Search Results (121)

The growth plate is a specialized cartilage structure near the ends of long bones that orchestrates longitudinal bone growth during fetal and postnatal stages. Within this region reside a dynamic population of growth plate skeletal stem cells (gpSSCs), primarily located in the resting zone, which possess self-renewal and multilineage differentiation capacity. Recent advances in cell-lineage tracing, single-cell transcriptomics, and in vivo functional studies have revealed distinct subpopulations of gpSSCs, which are defined by markers such as parathyroid hormone-related protein (PTHrP), CD73, axis inhibition protein 2 (Axin2), forkhead box protein A2 (FoxA2), and apolipoprotein E (ApoE). These stem cells interact intricately with their niche, particularly after the formation of the secondary ossification center, through stage-specific regulatory mechanisms involving several key signaling pathways. This review summarizes the current understanding of gpSSC identity, behavior, and regulation, focusing on how these cells sustain growth plate function through adapting to biomechanical and molecular cues. Full article

Cortical transcriptional dysregulation is widespread in Huntington’s disease (HD). We re-examined prefrontal Brodmann Area 9 (BA9) RNA-seq (GSE64810; 20 HD, 49 controls) using BH-FDR and GEO2R to obtain differential-expression statistics for downstream in silico integration. A compact, direction-aware 80-gene panel was assembled for visualization/ranking only, while inference relied on validated target sets and full-universe testing. At FDR < 0.05, we detected Up = 2923 and Down = 2448 genes (ratio 1.19), indicating a mild predominance of up-regulation. MIR219A2 was strongly down-regulated, and four experimentally validated targets (FOXC1, NFKBIA, SLC38A2, SLC6A20) overlapped the up-regulated core; as expected for n = 4, no GO/KEGG/Reactome term met FDR < 0.05, and STRING returned no high-confidence edges. Beyond the curated panel, we tested MIR219A2 (hsa-miR-219a-5p; hsa-miR-219a-1-3p; hsa-miR-219a-2-3p) targets against the full FDR-significant BA9 up-regulated universe. Two orthogonal, experimentally supported resources—miRTarBase functional assays and ENCORI/starBase CLIP—showed direction-consistent, FDR-controlled enrichment, with effect sizes and uncertainty reported in the main text, supporting a BA9-specific, MIR219A2-aligned association signal. On the TF axis, MSigDB C3:TFT (gene symbols) revealed significant over-representation of TF target sets among BA9-Up under the same BA9 expressed-gene background after BH-FDR (e.g., NFAT motifs, C/EBP, FOXA/HNF3), while TRRUST v2 applied to the MIR219A2 CLIP–BA9-Up subset provided target-level transparency. MIR219A2 enrichments were robust to composition sensitivity analyses (marker-excluded and neuron/glia-stratified backgrounds). Exploratory GO–Biological Process bubbles are shown for trend summarization only; no term met FDR < 0.05 in the primary analysis. All conclusions are analysis-only; no wet-lab or biofluid/peripheral assays were performed, and findings are BA9-specific—generalization to other regions remains hypothesis-generating. Full article

Prostate cancer (PCa) is the second most frequent tumor and the fifth leading cause of cancer-related death in men worldwide. PCa shows the largest clinical disparities across Asian, Caucasian, and African descendants among all cancer types, proving that the ethnic genetic background plays a significant role in PCa. Androgen Receptor (AR) gene malfunctioning represents the most prevalent cause of PCa. AR also displays a broad spectrum of genetic variability across ethnic backgrounds differently associated with cancer risk. We conducted a massive sequencing analysis of 15 genes highly relevant for PCa or the AR activation pathway in biopsies from 64 tumors and 36 benign prostate samples from Mexican patients. We identified 3414 genomic mutations and observed that AR, SPOP, TP53, FOXA1, and MTOR had the highest rate of pathogenic mutations in tumors, evidencing their relevance in PCa. AR showed 13 unique mutations, followed by SPOP (6), TP53 (5), FOXA1 (4), and MTOR (3). We discovered 19 novel mutations specific of Hispanic patients, a population only scarcely studied, thus adding critical information on the genetic diversity of the mutational landscape in genes key for PCa. We discuss the clinical relevance of these mutations and predict the structural consequences on the proteins. Mutations in FOXA1 showed significant negative association with patient survival and might be used as novel PCa markers, at least for Hispanic men. Full article

Background/Objectives: Colorectal cancer (CRC) is one of the most common malignancies worldwide. microRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally and have emerged as important regulators in cancer biology. This study aimed to investigate the roles of miR-379-5p and miR-519a-3p in CRC using Quantitative Real-Time PCR (RT-qPCR) and comprehensive bioinformatic analyses. Methods: Tumor tissues and matched adjacent normal tissues were collected from 54 patients with CRC. The expression levels of miR-379-5p and miR-519a-3p in these tissues were determined using the RT-qPCR method. To investigate the functional roles of differently expressed miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to construct miRNA–transcription factor (TF)–target gene–disease interaction networks. Results: It was found that the expression level of miR-379-5p was statistically significantly increased in tumor tissues compared to normal tissues, while miR-519a-3p was decreased (p < 0.05). GO analysis revealed enrichment in several important biological processes, including cellular protein metabolic processes, biosynthetic processes, response to stress, and nucleic acid binding TF activity. KEGG analysis exhibited that dysregulated miRNAs were associated with important pathways related to carcinogenesis, such as p53 signaling, TGF-beta signaling, and FoxO signaling pathways. Additionally, the miRNAs-TFs-Genes-Diseases Networks analysis identified ESR1 and FOXA1 as common target TFs of dysregulated miRNAs. Network analyses showed that dysregulated miRNAs interact with CRC-associated genes (Caspase 3 (CASP3), Adenomatous polyposis coli (APC), and AKT serine/threonine kinase 3 (AKT3)). Conclusions: The present study indicates that miR-379-5p and miR-519a-3p may be involved in CRC progression, with miR-379-5p being upregulated and miR-519a-3p being downregulated in tumor tissues. However, further functional studies are required to clarify their potential roles in tumor biology. The findings of the study suggest that miR-379-5p and miR-519a-3p may be associated with regulatory pathways related to CRC. These miRNAs have the potential to serve as diagnostic biomarkers or therapeutic targets in CRC. Full article

Ulcerative colitis (UC) is a chronic inflammatory bowel disease associated with disrupted lipid metabolism. This study aimed to uncover novel molecular subtypes and biomarkers by integrating sphingolipid metabolism-related genes (SMGs) with machine learning approaches. Using data from the GEO and GeneCards databases, 29 UC-related SMGs were identified. Consensus clustering was employed to define distinct molecular subtypes of UC, and a diagnostic model was developed through various machine learning algorithms. Further analyses—including functional enrichment, transcription factor prediction, single-cell localization, potential drug screening, molecular docking, and molecular dynamics simulations—were conducted to investigate the underlying mechanisms and therapeutic prospects of the identified genes in UC. The analysis revealed two molecular subtypes of UC: C1 (metabolically dysregulated) and C2 (immune-enriched). A diagnostic model based on three key genes demonstrated high accuracy in both the training and validation cohorts. Moreover, the transcription factor FOXA2 was predicted to regulate the expression of all three genes simultaneously. Notably, mebendazole and NVP-TAE226 emerged as promising therapeutic agents for UC. In conclusion, SMGs are integral to UC molecular subtyping and immune microenvironment modulation, presenting a novel framework for precision diagnosis and targeted treatment of UC. Full article

Thanatosomes (hyaline globules or death bodies) are histologically observed in various non-neoplastic and neoplastic conditions. Some of these globules are associated with apoptotic cell death. Only six documented cases of thanatosomes have been reported in breast tumors. In this rare case involving a 64-year-old Japanese woman diagnosed as having rectal cancer, preoperative computed tomography scanning revealed breast cancer in her right breast. Following a right total mastectomy, a tumor characterized as apocrine carcinoma (carcinoma with apocrine differentiation) containing thanatosomes was discovered. These globules are PAS positive and diastase resistant, exhibit deep fuchsinophilic staining with Masson’s trichrome, stain dark blue with PTAH, and are negative for mucin by Alcian blue. The tumor cells tested positive for the androgen receptor, FOXA1, and GCDFP15. Human epidermal growth factor type 2 (HER2)/neu score was 3+/positive, and the Ki-67 labeling index was 60%. Thus, the tumor represented high-grade, HER2-enriched apocrine carcinoma. Thanatosomes are immunoreactive to cleaved caspase-3 and are histological markers of high cell turnover and apoptotic cell death. Therefore, in this nonspecific microscopic neoplastic condition, they are typically linked to high-grade tumors, as this case showed. This report presents a rare case of apocrine breast cancer featuring a limited number of thanatosomes. Full article

Hypoxia is a hallmark of aggressive prostate cancer, but how it disrupts lineage-specific transcriptional programs to drive progression remains unclear. Here, we identify the HIF1α-PHD1-FOXA1 axis as a critical mediator of hypoxic adaptation and androgen signaling suppression. Using genome-wide profiling, we demonstrate that hypoxia reprograms HIF1α chromatin occupancy, shifting its cooperation from AR to FOXA1. Mechanistically, HIF1α physically interacts with FOXA1, destabilizing it via PHD1-mediated hydroxylation—a previously unrecognized post-translational regulatory node. Under hypoxia, loss of FOXA1 attenuates androgen-responsive transcription while activating hypoxia-inducible genes, demonstrating a dual role for this axis in hypoxia adaptation and prostate cancer progression. Genetic or pharmacological disruption of HIF1α-PHD1-FOXA1 impairs prostate cancer proliferation and migration, underscoring its translational relevance. Our findings establish oxygen-dependent FOXA1 degradation as a linchpin connecting microenvironmental stress to transcriptional plasticity in advanced prostate cancer, offering new therapeutic avenues. Full article

Per- and polyfluoroalkyl substances (PFAS) are used in consumer products and manufacturing. Perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), and perfluoroundecanoic acid (PFUnDA) are long-chain PFAS composed of 9, 10, and 11 carbons, respectively, which exert sublethal toxicity to aquatic species. Here, we review the data regarding the environmental fate and ecotoxicology of these understudied long-chain PFAS in fish. The objectives of this study were to (1) compile the literature to compare physiological or molecular signaling pathways disrupted by PFNA, PFDA, or PFUnDA; and (2) uncover potential biomarkers and pathways of toxicity of longer-chain PFAS using gene ontology computational approaches to shed light on their mechanism of action. Studies show that PFAS have a range of effects on fish, including developmental issues, changes in gene expression, and behavioral modifications. Based on our review, PFNA has been studied more frequently in fish compared to PFDA and PFUnDA; however, longer-chained PFAS are proposed to pose greater toxicity. Based on the computational approach, prominent pathways affected by PFNA include insulin signaling [“Insulin -> CEBPA/CTNNB/FOXA/FOXO”, “Insulin -> STAT Expression Targets”], immune system signaling [“TNF -> STAT Expression Targets”, “IL6 Expression Targets”, and “IL2 Expression Targets”], and growth hormone/prolactin signaling [“GH1/PRLR Expression Targets”, “PRL/GHR -> STAT Expression Targets”, “PRL/PRLR Expression Targets”]. Several transcripts related to cholesterol metabolism were also affected by PFNA. This review summarizes the current knowledge on the distribution, fate, and ecotoxicology of PFNA, PFDA, and PFUnDA in teleost fish, highlighting potential physiological and molecular responses that could aid in assessing long-chain PFAS toxicity in future studies. Full article

Human induced pluripotent stem cells (hiPSCs) hold great potential for regenerative medicine. However, optimizing their differentiation into specific lineages within three-dimensional (3D) scaffold-based culture systems that mimic in vivo environments remains challenging. This study examined the trilineage differentiation of hiPSCs under various 3D conditions using synthetic peptide hydrogel matrices with and without embryoid body (EB) medium induction. hiPSC 3D colonies (spheroids), naturally formed from single cells or small clusters in 3D culture, were used for differentiation into the three germ lineages. Differentiated spheroids exhibited distinct morphological characteristics and significantly increased expression of key lineage-specific markers—FOXA2 (endoderm), Brachyury (mesoderm), and PAX6 (ectoderm)—compared to undifferentiated controls. Marker expression varied depending on the 3D culture conditions. Differentiation efficiency improved significantly, increasing from 16% to 71% for endoderm, 61% to 80% for mesoderm, and 35% to 48% for ectoderm, by selecting the appropriate 3D matrix and applying EB induction. Comprehensive data analysis from RT-qPCR, immunocytochemistry staining, and flow cytometry confirmed that the Synthegel Spheroid (SGS) is a viable 3D matrix for evaluating all three germ lineages using a commercial trilineage differentiation kit. While EB induction is essential for endodermal differentiation, it is not required for mesodermal and ectodermal lineages. These findings are valuable not only for screening initial differentiation potential at the lineage level but also for optimizing 3D differentiation protocols for deriving somatic cells from hiPSCs. Full article

The piggyBac+TET-on transposon induction system has a high efficiency in integrating exogenous genes in multiple cell types, can precisely integrate to reduce genomic damage, has a flexible gene expression regulation, and a strong genetic stability. When used in conjunction with somatic cell nuclear transfer experiments, it can precisely and effectively reveal the intrinsic mechanisms of early biological development. This study successfully reprogrammed black-boned sheep fibroblasts (SFs) into induced pluripotent stem cells (iPSCs) using the piggyBac+TET-on transposon system and investigated their impact on early embryonic development. Seven exogenous reprogramming factors (bovine OCT4, SOX2, KLF4, cMyc, porcine NANOG, Lin-28, and SV40 Large T) were delivered into SFs, successfully inducing iPSCs. A growth performance analysis revealed that iPSC clones exhibited a raised or flat morphology with clear edges, positive alkaline phosphatase staining, and normal karyotypes. The transcriptome analysis indicated a significant enrichment of iPSCs in oxidative phosphorylation and cell proliferation pathways, with an up-regulated expression of the ATP5B, SDHB, Bcl-2, CDK1, and Cyclin D1 genes and a down-regulated expression of BAX (p < 0.05). Somatic cell nuclear transfer experiments demonstrated that the cleavage rate (85% ± 2.12) and blastocyst rate (52% ± 2.11) of the iPSCs were significantly higher than those of the SFs (p < 0.05). The detection of trilineage marker genes confirmed that the expression levels of endoderm (DCN, NANOS3, FOXA2, FOXD3, SOX17), mesoderm (KDR, CD34, NFH), and ectoderm (NEUROD) markers in iPSCs were significantly higher than in SFs (p < 0.01). The findings demonstrate that black-boned sheep iPSCs possess pluripotency and the potential to differentiate into all three germ layers, revealing the mechanisms by which reprogrammed iPSCs influence early embryonic development and providing a critical foundation for research on sheep pluripotent stem cells. Full article

Background/Objectives: The germline polymorphism in the HSD3B1 gene (c.1100 C) results in adrenal-permissive (CC) or adrenal-restrictive (AA) functions of the protein product by regulating the production of high-affinity ligands that activate androgen signaling. Prior studies have indicated that the CC genotype is associated with worse response to hormonal therapies in prostate cancer (PC) patients. Methods: To characterize the impact of germline HSD3B1 variants on somatic tumor features, we examined 6550 primary and metastatic PCs from the Caris Life Sciences database, in which the genomic and transcriptomic landscapes were acquired via paired whole-exome/whole-transcriptome sequencing. Results: The overall prevalence of the HSD3B1 AA genotype (restrictive–homozygous) was 48.8%, AC (permissive–heterozygous) was 32.8%, and CC (permissive–homozygous) was 14.9%. There was enrichment of the CC genotype in these PC patients as compared to prior reports that examined non-cancerous populations. However, the rates of the CC genotype varied between metastatic site and by race. Compared to the AA genotype, tumors harboring the CC genotype did not demonstrate increased AR alterations, nor higher expression of AR, FOXA1, HOXB13, or AR signaling signatures. We instead found significant changes in immune-associated hallmark pathways, immune cell fractions, and biomarkers that inform the use of immune therapies (TMB-high, MSI-high). Further, the CC and AA genotypes exhibited notable differences in the expression of immunoglobulins, MHC class I/II molecules, and cell surface targets. The differences in expression by HSD3B1 genotype were especially notable in lung and liver metastases. Conclusions: Our study indicates that in prostate cancers, HSD3B1 germline c.1100 allele status may not directly influence tumor-intrinsic genomics but is associated with novel functions beyond androgen signaling. Full article

The asb5 gene, a member of the Asb protein subfamily characterized by six ankyrin repeat domains, is highly conserved and comprises two subtypes, asb5a and asb5b, in zebrafish. Our previous research has demonstrated that a deficiency of the asb5 gene significantly impairs early cardiac contractile function, highlighting its close relationship with heart development. Zebrafish asb5 expression was disrupted by both morpholino (MO) antisense oligomer-mediated knockdown and a CRISPR-Cas9 system. A high-throughput RNA-Seq analysis was used to analyze the possible molecular regulatory mechanism of asb5 gene deletion leading to left–right (L-R) asymmetry defects in the heart. Whole-mount in situ hybridization (WISH) was conducted to evaluate gene expression patterns of Nodal signaling components and the positions of heart organs. Heart looping was defective in zebrafish asb5 morphants. Rescue experiments in the asb5-deficiency group (inactivating both asb5a and asb5b) demonstrated that the injection of either asb5a-mRNA or asb5b-mRNA alone was insufficient to rectify the abnormal L-R asymmetry of the heart. In contrast, the simultaneous injection of both asb5a-mRNA and asb5b-mRNA successfully rescued the morphological phenotype. A high-throughput RNA-Seq analysis of embryos at 48 h post fertilization (hpf) revealed that numerous genes associated with L-R asymmetry exhibited expression imbalances in the asb5-deficiency group. WISH further confirmed that the expression of genes such as fli1a, acta1b, hand2, has2, prrx1a, notch1b, and foxa3 were upregulated, while the expression of mei2a and tal1 was downregulated. These results indicated that loss of the asb5 gene in zebrafish led to the disordered development of L-R asymmetry in the heart, resulting in an imbalance in the expression of genes associated with the regulation of L-R asymmetry. Subsequently, we examined the expression patterns of classical Nodal signaling pathway-related genes using WISH. The results showed that the midline barrier factor gene lefty1 was downregulated at early stages in the asb5-deficiency group, and the expression of spaw and lefty2, which are specific to the left lateral plate mesoderm (LPM), was disrupted. This study reveals that the two subtypes of the asb5 gene in zebrafish, asb5a and asb5b, interact and jointly regulate the establishment of early cardiac L-R asymmetry through the Nodal-spaw-lefty signaling pathway. Full article

It has been shown that the pathogenic variants (PVs) of the DNA Damage Response (DDR) genes, whether of a germinal or somatic nature, represent a predictive biomarker of high sensitivity to treatment with inhibitors of the enzyme poly-ADP-ribose polymerase (PARP) in patients with hormone-resistant metastatic prostate cancer (HRPCa). Moreover, the detection of PVs of the Homologous Recombination Repair (HRR) genes in PCa patients can help to define the patient’s prognosis and the choice of the therapeutic procedure. Among men with metastatic PCa, the frequency of PVs in HRR genes ranges from 11% to 33%, which is a significantly higher rate compared to non-metastatic PCa, where the incidence is between 5% and 10%. Next-Generation Sequencing (NGS) results were more commonly obtained from newly acquired somatic samples compared to archived samples (prostate biopsy or prostatectomy). We developed an experimental multidisciplinary prospective study in patients with a new diagnosis of high-risk PCa at biopsy. The aim was to evaluate the presence of PVs of different HRR genes in patients with the first diagnosis of PCa in relation to a metastatic or non-metastatic stage, tumor aggressiveness, and early risk of progression. Among 43 initial tumor samples from 22 patients, 25 samples from 12 patients were selected for library preparation based on their DNA concentration and quality. After the NGS, 14 different DNA variants were prioritized. Oncogenetic and likely oncogenetic variants were found in the ATM, BRCA1, PTEN, KMT2D, and CDH1 genes. Moreover, variants of uncertain significance were found in ATM, DDR2, FANCA, FOXA1, PLCB4, PTCH1, and RB1. Full article

Extrachromosomal circular DNAs (eccDNAs) has been found to be widespread and functional in various organisms. However, comparative analyses of pre- and post-infection of virus are rarely known. Herein, we investigated the changes in expression patterns of eccDNA following infection with Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) and explore the role of eccDNA in viral infection. Circle-seq was used to analyze eccDNAs in the midgut of BmCPV-infected and BmCPV-uninfected silkworms. A total of 5508 eccDNAs were identified, with sizes varying from 72 bp to 17 kb. Most of eccDNAs are between 100 to 1000 bp in size. EccDNA abundance in BmCPV-infected silkworms was significantly higher than in BmCPV-uninfected silkworms. GO and KEGG analysis of genes carried by eccDNAs reveals that most are involved in microtubule motor activity, phosphatidic acid binding, cAMP signaling pathway, and pancreatic secretion signaling pathways. Several eccDNAs contain sequences of the transcription factor SOX6, sem-2, sp8b, or Foxa2. Association analysis of eccDNA-mRNA/miRNA/circRNA revealed that some highly expressed genes are transcribed from relevant sequences of eccDNA and the transcription of protein coding genes influenced the frequency of eccDNA. BmCPV infection resulted in changes in the expression levels of six miRNAs, but no known miRNAs with altered expression levels due to changes in eccDNA abundance were identified. Moreover, it was found that 1287 and 924 sequences representing back-spliced junctions of circRNAs were shared by the junctions of eccDNAs in the BmCPV-infected and uninfected silkworms, respectively, and some eccDNAs loci were shared by circRNAs on Chromosomes 2, 7, 11, 14, and 24, suggesting some eccDNAs may exert its function by being transcribed into circRNAs. These findings suggest that BmCPV infection alter the expression pattern of eccDNAs, leading to changes in RNA transcription levels, which may play roles in regulating BmCPV replication. In the future, further experiments are needed to verify the association between eccDNA-mRNA/miRNA/circRNA and its function in BmCPV infection. Full article

(1) Background: Prostate cancer treatment efficacy is significantly influenced by androgen receptor (AR) signaling pathways. SLC22A3, a membrane transporter, has been linked to SNP rs9364554 risk loci for drug efficacy in prostate cancer. (2) Methods: We examined the location of SNP rs9364554 in the genome and utilized TCGA and other publicly available datasets to analyze the association of this SNP with SLC22A3 transcription levels. We verified onco-mining findings in prostate cancer cell lines using quantitative PCR and Western blots. Additionally, we employed electrophoretic mobility shift assay (EMSA) to detect the binding affinity of transcription factors to this SNP. The ChIP-Seq was used to analyze the enrichment of H3K27ac on the SLC22A3 promoter. (3) Results: In this study, we revealed that SNP rs9364554 resides in the SLC22A3 gene and affects its transcription. The downregulation of SLC22A3 is associated with drug resistance. More importantly, we found that this SNP has different binding affinities with transcription factors, specifically FOXA1 and AR, which significantly affects their regulation of SLC22A3 transcription. (4) Conclusions: Our findings highlight the potential of using this SNP as a biomarker for predicting chemotherapeutic outcomes and uncover possible mechanisms underlying drug resistance in advanced prostate cancers. More importantly, it provides a clinical foundation for targeting FOXA1 to enhance drug efficacy in prostate cancer patients. Full article