM cases. A rare de novo OPA1 variant, c.563C>T (p.Pro188Leu), was identified in a DCM patient, which is absent in 100 healthy controls as well as in the 1000 Genomes, IndiGenomes and GenomeAsia 100k databases while it showed very low MAF (0.000069) in GnomAD. Structural modelling predicted the variant to be highly deleterious and revealed marked conformational distortion of the mutant protein (RMSD = 3.5 Angstrom). Molecular docking further demonstrated enhanced accessibility of mutant OPA1 to mitochondrial protease OMA1, suggesting increased OPA1 proteolytic processing and a consequent increase in mitochondrial fragmentation. Functional analysis in stable H9C2 cardiomyoblast cells, demonstrated significantly reduced OPA1 protein expression, extensive mitochondrial fragmentation in mutant-OPA1 expressing cells. The mutant protein caused significant reduction in mitochondrial membrane potential, ATP generation, and oxygen consumption rate (OCR), together with elevated cytosolic Calcium and reactive oxygen species (ROS) levels. qRT-PCR analysis further revealed depletion in mtDNA copy number and increased in expression of intrinsic apoptotic markers Caspase3, 9 and Bax/Bcl-2 ratio. The above findings collectively highlighted the significant impact of the OPA1 mutation on mitochondrial dynamics and cellular health, suggesting a significant correlation with the pathogenesis of DCM. Collectively, these findings suggest that OPA1-mediated mitochondrial dysfunction represents a potential therapeutic avenue for the management of DCM.

Ultraviolet-C (UV-C) radiation is a potent environmental stressor that induces DNA damage, accumulation of reactive oxygen species (ROS), and cellular dysfunction. This also initiates coordinated molecular responses to regulate cellular adaptation and recovery. Small extracellular vesicles (sEVs) have emerged as key mediators of intercellular communication through the selective incorporation of microRNAs (miRNAs), proteins, and lipids. However, the temporal changes of sEV-associated cargo during the progression from UV-C-induced damage to recovery remain uncharacterized. We hypothesised that UV-C exposure induces stage-specific changes in sEV cargo (miRNA and proteins) that promote the transition of cells from damage to the response and recovery phases. To examine this, a time-resolved UV-C exposure model was established using Caenorhabditis elegans (C. elegans). In this paper, we studied 2.5 hours of UV-C exposure, including cellular damage, intracellular ROS levels, and DNA integrity, to define the damage and repair state. Based on these temporal variations, samples were collected: i) immediately after exposure, ii) 6 hours post-exposure, and iii) 16 hours post-exposure were designated as damage, response, and recovery conditions, respectively. sEVs isolated from whole-worm preparations were characterised using biophysical and molecular approaches, followed by miRNA sequencing and proteomic analyses. Integrative analysis further identified miRNA-protein associations and associated them with pathways involved in stress adaptation, metabolism, signal transduction, and cellular homeostasis. Collectively, these findings provide a temporal molecular framework of sEV cargo associated with UV-C-induced damage, response, and recovery in C. elegans. Overall, this study identified candidate molecular signatures and miRNA-protein associations that underlie the temporally selective packaging of sEV-associated cargo following UV-C-induced damage, providing a basis for future tissue-specific and mechanistic investigations.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterised by a highly immunosuppressive tumour microenvironment and limited therapeutic responses. Tumour-derived extracellular vesicles (EVs) contribute to PDAC progression by transferring immunomodulatory molecules and tumour-associated signals, suggesting EV-associated processes as potential intervention opportunities. However, the heterogeneity of EV biology and the complexity of tumour-immune interactions make single-target intervention strategies challenging. Here, we developed a computation-driven dual-layer candidate-prioritisation framework to identify potential modulators associated with PDAC EV-mediated immune escape through complementary production-side and action-side strategies. For the production-side layer, we focused on upstream processes related to EV biogenesis, cargo regulation, inflammatory signalling, and tumour-associated pathways. An 88-gene PDAC EV-associated target framework was integrated with cell-type-resolved prognosis annotations from ctPANDA and predicted targets of 18 natural products derived from Scutellaria baicalensis, Epimedium spp., and Cornus officinalis to prioritise natural-product candidates with disease relevance and potential chemical tractability. In parallel, key targets with experimentally resolved ligand-binding structures were subjected to pocket-guided de novo small-molecule design based on co-crystal ligand-defined binding sites, followed by structural, docking-based, and physicochemical screening of generated compounds. For the action-side layer, VHH and scFv binders were computationally designed and screened against extracellular regions of MET and CD81 to prioritise candidates potentially suitable for EV recognition and capture. This study provides a computational strategy for narrowing candidate spaces across both EV-associated production pathways and released vesicle recognition. The resulting small molecules, antibody-like binder models, and screening workflows provide a resource for future experimental validation of strategies targeting PDAC EV-associated immune regulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/740294v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@11829b0org.highwire.dtl.DTLVardef@158efb5org.highwire.dtl.DTLVardef@1e17cc5org.highwire.dtl.DTLVardef@c69696_HPS_FORMAT_FIGEXP M_FIG C_FIG

Introduction: In both humans and experimental animals, obesity is associated with hypothalamic inflammation and neuronal metabolic dysfunction, which contribute to disrupting body energy homeostasis. Although ciliary neurotrophic factor (CNTF) is a neuroprotective cytokine with recognized anti-obesity effects in peripheral metabolic tissues, its role in obesity-associated hypothalamic dysfunction is still poorly characterized. We investigated whether CNTF exerts any direct effects on mHypoE-N41 (N41) hypothalamic neurons and whether it modulates the effects induced by palmitate (PA), an established model of obesity-associated neuronal metabolic dysfunction. Methods: N41 cells were administered CNTF alone or combined with PA to assess whether CNTF affects PA-induced lipotoxic stress. Gene and protein expression was assessed by qRT-PCR, western blotting, and immunofluorescence analysis. Results: In N41 cells, CNTF activated the STAT3, ERK and AMPK signaling pathways. It also upregulated genes involved in mitochondrial metabolism and fatty acid oxidation, including Ucp2, Cpt1 and Pgc1, as well as the proliferation-associated markers Ki-67 and PCNA. PA treatment induced inflammatory and endoplasmic reticulum stress responses and impaired insulin signaling. In PA-treated N41 cells, CNTF significantly attenuated the expression of pro-inflammatory markers Tnf, Mcp1 and Nfkb, restored insulin-induced AKT phosphorylation, and partially reversed PA-induced changes in the expression of metabolic genes Ucp2 and Cpt1. Conclusions: Collectively, these findings indicate that CNTF exerts direct protective metabolic effects on hypothalamic N41 neurons subjected to lipotoxic stress and supports a role for it in the preservation of neuronal metabolic function under obesogenic conditions.

Oligodendrocytes play an essential role in axonal metabolic support and myelination, and their dysfunction is associated with amyotrophic lateral sclerosis (ALS). LINGO1 is a major inhibitor of oligodendrocyte differentiation and axonal regeneration, identified as a promising therapeutic targeted for inflammatory demyelinating diseases. Here, we investigated the expression pattern of LINGO1 in the well-established SOD1(G93A) transgenic mouse model of ALS. We show that LINGO1 protein expression is significantly elevated in both grey and white matter of the mutant spinal cord during both the symptomatic and end stages of the disease. LINGO1 is also notably co-expressed with astroglial and neuronal markers. However, neither the levels of LINGO1 transcripts, nor levels of microRNAs predicted to regulate its expression were altered in the mutant spinal cord, suggesting the involvement of alternative regulatory mechanisms. Our analysis of microRNAs revealed in the mutant a significant downregulation of miR-138, a microRNA known to promote myelination. The differential expression of LINGO1 and miR-138 in ALS mice thus may drive deleterious processes during disease progression in adulthood. Moreover, our data show that white-matter pathology arises earlier than initially thought, as evidenced by significant alterations of oligodendrogenesis that manifest as early as postnatal day 5. Study of the molecular determinants of this developmental defect shows increased miR-138 expression, which may promote oligodendrocyte progenitor cell maturation and involve compensatory mechanisms. Overall, our work identifies disrupted expression of LINGO1 and/or miR-138 in brain during early oligodendrogenesis and at symptomatic disease stages. These findings open the way to further investigations that may consider miR-138 as a potential presymptomatic biomarker and LINGO1 as a therapeutic target to promote remyelination in the context of ALS.

The Epstein-Barr virus (EBV) is a highly prevalent virus worldwide that is associated with several lymphoid and epithelial malignancies. However, extensive research on EBV integral membrane proteins BILF1, LMP1 and LMP2, has been scarce due to their hydrophobic transmembrane domains. Our study applies the QTY code (glutamine, threonine, tyrosine) to design water-soluble analogs of BILF1, LMP1 and LMP2 with reduced hydrophobicity, where we systematically replaced hydrophobic amino acid residues leucine (L), isoleucine (I), valine (V), and phenylalanine (F) with structurally similar polar residues glutamine (Q), threonine (T), and tyrosine (Y). We retrieved their native sequences from UniProt, identified transmembrane domains using Protter, then performed QTY design through the Protein Solubilizing Server (PSS). We then predicted native and QTY structures using in silico prediction tools AlphaFold3, ColabFold, and Boltz-2. Our analyses demonstrate that despite significant protein sequence replacements in their transmembrane domains (54.15%-61.59%) and increased intrinsic solubility, the QTY analogs exhibited minimal changes in isoelectric point (0.00-0.15 decrease) and molecular weight (0.7-1.2 kDa increase). Additionally, structural superpositions between QTY analogs and native structures using PyMOL yield low RMSD values (0.217[A] -1.202[A]). Our results demonstrate the QTY codes ability to design detergent-free analogs of BILF1, LMP1 and LMP2 with substantially reduced hydrophobicity and aggregation propensity whilst preserving native-like structures. Our results may facilitate protein characterization studies, therapeutic research on EBV, and other protocols that typically require protein solubilization.

Obesity is a major public health challenge of the 21st century, particularly in low- and middle-income populations. Adipogenesis plays a central role in the development of obesity and associated metabolic disorders, as it determines adipocyte number, size, and function. The 14-3-3 protein family comprises seven paralogs in mammals that regulate multiple cellular processes, yet their specific roles during adipogenesis remain poorly understood. In this study, we characterized the expression profiles of 14-3-3 paralogs during the early and late stages of adipogenic differentiation using quantitative PCR under standard adipogenic differentiation medium and modified drug-supplemented conditions. We found that the expression of specific paralogs is strongly influenced by the composition of the differentiation medium. The absence of insulin led to an early increase in Ywhaz, which could not be maintained during late adipogenesis and was associated with impaired adipogenic differentiation. In contrast, stimulation with incretins in combination with insulin induced late expression of Ywhag and Ywhab paralogs and promoted the formation of a greater number of smaller lipid droplets. These findings indicate that individual 14-3-3 paralogs exert distinct and context-dependent effects on adipogenesis, highlighting their potential roles as modulators of adipocyte differentiation and metabolic function.

Deep learning structure predictors, most prominently AlphaFold2 (the field-standard tool benchmarked against throughout this study), have substantially expanded access to protein structural information, yet characteristically return a single static conformation per target. This is an incomplete representation of the binding-competent state for the many pharmacologically relevant targets whose recognition geometry is intrinsically dependent on receptor flexibility, including cryptic-pocket, induced-fit, and water-mediated binding mechanisms. We present a category-stratified, statistically powered benchmark comparing pose prediction from receptor conformational ensembles against AlphaFold2, used as a matched static-structure baseline, across 29 protein-ligand systems spanning cryptic-pocket, induced-fit, water-mediated, and autoimmune-indication target classes. Considering the most accurate pose available from each methods full candidate output, ensemble-derived poses achieved lower RMSD to the experimental structure than AlphaFold on 21 of 29 targets (72.4%), with a mean RMSD of 3.39 [A] versus 5.60 [A]: a clear, statistically decisive advantage (paired Wilcoxon signed-rank test, W = 93.0, p = 0.0060). Rather than being diffuse, this advantage was concentrated precisely where mechanistic theory predicts it should be: in induced-fit and water-mediated categories, the classes in which static-structure prediction is expected to be least representative of the bound state: a result that constitutes direct, quantitative confirmation of the ensemble hypothesis, not merely a favorable average. Independent assessment against a field-standard physical-validity framework confirmed that this accuracy gain was achieved without any trade-off in chemical or geometric realism. We further quantify, rather than assume, the extent to which this advantage is recoverable by fully autonomous pose selection, using a proprietary ensemble-aware scoring model with no access to the correct answer, and report a substantial, discriminative signal (cross-validated mean AUC 0.92) with a partial, and clearly characterized, recovery under the strictest accuracy criteria (mean AUPR 0.36), which we identify as the principal, now precisely quantified, determinant of near-term translational progress. Under this same fully autonomous, ground-truth-blind setting, AlphaFolds own top-ranked poses currently match or modestly exceed Mavchen-1s autonomously selected poses on strict success-rate criteria (e.g., 17.2% vs. 20.7% at the combined RMSD-and-validity threshold), a result we report without qualification as the clearest current benchmark for near-term development. Together, these results provide compelling, statistically rigorous evidence that conformational ensemble sampling is a mechanistically grounded and substantial source of improved pose accuracy relative to static-structure prediction, and establish a quantitative benchmark against which continued methodological development can be measured and demonstrably improved upon.

Adipose tissue is a key metabolic organ for carbohydrate and lipid metabolism. Multiple nutrient sensing pathways and metabolic enzymes operate in adipocytes to control energy production and lipid mobilization in response to physiological conditions. Important regulators of glycolytic and lipid metabolism in many species are members of the estrogen-related receptor (ERR) family of nuclear receptors. We previously showed that ERR is required for transcriptional regulation of glycolytic and pentose phosphate pathway enzymes in adult Drosophila females, consistent with what is observed in ERR mutant males and larvae. However, the cell-type specific targets of ERR in adipose and other tissues have not been fully elucidated. Here, using a modified targeted DamID approach (NanoDam), we identified ERR occupancy specifically in adult adipocytes at the loci that encode genes involved in glycolysis, the pentose phosphate pathway, and fatty acid metabolism. Overall, our results predict that ERR centrally functions in adipose tissue to regulate multiple metabolic pathways.

Immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown great promise in treating bladder cancer and are now part of the standard treatment for advanced disease. However, many patients still fail to respond to treatment and at present many biomarkers are assessed but have yet shown only limited results. Therefore, with the advent of combination treatments and the increase of immune related adverse event, the search for reliable predictive biomarkers is paramount. Using a multiplexed enhanced FRET-FLIM based technique (QF-Pro) we quantified the interaction of PD-1/PD-L1, CTLA-4/CD80 and TIGIT/CD155 immune checkpoints in a pre-treatment TMA of 46 patients treated with atezolizumab. The association between higher PD-1/PD-L1 ICP interaction state and treatment efficacy was demonstrated in the male sample cohort, where it identified patients with better PFS. Conversely, patients exhibiting higher CTLA-4/CD80 engagement had a worse response to atezolizumab. Remarkably, the dual assessment of patients with high PD-1/PD-L1 and low CTLA-4/CD80 allowed to identify the best responders. These results indicate that the monitoring of patients immune profile in urothelial carcinoma might be critical in identifying patients who may benefit from combination therapy.

Inadequate autophagy promotes smoking-induced cellular senescence involved in chronic obstructive pulmonary disease (COPD) pathogenesis. Transcription factor EB (TFEB) is a master regulator of the autophagy-lysosome axis. For the first time, we investigated the therapeutic potential of pemafibrate, a putative TFEB inducer. COPD lung epithelial cells showed reduced TFEB expression. Pemafibrate enhanced autophagy/mitophagy flux and restored lysosomal acidification observed during cigarette smoke (CS) extract exposure in human bronchial epithelial cells, resulting in reduced cellular senescence. TFEB knockdown demonstrated involvement of pemafibrate-induced TFEB in these effects. Pemafibrate induced TFEB expression, mitigated alveolar enlargement and airflow obstruction, and attenuated the CS-induced increase in static lung compliance in a long-term CS-exposed mouse model. It reduced the CS exposure-induced cellular senescence, possibly through autophagy/mitophagy, as suggested by bulk RNA sequencing of mouse lungs. A retrospective cohort study showed that patients given pemafibrate displayed attenuated FEV1.0 decline compared with those given bezafibrate or fenofibrate. In conclusion, pemafibrate is a promising therapeutic agent for COPD, potentially exerting its effects through the regulation of the TFEB-autophagy/mitophagy-lysosome axis.