Gene Ontology Terms Research Articles

The role and mechanism of “eight famous herbals in Zhejiang” in cancer via network pharmacology and experimental validation

In recent years, some components and active ingredients from the herbal formula “eight famous herbals in Zhejiang” (Zhe-Ba-Wei) have been reported to possess antitumor properties. However, there is still no systemic study on the role and mechanism of Zhe-Ba-Wei in cancer. To systematically investigate the anticancer efficacy of Zhe-Ba-Wei, we first identified 16 reported active ingredients with gene targets associated with various types of tumors. Second, we screened these active ingredients and their responding multiple shared targets by analyzing the convergence of diverse and tumor-specific target sites and identified four crucial active ingredients (ferulic acid, quercetin, rutin, luteolin), which were characterized by 27 overlapping gene targets. Third, these 27 gene targets were subsequently mapped onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology term, and among the 27 total potential targets, 12 were involved in plasma membrane function. Fourth, we investigated the binding affinities between the four crucial active ingredients and their potential targets such as EGFR and MET, both of which are well-known oncogenes in various cancers. Subsequently, an investigation of the computational ADMET properties showed that most of these four ingredients exhibited good ADMET properties. Finally, we found that three active ingredients (ferulic acid, luteolin, and quercetin) could inhibit the proliferation of NSCLC cells and decrease the protein expression of EGFR in a concentration-dependent manner. All these results shed light on the bioactive components, pharmacological effects, and drug development and utilization of Zhe-Ba-Wei, aiming to provide useful support for its further research and clinical application.

Targeting resident astrocytes attenuates neuropathic pain after spinal cord injury.

Astrocytes derive from different lineages and play a critical role in neuropathic pain after spinal cord injury (SCI). Whether selectively eliminating these main origins of astrocytes in lumbar enlargement could attenuate SCI-induced neuropathic pain remains unclear. Through transgenic mice injected with an adeno-associated virus vector and diphtheria toxin, astrocytes in lumbar enlargement were lineage traced, targeted, and selectively eliminated. Pain-related behaviors were measured with an electronic von Frey apparatus and a cold/hot plate after SCI. RNA sequencing, bioinformatics analysis, molecular experiment, and immunohistochemistry were used to explore the potential mechanisms after astrocyte elimination. Lineage tracing revealed that the resident astrocytes but not ependymal cells were the main origins of astrocytes-induced neuropathic pain. SCI-induced mice to obtain significant pain symptoms and astrocyte activation in lumbar enlargement. Selective resident astrocyte elimination in lumbar enlargement could attenuate neuropathic pain and activate microglia. Interestingly, the type I interferons (IFNs) signal was significantly activated after astrocytes elimination, and the most activated Gene Ontology terms and pathways were associated with the type I IFNs signal which was mainly activated in microglia and further verified in vitro and in vivo. Furthermore, different concentrations of interferon and Stimulator of interferon genes (STING) agonist could activate the type I IFNs signal in microglia. These results elucidate that selectively eliminating resident astrocytes attenuated neuropathic pain associated with type I IFNs signal activation in microglia. Targeting type I IFNs signals is proven to be an effective strategy for neuropathic pain treatment after SCI.

Targeting resident astrocytes attenuates neuropathic pain after spinal cord injury

Astrocytes derive from different lineages and play a critical role in neuropathic pain after spinal cord injury (SCI). Whether selectively eliminating these main origins of astrocytes in lumbar enlargement could attenuate SCI-induced neuropathic pain remains unclear. Through transgenic mice injected with an adeno-associated virus vector and diphtheria toxin, astrocytes in lumbar enlargement were lineage traced, targeted, and selectively eliminated. Pain-related behaviors were measured with an electronic von Frey apparatus and a cold/hot plate after SCI. RNA sequencing, bioinformatics analysis, molecular experiment, and immunohistochemistry were used to explore the potential mechanisms after astrocyte elimination. Lineage tracing revealed that the resident astrocytes but not ependymal cells were the main origins of astrocytes-induced neuropathic pain. SCI-induced mice to obtain significant pain symptoms and astrocyte activation in lumbar enlargement. Selective resident astrocyte elimination in lumbar enlargement could attenuate neuropathic pain and activate microglia. Interestingly, the type I interferons (IFNs) signal was significantly activated after astrocytes elimination, and the most activated Gene Ontology terms and pathways were associated with the type I IFNs signal which was mainly activated in microglia and further verified in vitro and in vivo. Furthermore, different concentrations of interferon and Stimulator of interferon genes (STING) agonist could activate the type I IFNs signal in microglia. These results elucidate that selectively eliminating resident astrocytes attenuated neuropathic pain associated with type I IFNs signal activation in microglia. Targeting type I IFNs signals is proven to be an effective strategy for neuropathic pain treatment after SCI.

Abstract A017: IGF2BP1 is essential for ETO2/GLIS2 leukemogenesis via stabilization of primitive myeloid transcriptional programs

Abstract Certain subtypes of pediatric leukemia continue to have dismal cure rates despite advances in targeted therapy. One such disease is acute megakaryoblastic leukemia (AMKL) with a rearrangement of ETO2/GLIS2 (also known as CBFA2T3/GLIS2.) Based on our preliminary data utilizing CRISPR/Cas9 screens in vivo in patient-derived xenografts, we have nominated IGF2BP1 as a potential vulnerability in ETO2/GLIS2-rearranged AMKL. For our discovery phase, we utilized a patient-derived E2G2r AMKL which successfully engrafts in NSGS mice. We created a stable Cas9-expressing subclone using lentiviral transduction followed by FACS enrichment and limiting dilution transplants. We then generated a custom library targeting the top 100 overexpressed genes between E2G2r leukemias versus other leukemia PDXs which we previously characterized, including eight transcription factors with motifs enriched in differentially expressed genes, as well as eight pan-essential positive controls. Mice were sacrificed at humane endpoints, and spleens and bone marrow underwent PCR amplification for gRNA sequences followed by sequencing and analysis with MAGeCK-VISPR (Wei L, et al. Genome Biol 2015). We observed the dropout of 38 genes with a false discovery rate < 0.25, including all positive control gRNAs. Among the most significantly depleted genes was the RNA binding protein IGF2BP1. We subsequently characterized phenotypic changes using shRNAs in the E2G2r cell line M07e and ETO2/GLIS2-transformed CD34+ umbilical cord blood cells. Notably, we observed impaired cell growth with IGF2BP1 knockdown in both cell lines as well as the parent xenograft. We also generated M07e lines expressing a degron (FKBPF36V, aka “dTAG”, Nabet et al. Nat Chem Biol 2018) knocked in at the endogenous IGF2BP1 locus and observed similar phenomena. Through flow cytometry of M07e following IGF2BP1 depletion, we observed changes in the leukemic immunophenotype as well, suggesting perturbation of megakaryocyte differentiation potential. To determine the mechanism underlying our observations, we performed enhanced UV crosslinking with IP and sequencing (Blue SM et al. Nat Protoc 2022) against both IGF2BP1 and m6A residues based on the putative role of IGF2BP1 as an m6A reader. We observed binding of IGF2BP1 predominantly in 3’UTRs, as well as the presence of m6A-modified bases at IGF2BP1 binding sites. Gene ontology (GO) analysis of IGF2BP1-bound transcripts demonstrated enrichment for GO terms pertaining to embryonic hematopoiesis and megakaryocyte maturation/development. We further evaluated global changes in gene expression following IGF2BP1 loss, and performed RNAseq 72 hours following shRNA-mediated knockdown. GO analysis showed that downregulated genes were highly enriched for E2F-mediated transcriptional programs. We hypothesize that IGF2BP1 regulates myeloid developmental transcripts essential for E2G2r leukemogenesis, likely via stabilization in an m6A-dependent fashion, and thus may represent a selective therapeutic target. Work is ongoing to further elucidate this proposed mechanism. Citation Format: Jason Clark, Mark Wunderlich, Jing Chen, Daniel Starczynowski, Lynn Lee. IGF2BP1 is essential for ETO2/GLIS2 leukemogenesis via stabilization of primitive myeloid transcriptional programs [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A017.

Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds.

Indigenous buffaloes, as the important livestock species contributing to economy of the country, are the lifeline of livelihood in Nepal. They are distributed across diverse geographical regions of the country and have adapted to various feeding, breeding, and management conditions. The larger group of these native buffalo breeds are present in narrow and stiff hilly terrains. Their dispersal indicates a possible environmental adaptation mechanism, which is crucial for the conservation of these breeds. We utilized whole-genome sequencing (WGS) to investigate the genetic diversity, population structure, and selection signatures of Nepalese indigenous buffaloes. We compared 66 whole-genome sequences with 118 publicly available sequences from six river and five swamp buffalo breeds. Genomic diversity parameters indicated genetic variability level in the Nepalese buffaloes comparable to those of Indian breeds, and population genetic structure revealed distinct geography-mediated genetic differentiation among these breeds. We used locus-specific branch length analysis (LSBL) for genome-wide scan, which revealed a list of potentially selected genes in Lime and Parkote breeds that inhabit the hilly region. A gene ontology (GO) analysis discovered that many GO terms were associated with cardiac function regulation. Furthermore, complementary analyses of local selection signatures, tissue expression profiles, and haplotype differences identified candidate genes, including KCNE1, CSF1R, and PDGFRB, related to the regulation of cardiac and pulmonary functions. This study is a comprehensive WGS-based genetic analysis of the native Nepalese buffalo breeds. Our study suggested that the Nepalese "hilly" buffaloes, especially the Lime and Parkote breeds, have undergone some characteristic genetic changes and evolved increased cardiac and pulmonary function for their adaptation to the steep hilly terrains of the country.

Exploring mechanisms of gene expression control during Ustilago maydis teliospore germination

Fungal plant pathogens produce spores for survival and dispersion. Developing an understanding of the mechanisms involved in spore dormancy and germination will aid in mitigating the impact of diseases they cause. The thick-walled diploid teliospores of Ustilago maydis were used as a model for studying fungal spore dormancy and germination. These spores develop only in infected maize tissue and can remain dormant for long periods of time. Teliospores germinate under favourable conditions, resume meiosis, and produce basidiospores to initiate new rounds of infection. Previous research identified changing gene transcripts during teliospore germination, but analysis was hampered by asynchronous germination. The more comprehensive RNA-seq analysis of U. maydis teliospore germination presented here aimed to identify gene altered transcript levels detectable above the background of fluctuating changes resulting from asynchronous germination. The analyses identified 18 different patterns of gene transcript level changes. It also indicated that gene expression is controlled at the transcriptional and post-transcriptional levels. Gene ontology term enrichment analyses of these patterns revealed genes that are involved in cell morphogenesis, metabolism, and RNA metabolism.

Integrating Physiology, Transcriptome, and Metabolome Analyses Reveals the Drought Response in Two Quinoa Cultivars with Contrasting Drought Tolerance

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa responses to drought are related to drought intensity and genotype. This study used two different drought-responsive quinoa cultivars, LL1 (drought-tolerant) and ZK1 (drought-sensitive), to reveal the important mechanisms of drought response in quinoa by combining physiological, transcriptomic, and metabolomic analyses. The physiological analysis indicated that Chla/Chlb might be important for drought tolerance in quinoa. A total of 1756 and 764 differentially expressed genes (DEGs) were identified in LL1 and ZK1, respectively. GO (Gene Ontology) enrichment analysis identified 52 common GO terms, but response to abscisic acid (GO:0009737) and response to osmotic stress (GO:0006970) were only enriched in LL1. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that glycerophospholipid metabolism (ko00564) and cysteine and methionine metabolism (ko00270) ranked at the top of the list in both cultivars. A total of 1844 metabolites were identified by metabolomic analysis. “Lipids and lipid-like” molecules had the highest proportions. The DEMs in LL1 and ZK1 were mainly categorized 6 and 4 Human Metabolome Database (HMDB) superclasses, respectively. KEGG analysis revealed that the ‘α-linolenic acid metabolism’ was enriched in both LL1 and ZK1. Joint KEGG analysis also revealed that the ‘α-linolenic acid metabolism’ pathway was enriched by both the DEGs and DEMs of LL1. There were 17 DEGs and 8 DEMs enriched in this pathway, and methyl jasmonate (MeJA) may play an important role in the drought response of quinoa. This study will provide information for the identification of drought resistance in quinoa, research on the molecular mechanism of drought resistance, and genetic breeding for drought resistance in quinoa.

Rfam 15: RNA families database in 2025.

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam's coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org.

Analysis of Rfo-Mediated Network in Regulating Fertility Restoration in Brassica oleracea

Ogura cytoplasmic male sterility (CMS) lines play a crucial role in the utilization of heterosis. However, valuable traits, such as disease resistance genes from Ogura CMS hybrids, are challenging to incorporate for germplasm innovation, particularly in cabbage and broccoli. To date, the Rfo-mediated network regulating fertility restoration remains largely unexplored. In this study, we conducted a transcriptomic analysis of broccoli flower buds from Ogura CMS SFB45 and its Rfo-transgenic fertility restoration line, pRfo, at different stages of pollen development. Gene Ontology (GO) terms such as “pollen exine formation”, “flavonoid metabolic and biosynthetic processes”, and “pollen wall assembly”, along with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including “flavonoid biosynthesis”, “MAPK signaling pathway-plant”, and “ABC transporters”, were significantly enriched. We identified five differentially expressed genes (DEGs) involved in tapetum-mediated callose metabolism, thirty-four DEGs related to tapetum-mediated pollen wall formation, three DEGs regulating tapetum programmed cell death (PCD), five MPKs encoding DEGs, and twelve DEGs associated with oxidative phosphorylation. Additionally, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays demonstrated that RFO directly interacts with ORF138 at the protein level. These findings provide valuable insights into the fertility recovery mechanisms regulated by Rfo in broccoli and offer important clues for breeders aiming to enhance Ogura CMS hybrids in Brassica oleracea.

QTL mapping and transcriptome analysis of seed germination under PEG-induced water stress in Lactuca spp.

The impact of limited water availability on lettuce growth has been well documented. However, the mechanisms by which lettuce controls seed germination under water stress remain unknown. Germination percentage was evaluated in the cv. Salinas (Lactuca sativa) (L. sativa) × US96UC23 (Lactuca serriola) (L. serriola) recombinant inbred line (RIL) population and USDA germplasm collection using 10% polyethylene glycol (PEG). About 50% of both populations displayed less than 90% germination. The average broad-sense heritability (H2) for germination percentage was 0.81 across both populations. Two quantitative trait loci (QTL) for germination percentage were identified on chromosomes 4 and 8 in the RIL population. The RNA-Seq and network analyses of wild lettuce, US96UC23, were performed using the control (distilled water, dH2O) and treatment (10% PEG) datasets. The number of differentially expressed genes (DEGs) was 4,095. The top 20 gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were assessed by enrichment analysis. The consensus network analysis captured 44 modules. Gene networks were constructed for the top 20 hub genes in 10 significant modules from each dataset. This study comprehensively explains QTL, GO terms, KEGG pathways, and gene networks associated with lettuce seed germination under osmotic stress.

Transcriptome analysis of mammary epithelial cell between Sewa sheep and East FriEsian sheep from different localities.

Mammary epithelial cells, the only milk-producing cell type in the mammary gland, undergo dynamic proliferation and differentiation during pregnancy, culminating in lactation postpartum. The East FriEsian sheep ranks among the world's most prolific dairy breeds, while the Sewa sheep, a unique dual-purpose breed autochthonous to the Qinghai-Tibet Plateau, exhibits significantly lower milk production. Employing tissue culture methods, we successfully established mammary epithelial cell lines from both breeds. Morphological assessment of mammary epithelial cells and immunofluorescence identification of Cytokeratin 7 and Cytokeratin 8 confirmed the epithelial identity of the isolated cells. Subsequent RNA-seq analysis of these in vitro epithelial cell lines revealed 1813 differentially expressed genes (DEGs). Among these, 1108 were significantly up-regulated and 705 were down-regulated in Sewa epithelial sheep cells compared to East FriEsian epithelial cells. KEGG enrichment analysis identified cellular processes, environmental information processing, human diseases, metabolism, and organismal systems as the primary functional categories associated with DEGs. Gene ontology (GO) terms annotation, categorized into molecular function, biological processes, and cellular component, yielded "binding and catalytic activity," "molecular function regulator activity," and "cellular process," "biological regulation," and "regulation of biological process" as the top three terms within each domain, respectively. Clusters of Orthologous Groups of proteins (KOG) classification further revealed that "signal transduction mechanisms" accounted for the largest proportion of DEGs among all KOG categories. Finally, based on these analyses, ATF3 and MPP7 were identified as promising candidate genes for regulating lactation.

RecGOBD: Accurate Recognition of Gene Ontology Related Brain Development Protein Functions through Multi-Feature Fusion and Attention Mechanisms

Abstract Motivation Protein function prediction is important in bioinformatics, driven by the increasing availability of protein sequence data from high-throughput sequencing technologies. Traditional methods for determining protein functions are costly and time-consuming, highlighting the need for computational approaches. Deep learning models are powerful tools in this area, but many are not optimized for brain development-related datasets. Understanding protein functions in brain development is essential for studying neurodevelopmental disorders. To address this, we developed RecGOBD (Recognition of Gene Ontology-related Brain Development protein function), designed to predict protein functions related to key brain development processes. Result RecGOBD focuses on ten critical Gene Ontology (GO) terms associated with brain development, extracting and embedding the protein sequences linked to these terms. Using advanced pre-trained models, we generated embeddings that capture both sequence and structural information, and applied attention mechanisms to align them with relevant GO terms. RecGOBD’s category attention layer improves prediction accuracy for brain development-related terms. Evaluated against five models using AUROC, AUPR, and Fmax metrics, RecGOBD outperformed in all measures. We also applied the model to predict protein functions related to autism spectrum disorder and analyzed how protein site mutations affect GO term changes. These results highlight RecGOBD’s potential for advancing protein function prediction, particularly in brain development, offering valuable insights into neurodevelopmental disorder research. Availability and implementation All Python codes associated with this study are available at https://github.com/ZL-Xia/RECGOBD.git. Supplementary information Supplementary data are available at Bioinformatics Advance online

Drosophila Toxicogenomics: genetic variation and sexual dimorphism in susceptibility to 4-Methylimidazole

Background4-methylimidazole is a ubiquitous and potentially carcinogenic environmental toxicant. Genetic factors that contribute to variation in susceptibility to its toxic effects are challenging to assess in human populations. We used the Drosophila melanogaster Genetic Reference Panel (DGRP), a living library of natural genetic variation, to identify genes with human orthologs associated with variation in susceptibility to 4-methylimidazole.ResultsWe screened 204 DGRP lines for survival following 24-hour exposure to 4-methylimidazole. We found extensive genetic variation for survival, with a broad sense heritability of 0.82; as well as genetic variation in sexual dimorphism, with a cross-sex genetic correlation of 0.59. Genome-wide association analyses identified a total of 241 candidate molecular polymorphisms in or near 273 unique genes associated with survival. These polymorphisms had either sex-specific or sex-antagonistic effects, and most had putative regulatory effects. We generated interaction networks using these candidate genes as inputs and computationally recruited genes with known physical or genetic interactions. The network genes were significantly over-represented for gene ontology terms involving all aspects of development (including nervous system development) and cellular and organismal functions as well as canonical signaling pathways, and most had human orthologs.ConclusionsThe genetic basis of variation in sensitivity to acute exposure to 4-methylimidazole in Drosophila is attributable to variation in genes and networks of genes known for their effects on multiple developmental and cellular processes, including possible neurotoxicity. Given evolutionary conservation of the underlying genes and pathways, these insights may be applicable to humans.

The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease

BackgroundBacterial wilt (BW), caused by Ralstonia solanacearum (Ral), results in substantial yield losses in pepper crops. Developing resistant pepper varieties through breeding is the most effective strategy for managing BW. To achieve this, a thorough understanding of the genetic information connected with resistance traits is essential. Despite identifying three major QTLs for bacterial wilt resistance in pepper, Bw1 on chromosome 8, qRRs-10.1 on chromosome 10, and pBWR-1 on chromosome 1, the genetic information of related BW pepper varieties has not been sufficiently studied. Here, we resequenced two pepper inbred lines, C. annuum ‘MC4’ (resistant) and C. annuum ‘Subicho’ (susceptible), and analyzed genomic variations through SNPs and Indels to identify candidate genes for BW resistance.ResultsAn average of 139.5 Gb was generated among the two cultivars, with coverage ranging from 44.94X to 46.13X. A total of 8,815,889 SNPs was obtained between ‘MC4’ and ‘Subicho’. Among them, 31,190 (0.35%) were non-synonymous SNPs (nsSNPs) corresponding to 10,926 genes, and these genes were assigned to 142 Gene Ontology (GO) terms across the two cultivars. We focused on three known BW QTL regions by identifying genes with sequence variants through gene set enrichment analysis and securing those belonging to high significant GO terms. Additionally, we found 310 NLR genes with nsSNP variants between ‘MC4’ (R) and ‘Subicho’ (S) within these regions. Also, we performed an Indel analysis on these genes. By integrating all this data, we identified eight candidate BW resistance genes, including two NLR genes with nsSNPs variations in qRRs-10.1 on chromosome 10.ConclusionWe identified genomic variations in the form of SNPs and Indels by re-sequencing two pepper cultivars with contrasting traits for bacterial wilt. Specifically, the four genes associated with pBWR-1 and Bw1 that exhibit both nsSNP and Indel variations simultaneously in ‘Subicho’, along with the two NLR genes linked to qRRs-10.1, which are known for their direct involvement in immune responses, are identified as most likely BW resistance genes. These variants in leading candidate genes associated with BW resistance can be used as important markers for breeding pepper varieties.

Increased Rab1a accelerates osteoarthritis by inhibiting autophagy via activation of the mTORC1-S6K pathway

IntroductionCartilage degradation is a critical alteration in the progression of osteoarthritis (OA) due to the disorder of chondrocyte metabolic homeostasis. Autophagy plays an important role in maintaining intracellular homeostasis. Recent investigations have increasingly underscored the importance of autophagy in modulating the pathological mechanisms underlying OA. Ras-related protein Rab-1a (Rab1a) has been illustrated to regulate autophagy in many diseases but not in OA. ObjectivesThis study aims to elucidate whether Rab1a could regulate the development of OA through modulation of chondrocyte autophagy and apoptosis. MethodsProteomic sequencing, Western blotting, and immunohistochemistry were applied to detect the expression level of Rab1a in vitro and in vivo. Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were rigorously identified. The effects of Rab1a and the interaction between Rab1a, mTORC1, autophagy and apoptosis were explored by qPCR, Western blotting, and immunofluorescence. An experimental mouse OA model was also performed to confirm the role of Rab1a in OA pathogenesis in vivo. Histological analysis was employed to demonstrate cartilage damage. ResultsRab1a expression was significantly upregulated in inflamed chondrocytes and knee OA cartilage. Inhibition of Rab1a partially attenuated the degradation of the extracellular matrix and cell apoptosis both in vitro and in vivo, whereas overexpression of Rab1a intensified cartilage matrix degradation and cellular apoptosis. Additionally, elevated Rab1a levels were observed to suppress autophagy and activate the mTORC1-S6K signaling pathway, thereby aggravating OA pathogenesis. ConclusionThe augmentation of Rab1a expression impairs autophagy and promotes apoptosis through the activation of the mTORC1-S6K signaling pathway, further exacerbating OA pathogenesis. This finding suggests that Rab1a serves as a promising and innovative therapeutic target for the prevention and treatment of OA.

Identification of key genes in diabetic nephropathy based on lipid metabolism.

Diabetic nephropathy (DN) is a common systemic microvascular complication of diabetes with a high incidence rate. Notably, the disturbance of lipid metabolism is associated with DN progression. The present study aimed to identify lipid metabolism-related hub genes associated with DN for improved diagnosis of DN. The gene expression profile data of DN and healthy samples (GSE142153) were obtained from the Gene Expression Omnibus database, and the lipid metabolism-related genes were obtained from the Molecular Signatures Database. Differentially expressed genes (DEGs) between DN and healthy samples were analyzed. The weighted gene co-expression network analysis (WGCNA) was performed to examine the relationship between genes and clinical traits to identify the key module genes associated with DN. Next, the Venn Diagram R package was used to identify the lipid metabolism-related genes associated with DN and their protein-protein interaction (PPI) network was constructed. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. The hub genes were identified using machine-learning algorithms. The Gene Set Enrichment Analysis (GSEA) was used to analyze the functions of the hub genes. The present study also investigated the immune infiltration discrepancies between DN and healthy samples, and assessed the correlation between the immune cells and hub genes. Finally, the expression levels of key genes were verified by reverse transcription-quantitative (RT-q)PCR. The present study determined 1,445 DEGs in DN samples. In addition, 694 DN-related genes in MEyellow and MEturquoise modules were identified by WGCNA. Next, the Venn Diagram R package was used to identify 17 lipid metabolism-related genes and to construct a PPI network. GO analysis revealed that these 17 genes were markedly associated with 'phospholipid biosynthetic process' and 'cholesterol biosynthetic process', while the KEGG analysis showed that they were enriched in 'glycerophospholipid metabolism' and 'fatty acid degradation'. In addition, SAMD8 and CYP51A1 were identified through the intersections of two machine-learning algorithms. The results of GSEA revealed that the 'mitochondrial matrix' and 'GTPase activity' were the markedly enriched GO terms in both SAMD8 and CYP51A1. Their KEGG pathways were mainly concentrated in the 'pathways of neurodegeneration-multiple diseases'. Immune infiltration analysis showed that nine types of immune cells had different expression levels in DN (diseased) and healthy samples. Notably, SAMD8 and CYP51A1 were both markedly associated with activated B cells and effector memory CD8 T cells. Finally, RT-qPCR confirmed the high expression of SAMD8 and CYP51A1 in DN. In conclusion, lipid metabolism-related genes SAMD8 and CYP51A1 may play key roles in DN. The present study provides fundamental information on lipid metabolism that may aid the diagnosis and treatment of DN.

Effect of GB1107, a novel galectin-3 inhibitor on pro-fibrotic signalling in the liver

Background and PurposeGalectin-3 (Gal-3) is a pro-fibrotic β-galactoside binding lectin highly expressed in fibrotic liver and implicated in hepatic fibrosis. GB1107 is a novel orally active Gal-3 small molecule inhibitor that has high affinity for Gal-3 >1000-fold selectively over other galectins. The aim of this study was to characterise GB1107 and galectin-3 in vitro and in vivo in the context of fibrosis signalling and liver disease. Experimental ApproachLiver fibrosis was induced by administration of CCl4 twice weekly by intraperitoneal injection in mice for 8 weeks. GB1107 was orally administered once daily (10 mg/kg) for the last 4 weeks of CCl4 treatment. Fibrosis was assessed by picrosirius red staining of FFPE sections. Liver enzymes, Gal-3 and downstream biomarkers were assessed in liver and plasma. Paired-end sequencing was performed on the NextSeq 2000 platform. Pathway enrichment analysis was performed to determine enrichment of differentially expressed genes (DEGs) within Reactome pathways and Gene Ontology (GO) terms. Key ResultsGB1107 significantly reduced plasma transaminases and liver Gal-3 and reduced liver fibrosis. RNAseq analysis of whole liver showed that 1,659 DEGs were identified with CCl4 treatment compared to control. Pathways enriched in up-regulated genes in the CCl4 group included those related to the extracellular matrix, collagen biosynthesis and assembly, cell cycle and the immune system. Comparing GB1107 treatment with CCl4 control 1147 DEGs were identified. GB1107 effectively reversed the majority of the CCl4 induced gene changes. Conclusions and ImplicationsGB1107 attenuated liver fibrosis and highlights Gal-3 as a therapeutic target for hepatic fibrosis.

The peripheral Atf3 + neuronal population is responsible for nerve regeneration at the early stage of nerve injury revealed by single-cell RNA sequencing.

Peripheral nerve injury (PNI) can transform primary somatosensory neurons to a regenerative state. However, the details of the transcriptomic changes associated with the nerve regeneration of somatosensory neurons remain unclear. In this study, single-cell RNA sequencing (scRNA-seq) is conducted on mouse dorsal root ganglion (DRG) cells after the early stage of nerve injury on day 3 after chronic constriction injury (CCI). We observe that a novel CCI-induced neuronal population (CIP) emerge and express high levels of activating transcription factor ( Atf3), a neuronal injury marker. CIP neurons highly express regeneration-associated genes (RAGs) and are enriched in regeneration-related gene ontology (GO) terms, suggesting that these neurons can constitute a pro-regenerative population. Moreover, intercellular communication networks show that CIP neurons closely communicate with satellite glial cells (SGCs) and specifically transmit strong Fgf3- Fgfr1 signaling to SGCs, which could initiate regeneration-associated transcriptional changes in SGCs. We also confirm that regenerative progress occurs at the early stage of nerve injury because immunohistochemistry shows that the expression of ATF3 is significantly increased beginning at 3 days post-CCI and decreased at 1 month post-CCI. Our bioinformatics analysis at single-cell resolution advances the knowledge of regenerative dynamic transcriptional changes in DRG cells after injury and the underlying molecular mechanisms involved.

Regulation of cell-mediated immune responses in dairy bulls via long non-coding RNAs from submandibular lymph nodes, peripheral blood, and the spleen

Cell-mediated immune responses (CMIRs) are critical to building a robust immune system and reducing disease susceptibility in cattle. Long non-coding RNAs (lncRNAs) regulate various biological processes. However, to the best of our knowledge, the characterization and functions of lncRNAs and their regulations on the bovine CMIR have not been investigated comprehensively. In this study, experimental bulls were immunized with a heat-killed preparation of Candida albicans (HKCA) to induce delayed-type hypersensitivity (DTH). Three bulls were classified as high- CMIR responders and three were low-CMIR responders, based on their classical DTH skin reactions. LncRNAs were identified in the submandibular lymph nodes, peripheral blood, and spleen of high- and low-CMIR animals using strand-specific RNA sequencing. A total of 21,003 putative lncRNAs were identified across tissues, and 420, 468, and 599 lncRNAs were differentially expressed between the two groups in the submandibular lymph node, peripheral blood, and spleen tissues, respectively. Functional analysis of the differentially expressed lncRNA (DElncRNA) target genes showed that a number of immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched, including immune response, cell adhesion, nucleosome, DNA packaging, antigen processing and presentation, and complement and coagulation cascades. Tissue specificity analysis indicated that lncRNA transcripts have stronger tissue specificity than mRNA. Furthermore, an interaction network was constructed based on DElncRNAs and DEGs, and 11, 14, and 11 promising lncRNAs were identified as potential candidate genes influencing immune response regulation in submandibular lymph nodes, peripheral blood, and spleen tissues, respectively. These results provide a foundation for further research into the biological functions of lncRNAs associated with bovine CMIR and identify candidate lncRNA markers for cell-mediated immune responses.

RUNX2 is stabilised by TAZ and drives pulmonary artery calcification and lung vascular remodelling in pulmonary hypertension due to left heart disease.

Calcification is common in chronic vascular disease, yet its role in pulmonary hypertension due to left heart disease is unknown. Here, we probed for the role of runt-related transcription factor-2 (RUNX2), a master transcription factor in osteogenesis, and its regulation by the HIPPO pathway transcriptional coactivator with PDZ-binding motif (TAZ) in the osteogenic reprogramming of pulmonary artery smooth muscle cells and vascular calcification in patients with pulmonary hypertension due to left heart disease. We similarly examined its role using an established rat model of pulmonary hypertension due to left heart disease induced by supracoronary aortic banding. Pulmonary artery samples were collected from patients and rats with pulmonary hypertension due to left heart disease. Genome-wide RNA sequencing was performed, and pulmonary artery calcification assessed. Osteogenic signalling via TAZ and RUNX2 was delineated by protein biochemistry. In vivo, the therapeutic potential of RUNX2 or TAZ inhibition by CADD522 or verteporfin was tested in the rat model. Gene ontology term analysis identified significant enrichment in ossification and osteoblast differentiation genes, including RUNX2, in pulmonary arteries of patients and lungs of rats with pulmonary hypertension due to left heart disease. Pulmonary artery calcification was evident in both patients and rats. Both TAZ and RUNX2 were upregulated and activated in pulmonary artery smooth muscle cells of patients and rats. Co-immunoprecipitation revealed a direct interaction of RUNX2 with TAZ in pulmonary artery smooth muscle cells. TAZ inhibition or knockdown decreased RUNX2 abundance due to accelerated RUNX2 protein degradation rather than reduced de novo synthesis. Inhibition of either TAZ or RUNX2 attenuated pulmonary artery calcification, distal lung vascular remodelling and pulmonary hypertension development in the rat model. Pulmonary hypertension due to left heart disease is associated with pulmonary artery calcification that is driven by TAZ-dependent stabilisation of RUNX2, causing osteogenic reprogramming of pulmonary artery smooth muscle cells. The TAZ-RUNX2 axis may present a therapeutic target in pulmonary hypertension due to left heart disease.