Search Results (9,231)

In this study, an exploratory transcriptomic investigation was conducted to evaluate the feasibility of using feather transcriptomics to detect sex differences and gene responses to physiological changes in chickens. Feathers represent a promising non-invasive biological source of RNA, as the feather pulp of growing feathers contains living cells capable of active transcription. Growing feathers were collected from 150-day-old male and female chickens (Bionda Piemontese, a slow-growing breed) raised under a free-range system and fed two finisher diets differing in lipid content: low-lipid (LL, ether extract 3.6%) and high-lipid (HL, ether extract 9.3%) diets. RNA was extracted from feather pulp, and 12 pools were subjected to whole RNA-Seq analysis. The study was designed as 2 × 2 factorial experiments investigating the effects of diet and sex on gene expression. A total of 17,360 transcripts were detected and used for downstream analyses. Differential gene expression and functional enrichment analyses were performed. The main effects of diet and sex were estimated with an additive design using the DEseq2 package, while for the sex-specific diet analyses, subgroup comparisons were conducted on the RaNA-Seq platform. The analysis of the main effect of diet reveals that three genes associated with ether lipid metabolism (PLA2G10, PLA2G4F, and ENPP6) were upregulated in chickens fed the HL diet. In roosters, HL feeding significantly altered the expression of APOA1 and SLC27A4, suggesting an effect on lipid transport and metabolic regulation within the PPAR signaling pathway. In contrast, hens showed differential expression primarily in pathways related to apelin signaling, extracellular matrix remodeling, and cardiovascular function, rather than classical lipid metabolism pathways; additionally, gene set enrichment analysis indicated a limited enrichment of linoleic acid metabolism, suggesting secondary involvement of lipid metabolic processes. These findings are consistent with those in the literature reporting sex-related differences between males and females. The results further suggest that transcriptomic responses to dietary lipid supplementation can be investigated through the expression of selected candidate genes in feather pulp. Among the genes identified, PLA2G10, PLA2G4F, ENPP6, APOA1, and SLC27A4 emerged as potential molecular markers associated with dietary treatment, and the importance of sex-dependent transcriptional responses was highlighted. In conclusion, this study demonstrates the potential of feather pulp as a viable source of RNA for transcriptomic analyses in live chickens, providing a minimally invasive alternative to conventional tissue sampling. These preliminary results also support the hypothesis that feathers represent a practical and ethically favorable tissue for future nutrigenomic and genetic improvement studies, ultimately supporting more sustainable poultry production. Full article

Gustatory perception in honeybees is a key determinant of foraging decisions and pollen source selection. However, the molecular mechanisms underlying this sensory discrimination remain poorly understood. To investigate these mechanisms during the collection of pollen from different floral sources, this study utilized antennae from worker bees foraging on pear and rapeseed pollen, and non-pollen-foraging workers as controls. Illumina high-throughput transcriptome sequencing was employed to identify differentially expressed genes (DEGs), perform functional annotation, and characterize gustatory receptor (GR) genes. Compared with the control group, 583 DEGs and 516 DEGs were identified in pear-pollen and rapeseed-pollen foragers, respectively, whereas only 73 DEGs were detected between the two pollen-foraging groups. Several DEGs were associated with chemosensory perception, signal transduction, energy metabolism, and immune responses. Notably, genes involved in membrane-associated signaling and stimulus response exhibited differential expression patterns among foraging groups, suggesting adaptive molecular responses to distinct floral resources. Gene Ontology (GO) analysis indicated that DEGs were primarily associated with cellular processes, membrane components, and binding functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted significant involvement in phagosome, phosphatidylinositol signaling system, oxidative phosphorylation, and extracellular matrix–receptor interaction. Notably, seven GR-related genes were identified in the antennal transcriptome, including five known GR genes and two novel candidates, all with complete open reading frames. Four of these genes featured the canonical seven-transmembrane domain structure of insect GRs. Phylogenetic analysis, in addition to the known sugar receptors AmelGR43a, AmelGR64f, and AmelGR64f-X1, based on GRs from Apis mellifera and Drosophila melanogaster suggested that AmelGR28b, AmelGR10, AmelGR12, and AmelGR13 may belong to the bitter taste receptor family. Quantitative real-time PCR (qRT-PCR) validation demonstrated that the expression patterns of the selected seven DEGs were consistent with the RNA-seq results. This study reveals differential expression patterns and potential functional divergence of gustatory receptor genes in Apis mellifera during pollen collection from different floral sources. It provides important molecular evidence for understanding how honeybees accurately recognize and preferentially forage specific pollen sources via gustatory perception, and offers valuable theoretical and practical insights for honeybee behavioral ecology and crop pollination management. Full article

The rising burden of diabetic kidney disease (DKD) and its associated lipid abnormalities underscores the need for new mechanistic insights. Uromodulin, a kidney-enriched protein, has been associated with metabolic disorders in human studies, yet its functional role in systemic lipid metabolism remains elusive. In this study, transcriptomic datasets were analyzed to investigate uromodulin expression and biological function in DKD. Subsequently, a diabetic model was induced in UMOD^+/+ and UMOD^−/− rats using a combination of a high-fat diet, unilateral nephrectomy, and streptozotocin to assess renal and metabolic phenotypes. Public RNA-seq data indicated that uromodulin expression was downregulated in DKD and was enriched in the fatty acid metabolism pathway. At baseline, UMOD^−/− rats resembled UMOD^+/+ rats in terms of growth, routine serum lipids, and major organ function. However, in diabetes, UMOD^−/− rats exhibited higher mortality and pronounced hyperlipidemia. Hyperlipidemia occurred prior to the onset of renal dysfunction. Of note, this exacerbated lipid dysregulation represented a lipodystrophy-like phenotype rather than secondary changes in the pancreas, liver, or circulating cytokines (IL-6, IL-1β, and TNF-α). Moreover, UMOD^−/− rats displayed exacerbated tubular injury and enhanced renal lipid accumulation in DKD relative to UMOD^+/+ rats. Collectively, uromodulin protects diabetic rats from death, prevents epididymal white adipose tissue from browning, and attenuates kidney injury. Our findings identify uromodulin as a novel regulator of the kidney–adipose axis. Full article

The Growth-Regulating Factor (GRF) family and their co-activators, GRF-Interacting Factors (GIFs), are key players in the trade-off between plant development and stress adaptation, functioning as canonical targets of the highly conserved miR396 family, which mediates responses to environmental stressors including high temperatures and water deficits. The “starlet” phenomenon in the allotetraploid Coffea arabica L. is a developmental disorder that results in malformed flowers, frequently associated with environmental stress and floral sterility. Since their underlying molecular mechanisms remain uncharacterized, we performed a genome-wide identification of the CaGRF and CaGIF families and quantified their transcriptional profiles in shoot apical meristems (SAMs) and across multiple stages of floral bud development. Our findings reveal significant differential expression of the GRF-GIF module between typical and starlet tissues throughout development, including the SAM. Intriguingly, these results do not correlate with the levels of a representative member of the miR396 family, indicating that the GRF-GIF expression shifts in starlet-flowers may be uncoupled from miR396 levels. This work provides the first molecular insights into the enigmatic starlet phenomenon in Coffea arabica L., addressing an understudied aspect of coffee reproductive development and its implications for the reproductive stability (and productivity) of this important tropical crop species. Full article

In this paper, we consider the extremal trace problem for the coupled Laplacian on the sets homeomorphic to the Stiefel manifold defined on the complex Euclidean space. The study is implemented via various mathematical methods, including topological and probabilistic approaches. A detailed, comprehensive classification of the stationary points is given, which itself deserves to be considered as a general method in the framework of the optimization theory. Finally, an application to biologically meaningful integration of heterogeneous datasets, in which the structure of molecular interactions serves as a significant constraint for the mathematical model, is proposed. The main advantage of the elaborated method in comparison with the previously used ones is the absence of any conditions on the structure of the initial heterogeneous datasets. This paper is a continuation of a series of papers by our research group devoted to the development of new mathematical methods for integrating multi-omics data. Full article

Calcium (Ca²⁺) functions as a second messenger in plants, coordinating development and stress responses through cytosolic Ca²⁺ dynamics. The P-type Ca²⁺-ATPases of the ECA (P-IIA) and ACA (P-IIB) subfamilies are central to Ca²⁺ homeostasis and signal termination by extruding Ca²⁺ from the cytosol. In this study, genome-wide identification was performed to identify the P-type Ca²⁺-ATPases according to the maize B73 v5 reference genome, followed by phylogenetic, structural, chromosomal, syntenic, network, and expression analyses. Nineteen genes were identified, comprising 4 ECAs and 15 ACAs. All 19 members retained the DKTGT phosphorylation site, while the CaATP_NAI (N- terminal autoinhibitory) extension distinguished all 15 ACAs from the 4 ECAs. Collinearity analysis revealed 11 maize–rice syntenic pairs, implicating segmental duplication. ECAs were preferentially expressed in reproductive tissues, whereas ACAs were broadly expressed across vegetative organs. RNA-seq-based profiling detected distinct stress-responsive expression patterns of Ca²⁺-ATPase genes. Under abiotic stress, ZmACA12-1 was consistently upregulated under drought, ZmACA6-2 dominated the heat response, and ZmACA4-2 showed the broadest cross-stress repression. Under biotic stress, ACA members again dominated, with ZmACA1-1 being the most broadly pathogen-responsive member, ZmECA1-3 the principal ECA-class responder, and ZmACA9 exhibiting consistent pathogen-associated repression. Additionally, ZmACA12-1 and ZmACA4-4 showed genotype-dependent regulation between resistant and susceptible lines. Collectively, these candidates represent priority targets for functional validation of the calcium efflux mechanisms that underlie maize adaptation to both abiotic and biotic stresses. Full article

The hormonal vitamin D metabolite, 1,25-dihydroxyvitamin D (1,25D), produced primarily in the kidney, acts in numerous end-organs via the nuclear vitamin D receptor (VDR) to trigger molecular events that orchestrate bone mineral homeostasis, immune responsiveness, and aspects of behavior. Tyrosine hydroxylase (TH) encodes a neuronally expressed enzyme that catalyzes the initial, rate-limiting step in the production of several catecholamine neurotransmitters and hormones, including dopamine, norepinephrine, and epinephrine. Herein we report that TH mRNA is significantly induced (2.5-fold) and NURR1 mRNA is induced 9.3-fold by 10 nM 1,25D in differentiated human SH-SY5Y neuroblastoma cells. Similar results were observed in human U87 glioblastoma cells (TH, 2.6-fold; NURR1, 3.6-fold). Comparative analysis of TH gene promoter-proximal sequences from human, mouse, and rat identifies candidate NURR1-responsive elements (NBREs) at the following positions: −35, −855, −1470, and −2343 bp in the human gene; −34 and −961 bp in the mouse gene; and −34, −350, and −873 bp in the rat gene, consistent with NURR1 acting as a recurring regulatory factor at TH promoters across mammalian species. Furthermore, by interrogating VDR ChIP-seq/cistrome datasets, we identified candidate vitamin D-responsive elements (VDREs) at the human NURR1 locus that provide a plausible genomic framework for direct regulation of NURR1 by 1,25D/VDR. We propose that 1,25D-liganded VDR acts as a primary inducer of NURR1, which in turn secondarily activates expression of the TH gene, thereby defining a transcriptional route through which 1,25D/VDR signaling may influence TH-linked dopaminergic gene programs. Retinoid X receptor (RXR) may facilitate both NURR1-dependent and -independent potentiation of TH transcription because the rexinoid, bexarotene, significantly enhances TH mRNA in human U87 cells, either alone (2.0-fold) or in combination with 1,25D (4.1-fold). In addition, bexarotene and its novel analogs, A41 and A55, induce NURR1 mRNA expression in U87 cells by 2.8-, 3.1-, and 4.8-fold, respectively, with A55 outperforming the parent compound at matched concentration. Because Parkinson’s disease is characterized by the selective degeneration of dopaminergic neurons and impaired NURR1-dependent transcriptional programs, our findings identify a 1,25D/VDR–NURR1–RXR transcriptional axis as a previously underappreciated regulatory framework for studying TH gene expression and dopaminergic gene regulation in Parkinson’s disease-relevant neural contexts. Full article

Background/Objectives: While traditional transcriptomics and single-cell RNA sequencing can reveal differences in cell type and gene expression, they cannot provide spatial information within tissues. Spatial transcriptomics (ST), as an emerging technology in recent years, has achieved significant progress in resolving gene expression along the spatial dimension. This technology quantifies gene expression at defined spatial coordinates and describes the spatial distribution of transcripts and the co-localization patterns between cells within intact tissue, allowing for an integrated analysis of molecular and spatial information. This review aims to systematically trace the development of ST and highlight its application value in breast cancer research. Methods: We systematically reviewed the recent literature on ST platforms, on combined analyses of single-cell RNA sequencing (scRNA-seq) and ST, and on integrated spatial multi-omics in breast cancer. Key topics include tumor microenvironment organization, intra-tumor heterogeneity, the spatial distribution of immune cells, cancer-associated fibroblast function, treatment-response prediction, and personalized-treatment strategy development. Results: ST can characterize the spatial organization of interactions between breast cancer cells and the tumor microenvironment, describe the spatial dimensions of tumor heterogeneity, and provide multi-dimensional information that may support refined subtype classification and prognostic assessment. Existing studies indicate that ST shows significant potential to inform personalized treatment strategies, but the technology also faces bottlenecks in data integration, spatial resolution, standardization, and the need for functional validation. Conclusions: ST provides an important tool for an in-depth description of the complex spatial organization within breast cancer tumors. When integrated with functional perturbation, longitudinal cohorts, and orthogonal omics, it has the potential to ultimately improve clinical outcomes for breast cancer patients. Full article

Background/Objectives: Atherosclerotic plaque instability is driven by complex interactions among inflammatory, structural, and cellular remodeling programs. While bulk RNA sequencing provides insight into tissue-level transcriptional states and single-cell RNA sequencing (scRNA-seq) defines cellular heterogeneity, integration across these transcriptomic layers remains limited. We aimed to identify coordinated transcriptional programs associated with stable and unstable plaque phenotypes and map these programs to specific cellular compartments and regulatory networks. Methods: Paired bulk RNA-seq data from stable and unstable human carotid plaques (GSE120521) and scRNA-seq data from human coronary atherosclerotic lesions (GSE131778) were analyzed. Differential expression and Hallmark gene set enrichment analyses were performed using limma and clusterProfiler. Bulk-derived inflammatory and structural signatures were projected onto single-cell data using Seurat module scoring. Compartment-level transcriptional scores, an inflammatory–structural endotype index, and transcription factor activity inference using decoupleR and DoRothEA were used to characterize plaque-associated transcriptional states. Results: Unstable plaques demonstrated enrichment of inflammatory pathways, including interferon gamma response, inflammatory response, TNFα/NF-κB signaling, IL6/JAK/STAT3 signaling, complement activation, and reactive oxygen species pathways. In contrast, stable plaques demonstrated relative enrichment of myogenesis and structural remodeling programs. Projection of bulk-derived signatures onto single-cell data localized inflammatory programs predominantly to TREM2hi and inflammatory macrophage populations, whereas structural programs localized to smooth muscle cell and fibromyocyte-like compartments. Compartment-level analyses showed increased myeloid and adaptive immune signatures in unstable plaques and increased smooth muscle cell/fibro-remodeling signatures in stable plaques. Transcription factor activity analysis identified increased SPI1, NFKB1, RELA, and STAT1 activity in unstable plaques and higher SRF and TEAD1 activity in stable plaques. Conclusions: Integrative analysis of bulk and single-cell transcriptomic data identified distinct inflammatory and structural plaque transcriptional states associated with unstable and stable plaque phenotypes, respectively. These findings support a systems-level framework linking tissue-level plaque behavior to specific cellular and regulatory programs and provide evidence for inflammatory and structural plaque endotypes in human atherosclerosis. Full article

The pituitary and gonads serve as central regulatory hubs and functional organs for gametogenesis and maturation. In this study, we performed single-cell RNA sequencing (scRNA-seq) of the pituitary and ovary in pre-spawning Pelteobagrus fulvidraco to elucidate the cellular landscape and regulatory pathways governing gonadal development and oocyte maturation. Pituitaries from four female fish (weight: 43.8 ± 3.2 g; length: 14.1 ± 0.7 cm) and four male fish (weight: 78.2 ± 11.2 g; length: 18.9 ± 1.1 cm) were subjected to single-cell transcriptomic analysis. A total of 17 distinct cell types were identified in the female pituitary, whereas 15 cell types were detected in the male pituitary. Both male and female pituitaries comprised multiple hormone-secreting endocrine populations, indicating a largely conserved cellular composition. However, sex-specific differences were observed in thyrotrope subtypes, suggesting potential sexual dimorphism in pituitary endocrine regulation. Examination of receptor gene expression revealed cell-type-specific regulatory capacities, highlighting gonadotropin, steroid, and neuropeptide responsiveness across pituitary populations. In the ovary, 10 cell types were identified, with granulosa cells (~22.9%) and theca cells (~8.6%) showing distinct transcriptional profiles. Follicle-stimulating hormone receptor (fshr) was highly expressed in granulosa cells, whereas luteinizing hormone receptor (lhcgr) and steroidogenic genes (hsd3b1, pgr) were predominantly localized in theca cells, indicating functional compartmentalization of gonadotropin and steroid signaling. Prostaglandin (PG) and melatonin (MT) pathways were implicated in paracrine regulation: the prostaglandin synthase ptgs2a was expressed in theca, germ, and immune cells, while ptger2a was expressed in granulosa cells; melatonin synthesis genes (aanat1, aanat2, asmtl) were confined to granulosa cells, with receptors (mtnr1ab) in germ cells. These findings suggest that ovarian paracrine signaling complements systemic endocrine control to modulate oocyte maturation and ovulation. This single-cell atlas provides a high-resolution framework of reproductive cell types and signaling networks in P. fulvidraco, offering insights for improving artificial breeding and reproductive management in aquaculture. Full article

The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (Equus asinus, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (Equus caballus, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searches (Pfam PF00019), followed by phylogenetic, conserved motif, synteny, Ka/Ks, mutation prediction, subcellular localization, and tissue-specific expression analyses. We identified 40 TGF-β genes in donkeys, exceeding the numbers reported in several mammals, suggesting possible lineage-specific expansion or differential gene retention within Equidae. Phylogenetic and motif analyses demonstrated strong evolutionary conservation across the two principal clades (TGF-β-like and BMP-like). Four segmental duplications were identified, with Ka/Ks ratios ranging from 0.28 to 0.43, indicating strong purifying selection on duplicated genes. Synteny analysis revealed extensive collinearity with the horse genome, supporting conserved equid genomic architecture. Comparative sequence analysis identified 160 amino acid variants, including 11 predicted deleterious mutations in key genes (GDF6, GDF9, GDF10, BMP15, and RGMA), suggesting potential functional divergence associated with reproductive and developmental pathways. Importantly, transcriptomic validation using publicly available donkey RNA-seq tissue expression data (NCBI BioProject: PRJNA1017964) revealed distinct tissue-specific expression patterns, with reproductive tissues (ovary and uterus) displaying enriched expression of TGF-β/BMP signaling components, particularly TGFBR1, TGFBR2, TGFB1, BMP2, BMP4, and BMP7, while canonical fecundity genes (GDF9 and BMP15) exhibited ovary-associated expression. This receptor-dominant signaling profile may have a coordinated TGF-β regulatory network underlying folliculogenesis, reproductive tissue remodeling, and fertility-related processes in donkeys. Subcellular localization predictions showed that most proteins (22/40) were extracellularly localized, consistent with conserved signaling functions. Together, this study provides the first integrated genomic and tissue-expression atlas of the donkey TGF-β superfamily, offering new insights into equid-specific evolutionary conservation, reproductive signaling, and functional divergence. Full article

RNA interference (RNAi) represents a promising alternative to chemical insecticides, but its efficacy depends on efficient double-stranded RNA (dsRNA) uptake, a process poorly characterized in thrips. To enable sufficient dsRNA production for functional studies, we first optimized an E. coli expression system by constructing a vector containing three tandem terminators, which substantially enhanced dsRNA yield by approximately 11-fold. Using this optimized production system, this study identified a conserved muscle actin fragment for dsRNA synthesis and evaluated RNAi responses in Megalurothrips usitatus and Frankliniella occidentalis. Insect mortality, target-gene suppression, and transcriptomic responses were evaluated via RT-qPCR and RNA-seq analyses using artificial diets supplemented with muscle actin dsRNA. The designed dsactin shared > 97% sequence identity between the two species. Oral ingestion of 1500 ng µL⁻¹ dsRNA caused concentration-dependent mortality (72% in M. usitatus, 48% in F. occidentalis) and significant down-regulation of muscle actin mRNA within 72 h. Transcriptomic analysis in M. usitatus revealed upregulation of genes associated with clathrin-mediated endocytosis and SID-1-like transmembrane transport, suggesting a potential dual-pathway model for dsRNA uptake. These findings provide correlative insights into RNAi efficiency in thrips. Full article

The European perch (Perca fluviatilis) is highly susceptible to heat stress, limiting its sustainable aquaculture. While single-organ thermal responses are partially understood, the systemic, multi-organ cooperative survival mechanisms under acute heat stress remain poorly characterized. To elucidate the underlying tolerance mechanisms and provide genetic markers for breeding, this study investigated the multi-organ responses of European perch (n = 90; body length: 13.15 ± 1.75 cm; body weight: 30.54 ± 7.17 g) transferred from 24 °C to an acute heat stress challenge (31 °C) at an increasing rate of 2 °C/h, and the histopathological changes (liver and gill), hepatic biochemical biomarkers (CAT, SOD, GSH-Px, GST, LDH, and MDA), and transcriptomic changes (liver and kidney) were evaluated over a 24 h period. Heat stress induced progressive structural damage, including gill lamellar edema and hepatocyte necrosis, accompanied by significant hepatic oxidative stress and lipid peroxidation. RNA-seq transcriptome profiling uncovered distinct sets of genes with significant expression changes, comprising 1343 DEGs in liver tissue and 722 DEGs in kidney samples. Both organs shared a systemic endoplasmic reticulum stress response but exhibited highly divergent survival strategies. The liver underwent severe metabolic reprogramming towards anaerobic glycolysis and gluconeogenesis, coupled with vesicle-mediated membrane repair attempts and apoptosis. Conversely, the kidney adopted a strict “energy triage” strategy, suppressing highly energy-consuming immune and osmoregulatory functions while actively silencing pro-apoptotic signals. These findings highlight organ-specific adaptations and identify potential metabolic markers for the future breeding of new heat-tolerant varieties. Full article

Total RNA was isolated from sections of healthy testes and Leydig cell tumors of mixed-breed dogs using TMA Master II device. The RNA-seq libraries were sequenced on the Illumina platform. Following differential expression analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were applied with quality control obtained using FastQC and Trimmomatic. This analysis revealed 1500 transcripts, including 982 upregulated and 168 downregulated genes. The results demonstrated that a significant proportion of these differentially expressed genes are directly involved in the control of sex steroid production (CYP11A1, STAR, and 3β-HSD3B1) or tube formation, angiogenesis, and extracellular matrix remodeling in interstitial cells (ESM1, FGG, and VEGFA). Moreover, we identified the upregulation of transcripts responsible for neurotransmitter or neuroendocrine signaling (SLC6A4, GRIN2C, GABRB3) and cholesterol metabolism and its regulation (GPX3, MSMO1, DHCR24). These genes were strongly associated with the phosphatidylinositol-3-kinase (PI3K)-Protein Kinase B (Akt) cascade and extracellular matrix interactions, features shared with various malignancies. Alterations in estrogen and relaxin signaling appear to be distinctive, understudied mechanisms specific to canine Leydig cell tumors. Concurrently, downregulated genes (e.g., DMRTC2, SEMA3C, ALOX12) were linked with cell differentiation, signaling and immunoregulatory pathway suppression involved in tumorigenesis. A complex transcriptomic profile of canine Leydig cell tumors was developed, revealing a conserved oncogenic core shared in some aspects with human malignancies alongside unique species-specific alterations. Findings seem to be useful for identifying novel diagnostic biomarkers and targeted therapies in veterinary oncology, establishing canine reproductive tissues as a valuable comparative biomedical model for research in human. Full article

Background: Angiopoietin-like 3 (ANGPTL3) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are key regulators of lipid homeostasis. We have previously shown that gene silencing of ANGPTL3 significantly induces PCSK9 expression in the human hepatoma cell line Huh7. Here, we investigated the biological significance of this regulation in the cultured human hepatoma cell line Huh7. Methods: We performed an RNA-seq analysis in Huh7 cells transfected with siRNA-ANGPTL3, siRNA-PCSK9, and double siRNA-ANGPTL3/PCSK9. Selected findings were assessed by RT-qPCR, Western blotting, and ELISA. Results: Among 13,945 detected transcripts, 192 genes were differentially expressed after ANGPTL3 silencing, 88 after PCSK9 silencing, and 219 after combined ANGPTL3/PCSK9 silencing, compared with scramble-siRNA controls. When ANGPTL3 gene expression was silenced, we observed a compensatory induction in PCSK9 mRNA and protein expression. Bioinformatic analysis revealed that gene silencing of ANGPTL3 or both ANGPTL3/PCSK9 suppresses serpin family A member 1 (SERPINA1), which encodes α1-antitrypsin, and lectin mannose-binding 1 (LMAN1). These data were confirmed by Western blot and RT-PCR analysis. In addition, ANGPTL3-siRNA, alone or combined with PCSK9-siRNA, significantly increased FV and FVIII mRNA expression and secretion in conditioned medium. Conclusions: Our data identified SERPINA1 and LMAN1 as genes downregulated in response to ANGPTL3 silencing in Huh7 hepatoma cells, which was also associated with increased expression of FV and FVIII. Our study suggests a potential link between ANGPTL3 silencing and coagulation-related processes, extending the biological relevance of ANGPTL3 beyond lipid metabolism. Full article