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.

Photobiomodulation (PBM) is a therapeutic approach based on illumination with red or near-infrared (NIR) light. Cytochrome c oxidase (COX), a terminal enzyme of the mitochondrial respiratory chain, contains copper centers (CuA and CuB) that absorb light within the red and NIR spectral range, making it a potential primary photoacceptor at wavelengths around 820 nm. PBM appears to be a promising strategy for the treatment and prevention of neurological disorders. Elucidating its precise molecular mechanisms may help optimize therapeutic outcomes. Using patch-clamp method, we showed that illumination with 820 nm light activates mitochondrial large-conductance calcium-activated potassium (mitoBKCa) channels in rat hippocampal mitochondria. Moreover, 820 nm light caused neuroprotective effect in NMDA-treated organotypic hippocampal cultures. Consistently, activation of mitoBKCa channel by 820 nm light illumination was observed in mitochondria isolated from glioma U-87 MG cells. To further investigate the role of mitoBKCa channel, we used CRISPR/Cas9- developed U-87 MG cells lacking the -subunit of the BKCa channel (dBK cells). Comparative transcriptomic analysis of illuminated wild-type and dBK cells revealed significant differences in gene expression profiles. In summary, our results show two types of cellular responses to the PBM. An acute effect involving activation of the mitoBKCa channel and a long-term effect associated with extensive transcriptome remodeling. Both mechanisms may contribute to the cytoprotective effect of 820 nm near-infrared light. HighlightsO_LI820 nm light activates hippocampal mitochondrial BKCa channels C_LIO_LI820 nm light induces hippocampal neuroprotection under excitotoxic conditions C_LIO_LI820 nm light causes intensive transcriptome remodeling in glioma cells C_LIO_LIBKCa channels modulate a subset of transcriptomic responses to 820 nm light C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/731043v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@5a5595org.highwire.dtl.DTLVardef@a8ddb2org.highwire.dtl.DTLVardef@72ec20org.highwire.dtl.DTLVardef@ec46da_HPS_FORMAT_FIGEXP M_FIG C_FIG

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome is a genetic disorder characterized by progressive neuromuscular and multisystem symptoms. MELAS typically manifests during childhood, can be difficult to diagnose, and has no cure. Extracellular vesicles (EVs) are lipid-enclosed nanoparticles secreted from cells that contain biological cargo and have demonstrated potential as biomarkers. We investigated the potential of plasma-derived EVs as diagnostic biomarkers of MELAS and examined their functional effects on mitochondrial respiration in treated skeletal muscle myotubes. Plasma-derived EVs were isolated from MELAS patients and age- and sex-matched control individuals, and biophysical characteristics and cargo of EVs analyzed. A Mito Stress Test was performed to assess oxygen consumption rate (OCR) in healthy myotubes treated with Control- or MELAS-EVs to determine the functional effects of circulatory EVs. Nine MELAS patients from two families were studied, and the results were categorized by age, sex and mtDNA heteroplasmy level. EV size and zeta potential remained unchanged. However, total EV concentration was higher in MELAS patients, particularly for small-EVs (<200 nm) and in younger patients (<25 years old). Relative protein yield per EV was lower in the MELAS group, especially among female and younger individuals. EV double-stranded DNA (dsDNA) concentration did not differ between MELAS- and Control-EVs overall, but was higher in male MELAS patients. Protein markers typically enriched in small-EVs showed altered expression in MELAS EVs: TSG101 and CD63 were lower, while flotillin-1 was higher compared to Control-EVs. A decrease in basal OCR was shown in cells treated with MELAS-EVs, with a similar response noted in the group treated with EVs from female MELAS patients. Post-treatment analysis showed no differences in oxidative phosphorylation (OXPHOS) subunit levels between cells treated with MELAS- and Control-EVs. In conclusion, plasma-derived EVs show promise as potential biomarkers for MELAS, and circulating EVs in this patient population may contribute to systemic metabolic dysfunction.

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.

Hereditary transthyretin amyloidosis (ATTRv) is driven by mutations that destabilize the native tetrameric transthyretin (TTR), promoting monomer formation and amyloid aggregation. The H88R variant has been considered fully monomeric, yet its behavior in heterozygous patients has remained unclear. Here, we demonstrate that H88R TTR can form hybrid tetramers with wild-type chains, both in vitro and in patient sera. We considered all possible tetramers, along with various trimer and dimer constructions, and found that the stability of hybrid tetramers containing one or two mutant chains is not significantly reduced in comparison with of the wild-type tetramer, suggesting a practically unhindered entry for H88R TTR monomers into such hybrid tetrameric assemblies, facilitating their secretion. Mass spectrometry confirms incorporation of H88R chains into tetramers in vitro, and show that the H88R TTR variant is present in the serum of carriers albeit in low concentration. We propose that the scarcity of this variant is the result of its retention in the endoplasmic reticulum and present a model for the association of H88R TTR with the endoplasmic reticule chaperone Binding immunoglobulin Protein (BiP). These findings revise the current monomeric view of H88R TTR, with direct implications for the efficacy of tetramer-stabilizing therapeutics. Our results highlight a delicate balance between cellular retention and hybridization, informing mechanistic understanding and treatment strategies in heterozygous ATTRv patients.

Significance Missense mutations can lead to pathological effects in human cells. Predictive methods that account for structural context, such as AlphaMissense, can provide pathogenicity scores. The accumulation of pathogenicity hotspots can reveal important structural features within individual proteins of protein families, such as GLUT transporters. Mapping pathogenicity scores onto the structure can thus provide a mechanistic explanation of the protein function necessary for its role in the cell. Abstract Non-synonymous amino acid substitutions (missense mutations) are common in the general population; some are causative of serious disease. Depending on their structural context, they can disrupt protein function, folding, or dynamics. Computational predictive methods developed in recent years, such as AlphaMissense, provide new insights into how missense mutations affect protein structure by predicting and mapping their pathogenicity across each amino acid in the human proteome. In this study, we identify recurring patterns of pathogenicity prediction across the GLUT family membrane transporters encoded by genes slc2a1-14. Within the GLUT transporter family, we observe higher pathogenicity profiles in the transmembrane domains, particularly in pore-lining and binding-site residues. Predicted missense pathogenicity is elevated throughout residues assigned to the central cavity, suggesting sensitivity of the transport pathway. Another finding shows higher pathogenicity in specific transmembrane helices of the protein, with the same pattern across all proteins. On the other hand, we observed lower pathogenicity values in some representatives of the GLUT family. These findings show that the pathogenicity of glucose transport within the GLUT family may be shaped by functional redundancy and physiological essentiality across GLUT groups.

BackgroundTriple-negative breast cancer (TNBC) is an aggressive subtype with limited therapeutic options. While PARP inhibitors, such as olaparib, show promise in BRCA1-deficient TNBC through synthetic lethality, up to 50% of patients fail to respond, highlighting the need to understand the molecular mechanisms underlying PARP inhibitors efficacy. Transposable elements (TEs), particularly LINE-1 elements, are increasingly recognized as modulators of genomic instability associated with DNA repair processes and potential key players in synthetic lethality. Here, we investigate the functional relationship between TE activity and olaparib treatment in TNBC with distinct BRCA1 functional status. MethodsWe performed comprehensive multi-OMICs analysis of four TNBC cell lines (two BRCA1-deficient: SUM1315 and MDA-MB-436; two BRCA1-proficient: MDA-MB-468 and BT549) treated with olaparib. We analyzed expression and differential expression of protein-coding genes, TEs, and gene-TE chimeric transcripts. Long-read whole-genome sequencing was employed to detect de novo TE insertions, complemented by a functional assay to quantify LINE-1 retrotransposition activity in olaparib-treated cells. ResultsOlaparib treatment induces extensive transcriptomic and genomic disorganization mediated by TEs, especially LINE-1, exclusively in BRCA1-deficient cells. We observed aberrant overexpression of both genes and TEs, including gene-TE chimeric transcripts harboring poison exons within tumorigenic genes and multi-exonic TE-TE chimeras capable of forming immunostimulatory double-stranded RNA (dsRNA) structures. Functional enrichment analyses revealed activation of antiviral immune pathways linked to LINE-1 activity. Consistently, orthogonal assays confirmed LINE-1 retrotransposition in BRCA1-deficient cells following olaparib exposure. ConclusionsOur findings demonstrate that olaparib treatment induces TE activation especially in BRCA1-deficient cells, a novel mechanism that may underlie synthetic lethality in TNBC. This TE activation triggers immune responses and genomic instability, providing new therapeutic opportunities through immunotherapy combinations and suggesting that TE activity may serve as a potential biomarker for treatment stratification of TNBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/738694v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@e8b202org.highwire.dtl.DTLVardef@fea1c5org.highwire.dtl.DTLVardef@12ea397org.highwire.dtl.DTLVardef@f60f1c_HPS_FORMAT_FIGEXP M_FIG C_FIG

Positron emission tomography (PET) tracers targeting amyloid-{beta} (A{beta}) are central to the diagnosis and staging of Alzheimers disease (AD). However, growing evidence indicates that these tracers can engage off-target molecules, complicating signal interpretation. Sulfotransferases (SULTs) have been experimentally identified as binding partners of 11C-Pittsburgh Compound-B (PiB). However, whether the clinically used fluorinated PiB derivatives flutemetamol and flutafuranol interact with brain-expressed SULTs is yet unexplored. Here, we combined multi-omic transcriptomic profiling with molecular docking and molecular dynamics (MD) simulations to assess the structural interactions of SULT-tracer complexes. Analysis of the Genotype-Tissue Expression project and the Human Protein Atlas identified SULT1A1, SULT1A3, and SULT4A1 as the SULT isoforms predominantly expressed in the human brain. Docking and MD simulations showed that all three tracers form energetically comparable complexes within the catalytic pockets of these isoforms, yet their dynamic stability varied in an enzyme- and tracer-specific manner. PiB and flutemetamol were stably accommodated in SULT1A1, but PiB lost its initial pose in SULT4A1. Flutafuranol showed weaker binding in SULT1A1, yet formed stable complexes in SULT1A3 and SULT4A1. Notably, SULT1A1, SULT1A3, and SULT4A1 are all expressed in the cerebellum, the brain region used as a reference for A{beta} PET signal normalization. These findings provide a structural framework for off-target tracer interaction with brain SULTs and suggest that the intracellular enzymatic environment may contribute to variability in A{beta} PET signals beyond fibrillar A{beta} deposition.

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.

White, beige and brown adipocytes store energy as lipids, secrete hormones and produce heat, playing an important role in the regulation of energy balance through not completely defined mechanisms. We investigate herein the impact of the almost complete absence of mature adipocytes (severe lipoatrophy) in the determination of energy balance (energy intake and expenditure) and homeothermy in mice. For this, mice with severe lipoatrophy induced by adipocyte deletion of peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) (PPAR{gamma} flox adiponectin-Cre) and littermate controls (PPAR{gamma} flox) were evaluated for energy balance, thermoneutral zone, core body temperature, locomotor activity, and gene expression profiles at different ambient temperatures. Severely lipoatrophic mice are heavier, hypermetabolic and hyperphagic and feature a widened thermoneutral zone, lower ambulatory activity, and metabolic inflexibility at both 23 and 17{degrees}C, along with unstable thermal behavior characterized by hyperthermia at 30{degrees}C, normothermia at 23{degrees}C, and bouts of hypothermia at 17{degrees}C. Noteworthy, lipoatrophic mice hypermetabolism at 30{degrees}C is not due to thyroid hormones, impaired insulation or increased body and lean masses and is not altered by pharmacological blockade of either {beta}-adrenergic receptor signaling with propranolol or skeletal muscle sarcoplasmic/endoplasmic reticulum Ca2+-ATPases (SERCA) and sarcolipin (SLN)-mediated calcium cycling with dantrolene, but is partially attenuated by pharmacological inhibition of acetyl-CoA carboxylase (ACC) and de novo lipogenesis with ND-630. In conclusion, severe lipoatrophy causes hypermetabolism and hyperthermia at 30{degrees}C partly through the activation of liver de novo fatty acid synthesis.

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.

BackgroundCatecholamines play a central role in cardiac performance, coordinating myocardial contractility, conduction, metabolism, and electrophysiological stability. In the heart, their actions have been attributed primarily to sympathetic nerve terminals and circulating adrenal catecholamines. The discovery of an intrinsic non-neuronal cholinergic system within cardiomyocytes challenges this neurocentric paradigm and raises the possibility that cardiomyocytes also possess an intrinsic catecholaminergic programme. Here, we investigated whether cardiomyocytes possess an intrinsic catecholaminergic programme and its contribution to cardiomyocyte homeostasis and stress responses. MethodsWe investigated catecholamine biosynthesis and handling in human induced pluripotent stem cell-derived cardiomyocytes, adult mouse cardiomyocytes, H9C2 cells, rat ventricular tissue, and Langendorff-perfused mouse hearts. Protein expression of catecholamine biosynthetic enzymes and vesicular monoamine transporters was assessed by immunoblotting and immunohistochemistry, while vesicular monoamine uptake was evaluated using fluorescent false neurotransmitters. Functional consequences of catecholamine biosynthesis inhibition were examined using pharmacological approaches, assessing cell viability, apoptosis, organelle homeostasis, metabolic signalling, and cardiac electrophysiology. ResultsTyrosine hydroxylase, aromatic L-amino acid decarboxylase, dopamine {beta}-hydroxylase, and vesicular monoamine transporters were detected in cardiomyocytes across models. Expression of catecholamine biosynthetic enzymes increased following ischaemia-reperfusion injury in rat heart tissue (TH p=0.008, AADC p=0.031, DBH p=0.008). Pharmacological inhibition of catecholamine biosynthesis caused dose-dependent reductions in cardiomyocyte viability (p<0.0001), increased apoptosis, organelle stress, and mitochondrial dysfunction, with greater effects under oxidative stress. Mechanistically, catecholamine depletion suppressed mTORC1 signalling and activated LKB1-AMPK-ULK1 pathways. In Langendorff-perfused hearts, tyrosine hydroxylase inhibition induced ventricular arrhythmias in 5 of 6 hearts, including sustained ventricular tachycardia, polymorphic ventricular tachycardia, and ventricular fibrillation. ConclusionsThese findings identify cardiomyocytes as previously unrecognised catecholamine-competent cells expressing intrinsic machinery for catecholamine biosynthesis and vesicular handling. Disruption of this pathway compromises metabolic and organelle homeostasis, activates energy-stress and autophagy-related signalling, and promotes malignant ventricular arrhythmias. Intrinsic cardiomyocyte catecholamine biology therefore represents a non-neuronal regulatory axis essential for myocardial resilience and electrical stability, with potential relevance to ischaemic injury and stress-induced dysfunction.

Despite advances in the understanding of the cellular and molecular mechanisms involved in erythropoiesis, there are still unanswered questions regarding the coordination between autophagy, vesicular trafficking, and endocytic signaling during this process. The complexity of these events suggests the existence of regulatory mechanisms capable of integrating these pathways. In this context, low-density lipoprotein receptor-related protein 1 (LRP1) emerges as a potential modulator given its function as a multifunctional endocytic receptor and its involvement in the regulation of degradation and signaling processes in various cellular models. However, its role in modulating mitophagy, a particular type of autophagy, and its link to vesicular trafficking associated with multivesicular bodies (MVBs) and the release of exosomes during erythroid maturation has been poorly explored. In this regard, alpha-2-Macroglobulin (2M), the main physiological ligand of LRP1, has been identified in extracellular vesicles (EVs) in various pathophysiological contexts, suggesting that it may be involved in vesicular dynamics and cellular clearance. In this study, we demonstrate that activated 2M (2M*), induces autophagy and particularly mitophagy, in K562 cells, and that LRP1 is directly responsible for this activation. Furthermore, we observed that 2M* stimulates the interaction of autophagosomes with MVBs/amphisomes and that EVs from K562 cells are positive for LC3, supporting a close relationship between the endocytic pathway and the autophagic pathway mediated by the 2M-LRP1 interaction. Taken together, these findings expand our understanding of erythroid biology and provide a conceptual foundation for exploring altered mechanisms in erythropoietic diseases and for the development of diagnostic and therapeutic strategies.

Pathogenic mutations in the ABCA4 gene cause several inherited retinal diseases, particularly Stargardt disease (STGD1). However, many missense variants remain classified as variants of uncertain significance (VUS) due to inconclusive evidence regarding their pathogenic impact. The missense VUS span across all the domains of ABCA4, with the majority found in the larger extracellular domains (ECDs). The largest uncharacterized region of ABCA4 is located in ECD1, where limited structural information and inconsistent computational predictions hinder clinical interpretation of missense VUS in this region. Here, we integrated in silico analysis with in vitro functional assays to evaluate the pathogenicity of VUS in this region and improve their diagnostic classification. Missense VUS in the ECD1 uncharacterized region were curated from ClinVar. Six multiallelic sites were identified in the uncharacterized region and 13 missense VUS on these multiallelic sites were characterized using the integrated analysis. In the in silico platform, the pathogenicity of the VUS were predicted using multiple algorithms, and the structural effects of the variants were analyzed compared to the wild type. Recombinant variants were expressed in virus-like particles (VLPs), and protein expression, membrane localization, and ATPase activity were quantified relative to wild type to identify potential disease-causing variants. From the integrated analysis, variants with pronounced structural destabilization, impaired membrane trafficking, and reduced or absent N-retinylidene-phosphatidylethanolamine (NRPE) substrate stimulated ATPase activities were identified as potentially deleterious. Notably, VUS at p.H193P and p.I214N showed loss of function, with p.I214N reflecting selectively impaired membrane targeting and p.H193P reflecting combined expression and trafficking defects. Additionally, NRPE-stimulated ATPase activities were impaired in VUS, p.V195L, p.V195I, p.D197H, p.I214F and p.N269S. Overall structural destabilization interfered with the NRPE-stimulated ATPase activities of p.N269S, while the lack of NRPE-stimulated ATPase activities of p.D197H, p.V195L, p.V195I and p.I214F are thought to be due to impaired NRPE interactions with ABCA4. All the VUS at p.R140, p.H193Y, p.D197N and p.N269H showed both the basal and NRPE-stimulated ATPase activities but less than that of the wild type, displaying a mild functional deficit. Together, these findings demonstrated that certain VUS within the unresolved ECD1 region disrupt ABCA4 stability and function, supporting their contribution to disease pathogenesis. This integrative approach highlights key residues likely to be pathogenic and advances the interpretation of VUS in inherited retinal disorders.

AnnotationMitochondrial heteroplasmy --the coexistence of both wild-type and mutant copies of mitochondrial DNA (mtDNA) within a cell--is a key factor in the pathogenesis of mitochondrial diseases. Classical approaches, which rely solely on the scalar fraction of mutant DNA, fail to fully account for threshold effects, the stochastic nature of heteroplasmy dynamics, and tissue specificity. The aim of the work is to construct a complex stochastic model of heteroplasmy dynamics, which for the first time combines the effects of selection, genetic drift, migration of mitochondrial genomes between tissues and threshold mechanisms of pathology development, for a quantitative assessment of the risk of mitochondrial diseases. In this paper, we propose a complex-phase formalism in which the state of a cells mitochondrial genome is described by a complex number Z = a + ib, where a and b are the absolute numbers of normal and mutant mtDNA copies, respectively. This approach naturally combines information on copy number and heteroplasmy level, and the argument{phi} = arctan (b / a) is interpreted as a phase characterizing the mutant load. Based on this formalism, we developed a stochastic model of tissue dynamics that includes the processes of selection, genetic drift, and intertissue migration of mitochondrial genomes. Using Monte Carlo methods (1000 simulations), we demonstrated that neuronal tissues are characterized by high heteroplasmy variability and a significant probability of reaching a pathological threshold even with a relatively low systemic mutant load. Kaplan-Meier survival analysis demonstrates that the development of pathology is probabilistic and can be described as a time -to-event process . The proposed approach enables quantitative assessment of the individual risk of developing mitochondrial diseases and opens the door to personalized prognosis.

Purpose: To identify transcript-level variants in crystallin genes in paediatric patients with unilateral cataracts. Methods: Anterior capsulorhexis (n=12) from patients underwent surgical management of congenital unilateral cataracts was collected. Total RNA was isolated from lens epithelial cells, and complementary DNA (cDNA) was synthesized. Full-length RNA transcripts of 10 lens-specific crystallin genes were PCR-amplified and analysed via Sanger sequencing. Identified transcript variants were further validated using genomic DNA (gDNA) through Sanger sequencing. In addition, the full-length (~7,535 bp) CRYBA1 genomic region was sequenced using Oxford Nanopore Technology. Results: Aberrant low molecular weight (LMW) amplicons (~370 bp) of the CRYBA1 transcript were identified in three patients presented with unilateral cataract. Of 3 patients, 2 had persistent fetal vasculature (PFV) and 1 had pre-existing posterior capsular defect (PPCD). Sanger sequencing revealed a precise loss of exons 2 to 4 in the CRYBA1 RNA transcript. No coding, splice-site, or large deletion variants were detected in the genomic DNA of the patients or their parents. In silico analysis predicted two possible truncated proteins arising from these alternatively spliced transcripts: one comprising the first 11 amino acids of the N-terminal region with a loss of all Greek key motifs, and another comprising 90 amino acids encoded by exons 5 and 6, initiated from an alternative start codon in exon 5, and loss of Greek key motifs 1 & 2. Conclusion: The precise skipping of exons 2 to 4, consistent with canonical splicing signals (5-prime-GU...AG-3-prime), in the absence of genomic alterations, suggests the presence of alternatively spliced (AS) CRYBA1 transcripts in human lenses. This is the first report documenting AS-CRYBA1 transcripts in association with childhood cataracts with PFV and PPCD.

A priori assessment of target proteins' druggability remains an unsolved problem in the field of drug development. The empirical approaches widely used to solve this problem demonstrate low efficiency. In this work, we investigated the factor of hydration of a representative set of 65 evolutionarily and structurally unrelated human enzymes in a water environment. This factor depends only on the structure of the proteins, and not on the physical and chemical properties of any potential ligands. The results show that, unlike the widely used approaches based on calculations of the accessible surface area (ASA), the content of low-entropy water molecules (LEW) in the active sites of human enzymes is systematically higher than that in other areas of their surface, including inactive cavities. Optimal criteria and a step-by-step procedure for identifying protein ligand binding sites are proposed. The proposed approach, based on the calculation of the LEW content in the first hydration layer of potentially interesting target proteins, makes it possible to evaluate their medicinal suitability even before the development of any ligands. The article also presents the results of a comparative analysis of experimental Raman spectroscopy data and the results of molecular dynamics simulations of water hydrogen bonds using three widely used water models (TIP3P, OPC3, and TIP5P) and standard algorithms for calculating hydrogen bond networks.

Dysregulated gut homing of leukocytes drives chronic inflammation in Crohns disease (CD). We employed phage display selection campaigns with libraries of stabilized, constrained peptides against endogenous conformation states of the cannabinoid receptor CB2R on human T cells, to discover novel receptor antagonists with potential to inhibit gut homing. Cluster and frequency analysis of 50,000 enriched sequences resulted in expression and functional characterisation of 10 protein candidates using assays of glucose uptake, ERK phosphorylation (pERK) and beta-arrestin recruitment. Each candidate antagonised CB2R activity with recorded IC50 values of between 5-10 nM. Cannabinoid receptor nanodisc binding experiments and SPR confirmed CB2R selectivity. SLKC_09 with an IC50 of 5.4 nM, was studied in a mouse model of chronic ileitis where it significantly inhibited gut homing of CD4+ & CD8+ naive, effector and memory cell types. Our findings highlight an alternative route to therapeutic inhibition of leukocyte trafficking in CD with a biologic inhibitor of CB2R.