Search Results (33)

H3K4me3, a well-established histone modification associated with active promoters, plays a critical role in orchestrating gene expression programs that govern mammary gland development and lactation. In this study, we present the first comprehensive epigenomic profiling of H3K4me3 modifications during mammary gland development in Yili horses using Cleavage Under Targets and Tagmentation (CUT&Tag) and RNA sequencing. Mammary gland tissues were collected from two developmental stages—early lactation and peak lactation. A total of 393 differentially expressed genes (DEGs) were identified between two groups, among which 72 DEGs (54 upregulated H3K4me3 targets and 18 downregulated targets) were directly regulated by H3K4me3. KEGG enrichment analyses revealed that these DEGs were involved in ECM–receptor interaction, focal adhesion, the PI3K-Akt signaling pathway, and the calcium signaling pathway. In these pathways, five genes were identified as potential regulators of mammary gland development. Among these, PTGES, COL1A1, PDGFRB, and RYR1 exhibited consistent upregulation at both the transcriptomic and chromatin levels, whereas PRKAG3 showed significant downregulation. These findings offer novel insights into the epigenetic regulation of lactation in horses and lay a theoretical foundation for improving milk production traits through targeted molecular breeding strategies. Full article

Background: PRKAG2 cardiac syndrome is a rare autosomal dominant glycogen-storage cardiomyopathy that mimics sarcomeric hypertrophic cardiomyopathy (HCM) but features ventricular pre-excitation, progressive conduction disease and concentric hypertrophy due to intracellular glycogen accumulation. The c.905G>A (p.Arg302Gln) variant is one of the most frequently reported pathogenic substitutions. Case summary: We describe a three-generation family carrying the heterozygous PRKAG2 p.Arg302Gln variant. The proband, a 41-year-old man, presented with paroxysmal atrial fibrillation, short PR interval and abnormal intraventricular conduction associated with concentric left ventricular hypertrophy and preserved ejection fraction. Holter monitoring disclosed episodes of high-grade atrioventricular block, prompting implantation of a primary-prevention dual-chamber ICD. Two gene-positive brothers exhibited milder hypertrophy but shared sinus bradycardia, ventricular pre-excitation and supraventricular arrhythmias; one underwent catheter ablation of a posteroseptal accessory pathway. The affected mother displayed a hypertrophic phenotype complicated by sick sinus syndrome and permanent atypical atrial flutter requiring pacemaker implantation. No relevant extracardiac involvement was detected in any family member. Review and novelty: Using this family as a starting point, we provide a concise narrative review of PRKAG2 syndrome with emphasis on the Arg302Gln genotype, molecular mechanisms and emerging treatment strategies. We highlight key multimodality imaging and tissue-characterization features that help distinguish diffuse, concentric glycogen-storage hypertrophy from the often-asymmetric pattern of sarcomeric HCM. Integration of our findings with published Arg302Gln cohorts illustrates the broad phenotypic variability in conduction disease, pre-excitation and atrial arrhythmias. Conclusions: PRKAG2 p.Arg302Gln-related cardiomyopathy should be suspected in patients with otherwise unexplained left ventricular hypertrophy associated with short PR interval, pre-excitation or early brady–tachy arrhythmias. Early recognition of red-flag features, systematic genetic testing, family screening and tailored arrhythmia/device management are crucial, while emerging gene- and pathway-targeted therapies may offer future disease-modifying potential. Full article

Background: The Tibetan pig, a highland breed with exceptional adaptability to harsh environments (cold, hypoxia, coarse feed) but poor growth/reproductive traits, was studied to uncover genetic mechanisms and support breeding improvements. Methods: We conducted de novo genome assembly of a male Tibetan pig using stLFR sequencing, supplemented with ONT data, and compared the assembly to the Duroc pig genome (v11.1). Results: The assembled genome (2.25 Gb, contig N50 = 136.5 Mb, GC content = 41.74%, 94.16× coverage) showed 96.9% BUSCO completeness. Structural variant (SV) analysis identified 22,008 insertions and 27,639 deletions, with an SV genotyping accuracy of 0.9735. Selective sweep analysis highlighted adaptive genes: XIRP2 (cardiac function), KSR2/CACNA1A (fat metabolism), COL11A1 (cartilage), and ADORA2A (vascular regulation). Tibetan pigs exhibited the fewest and shortest runs of homozygosity (ROHs) among four breeds, with ROH-linked SNPs implicating lipid catabolism genes (LIPE, PNPLA2, MGLL, DGAT1). An SNP-based GWAS revealed reproductive trait associations: immune gene IL2RB, energy metabolism genes PRKAG2, ADGRA1, and PTPRN2, and growth genes SLIT2 and BMP6. SV analysis identified additional candidates: energy metabolism genes HAO2 and NRG4, growth genes MTUS2 and FGF12, and immune genes SCGB1A1 and C8A. Conclusions: This study provides a chromosome-level genome assembly of a male Tibetan pig (generated from stLFR and ONT data), and, through whole-genome resequencing of 124 Tibetan sows, identifies key genetic factors underlying Tibetan pigs’ environmental adaptability and reproductive limitations, enabling genomic strategies to enhance breeding efficiency while preserving adaptive traits. Full article

Pigs are a major source of animal protein for humans and serve as valuable biomedical models. Compared to Western commercial pig breeds, Jinhua pigs are characterized by superior meat quality due to dynamic muscle development and fat deposition. However, studies investigating dynamic transcriptional regulation of swine meat quality traits across developmental stages remain limited. In this work, we collected longissimus dorsi muscle tissue from three Jinhua and three Landrace × Yorkshire pigs at 1, 90, and 180 days of age, respectively. We have uncovered differentially expressed genes and transcripts, alternative splicing events, and gene fusion events across development stages utilizing RNA sequencing data. CKM exhibited consistent breed-specific alternative splicing and gene fusion events across all three stages, representing a stable regulator of muscle development in Jinhua pigs. On the other hand, our findings highlight day 90 as a critical “window phase” for muscle development and meat quality differences between Jinhua and Landrace × Yorkshire pigs at this stage, exhibiting the greatest number of inter-breed differences in transcriptomic genetic regulation. Additionally, time series analysis revealed that genes with peak expression at day 90 were significantly enriched in pathways associated with muscle development and function. Finally, we identified PFKM, PRKAG3, and CKM as candidate genes with age-specific expression and post-transcriptional regulation that likely influence muscle development. This study advances understanding of transcriptional regulation in pig muscle with implications for meat quality improvement. Full article

This study investigated meat quality, nutritional characteristics, and transcriptomic regulation in Yunan (YN) black pigs and Huainan (HN) black pigs (n = 6 each). Analysis of fatty acid composition revealed that HN black pigs possessed significantly higher levels of most fatty acids compared to YN black pigs. Notably, the contents of monounsaturated fatty acid C18:1n9c and polyunsaturated fatty acid C18:2n6c in HN black pigs were 1.94-fold and 2.65-fold higher, respectively, than those in YN black pigs. The α-linolenic acid content was also significantly elevated in HN black pigs, indicating an overall higher fatty acid content. Regarding amino acid differences, HN black pigs exhibited significantly higher levels of aspartic acid, glutamic acid, histidine, as well as superior composition of total amino acids, total umami amino acids, and essential amino acids, which contribute to enhanced flavor characteristics and nutritional balance. Transcriptome analysis identified 526 differentially expressed genes in HN vs. YN. KEGG enrichment analysis showed that these genes were involved in many adipogenesis and lipid metabolism signaling pathways, such as biosynthesis of unsaturated fatty acids, fatty acid elongation, apelin signaling pathway and lysine degradation. By integrating transcriptome and protein–protein interaction (PPI) network analyses, we identified key meat quality-related genes: ELOVL6, PRKAG3, ROCK2, and MYH11. miRNA profiling identified ssc-miR-133b, ssc-miR-206, and miR-205 as key regulators of meat quality. This study provides a valuable theoretical foundation for understanding the molecular mechanisms underlying pork quality and offers insights for its future improvement. Full article

Background: PRKAG2-related disease is an autosomal dominant disorder caused by pathogenic variants in the PRKAG2 gene, leading to glycogen accumulation in cardiomyocytes. It is characterized by left ventricular hypertrophy (LVH), ventricular pre-excitation, and conduction disease. Due to the rarity of the condition and the frequent occurrence of private variants, functional or pathological testing is required for definitive pathogenicity classification. Case Presentation: We describe a 22-year-old male referred for evaluation after experiencing exertional dyspnea and a syncopal episode. Family history revealed sudden cardiac deaths and conduction disease requiring pacemaker implantation. The patient exhibited mild LVH on imaging, conduction abnormalities on electrophysiological study, and a heterozygous PRKAG2 variant (c.1643C>T; p.Ser548Leu), classified as likely pathogenic according to ACMG guidelines. Cascade screening identified the variant in three family members, one of whom exhibited a positive phenotype. Endomyocardial biopsy revealed glycogen accumulation, providing histopathological confirmation of PRKAG2-related disease. Conclusions: This case underscores the importance of integrating genetic, clinical, and histopathological data in variant interpretation. Endomyocardial biopsy can provide definitive evidence to reclassify a PRKAG2 variant as pathogenic, thereby guiding management and family screening. Full article

Background: Alcohol-associated liver disease (ALD) is characterized by gut–liver axis dysfunction and metabolic dysregulation, yet the therapeutic potential of probiotics remains underexplored. This study aimed to investigate the protective effects and mechanisms of Lacticaseibacillus paracasei 36 (LP36) against ethanol-induced ALD in mice. Methods: Mice were pretreated with LP36 prior to ethanol exposure. Liver injury was assessed through serum ALT/AST levels, hepatic steatosis (TC/TG content), and ethanol detoxification capacity (ADH/ALDH activity). Intestinal barrier integrity was evaluated via Mucin2 and ZO-1 expression, and gut microbiota alterations were analyzed by 16S rRNA sequencing. Hepatic transcriptomics (RNA-seq) was performed to identify key regulatory pathways. Results: LP36 significantly attenuated ethanol-induced liver injury, evidenced by reduced ALT/AST, improved hepatic steatosis (lower TC/TG), and enhanced ADH/ALDH activity. Mechanistically, LP36 restored intestinal barrier function (upregulated Mucin2 and ZO-1), modulated gut microbiota (suppressed Parasutterella, Romboutsia, and Christensenellaceae_R-7_group; enriched Faecalibaculum and Tuzzerella), and reduced systemic inflammation. Transcriptomics revealed LP36-mediated rescue of AMPK signaling, involving regulation of Stk11, Prkag3, lipid synthesis genes (Fasn, Acaca), and metabolic modulators (Creb3l3, G6pc3, mTOR, Rps6kb2).Conclusions: LP36 ameliorates ethanol-induced ALD by enhancing intestinal barrier integrity, reshaping gut microbiota, and restoring AMPK-dependent metabolic homeostasis. These findings highlight LP36 as a promising probiotic candidate for ALD prevention. Full article

Tilapia (Oreochromis spp.) is a globally important farmed fish. Analyses of genetic variation across different types of tilapia are essential for the development of superior breeding populations. We investigated the genetic structures of breeding populations of blue tilapia (Oreochromis aureus) (OA), Nile tilapia (Oreochromis niloticus) (ON), and red tilapia (Oreochromis spp.) (OS) by whole-genome resequencing. The results showed that the OS population had maintained high genetic diversity but significant genetic differentiation from the OA population. Principal component analysis, phylogenetic analysis, and genetic clustering analysis revealed a clear pattern of genetic differentiation among the three populations. The genetic structure of the ON population differed from that of the OA population but was similar to that of the OS population. Population kinship analysis revealed a close relationship between the ON and OS populations. Selective scanning analyses of three comparison groups (OA vs. ON, OA vs. OS, and ON vs. OS) revealed population-selected regions related to metabolism, endocrine, and immune systems, harboring key genes (qrsl1, pde4d, hras, ikbkb, prkag1, prkaa2, prkacb, irs2, and eif4e2). These key genes were related to growth, reproduction, and disease resistance, indicating that breeding programs have selected for these traits. Due to the lack of stable morphological characteristics of juvenile fish and the changes in external environmental conditions that lead to changes in individual morphological characteristics, SNP fingerprints were successfully constructed for the identification of the three populations based on the differences in SNPs. Based on the five core SNP markers, two combinations of SNP markers were developed to accurately identify the three populations of tilapia at the genomic level. These results provide new information about tilapia genetic resources and reference data for identification and breeding purposes. Full article

The improvement of carcass traits is a key focus in pig genetic breeding programs. To identify quantitative trait loci (QTLs) and genes linked to key carcass traits, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 1118 commercial pigs (Duroc sires and Yorkshire/Landrace F1 dams). This study focused on six phenotypes: iodine value, belly firmness, belly side fat, total side thickness (belly SThK), belly subcutaneous fat (Subq), and belly seam. Phenotypes were measured using image analysis, DEXA, and fatty acid profiling, and genotyping was performed using low-pass sequencing (SkimSeq). After quality control, 18,911,793 single nucleotide polymorphisms (SNPs) were retained for further analysis. A GWAS was conducted using a linear mixed model implemented in GCTA. Key findings include a significant QTL on SSC15 (110.83–112.23 Mb), which is associated with the iodine value, containing genes such as COX15, CHUK, SCD, and HIF1AN, which have known roles in fatty acid metabolism. Additionally, PNKD, VIL1, and PRKAG3 (120.74–121.88 Mb on SSC15) were linked to belly firmness, influencing muscle structure and fat composition. Three QTLs for belly side fat were identified on SSC1, SSC2, and SSC3, highlighting genes like SLC22A18, PHLDA2, and OSBPL5, which regulate fat deposition and lipid metabolism. The results provide novel molecular markers that can be incorporated into selective breeding programs to improve pork quality, fat distribution, and meat composition. These findings enhance our understanding of the genetic mechanisms underlying carcass belly traits while offering tools to improve pork quality, optimize fat composition, and align with consumer preferences in the meat production industry. Full article

Background/Objectives: PRKAG2 syndrome (PS) is a rare genocopy of hypertrophic cardiomyopathy (HCM). Our goal was to expand knowledge about PS by analyzing patient clinical, imaging, and follow-up data. Methods: The study included carriers of likely pathogenic or pathogenic PRKAG2 variants identified in the years 2011–2022. Cardiac involvement was assessed by electrocardiography, echocardiography, cardiac magnetic resonance imaging, and endomyocardial biopsy (EMB). We recorded concomitant diseases and cardiac events, including the implantation of electronic cardiac devices, arrhythmia, heart failure (HF), and death. Results: Seven patients from four families (median age 43 years) with PRKAG2 variants: Phe293Leu, Val336Leu, Arg302Gln, and His530Arg were included. At the first evaluation, 3 carriers were in New York Heart Association (NYHA) functional class II–III, while the remaining were in NYHA class I. Left ventricular hypertrophy (LVH) was present in 5 patients; 2 had ventricular pre-excitation, one was in atrial flutter and pacemaker-dependent; 2 had bradycardia. Two female carriers had concomitant chronic renal disease. In the EMB of one of the patients, staining for glycogen deposits was positive. Furthermore, we provide a link between the Val336Leu PRKAG2 variant and autophagy identified on EMB. After a median follow-up of 13.1 years, 6 carriers had LVH, 3 required admission for HF, and 1 had sustained ventricular tachycardia with subsequent cardioverter defibrillator implantation, and despite this, died suddenly; there were two de novo pacemaker implantations due to symptomatic bradycardia. Conclusions: PR is a distinctive disorder with an early onset of arrhythmic events, often leading to HF. Full article

Meat quality is a complex trait that exhibits significant variation across pig breeds, and the regulatory mechanisms governing pork meat quality are not fully elucidated. We compared the transcriptomics and metabolomics of the longissimus dorsi (LD) muscle between the Songliao Black Pig (SBP) and Large White × Landrace Pig (LWLDP) to investigate breed-specific differences in meat quality and underlying regulatory pathways. The results showed that SBP meat had a higher marbling score and backfat thickness, a richer color, a lower shear force, and reduced drip loss. Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. Protein–protein interaction (PPI) network analysis found 25 key genes, which are associated with muscle development, fat deposition, and overall meat quality, while genes in the insulin signaling pathway, such as PPP1R3B, PPARGC1A, SOCS1, EIF4E, PRKAR2A, PRKAG2, and FASN, play a crucial role in balancing fat metabolism and catabolism. Metabolomic analysis identified 89 upregulated and 10 downregulated metabolites in the SBP, primarily involved in fructose and mannose metabolism, amino acid biosynthesis, nucleotide sugar metabolism, and glucagon signaling pathways. Gene–metabolite association analysis found that the PPP1R3B gene had a strong association with Thr-Leu, Maltol, D-myo-Inositol-4-phosphate, and Fructose-6-phosphate, while MYOG correlated with Mannose-6-phosphate, Fructose-1-phosphate, Mannose-1-phosphate, and Glucose-6-phosphate. In contrast, NR4A3 and PPARGC1A showed a strong negative correlation with most upregulated metabolites. In conclusion, this study identified functional genes, elucidated the mechanisms associated with meat quality traits, and identified gene–metabolite associations involved in energy metabolism, muscle development, and fat deposition, providing valuable insights into the molecular mechanisms that regulate meat quality between pig breeds. Full article

Background: Cardiomyopathy, including dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), is a major cause of heart failure (HF) and a leading indication for heart transplantation. Of these patients, 20–50% have a genetic cause, so understanding the genetic basis of cardiomyopathy will provide knowledge about the pathogenesis of the disease for diagnosis, treatment, prevention, and genetic counseling for families. Methods: This study collected nine patients from different Vietnamese families for genetic analysis at The Cardiovascular Center, E Hospital, Hanoi, Vietnam. The patients were diagnosed with cardiomyopathy based on clinical symptoms. Whole-exome sequencing (WES) was performed in the Vietnamese patients to identify variants associated with cardiomyopathy, and the Sanger sequencing method was used to validate the variants in the patients’ families. The influence of the variants was predicted using in silico analysis tools. Results: Nine heterozygous variants were detected as a cause of disease in the patients, three of which were novel variants, including c.284C>G, p.Pro95Arg in the MYL2 gene, c.2356A>G, p.Thr786Ala in the MYH7 gene, and c.1223T>A, p.Leu408Gln in the DES gene. Two other variants were pathogenic variants (c.602T>C, p.Ile201Thr in the MYH7 gene and c.1391G>C, p.Gly464Ala in the PTPN11 gene), and four were variants of uncertain significance in the ACTA2, ANK2, MYOZ2, and PRKAG2 genes. The results of the in silico prediction software showed that the identified variants were pathogenic and responsible for the patients’ DCM. Conclusions: Our results contribute to the understanding of cardiomyopathy pathogenesis and provide a basis for diagnosis, treatment, prevention, and genetic counseling. Full article

PRKAG2 cardiomyopathy is a rare genetic disorder that manifests early in life with an autosomal dominant inheritance pattern. It harbors left ventricular hypertrophy (LVH), ventricular pre-excitation and progressively worsening conduction system defects. Its estimated prevalence among patients with LVH ranges from 0.23 to about 1%, but it is likely an underdiagnosed condition. We report the association of the PRKAG2 missense variant c.1006G>A p. (Val336Ile) with LVH, conduction abnormalities (short PR interval and incomplete right bundle branch bock) and early-onset arterial hypertension (AH) in a 44-year-old Caucasian patient. While cardiac magnetic resonance (CMR) showed a mild hypertrophic phenotype with maximal wall thickness of 17 mm in absence of tissue alterations, the electric phenotype was relevant including brady–tachy syndrome and recurrent syncope. The same variant has been detected in the patient’s sister and daughter, with LVH + early-onset AH and electrocardiographic (ECG) alterations + lipothymic episodes, respectively. Paying close attention to the coexistence of LVH and ECG alterations in the proband has been helpful in directing genetic tests to exclude primary cardiomyopathy. Hence, identifying the genetic basis in the patient allowed for familial screening as well as a proper follow-up and therapeutic management of the affected members. A review of the PRKAG2 cardiomyopathy literature is provided alongside the case report. Full article

A 72-year-old Brazilian woman presented with a 4-year history of rest tremors of the hands, followed by slowness of movement, and a diagnosis of idiopathic Parkinson’s disease. She was started on dopamine agonists with significant improvement. After three years, she complained about slowly progressive dysphagia, dysphonia, quadriparesis, and cramps and fasciculations. A neurological examination disclosed distal-dominant quadriparesis, dysarthria, atrophy and fasciculation of the tongue, global brisk tendon reflexes, fasciculations, bilateral ankle clonus, and moderate spasticity of the lower limbs. She had also palpitations, dyspnea, and one episode of paroxysmal atrial fibrillation. Electrocardiography revealed a short PR interval, a widened QRS complex, and the delta wave, suggestive of Wolff–Parkinson–White syndrome. Brain and spine MR imaging, a cerebrospinal fluid analysis, and general serum lab exams were unremarkable. Needle electromyography disclosed chronic denervation involving cervical, thoracic, lumbosacral, and bulbar levels associated with acute denervation, including positive sharp waves, fasciculations, and fibrillation potentials. This patient fulfilled the diagnostic criteria for amyotrophic lateral sclerosis associated with parkinsonism. A broad next-generation sequencing-based panel disclosed the presence of the novel heterozygous variant c.1247C > T (p.Pro416Leu) in the PRKAG2 gene (NM_016203.4). Clinicians must be aware of the possibility of PRKAG2 variants in complex clinical scenarios associating cardiac arrhythmia, preexcitation syndromes, hypertrophic cardiomyopathy, motor neuron disease, and parkinsonism. Full article

Background: Recent genome-wide association studies demonstrated the association between the prevalence of chronic kidney disease (CKD) and rs11959928, rs626277, and rs7805747 polymorphisms. Materials and Methods: In this study, we investigated the association between CKD and these polymorphisms in patients and controls according to gender. High-resolution melting analysis was performed to detect DAB2 rs11959928, DACH1 rs626277, and PRKAG2 rs7805747 single nucleotide polymorphisms. Genomic DNA was extracted from the buffy coat of 163 patients with chronic renal disease and 218 control individuals. Ten percent of the results were also randomly confirmed by direct DNA sequencing. Results: Multivariable logistic regression analysis with adjustment for confounders showed rs7805747 (dominant model) has a statistically significant protective effect in females, and rs11959928 (additive and dominant models) was significantly associated with the prevalence of CKD in males. rs7805747 (recessive model) was significantly associated with the prevalence of CKD in males. Conclusion: The very same genetic variants have different effects in males and females separately. Our results warrant the need for similar studies in larger cohorts. Full article