Search Results (21)

The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-quality data after quality control. The single nucleotide polymorphisms (SNPs) were primarily distributed in intergenic regions, followed by intronic regions. Principal component analysis (PCA) and STRUCTURE revealed clear distinctions among the generations, with a notable overlap between CY and F3. Using the SNP dataset, we analyzed the number and length distribution patterns of runs of homozygosity (ROHs) in the genomes of different generational groups of Grassland-Thoroughbreds. Short ROHs ranging from 0.5 to 2 Mb were the most abundant, with the following distribution: F1 (85.15%) > F2 (82.92%) > CY (78.75%) > F3 (77.51%). Medium-length ROHs (2–8 Mb) and long ROHs (>8 Mb) together exhibited a similar but opposite trend. The average length of ROHs was 1.57 Mb. The inbreeding coefficients (F_ROH) among different generational groups of Grassland-Thoroughbreds were as follows: F1 (0.0942) < F2 (0.1197) < CY (0.1435) < F3 (0.1497). Through ROH island analysis, 10 high-frequency ROH regions were identified and annotated with 120 genes. Genomic regions and candidate genes associated with athletic traits—ACAD8, OPCML, PRDX2, NTM, NDUFB7, SCL25A15, FOXO1, and SLC4A10—were identified. These genes may play important roles in regulating muscle performance, mitochondrial energy supply, and learning and memory processes in horses and are closely associated with the athletic ability of the Grassland-Thoroughbred population. This study is the first to systematically characterize the genomic diversity and inbreeding dynamics of the Grassland-Thoroughbred during the breeding process. It identifies candidate genes that may influence athletic performance, thereby providing an important molecular foundation and theoretical basis for the genetic improvement and performance-based selection of this emerging breed. Full article

Meat color is the most intuitive measure of meat quality and has a significant impact on consumer preference. To explore the molecular mechanisms affecting duck pectoralis meat color, the phenotypic traits of Cherry Valley duck (CV, eight males and eight females) and Huai Fu duck (HF, eight males and eight females) were compared; three males and three females of each variety were later selected for transcriptomic and metabolomic analyses to reveal key molecular processes. This study found that the expression level of CA3 (carbonic anhydride enzyme 3) is positively correlated with the meat color phenotype, suggesting that it may play a positive regulatory role in the formation of meat color. The expression trend of the ST13 gene is opposite to the phenotype, suggesting that it may play a negative regulatory role. With the participation of CA3 and NDUF family genes (such as NDUFC2, NDUFB2, etc.), the oxidative phosphorylation pathway plays a key role in meat color formation by regulating the oxygenation/deoxygenation state of myoglobin and intracellular pH value. Although the effects of these genes and pathways on meat color have been discovered, their specific genetic mechanisms and molecular functions still need further verification. This provides important clues for further understanding the molecular mechanism of meat color formation and may offer potential molecular targets for improving meat color or breeding new varieties. Full article

Antlers, as the only fully regenerable bone tissue in mammals, serve as an exceptional model for investigating bone growth, mineralization, articular cartilage repair, and the pathophysiology of osteoporosis. Nevertheless, the exact molecular mechanisms governing osteogenesis, particularly the dynamic cellular interactions and signaling pathways coordinating these processes, remain poorly characterized. This study used single-cell RNA sequencing (scRNA-seq) on the 10× Genomics Chromium platform, combined with bulk-RNA sequencing results, to comprehensively analyze molecular regulatory mechanisms in rapid antler osteogenesis. The results showed that eight cell types were identified in sika deer antler during the growth and ossification stages: mesenchymal, chondrocyte, osteoblast, pericyte, endothelial, monocyte/macrophage, osteoclast, and NK cells. Chondrocytes were predominantly found during the growth stage, while osteoblasts were more abundant during the ossification stage. Mesenchymal cells were subclassified into three subcategories: MSC_1 (VCAN and SFRP2), MSC_2 (TOP2A, MKI67), and MSC_3 (LYVE1 and TNN). MSC_3 was predominantly present during the growth stage. During the growth stage, MSC_1 and MSC_2 upregulated genes related to vasculature development (COL8A1, NRP1) and cell differentiation (PTN, SFRP2). During the ossification stage, these subcategories upregulated genes involved in the positive regulation of p53 class mediator signal transduction (RPL37, RPL23, RPS20, and RPL26), osteoblast differentiation (SPP1, IBSP, BGLAP), and proton-motive ATP synthesis (NDUFA7, NDUFB3, NDUFA3, NDUFB1). Endothelial cells were categorized into five subpopulations: Enc_1 (SPARCL1, VWF), Enc_2 (MCM5), Enc_3 (ASPM, MKI67), Enc_4 (SAT1, CXCL12), and Enc_5 (ZFHX4, COL6A3). Combined scRNA-seq and bulk RNA-seq analysis revealed that the ossification stage’s upregulation genes included osteoclast- and endothelial cell-specific genes, while the growth stage’s upregulation genes were mainly linked to collagen organization, osteoblast differentiation, mitotic cell cycle, and chondrocyte differentiation. Overall, this study offers a detailed single-cell analysis of gene expression patterns in antlers during the growth and ossification stages, providing insights into the molecular mechanisms driving rapid osteogenesis. Full article

As ovarian cancer progresses, increased glucose use causes a glucose shortage in the tumor microenvironment. Therefore, it is crucial to find drugs that can effectively kill cancer cells in this energy stress setting. Here, we propose an effective therapeutic strategy that combines nutrient restriction with metformin to combat tumors. This study investigated the effects of metformin on ovarian cancer cells under energy stress conditions, mimicking the nutrient-deprived tumor microenvironment. We revealed that Metformin (10 mM) significantly reduced cell viability and proliferation under glucose deprivation conditions. Furthermore, it enhanced apoptosis and ferroptosis, as demonstrated by alterations in apoptotic protein expression and elevated levels of lipid reactive oxygen species (ROS), malondialdehyde (MDA), lipid peroxidation (LPO), and Fe²⁺. Transcriptional profiling revealed significant alterations in genes related to iron homeostasis and oxidative phosphorylation. Moreover, Metformin was found to induce mitochondrial dysfunction without affecting mitochondrial DNA or the expression of enzymes in the tricarboxylic acid (TCA) cycle, resulting in decreased ATP production and compromised activities of the respiratory chain complexes. The direct interaction between metformin and the NDUFB4 subunit in mitochondrial complex I was corroborated through the application of cellular thermal shift assay (CETSA) and drug affinity responsive target stability (DARTS) assays. In vivo, the combination of metformin and fasting cycles significantly inhibited SKOV3 cell-derived xenograft tumors in immunodeficient mice. Altogether, we have demonstrated that Metformin potentiates apoptosis and ferroptosis in ovarian cancer cells under energy stress conditions by targeting the NDUFB4 subunit of mitochondrial complex I, thus laying the groundwork for clinical testing. This study, though limited to cellular and animal levels, provides valuable insights into the therapeutic potential of metformin in ovarian cancer treatment. Full article

Psoriasis (Ps) is a debilitating immune-mediated chronic skin condition. It affects about 1–3% of the world population, with an 8–11% prevalence in Northern European populations. Tyrosine kinase 2 (TYK2) is a newly identified target for Ps. An independent non-coding genetic association with Ps has been identified ~400 kb upstream of TYK2. The variants making up the credible Ps Single-Nucleotide Polymorphism (SNP) set were identified in their genomic context with the potential to influence TYK2 expression by interacting with regulatory elements involved in gene regulation. Previous evidence from our laboratory has suggested that credible SNP sets in intronic regions can be distal regulators of the genes of interest through long-range chromatin interactions. We hypothesise that SNPs at ILF3 are distal regulators of TYK2 expression via long-range chromatin interactions and Ps risk. The dysregulation of the TYK2 pathway in Ps may be mediated by a combination of GWAS risk SNPs at ILF3 and TYK2 and downstream genes. We investigated this by employing functional genomics and molecular biology methods. We developed a CD4 T cell model system with Jurkat-dCAS9-VP64 and Jurkat-dCAS9-KRAB cells using CRISPR activation and CRISPR inhibition of the risk variants rs892086 and rs7248205, selected from the latest Ps GWAS SNP set for their long-range interaction and light Linkage Disequilibrium (R² > 0.8), respectively. Using CRISPR activation, we demonstrate here that these risk SNPs, although distal to TYK2, do indeed regulate the TYK2 gene. Investigations into annotating the TYK2 pathway using RNA-seq analysis revealed differentially regulated genes, including VEGFA, C1R, ADORA1, GLUD2, NDUFB8, and FCGR2C, which are thought to be implicated in Ps. These genes were observed to be associated with conditions such as psoriatic arthritis, atopic dermatitis, and systemic sclerosis when compared using published databases, which confirms their relevance and importance in inflammatory conditions. With the developed cell model systems using CRISPR technology and differential gene regulation, we demonstrate here that these genes have the potential to define the TYK2/Ps pathway and our understanding of the disease biology. Full article

A prenatal low-protein (LP) diet disrupts glucose homeostasis in adult offspring. Skeletal muscles are one of the main sites of glucose clearance, and mitochondria residing in the muscle fibers are central to glucose homeostasis. Our previous studies indicated that impaired mitochondrial health is central to dysregulated glucose metabolism in the gastrocnemius muscle of the LP-programmed female rats. In addition, dysfunctional mitochondria are often an indicator of underlying irregularities in energy metabolism and metabolic inflexibility. Therefore, this study examined the mitochondrial function and metabolic flexibility in the skeletal muscles of prenatal LP-programmed adult male rats. Pregnant Wistar rats were randomly allotted to a control diet (20% protein) or an isocaloric LP diet (6% protein). Standard laboratory rat chow was given to the dams and the pups after delivery and weaning. Gene and protein expressions, mtDNA copy number, and electron microscopy were assessed in gastrocnemius (GS) muscle, and the mitochondrial oxygen consumption rate was determined using isolated flexor digitorum brevis muscle fibers. The genes associated with mitochondrial outer membrane fusion, mitofusin1 and 2 (Mfn1 and Mfn2), fission (Fis1), and biogenesis (Pgc1B, Nrf1, and Esrra) were lower in the LP group. Further, our functional studies showed that the ATP-linked oxygen consumption rate (OCR), maximal, spare respiratory, and non-mitochondrial respiration-associated OCRs were lower in the LP rats. Further, the mRNA and protein expressions of Ndufb8, a key factor involved in the complex-I catalytic activity, were downregulated in the LP group. In addition, the expression of genes linked to mitochondrial pyruvate transport (Mpc1) and metabolism (Pdha1) was lower in the LP group. In contrast, the expression of mitochondrial fatty acid transporters (Cpt1a and Cpt2) was higher in the LP when compared to the control group. However, electron microscopic analysis exhibited no difference in the mitochondrial ultrastructure in the LP muscle compared to the control. Altogether, our results indicate that the LP diet affects the mitochondrial complex-I integrity and dynamics and leads to altered expression of genes associated with substrate oxidation and mitochondrial dysfunction in the skeletal muscle of the male LP offspring. Full article

In recent years, research has gradually uncovered the mechanisms of animal adaptation to hypoxic conditions in different altitude environments, particularly at the genomic level. However, past genomic studies on high-altitude adaptation have often not delved deeply into the differences between varying altitude levels. This study conducted whole-genome sequencing on 60 Tibetan sheep (Medium Altitude Group (MA): 20 Tao sheep (TS) at 2887 m, High Altitude Group (HA): 20 OuLa sheep (OL) at 3501 m, and Ultra-High Altitude Group (UA): 20 AWang sheep (AW) at 4643 m) from different regions of the Tibetan Plateau in China to assess their responses under varying conditions. Population genetic structure analysis revealed that the three groups are genetically independent, but the TS and OL groups have experienced gene flow with other northern Chinese sheep due to geographical factors. Selection signal analysis identified FGF10, MMP14, SLC25A51, NDUFB8, ALAS1, PRMT1, PRMT5, and HIF1AN as genes associated with ultra-high-altitude hypoxia adaptation, while HMOX2, SEMA4G, SLC16A2, SLC22A17, and BCL2L2 were linked to high-altitude hypoxia adaptation. Functional analysis showed that ultra-high-altitude adaptation genes tend to influence physiological mechanisms directly affecting oxygen uptake, such as lung development, angiogenesis, and red blood cell formation. In contrast, high-altitude adaptation genes are more inclined to regulate mitochondrial DNA replication, iron homeostasis, and calcium signaling pathways to maintain cellular function. Additionally, the functions of shared genes further support the adaptive capacity of Tibetan sheep across a broad geographic range, indicating that these genes offer significant selective advantages in coping with oxygen scarcity. In summary, this study not only reveals the genetic basis of Tibetan sheep adaptation to different altitudinal conditions but also highlights the differences in gene regulation between ultra-high- and high-altitude adaptations. These findings offer new insights into the adaptive evolution of animals in extreme environments and provide a reference for exploring adaptation mechanisms in other species under hypoxic conditions. Full article

Collagen VI-related dystrophies (COL6RD) are a group of rare muscle disorders caused by mutations in specific genes responsible for type VI collagen production. It affects muscles, joints, and connective tissues, leading to weakness, joint problems, and structural issues. Currently, there is no effective treatment for COL6RD; its management typically addresses symptoms and complications. Therefore, it is essential to decipher the disease’s molecular mechanisms, identify drug targets, and develop effective treatment strategies to treat COL6RD. In this study, we employed differential gene expression analysis, weighted gene co-expression network analysis, and genome-scale metabolic modeling to investigate gene expression patterns in COL6RD patients, uncovering key genes, significant metabolites, and disease-related pathophysiological pathways. First, we performed differential gene expression and weighted gene co-expression network analyses, which led to the identification of 12 genes (CHCHD10, MRPS24, TRIP10, RNF123, MRPS15, NDUFB4, COX10, FUNDC2, MDH2, RPL3L, NDUFB11, PARVB) as potential hub genes involved in the disease. Second, we utilized a drug repurposing strategy to identify pharmaceutical candidates that could potentially modulate these genes and be effective in the treatment. Next, we utilized context-specific genome-scale metabolic models to compare metabolic variations between healthy individuals and COL6RD patients. Finally, we conducted reporter metabolite analysis to identify reporter metabolites (e.g., phosphatidates, nicotinate ribonucleotide, ubiquinol, ferricytochrome C). In summary, our analysis revealed critical genes and pathways associated with COL6RD and identified potential targets, reporter metabolites, and candidate drugs for therapeutic interventions. Full article

The tiger pufferfish (Takifugu rubripes), also known as fugu, has recently suffered from severe C. irritans infections under aquaculture environment, yet the underlying immune mechanisms against the parasite remain poorly understood. In this study, we conducted a comprehensive transcriptome analysis of the gill tissue from infected and uninfected fish using PacBio long-read (one pooled sample each for seriously infected and healthy individuals, respectively) and Illumina short-read (three pools for mildly infected, seriously infected, and healthy individuals, respectively) RNA sequencing technologies. After aligning sequence data to fugu’s reference genome, 47,307 and 34,413 known full-length transcripts were identified and profiled in healthy and infected fish, respectively. Similarly, we identified and profiled 1126 and 803 novel genes that were obtained from healthy and infected fish, respectively. Interestingly, we found a decrease in the number of alternative splicing (AS) events and long non-coding RNAs (lncRNAs) after infection with C. irritans, suggesting that they may be involved in the regulation of the immune response in fugu. There were 687 and 1535 differentially expressed genes (DEGs) in moderately and heavily infected fish, respectively, compared to uninfected fish. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that immune-related DEGs in the two comparison groups were mainly enriched in cytokine-cytokine receptor interactions, ECM-receptor interactions, T-cell receptor signaling pathways, Th1 and Th2 cell differentiation, and Th17 cell differentiation pathways. Further analysis revealed that a large number of immune-related genes were downregulated in infected fish relative to uninfected ones, such as CCR7, IL7R, TNFRSF21, CD4, COL2A1, FOXP3B, and ITGA8. Our study suggests that C. irritans is potentially a highly efficient parasite that may disrupt the defense mechanisms of fugu against it. In addition, in combination of short-read RNA sequencing and previous genome-wide association analyses, we identified five key genes (NDUFB6, PRELID1, SMOX, SLC25A4, and DENND1B) that might be closely associated with C. irritans resistance. This study not only provides valuable resources of novel genic transcripts for further research, but also provides new insights into the immune mechanisms underlying C. irritans infection response in farmed fugu. Full article

The cellular events leading to the development of the woody breast myopathy in broiler breast muscle are unclear. Affected woody breast muscle exhibits muscle fiber degeneration/regeneration, connective tissue accumulation, and adverse morphological changes in mitochondria. Ribonucleotide reductase (RNR) is an enzyme for the synthesis of dNTP, which is important for mitochondria DNA content (mtDNA). RNR consists of two subunits: RRM1/RRM2. A decrease in RRM2 is associated with a decrease in mtDNA and mitochondria proteins, leading to impaired ATP production. The objective of this study was to investigate potential RNR differences between woody breast (WB) and normal (N) breast muscle by examining RRM2 expression and associated pathways. Gene expression and enzyme activities were examined by qPCR and commercial kits. Results showed that RRM2 expression reduced for WB (p = 0.01) and genes related to mitochondria, including ATP6 (p = 0.03), COX1 (p = 0.001), CYTB (p = 0.07), ND2 (p = 0.001) and ND4L (p = 0.03). Furthermore, NDUFB7 and COX 14, which are related to mitochondria and ATP synthesis, tended to be reduced in WB. Compared to N, GLUT1 reduced for WB (p = 0.05), which is responsible for glucose transport in cells. Consequently, PDK4 (p = 0.0001) and PPARG (p = 0.008) increased in WB, suggesting increased fatty acid oxidation. Citric synthase activity and the NAD/NADH ratio (p = 0.02) both reduced for WB, while WB increased CHRND expression (p = 0.001), which is a possible indicator of high reactive oxygen species levels. In conclusion, a reduction in RRM2 impaired mitochondria function, potentially ATP synthesis in WB, by increasing fibrosis and the down-regulation of several genes related to mitochondria function. Full article

Obesity is associated with excessive fat accumulation in adipose tissue and other organs, such as skeletal muscle, whereas aerobic exercise (AE) plays an important role in managing obesity through profound protein regulation. Our study aimed to investigate the impact of AE on proteomic changes in both the skeletal muscle and the epididymal fat pad (EFP) of high-fat-diet-induced obese mice. Bioinformatic analyses were performed on differentially regulated proteins using gene ontology enrichment analysis and ingenuity pathway analysis. Eight weeks of AE significantly reduced body weight, increased the serum FNDC5 level, and improved the homeostatic model assessment of insulin resistance. A high-fat diet caused alterations in a subset of proteins involved in the sirtuin signaling pathway and the production of reactive oxygen species in both skeletal muscle and EFP, leading to insulin resistance, mitochondrial dysfunction, and inflammation. On the other hand, AE upregulated skeletal muscle proteins (NDUFB5, NDUFS2, NDUFS7, ETFD, FRDA, and MKNK1) that enhance mitochondrial function and insulin sensitivity. Additionally, the upregulation of LDHC and PRKACA and the downregulation of CTBP1 in EFP can promote the browning of white adipose tissue with the involvement of FNDC5/irisin in the canonical pathway. Our study provides insights into AE-induced molecular responses and may help further develop exercise-mimicking therapeutic targets. Full article

We report a neonatal patient with hypertrophic cardiomyopathy (HCM), lactic acidosis and isolated complex I deficiency. Using a customized next-generation sequencing panel, we identified a novel hemizygous variant c.338G>A in the X-linked NDUFB11 gene that encodes the NADH: ubiquinone oxidoreductase subunit B11 of the mitochondrial respiratory chain (MRC) complex I (CI). Molecular and functional assays performed in the proband’s target tissues—skeletal and heart muscle—showed biochemical disturbances of the MRC, suggesting a pathogenic role for this variant. In silico analyses initially predicted an amino acid missense change p.(Arg113Lys) in the NDUFB11 CI subunit. However, we showed that the molecular effect of the c.338G>A variant, which is located at the last nucleotide of exon 2 of the NDUFB11 gene in the canonical ‘short’ transcript (sized 462 bp), instead causes a splicing defect triggering the up-regulation of the expression of an alternative ‘long’ transcript (sized 492 bp) that can also be detected in the control individuals. Our results support the hypothesis that the canonical ‘short’ transcript is required for the proper NDUFB11 protein synthesis, which is essential for optimal CI assembly and activity, whereas the longer alternative transcript seems to represent a non-functional, unprocessed splicing intermediate. Our results highlight the importance of characterizing the molecular effect of new variants in the affected patient’s tissues to demonstrate their pathogenicity and association with the clinical phenotypes. Full article

Molecular heterogeneity has great significance in the disease biology of multiple myeloma (MM). Thus, the analysis combined single-cell RNA-seq (scRNA-seq) and bulk RNA-seq data were performed to investigate the clonal evolution characteristics and to find novel prognostic targets in MM. The scRNA-seq data were analyzed by the Seurat pipeline and Monocle 2 to identify MM cell branches with different differentiation states. Marker genes in each branch were uploaded to the STRING database to construct the Protein-Protein Interaction (PPI) network, followed by the detection of hub genes by Cytoscape software. Using bulk RNA-seq data, Kaplan-Meier (K-M) survival analysis was then carried out to determine prognostic biomarkers in MM. A total of 342 marker genes in two branches with different differentiation states were identified, and the top 20 marker genes with the highest scores in the network calculated by the MCC algorithm were selected as hub genes in MM. Furthermore, K-M survival analysis revealed that higher NDUFB8, COX6C, NDUFA6, USMG5, and COX5B expression correlated closely with a worse prognosis in MM patients. Moreover, ssGSEA and Pearson analyses showed that their expression had a significant negative correlation with the proportion of Tcm (central memory cell) immune cells. Our findings identified NDUFB8, COX6C, NDUFA6, USMG5, and COX5B as novel prognostic biomarkers in MM, and also revealed the significance of genetic heterogeneity during cell differentiation in MM prognosis. Full article

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ² = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish. Full article

Primary brain malignancy is a rare tumor with a global incidence of less than 10 per 100,000 people. Hence, there is limited power for identifying risk loci in individual studies, especially for Han Chinese. We performed a genome-wide association study (GWAS) in Taiwan, including 195 cases and 195 controls. We identified five new genes for malignant neoplasms of the brain: EDARADD (rs645507, 1p31.3, p = 7.71 × 10⁻⁵, odds ratio (OR) = 1.893), RBFOX1 (rs8044700, p = 2.35 × 10⁻⁵, OR = 2.36), LMF1 (rs3751667, p = 7.24 × 10⁻⁷, OR = 2.17), DPP6 (rs67433368, p = 8.32 × 10⁻⁵, OR = 3.94), and NDUFB9 (rs7827791, p = 9.73 × 10⁻⁶, OR = 4.42). These data support that genetic susceptibility toward GBM or non-GBM tumors is highly distinct, likely reflecting different etiologies. Combined with signaling analysis, we found that RNA modification may be related to major risk factors in primary malignant neoplasms of the brain. Full article