Changes In Gene Expression Profiles Research Articles

Integrative analysis highlights molecular and immune responses of tick Amblyomma americanum to Escherichia coli challenge.

Ticks are ectoparasites that can transmit various pathogens capable of causing life-threatening illnesses in people and animals, making them a severe public health threat. Understanding how ticks respond to bacterial infection is crucial for deciphering their immune defense mechanisms and identifying potential targets for controlling tick-borne diseases. In this study, an in-depth transcriptome analysis was used to investigate the molecular and immune responses of Amblyomma americanum to infection caused by the microinjection of Escherichia coli. With an abundance of differentially expressed genes discovered at different times, the analysis demonstrated significant changes in gene expression profiles in response to E. coli challenge. Notably, we found alterations in crucial immune markers, including the antimicrobial peptides defensin and microplusin, suggesting they may play an essential role in the innate immune response. Furthermore, KEGG analysis showed that following E. coli exposure, a number of key enzymes, including lysosomal alpha-glucosidase, fibroblast growth factor, legumain, apoptotic protease-activating factor, etc., were altered, impacting the activity of the lysosome, mitogen-activated protein kinase, antigen processing and presentation, bacterial invasion, apoptosis, and the Toll and immune deficiency pathways. In addition to the transcriptome analysis, we constructed protein interaction networks to elucidate the molecular interactions underlying the tick's response to E. coli challenge. Hub genes were identified, and their functional enrichment provided insights into the regulation of cytoskeleton rearrangement, apoptotic processes, and kinase activity that may occur in infected cells. Collectively, the findings shed light on the potential immune responses in A. americanum that control E. coli infection.

Increased cholesterol uptake is associated with the altered gene expression in white adipose tissue of ApoE−/− mice fed a high-fat high-cholesterol diet

Apolipoprotein E knock out (ApoE−/−) mice, the widely used model for atherosclerosis, exhibits anti-obesity characteristics due to the impaired lipoprotein internalization. Since excessive accumulation of triglycerides and cholesterol in white adipose tissue (WAT) is shown to increase the risk of metabolic diseases, we investigated the effects of dietary high-fat high-cholesterol (HFHC) on gene expression profile and the possible role of cholesterol accumulation in WAT of ApoE−/− mice. Control (CON) and HFHC diets were provided to wild-type mice (WC, WH) and ApoE−/− mice (EC, EH) for 10 weeks. Although body and WAT weights were lower in the ApoE−/− group compared to the wild-type group, increases in cholesterol and lipid peroxides in WAT were only observed in the ApoE−/− group. Transcriptome analysis revealed 3660 and 839 differentially expressed genes (DEGs) in the EC/WC and EH/WH comparison, respectively. “Thermogenesis” and “Oxidative phosphorylation” KEGG pathways were found in the EC/WC comparison, but not in the EH/WH comparison. We identified 142 and 2585 DEGs in the WH/WC and EH/EC comparison respectively, indicating a stronger effect of HFHC on WAT of ApoE−/− mice. Gene ontology analysis of DEGs revealed the association of DEGs with “Regulation of inflammatory response” term, in the EH/EC comparison, but not in the WH/WC comparison. Especially, genes encoding scavenger receptors and toll-like receptors were associated with cholesterol and lipid peroxide levels in WAT of ApoE−/− mice, but not in wild-type mice. In conclusion, changes in gene expression profile of WAT were more pronounced in ApoE−/− mice compared to wild-type mice in response to HFHC, and these altered genes were related to inflammatory response. These data suggest that increased cholesterol accumulation in WAT by dietary HFHC may play a pivotal role in the regulation of gene expression in ApoE−/− mice.

Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

BackgroundDurum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains.ResultsTo enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example.ConclusionWe provide a valuable resource for studying endosperm development in this increasingly important crop species.

Early-Life Exposure to Lipopolysaccharide Induces Persistent Changes in Gene Expression Profiles in the Liver and Spleen of Female FVB/N Mice.

The objective of this study was to investigate how subcutaneous (sc) lipopolysaccharide (LPS) administration affects the gene expression profiles of insulin signaling as well as innate and adaptive immunity genes in mouse livers and spleens. FVB/N female mice were randomly assigned to one of two treatment groups at 5 weeks of age: (1) a six-week subcutaneous injection of saline at 11 μL/h (control-CON), or (2) a six-week subcutaneous injection of LPS from Escherichia coli 0111:B4 at 0.1 μg/g body weight at 11 μL/h. At 106 weeks (i.e., 742 days) after the last treatment, mice were euthanized. Following euthanasia, liver and spleen samples were collected, snap frozen, and stored at -80 °C until gene expression profiling. LPS upregulated nine genes in the liver, according to the findings (Pparg, Frs3, Kras, Raf1, Gsk3b, Rras2, Hk2, Pik3r2, and Myd88). With a 4.18-fold increase over the CON group, Pparg was the most up-regulated gene in the liver. Based on the annotation cluster analysis, LPS treatment upregulated liver genes which are involved in pathways associated with hepatic steatosis, B- and T-cell receptor signaling, chemokine signaling, as well as other types of cancers such as endometrial cancer, prostate cancer, and colorectal cancer. LPS increased the spleen expression of Ccl11, Ccl25, Il6, Cxcl5, Pparg, Tlr4, Nos2, Cxcl11, Il1a, Ccl17, and Fcgr3, all of which are involved in innate and adaptive immune responses and the regulation of cytokine production. Furthermore, functional analysis revealed that cytokine-cytokine receptor interaction and chemokine signaling pathways were the most enriched in LPS-treated mice spleen tissue. Our findings support the notion that early-life LPS exposure can result in long-term changes in gene expression profiling in the liver and spleen tissues of FVB/N female mice.

Synergistic Effect of Treatment with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Lipopolysaccharide on the Inflammatory Response of Porcine Pulmonary Microvascular Endothelial Cells.

The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) often causes secondary bacterial infection in piglets, resulting in inflammatory lung injury and leading to high mortality rates and significant economic losses in the pig industry. Microvascular endothelial cells (MVECs) play a crucial role in the inflammatory response. Previous studies have shown that HP-PRRSV can infect porcine pulmonary MVECs and damage the endothelial glycocalyx. To further understand the role of pulmonary MVECs in the pathogenesis of HP-PRRSV and its secondary bacterial infection, in this study, cultured porcine pulmonary MVECs were stimulated with a HP-PRRSV HN strain and lipopolysaccharide (LPS). The changes in gene expression profiles were analyzed through transcriptome sequencing, and the differentially expressed genes were verified using qRT-PCR, Western blot, and ELISA. Furthermore, the effects on endothelial barrier function and regulation of neutrophil trans-endothelial migration were detected using the Transwell model. HP-PRRSV primarily induced differential expression of numerous genes associated with immune response, including IFIT2, IFIT3, VCAM1, ITGB4, and CCL5, whereas LPS triggered an inflammatory response involving IL6, IL16, CXCL8, CXCL14, and ITGA7. Compared to the individual effect of LPS, when given after HN-induced stimulation, it caused a greater number of changes in inflammatory molecules, such as VCAM1, IL1A, IL6, IL16, IL17D, CCL5, ITGAV, IGTB8, and TNFAIP3A, a more significant reduction in transendothelial electrical resistance, and higher increase in neutrophil transendothelial migration. In summary, these results suggest a synergistic effect of HP-PRRSV and LPS on the inflammatory response of porcine pulmonary MVECs. This study provides insights into the mechanism of severe lung injury caused by secondary bacterial infection following HP-PRRSV infection from the perspective of MVECs, emphasizing the vital role of pulmonary MVECs in HP-PRRSV infection.

Microglia and Astroglia-The Potential Role in Neuroinflammation Induced by Pre- and Neonatal Exposure to Lead (Pb).

Neuroinflammation is one of the postulated mechanisms for Pb neurotoxicity. However, the exact molecular mechanisms responsible for its pro-inflammatory effect are not fully elucidated. In this study, we examined the role of glial cells in neuroinflammation induced by Pb exposure. We investigated how microglia, a type of glial cell, responded to the changes caused by perinatal exposure to Pb by measuring the expression of Iba1 at the mRNA and protein levels. To assess the state of microglia, we analyzed the mRNA levels of specific markers associated with the cytotoxic M1 phenotype (Il1b, Il6, and Tnfa) and the cytoprotective M2 phenotype (Arg1, Chi3l1, Mrc1, Fcgr1a, Sphk1, and Tgfb1). Additionally, we measured the concentration of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α). To assess the reactivity and functionality status of astrocytes, we analyzed the GFAP (mRNA expression and protein concentration) as well as glutamine synthase (GS) protein level and activity. Using an electron microscope, we assessed ultrastructural abnormalities in the examined brain structures (forebrain cortex, cerebellum, and hippocampus). In addition, we measured the mRNA levels of Cxcl1 and Cxcl2, and their receptor, Cxcr2. Our data showed that perinatal exposure to Pb at low doses affected both microglia and astrocyte cells' status (their mobilization, activation, function, and changes in gene expression profile) in a brain-structure-specific manner. The results suggest that both microglia and astrocytes represent a potential target for Pb neurotoxicity, thus being key mediators of neuroinflammation and further neuropathology evoked by Pb poisoning during perinatal brain development.

Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence

Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNA (hetsiRNA) loci/regions whose transcriptional activity was significantly changed in the absence of NDX. In addition, data obtained from inflorescence were compared with seedling transcriptomics data, which revealed development-specific changes in gene expression profiles. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further research on NDX function.

Transcriptomic profiling reveals differential cellular response to copper oxide nanoparticles and polystyrene nanoplastics in perfused human placenta

The growing nanoparticulate pollution (e.g. engineered nanoparticles (NPs) or nanoplastics) has been shown to pose potential threats to human health. In particular, sensitive populations such as pregnant women and their unborn children need to be protected from harmful environmental exposures. However, developmental toxicity from prenatal exposure to pollution particles is not yet well studied despite evidence of particle accumulation in human placenta. Our study aimed to investigate how copper oxide NPs (CuO NPs; 10–20 nm) and polystyrene nanoplastics (PS NPs; 70 nm) impact on gene expression in ex vivo perfused human placental tissue. Whole genome microarray analysis revealed changes in global gene expression profile after 6 h of perfusion with sub-cytotoxic concentrations of CuO (10 µg/mL) and PS NPs (25 µg/mL). Pathway and gene ontology enrichment analysis of the differentially expressed genes suggested that CuO and PS NPs trigger distinct cellular response in placental tissue. While CuO NPs induced pathways related to angiogenesis, protein misfolding and heat shock responses, PS NPs affected the expression of genes related to inflammation and iron homeostasis. The observed effects on protein misfolding, cytokine signaling, and hormones were corroborated by western blot (accumulation of polyubiquitinated proteins) or qPCR analysis. Overall, the results of the present study revealed extensive and material-specific interference of CuO and PS NPs with placental gene expression from a single short-term exposure which deserves increasing attention. In addition, the placenta, which is often neglected in developmental toxicity studies, should be a key focus in the future safety assessment of NPs in pregnancy.

Starch deficiency in tomato causes transcriptional reprogramming that modulates fruit development, metabolism and stress responses.

Tomato fruit (Solanum lycopersicum) store carbon as starch during early development and mobilize it at the onset of ripening. Starch accumulation has been suggested to buffer fluctuations in carbon supply to the fruit under abiotic stress, and contribute to sugar levels in ripe fruit. However, the role of starch accumulation and metabolism during fruit development is still unclear. Here we show that the tomato mutant adpressa (adp) harbors a mutation in a gene encoding the small subunit of ADP-glucose pyrophosphorylase (AGPase), which abolishes starch synthesis. The disruption of starch biosynthesis causes major transcriptional and metabolic remodeling in adp fruit but only minor effects on fruit size and ripening. Changes in gene expression and metabolite profiles indicate that the lack of carbon flow into starch increases levels of soluble sugars during fruit growth, triggers a readjustment of central carbohydrate and lipid metabolism, and activates growth and stress protection pathways. Accordingly, adp fruits are remarkably resistant to blossom-end rot, a common physiological disorder induced by environmental stress. Our results provide insights into the effects of perturbations of carbohydrate metabolism on tomato fruit development, with potential implications for the enhancement of protective mechanisms against abiotic stress in fleshy fruit.

Time-series transcriptome analysis of peripheral blood mononuclear cells obtained from individuals who received the SARS-CoV-2 mRNA vaccine.

Messenger ribonucleic acid (mRNA) vaccination against coronavirus disease 2019 (COVID-19) is an effective prevention strategy, despite a limited understanding of the molecular mechanisms underlying the host immune system and individual heterogeneity of the variable effects of mRNA vaccination. We assessed the time-series changes in the comprehensive gene expression profiles of 200 vaccinated healthcare workers by performing bulk transcriptome and bioinformatics analyses, including dimensionality reduction utilizing the uniform manifold approximation and projection (UMAP) technique. For these analyses, blood samples, including peripheral blood mononuclear cells (PBMCs), were collected from 214 vaccine recipients before vaccination (T1) and on Days 22 (T2, after second dose), 90, 180 (T3, before a booster dose), and 360 (T4, after a booster dose) after receiving the first dose of BNT162b2 vaccine (UMIN000043851). UMAP successfully visualized the main cluster of gene expression at each time point in PBMC samples (T1-T4). Through differentially expressed gene (DEG) analysis, we identified genes that showed fluctuating expression levels and gradual increases in expression levels from T1 to T4, as well as genes with increased expression levels at T4 alone. We also succeeded in dividing these cases into five types based on the changes in gene expression levels. High-throughput and temporal bulk RNA-based transcriptome analysis is a useful approach for inclusive, diverse, and cost-effective large-scale clinical studies.

Effect of preventive training in cardiac transcriptoma in rats with pulmonary hypertension

Abstract Funding Acknowledgements Type of funding sources: None. Introduction Pulmonary hypertension (PH) is a progressive disease characterized by elevated right ventricular afterload, vascular remodeling, right ventricular hypertrophy and dysfunction, and ultimately heart failure. Physical exercise has been recognized as a treatment for this condition. Although different mechanisms have been proposed to explain PH development, the influence of preventive exercise training interventions onset of pulmonary hypertension in right ventricular hypertrophy is underexplored. Purpose Analyze the effect of preventive training in global gene expression profiling of right ventricular in PH from rats. Methods Twenty-four male Wistar rats (206-220 g) were divided into three four groups (n=8/group): S, sedentary control; SPH, sedentary pulmonary hypertension; and TPH, trained pulmonary hypertension group. The preventive training protocol was performed on a treadmill for 13 weeks, five times/week. Cardiac hypertrophy by PH was experimentally induced by a single intraperitoneal injection (60 mg/kg) of monocrotaline after the protocol training. The S were injected with saline solution. The rats were evaluated 28 days after monocrotaline administration, in the early stage of the PH. Left ventricle weight, right ventricle weight, and atrium weight normalized by body weight were used as indexes of heart hypertrophy. Gene expression profiling was performed using the Rat Gene ST Array platform. To further understand the biological relevance of differential expressed genes, we performed a functional enrichment analysis in the context of the gene ontology (biological process, molecular function, and cellular component) and interaction networks (KEGG, Reactome, Wikipathways and BioPlanet). Results Through the analysis, the HP group had cardiac hypertrophy, and the training mitigated this change p< 0.05. Global gene expression profiling identified 687 differentially expressed genes (S vs. SPH), in the hypertrophy right ventricular during PH, and when compared to preventive training, 91 genes were dysregulated (SPH vs TPH). Gene ontology analysis on expression profiling data revealed alteration on genes that regulate the inflammatory process, muscle growth, metabolic processes, cell death, and ion regulation comparison between SPH vs. TPH The genes that were altered in the hypertrophy phase of PH and modified by the exercise were platelet alpha granule lumen (genes Fgg and Qsox1), NAD + binding (gene Cryl1), positive regulation of cAMP-mediated signaling (gene Cxcl11), positive regulation of macrophage differentiation (Il34 gene), mRNA cleavage (Cstf3 gene), negative regulation of transporter activity (Wwp2 gene), regulation of respiratory system process (Mtg2 gene) p< 0.05. Conclusion Preventive training influences changes in cardiac gene expression profile in the hypertrophy stage of PH. New genes have been identified, and these could be biomarkers and potential therapeutic targets in the early stage of PH.

High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

BackgroundThe adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear.ResultsIn this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated ~ 1.5 kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response.ConclusionsOur study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.

Transcriptome-based analysis of the effects of compound microbial agents on gene expression in wheat roots and leaves under salt stress.

Salt stress inhibits the beneficial effects of most plant growth-promoting rhizobacteria. The synergistic relationship between beneficial rhizosphere microorganisms and plants helps achieve more stable growth-promoting effects. This study aimed 1) to elucidate changes in gene expression profiles in the roots and leaves of wheat after inoculation with compound microbial agents and 2) to determine the mechanisms by which plant growth-promoting rhizobacteria mediate plant responses to microorganisms. Following inoculation with compound bacteria, transcriptome characteristics of gene expression profiles of wheat, roots, and leaves at the flowering stage were investigated using Illumina high-throughput sequencing technology. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the genes that were significantly differentially expressed. The expression of 231 genes in the roots of bacterial preparations (BIO) -inoculated wheat changed significantly (including 35 upregulated and 196 downregulated genes) compared with that of non-inoculated wheat. The expression of 16,321 genes in leaves changed significantly, including 9651 upregulated genes and 6670 downregulated genes. The differentially expressed genes were involved in the metabolism of carbohydrates, amino acids, and secondary compounds as well as signal transduction pathways. The ethylene receptor 1 gene in wheat leaves was significantly downregulated, and genes related to ethylene-responsive transcription factor were significantly upregulated. GO enrichment analysis showed that metabolic and cellular processes were the main functions affected in the roots and leaves. The main molecular functions altered were binding and catalytic activities, among which the cellular oxidant detoxification enrichment rate was highly expressed in the roots. The expression of peroxisome size regulation was the highest in the leaves. KEGG enrichment analysis showed that linoleic acid metabolism expression was highest in the roots, and the expression of photosynthesis-antenna proteins was the highest in leaves. After inoculation with a complex biosynthesis agent, the phenylalanine ammonia lyase (PAL) gene of the phenylpropanoid biosynthesis pathway was upregulated in wheat leaf cells while 4CL, CCR, and CYP73A were downregulated. Additionally, CYP98A and REF1 genes involved in the flavonoid biosynthesis pathway were upregulated, while F5H, HCT, CCR, E2.1.1.104, and TOGT1-related genes were downregulated. Differentially expressed genes may play key roles in improving salt tolerance in wheat. Compound microbial inoculants promoted the growth of wheat under salt stress and improved disease resistance by regulating the expression of metabolism-related genes in wheat roots and leaves and activating immune pathway-related genes.

A comparison of machine learning approaches for the quantification of microglial cells in the brain of mice, rats and non-human primates.

Microglial cells are brain-specific macrophages that swiftly react to disruptive events in the brain. Microglial activation leads to specific modifications, including proliferation, morphological changes, migration to the site of insult, and changes in gene expression profiles. A change in inflammatory status has been linked to many neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. For this reason, the investigation and quantification of microglial cells is essential for better understanding their role in disease progression as well as for evaluating the cytocompatibility of novel therapeutic approaches for such conditions. In the following study we implemented a machine learning-based approach for the fast and automatized quantification of microglial cells; this tool was compared with manual quantification (ground truth), and with alternative free-ware such as the threshold-based ImageJ and the machine learning-based Ilastik. We first trained the algorithms on brain tissue obtained from rats and non-human primate immunohistochemically labelled for microglia. Subsequently we validated the accuracy of the trained algorithms in a preclinical rodent model of Parkinson's disease and demonstrated the robustness of the algorithms on tissue obtained from mice, as well as from images provided by three collaborating laboratories. Our results indicate that machine learning algorithms can detect and quantify microglial cells in all the three mammalian species in a precise manner, equipotent to the one observed following manual counting. Using this tool, we were able to detect and quantify small changes between the hemispheres, suggesting the power and reliability of the algorithm. Such a tool will be very useful for investigation of microglial response in disease development, as well as in the investigation of compatible novel therapeutics targeting the brain. As all network weights and labelled training data are made available, together with our step-by-step user guide, we anticipate that many laboratories will implement machine learning-based quantification of microglial cells in their research.

Transcriptome sequencing reveals the effects of circRNA on testicular development and spermatogenesis in Qianbei Ma goats.

Circular RNAs (circRNAs) play an important role in regulating the mammalian reproductive system, especially testicular development and spermatogenesis. However, their functions in testicular development and spermatogenesis in the Qianbei Ma goat, the Guizhou endemic breed are still unclear. In this study, tissue sectioning and circRNAs transcriptome analysis were conducted to compare the changes of morphology and circular RNAs gene expression profile at four different developmental stages (0Y, 0-month-old; 6Y, 6-month-old; 12Y, 12-month-old; 18Y, 18-month-old). The results showed that the circumferences and area of the seminiferous tubule gradually increased with age, and the lumen of the seminiferous tubule in the testis differentiated significantly. 12,784 circRNAs were detected from testicular tissues at four different developmental stages by RNA sequencing, and 8,140 DEcircRNAs (differentially expressed circRNAs) were found in 0Y vs. 6Y, 6Y vs. 12Y, 12Y vs. 18Y and 0Y vs. 18Y, 0Y vs. 12Y, 6Y vs. 18Y Functional enrichment analysis of the source genes showed that they were mainly enriched in testicular development and spermatogenesis. In addition, the miRNAs and mRNAs associated with DECircRNAs in 6 control groups were predicted by bioinformatics, and 81 highly expressed DECircRNAs and their associated miRNAs and mRNAs were selected to construct the ceRNA network. Through functional enrichment analysis of the target genes of circRNAs in the network, some candidate circRNAs related to testicular development and spermatogenesis were obtained. Such as circRNA_07172, circRNA_04859, circRNA_07832, circRNA_00032 and circRNA_07510. These results will help to reveal the mechanism of circRNAs in testicular development and spermatogenesis, and also provide some guidance for goat reproduction.

Ornithine δ-aminotransferase OsOAT is critical for male fertility and cold tolerance during rice plant development.

Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ-aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature-sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild-type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold-inducible in WYG but cold-irresponsive in HHZ. Further studies showed that indica varieties carry both WYG-type and HHZ-type OsOAT, whereas japonica varieties mostly carry WYG-type OsOAT. Cultivars carrying HHZ-type OsOAT are mainly distributed in low-latitude regions, whereas varieties carrying WYG-type OsOAT are distributed in both low- and high-latitude regions. Moreover, indica varieties carrying WYG-type OsOAT generally have higher seed-setting rates than those carrying HHZ-type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG-type OsOAT during domestication and breeding to cope with low temperatures.

CD30 stimulation induces multinucleation and chromosomal instability in HTLV-1-infected cell lines.

A recent report indicated involvement of CD30 in progression of human leukemia virus type 1 (HTLV-1) infection, but the exact roles of CD30 in this process remain unclear. This study was conducted to determine the role of CD30 by stimulating CD30 expressed on HTLV-1-infected cell lines with CD30 ligand and observing its effects. CD30 stimulation increased multinucleated cells and inhibited proliferation of HTLV-1-infected cells. This inhibition was recovered by interruption of CD30 stimulation. Chromatin bridges found in multinucleated cells suggested DNA damage. CD30 stimulation triggered DNA double-strand breaks (DSBs) and chromosomal imbalances. CD30 stimulation induced reactive oxygen species (ROS), which induced DSBs. Generation of ROS and multinucleated cells by CD30 was dependent on phosphoinositide 3-kinase. RNA sequencing showed that CD30 stimulation produced significant changes in gene expression profiles, including upregulation of programmed death ligand 1 (PD-L1). Tax, which has also been shown to induce multinucleation and chromosomal instability, failed to induce CD30. These results suggest that induction of CD30, independent of Tax, triggers morphological abnormalities, chromosomal instability, and alteration of gene expression in HTLV-1-infected cells.

Adipose-Derived Stem Cells Improve Angiogenesis and Lymphangiogenesis in a Hypoxic Dermal Regeneration Model In Vitro.

Background and Objectives: Impaired wound healing represents an unsolved medical issue with a high impact on patients' quality of life and global health care. Even though hypoxia is a significant limiting factor for wound healing, it reveals stimulating effects in gene and protein expression at cellular levels. In particular, hypoxically treated human adipose tissue-derived stem cells (ASCs) have previously been used to stimulate tissue regeneration. Therefore, we hypothesized that they could promote lymphangiogenesis or angiogenesis. Materials and Methods: Dermal regeneration matrices were seeded with human umbilical vein endothelial cells (HUVECs) or human dermal lymphatic endothelial cells (LECs) that were merged with ASCs. Cultures were maintained for 24 h and 7 days under normoxic or hypoxic conditions. Finally, gene and protein expression were measured regarding subtypes of VEGF, corresponding receptors, and intracellular signaling pathways, especially hypoxia-inducible factor-mediated pathways using multiplex-RT-qPCR and ELISA assays. Results: All cell types reacted to hypoxia with an alteration of gene expression. In particular, vascular endothelial growth factor A (VEGFA), vascular endothelial growth factor B (VEGFB), vascular endothelial growth factor C (VEGFC), vascular endothelial growth factor receptor 1 (VEGFR1/FLT1), vascular endothelial growth factor receptor 2 (VEGFR2/KDR), vascular endothelial growth factor receptor 3 (VEGFR3/FLT4), and prospero homeobox 1 (PROX1) were overexpressed significantly depending on upregulation of hypoxia-inducible factor 1 alpha (HIF-1a). Moreover, co-cultures with ASCs showed a more intense change in gene and protein expression profiles and gained enhanced angiogenic and lymphangiogenic potential. In particular, long-term hypoxia led to continuous stimulation of HUVECs by ASCs. Conclusions: Our findings demonstrated the benefit of hypoxic conditioned ASCs in dermal regeneration concerning angiogenesis and lymphangiogenesis. Even a short hypoxic treatment of 24 h led to the stimulation of LECs and HUVECs in an ASC-co-culture. Long-term hypoxia showed a continuous influence on gene expressions. Therefore, this work emphasizes the supporting effects of hypoxia-conditioned-ASC-loaded collagen scaffolds on wound healing in dermal regeneration.

PD02-02 THE ROLE OF TRANSFORMING GROWTH FACTOR Β IN A PROSTATIC FIBROSIS UNDER SUPPRESSION OF DIHYDROTESTOSTERONE IN HIGH FAT DIET INDUCED OBESITY RAT MODEL

You have accessJournal of UrologyCME1 Apr 2023PD02-02 THE ROLE OF TRANSFORMING GROWTH FACTOR Β IN A PROSTATIC FIBROSIS UNDER SUPPRESSION OF DIHYDROTESTOSTERONE IN HIGH FAT DIET INDUCED OBESITY RAT MODEL Shinsuke Mizoguchi, Kenichi Mori, Hiromitsu Mimata, and Toshitaka Shin Shinsuke MizoguchiShinsuke Mizoguchi More articles by this author , Kenichi MoriKenichi Mori More articles by this author , Hiromitsu MimataHiromitsu Mimata More articles by this author , and Toshitaka ShinToshitaka Shin More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003219.02AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Although 5 alpha reductase inhibitors (5ARIs) can reduce prostatic volume by blocking production of dihydrotestosterone (DHT) and is widely used to treat symptomatic benign prostatic hyperplasia (BPH), the histological response to the treatment by 5ARIs is often heterogeneous and lower urinary tract symptoms can persist. Thus, a 5ARIs induced pathway related to treatment refractory is supposed to exist. To elucidate the pathways implicated to unsuccessful treatment for BPH patients, this study investigated changes in morphological and gene expression profiles in the prostate under DHT suppression using high fat diet induced obesity rat model. METHODS: Male Wistar rats at 8 weeks old were divided into four groups; rats with normal diet group (ND, n=5), rats with high fat diet induced obesity group (HFD, n=5), HFD treated by dutasteride (D, n=4), and HFD treated by dutasteride and tranilast (D+T, n=4), which is known to inhibit TGFβ. The high fat diet contains 32% fat. These rats were maintained for twelve weeks followed by two weeks treatment by oral administration of placebo or dutasteride (0.5 mg/kg) or tranilast (150 mg/kg) daily. Lateral lobes of prostate were harvested to evaluate prostatic weight, histological change and mRNA expression of IL1β and TGFβ in the prostate by qPCR. RESULTS: HFD showed significantly increased body weight, visceral fat and prostatic weight as well as significant upregulation of gene expressions in IL1β and TGFβ compared to ND. In contrast, HFD treated by dutasteride demonstrated significantly decreased prostatic weight in association with downregulation of IL1β and upregulation of TGFβ with compared to HFD with placebo. Furthermore, dutasteride administration induced prostatic fibrosis as evidenced by masson trichrome staining whereas the addition of tranilast to dutasteride suppressed prostatic tissue fibrosis in association with reduced weight of prostatic tissue and downregulation of TGFβ in group D+T compared to group D. CONCLUSIONS: This study demonstrated prostatic fibrosis in association with upregulation of TGFβ as well as decreased prostatic weight and improvement of prostatic fibrosis by TGFβ inhibition. These results suggest that TGFβ signaling has an important role in development of prostatic fibrosis under 5ARIs treatment possibly leading to treatment refractory. Therefore, TGFβ signaling pathway could be an therapeutic target for BPH. Source of Funding: JSPS KAKENHI Grant Number 20K18094 © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e69 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Shinsuke Mizoguchi More articles by this author Kenichi Mori More articles by this author Hiromitsu Mimata More articles by this author Toshitaka Shin More articles by this author Expand All Advertisement PDF downloadLoading ...

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

Oilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.