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A Novel Long Noncoding RNA-LNC000133 Associated With Steroid-Induced Osteonecrosis of the Femoral Head Promotes Osteoblast Differentiation Through Bone Marrow Mesenchymal Stem Cells-Derived Exosomes Pathway: A Bioinformatics Validation and Detailed Mechanistic Study.

Steroid-induced osteonecrosis of the femoral head (SONFH) is a debilitating disease caused by glucocorticoid abuse, characterized by complex pathogenesis and unclear molecular mechanisms. Dysfunction of bone marrow mesenchymal stem cells (BMSCs) and their exosome-mediated signalling is a key contributor to SONFH, although the precise mechanisms remain to be elucidated. In this study, the differential expression profiles of long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and messenger RNAs (mRNAs) in exosomes derived from human BMSCs (hBMSCs) obtained from patients with SONFH compared to controls with femoral neck fractures were identified. Through next-generation sequencing, a novel lncRNA, LNC000133, associated with SONFH was discovered. Using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and competing endogenous RNA (ceRNA) network construction, the LNC000133/miR-362-5p/TGF-β3/SMAD3/BMP2 signalling axis was established. The definitive expression, localization and full-length sequence of LNC000133 in BMSCs were subsequently validated by Northern blot, quantitative real-time polymerase chain reaction (qRT-PCR), fluorescence in situ hybridization (FISH) and rapid amplification of cDNA ends (RACE). Most notably, mechanistic studies demonstrated that LNC000133-modified BMSCs-derived exosomes were efficiently taken up by osteoblasts, which promoted proliferation and osteogenic differentiation by targeting the miR-362-5p/TGF-β3/SMAD3/BMP2 signalling pathway.

Humans

The shikimate pathway. III. 3-dehydroquinate synthetase of E. coli. Mechanistic studies by kinetic isotope effect.

The conversion of 3-deoxy D-arabino heptulosonate 7-phosphate to 3-dehydroquinate by the 3-dehydroquinate synthetase from E. coli is characterized by a low but significant kinetic isotope effect for tritium carried in position-5 of DAHP, while no isotope effect was detectable for tritium in position-4. This effect was observed at different pH nad is interpreted as a result of theintermediary of a 5-ketonic form of the substrate, formed in a preliminary non limiting step during the enzymic cyclization reaction. A tentative scheme for the 3-DHQ synthetase reaction is proposed involving five steps: oxidation by NAD+ in position-5, phsophate elimination after enolization, reduction with precedently formed NADH and cyclization by attack of the 2-carbonyl by the C-7 methylene group.

Chemical Phenomena

Mechanistic studies of glutamine synthetase from Escherichia coli. An integrated mechanism for biosynthesis, transferase, ATPase reaction.

The mechanism of biosynthetic, transferase, ATPase, and transphosphorylation reactions catalyzed by unadenylylated glutamine synthetase from E. coli was studied. Activation complex(es) involved in the biosynthetic reaction are produced in the presence of either Mg2+ or Mn2+ ; however, with the Mn2+-enzyme inhibition by the product, ADP, is so great that the overall forward biosynthetic reaction cannot be detected with the known assay methods. Binding studies show that substrates (except for NH3 and NH2OH which are not reported here) can bind to the enzyme in a random manner and that binding of the ATP-glutamate, ADP-Pi or ADP-arsenate pairs is strongly synergistic. Inhibition and binding studies show that the same binding site is utilized for glutamate and glutamine in biosynthetic and transferase reactions, respectively, and that a common nucleotide binding site is used for all reactions studied. Studies of the reverse biosynthetic reaction and results of fluorescent titration experiments suggest that both arsenate and orthophosphate bind at a site which overlaps the gamma-phosphate site of nucleoside triphosphate. In the reverse biosynthetic and transferase reactions, ATP serves as a substrate for the Mn2+-enzyme but not for the Mg2+-enzyme. The ATP supported transferase activity of Mn2+-enzyme is probably facilitated by the generation of ADP through ATP hydrolysis. When AMP was the only nucleotide substrate added, it was converted to ATP with concomitant formation of two equivalents of glutamate, under the reverse biosynthetic reaction conditions, and no ADP was detected. The reversibility of 180 transfer between orthophosphate and gamma-acyl group of glutamate was confirmed. ATPase activity of Mg2+ and Mn2+ unadenylylated enzymes is about the same. Both enzymes forms catalyze transphosphorylation reactions between various purine nucleoside triphosphates and nucleoside diphosphates under biosynthetic reaction conditions. The data are consistent with the hypothesis that a single active center is utilized for all reactions studied. Two stepwise mecanisms that could explain the results are discussed.

Adenosine Diphosphate

Mechanistic studies of glutamine synthetase from Escherichia coli: kinetics of ADP and orthophosphate binding to the unadenylylated enzyme.

The kinetics of protein fluorescence change exhibited by ADP or orthophosphate addition to the Mg2+-or Mn2+-activated unadenylylated glutamine synthetase from Escherichia coli were studied. The kinetic patterns of these reactions are incompatible with a simple bimolecular binding process and a mechanism which required protein isomerization prior to substrate binding. They are consistent with a mechanism in which direct substrate binding is followed by a substrate-induced conformational change step, ES in equilibrium ES. At pH 7.0 and 15 degrees C, the association constants for the direct binding (K1) of ADP to MnE1.0 and of Pi to MnE1.0ADP are 3.9 X 10(4) and 2.28 X 10(2) M(-1), respectively. The association constant for the direct binding of ADP to MnE1.0Pi is 2.3 X 10(4) M(-1) at pH 7.0 and 19 degrees C. The deltaG degrees for the substrate-induced conformational step are -3.5 and -1.3 kcal mol(-1) due to ADP binding to MnE1.0Pi and MnE1.0, respectively, and -1.4 kcal mol(-1) due to Pi binding to MnE1.0ADP. Rate constants, k2 and k(-2), for the isomerization step are: 90 and 9.5 s(-1) for ADP binding to MnE1.0, 440 and 0.36 s(-1) for ADP binding to MnE1.0Pi, and 216 and 1.8 s(-1) for Pi binding to MnE1.0ADP. Due to low substrate affinity, the association constant for direct Pi binding to MnE1.0 was roughly estimated to be 230 M(-1) and k2 = 750 s(-1), k(-2) = 250 s(-1). At 9 degrees C and pH 7.0, the estimated association constants for the direct ADP binding to MgE1.0 and MgE1.0 Pi are 1.8 X 10(4) and 1.6 X 10(4) M(-1), respectively; and the rate constants for the isomerization step associated with the corresponding reaction are k2 = 550 s(-1), k(-2) = 500 s(-1), and k2 = 210 s(-1), k(-2) = 100 s(-1). From the kinetic analysis it is evident that the inability of Mn2+ to support biosynthetic activity of the unadenylylated enzyme is due to the slow rate of ADP release from the MnE1.0PiADP complex. In contrast the large k(-2) obtained for ADP release from the MgE1.0ADP or MgE1.0PiADP complex indicates that this step is not rate limiting in the biosynthesis of glutamine since the k catalysis obtained under the same conditions is 7.2 s(-1).

Adenosine Diphosphate

Mechanistic studies of glutamine synthetase from Escherichia coli: kinetic evidence for two reaction intermediates in biosynthetic reaction.

Fast reaction techniques were used to study the kinetics of protein fluorescence intensity changes that are associated with the reactions of unadenylylated Escherichia coli glutamine synthetase [L-glutamate: ammonia ligase (ADP-forming), EC 6.3.1.2] with its substrates. It was established that the synthesis of glutamine occurs by a stepwise mechanism. During the catalytic process two fluorometrically distinct intermediates were observed. Both forward and reverse rate constants which lead to the formation and consumption of these intermediates were evaluated. The catalytic rate constant, kc, which was calculated from these rate constants agrees well with the values of kc which were determined by direct measurement of the overall biosynthetic activities by means of stopped-flow technique or the steady-state assay method.

Enzyme Activation

The use of a basic dye (azure A or toluidine blue) plus a cationic surfactant for selective staining of RNA: a technical and mechanistic study.

Selective purple staining of RNA-rich structures such as basophilic cytoplasms of exocrine pancreas and plasma cells, Nissl substance, and nucleoli was achieved by treating tissue sections as follows. Stain dewaxed sections for 1/2 hour in a dyebath containing 0.1% w/v axure A or toluidine blue and 1% cationic surfactant (Hyamine 2389, a 50% w/v aqueous solution of diisobutylphenoxyethoxyethyldimethylbenzylammonium chloride; or benzyldimethylammonium chloride, or cetylpyridinium bromide, or cetyltrimethylammonium bromide) buffered to pH 7 with phosphate. Rinse in water, blot, air dry and mount in synthetic resin. Intense purple staining of RNA-rich regions occurred after fixation in neutral formalin or in Carnoy's or Gendre's fluids, though satisfactory results were also found after fixation in acetone or alcohol. Chromatin generally stained a very pale azure after all fixations, though occasionally nuclei were unstained (Gendre's or Zenker's fluids). Subjecting tissue sections to acid hydrolysis or to digestion by RNAase eliminated or reduced the purple staining, but left the azure staining of nuclei unaffected. Satisfactory staining of RNA-rich structures was not critically dependent on the precise concentrations of dye, surfactant or inorganic salts in the dyebath, nor on pH, staining time or chemical nature of the surfactant. The staining patterns can be rationalized with a tissue model that considers both surface charge and permeability factors, since present in the dyebath are small dye cations and large cationic surfactant micelles. As micelles and dye will both quickly penetrate basophilic structures considered to be porous, such as chromatin, competition will then greatly reduce staining of such substrates. But the large micelles will only slowly penetrate regions considered to be more impermeable, such as basophilic cytoplasms, so consequently small fast moving dye ions may enter and stain without competition.

Animals

Mechanistic studies with purified components of the liver microsomal hydroxylation system: spectral intermediates in reaction of cytochrome P-450 with peroxy compounds.

Recent investigations in this laboratory on the mechanism of action of liver microsomal cytochrome P-450 (P-450 LM) and its interaction with other components of the hydroxylation system are presented. Two electrophoretically homogeneous forms of the cytochrome, phenobarbital-inducible P-450 LM2 and 5,6-benzoflavone-inducible P-450 LM4, so designated according to their relative electrophoretic mobilities, were used in these studies. Phosphatidylcholine is required in the reconstituted enzyme system for rapid electron transfer from NADPH to P-450 LM, catalyzed by NADPH-cytochrome P-450 reductase, as well as for maximal hydroxylation activity with either molecular oxygen or a peroxy compound serving as oxygen donor to the substrate. The phospholipid facilitates the binding of both substrate and reductase to P-450 LM and apparently causes a structural change in the cytochrome as shown by an increase in alpha-helical content, determined by circular dichroic spectrometry. P-450LM3 and LM4 are one-electron acceptors under anaerobic conditions, in accord with previous potentiometric titrations and product yield data, but in disagreement with previous titrations with reducing agents. The cause for the discrepancy between the present and earlier results is not yet fully understood. Stopped flow spectrophotometry was employed to detect intermediates in the reaction of peroxy compounds with P-450LM2. With m-chloroperbenzoic acid the intermediate formed has absorption maxima at 375, 425, and 540 nm in the absolute spectrum and at 370, 436, and 540 nm in the difference spectrum (intermediate minus oxidized form). A study of the magnitude of the spectral change at various peracid concentrations indicated that with this oxidant the reaction shows a dependence resembling a binding curve. These and other experiments with various oxidants, including cumente hydroperoxide, suggest a reversible two-step mechanism according to the reaction: P-450 LM + oxidant equilibrium C equilibrium D, where C may be an enzyme-oxidant complex and D is a spectral intermediate of unknown structure. A scheme is proposed for the mechanism of action of P-450 LM based on these and earlier studies, including evidence from deuterium isotope experiments for the formation of a substrate carbon radical prior to oxygen transfer.

Anaerobiosis

Function-based selection of synthetic communities enables mechanistic microbiome studies.

Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.

Animals

Teleost lincRNAs: Functional roles, regulatory mechanisms, and future applications in aquaculture.

Long intergenic non-coding RNAs (lincRNAs) regulate gene expression across vertebrate physiological systems, yet their functional roles in teleost fish remain incompletely synthesized. This review systematically integrates current evidence through PRISMA-guided searches across PubMed, Web of Science, and Scopus, identifying ten lincRNA-focused functional studies with genetic, mechanistic, or developmental validation, complemented by twenty two supplementary contextual references. Findings span development, immunity, environmental adaptation, reproduction, regeneration, and toxicology, with each association graded as experimentally validated, bioinformatically predicted, correlational, or speculative. This synthesis offers three core contributions. First, it shows that cis-acting regulation on neighboring genes, mediated through Wnt, NF-κB, and AHR signaling, is the dominant validated lincRNA mechanism across teleost physiological domains. Second, it demonstrates that direct experimental validation, primarily via CRISPR-Cas9 and chromatin-capture assays, remains concentrated in zebrafish, whereas aquaculture-species associations remain largely correlational. Third, it identifies two findings that challenge current lincRNA classification: unexpected regulatory directionality at the slincR-sox9b locus, and micropeptide-encoding potential within annotated lincRNAs. Together, these contributions establish an evidence-graded foundation for future mechanistic studies and translational aquaculture applications.

Aquaculture

Transcriptomic insights into the coordinated regulation of signaling, apoptosis, immunity, and metabolism during Sinonovacula constricta larval metamorphosis.

Metamorphosis is a critical ontogenetic transition for marine bivalves, marking the shift from planktonic to benthic lifestyles, where successful transformation dictates survival. The razor clam Sinonovacula constricta is economically important; however, low larval metamorphosis rates remain a major bottleneck in seedling production. To elucidate the mechanisms governing this process, we performed a comparative transcriptome analysis of S. constricta larvae at pre- and post-metamorphosis stages using Illumina sequencing. A total of 3701 differentially expressed genes (DEGs) were identified, including 3254 up-regulated and 447 down-regulated genes. Functional annotation of the respective top 20 significantly up-regulated and down-regulated DEGs indicated their potential pivotal roles in signal transduction (e.g., up-regulated: CAV1, CHRNA2; down-regulated: APP, NOTCH1), cellular proliferation and differentiation (e.g., up-regulated: TUBA, EGF1; down-regulated: KIF23, TTC25), transcriptional and epigenetic regulation (e.g., up-regulated: NFIL3; down-regulated: OVO, HMX1), substance transport (e.g., up-regulated: LRP2, LRP1B; down-regulated: SLC51A, Slc33a1), substance metabolism (e.g., up-regulated: CPK3, CYP26A1; down-regulated: RDMT1, ADAC), immunomodulation (e.g., up-regulated: CPN2, CRISP2), and protein homeostasis (e.g., up-regulated: HSP27, NAS-27). Functional enrichment analysis further revealed that DEGs were significantly enriched in pathways related to signal transduction and developmental regulation (e.g., Ras, TNF), cell death and homeostasis (e.g., apoptosis), immune responses (e.g., Toll-like receptor), energy metabolism (e.g., lipid), cardiovascular related (e.g., Fluid shear stress), cell junction and architecture (e.g., Tight junction), and infectious disease (e.g., measles). These results suggest a synergistic interplay between signaling, apoptosis, immunity, and metabolism during S. constricta metamorphosis. This study advances our understanding of marine bivalve metamorphosis and offers candidate genes for further mechanistic studies.

Animals

Repurposing screens reveal a role for PKCη and NF1 in SARS-CoV-2 infection.

SARS-CoV-2 continues to circulate with the emergence of variants that evade existing immunity. However, all strains rely on conserved host factors for entry, making them attractive targets for host-directed antivirals. SARS-CoV-2 engages the ACE2 receptor and can enter cells through two alternative pathways depending on cell type: Spike cleavage at the plasma membrane by TMPRSS2, or within endocytic compartments by cathepsins. Cleavage triggers Spike-mediated membrane fusion and release of the viral genome. To discover small-molecule inhibitors of entry, we first screened compounds against live virus and active candidates were then tested using recombinant VSV expressing SARS-CoV-2 Spike, with VSV expressing its native glycoprotein serving as a control. This approach identified known and novel TMPRSS2 inhibitors, as well as Staurosporine and Retro-2.1. Both compounds inhibited infection in both TMPRSS2-dependent and -independent cell types. Entry bypass studies revealed that Staurosporine acts upstream of Spike cleavage, while Retro-2.1 functions downstream. Mechanistic studies in Calu-3 cells showed that Staurosporine, a pan-PKC inhibitor, blocks entry via PKCη, a pro-viral factor acting before Spike cleavage. Retro-2.1 targets NF1, which promotes infection downstream of Spike cleavage. Together, our screening pipeline identified inhibitors that block SARS-CoV-2 entry at distinct stages and revealed host factors that may inform the development of current and novel antiviral strategies.

Humans

Dc Polarographic assay of tetracyclines.

The inhibitory effect of dioctyl sodium sulfosuccinate on hog pepsin activity was investigated over the pH 1.5-3.0 range. The inhibitory effect was studied using a natural substrate, hemoglobin, and a synthetic substrate, N-acetyl-L-diiodotyrosine. The mechanistic studies revealed that a substrate-inhibitor interaction was the major mechanism of inhibition with hemoglobin. However, some direct enzyme inhibition also was involved. With the synthetic substrate, the inhibition las due to a competition between the substrate and the inhibitor molecules for the enzyme. The possible therapeutic significance of the inhibitory effect of the medicinal surfactant is discussed.

Buffers

Modeling meningioma in vitro in the omics era.

Meningioma biology has been substantially clarified by recent omics-based studies, which have identified recurrent mutations, copy-number alterations, and distinct molecular subgroups. However, although these approaches have provided a valuable framework, they are inherently limited in their ability to establish direct causal relationships. The mechanistic studies are therefore indispensable for translating these molecular observations into biological understanding. Nevertheless, the mechanistic literature has often evolved in a fragmented manner, with individual pathways and model systems studied in relative isolation from the broader multi-omic landscape. In this review, we synthesize these complementary bodies of work into an integrated framework and outline a clear roadmap for future studies. We first review the historical development of established meningioma cell lines, their current molecular characterization, and the recent emergence of 3D models and organoids. Intrinsic challenges in modeling meningioma in vitro are discussed, including the difficulty of establishing immortalized cell lines from predominantly benign tumors, genetic alterations introduced during immortalization, and drift under culture conditions that differ substantially from those of the parental tumors. Next, insights from functional studies centered on these models are integrated within the molecular framework established by large-scale omics analyses. To avoid fragmentation and overemphasis on isolated findings, prior studies are organized into six categories based on major signaling pathways: Hippo, PI3K/Akt/mTOR, MAPK, Wnt/β-catenin, FOXM1, and Notch. Finally, lessons from other cancer models, including experimental approaches to chromosome-scale genomic disturbances, are considered to provide a more integrated view of meningioma biology and to highlight directions for future research.

Meningioma

Loss of chromosome Y in hematopoietic cells: mechanisms and implications for human disease.

The chromosome Y, once thought to function primarily in male reproduction, is now recognized to have broader biological roles. Hematopoietic loss of chromosome Y (LOY) is one of the most frequent somatic genomic alterations in male blood, with prevalence increasing markedly with age. Advances in technology have enabled robust detection of LOY in blood at both the population scale and the single-cell level. Hematopoietic LOY arises from mitotic chromosome mis-segregation and is influenced by inherited genetic variation, environmental exposures, and aging. Population-based genome-wide association study (GWAS) analyses have identified robust epidemiological associations between hematopoietic LOY and cardiovascular disease, brain disease, immune disorders, and cancer. Mechanistic studies demonstrate that LOY has functional consequences, including altered gene expression, immune dysregulation, and clonal expansion. Some findings are strongly supported by CRISPR-based LOY mouse and cellular models, which recapitulate key disease-related phenotypes. Collectively, these findings establish hematopoietic LOY as a biologically meaningful form of somatic mosaicism with important implications for disease susceptibility.

Humans

Deep learning and statistical methods identify novel asthma risk variants in Europeans.

BACKGROUND: Asthma is a common heritable respiratory disorder with a complex genetic basis. Although large-scale genome-wide association studies have identified many risk loci, the full spectrum of its polygenic architecture remains to be defined. OBJECTIVE: We refined the genetic landscape of asthma in individuals of European ancestry and improve polygenic risk prediction through statistical and deep learning-based methods. METHODS: We conducted the largest genome-wide association study meta-analysis of asthma in individuals of European ancestry, combining data from the Global Biobank Meta-analysis Initiative (121,940 cases, 1,254,131 controls) and the Million Veteran Program (36,823 cases, 398,278 controls). To enhance discovery, we applied pleiotropy-informed multitrait analysis and conditional false discovery rate approaches, each incorporating eosinophil counts as a secondary trait. In parallel, we used a Transformer-based deep learning framework to further prioritize variants and improve polygenic risk prediction. RESULTS: The meta-analysis identified 69 independent genome-wide significant loci (P&#x2009;<&#x2009;5 &#xd7; 10-8) not previously reported in asthma. Multitrait analysis of genome-wide association studies, conditional false discovery rate, and deep learning approaches uncovered additional candidate loci. Functional annotation and expression quantitative trait locus mapping implicated novel genes in immune regulation, airway remodeling, and metabolic processes. Polygenic risk score models derived from deep learning-prioritized variants outperformed those based on conventional genome-wide association study and standard statistical approaches. CONCLUSIONS: Our study yields a comprehensive map of asthma-associated loci in European ancestry populations, improves genetic risk prediction, and informs future mechanistic studies.

Humans

APOL1 kidney disease: a critical narrative review of molecular mechanisms, clinical heterogeneity, and the emerging therapeutic landscape.

BACKGROUND: The G1 and G2 variants of the APOL1 gene represent significant genetic risk factors for APOL1 kidney disease and contribute substantially to the excess burden of renal disease observed in individuals of African ancestry. Importantly, both variants exhibit incomplete penetrance, with only approximately 15-20% of high-risk genotype carriers ultimately developing overt nephropathy. OBJECTIVE: To provide a critically appraised, clinically oriented narrative synthesis of APOL1 kidney disease that (i) assigns an explicit certainty rating to each major mechanistic and clinical claim, (ii) identifies where published estimates diverge, where associations remain contested, and where conclusions have been overstated in the secondary literature, and (iii) aligns terminology, testing guidance and therapeutic expectations with the conclusions of the 2025 KDIGO Controversies Conference and with clinical trial data available to August 2026. METHODS: This literature narrative review was performed using a literature search of PubMed and Scopus focusing on APOL1-related nephropathy. Mainly studies published from 2010 to 2026 were considered; however, some selected historical papers from 2005 to 2010 were used for better understanding of the underlying mechanisms and history. Used search terms were "APOL1," "APOL1 risk variants," "chronic kidney disease," AMPLITUDE trial, MZE829, HORIZON trial, "focal segmental glomerulosclerosis," "HIV-associated nephropathy," "podocyte injury," "inaxaplin," "VX-147," KDIGO 2025, and "antisense oligonucleotides." Trial status and topline results for agents in development were additionally verified against ClinicalTrials.gov registrations and sponsor disclosures. The literature search was last updated on 10 August 2026. The inclusion criteria of the study were peer-reviewed original articles, genome-wide association studies, randomised controlled trials, translational studies, mechanistic investigations, and high-quality review articles published in the English language. Exclusion criteria included conference abstracts without peer review, duplicate papers, non-English publications with unreliable translation, and case reports with no relevance to the underlying mechanisms. More attention was paid to studies focusing on molecular pathogenesis of APOL1 nephropathy, second-hit pathophysiology, genotypes/phenotypes, and new therapies (e.g. inhibitors such as Inaxaplin). The review method and design have been prepared according to SANRA (Scale for the Assessment of Narrative Review Articles) criteria. Among eligible articles, priority was given to studies with larger sample sizes, more recent publication dates, higher-impact peer-reviewed journals, and direct clinical or mechanistic relevance to APOL1-associated nephropathy; where multiple studies addressed the same question, the most methodologically rigorous and most recent source was preferentially cited. To move beyond description, each principal claim carried forward into this review was assigned a qualitative certainty rating (high, moderate, low or very low) on the basis of study design, consistency across independent cohorts, directness of the evidence to human disease, and precision of the estimate. These ratings, together with the study design that would be required to resolve each remaining uncertainty, are presented in Table&#xa0;5. This grading represents a structured judgement by the authors and is not a formal GRADE assessment. RESULTS: Pathogenic actions of APOL1 risk alleles depend on toxic gain-of-function activities that result from the disruption of ion channels. Mitochondrial dysfunction, endoplasmic reticulum stress, and inflammasome activation play roles as secondary downstream modulators of podocyte damage. The existence of incomplete penetrance and lack of symptoms in people with high-risk alleles highlights the need for secondary triggers, including environmental, infectious, and inflammatory factors, for disease onset and progression. High-risk APOL1 genotypes increase the likelihood of rapidly progressing kidney diseases like FSGS, which amplify susceptibility in HIVAN when accompanied by secondary causes like HIV infection. Management is mainly through renin-angiotensin antagonists, but recent treatments include antisense oligonucleotides, immunomodulators, and small molecule inhibitors like inaxaplin. Although promising, inaxaplin (VX-147) showed a ~47% reduction in urine protein/creatinine ratio (UPCR) in Phase 2a trial; however, these findings are based on a relatively small sample size, an open-label study design, and short-term follow-up, and therefore require confirmation in ongoing Phase 3 studies. As this is a narrative review rather than a primary study, no new patient-level data are reported. Across the studies synthesised, high-risk APOL1 genotypes were consistently associated with podocyte injury and with a faster decline in kidney function than low-risk genotypes; however, the magnitude of this association varied substantially with how cohorts were ascertained. The association is robust and reproducible for focal segmental glomerulosclerosis, HIV-associated nephropathy, and hypertension-attributed kidney failure, and remains inconsistent for diabetic kidney disease. Therapeutic development has accelerated, but the supporting clinical evidence remains early phase. Inaxaplin (VX-147) reduced the urine protein-to-creatinine ratio by approximately 47.6% at week 13 in a 16-participant, single-group, open-label Phase 2a study, and is now being evaluated in the randomised, double-blind, placebo-controlled Phase 2/3 AMPLITUDE trial (NCT05312879), whose pre-specified week 48 interim analysis is anticipated in early 2027. MZE829, an orally administered APOL1 inhibitor, produced a mean 35.6% reduction in the urine albumin-to-creatinine ratio at 12&#xa0;weeks in the Phase 2 HORIZON study; because HORIZON was a small, open-label, single-arm basket study (15 participants enrolled, 12 evaluable) whose primary endpoints were safety and tolerability, this reduction is neither placebo adjusted nor the result of a formal test of efficacy. To date, no APOL1-targeted agent has demonstrated benefit on a hard kidney endpoint. CONCLUSION: APOL1 is the clearest current example of a genetically defined, mechanism-targetable kidney disease, but its evidence base is uneven. The genetic association is firmly established; whereas much of the mechanistic literature derives from overexpression systems, several downstream pathways remain contested, and every APOL1-targeted therapy is so far supported only by short-term, surrogate-endpoint data. The principal unresolved issues are the determinants of incomplete penetrance, the absence of a validated progression biomarker and of any model reproducing the common slowly progressive phenotype, and the long-term efficacy and safety of APOL1-directed therapy. Genotype-guided risk stratification is therefore best regarded as clinically reasonable but not yet proven, and routine population-level screening is not currently supported.

AMPLITUDE trial

A Multitrait Locus Regulates Sarbecovirus Pathogenesis.

Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to severe acute respiratory syndrome coronavirus (SARS-CoV) disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6, that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2, and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species. IMPORTANCE Host genetic variation is an important determinant that predicts disease outcomes following infection. In the setting of highly pathogenic coronavirus infections genetic determinants underlying host susceptibility and mortality remain unclear. To elucidate the role of host genetic variation on sarbecovirus pathogenesis and disease outcomes, we utilized the Collaborative Cross (CC) mouse genetic reference population as a model to identify susceptibility alleles to SARS-CoV and SARS-CoV-2 infections. Our findings reveal that a multitrait loci found in chromosome 9 is an important regulator of sarbecovirus pathogenesis in mice. Within this locus, we identified and validated CCR9 and CXCR6 as important regulators of host disease outcomes. Specifically, both CCR9 and CXCR6 are protective against severe SARS-CoV, SARS-CoV-2, and SARS-related HKU3 virus disease in mice. This chromosome 9 multitrait locus may be important to help identify genes that regulate coronavirus disease outcomes in humans.

Animals

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.

Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.

Dysbiosis