Search Results (226)

Background/Objectives: Genetic testing is important for diagnosing inherited retinal diseases (IRDs), but further evidence is needed on the utility of singleton genetic testing in an Australian cohort. Methods: A consecutive series of individuals with clinically diagnosed IRDs without prior genetic testing underwent commercial panel-based sequencing (Invitae or Blueprint Genetics), clinical assessment, and multimodal imaging. Retinal images were graded using the Human Phenotype Ontology terms. Binary logistic regression was used to evaluate clinical predictors of a positive molecular diagnosis. Results: Among 140 participants (mean age 49 ± 19 years), genetic testing was undertaken, on average, 23 ± 17 years after the initial clinical IRD diagnosis. Of the 60% who received a probable molecular diagnosis, 40% require further phase testing, highlighting the limitations of singleton genetic testing. USH2A, ABCA4, and RPGR were the most common encountered genes; 67% of the probably solved participants had causative genes with targeted experimental treatments in ongoing human clinical trials. Symptom onset before the age of 30 (OR = 3.06 [95% CI: 1.34–7.18]) and a positive IRD family history (OR = 2.87 [95% CI: 1.27–6.78]) were each associated with higher odds of receiving a molecular diagnosis. Diagnostic rates were comparable across retinal imaging phenotypes (atrophy and autofluorescence patterns in widespread IRD, and the extent of dystrophy in macular IRDs). Conclusions: In an Australian IRD population without prior genetic testing, commercial panels yielded higher diagnostic rates in individuals with IRD onset before the age of 30 and those with an IRD family history. Further research is needed to understand the genetic basis of IRDs, especially isolated and late-onset cases, to improve diagnosis and access to emerging therapies. Full article

Background/Objectives: Cardiovascular diseases are a global health issue with an increasing burden and are exacerbated by hypertension. High blood pressure is partly attributed to genetic variants that are generally not well understood or extensively studied in sub-Saharan African populations. Variants linked to blood pressure have been found through genome-wide association studies (GWASs), which were mostly conducted among European ancestry populations; however, limited research has been undertaken in Africa. The current study evaluated single-nucleotide polymorphisms (SNPs) of PCSK9, ABCA1, LPL, and PON1 in relation to blood pressure measurements of 1839 Ghanaian adults. Methods: Genotypes were extracted from data generated by the H3Africa SNP array. After adjusting for sex, age, smoking, and body mass index (BMI), inferential statistics were used to investigate the relationships between SNPs and blood pressure (BP) indices. Additionally, Bonferroni correction was used to adjust for multiple testing. Results: Diastolic blood pressure (DBP) and the minor allele T of the PCSK9 variant (rs17111557) were positively associated at p = 0.006 after covariate adjustments. Although this novel DBP-associated variant is located in the 3′ untranslated region (3′ UTR) of the PCSK9 gene, in silico functional prediction suggests it is an expression quantitative trait locus (eQTL) that may change the binding site of transcription factors, potentially altering the rate of transcription and impacting DBP in this Ghanaian population. Conclusions: Our findings highlight the role of genetics in hypertension risk and the potential of discovering new therapies targeting isolated diastolic blood pressure in this rural African population. Full article

Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over 1200 pathogenic/likely pathogenic ABCA4 variants highlight the genetic heterogeneity of STGD1, which manifests as progressive central vision loss, with phenotype influenced by deep intronic variants, modifier genes, and environmental factors like light exposure. ABCA4 variants also show variable penetrance and geographical prevalence. With no approved treatment, investigational therapies target different aspects of disease pathology. Small-molecule therapies target vitamin A dimerization (e.g., ALK-001), inhibit lipofuscin accumulation (e.g., soraprazan), or modulate the visual cycle (e.g., emixustat hydrochloride). Gene therapy trials explore ABCA4 supplementation including strategies like RNA exon editing (ACDN-01) and bioengineered ambient light-activated OPSIN. RORA gene therapy (Phase 2/3) addresses oxidative stress, inflammation, lipid metabolism, and complement system dysregulation. Trials like DRAGON (Phase 3, tinlarebant), STARLIGHT (phase 2, bioengineered OPSIN) show promise, but optimizing efficacy remains challenging. With the key problem of establishing genotype–phenotype correlations, the future of STGD1 therapy may rely on approaches targeting oxidative stress, lipid metabolism, inflammation, complement regulation, and genetic repair. Full article

Background/Objectives: Breast milk provides essential nutrition and immune protection to support infant growth and development. However, insufficient breast milk remains a serious issue, and bioactive peptides represent a potential strategy to promote lactation. In this study, we investigated the impact of a methionine-containing dipeptide, EM, on MCF-10A mammary epithelial cells. Methods: MCF-10A cells were treated with EM, and cell proliferation and the expression of key milk protein genes were assessed. Integrated transcriptomic and untargeted metabolomic analyses were performed to identify EM-induced changes in metabolic and gene expression pathways. Results: EM treatment significantly enhanced cell proliferation and upregulated the expression of key milk protein genes (CSN1S1 (casein alpha-S1, encoding alpha-S1 casein), CSN2 (casein beta, encoding beta-casein), and CSN3 (casein kappa, encoding kappa-casein)) at both transcriptional and protein levels compared to controls. Integrated transcriptomic and metabolomic analyses revealed that EM reprogrammed amino acid metabolism, lipid biosynthesis, and nutrient transport pathways. Core genes such as SLC7A11, APOE, and ABCA1 were identified as critical nodes linking metabolic and transcriptional networks. Conclusions: These findings indicate that EM may promote lactogenic activity by modulating metabolic and transcriptional networks in vitro, highlighting the potential of dipeptide-based nutritional interventions, which warrants further in vivo validation. Full article

Background/Objectives: Long non-coding RNAs (lncRNAs) play significant roles in tissue development and disease progression and have emerged as crucial regulators of gene expression. The hepatocyte nuclear factor alpha antisense RNA 1 (HNF1A-AS1) lncRNA is a particularly intriguing regulatory molecule in liver biology that is involved in the regulation of cytochrome P450 enzymes via epigenetic mechanisms. Despite the growing recognition of lncRNAs in liver disease, the comprehensive role of HNF1A-AS1 in liver function remains unclear. This study aimed to investigate the roles of the mouse homolog of the human HNF1A-AS1 lncRNA HNF1A opposite strand 1 (Hnf1aos1) in liver function, gene expression, and cellular processes using a mouse model to identify potential therapeutic targets for liver disorders. Methods: The knockdown of Hnf1aos1 was performed in in vitro mouse liver cell lines using siRNA and in vivo livers of AAV-shRNA complexes. Changes in the global expression landscapes of mRNA and proteins were revealed using RNA-seq and proteomics, respectively. Changes in the selected genes were further validated via real-time quantitative polymerase chain reaction (RT-qPCR). Phenotypic changes were assessed via histological and absorbance-based assays. Results: After the knockdown of Hnf1aos1, RNA-seq and proteomics analysis revealed the differential gene expression of the mRNAs and proteins involved in the processes of molecular transport, liver regeneration, and immune signaling pathways. The downregulation of ABCA1 and SREBF1 indicates their role in cholesterol transport and fatty acid and triglyceride synthesis. Additionally, significant reductions in hepatic triglyceride levels were observed in the Hnf1aos1-knockdown group, underscoring the impact on lipid regulation. Notably, the knockdown of Hnf1aos1 also led to an almost complete depletion of CYP7A1, the rate-limiting enzyme in bile acid synthesis, highlighting its role in cholesterol homeostasis and hepatotoxicity. Histological assessments confirmed these molecular findings, with increased hepatic inflammation, hepatocyte swelling, and disrupted liver architecture observed in the Hnf1aos1-knockdown mice. Conclusions: This study illustrated that Hnf1aos1 is a critical regulator of liver health, influencing both lipid metabolism and immune pathways. It maintains hepatic lipid homeostasis, modulates lipid-induced inflammatory responses, and contributes to viral immunity, indirectly affecting glucose and lipid metabolic balance. Full article

Background/Objectives: Lumbar disc herniation (LDH) is the most common condition associated with low back pain, and it adversely impacts individuals’ health. The interplay between energy metabolism and apoptosis is critical, as the loss of viable cells in the intervertebral disc (IVD) can lead to a cascade of degenerative changes. Efferocytosis is a key biological process that maintains homeostasis by removing apoptotic cells, resolving inflammation, and promoting tissue repair. Therefore, enhancing mitochondrial energy metabolism and efferocytosis function in IVD cells holds great promise as a potential therapeutic approach for LDH. Methods: In this study, energy metabolism and efferocytosis-related differentially expressed genes (EMERDEGs) were identified from the transcriptomic datasets of LDH. Machine learning approaches were used to identify key genes. Functional enrichment analyses were performed to elucidate the biological roles of these genes. The functions of the hub genes were validated by RT-qPCR. The CIBERSORT algorithm was used to compare immune infiltration between LDH and Control groups. Additionally, we used single-cell RNA sequencing dataset to analyze cell-specific expression of the hub genes. Results: By using bioinformatics methods, we identified six EMERDEGs hub genes (IL6R, TNF, MAPK13, ELANE, PLAUR, ABCA1) and verified them using RT-qPCR. Functional enrichment analysis revealed that these genes were primarily associated with inflammatory response, chemokine production, and cellular energy metabolism. Further, we identified candidate drugs as potential treatments for LDH. Additionally, in immune infiltration analysis, the abundance of activated dendritic cells, neutrophils, and gamma delta T cells varied significantly between the LDH group and Control group. The scRNA-seq analysis showed that these hub genes were mainly expressed in chondrocyte-like cells. Conclusions: The identified EMERDEG hub genes and pathways offer novel insights into the molecular mechanisms underlying LDH and suggest potential therapeutic targets. Full article

Background: Children’s interstitial and diffuse lung diseases, commonly referred to as “chILDs”, include around 200 rare conditions that disrupt normal lung function. They are classified, based on etiopathogenesis, into several subgroups, having a varied and multifaceted clinical presentation depending on the type of genetic mutation present. Methods and Results: We describe the case of a late preterm newborn presenting soon after birth with respiratory distress syndrome poorly responsive to surfactant administration, in whom a targeted gene panel analysis for pulmonary congenital diseases, performed using next-generation sequencing (NGS), revealed a novel compound heterozygous variant of the ATP-Binding-Cassette-Subfamily-A-Member-3 (ABCA3) gene. A review of the literature on the subject completes our work. Conclusions: Molecular genetic analysis has become crucial for a more targeted therapeutic treatment, along with the only current curative treatment option that is lung transplantation. Full article

Bacterial tolerance, especially in Staphylococcus aureus (S. aureus), may arise under intermittent antibiotic regimens and act as a stepping stone toward resistance development. However, the transition from tolerance to resistance and its contributing factors remain poorly understood. This study explores the role of the efflux pump gene abcA in this process. abcA mutants (overexpression, knockout, and complementation) were constructed via homologous recombination. These strains were subjected to 21 cycles of intermittent exposure to oxacillin at 20× MIC, and the resistance evolution was monitored. Spontaneous mutation frequencies and survival abilities in these mutants were also measured to determine their involvement in resistance development. The abcA overexpression mutant exhibited a faster development of resistance compared to the wildtype strain. Conversely, the abcA knockout mutant maintained susceptibility to oxacillin, with no significant changes in the relative MIC. Increased mutation frequency and enhanced survival were observed in the overexpression strain, whereas both were reduced in the knockout. abcA overexpression significantly accelerated the development of oxacillin resistance in S. aureus by promoting spontaneous mutations and bacterial survival. Disrupting abcA may offer a novel strategy to prevent the evolution of antibiotic resistance. Full article

Guanidinoacetic acid (GAA) has been used in ruminant feeding, but it is still unclear whether the exogenous addition of methyl donors, such as methionine (Met), can enhance the effects of GAA. This study investigated the effects of dietary GAA alone or combined with Met on beef cattle growth performance and explored the underlying mechanisms via blood analysis, liver metabolomics, and transcriptomics. Forty-five Simmental bulls (453.43 ± 29.05 kg) were assigned to three groups for 140 days: CON (control), GAA (0.1% GAA), and GAM (0.1% GAA + 0.1% Met), where each group consisted of 15 bulls. Compared with the CON group, the average daily gain (ADG) and feed conversion efficiency (FCE) of the two feed additive groups were significantly increased, and the digestibility of neutral detergent fiber (NDF) was improved (p < 0.05). Among the three treatment groups, the GAM group showed a higher rumen total volatile fatty acids (TVFAs) content and digestibility of dry matter (DM) and crude protein (CP) in the beef cattle. The serum indices showed that the contents of indicators related to protein metabolism, lipid metabolism, and creatine metabolism showed different increases in the additive groups (p < 0.05). It is worth noting that the antioxidant indexes in the serum and liver tissues of beef cattle in the two additive groups were significantly improved (p < 0.05). The liver metabolites related to protein metabolism (e.g., L-asparagine, L-glutamic acid) and lipid metabolism (e.g., PC (17:0/0:0)) were elevated in two additive groups, where Met further enhanced the amino acid metabolism in GAM. In the two additive groups, transcriptomic profiling identified significant changes in the expression of genes associated with protein metabolism (including PIK3CD, AKT3, EIF4E, HDC, and SDS) and lipid metabolism (such as CD36, SCD5, ABCA1, APOC2, GPD2, and LPCAT2) in the hepatic tissues of cattle (p < 0.05). Overall, the GAA and Met supplementation enhanced the growth performance by improving the nutrient digestibility, serum protein and creatine metabolisms, antioxidant capacity, and hepatic energy and protein and lipid metabolisms. The inclusion of Met in the diet was shown to enhance the nutrient digestibility and promote more efficient amino acid metabolism within the liver of the beef cattle. Full article

Stress-induced demyelination resulting from oligodendrocyte (OLG) dysfunction is one of the key pathological mechanisms of depression, yet its dynamic regulatory network remains unclear. This study integrates single-cell transcriptomics, lineage tracing, and functional interventions to uncover a temporally disordered OLG cholesterol metabolism in a restraint stress mouse model: After 3 days of stress, upregulation of efflux genes Abca1/Abcg1 triggers a compensatory response; however, by day 14, persistent suppression of transport genes (Apoe, Apod) and homeostatic regulatory genes (Dhcr24, Srebf2, etc.) leads to intracellular accumulation of “ineffective cholesterol”, with compensatory activation of the AMPK pathway unable to restore cholesterol conversion into myelin. Pseudotime analysis further reveals that stress alters OLG differentiation trajectories, decreasing the proportion of mature OLGs and causing immature precursors to abnormally stall at the late pre-differentiation stage, resulting in myelin regeneration failure. Moreover, an immune OLG_C10 subpopulation expressing complement component C3 and P2ry12 is identified, indicating that OLGs may contribute to neuroinflammatory cascades through immune reprogramming. In summary, these findings reveal a novel mechanism from the dynamic perspective of OLGs, in which the interplay of “metabolic imbalance, differentiation blockade, and immune activation” collaboratively drives stress-induced demyelination, providing a theoretical foundation for depression treatment targeting OLG functional restoration. Full article

Oysters are a globally distributed aquatic economic shellfish with a remarkable ability to accumulate cadmium (Cd). The phenomenon of Cd content exceeding safety standards in oysters occurs frequently, posing a significant risk to food safety. In this study, Portuguese oysters (Crassostrea angulata) were exposed to 2 μg/L of Cd for 15 days. Individuals with significantly different Cd accumulation were selected for transcriptomic sequencing analysis. KEGG enrichment analysis revealed that the differentially expressed genes (DEGs) between high- and low-Cd-accumulation individuals, as well as those before and after Cd exposure, were primarily enriched in metabolic pathways (33.8%) and organismal systems (32.2%). ABC transporters, phagosomes, glutathione metabolism, and the biosynthesis of amino acids played crucial roles in Cd accumulation and detoxification processes. Metal cation transport-related genes, including zip1, copt5.1, and orct2, may be involved in the Cd transport process in Portuguese oysters, and their differential expression influences Cd accumulation in the soft tissues. Meanwhile, genes such as sod3, cyp4f22, and abca3 are likely to play significant roles in detoxification under Cd exposure. Additionally, alternative splicing analysis identified 13 potential genes associated with Cd response in Portuguese oysters, including cs2, gfpt1, and acox1. Full article

Stargardt disease (STGD1), the most common retinal dystrophy caused by pathogenic variants of the biallelic ABCA4 gene, results in irreversible vision loss. This cross-sectional case series study analyzes 18 unrelated Stargardt disease (STGD1) patients from southeast China, examining clinical and genetic features. Ophthalmological assessments included BCVA, ophthalmoscopy, fundus photography, and autofluorescence, with ultra-widefield OCT angiography carried out on one patient. Genetic testing uses targeted exome sequencing for eye disease genes. The mean age of onset was 44.3 years for adult onset (6 patients) and 9.6 years for childhood/adolescent onset (12 patients). The mean logMAR visual acuity was 0.96 (right eye) and 0.91 (left eye). Eight novel ABCA4 variants were found, including two nonsense, two frameshift deletions, one copy number variant, one splice-site alternation, and two deep intronic variants. The genotypes are as follows: 77.8% (14/18) biallelic heterozygous, 16.7% (3/18) homozygous, and one patient with three variants. The study underscores STGD1’s phenotypic and genotypic diversity, expands the ABCA4 mutation spectrum, and offers insights into therapeutic strategies. Full article

We introduce an innovative, non-invasive prenatal screening approach for detecting fetal monogenic alterations and copy number variations (CNVs) from maternal blood. Method: Circulating free DNA (cfDNA) was extracted from maternal peripheral blood and processed using the VeriSeq NIPT Solution (Illumina, San Diego, CA, USA), with shallow whole-genome sequencing (sWGS) performed on a NextSeq550Dx (Illumina). A customized gene panel and bioinformatics tool, named the “VERA Revolution”, were developed to detect variants and CNVs in cfDNA samples. Results were compared with genomic DNA (gDNA) extracted from fetal samples, including amniotic fluid and chorionic villus sampling and buccal swabs. Results: The study included pregnant women with gestational ages from 10 + 3 to 15 + 2 weeks (mean: 12.1 weeks). The fetal fraction (FF), a crucial measure of cfDNA test reliability, ranged from 5% to 20%, ensuring adequate DNA amount for analysis. Among 36 families tested, 14 showed a wild-type genotype. Identified variants included two deletions (22q11.2, and 4p16.3), two duplications (16p13 and 5p15), and eighteen single-nucleotide variants (one in CFTR, three in GJB2, three in PAH, one in RIT1, one in DHCR7, one in TCOF1, one in ABCA4, one in MYBPC3, one in MCCC2, two in GBA1 and three in PTPN11). Significant concordance was found between our panel results and prenatal/postnatal genetic profiles. Conclusions: The “VERA Revolution” test highlights advancements in prenatal genomic screening, offering potential improvements in prenatal care. Full article

Background: Understanding gene–diet interactions is crucial for establishing dietary guidelines for cardiovascular diseases (CVD). This study analyzed the interaction between dietary intake and six genome-wide association study (GWAS)-identified single nucleotide polymorphisms (SNP) associated with high-density lipoprotein (HDL) cholesterol levels and their impact on CVD risk. Methods: A total of 68,806 participants in the Korean Genome and Epidemiology Study (KoGES) were analyzed. Six target SNPs (LPL: rs17482753; ABCA1: rs1883025; APOA5: rs651821; LIPC: rs1077835; CETP: rs17231506; and LIPG: rs9953437) were extracted from genome-wide SNP genotype data. Dietary intake was assessed using a food frequency questionnaire. SNP genotyping was conducted using the Korea Biobank Array (Korean Chip), a specialized genotyping platform designed for GWAS of blood biochemical traits in the Korean population. SNP–diet interactions on CVD risk were analyzed using generalized linear models (GLM). Results: Among the six SNPs, ABCA1: rs1883025 and APOA5: rs651821 showed significant gene–diet interactions. For rs1883025 (ABCA1), carriers of the T allele exhibited reduced HDL cholesterol levels. However, in the high-protein intake group, individuals with the T/T genotype had a significantly lower risk of ischemic stroke compared to those in the low-protein intake group (interaction p-value = 0.044). For rs651821 (APOA5), carriers of the T allele also had lower HDL cholesterol levels, but individuals with the C/C genotype (wild-type homozygotes) in the low-fat intake group showed a significantly reduced risk of coronary artery disease (interaction p-value = 0.0155). Conclusions: This study suggests potential interactions between polymorphisms associated with low HDL cholesterol and dietary patterns, particularly high-protein and low-fat diets, in relation to CVD risk. These findings highlight the importance of personalized dietary recommendations based on genetic profiles to reduce CVD risk. They provide a basis for future research aimed at developing precision nutrition guidelines and targeted interventions to manage hypo-HDL cholesterolemia and nutrition-related CVD risks. Full article

Background/Objectives: This research investigated the effects of myricitrin on hypercholesterolemia and non-alcoholic fatty liver disease (NAFLD) in mice given a high-cholesterol diet (HCD). Methods: C57BL/6J mice were maintained for 20 weeks on an HCD with or without myricitrin. Results: Myricitrin had no impact on the food consumption, body weight, or plasma triglyceride concentrations. However, myricitrin-supplemented mice had lower plasma total cholesterol (TC) concentrations and LDL + VLDL-cholesterol/TC proportion, and higher HDL-cholesterol/TC proportion than control mice, which resulted in a markedly decreased atherogenic index. Moreover, the levels of plasma C-reactive protein, oxidized LDL, lipoprotein(a), and plasminogen activator inhibitor-1, which are indicators for cardiovascular disease (CVD), were reduced, while levels of plasma paraoxonase, a cardioprotective enzyme, were greater in myricitrin-supplemented mice than in control mice. Myricitrin also meaningfully reduced liver weight and hepatic cholesterol content, and slightly alleviated fatty liver and fibrosis caused by an HCD. The plasma and hepatic cholesterol-lowering effects of myricitrin were partly associated with decreased activities of hepatic 3-hydroxy-3-methylglutaryl-CoA reductase and acyl-CoA:cholesterol acyltransferase, which are involved in cholesterol synthesis and esterification, respectively, as well as mRNA expression. Myricitrin also altered other hepatic genes implicated in cholesterol homeostasis, including the downregulation of SREBP2 and ABCA1 mRNA expression and the upregulation of LDLR mRNA expression. Moreover, myricitrin decreased TBARS levels in the liver and erythrocytes by activating antioxidant enzymes (SOD and catalase). Conclusions: These results indicate that dietary myricitrin may offer therapeutic benefits for HCD-caused hypercholesterolemia and NAFLD, and may help reduce CVD risk. Full article