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Age-related hearing loss (ARHL) disrupts ascending auditory inputs, impairing auditory signal transmission, triggering cortical hyperexcitability, and increasing the risk of age-related cognitive decline. In early aging, multisession epidural direct current stimulation (DCS) of the auditory cortex (AC) preserves auditory thresholds and prevents cortical hyperexcitability in Wistar rats. Here, we hypothesized that multisession DCS could halt transcriptional dysregulation in the AC at the earliest stages of aging. We have characterized age-related transcriptional changes in the AC to assess DCS-mediated effects by RNA-seq. At 18.13 months, non-stimulated, aged rats (NES) showed 194 differentially expressed genes (DEGs) in relation to young controls (YG), with enrichment in pathways associated with GABAergic, glutamatergic, and dopaminergic synapses, long-term potentiation/depression, inflammaging, autophagy, apoptosis and neurodegeneration. The upregulated genes included Gabrb1, Grin2b, Rac3c, Tnr, and Ndst1, suggesting compensatory hyperactivity, excitatory/inhibitory imbalance, and stiffening of perineuronal nets (PNN) around parvalbumin (PV) interneurons. Electrically stimulated (ES) rats showed 86 DEGs in relation to YG, with no significant enrichment in aging-related pathways. By contrast, NES vs ES showed 1393 DEGs, with strong enrichment in aging-related pathways. Also, many of the 121 common DEGs across comparisons, which are upregulated in NES and downregulated in ES, are related to neurotransmission (Gabrb1, Grin2b), synaptic scaffolding (Dlg2, Prkca), trophic signaling (Ntrk2, Igf1r) and PNN (Tnr, Ndst1). Based on these findings, multisession DCS curbs maladaptive genomic reprogramming in the aged AC most likely by preserving excitatory/inhibitory balance and maintaining PNN integrity, thereby protecting the AC from ARHL and cognitive vulnerability. Show less

Ambient air pollution contributes to chronic obstructive pulmonary disease (COPD), but the genetic factors that may influence susceptibility remain poorly defined. We conducted a genome-wide interaction analysis to identify genetic markers that may modify the association between air pollution and COPD. We analyzed data from 16,839 Canadian Longitudinal Study of Aging participants, including spirometry, genome-wide genotype data (645,625 single-nucleotide polymorphisms [SNPs]), and air pollution exposure estimates. COPD was defined as a forced expiratory volume in 1 second to forced vital capacity ratio (FEV Show less

Neurotoxicity induced by excessive glutamatergic signaling is associated with synaptic dysfunction, calcium imbalance, and oxidative stress, which are key molecular events implicated in several neurodegenerative conditions. Monosodium glutamate (MSG), a common flavor enhancer, may exert neurotoxic effects, particularly on synaptic integrity, though mechanisms remain unclear. Tannic acid (TA), a natural polyphenol, has been proposed as a neuroprotective compound. This study investigated the impact of MSG on synaptic components beyond classical AD markers and assessed the protective potential of TA. Rats were randomly divided into four groups (n = 6 per group) and treated with MSG (2 g/kg) and/or TA (50 mg/kg) by oral gavage for 21 consecutive days. Gene and protein expression levels of the synaptic markers (GRIN2A, GRIN2B, DLG2, SNAP25, SCN2A, and ATP2B2) in the cerebral cortex were analyzed using qPCR and western blot. MSG treatment significantly downregulated SNAP25, GRIN2B, DLG2, and SCN2A at both mRNA and protein levels, indicating synaptic dysfunction. GRIN2A and ATP2B2 showed reduced mRNA expression, but protein levels were inconsistent. MSG+TA group showed no significant difference compared with the control group, while TA alone produced minimal changes, suggesting that its role is primarily protective under toxic stress. These findings suggest that chronic MSG exposure disrupts synaptic molecular architecture, whereas the restorative effect of TA may be attributed to its ability to modulate MSG-induced molecular alterations. The data emphasize synaptic pathways as alternative neurotoxicity targets and highlight TA's potential in mitigating diet-related excitotoxic synaptic alterations. Further functional and pathway-based studies are needed to confirm the underlying mechanisms. Show less

A low ankle-brachial Index (ABI) is an established condition for peripheral artery disease (PAD) and cardiovascular disease risk. The search for genetic determinants of the ankle-brachial index (ABI) is important to better understand molecular patho-cmechanisms of PAD and its commonalities with cardiovascular diseases (CVD), supporting development of new drug targets and tailored preventive or therapeutic measures. To search for genetic factors contributing to ankle-brachial index, we integrated genome-wide association meta-analysis and transcriptome-wide association meta-analysis (TWAMA) of two German cohorts, the population-based LIFE-Adult cohort and LIFE-Heart, a cohort of patients with suspected or confirmed coronary artery disease. Pathway analysis of identified genes was used to explore biological mechanisms potentially involved in ABI pathophysiology. Finally, we analysed co-associations of known CAD or carotid plaque associations with ABI to detect possible genetic commonalities. By our GWAS meta-analysis, we identified four new gene loci associated with ABI that are also linked with coronary artery diseases (CAD) (6q26: LPA and 11q14.1: DLG2) or cholesterol levels (12q21.31: TMTC2 and Xp21.1: DMD). Furthermore, we replicated a known ABI locus on cytoband 9p21.3 (CDKN2B) and four loci associated with PAD. In our TWAMA, we identified 145 blood transcripts associated with ABI at FDR 5% level. Gene set enrichment analysis of all TWAMA results revealed the inflammation-related pathways interferon gamma response, neutrophil degranulation, and interferon alpha response as the top three upregulated pathways in patients with lower ABI. Among overlapping genes between blood TWAMA and tissue-specific genetically regulated gene-expression association analysis, 24 genes showed consistent effect directions at nominal significance, with lower ABI-associated genes relating to stress response and vascular integrity, while higher ABI-associated genes linked to cellular homeostasis and metabolism. In our integrated genome- and transcriptome-wide meta-analysis, we identified novel and confirmed known candidate genes and pathways associated with ABI. Association signals partly overlap with those of other cardiovascular traits such as CAD and carotid plaque formation. The integration of gene-expression data, validated known and added new molecular insight how inflammatory signalling can contribute to atherosclerosis and vascular dysfunction. These findings pave the way for improved understanding of the molecular underpinnings of PAD and inform future strategies for targeted prevention and therapy. Show less

Genome-wide scan for run of homozygosity (ROH) stretches, effective population size (Ne) and selection signatures can help to elucidate mechanisms of selection and pinpoint genomic regions linked with phenotypic traits. This study aimed to identify the genomic patterns of ROH, Ne and selection signatures in two Iranian main sheep breeds including Afshari and Qezel (known as meat and dairy sheep, respectively) using 49,017 single nucleotide polymorphisms (SNPs) generated using the ovine 50K SNP BeadChips. Analysis of ROH in Iranian sheep breeds revealed the differences in the pattern of ROH length and burden in these breeds. Inbreeding estimated based on ROH stretches showed very low amount of inbreeding in these indigenous sheep breeds. The Qezel breed displayed a higher Ne than Afshari breed. Furthermore, the potential selection was detected in genomic regions using three complementary approaches including FST (fixation index), XP-EHH (cross-population extended haplotype homozygosity), and hapFLK (haplotype differentiation). Our results identified the genomic regions that were enriched with the genes associated with immune response (e.g., IL23A, STAT2 and DOCK5), milk traits (e.g., PCCA, ACAP3, TTK and BTG3), energy metabolisms (e.g., GLS2), reproduction (e.g., ANGPT2), fecundity (e.g., BMP5), nervous system (e.g., DLG2, PCDH9, and FRMPD4), growth traits and muscle formation (NPY, MYF5 and PPP1R12A), and sweat gland development (SCNN1D). Some regions were also detected for the first time and overlapped with no genes suggesting novel loci associated with traits that differentiate these breeds. Overall, the finding of this study may shed light on the genomic regions linked to economically important traits in sheep as well as for developing the conservation and selection breeding programs. Show less

Reproductive and growth traits are key economic traits in sheep. This study aims to identify key single nucleotide polymorphisms (SNPs) and candidate genes associated with reproductive and growth traits in Tianmu polytocous sheep through a genome-wide association study (GWAS). The findings are expected to provide both a theoretical foundation for molecular breeding in this breed and novel insights into the genetic basis of ovine reproductive and growth performance. This study took 483 adult Tianmu polytocous ewes as the research subjects, collected their lambing records, measured their phenotypic values of growth traits (3 weight and 11 body size traits), and collected their blood samples for whole-genome resequencing to identify SNPs in the Tianmu polytocous sheep genome. The results identified a total of 9,499,019 (3× coverage) and 27,413,216 (30× coverage) high-quality SNPs in the Tianmu polytocous sheep genome. Subsequently, the association analysis between SNPs and reproductive and growth traits was conducted using a mixed linear model. A total of 92, 66, 18, 28, 6, 42, 3, 3, 6, 1, 12, 3, 22, 8, 6, and 3 SNPs were found associated with litter size at first parity, litter size at second parity, litter size at third parity, litter size at fourth parity, birth weight, weaning weight, body height, withers height, body length, head length, head width, cannon bone circumference, forelimb height, chest girth, chest depth, and withers width, respectively. Further, based on SNP annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, candidate genes associated with the reproductive and growth traits were identified. Among these genes, 11 Show less

Osteosarcoma (OS) is the most common bone tumor in both dogs and humans. It predominantly occurs in the appendicular skeleton, with about 25% of cases occurring within the axial skeleton. Progression of local disease is often the life-limiting factor for patients with axial OS, in contrast to appendicular OS, where local disease is addressed surgically, and metastatic disease remains the primary obstacle. While OS is a rare human cancer, limiting the availability of samples, its higher incidence in dogs provides a valuable comparative model for study. Both canines and humans share commonalities in clinical presentation, but dogs have an accelerated progression. Similarly, complex structural genetic changes define appendicular OS in both dogs and people, but it is unclear whether the genomic landscape of axial OS exhibits different alterations that may separate it from appendicular OS. We performed pilot whole genome sequencing of canine primary oral (maxillary or mandibular) OS tumors (n = 8) and matched normal tissue. We found that the genetics of canine oral OS largely parallel the genetics of canine appendicular OS, including an overall low number of recurrent point mutations affecting the same gene (TP53 and SETD2, 3/8 samples). Structural variants dominated the landscape of mutational changes, with recurrent variants in DMD (4/8) and DLG2 (3/8) found at a similar incidence to appendicular OS. This pilot suggests genomic similarities between oral and appendicular OS. Show less

Discs large homolog 2 (DLG2) has been implicated in cancer development, yet its role in cervical cancer remains unclear. This study aims to explore the regulatory mechanism of DLG2 in cervical cancer and its clinical implications. Quantitative reverse transcription polymerase chain reaction and western blotting assays were employed to detect RNA and protein expression, respectively. Colony formation assay, 5-Ethynyl-2'-deoxyuridine assay, flow cytometry, and transwell assays were conducted for cell functional analysis. A xenograft mouse model assay was performed to analyze tumor tumorigenesis in vivo. m6A RNA immunoprecipitation assay was used to analyze the association of METTL3 and DLG2. DLG2 was underexpressed in cervical cancer tissues and cells. Elevating DLG2 levels significantly suppressed cervical cancer cell proliferation, migration, and invasion, while promoting apoptosis. Additionally, DLG2 overexpression led to the deactivation of the Hippo/YAP signaling pathway. In vivo, DLG2 overexpression was shown to reduce tumor formation. We also discovered that METTL3 destabilized DLG2 mRNA through an m6A-dependent mechanism. Moreover, lowering DLG2 expression mitigated the effects of METTL3 silencing on cervical cancer cell malignancy. DLG2 acted as a tumor suppressor in cervical cancer by inhibiting the Hippo/YAP signaling pathway. The METTL3-dependent regulation of DLG2 mRNA stability could be a critical factor in cervical cancer progression. Show less

1. Copy number variation (CNV) is an important source for identifying genetic differences. This study compared the genome-wide CNV and their regions (CNVR) across 16 Chinese local duck breeds and detected key genes and pathways involved in growth and reproduction-related traits using this dataset.2. Breakdancer, Pindel and CNVnator were used to detect reliable CNV, and HandyCNV was used to obtain CNVR. Selection signatures were analysed in meat (MD) and egg-laying ducks (ED) compared to wild ducks (WD) using fixation and differentiation index DIsv methods. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was carried out to identify key pathways and related genes.3. Principal component analysis (PCA) using CNV data clustered 127 ducks into 4 populations: WD, MD, ED and meat+egg-type ducks (MED). In total, 237,630 CNV and 6,176 CNVR were detected across these samples. Intersection analysis identified 1,384 common CNVR and 2,105 unique CNVR. The KEGG analysis showed that common CNVR were enriched in 7 basic life activity pathways, while unique CNVR were enriched in 9 population-specific pathways. Compared to WD, MD selection signatures were found in 4 enriched pathways and 8 genes ( Show less

Avian leukosis (AL), a major vertically transmitted infectious disease, poses a significant challenge to the conservation and industrial development of indigenous chicken breeds in China. In this study, Chengkou mountain chickens were used as a model to systematically identify genetic markers associated with resistance to avian leukosis virus subgroup J (ALV-J) through a genome-wide association study (GWAS). Genomic DNA was extracted from 500 hens at 300 days of age, and cloacal swabs, plasma, and egg white samples were collected to assess the ALV-J infection status. A total of 325 ALV-positive (ALV+) and 175 ALV-negative (ALV-) individuals were identified. Based on 10× whole-genome resequencing and stringent quality control, 12,644,463 high-quality SNPs were obtained. GWAS revealed a significant enrichment of SNPs on chromosome 6 (Chr6), from which 218 SNPs significantly associated with ALV-J resistance and 49 candidate genes were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that many of these genes, including Show less

Phosphorylation of alpha-synuclein (αsyn) at serine 129 (PS129) marks aggregates in synucleinopathies but also occurs physiologically, potentially signaling protein interactions during neuronal activity. Technical barriers, including postmortem dephosphorylation, have hindered the study of physiological PS129 in the human brain. Using biotinylation by antibody recognition (BAR) on surgically resected temporal lobectomy tissues (without post-mortem interval), we mapped physiological PS129 and total αsyn interactomes. BAR identified 1,095 interactions with 513 αsyn-specific, 524 shared, and 58 PS129-specific, mostly associated with vesicles at presynaptic nerve terminals. PS129-specific interactions were uniquely associated with postsynaptic density proteins SHANK1/3, DLGAP1-4, DLGAP1-3, and DLG2-4, as well as nuclear-associated proteins HUWE1, HNRNPM, RBM14, ITCH, OGT, PHF24, and PPP2R5E. Fluorescent staining confirmed physiological PS129 proximal to dendrites and within the nucleus. Confirmation in healthy cynomolgus macaques (62% αsyn and 41% PS129 overlap) demonstrated that the interactomes were physiological rather than disease- or aggregate-associated. We conclude that physiological PS129 plays a unique and underappreciated role in postsynaptic neurons extending from the postsynaptic active zone to the nucleus. These interactomes benchmark normal αsyn biology, illuminating the transition to synucleinopathy pathology. Disease-associated αsyn phosphorylation (PS129) was recently identified in healthy mammalian brain and may signal αsyn-protein interactions during neuronal activity. Here, we surmounted technical hurdles and characterized αsyn and PS129 interactomes directly in the human brain. Results showed a unique significance for PS129 in post-synaptic active zones and nuclear compartments, which was confirmed in healthy non-human primates. These αsyn interactomes will be a valuable reference for understanding synucleinopathy mechanisms in the context of normal αsyn biology. Show less

Schizophrenia (SZ) is a severe mental disorder with high heritability. DLG2 encodes the postsynaptic scaffolding protein DLG2 (PSD93, Postsynaptic Density Protein 93), and its variants were associated with an increased risk of SZ. However, the role of DLG2 locus variation in SZ remains elusive. This study aims to investigate the association between DLG2 gene polymorphisms and SZ susceptibility and the relationship between DLG2 and altered brain function and clinical symptoms in SZ patients. Single nucleotide polymorphisms (SNPs) rs11607886 and rs7479949 were genotyped in 350 SZ patients and 407 healthy controls (HCs). 47 SZ patients and 79 HCs were genotyped into two groups: the risk A allele carrier group and the GG-pure group. Functional magnetic resonance imaging (fMRI) indices were further analyzed. Subsequently, data from different brain regions were correlated with clinical symptom assessment. DLG2 rs11607886 was significantly associated with SZ. Significant main effects were found in the ALFF and ReHo, especially for the left precuneus gyrus (PCu). A significant interaction between genotype and diagnosis had a significant effect on FC, which was increased between the left PCu and the right middle temporal gyrus in carriers of the A allele with SZ (r = -0.336, P The rs11607886 polymorphism in DLG2 may influence the pathogenesis of SZ and have potential effects on cognitive function. The present study emphasizes DLG2 as a candidate gene for SZ and suggests an important role for PCu in SZ. Show less

Multiple studies suggest an association between DLG2 and neurodevelopmental disorders and indicate the haploinsufficiency of this gene; however, few cases have been thoroughly described. We performed additional studies to confirm this clinical association and DLG2 haploinsufficiency. Chromosomal microarray analysis was performed on 11,107 patients at the Cytogenetics Laboratory at the University of Alabama at Birmingham. The Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database were selected for the association analysis. Fifty-nine patients from the literature and DECIPHER, all having DLG2 intragenic deletions, were included for comprehensive analysis of the distribution of these deletions. A total of 13 patients with DLG2 intragenic deletions, from 10 families in our cohort, were identified. Nine of 10 probands presented with clinical features of neurodevelopmental disorders. Congenital anomalies and dysmorphism were common in our cohort of patients. Association analysis showed that the frequency of DLG2 deletions in our cohort is significantly higher than those in the Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database. Most of DLG2 intragenic deletions identified in 69 unrelated patients from our cohort, the literature, and DECIPHER map to the 5' region of the gene, with a hotspot centered around HPin7, exon 8, and HPin8. Our findings reinforce the link between DLG2 intragenic deletions and neurodevelopmental disorders, strongly support the haploinsufficiency of this gene, and indicate that these deletions might also have an association with congenital anomalies and dysmorphism. Show less

Even though the enhanced permeability and retention (EPR) effect is applicable for the passive targeting of solid tumors, many nanodrugs have failed to achieve meaningful clinical outcomes due to the heterogeneity of EPR effect. Therefore, understanding the mechanism of the EPR effect is crucial to overcome the obstacles nanomedicines face in clinical translation. The aim of this study was to establish a reliable method to increase awareness of the critical influencing factors of nanoparticle (NP) transport into tumors based on the EPR effect using a combined radiogenomics and clinical magnetic resonance imaging (MRI) technique and gene set pathway enrichment analysis. Employing poly(lactic- Show less

Tumor-associated astrocytes (TAAs) in the glioblastoma microenvironment play an important role in tumor development and malignant progression initiated by glioma stem cells (GSCs). In the current study, normal human astrocytes (NHAs) were cultured and continuously treated with GSC-derived exosomes (GSC-EXOs) induction to explore the mechanism by which GSCs affect astrocyte remodeling. This study revealed that GSC-EXOs can induce the transformation of NHAs into TAAs, with relatively swollen cell bodies and multiple extended processes. In addition, high proliferation, elevated resistance to temozolomide (TMZ), and increased expression of TAA-related markers (TGF-β, CD44, and tenascin-C) were observed in the TAAs. Furthermore, GSC-derived exosomal miR-3065-5p could be delivered to NHAs, and miR-3065-5p levels increased significantly in TAAs, as verified by miRNA expression profile sequencing and Reverse transcription polymerase chain reaction. Overexpression of miR-3065-5p also enhanced NHA proliferation, elevated resistance to TMZ, and increased the expression levels of TAA-related markers. In addition, both GSC-EXO-induced and miR-3065-5p-overexpressing NHAs promoted tumorigenesis of GSCs in vivo. Discs Large Homolog 2 (DLG2, downregulated in glioblastoma) is a direct downstream target of miR-3065-5p in TAAs, and DLG2 overexpression could partially reverse the transformation of NHAs into TAAs. Collectively, these data demonstrate that GSC-EXOs induce the transformation of NHAs into TAAs via the miR-3065-5p/DLG2 signaling axis and that TAAs can further promote the tumorigenesis of GSCs. Thus, precisely blocking the interactions between astrocytes and GSCs via exosomes may be a novel strategy to inhibit glioblastoma development, but more in-depth mechanistic studies are still needed. Show less

Hepatitis B is a significant public health issue worldwide. Long noncoding RNAs (lncRNAs) are pivotal in biological mechanisms. The involvement of lncRNAs in hepatitis Hepatitis B remains incompletely understood. This study sought to explore the potential of certain lncRNAs as diagnostic and prognostic markers in hepatitis B, and their ability to differentiate between clinical disease subgroups. Plasma samples from 204 individuals diagnosed with hepatitis B were meticulously examined for the presence of specific lncRNAs, focusing on those known to be associated with hepatitis B as indicated in the literature. In this study, gene expression levels of 14 lncRNAs were analyzed in three subgroups (chronic, recovered and inactive HBsAg carriers) and compared with those in the healthy control group. The downregulation of the RN7SL1 and Alpha-280 genes in all patients indicates potential diagnostic lncRNAs. ZFHX2-AS1 expression was consistently lower in all subgroups, while SRA1 showed high expression in recovered hepatitis B patients, indicating that it is a descriptive marker. DLG2-AS2 expression increased in the chronic hepatitis B but decreased in the other groups. These findings reveal the prognostic importance of lncRNAs in hepatitis B. The expression levels of ZFHX2-AS1, RN7SL1, PCAT-1, PCA3, SRA1 and Alpha-280 have been identified as crucial biomarkers for the diagnosis of hepatitis B and for distinguishing between its clinical subgroups. A strong association between hepatitis B disease and the gene expression of the DLG2-AS2, HOTTIP, HOTAIRM1, HOXA11-AS, NOS2P3, LINC02665, MEG9, and RNY5 lncRNAs has been suggested. Show less

Cognitive decline, and more specifically Alzheimer's disease, continues to increase in prevalence globally, with few, if any, adequate preventative approaches. Several tests of cognition are utilized in the diagnosis of cognitive decline that assess executive function, short- and long-term memory, cognitive flexibility, and speech and motor control. Recent studies have separately investigated the genetic component of both cognitive health, using these measures, and circulating fatty acids. We aimed to examine the potential moderating effect of main species of ω-3 polyunsaturated fatty acids (PUFAs) on an individual's genetically conferred risk of cognitive decline. The Offspring cohort from the Framingham Heart Study was cross-sectionally analyzed in this genome-wide interaction study (GWIS). Our sample included all individuals with red blood cell ω-3 PUFA, genetic, cognitive testing (via Trail Making Tests [TMTs]), and covariate data (N = 1620). We used linear mixed effects models to predict each of the 3 cognitive measures (TMT A, TMT B, and TMT D) by each ω-3 PUFA, single nucleotide polymorphism (SNP) (0, 1, or 2 minor alleles), ω-3 PUFA by SNP interaction term, and adjusting for sex, age, education, APOE ε4 genotype status, and kinship (relatedness). Our analysis identified 31 unique SNPs from 24 genes reaching an exploratory significance threshold of 1×10 In this GWIS of ω-3 PUFA species on cognitive outcomes, we identified 8 unique genes with plausible biology suggesting individuals with specific polymorphisms may have greater potential to benefit from increased ω-3 PUFA intake. Additional replication in prospective settings with more diverse samples is needed. Show less

Kawasaki disease (KD) is an acute vasculitis that primarily affects children under age 5 years. Approximately 20-25% of untreated children with KD and 3-5% of those treated with intravenous immunoglobulin therapy develop coronary artery aneurysms (CAAs). The prevalence of CAAs is much higher in male than in female patients with KD, but the underlying factors contributing to susceptibility to CAAs in patients with KD remain unclear. This study aimed to identify sex-specific susceptibility loci associated with CAAs in KD patients. A sex-stratified genome-wide association study (GWAS) was performed using previously obtained GWAS data from 296 KD patients and a new replication study in an independent set of 976 KD patients by comparing KD patients without CAA (controls) and KD patients with aneurysms (internal diameter ≥5 mm) (cases). Six male-specific susceptibility loci, A sex-stratified GWAS identified 6 male-specific ( Show less

Environmental factors serve as one of the important pathogenic factors for gliomas. Yet people focus only on the effect of electromagnetic radiation on its pathogenicity, while metals in the environment are neglected. This study aimed to investigate the relationship between metal ion stimulation and the clinical characteristics and immune status of GM patients. Firstly, mRNA expression profiles of GM patients and normal subjects were obtained from Chinese GM Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) to identify differentially expressed metal ion stimulation-related genes(DEMISGs). Secondly, two molecular subtypes were identified and validated based on these DEMISGs using consensus clustering. Diagnostic and prognostic models for GM were constructed after screening these features based on machine learning. Finally, supervised classification and unsupervised clustering were combined to classify and predict the grade of GM based on SHAP values. GM patients are divided into two different response states to metal ion stimulation, M1 and M2, which are related to the grade and IDH status of the GM. Six genes with diagnostic value were obtained: SLC30A3, CRHBP, SYT13, DLG2, CDK1, and WNT5A. The AUC in the external validation set was higher than 0.90. The SHAP value improves the performance of classification prediction. The gene features associated with metal ion stimulation are related to the clinical and immune characteristics of transgenic patients. XGboost/LightGBM Kmeans has a higher classification prediction accuracy in predicting glioma grades compared to using purely supervised classification techniques. Show less

The retina is composed of neuronal layers that include several types of interneurons and photoreceptor cells, and separate underlying retinal pigment epithelium (RPE), Bruch's membrane, and choroid. Different regions of the human retina include the fovea, macula, and periphery, which have unique physiological functions and anatomical features. These regions are also unique in their protein expression, and corresponding cellular and molecular responses to physiological and pathophysiological stimuli. Skeie and Mahajan analyzed regional protein expression in the human choroid-RPE complex. Mitogen-Activated Protein Kinase (MAPK) signaling pathways have been implicated in responses to stimuli such as oxidative stress and inflammation, which are critical factors in retina diseases including age-related macular degeneration. We, therefore, analyzed the Skeie and Mahajan, 2014, dataset for regional differences in the expression of MAPK-related proteins and discussed the potential implications in retinal diseases presenting with regional signs and symptoms. Regional protein expression data from the Skeie and Mahajan, 2014, study were analyzed for members of signaling networks involving MAPK and MAPK-related proteins, categorized by specific MAPK cascades, such as p38, ERK1/2, and JNK1/2, both upstream or downstream of the respective MAPK and MAPK-related proteins. We were able to identify 207 MAPK and MAPK-related proteins, 187 of which belonging to specific MAPK cascades. A total of 31 of these had been identified in the retina with two proteins, DLG2 and FLG downstream, and the other 29 upstream, of MAPK proteins. Our findings provide evidence for potential molecular substrates of retina region-specific disease manifestation and potential new targets for therapeutics development. Show less

Neuroblastoma is the most common extracranial solid tumour in children, comprising close to 10% of childhood cancer-related deaths. We have demonstrated that activation of NTRK1 by TP53 repression of PTPN6 expression is significantly associated with favourable survival in neuroblastoma. The molecular mechanisms by which this activation elicits cell molecular changes need to be determined. This is critical to identify dependable biomarkers for the early detection and prognosis of tumours, and for the development of personalised treatment. In this investigation we have identified and validated a gene signature for the prognosis of neuroblastoma using genes differentially expressed upon activation of the NTRK1-PTPN6-TP53 module. A random survival forest model was used to construct a gene signature, which was then assessed across validation datasets using Kaplan-Meier analysis and ROC curves. The analysis demonstrated that high Show less

Many sex-specific biomarkers have been recently revealed in Alzheimer's disease (AD); however, cerebral glial cells were rarely reported. This study analyzed 220,095 single-nuclei transcriptomes from the frontal cortex of thirty-three AD individuals in the GEO database. Sex-specific Differentially Expressed Genes (DEGs) were identified in glial cells, including 243 in astrocytes, 1,154 in microglia, and 572 in oligodendrocytes. Gene Ontology (GO) functional annotation analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed functional concentration in synaptic, neural, and hormone-related pathways. Protein-protein interaction network (PPI) identified MT3, CALM2, DLG2, KCND2, PAKACB, CAMK2D, and NLGN4Y in astrocytes, TREM2, FOS, APOE, APP, and NLGN4Y in microglia, and GRIN2A, ITPR2, GNAS, and NLGN4Y in oligodendrocytes as key genes. NLGN4Y was the only gene shared by the three glia and was identified as the biomarker for the gender specificity of AD. Gene-transcription factor (TF)-miRNA coregulatory network identified key regulators for NLGN4Y and its target TCMs. Ecklonia kurome Okam (Kunbu) and Herba Ephedrae (Mahuang) were identified, and the effects of the active ingredients on AD were displayed. Finally, enrichment analysis of Kunbu and Mahuang suggested that they might act as therapeutic candidates for gender specificity of AD. Show less

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with considerable genetic heterogeneity. The disorder is clinically diagnosed based on DSM-5 criteria, featuring deficits in social communication and interaction, along with restricted and repetitive behaviours. Here, we performed whole-genome sequencing (WGS) on four individuals with ASD from two multiplex families (MPX), where more than one individual is affected, to identify potential single nucleotide variants (SNVs) and structural variants (SVs) in coding and non-coding regions. A rigorous bioinformatics pipeline was employed for variant detection, followed by segregation analysis. Our investigation revealed an unreported splicing variant in the DYRK1A gene (c.-77 + 2T > C; IVS1 + 2T > C; NM₀₀₁₃₉₆.5), in heterozygote form in two affected children in one of the families (family B), which was absent in the healthy parents and siblings. This finding suggests the presence of gonadal mosaicism in one of the parents, representing the first documented instance of such inheritance for a variant in the DYRK1A gene associated with ASD. Furthermore, we identified a 50 bp deletion in intron 9 of the DLG2 gene in two affected patients from the same family, confirmed by PCR and Sanger sequencing. In Family A, we identified potential candidate variants associated with ASD shared by the two patients. These findings enhance our understanding of the genetic landscape of ASD, particularly in MPX families, and highlight the utility of WGS in uncovering novel genetic contributions to neurodevelopmental disorders. Show less

Cancer is rarely the straightforward consequence of an abnormality in a single gene, but rather reflects a complex interplay of many genes, represented as gene modules. Here, we leverage the recent advances of model-agnostic interpretation approach and develop CGMega, an explainable and graph attention-based deep learning framework to perform cancer gene module dissection. CGMega outperforms current approaches in cancer gene prediction, and it provides a promising approach to integrate multi-omics information. We apply CGMega to breast cancer cell line and acute myeloid leukemia (AML) patients, and we uncover the high-order gene module formed by ErbB family and tumor factors NRG1, PPM1A and DLG2. We identify 396 candidate AML genes, and observe the enrichment of either known AML genes or candidate AML genes in a single gene module. We also identify patient-specific AML genes and associated gene modules. Together, these results indicate that CGMega can be used to dissect cancer gene modules, and provide high-order mechanistic insights into cancer development and heterogeneity. Show less

Vogt-Koyanagi-Harada (VKH) disease is a leading cause of blindness in young and middle-aged people. However, the etiology of VKH disease remains unclear. Here, we performed the first trio-based whole-exome sequencing study, which enrolled 25 VKH patients and 50 controls, followed by a study of 2081 VKH patients from a Han Chinese population to uncover detrimental mutations. A total of 15 de novo mutations in VKH patients were identified, with one of the most important being the membrane palmitoylated protein 2 (MPP2) p.K315N (MPP2-N315) mutation. The MPP2-N315 mutation was highly deleterious according to bioinformatic predictions. Additionally, this mutation appears rare, being absent from the 1000 Genome Project and Genome Aggregation Database, and it is highly conserved in 10 species, including humans and mice. Subsequent studies showed that pathological phenotypes and retinal vascular leakage were aggravated in MPP2-N315 mutation knock-in or MPP2-N315 adeno-associated virus-treated mice with experimental autoimmune uveitis (EAU). In vitro, we used clustered regularly interspaced short palindromic repeats (CRISPR‒Cas9) gene editing technology to delete intrinsic MPP2 before overexpressing wild-type MPP2 or MPP2-N315. Levels of cytokines, such as IL-1β, IL-17E, and vascular endothelial growth factor A, were increased, and barrier function was destroyed in the MPP2-N315 mutant ARPE19 cells. Mechanistically, the MPP2-N315 mutation had a stronger ability to directly bind to ANXA2 than MPP2-K315, as shown by LC‒MS/MS and Co-IP, and resulted in activation of the ERK3/IL-17E pathway. Overall, our results demonstrated that the MPP2-K315N mutation may increase susceptibility to VKH disease. Show less

In this issue, Griesius et al report that heterozygous Dlg2+/- rats showed a reversal learning impairment on a specific bowl-digging task, whereas other reversal tasks were unaffected. The study suggests that Dlg2 gene disruption, which has been linked to neuropsychiatric disorders, including schizophrenia, may cause relatively specific impairments in reversal learning, an important aspect of cognitive flexibility. The study draws attention to two important issues regarding the neuro-behavioral mechanisms of reversal learning, namely that hippocampal dysfunction, which is prominent in Dlg2+/- rats, may contribute to reversal learning impairments and that, depending on the task and previous experience, brain and behavioral mechanisms of reversal learning may differ. Show less

Copy number variants (CNVs) are among the main genetic factors identified in schizophrenia (SZ) through genome-scale studies conducted mostly in Caucasian populations. However, to date, there have been no genome-scale CNV reports on patients from India. To address this shortcoming, we generated, for the first time, genome-scale CNV data for 168 SZ patients and 168 controls from South India. In total, 63 different CNVs were identified in 56 patients and 46 controls with a significantly higher proportion of medium-sized deletions (100 kb-1 Mb) after multiple testing (FDR = 2.7E-4) in patients. Of these, 13 CNVs were previously reported; however, when searched against GWAS, transcriptome, exome, and DNA methylation studies, another 17 CNVs with candidate genes were identified. Of the total 30 CNVs, 28 were present in 38 patients and 12 in 27 controls, indicating a significantly higher representation in the former ( Show less

Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and is highly metastatic. Our prior studies have demonstrated the critical role of axon guidance pathway genes in PDAC and the connection between neuronal development and the tumor microenvironment. A recent study newly identified 20 neuronal development genes [disks large homolog 2 ( We hence applied the sequential multiplex immunohistochemistry results of biopsy specimens from 63 PDAC patients to investigate this relationship. We found that, except for Our study suggested that neuronal development genes play a role in modulating TME in a pancreatic cancer setting. Show less

Variations in the Dlg2 gene have been linked to increased risk for psychiatric disorders, including schizophrenia, autism spectrum disorders, intellectual disability, bipolar disorder, attention deficit hyperactivity disorder, and pubertal disorders. Recent studies have reported disrupted brain circuit function and behaviour in models of Dlg2 knockout and haploinsufficiency. Specifically, deficits in hippocampal synaptic plasticity were found in heterozygous Dlg2+/- rats suggesting impacts on hippocampal dependent learning and cognitive flexibility. Here, we tested these predicted effects with a behavioural characterisation of the heterozygous Dlg2+/- rat model. Dlg2+/- rats exhibited a specific, mild impairment in reversal learning in a substrate deterministic bowl-digging reversal learning task. The performance of Dlg2+/- rats in other bowl digging task, visual discrimination and reversal, novel object preference, novel location preference, spontaneous alternation, modified progressive ratio, and novelty-suppressed feeding test were not impaired. These findings suggest that despite altered brain circuit function, behaviour across different domains is relatively intact in Dlg2+/- rats, with the deficits being specific to only one test of cognitive flexibility. The specific behavioural phenotype seen in this Dlg2+/- model may capture features of the clinical presentation associated with variation in the Dlg2 gene. Show less