Inositol polyphosphate multikinase (IPMK) is emerging as a critical regulator of nuclear functions. While earlier studies in yeast and cell lines linked IPMK to gene expression, recent work reveals its role in modulating histone acetylation through the activation of histone deacetylases 1/3 (HDAC1/3). Interestingly, HDAC1/3 interact with DNA methyltransferase 1 (DNMT1), stabilizing DNMT1 and promoting DNA methylation. As an HDAC1/3 activator, IPMK may thereby influence DNA methylation dynamics. This study investigates how the genetic depletion of IPMK influences DNA methylation, though the role of its kinase activity remains untested. Using long-read Oxford nanopore sequencing, we conducted methylation analysis for >28 millions of CpG sites and discovered that IPMK deletion results in over 22,000 differentially methylated regions (DMRs). Integrating affected genes by DMRs and RNA-seq data, we found that 35 genes show an inverse correlation between methylation in promoter regions and gene expression. Pathway analysis revealed that genes related to tissue remodeling and hematopoiesis are affected. Notably, MMP14 and LIF showed significant methylation changes in promoter regions under IPMK deletion, resulting in decreased mRNA and protein expression. Collectively, this study identifies IPMK as a novel regulator of DNA methylation. While this study did not investigate the role of IPMK's kinase activity in regulating DNA methylation, future studies will determine whether IPMK's effects on DNA methylation are driven by its kinase activity or by kinase-independent mechanisms.

Bone is a common site for metastasis of solid cancers. The diversity of histological and molecular characteristics of bone metastases (BMs) remains poorly studied. Here, we performed single-cell RNA sequencing on 42 BMs from eight cancer types, identifying three distinct ecosystem archetypes, each characterized by an enrichment of specific immune cells: macrophages/osteoclasts, regulatory/exhausted T cells, or monocytes. We validated these archetypes by immunostaining on tissue sections and bioinformatic analysis of bulk RNA sequencing/microarray data from 158 BMs across more than 10 cancer types. Interestingly, we found only a modest correlation between the BM archetypes and the tissues of origin; BMs from the same cancer type often fell into different archetypes, while BMs from different cancer types sometimes converged on the same archetype. Additional analyses revealed parallel immunosuppression and bone remodeling mechanisms, some of which were experimentally validated. Overall, we discovered unappreciated heterogeneity of BMs across different cancers.

The sense of smell is essential for human perception. Olfactory function declines with increasing age, affecting a substantial portion of the elderly population, and this decline is more pronounced in men. This reduction can be attributed to anatomical and degenerative changes in the brain and olfactory receptors. There is robust clinical evidence indicating an association between olfactory perception decline/deficit (OPD) and major neurodegenerative diseases, with severe deficits observed in Alzheimer's and Parkinson's disease and milder effects noted in other conditions. However, its molecular bases have not yet been identified. Here, we explored the molecular connection between OPD and Parkinson's disease by conducting data-mining, gene enrichment analysis, and examining protein-interaction networks using systems biology approaches. We found pathways associated with both OPD and Parkinson's disease, identifying over 300 relevant genes. These genes belong to biologically relevant gene families, including transporters, kinases, nuclear receptors, transcription factors, and olfactory and other G protein-coupled receptors. Functional enrichment analysis revealed shared biological processes between OPD and Parkinson's disease, such as synaptic signalling and neuroinflammation. Mitochondrial gene enrichment was unique to Parkinson's. Both conditions exhibited a scarcity of associated genes on the Y chromosome but an even distribution on the non-pseudoautosomal region of the X chromosome, potentially explaining sex prevalence differences. In conclusion, our study suggests olfactory testing may help diagnose cognitive decline in neurodegenerative diseases. Further research is needed to understand the connection between OPD, aging, and other diseases and to examine olfactory performance in screening individuals at risk of Parkinson's disease and similar conditions.

Understanding the genetic mechanisms underlying egg production is crucial for improving laying performance in chickens. However, traditional genome-wide association studies (GWAS) have not effectively utilized the information regarding the longitudinal trajectories and dynamics of egg-laying phenotype. In this study, based on individual egg production records over time, we first utilized the Yang-Ning model to characterize four egg production parameters. Our SNP-based GWAS on these parameters, along with three multidimensional GWAS models, captured different aspects of egg-laying dynamics. The novel significant associations and candidate genes identified, including C3, CADPS2, and TLN2, contribute significantly to egg-laying traits. By quantifying both direct and indirect effects of egg production parameters on egg number (EN) through the integration of Bayesian networks and structural equation modeling, we demonstrated that an earlier age at first egg directly promotes EN. The findings from this study enhance our understanding of the genetic mechanisms involved in egg production and provide valuable insights for optimizing chicken breeding strategies.

The accumulation of plastic waste in the environment, breaking down into micro- and nanoplastics, poses significant threats to ecosystem and human health. Plastic particles have been detected in human blood, urine, and placental tissue, indicating widespread exposure. While their long-term health impacts remain unclear, developing brains, especially in fetuses and children, may be vulnerable, potentially resulting in behavioral changes or neurodevelopmental disorders. This study explores the effects of chronic exposure to 23-nm polystyrene nanoplastics at 10 µg/day/kg in wild-type mice across life stages, using exposure levels reflective of human reality. Maternal exposure disrupted critical developmental milestones in pups. In adulthood, exposed mice exhibited Attention-Deficit Hyperactivity Disorder (ADHD)-like traits, including hyperactivity, increased risk-taking behaviors, and impaired motor learning and executive functions. In aging mice, exposure was associated with a lower epileptic threshold, with developing seizures. These behavioral changes were linked to altered gene and synaptic protein expression associated with ADHD and epilepsy. At the cellular level, lifelong nanoplastic exposure caused lysosomal dysfunctions and increased lipofuscin accumulation, indicative of accelerated brain aging. These findings align with the growing prevalence of ADHD and epilepsy in humans, particularly children and the elderly, emphasizing the urgent need to address plastic pollution and its health implications.

Focusing on the early stages of Alzheimer's disease (AD) holds great promise. However, the specific events in neural cells preceding AD onset remain elusive. To address this, we utilized human-induced pluripotent stem cells carrying APPswe mutation to explore the initial changes associated with AD progression. We observed enhanced neural activity and early neuronal differentiation in APPswe cerebral organoids cultured for one month. This phenomenon was also evident when neural progenitor cells (NPCs) were differentiated into neurons. Furthermore, transcriptomic analyses of NPCs and neurons confirmed altered expression of neurogenesis-related genes in APPswe NPCs. We also found that the upregulation of reactive oxygen species (ROS) is crucial for early neuronal differentiation in these cells. In addition, APPswe neurons remained immature after initial differentiation with increased susceptibility to toxicity, providing valuable insights into the premature exit from the neural progenitor state and the increased vulnerability of neural cells in AD.

Mendelian randomization (MR) leverages trait associated genetic variants as instrumental variables (IVs) to determine causal relationships in epidemiology. However, genetic IVs for complex traits are typically highly heterogeneous and, at a molecular level, exert effects on different biological processes. Exploration of the biological underpinnings of such heterogeneity can enhance our understanding of disease mechanisms and inform therapeutic strategies. Here, we introduce a new approach to instrument partitioning based on enrichment of Mendelian disease categories (pathway-partitioned) and compare it to an existing method based on genetic colocalization in contrasting tissues (tissue-partitioned).

We employed individual- and summary-level MR methodologies using SNPs grouped by pathway informed by proximity to Mendelian disease genes affecting the renal system or vasculature (for blood pressure (BP)), or mental health and metabolic disorders (for body mass index (BMI)). We compared the causal effects of pathway-partitioned SNPs on cardiometabolic outcomes with those derived using tissue-partitioned SNPs informed by colocalization with gene expression in kidney, artery (BP), or adipose and brain tissues (BMI). Additionally, we assessed the likelihood that estimates observed for partitioned exposures could emerge by chance using random SNP sampling.

Our pathway-partitioned findings suggest the causal relationship between systolic BP and heart disease is predominantly driven by vessel over renal pathways. The stronger effect attributed to kidney over artery tissue in our tissue-partitioned MR hints at a multifaceted interplay between pathways in the disease aetiology. We consistently identified a dominant role for vessel (pathway) and artery (tissue) driving the negative directional effect of diastolic BP on left ventricular stroke volume and positive directional effect of systolic BP on type 2 diabetes. We also found when dissecting the BMI pathway contribution to atrial fibrillation that metabolic-pathway and brain-tissue IVs predominantly drove the causal effects relative to mental health and adipose in pathway- and tissue-partitioned MR analyses, respectively.

This study presents a novel approach to dissecting heterogeneity in MR by integrating clinical phenotypes associated with Mendelian disease. Our findings emphasize the importance of understanding pathway-/tissue-specific contributions to complex exposures when interpreting causal relationships in MR. Importantly, we advocate caution and robust validation when interpreting pathway-partitioned effect size differences.

Precise gene editing with conventional CRISPR/Cas9 is often constrained by low knock-in (KI) efficiencies (≈ 2-20 %) in human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). This limitation typically necessitates labour-intensive manual isolation and genotyping of hundreds of colonies to identify correctly edited cells. Fluorescence- or antibiotic-based enrichment methods facilitate the identification process but can compromise cell viability and genomic integrity. Here, we present a footprint-free editing strategy that combines low-density seeding with next-generation sequencing (NGS) to rapidly identify cell populations containing precisely modified clones. By optimising the transfection workflow and adhering to CRISPR/Cas9 KI design principles, we achieved high average editing efficiencies of 64 % in hiPSCs (introducing a Brugada syndrome-associated variant) and 51 % in hESCs (introducing a neurodevelopmental disorder (NDD)-associated variant). Furthermore, under suboptimal CRISPR design conditions, this approach successfully identified hESC clones carrying a second NDD-associated variant, despite average KI efficiencies below 1 %. Importantly, genomic integrity was preserved throughout subcloning rounds, as confirmed by Sanger sequencing and single nucleotide polymorphism (SNP) array analysis. Hence, this NGS-based enrichment strategy reliably identifies desired KI clones under both optimal and challenging conditions, reducing the need for extensive colony screening and offering an effective alternative to fluorescence- and antibiotic-based selection methods.

Effective exploration and analysis tools are vital for the extraction of insights from single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., samples) require restrictive assumptions or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that reduction and insight in single-cell exploration (RISE), an adaptation of the tensor decomposition method PARAFAC2, enables the dimensionality reduction and analysis of single-cell data across conditions. We demonstrate the benefits of RISE across distinct examples of single-cell RNA-sequencing experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus patient samples. RISE enables associations of gene variation patterns with patients or perturbations while connecting each coordinated change to single cells without requiring cell-type annotations. The theoretical grounding of RISE suggests a unified framework for many single-cell data modeling tasks while providing an intuitive dimensionality reduction approach for multi-sample single-cell studies across biological contexts. A record of this paper's transparent peer review process is included in the supplemental information.

Changes in biological pathways provide essential clues about metabolism. Genome-scale metabolic models (GEM) are network-based templates that computationally describe all stoichiometric associations and gene-protein reaction (GPR) relations found in an organism for all its metabolic genes and metabolites. Using reaction stoichiometry as input, GEMs mathematically simulate metabolic reaction fluxes occurring in an organism and predict changes in the metabolic system under the relevant condition. Multiple tools and approaches in the literature can capture fluxes sensitive to a given condition by using GEMs. However, functional enrichment analysis of these reaction lists in a systems biology perspective is not straightforward. Here, we introduce RSEA to annotate given reaction sets to significantly related metabolic pathways: Reaction Set Enrichment Analysis web server tool. RSEA converts given reaction list derived from GEMs into proper reaction identifiers and statistically analyze its enrichment in metabolic pathways. RSEA is designed to provide researchers with a practical and user-friendly platform to explore and interpret sets of reactions in biological pathways and freely available online (https://rseatool.com/).

Chromosomal instability (CIN) drives tumor heterogeneity, complicating cancer therapy. Although Polo-like kinase 1 (PLK1) overexpression induces CIN, direct inhibition of PLK1 has shown limited clinical benefits. We therefore performed a genome-wide synthetic dosage lethality (SDL) screen to identify effective alternative targets and validated over 100 candidates using in vivo and in vitro secondary CRISPR screens. We employed direct-capture Perturb-seq to assess the transcriptional consequences and viability of each SDL perturbation at a single-cell resolution. This revealed IGF2BP2 as a critical genetic dependency that, when targeted, downregulated PLK1 and significantly restricted tumor growth. Mechanistic analyses showed that IGF2BP2 loss disrupted cellular energy metabolism and mitochondrial ATP production by downregulating PLK1 levels as well as genes associated with oxidative phosphorylation. Consistent with this, pharmacological inhibition of IGF2BP2 severely impacts the viability of PLK1-overexpressing cancer cells addicted to higher metabolic rates. Our work offers a novel therapeutic strategy against PLK1-driven heterogeneous malignancies.

Regulatory B cells (Bregs) are crucial for maintaining homeostasis and controlling inflammation. Although interleukin (IL)-10 has been traditionally suggested as the primary suppressive mechanism of Bregs in both mice and humans, the key functional differences between Bregs in these two species, particularly in the context of disease, is still largely unresolved. IL-37, the latest described immunosuppressive cytokine, is produced in humans but not in mice. Herein we identified the characteristics and functions of IL-37-producing Bregs, that naturally exist in human and can be induced by recombinant IL-37 (rIL-37) and/or Toll-like receptor 9 agonist CpG via different mechanisms. rIL-37 alone is sufficient to prompt IL-37, but not IL-10, production and proliferation of Bregs, whereas CpG elicits IL-37 expression in Bregs independently of IL-10, but dependent on HIF-1α which binds on the enhancer/promoter of the IL-37 gene. Functionally, IL-37+ Bregs exhibit superior anti-inflammatory efficacy than IL-37- Bregs in vitro, as well as in psoriasis and colitis models. However, the frequency of IL-37+ Bregs is reduced in patients with psoriasis. Thus, IL-37+ Bregs hold significant therapeutic potential for treating various inflammatory disorders, including psoriasis and colitis.

Temporal lobe epilepsy (TLE) is a brain network disorder closely associated with synaptic loss and has a genetic basis. However, the in vivo whole-brain synaptic changes at the network-level and the underlying gene expression patterns in patients with TLE remain unclear.

In this study, we utilized a positron emission tomography with the synaptic vesicle glycoprotein 2 A radioligand [18F]SynVesT-1 cohort and two independent transcriptome datasets to investigate the topological properties of the synaptic density similarity network (SDSN) in TLE and its correlation with significantly dysregulated risk genes.

We observed an overall decrease in strength, reduced clustering coefficient, and increased path length of SDSN in TLE, suggesting a loss of connectivity that is accompanied by network reorganization. These changes were predominantly distributed in the temporo-limbic circuit and fronto-parietal networks. Moreover, connectivity changes in SDSN were found to be spatially correlated with the brain-wide expression of TLE risk genes, and the transcriptional correlate of SDSN changes showed a significant relationship with gene dysregulation. In particular, we identified a total of 183 downregulated genes that were functionally enriched for synaptic transmission pathways, forming a highly connected genetic interaction network. Within this set of genes, GABAergic genes such as RBFOX1 play a central role.

Our study provides the first evidence that the spatial expression patterns of downregulated risk genes underlie in vivo synaptic density network dysfunction in TLE. These imaging-transcriptomic findings have the potential to guide the development of molecular and genetic network-based therapeutic approaches for TLE.

Complement 3 (C3) glomerulopathy (C3G) is a rare but clinically significant glomerulopathy. However, little is known about its transcriptomic profile. We investigated the substructure-specific gene expression profile of C3G using the recently introduced spatial transcriptomics technology.

We performed spatial transcriptomic profiling using GeoMx Digital Spatial Profiler with formalin-fixed paraffin-embedded kidney biopsy specimens of three C3G cases and seven controls from donor kidney biopsy. Additionally, 41 samples of other glomerulonephritis, including focal segmental glomerulosclerosis, membranous nephropathy and minimal change disease, were included as disease controls. We identified differentially expressed genes (DEGs) specific to C3G, followed by in vitro validation analysis of consistently upregulated DEGs in human glomerular endothelial cells through a co-culture with complement-stimulated macrophages.

We found 229 and 157 highly expressed DEGs in the glomeruli of C3G compared with those of donor and disease controls, respectively, including POSTN, COL1A2 and IFI44L. Protease binding, structural molecule activity and extracellular matrix (ECM) structural constituent were among the top enriched Gene Ontology terms in the glomeruli of C3G. Specifically, genes related to the ECM and interferon activity were the most upregulated, with network analysis suggesting possible interactions between complement C3 and the ECM through CD11c. The in vitro experimental validation using iC3b-stimulated CD11c+ macrophages supported these findings, inducing elevated expression of fibrosis markers and ECM components in glomerular endothelial cells.

Significant disease-specific transcriptomic alterations in C3G, including upregulation of genes related to the ECM, provide potential insights into the pathophysiology.

Despite the successful development of vaccines and antiviral therapeutics against SARS-CoV-2, its tendency to mutate rapidly has emphasized the need for continued research to better understand this virus's mechanism of pathogenesis and interactions with host signaling pathways. In this study, we sought to explore how the SARS-CoV-2 non-structural protein 13 (Nsp13) helicase, a highly conserved coronavirus protein that is essential for viral replication, influences host biological and cellular processes. Global transcriptomic analyses of Nsp13-transfected A549 cells identified changes in pathways involved in post-transcriptional gene silencing and translational repression by RNA, such as microRNAs (miRNAs). Upon further bioinformatic analyses, we identified miR-146a-mediated signaling pathways to be of interest as this miRNA has been previously linked to the regulation of host inflammation and innate immune responses. We found that miR-146a was induced in Nsp13-transfected cells and observed a corresponding decrease in the gene expression of two miR-146a targets, TRAF6 and IRAK1, which are important upstream regulators of NF-kB activation and IFN signaling. These results suggest that Nsp13-induced miR-146a signaling cascades, namely NF-kB activation and SMAD4 signaling, may provide valuable insight for the development of novel antiviral therapeutics against COVID-19 variants.

Over 10% of the US population over 12 years old meets criteria for alcohol use disorder (AUD), yet few effective, long-term treatments are currently available. Glycogen synthase kinase 3-beta (GSK3β) has been implicated in ethanol behaviours and poses as a potential therapeutic target in the treatment of AUD. Here, we investigated the preclinical evidence for tideglusib, a clinically available selective GSK3β inhibitor, in modulating chronic and binge ethanol consumption. Tideglusib decreased ethanol consumption in both a model of daily, progressive ethanol intake (two-bottle choice, intermittent ethanol access) and binge-like drinking behaviour (drinking in the dark) without effecting water intake. With drinking in the dark, tideglusib was more potent in males (ED50 = 64.6, CI = 58.9-70.8) than females (ED50 = 79.4, CI = 70.8-93.3). Further, we found tideglusib had no effect on ethanol pharmacokinetics, taste preference or anxiety-like behaviour, although there was a transient increase in total locomotion following treatment. Additionally, tideglusib treatment did not alter liver function as measured by serum activity of alanine aminotransferase and aspartate aminotransferase but did cause a decrease in serum alkaline phosphatase activity. RNA sequencing analysis of tideglusib actions on ethanol consumption revealed alterations in genes involved in synaptic plasticity and transmission, as well as genes downstream of the canonical Wnt signalling pathway, suggesting tideglusib may modulate ethanol consumption via β-catenin binding to the transcription factors TCF3 and LEF1. The data presented here further implicate GSK3β in alcohol consumption and support the use of tideglusib as a potential therapeutic in the treatment of AUD.

Cutaneous leishmaniasis (CL) is characterized by polymorphic dermal lesions and remains a major public health concern worldwide. This study assessed the impact of different Moroccan Leishmania major strains on host immunopathology. Swiss mice were infected with five L. major strains from Tinghir and Zagora Moroccan endemic foci and sacrificed at 3 and 13 weeks post-infection (p.i). Mice exhibited distinct infection profiles, with lesions appearing between the 2nd and 3rd weeks p.i and stabilizing between the 8th and 12th weeks pi. Two-way ANOVA showed a significant association between lesion size and strain region (p < 0.01), with Zagora strains exhibiting the largest lesions. RT-qPCR analysis revealed that Zagora strains downregulated IL-1β in draining lymph nodes (DLNs) and footpads at 3 and 13 weeks p.i respectively; they also downregulated iNOS in footpads and DLNs at 13 weeks p.i. Unsupervised principal component analysis, integrating lesion size, IL-1β, and iNOS expression with strain region, organ, and infection time, revealed significant associations among these parameters. By integrating these significant parameters, we built a multivariable model with IL-1β quantification as the outcome. This model revealed a positive association of IL-1β with iNOS (p < 0.001), as well as with the spleen (p < 0.001) and footpad (p < 0.01). Conversely, it showed a negative association of IL-1β with the Zagora strains (p < 0.05) and with infection time (13 weeks pi; p < 0.05). Transcriptome analysis highlighted early IL-1β induction in L. major infection, associated with an inflammatory response. Thus, IL-1β and iNOS modulation by L. major strains may explain the clinical polymorphism of CL patients' lesions.

Hirschsprung disease (HSCR) is a rare, congenital disease characterized by the absence of enteric ganglia in the hindgut. Common genetic variation contributes substantially to the heritability of the disease yet only three HSCR-associated loci were identified from genome-wide association studies (GWAS) thus far.

We performed the largest multi-ancestry meta-analysis of GWAS to date, totalling 1250 HSCR cases and 7140 controls. Prioritized candidate genes were further characterized using single-cell transcriptomic data of developing human and mouse gut for their roles in development of enteric nervous system (ENS). Functional characterisation using human cells and zebrafish models was performed. Global and ancestry-matched polygenic risk score (PRS) models were derived and evaluated for predicting risk of HSCR.

We identified four HSCR-susceptibility loci, with three loci (JAG1, HAND2 and ZNF25) reaching genome-wide significance and one putative locus (UNC5C) prioritized by functional relevance. Spatiotemporal analysis revealed hotspots of gene dysregulation during ENS development. Functional analyses further demonstrated that knockdown of the candidate genes impaired cell migration and zebrafish knockouts displayed abnormal ENS development. We also demonstrated comparable performance for a PRS model derived from multi-ancestry meta-analysis to those of ancestry-matched PRS models, supporting its potential clinical application in risk prediction of HSCR across populations.

Overall, the meta-analysis implicated novel genes, pathways and spatiotemporal developmental hotspots in the genetic aetiology of HSCR. Development of a PRS universally applicable irrespective of ancestries may leverage its clinical utility in risk prediction.

The full list of funding bodies can be found in the Acknowledgements section.

Understanding the interplay among clinical variables-such as demographics, symptoms, and laboratory results-and their relationships with disease outcomes is critical for advancing diagnostics and understanding mechanisms in complex diseases. Existing methods fail to capture indirect or directional relationships, while existing Bayesian network learning methods are computationally expensive and only infer general associations without focusing on disease outcomes. Here we introduce random walk- and genetic algorithm-based network inference (RAMEN), a method for Bayesian network inference that uses absorbing random walks to prioritize outcome-relevant variables and a genetic algorithm for efficient network refinement. Applied to COVID-19 (Biobanque québécoise de la COVID-19), intensive care unit (ICU) septicemia (MIMIC-III), and COPD (CanCOLD) datasets, RAMEN reconstructs networks linking clinical markers to disease outcomes, such as elevated lactate levels in ICU patients. RAMEN demonstrates advantages in computational efficiency and scalability compared to existing methods. By modeling outcome-specific relationships, RAMEN provides a robust tool for uncovering critical disease mechanisms, advancing diagnostics, and enabling personalized treatment strategies.

Pathogenic mutation of the zinc-finger transcription factor ZNF292 is a recently defined contributor to human neurodevelopmental disorders (NDDs). However, the gene's roles in cortical development and regulatory networks under its control were previously undefined. Here, human stem cell models of ZNF292 deficiency, resembling pathogenic haploinsufficiency, are used to derive cortical inhibitory neuron progenitors and neurons. ZNF292-deficient progenitors undergo precocious differentiation but subsequently exhibit compromised interneuron maturation and function. In progenitors, genome-wide occupancy and transcriptomic analyses identify direct target genes controlling neuronal differentiation and synapse formation that are upregulated upon ZNF292 deficiency. By contrast, deficiency in interneurons compromises ZNF292 genome-wide association with and causes downregulation of direct target genes promoting interneuron maturation and function, including other NDD genes. ZNF292-deficient interneurons also exhibit altered channel activities, elevated GABA responsiveness, and hallmarks of neuronal hyperactivity. Together, the results of this work define neurodevelopmental requirements for ZNF292, some of which may contribute to pathogenic ZNF292 mutation-related NDDs.

Wilms Tumor (WT), a prevalent pediatric renal malignancy, exhibits marked heterogeneity and variable clinical outcomes. Epithelial-mesenchymal transition (EMT), a biological process enabling epithelial cells to acquire mesenchymal traits associated with enhanced migratory and invasive capacities, plays a crucial role in cancer progression. Protein Regulator of Cytokinesis 1 (PRC1) is a critical protein in cell division, whose overexpression is linked to poor prognosis in various cancers. This study investigates the role of PRC1 as a key prognostic factor in WT and explore the mechanism through comprehensive bioinformatic and experimental approaches. Through bulk RNA-seq data from the TARGET database, we identified PRC1 as significantly up-regulated in WT and associated with poor overall survival. Functional enrichment analyses (GO, KEGG, GSEA) demonstrated PRC1's involvement in cell division, chromatin dynamics, and activation of oncogenic pathways including Wnt/β-catenin, PI3K/AKT/mTOR, and Hedgehog signaling. Immunological analysis showed that elevated PRC1 expression correlates with diminished immune cell activity, particularly in NK cells, suggesting potential immune evasion mechanisms. Single-cell RNA-seq analysis (GSE200256) confirmed PRC1's elevated expression in anaplastic Wilms tumor (AWT) compared to favorable Wilms tumor (FWT), and highlighted its involvement in intercellular communication and metastasis via the EMT process. Genomic analyses identified copy number variations (CNVs) and downregulated PRC1-targeting microRNAs as drivers of its overexpression. In vitro, PRC1 knockdown in WIT-49 cells significantly impaired migratory capacity, invasive potential, EMT progression, and glycolytic metabolism. These findings collectively position PRC1 as a promising therapeutic target and prognostic biomarker in WT.

Both schizophrenia (SCZ) and Alzheimer's disease (AD) are highly heritable brain disorders. Despite of the observed comorbidity and shared psychosis and cognitive decline between the two disorders, the genetic risk architecture shared by SCZ and AD remains largely unknown. Based on summary statistics of the currently available largest genome-wide association studies for SCZ (n = 130,644) and AD (n = 455,258) in individuals of European ancestry, we conducted conditional/conjunctional false discovery rate (FDR) analysis to enhance the statistical power for discovering more genetic associations with SCZ or AD and to detect the common genetic variants shared by both disorders. We found shared genetic architecture in SCZ conditioned on AD and vice versa across different levels of significance, indicating polygenic overlap. We found 268 (78 novel) SCZ-only and 125 (55 novel) AD-only SNPs at conditional FDR < 0.01, and 16 lead SNPs shared by SCZ and AD at conjunctional FDR < 0.05. Only half of the shared SNPs showed concordant effect direction, which was consistent with the modest genetic correlation (r = 0.097; P = 0.026) between the two disorders. This study provides evidence for polygenic overlap between SCZ and AD, suggesting the existence of the shared molecular genetic mechanisms, which may inform therapeutic targets that are applicable for both disorders.

Monocytes differentiate into macrophages (Mφs) to facilitate lung metastasis, but the monocyte-to-Mφ transition during this process is not well understood. To investigate, we performed bulk RNA sequencing on Mφs isolated from the lungs of mice bearing Lewis lung carcinoma tumors and from naive lungs. Our results showed impaired differentiation of monocytes into major histocompatibility complex (MHC) class II+ Mφs, with an upregulation of PGE2-inducible genes, including Arg1, in tumor-associated Mφs (TAMs). In vitro experiments confirmed that prostaglandin E2 (PGE2) inhibits the differentiation of MHC class II+ Mφs while promoting Arg1+ Mφs via the E prostanoid 2 (EP2) receptor, accompanied by DNA methylation. Whole-genome bisulfite sequencing revealed that PGE2-EP2 signaling drives the hypermethylation and downregulation of gene sets related to myeloid cells in non-neoplastic tissues. Our study highlights PGE2-EP2-driven DNA methylation in the monocyte-to-TAM transition, suggesting potential therapeutic avenues for lung metastasis.

Leflunomide's anti-tumor effects have been investigated in various types of tumors; however, its impact on pituitary adenoma, particularly prolactinoma, is unclear. Hence, the current study evaluates the effects of leflunomide on prolactinoma cells in vitro and in vivo and elucidates the potential underlying mechanism(s). Cell Counting Kit-8 results revealed that leflunomide inhibits the proliferation of rat pituitary tumor cell lines (GH3 and MMQ) in a concentration-dependent manner in vitro. However, combination therapy of cabergoline and leflunomide exerted stronger inhibitory effects than cabergoline in MMQ cells in vitro and in vivo. Transcriptomics and gene ontology (GO) analyses identified genes significantly enriched in apoptotic processes and programmed cell death. Protein-Protein Interaction (PPI) networks defined the roles of hub genes (Mdm2, Cdkn1a, Plk2, and Ccng1) in leflunomide-induced cell death. GO and pathway enrichment analyses showed that the combination drug-specific differentially expressed genes were associated with inhibiting protein translation, but were active in gene expression processes. Hence, the anti-proliferative effects of leflunomide on prolactinoma cell lines may be mediated through programmed cell death pathways. Importantly, combining cabergoline with leflunomide effectively enhances the toxic effect of cabergoline, suggesting a potential therapeutic role for leflunomide in drug-resistant prolactinoma.

The brain overlapping system-level architecture is associated with functional information integration in the multiple roles of the same region, and it has been developed as an underlying novel biomarker of brain disease and may characterise the indicators for the treatment of Alzheimer's disease (AD). However, it remains uncertain whether these changes are influenced by external magnetic stimulation and internal gene expression. A total of 73 AD-spectrum patients (52 with true stimulation and 21 with sham stimulation) were underwent four-week neuronavigated transcranial magnetic stimulation (rTMS). Shannon-entropy diversity coefficient analysis was used to explore the brain overlapping system of the neuroimaging data in these pre- and posttreatment patients. Transcription-neuroimaging association analysis was further performed via gene expression data from the Allen Human Brain Atlas. Compared with the rTMS_sham stimulation group, the rTMS_true stimulation group achieved the goal of cognitive improvement through the reconstruction of functional information integration in the multiple roles of 27 regions associated with the brain overlapping system, involving the attentional network, sensorimotor network, default mode network and limbic network. Furthermore, these overlapping regions were closely linked to gene expression on cellular homeostasis and immune inflammation, and support vector regression analysis revealed that the baseline diversity coefficients of the attentional and sensorimotor networks can effectively predict memory improvement after rTMS treatment. These findings highlight the brain overlapping system associated with cognitive improvement, and provide the first evidence that external magnetic stimulation and internal gene expression could influence these overlapping regions in AD-spectrum patients.

Schizophrenia (SCZ) and depression are two prevalent mental disorders characterized by comorbidity and overlapping symptoms, yet the underlying genetic and neural mechanisms remain largely elusive. Here, we investigated the genetic variants and neuroimaging changes shared by SCZ and depression in Europeans and then extended our investigation to cross-ancestry (Europeans and East Asians) populations. Using conditional and conjunctional analyses, we found 213 genetic variants shared by SCZ and depression in Europeans, of which 82.6% were replicated in the cross-ancestry population. The shared risk variants exhibited a higher degree of deleteriousness than random and were enriched for synapse-related functions, among which fewer than 3% of shared variants showed horizontal pleiotropy between the two disorders. Mendelian randomization analyses indicated reciprocal causal effects between SCZ and depression. Using multiple trait genetic colocalization analyses, we pinpointed 13 volume phenotypes shared by SCZ and depression. Particularly noteworthy were the shared volume reductions in the left insula and planum polare, which were validated through large-scale meta-analyses of previous studies and independent neuroimaging datasets of first-episode drug-naïve patients. These findings suggest that the shared genetic risk variants, synapse dysfunction, and brain structural changes may underlie the comorbidity and symptom overlap between SCZ and depression.

Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains largely unexplored. In this study, we systematically analyzed 17,329 human transcriptomes to investigate how TEs influence gene transcription across 47 adult tissues. Our findings reveal that TE-derived transcripts are broadly expressed in human tissues, contributing to both housekeeping functions and tissue-specific gene regulation. We identified sex-specific expression of TE-derived transcripts regulated by sex hormones in breast tissue between females and males. Our results demonstrated that TE-derived alternative transcription initiation significantly enhances the variety of translated protein products, e.g., changes in the N-terminal peptide length of WNT2B caused by TE-derived transcription result in isoform-specific subcellular localization. Additionally, we identified 68 human-specific TE-derived transcripts associated with metabolic processes and environmental adaptation. Together, these findings highlight the pivotal evolutionary role of TEs in shaping the human transcriptome, demonstrating how conserved and human-specific TEs contribute to transcriptional and translational innovation in human genome evolution.

Simiao Biejia (SMBJ) granules, a traditional Chinese herbal remedy, have been used to treat erectile dysfunction caused by diabetes mellitus (DMED). However, the molecular mechanisms underlying SMBJ's therapeutic effects remain unclear. This study aimed to investigate the effects and mechanisms of SMBJ in a rat model of DMED using network pharmacology, proteomics, and molecular docking.

A rat model of DMED was established, and SMBJ granules were administered (0, 7.1, 14.2, and 28.4 mg/kg/d, respectively) for 4 weeks. Erectile function was evaluated by measuring intracavernous pressure and mean arterial pressure. The active compounds in SMBJ were analyzed by gas chromatography and identified using network pharmacology and bioinformatics. Potential targets in the penile tissue was identified via proteomics and validated by Western blotting. Molecular docking was used to assess the binding affinity between bioactive compounds and primary targets.

SMBJ significantly improves erectile function and ameliorates DMED in rats by reducing corpus cavernosum fibrosis, decreasing eNOS and nNOS levels, alleviating oxidative stress in penile tissue, and mitigating damage to smooth muscle cells (SMCs) and vascular endothelial cells (VECs). Network pharmacology and proteomics identified 24 potential SMBJ targets in DMED. The 4 drug molecules identified were involved in the therapeutic effects of SMBJ, among which luteolin was predicted to be the core drug component. Luteolin bound directly with AKT1, a key differentially expressed protein in the penile tissue of DMED rats. Further analysis showed that luteolin in SMBJ activates the PI3K/Akt pathway and regulation of nNOS and NF-kB expression in the penile tissue of DMED rats to improve erectile function.

SMBJ improved oxidative stress damage, vascular endothelial repair, and angiogenesis in the penile tissue of DMED rats. Luteolin is one of the core drug components of SMBJ in DMED treatment that regulates PI3K/AKT-related pathways.

Neuropathic pain is a debilitating chronic condition that remains difficult to treat. More efficacious and safer therapeutics are needed. A potential target for therapeutic intervention recently identified by our group is the G-protein coupled receptor 160 (GPR160) and the cocaine- and amphetamine-regulated transcript peptide (CARTp) as a ligand for GPR160. Intrathecal administration of CARTp in rodents causes GPR160-dependent behavioral hypersensitivities. However, the molecular and biochemical mechanisms underpinning GPR160/CARTp-induced behavioral hypersensitivities in the spinal cord remain poorly understood. Therefore, we performed an unbiased RNA transcriptomics screen of dorsal horn spinal cord (DH-SC) tissues harvested at the time of peak CARTp-induced hypersensitivities and identified nucleotide-binding oligomerization domain-containing protein 2 ( Nod2 ) as a gene that is significantly upregulated. Nucleotide-binding oligomerization domain-containing protein 2 is a cytosolic pattern-recognition receptor involved in activating the immune system in response to bacterial pathogens. While NOD2 is well studied under pathogenic conditions, the role of NOD2-mediated responses in nonpathogenic settings is still not well characterized. Genetic and pharmacological approaches reveal that CARTp-induced behavioral hypersensitivities are driven by NOD2, with co-immunoprecipitation studies indicating an interaction between GPR160 and NOD2. Cocaine- and amphetamine-regulated transcript peptide-induced behavioral hypersensitivities are independent of receptor-interacting protein kinase 2 (RIPK2), a common adaptor protein to NOD2. Immunofluorescence studies found NOD2 co-expressed with endothelial cells rather than glial cells, implicating potential roles for CARTp/NOD2 signaling in these cells. While these findings are based only on studies with male mice, our results identify a novel pathway by which CARTp causes behavioral hypersensitivities in the DH-SC through NOD2 and highlights the importance of NOD2-mediated responses in nonpathogenic settings.

Senescence is a tumor suppressor mechanism triggered by oncogene expression and chemotherapy treatment. It orchestrates a definitive cessation of cell proliferation through the activation of the p53-p21 and p16-Rb pathways, coupled with the compaction of proliferative genes within heterochromatin regions. Some cancer cells have the ability to elude this proliferative arrest but the signaling pathways involved in circumventing senescence remain to be characterized. We have recently described that malignant cells capable of evading senescence have an increased expression of specific tRNAs, such as tRNA-Leu-CAA and tRNA-Tyr-GTA, alongside the activation of their corresponding tRNA ligases, namely LARS and YARS. We have previously shown that YARS promotes senescence escape by activating proliferation and cell cycle genes but its functions during this proliferative arrest remain largely unknown. In this study, we have continued to characterize the functions of YARS, describing non-canonical transcriptional functions of the ligase. Our results show that YARS is present in the nucleus of proliferating and senescent cells and interacts with the Trim28 transcriptional regulator. Importantly, YARS binds to the LIN9 promoter, a critical member of the Dream complex responsible for regulating cell cycle gene transcription. The ligase facilitates the binding and the phosphorylation of the type II RNA polymerase and promotes the deposition of activating epigenetic marks on the LIN9 promoter. Consequently, during senescence escape, YARS activates LIN9 expression and both proteins are necessary to induce the proliferation of emergent cells. These results underscore unconventional transcriptional functions of YARS in activating LIN9 expression in proliferating cells and during senescence escape.

The amygdala is a small but critical multi-nucleus structure for emotion, cognition and neuropsychiatric disorders. Although genetic associations with amygdala volumetric traits have been investigated in sex-combined European populations, cross-ancestry and sex-stratified analyses are lacking. Here we conducted cross-ancestry and sex-stratified genome-wide association analyses for 21 amygdala volumetric traits in 6,923 Chinese and 48,634 European individuals. We identified 191 variant-trait associations (P < 2.38 × 10-9), including 47 new associations (12 new loci) in sex-combined univariate analyses and seven additional new loci in sex-combined and sex-stratified multivariate analyses. We identified 12 ancestry-specific and two sex-specific associations. The identified genetic variants include 16 fine-mapped causal variants and regulate amygdala and fetal brain gene expression. The variants were enriched for brain development and colocalized with mood, cognition and neuropsychiatric disorders. These results indicate that cross-ancestry and sex-stratified genetic association analyses may provide insight into the genetic architectures of amygdala and subnucleus volumes.

Dilated cardiomyopathy (DCM) is the most common type of myocardial dysfunction, affecting mostly young adults, but its therapeutic diagnosis and biomarkers for prognosis are lacking. This study aimed to investigate the possible effect of the common food additive monosodium glutamate (MSG) and tannic acid (TA), a phenolic compound, on the key molecular actors responsible for DCM. DCM-related publicly available microarray datasets (GSE120895, GSE17800, and GSE19303) were downloaded from the comprehensive Gene Expression Omnibus (GEO) database, and analyzed to identify differentially expressed genes (DEGs). By integrating DEGs and gene-disease validity curation results, overlapping genes were screened and identified as hub genes. Protein-protein interaction (PPI) network and ontology analysis were performed to make sense of the identified biological data. Finally, mRNA expression changes of identified hub genes in the heart tissues of rats treated with MSG and TA were measured by the qPCR method. Six upregulated (IGF1, TTN, ACTB, LMNA, EDN1, and NPPB) DEGs were identified between the DCM and healthy control samples as the hub genes. qPCR results revealed that the mRNA levels of these genes involved in DCM development increased significantly in rat heart tissues exposed to MSG. In contrast, this increase was remarkably alleviated by TA treatment. Our results provide new insights into critical molecular mechanisms that should be focused on in future DCM studies. Moreover, MSG may play a critical role in DCM formation, and TA may be used as a promising therapeutic agent in DCM.