Pathway Genes Research Articles

Clinical significance of upregulated Rho GTPase activating protein 12 causing resistance to tyrosine kinase inhibitors in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a major health challenge with high incidence and poor survival rates in China. Systemic therapies, particularly tyrosine kinase inhibitors (TKIs), are the first-line treatment for advanced HCC, but resistance is common. The Rho GTPase family member Rho GTPase activating protein 12 (ARHGAP12), which regulates cell adhesion and invasion, is a potential therapeutic target for overcoming TKI resistance in HCC. However, no studies on the expression of ARHGAP12 in HCC and its role in resistance to TKIs have been reported. To unveil the expression of ARHGAP12 in HCC, its role in TKI resistance and its potential associated pathways. This study used single-cell RNA sequencing (scRNA-seq) to evaluate ARHGAP12 mRNA levels and explored its mechanisms through enrichment analysis. CellChat was used to investigate focal adhesion (FA) pathway regulation. We integrated bulk RNA data (RNA-seq and microarray), immunohistochemistry and proteomics to analyze ARHGAP12 mRNA and protein levels, correlating with clinical outcomes. We assessed ARHGAP12 expression in TKI-resistant HCC, integrated conventional HCC to explore its mechanism, identified intersecting FA pathway genes with scRNA-seq data and evaluated its response to TKI and immunotherapy. ARHGAP12 mRNA was found to be highly expressed in malignant hepatocytes and to regulate FA. In malignant hepatocytes in high-score FA groups, MDK-[integrin alpha 6 (ITGA6) + integrin β-1 (ITGB1)] showed specificity in ligand-receptor interactions. ARHGAP12 mRNA and protein were upregulated in bulk RNA, immunohistochemistry and proteomics, and higher expression was associated with a worse prognosis. ARHGAP12 was also found to be a TKI resistance gene that regulated the FA pathway. ITGB1 was identified as a crossover gene in the FA pathway in both scRNA-seq and bulk RNA. High expression of ARHGAP12 was associated with adverse reactions to sorafenib, cabozantinib and regorafenib, but not to immunotherapy. ARHGAP12 expression is elevated in HCC and TKI-resistant HCC, and its regulatory role in FA may underlie the TKI-resistant phenotype.

Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments

Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.

Spatial transcriptomics of human and murine Neurofibromatosis Type I fracture pseudarthroses reveal impaired BMP signaling

Abstract Introduction/Objective In Neurofibromatosis Type 1 (NF1), caused by mutations in the NF1 tumor-suppressor gene, children form fibrotic nonunions known as pseudarthroses following long bone fractures. Here, we integrate spatial transcriptomics of human and murine samples to investigate the pathogenesis underlying pseudoarthrosis development. Methods/Case Report We performed spatial transcriptomics on 10-day post-fracture calluses from control and periosteum-specific Nf1-deficient (Nf1Postn) mice as well as a human NF1 patient pseudarthrosis specimen. Differential gene expression and SpatialTime analyses were performed. BMP signaling was validated by immunohistochemical staining of tissues for phospho-SMAD1/5/8. Results (if a Case Study enter NA) Spatial transcriptomics detected eight cell clusters, including bone, cartilage, and muscle within mouse fracture calluses. In the control, clusters involved in fracture repair were enriched for genes associated with extracellular matrix and collagen formation (progenitor and cartilage clusters), cartilage and endochondral bone processes (ossifying perichondrium cluster), and bone remodeling (woven bone cluster). Expression of TGF-beta pathway genes was highest near the fracture plane, while BMP and Wnt pathways were activated further from the fracture. In the Nf1Postn fracture, healing was significantly delayed, lacking a robust callus and with a lower abundance of reparative skeletal cell clusters. While expression of TGF-beta pathway genes was similar to control, BMP pathway expression was minimal within the Nf1Postn fracture, which was further demonstrated by a lack of phospho-SMAD1/5/8 staining. In the human pseudarthrosis, while TGF-beta pathway genes were expressed near the fracture plane as expected, there was no enrichment of BMP pathway expression in the pseudarthrosis tissue and no significant phospho-SMAD1/5/8 staining. Conclusion Spatial transcriptomics allows for the simultaneous unbiased analysis of multiple signal transduction pathways within their native tissue environment. Our analyses 1) revealed the cellular diversity required for fracture healing, 2) demonstrated the spatially-restricted expression of key morphogenetic pathways within a fracture callus, and 3) provides in situ evidence for impaired BMP pathway activation associated with NF1 fracture pseudarthroses.

The potential role of Circular RNA New biomarkers for the prognosis of hepatocellular carcinoma

Abstract Introduction/Objective Hepatocellular carcinoma (HCC) is the most commonly diagnosed cancer with related deaths worldwide. The non-coding RNAs as the functions of circRNAs in tumor progression have attracted great attention to the clinicopathological characteristics of HCC. Methods/Case Report The present study was conducted to investigate and evaluate the expression level of hsa_circ_2124, and hsa_circ_4018 downstream target gene pathways related to clinico-pathological parameters of HCC. Cell proliferation was examined by West-1 assay and protein expression levels by using western blotting analysis. Results (if a Case Study enter NA) The hsa_circ_2124 expression level was up-regulated in HepG2 and Hep3B cells, respectively compared to normal liver cells. Furthermore, hsa_circ_4018 was down-regulated in two HCC cell lines compared to the normal cell line (LO2 cells), demonstrating the heterogeneity characteristics of the circRNA expressions in different HCC cell lines. Our data showed a significant inhibition of hsa_circ_4018 in HCC cell lines which in turn inhibited cell proliferation and migration. Besides, there is an inhibition in cell proliferation after hsa_circ_2124 knockdown in the tested cell lines. In addition, our data reported that the Knockdown of hsa_circ_2124 reduced the expression of ERK, c-Myc, and β-catenin expression in Hep-G2 cells. Furthermore, hsa_circ_4018 showed significant inhibition in β-catenin and c-Myc expression levels in Hep3B cells compared to the control. The knockdown of hsa_circ_2124 induced G1-phase arrest in HepG2 cells compared to control, suggesting the role of hsa_circ_2124 in the inhibition of HCC progression. Conclusion All in all, our data revealed that hsa_circ_2124 or hsa_circ_4018 plays a role in the regulation of MAPK and Wnt/β-catenin signaling pathways, which might be potential therapeutic biomarkers for HCC.

MiR-210 as a therapeutic target in diabetes-associated endothelial dysfunction.

MicroRNA (miR)-210 function in endothelial cells and its role in diabetes-associated endothelial dysfunction are not fully understood. We aimed to characterize the miR-210 function in endothelial cells and study its therapeutic potential in diabetes. Two different diabetic mouse models (db/db and Western diet-induced), miR-210 knockout and transgenic mice, isolated vessels and human endothelial cells were used. miR-210 levels were lower in aortas isolated from db/db than in control mice. Endothelium-dependent relaxation (EDR) was impaired in aortas from miR-210 knockout mice, and this was restored by inhibiting miR-210 downstream protein tyrosine phosphatase 1B (PTP1B), mitochondrial glycerol-3-phosphate dehydrogenase 2 (GPD2), and mitochondrial oxidative stress. Inhibition of these pathways also improved EDR in both diabetic mouse models. High glucose reduced miR-210 levels in endothelial cells and impaired EDR in mouse aortas, effects that were reversed by overexpressing miR-210. However, plasma miR-210 levels were not affected in individuals with type 2 diabetes (T2D) following improved glycaemic status. Of note, genetic overexpression using miR-210 transgenic mice and pharmacological overexpression using miR-210 mimic in vivo ameliorated endothelial dysfunction in both diabetic mouse models by decreasing PTP1B, GPD2 and oxidative stress. Genetic overexpression of miR-210 altered the aortic transcriptome, decreasing genes in pathways involved in oxidative stress. miR-210 mimic restored decreased nitric oxide production by high glucose in endothelial cells. This study unravels the mechanisms by which down-regulated miR-210 by high glucose induces endothelial dysfunction in T2D and demonstrates that miR-210 serves as a novel therapeutic target.

Identification of Biomarkers and Mechanisms Associated with Apoptosis in Recurrent Pregnancy Loss.

In this study, we employed bioinformatics techniques to identify genes associated with apoptosis in recurrent pregnancy loss (RPL). We retrieved the RPL expression profile datasets GSE165004 and GSE73025 from the Gene Expression Omnibus (GEO) database. We also obtained data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway of Apoptosis (hsa04210) to identify apoptosis-related genes. In addition, we performed Friends analysis to explore the interactions between differential apoptosis genes and other genes in the functional pathway. We identified six differentially expressed genes related to apoptosis, including CTSZ, BCL2, PIK3CD, KRAS, GADD45G, and CASP8, with GADD45G as the most gene. Functional fertility analysis revealed that differentially expressed genes primarily regulated protein stability, cell number homeostasis, myeloid cell homeostasis, hematopoietic progenitor cell differentiation, lytic vacuole and lysosome functions, vacuolar and lysosomal membranes, transmembrane transporter binding, protein domain-specific binding, G-protein beta-subunit binding, phospholipid binding, and were involved in pathways such as Rap1 signaling, regulation of actin cytoskeleton, and NOD-like receptor signaling. KRAS exhibited the highest mutation rate in RPL-related cancer CESC. There was also a positive correlation between differentially expressed genes and B cell memory, CD4 memory resting T cells, follicular helper T cells, naïve B cells, and resting dendritic cells. We identified six differentially expressed genes related to apoptosis in RPL, with GADD45G as the most important. NOD-like receptor signaling pathway and regulation of actin cytoskeleton could be therapeutic targets for RPL.

Glycolytic pathway analysis and gene expression profiles of combination of aloe vera and paclitaxel on non-small cell lung cancer and breast cancer.

The purpose of this study is to enhance the effectiveness of known anticancer medications using natural compounds. The study investigated the impact of combining AVE with PAX on non-small cell lung cancer (A549) and breast cancer (MCF7). In this study, A549 and MCF7 cells were treated with PAX (5μM), AVE (24μg/mL), and a combination of PAX and AVE (5μM + 24μg/mL). The glucose consumption rates of the cells were determined by extracellular acidification rate (ECAR) thanks to the SeaHorse XFe24 instrument. In addition, gene expression profiles were determined by performing Total RNA sequencing with the Novaseq 6000 instrument. Finally, the expressions of GAPDH, BAX, and BCL-2 genes involved in the apoptotic pathway were detected by RT-qPCR. The combined application of PAX and AVE reduced the ECAR value in both cell lines. According to the RT-qPCR results, the expression level of the apoptotic gene BAX increased in both cell lines (p < 0.05). Total RNA sequencing revealed that the combination effects of PAX and AVE play a role in the ribosome mechanism, thereby affecting the protein translation system in MCF7 while apoptosis and cell cycle have come to the forefront in A549.

Toxicological effects and defense mechanisms induced by beta-cypermethrin in Drosophila melanogaster

Widespread use of the pyrethroid insecticide beta-cypermethrin (beta-CYP) has led to adverse effects on nontarget populations within agroecosystems. Despite the efficacy of beta-CYP in pest control, its toxicological and defense mechanisms remain incompletely understood. In the present study, we explored the toxicological effects, antioxidant mechanisms and immune response against beta-CYP using Drosophila melanogaster, a well-established model organism for the study of insect biology, to represent the broader class of nontarget organisms. We exposed Drosophila larvae to 0.667 μg/mL beta-CYP and revealed that delayed development and caused intestinal epithelial damage in larvae. To gain insights into the molecular underpinnings of these effects, RNA sequencing analysis and quantitative polymerase chain reaction validation were performed. These analyses revealed that the messenger RNA levels of glutathione S-transferase were increased, third instar larvae exhibited an increase in reactive oxygen species content and a corresponding increase in antioxidant enzyme activity in response to beta-CYP exposure, indicating an upregulated response to oxidative stress. Beta-CYP also activated Hippo pathway to resist apoptosis and promote cell proliferation. Moreover, beta-CYP induced melanization and Toll immune pathways involved in immune response in Drosophila larvae, specifically the Toll pathway gene Drs. This activation suggests that Drosophila increases antioxidant defenses and promotes mitosis in damaged tissues as compensatory mechanisms to mitigate the cytotoxic effects of beta-CYP. These findings provide new insight into the mechanisms of beta-CYP–induced toxicity and the defense mechanisms in insects; they may also inform strategies for the sustainable use of insecticides and the development of mitigation measures to protect nontarget species in agroecosystems.

HIF-1α regulates mitochondrial function in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages.

HIF-1α plays a critical role in shaping macrophage phenotype and effector function. We have previously shown that tissue-resident alveolar macrophages (TR-AMs) have extremely low glycolytic capacity at steady-state, but can shift toward glycolysis under hypoxic conditions. Here, using inducible HIF-1α knockout ( Hif1a -/- ) TR-AMs and bone marrow-derived macrophages (BMDMs) and show that TR-AM HIF-1α is required for the glycolytic shift under prolyl hydroxylase inhibition, but is dispensable at steady-state for inflammatory effector function. In contrast, HIF-1α deletion in BMDMs led to diminished glycolytic capacity at steady-state and reduced inflammatory capacity, but higher mitochondrial function. Gene set enrichment analysis revealed enhanced c-Myc transcriptional activity in Hif1a -/- BMDMs, and upregulation of gene pathways related to ribosomal biogenesis and cellular proliferation. The findings highlight the heterogeneity of HIF-1α function in distinct macrophage populations and provide new insight into how HIF-1α regulates gene expression, inflammation, and metabolism in macrophages.

Gene Enrichment and Pathway Analysis for Ketosis Resistance in Dairy Cattle: A GWAS-Based Approach

Ketosis in dairy cattle is a common metabolic disorder that arises during the transition period from late gestation to early lactation. It is primarily caused by an imbalance between energy intake and expenditure, leading to an excessive accumulation of ketone bodies. This condition can significantly affect cattle health and productivity. Recent advances in genomic research, especially genome-wide association studies (GWAS), offer an opportunity to explore the genetic factors that contribute to ketosis resistance. The aim of this study is to comprehensively review and analyze existing GWAS data using gene enrichment analysis to identify potential functional candidate gene pathways associated with ketosis resistance in dairy cattle. In this study, data obtained from seven different studies were examined and 640 non-repetitive genes were obtained after filtering. Using Enrichr, an online tool for gene annotation, pathway analysis was performed with human homologs of the identified genes. Our findings highlight the acylglycerol homeostasis pathway, the regulation of triglyceride metabolism, and the role of chylomicrons in maintaining metabolic balance during ketosis. Additionally, immune response pathways were found to be linked to the genes associated with ketosis, offering insights into the intricate interplay between metabolic and immune pathways in ketosis. This study emphasizes the importance of understanding genetic factors in developing breeding strategies aimed at enhancing metabolic health and productivity in dairy cattle. Future research should focus on validating these candidate genes and exploring their mechanistic roles to facilitate targeted interventions and improve resistance to ketosis in dairy herds.

Molecular Landscape of Bladder Cancer: Key Genes, Transcription Factors, and Drug Interactions.

Bladder cancer is among the most prevalent tumors in the urinary system and is known for its high malignancy. Although traditional diagnostic and treatment methods are established, recent research has focused on understanding the molecular mechanisms underlying bladder cancer. The primary objective of this study is to identify novel diagnostic markers and discover more effective targeted therapies for bladder cancer. This study identified differentially expressed genes (DEGs) between bladder cancer tissues and adjacent normal tissues using data from The Cancer Genome Atlas (TCGA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to explore the functional roles of these genes. A protein-protein interaction (PPI) network was also constructed to identify and analyze hub genes within this network. Gene set variation analysis (GSVA) was conducted to investigate the involvement of these genes in various biological processes and pathways. Ten key genes were found to be significantly associated with bladder cancer: IL6, CCNA2, CCNB1, CDK1, PLK1, TOP2A, AURKA, AURKB, FOXM1, and CALML5. GSVA analyses revealed that these genes are involved in a variety of biological processes and signaling pathways, including coagulation, UV-response-down, apoptosis, Notch signaling, and Wnt/beta-catenin signaling. The diagnostic relevance of these genes was validated through ROC curve analysis. Additionally, potential therapeutic drug interactions with these key genes were identified. This study provides valuable insights into key genes and their roles in bladder cancer. The identified genes and their interactions with therapeutic drugs could serve as potential biomarkers, presenting new opportunities for enhancing the diagnosis and prognosis of bladder cancer.

Transcriptomics combined with physiological analysis provided new insights into the enhancing Dendrobium nobile resilience to Cu stress through Ce modulation

In the face of escalating environmental challenges, understanding the mechanisms through which plants can resist heavy metal stress is paramount. This study delves into the efficacy of cerium (Ce), a rare earth element, in mitigating copper (Cu) toxicity in Dendrobium nobile Lindl., an orchid plant with significant medicinal and ornamental value. Through a comprehensive experimental approach that encompasses physiological, biochemical, and molecular analyses, we demonstrate that Ce application notably enhances D. nobile's tolerance to Cu stress. The investigation revealed that Ce supplementation significantly ameliorated the adverse effects of Cu on plant growth, evidenced by a notable decrease in Cu accumulation within the plant tissues. At the molecular level, transcriptome sequencing uncovered the upregulation of genes involved in antioxidant defense mechanisms, heavy metal chelation, and stress response signaling pathways. Key findings include the enhanced activities of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase, alongside an increase in the levels of antioxidants and phytochelatins, which collectively contribute to the detoxification of Cu. Furthermore, Ce was found to influence the subcellular distribution of Cu, promoting its sequestration in less harmful cellular compartments. Our study provides novel insights into the role of Ce in modulating plant responses to heavy metal stress, highlighting its potential as a mitigative agent against Cu toxicity. The elucidation of specific gene regulations and pathway activations offers a foundation for future research aimed at enhancing plant resilience to environmental stresses through biotechnological interventions.

Identification of potential microRNAs involved in pathogenesis of venous thromboembolism (VTE): A meta analysis

ObjectiveMicroRNAs (MiRNAs) are master regulators of gene expression and have been suggested as potential diagnostic and therapeutic biomarkers in variety of complex diseases. Venous thromboembolism is a major cause of morbidity and mortality worldwide. Several miRNA expression studies have been conducted to identify miRNAs linked to VTE prognosis. These studies reveal that various miRNAs are significantly up-regulated and down-regulated in VTE patients in comparison to healthy controls. Present meta-analysis deliberate findings of such studies to identify most potential miRNA targets associated with VTE. MethodologyComprehensive literature review on Pubmed was conducted. Present analysis assessed 20 research article out of a total of 383 articles screened, based on inclusion and exclusion criteria. The up-regulated and down-regulated miRNAs obtained from selected research articles were subjected to meta-analysis. The differentially expressed miRNAs so obtained and were used for further bioinformatic analysis, including gene ontology and pathway analysis of their target genes, to study their potential involvement in VTE pathogenesis. ResultsTwenty articles selected for meta-analysis included a total of 808 patients. These included 26 up-regulated miRNAs and 11 down-regulated miRNAs. The meta-analysis based on Odds ratio suggested that one up-regulated miRNA (hsa-miR-1233-3p) and two down-regulated miRNAs (hsa-miR-103a-3p and hsa-miR-200c) returned significantly higher Odds compared to other miRNAs. Further bioinformatics analysis of their target genes revealed that these miRNAs target a large number of genes involved in cell adhesion, cell migration, endothelial activation and inflammation genes. ConclusionsThree miRNAs, viz.; hsa-miR-1233-3p, hsa-miR-103a-3p and hsa-miR-200c may play a crucial role in VTE pathogenesis and has potential to serve as reliable diagnostic or therapeutic biomarkers for VTE.

Gene expression profiling in Venous thromboembolism: Insights from publicly available datasets

BackgroundVenous thromboembolism (VTE) is the third most common cardiovascular disease and is a major cause of mobility and mortality worldwide. VTE is a complex multifactorial disease and genetic mechanisms underlying its pathogenesis is yet to be completely elucidated. The aim of the present study was to identify hub genes and pathways involved in development and progression of blood clot during VTE using gene expression data from public repositories. MethodologyDifferential gene expression (DEG) data from two datasets, GSE48000 and GSE19151 were analysed using GEO2R tool. Gene expression data of VTE patients were compared to that of healthy controls using various bioinformatics tools. ResultsWhen the differentially expressed genes of the two datasets were compared, it was found that 19 genes were up-regulated while 134 genes were down-regulated. Gene ontology (GO) and pathway analysis revealed that pathways such as complement and coagulation cascade and B-cell receptor signalling along with DNA methylation, DNA alkylation and inflammatory genes were significantly up-regulated in VTE patients. On the other hand, differentially down-regulated genes included mitochondrial translation elongation, termination and biosysthesis along with heme biosynthesis, erythrocyte differentiation and homeostasis. The top 5 up-regulated hub genes obtained by protein-protein interaction (PPI) network analysis included MYC, FOS, SGK1, CR2 and CXCR4, whereas the top 5 down-regulated hub genes included MRPL13, MRPL3, MRPL11, RPS29 and RPL9. The up-regulated hub genes are functionally involved in maintain vascular integrity and complementation cascade while the down-regulated hub genes were mostly mitochondrial ribosomal proteins. ConclusionPresent study highlights significantly enriched pathways and genes associated with VTE development and prognosis. The data hereby obtained could be used for designing newer diagnostic and therapeutic tools for VTE management.

Myeloid-Specific JAK2 Contributes to Inflammation and Salt Sensitivity of Blood Pressure.

Salt sensitivity of blood pressure (SSBP), characterized by acute changes in blood pressure with changes in dietary sodium intake, is an independent risk factor for cardiovascular disease and mortality in people with and without hypertension. We previously found that elevated sodium concentration activates antigen-presenting cells (APCs), resulting in high blood pressure, but the mechanisms are unknown. Here, we hypothesized that APC-specific JAK2 (Janus kinase 2) through STAT3 (signal transducer and activator of transcription 3) and SMAD3 (small mothers against decapentaplegic homolog 3) contributes to SSBP. We performed bulk or single-cell transcriptomic analyses following in vitro monocytes exposed to high salt and in vivo high sodium treatment in humans using a rigorous salt-loading/depletion protocol to phenotype SSBP. We also used a myeloid cell-specific CD11c+ JAK2 knockout mouse model and measured blood pressure with radiotelemetry after N-omega-nitro-L-arginine-methyl ester and a high salt diet treatment. We used flow cytometry for immunophenotyping and measuring cytokine levels. Fluorescence in situ hybridization and immunohistochemistry were performed to spatially visualize the kidney's immune cells and cytokine levels. Echocardiography was performed to assess cardiac function. We found that high salt treatment upregulates gene expression of the JAK/STAT/SMAD pathway while downregulating inhibitors of this pathway, such as suppression of cytokine signaling and cytokine-inducible SH2, in human monocytes. Expression of the JAK2 pathway genes mirrored changes in blood pressure after salt loading and depletion in salt-sensitive but not salt-resistant humans. Ablation of JAK2, specifically in CD11c+ APCs, attenuated salt-induced hypertension in mice with SSBP. Mechanistically, we found that SMAD3 acted downstream of JAK2 and STAT3, leading to increased production of highly reactive isolevuglandins and proinflammatory cytokine IL (interleukin)-6 in renal APCs, which activate T cells and increase production of IL-17A, IL-6, and TNF-α (tumor necrosis factor-alpha). Our findings reveal the APC JAK2 signaling pathway as a potential target for the diagnosis and treatment of SSBP in humans.

Loss of function in Drosophila transcription factor Dif delays brain development in larvae resulting in aging adult brain

Drosophila NF-κB transcription factor Dif has been well known for its function in innate immunity, and recent study also reveals its role in neuronal cells. However, the underlying mechanisms of Dif in the brain remain elusive. In this study, we aim to investigate the function of Dif in Drosophila brain development and how Dif regulates structure and plasticity of the brain to affect aging and behaviors. Based on the analysis of differentially expressed genes, we identified key genes associated with cell division, development and aging in the brain of Dif1 loss of function mutant. In Dif1 larvae, we found that the metamorphosis and brain development were delayed, and cell division was decreased. In Dif1 adults, the number of neuron cells was reduced in the brain, the lifespan and locomotor activity were decreased, protein markers associated with aging-related neurodegenerative diseases in the brain were altered in abundance or activity. Our results indicated that Dif plays a crucial role in brain plasticity and neurogenesis, dysfunction of Dif delays larval brain development and impacts proliferation of neuronal cells, resulting in aging adult brain by regulating expression of key genes in multiple signaling pathways involved in cell division, neurogenesis and aging.

A spray-induced gene silencing strategy for Spodoptera frugiperda oviposition inhibition using nanomaterial-encapsulated dsEcR

Although RNAi-based pest management holds great potential as an alternative to traditional chemical control, its efficiency is restricted by dsRNA instability and limited cellular uptake. Using nanomaterials to facilitate dsRNA delivery has shown promise in solving these challenges. In this study, we firstly used RNAi to investigate the role of the juvenile hormone and ecdysteroid signaling pathways genes in reproduction of Spodoptera frugiperda, the fall armyworm. Females in knocked-down treatments of any of the Met, EcR, and USP genes had greatly reduced fertility with the most pronounced inhibitory effects on oviposition observed following EcR knockdown, and thus the dsEcR could be a candidate target for RNAi-based oviposition inhibitory agency. Then a combinatorial spray-induced and nanocarrier-delivered gene silencing (SI-NDGS) approach that targeted EcR was conducted. At 72 h post-spay, the transcript levels of EcR and the oviposition were successfully reduced and inhibited. These findings support the groundwork for further developing novel RNAi-based pest management strategies for S. frugiperda.

Molecular Characterization of Sterol C4-Methyl Oxidase in Leishmania major.

Sterol biosynthesis requires the oxidative removal of two methyl groups from the C-4 position by sterol C-4-demethylase and one methyl group from the C-14 position by sterol C-14-demethylase. In Leishmania donovani, a CYP5122A1 (Cytochrome P450 family 5122A1) protein was recently identified as the bona fide sterol C-4 methyl oxidase catalyzing the initial steps of C-4-demethylation. Besides CYP5122A1, Leishmania parasites possess orthologs to ERG25 (ergosterol pathway gene 25), the canonical sterol C-4 methyl oxidase in Saccharomyces cerevisiae. To determine the contribution of CYP5122A1 and ERG25 in sterol biosynthesis, we assessed the essentiality of these genes in Leishmania major, which causes cutaneous leishmaniasis. Like in L. donovani, CYP5122A1 in L. major could only be deleted in the presence of a complementing episome. Even with strong negative selection, L. major chromosomal CYP5122A1-null mutants retained the complementing episome in both promastigote and amastigote stages, demonstrating its essentiality. In contrast, the L. major ERG25-null mutants were fully viable and replicative in culture and virulent in mice. Deletion and overexpression of ERG25 did not affect the sterol composition, indicating that ERG25 is not required for C-4-demethylation. These findings suggest that CYP5122A1 is the dominant and possibly only sterol C-4 methyl oxidase in Leishmania, and inhibitors of CYP5122A1 may have strong therapeutic potential against multiple Leishmania species.

Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression

Dominant X-linked diseases are uncommon due to female X chromosome inactivation (XCI). While random XCI usually protects females against X-linked mutations, Rett syndrome (RTT) is a female neurodevelopmental disorder caused by heterozygous MECP2 mutation. After 6-18 months of typical neurodevelopment, RTT girls undergo a poorly understood regression. We performed longitudinal snRNA-seq on cerebral cortex in a construct-relevant Mecp2e1 mutant mouse model of RTT, revealing transcriptional effects of cell type, mosaicism, and sex on progressive disease phenotypes. Across cell types, we observed sex differences in the number of differentially expressed genes (DEGs) with 6x more DEGs in mutant females than males. Unlike males, female DEGs emerged prior to symptoms, were enriched for homeostatic gene pathways in distinct cell types over time and correlated with disease phenotypes and human RTT cortical cell transcriptomes. Non-cell-autonomous effects were prominent and dynamic across disease progression of Mecp2e1 mutant females, indicating that wild-type-expressing cells normalize transcriptional homeostasis. These results advance our understanding of RTT progression and treatment.

The utilization of N-acetylgalactosamine and its effect on the metabolism of amino acids in Erysipelotrichaceae strain

BackgroundThe metabolism of gut microbiota produces bioactive metabolites that modulate host physiology and promote self-growth. Erysipelotrichaceae is one of the most common anaerobic microorganism families in the gut, which has been discovered to play a vital role in host metabolic disorders and inflammatory diseases. Our previous study found that N-acetylgalactosamine (GalNAc) in caecal content of pigs significantly affected the abundance of Erysipelotrichaceae strains. However, it remains unknown how GalNAc feeding in vitro culture affects the expression levels of genes in the GalNAc metabolic pathway and the concentrations of intermediate metabolites in the Erysipelotrichaceae strain. Whether GalNAc feeding should influence the metabolism of other nutrients, such as amino acids, remains unrevealed.ResultsIn this study, whole-genome sequence, transcriptome, and metabolome data were analyzed to assess the utilization of a Erysipelotrichaceae strain on GalNAc. The results showed the presence of a complete GalNAc catabolism pathway in the genome of this Erysipelotrichaceae strain. GalNAc feeding to this Erysipelotrichaceae strain significantly changed the expression levels of genes involved in glycolysis and tricarboxylic acid (TCA) cycle. Meanwhile, the concentrations of lactate, pyruvate, citrate, succinate and malate from the glycolysis and TCA cycle were significantly increased. In addition, transcriptome analysis indicated that the genes involved in the metabolism of amino acids were affected by GalNAc, including lysA (a gene involved in lysine biosynthesis) that was significantly down-regulated. The intracellular concentrations of 14 amino acids in the Erysipelotrichaceae strain were significantly increased after feeding GalNAc.ConclusionsOur findings comfirmed and extended our previous works that demonstrated the utilization of GalNAc by Erysipelotrichaceae strain, and explained the possible mechanism of GalNAc affecting the abundance of Erysipelotrichaceae strain in vitro.