Expression Of Differentially Expressed Genes Research Articles

Abstract TMP112: Histological and Transcriptomic Analysis of Ischemic Stroke Thrombi Identifies Neutrophil Extracellular Trap Enrichment as an Indicator of First Pass Outcome

Introduction: Both histological and transcriptomic analyses of acute ischemic stroke (AIS) clots have identified features associated with mechanical thrombectomy (MT) outcome. However, few studies have explored how fluorescence histology and mRNA sequencing from the same clot can pinpoint specific biological phenomena associated with MT failure. Hypothesis: Joint analysis of paired clot immunofluorescence histology and mRNA sequencing will identify Neutrophil Extracellular Trap (NET) enrichment as a biomarker of MT first pass (FP) outcome. Methods: We performed paired histological and transcriptomic analysis of 32 stroke clots retrieved by MT (n=16 each of FP success and failure). Immunofluorescence histology was completed by co-staining 4µm clot tissue sections with antibodies against NET components (neutrophil elastase [ELANE], citrullinated histone [CitHis]) and super resolution imaging with instant structured illumination microscopy (ISIM) at 100X magnification. Differentially expressed genes (DEGs) were identified between transcriptomes of FP success and failure using the criteria of logFC≥1.5 and q<0.05. Principal component analysis (PCA) and Ingenuity Pathway Analysis (IPA) were completed to evaluate how well DEGs separated clots based on FP outcome and to identify enriched biological processes. Results: 44 DEGs were identified, most of which were downregulated in clots with successful FP. Expression of DEGs was able to separate clots by FP outcome. The NET signaling pathway was identified as the most enriched biological process in the FP failure group, with related genes downregulated in the FP success group. NETs were detected in clots with FP failure. Conclusion: Our results suggest that future multi-omic models, upon integration with pre-MT CT radiomics, can be developed to inform thrombolytic therapy and device selection, as well as predict FP outcome.

Effects of maternal Escherichia coli lipopolysaccharide exposure on offspring: insights from lncRNA analysis in laying hens

Parental living environment significantly impacts on offspring, yet related studies are lacking in livestock and poultry production. The present study found that lipopolysaccharide (LPS, Escherichia coli, 0.2 mg/kg) stimulation in F0 hens led to growth retardation and a decrease in egg-laying rate in the unchallenged F1 hens. Using strand-specific transcriptomic data of peripheral blood mononuclear cells (PBMCs) in F1 hens, we identified 100 differentially expressed lncRNAs (DELs) and 452 differentially expressed genes (DEGs). LPS primarily affected the metabolic pathways of the offspring, possibly reducing the egg-laying rate of the F1 hens by inhibiting the ferroptosis signaling pathway and the expression of DEGs involved, such as NCOA4, SLC40A1, STEAP3, and TFRC. Using Pearson correlation analysis, we constructed a lncRNA-mRNA-egg-laying rate regulation network and found that the newly identified lncRNA MSTRG.6500.1 and its positively regulated target genes (ENSGALT00000051184, ENSGALT00000053276, NPPA, OSBP2, and TRARG1) were significantly downregulated in the F1 LPS group, which might be the main reason for the decrease in egg-laying rate of the LPS group. These results provide important references for the study of growth and reproductive performance in laying hens, revealing the impact of parental living environment on animal health and production performance, and providing a theoretical basis for future related research and breeding practices.

Pan-cancer transcriptomic analysis reveals HSPB8 as a prognostic and immunological biomarker in colorectal cancer

Abstract Background Heat shock protein B8 (HSPB8) is implicated in autophagy, and its aberrant expression has been linked to both the initiation and progression of tumors. However, the role and function of HSPB8 in colorectal cancer (CRC) and across multiple cancer types remain unclear. This study aimed to map the transcriptome of autophagy-related genes in CRC and to conduct a pan-cancer analysis of HSPB8 as both a prognostic and immunological biomarker. Methods We performed bioinformatics analyses on GSE113513 and GSE74602 to identify differentially expressed genes (DEGs) in CRC. These DEGs were then compared with autophagy-related genes to identify critical overlapping genes. The Kaplan-Meier plotter was used to verify the expression of autophagy-linked DEGs and evaluate its prognostic value. The protein expression of Hub gene in CRC was analyzed using the Human Protein Atlas database. The cBioPortal was used to analyze the type and frequency of Hub gene mutations. The TIMER (Tumor Immune Estimation Resource) database was used to study the correlation between HSPB8 and immune infiltration in CRC. Results In total, 825 DEGs were identified, including 8 autophagy-linked DEGs: ATIC, MYC, HSPB8, TNFSF10, BCL2, TP53INP2, ITPR1, and NKX2-3. Survival analysis showed that increased HSPB8 expression significantly correlates with poor prognosis in patients with CRC (p < 0.05). HSPB8 was also found to be differentially expressed in various cancer types, correlating with both prognosis and immune infiltration. Further, changes in HSPB8 methylation and phosphorylation status were observed across several cancers, suggesting potential regulatory mechanisms. Therefore, HSPB8 may serve as a crucial prognostic and immunological biomarker in CRC and other cancers. Conclusions This study provides new insights into the role of autophagy-related genes in cancer progression and highlights HSPB8 as a potential target for cancer diagnostics and therapy.

Growth and physiological response of Yulu Hippophae rhamnoides to drought stress and its omics analysis

ABSTRACT Hippophae rhamnoides (H. rhamnoides) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of H. rhamnoides roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu H. rhamnoides was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu H. rhamnoides may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of H. rhamnoides were discussed in greater detail.

Identification of Oxidative Stress-Related Genes in Hyperlipidemia Based on Bioinformatic Analysis.

Oxidative stress(OS) is thought to mediate the processes of glycolipid disorders of a number of metabolic diseases and recent data suggest that OS may be involved in the pathophysiology of hyperlipidemia. The gene expression profiles of hyperlipidemia samples were downloaded from the Gene Expression Omnibus(GEO) database. Oxidative stress-related genes (ORGs) was the intersection of all valid data of discovery dataset and the ORGs in Genecards. The Differentially expressed genes(DEGs) between hyperlipidemia and control samples were obtained via "limma" R package, and differentially expressed oxidative stress-related genes (DEORGs) associated with hyperlipidemia were screened via OS gene sets. Gene Ontology (GO) and Kyoto encyclopaedia of Genes and Genomes (KEGG) enrichment analyses were performed to study the biological function of DEORGs, and protein-protein interaction(PPI) network analysis was conducted to screen hub genes. Then we constructed microRNA(miRNA), transcription factor (TF) and drug component targets network to explain the regulatory mechanism of ORGs in hyperlipidemia. After screening and evaluating we took GSE1010 as the discovery dataset and the GSE13985 as the validation set. There were 395 ORGs and 14 DEORGs retained from the hyperlipidemia. GO and KEGG results showed that DEORGs were mostly related to OS and lipid metabolism. Then, we used miRNA, TF, and drug component targets network to reveal the regulatory mechanism of hub genes. Finally, we verified expression of DEGs and hub gene in validation set. Our study has further confirmed the relationships between OS and hyperlipidemia, providing oxidative stress-related hub genes with possible function analysis and pathways summarized. These molecules might play a crucial role in the progression of hyperlipidemia and serve as potential biomarkers and therapeutic targets, giving us additional insight into the genes and the mechanism linking the OS system and metabolic disorders. We have not only proved hyperlipidemia is associated with OS but also gave foundation and reference for future researches.

Insulin Resistance Mediates the Association Between Vitamin D and Non-Alcoholic Fatty Liver Disease.

Vitamin D (VD) deficiency and insulin resistance (IR) increase the risk of non-alcoholic fatty liver disease (NAFLD), but few studies have explored the potential mechanisms by which IR mediates the association between VD and the pathogenesis of NAFLD at the genetic level using publicly available databases. This is a cross-sectional study, and we utilized the National Health and Nutrition Examination Survey (NHANES) dataset, as well as data from GSE200765 obtained from the Gene Expression Omnibus (GEO) website. A total of 723 individuals who had completed liver ultrasound examination and the detection of VD levels were included in the final analysis. A gene expression dataset, GSE200765, was also downloaded from the GEO website, to explore the potential mechanism of VD and NAFLD. In the NHANES data, covariates significantly differed in four VD categories, and the controlled attenuation parameter (CAP), vibration-controlled transient elastography-liver stiffness measurement (VCTE-LSM), and IR were reduced with an increase in VD levels. Mediation analysis revealed that IR mediated the association between VD and both CAP and LSM, and the estimated mediation effects were 29.0% and 39.8%, respectively. Bioinformatics analysis showed that seven differentially expressed genes (DEGs) (solute carrier family 2 member 2 [SLC2A2], protein phosphatase 1 regulatory subunit 3E [PPP1R3E], CAMP responsive element binding protein 3-like 3 [CREB3L3], Interleukin-6 [IL-6], peroxisome proliferator-activated receptor gamma coactivator 1-alpha [PPARGC1A], nuclear factor kappa B inhibitor alpha [NFKBIA], and phosphoenolpyruvate carboxykinase 2 [PCK2]) were enriched in the IR pathway in comparison groups (VD group vs. lipid group), suggesting that VD improved NAFLD via changed IR. VD deficiency and IR were the risk factors for NAFLD, and increased VD levels improved the status of NAFLD. The underlying mechanism may be that elevated VD levels reduced IR, which improved the expression of DEGs involved in the IR pathway.

Lactiplantibacillus plantarum Ameliorated Morphological Damage and Barrier Dysfunction and Reduced Apoptosis and Ferroptosis in the Jejunum of Oxidatively Stressed Piglets.

Oxidative stress induces apoptosis and ferroptosis, leading to intestinal injury of piglets. Lactiplantibacillus plantarum P8 (P8) has antioxidant capacity, but its roles in intestinal apoptosis and ferroptosis remain unclear. Here, 24 weaned piglets were assigned to three treatments: control (Con), diquat injection (DQ), and P8 supplementation + DQ injection (DQ + P8). The results showed that the increased jejunal oxidative stress, jejunal morphology impairment, and barrier dysfunction in the DQ-treated piglets were decreased by P8 supplementation. TUNEL and apoptosis-related gene expressions showed increased jejunal apoptosis of DQ-treated piglets; however, reduced apoptosis was observed in the DQ + P8 group. In addition, the mitochondrial morphology and ferroptosis-related gene expressions indicated elevated jejunal ferroptosis in the DQ-treated piglets, and the DQ + P8 treatment attenuated the ferroptosis. Transcriptome identified various differentially expressed genes (DEGs) between different treatments. KEGG analysis indicated that the DEGs were enriched in the PI3K-AKT, NF-κB, and apoptosis pathways. The expressions of key DEGs and key proteins in the PI3K-AKT and NF-κB pathways were further verified. In summary, our results indicate that P8 supplementation ameliorated jejunal oxidative stress, morphological damage, barrier dysfunction, apoptosis, and ferroptosis in the DQ-treated piglets. Moreover, the beneficial effect of P8 may be related to the regulation of PI3K/AKT and NF-κB pathways.

Transcriptomic Profiling Unravels the Disruption of Photosynthesis Apparatuses and Induction of Immune Responses by a Bipartite Begomovirus in Tomato Plants.

Diseases caused by begomoviruses such as tomato yellow leaf curl disease (TYLCD) are major constraints in agriculture. While the interactions between plants and monopartite begomoviruses during TYLCD pathogenesis have been explored extensively, how bipartite begomoviruses interact with tomato plants are understudied. Here we first found that a bipartite begomovirus tomato yellow leaf curl Thailand virus (TYLCTHV) induced stunted growth, leaf curl and yellowing in tomato plants. We then profiled the tomato transcriptomic changes in response to TYLCTHV infection. In total, we identified 2322 upregulated and 1377 downregulated genes. KEGG enrichment analysis of the differentially expressed genes (DEGs) revealed that many KEGG pathways regulating plant photosynthesis processes and defenses were enriched. Specifically, TYLCTHV infection disrupted the expression of DEGs that function in the light-harvesting chlorophyll protein complex, photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase. Additionally, the expression of many DEGs regulating plant defenses including pathogen-associated molecular pattern (PAMP)-triggered immunity, effector-triggered immunity and hypersensitive response was upregulated upon TYLCTHV infection. Taken together, we found that during the pathogenesis of TYLCD induced by TYLCTHV, the virus actively disrupts plant photosynthesis processes and induces defense responses. Our findings add to our knowledge of TYLCD pathogenesis and plant-virus interactions in general.

Transcriptome profiling uncovers differentially expressed genes linked to nutritional quality in vegetable soybean.

Vegetative soybean (maodou or edamame) serves as a nutrient-rich food source with significant potential for mitigating global nutritional deficiencies. This study undertook a thorough examination of the nutritional profiles and transcriptomic landscapes of six soybean cultivars, including three common cultivars (Heinong551, Heinong562, and Heinong63) and three fresh maodou cultivars (Heinong527, HeinongXS4, and HeinongXS5). Nutrient analysis of the seeds disclosed notable differences in the levels of protein, fat, soluble sugars, vitamin E, calcium, potassium, magnesium, manganese, iron, and zinc across the cultivars. Through comparative transcriptome profiling and RNA sequencing, distinct variations in differentially expressed genes (DEGs) were identified between fresh and traditional maodou cultivars. Functional enrichment analyses underscored the involvement of DEGs in critical biological processes, such as nutrient biosynthesis, seed development, and stress responses. Additionally, association studies demonstrated robust correlations between specific DEG expression patterns and seed nutrient compositions across the different cultivars. Sankey diagrams illustrated that DEGs are strongly linked with seed quality traits, revealing potential molecular determinants that govern variations in nutritional content. The identified DEGs and their relationships with nutritional profiles offer valuable insights for breeding programs focused on developing cultivars with improved nutritional quality, tailored to specific dietary needs or industrial applications.

Deciphering Carotenoid and Flowering Pathway Gene Variations in Eastern and Western Carrots (Daucus carota L.).

Carrot is a major root vegetable in the Apiaceae owing to its abundant carotenoids, antioxidants, vitamins, and minerals. The modern dark orange western carrot was derived from sequential domestication events from the white-rooted wild form to the pale orange-, purple-, or yellow-rooted eastern carrot. Genetic and molecular studies between eastern and western carrots are meager despite their evolutionary relatedness. Twelve RNA seq libraries obtained from distinct eastern and western cultivars at vegetative and reproductive developmental stages were utilized to identify differentially expressed genes (DEGs) to decode the key molecular genetic changes in carotenoid and flowering pathways. In the carotenoid pathway, an upregulation of the PSY, CRTISO, and LCYE genes was observed in the western cultivar, while the eastern cultivar exhibited a higher abundance of downstream enzymes, particularly CCD and NCED1. These later enzymes are crucial in linking apocarotenoids and xanthin-mediated ABA signaling. In the flowering pathway, we noted a greater expression of DEGs associated with the photoperiod and vernalization pathways in the western cultivar. In contrast, the eastern cultivar displayed a dominance of genes from the autonomous pathway (FLD, LD, FLK, and PEBP) that function to repress FLC. The experimental validation of 12 key genes through quantitative real-time PCR further confirms their functional role in carrots. The identified key regulatory genes in these major pathways are valuable for designing breeding strategies for manipulating carotenoid content and flowering time while developing climate-specific carrots. The knowledge of carotenoid and flowering pathways is advantageous in producing nutritionally improved roots and seeds in carrots across diverse climates.

Investigation of GPM6B as a novel therapeutic target in Osteoarthritis

BackgroundOsteoarthritis (OA) is the most common motor system disease in older people, characterized by a high incidence and significant social and economic burden. Women have a higher risk of OA, more severe clinical symptoms, and a higher rate of disabilities than men. However, the pathogenesis of OA remains unclear. Therefore, we screened for differentially expressed genes (DEGs) in OA patients of different sex and searched for new targets that may be involved in regulating the development of OA.MethodsThe study compared the expression of DEGs in synovial fluid exosomes between male and female patients with OA through RNA sequencing combined with bioinformatics analysis using public data. To evaluate the screened DEGs, synovial tissue and fluid samples were obtained from patients with OA who underwent joint replacement surgery. SiRNA-mediated knockdown in vitro experiments were performed to investigate the role of glycoprotein membrane 6B (GPM6B). Meanwhile, GPM6B gene knockout mice were used to assess the in vivo pathological roles of GPM6B in OA.ResultsThe results revealed that GPM6B is a potential target associated with OA. Immunofluorescence staining demonstrated that GPM6B was expressed in fibroblast-like synoviocytes (FLS) and macrophage-like synoviocytes in patients with OA. In vitro experiments confirmed that GPM6B knockdown can reduce the expression of inflammatory factors in primary FLS from patients with OA. Under inflammatory conditions, GPM6B knockdown can reduce the expression of matrix metalloproteinases as well as proliferation of FLS. In addition, using a destabilization of the medial meniscus-induced OA model, we revealed that GPM6B is associated with OA progression in mice.ConclusionThus, we provided evidence that GPM6B act as a new target associated with OA.

Transcriptomic analysis reveals the mechanism underlying salinity-induced morphological changes in Skeletonema subsalsum.

Diatom cell walls are diverse and unique, providing the basis for species identification and supporting the ecological and economic value of diatoms. However, these important structures sometimes change in response to environmental fluctuations, especially under salt adaptation. Although studies have shown that salinity induces morphological plasticity changes in diatom cell walls, most research has focused on physiological responses rather than molecular mechanisms. In this study, Skeletonema subsalsum was cultured under four salinity conditions (0, 3, 6, 12). Through morphological and physiological methods, we found that salinity increased the cell diameter, protrusion lengths, distance between adjacent cells (DBCs), and nanopore size, while reducing cell height and silicification degree. To further investigate the mechanism underlying morphological changes in S. subsalsum, complementary transcriptome analysis was performed. In total, 20,138 differentially expressed genes (DEGs) were identified among the four treatments. Among them, 231 DEGs were screened and found to be closely associated with morphological changes, of which 107 were downregulated and 124 were upregulated. The findings demonstrated that elevated salinity inhibited silicon transport and deposition via downregulating the expression of DEGs involved in functions including chitin metabolism, putrescine metabolism, and vesicle transport, resulting in reduced silicon content and cell height. Increased salinity promoted the expression of DEGs related to microtubules (MTs), actin, and ubiquitin, which synchronously induced morphological changes. These findings provide a more comprehensive understanding of the salt tolerance of algae and a foundation for future studies on cell wall morphogenesis.

Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets.

The forkhead box (FOX) family members regulate gene transcription and expression. FOX family members regulate various biological processes, such as cell proliferation and tumorigenesis. FOXD, a FOX protein subfamily, is associated with poor prognosis for various cancers. However, the potential clinical value of FOXD subfamily members in colorectal cancer (CRC) has not yet been elucidated. Therefore, in this study, we aimed to determine the role of the FOXD subfamily members in CRC development. Using HTSeq-count data, clinical data, and single-nucleotide polymorphisms (obtained from The Cancer Genome Atlas Project), and bioinformatics analyses (using DESEQ2 software), we identified differentially expressed genes (DEGs) in CRC. Next, each DEG expression was validated in vitro using reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry (IHC). Among the FOXD subfamily members, the area under the receiver operating characteristic curve of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. Gene Set Enrichment Analysis revealed that FOXD-DEGs were mainly related to pathways such as cytokine, cytokine, and extracellular matrix receptor interactions. Kaplan-Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. In conclusion, FOXD subfamily members (especially FOXD3) could serve as diagnostic and prognostic biomarkers for CRC and an immunotherapy target in patients with CRC.

Integration of Transcriptome and Metabolome Reveals Wax Serves a Key Role in Preventing Leaf Water Loss in Goji (Lycium barbarum)

Drought stress is one of the main abiotic stresses that limit plant growth and affect fruit quality and yield. Plants primarily lose water through leaf transpiration, and wax effectively reduces the rate of water loss from the leaves. However, the relationship between water loss and the wax formation mechanism in goji (Lycium barbarum) leaves remains unclear. ‘Ningqi I’ goji and ‘Huangguo’ goji are two common varieties. In this study, ‘Ningqi I’ goji and ‘Huangguo’ goji were used as samples of leaf material to detect the differences in the water loss rate, chlorophyll leaching rate, wax phenotype, wax content, and components of the two materials. The differences in wax-synthesis-related pathways were analyzed using the transcriptome and metabolome methods, and the correlation among the wax components, wax synthesis genes, and transcription factors was analyzed. The results show that the leaf permeability of ‘Ningqi I’ goji was significantly lower than that of ‘Huangguo’ goji. The total wax content of the ‘Ningqi I’ goji leaves was 2.32 times that of the ‘Huangguo’ goji leaves, and the epidermal wax membrane was dense. The main components of the wax of ‘Ningqi I’ goji were alkanes, alcohols, esters, and fatty acids, the amounts of which were 191.65%, 153.01%, 6.09%, and 9.56% higher than those of ‘Huangguo’ goji, respectively. In the transcriptome analysis, twenty-two differentially expressed genes (DEGs) and six transcription factors (TFs) were screened for wax synthesis; during the metabolomics analysis, 11 differential metabolites were screened, which were dominated by lipids, some of which, like D-Glucaro-1, 4-Lactone, phosphatidic acid (PA), and phosphatidylcholine (PE), serve as prerequisites for wax synthesis, and were significantly positively correlated with wax components such as alkanes by the correlation analysis. A combined omics analysis showed that DEGs such as LbaWSD1, LbaKCS1, and LbaFAR2, and transcription factors such as LbaMYB306, LbaMYB60, and LbaMYBS3 were strongly correlated with wax components such as alkanes and alcohols. The high expression of DEGs and transcription factors is an important reason for the high wax content in the leaf epidermis of ‘Ningqi I’ goji plants. Therefore, by regulating the expression of wax-synthesis-related genes, the accumulation of leaf epidermal wax can be promoted, and the epidermal permeability of goji leaves can be weakened, thereby reducing the water loss rate of goji leaves. The research results can lay a foundation for cultivating drought-tolerant goji varieties.

Transcriptomic profiling reveals the effect of amino acid metabolism on the production capacity of Volvariella volvacea during repeated subculture

Tissue separation is commonly employed for the purification and rejuvenation of edible mushroom species. However, repeated or continuous tissue separation can result in strain degradation. In this study, cultivation experiments were conducted in Volvariella volvacea V844 (T0). Tissue separation subculture was repeated 16 times to obtain the succession strains T1–T16. Of these, T4, T8, T12, and T16 were selected as experimental strains, and their production traits were evaluated. Additionally, transcriptome sequencing technology was used to analyze the transcription spectrum of these strains. The results showed that with the increase in subculture cycles, the colony diameter, mycelial growth rate, mycelial biomass, and biological efficiency of V. volvacea first increased and then decreased, and the growth cycle was gradually prolonged. Transcriptome sequencing revealed the presence of 1375, 1015, 651, and 1648 differentially expressed genes (DEGs) in T4, T8, T12, and T16, respectively, versus T0. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis demonstrated that these DEGs were mainly involved in amino acid metabolic pathways. Further annotation analysis revealed that in V. volvacea subculture strains, the number of DEGs involved in histidine metabolism (Ko00340) and arginine and proline metabolism (Ko00330) was the highest. Amino acid analysis demonstrated that the proline and arginine content first rose and then fell across successive subculture strains, whereas the histidine content first decreased and then increased. The results indicated that the change in the production capacity of V. volvacea during repeated subculture may be due to the altered expression of DEGs involved in amino acid metabolism, leading to changes in the amino acid content of V. volvacea and further affecting the accumulation of reactive oxygen species, free radical scavenging, energy acquisition, nutrient absorption, and redox balance. These changes could result in the rejuvenation (<8) of the V. volvacea strain or cause its degradation (>12). The results of this study provide a theoretical framework for studying the mechanisms of rejuvenation and degradation in V. volvacea and also offer insights valuable for studying the molecular functions of genes involved in the growth of V. volvacea and other edible fungi.

Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs

BackgroundBackfat serves as a vital fat reservoir in pigs, and its excessive accumulation will adversely impact pig growth performance, farming efficiency, and pork quality. The aim of this research is to integrate assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to explore the molecular mechanisms underlying porcine backfat deposition.ResultsATAC-seq analysis identified 568 genes originating from 698 regions exhibiting differential accessibility, which were significantly enriched in pathways pertinent to adipocyte differentiation and lipid metabolism. Besides, a total of 283 transcription factors (TFs) were identified by motif analysis. RNA-seq analysis revealed 978 differentially expressed genes (DEGs), which were enriched in pathways related to energy metabolism, cell cycle and signal transduction. The integration of ATAC-seq and RNA-seq data indicates that DEG expression levels are associated with chromatin accessibility. This comprehensive study highlights the involvement of critical pathways, including the Wnt signaling pathway, Jak-STAT signaling pathway, and fatty acid degradation, in the regulation of backfat deposition. Through rigorous analysis, we identified several candidate genes (LEP, CTBP2, EHHADH, OSMR, TCF7L2, BCL2, FGF1, UCP2, CCND1, TIMP1, and VDR) as potentially significant contributors to backfat deposition. Additionally, we constructed TF-TF and TF-target gene regulatory networks and identified a series of potential TFs related to backfat deposition (FOS, STAT3, SMAD3, and ESR1).ConclusionsThis study represents the first application of ATAC-seq and RNA-seq, affording a novel perspective into the mechanisms underlying backfat deposition and providing invaluable resources for the enhancement of pig breeding programs.

Transcriptome analysis unveils PLSCR1 associated with microglial polarization in neuropathic pain

Neuropathic pain (NP) continues to be a significant problem that lacks effective treatment. Our study sought to explore a new promising gene target for the treatment of NP. Differential and enrichment analyses were performed on 24,197 genes and 12,088 genes from the NP microglial microarray and sequencing dataset. Candidate differentially expressed genes (DEGs), functions, and signaling pathways that are closely related to NP were identified by analyzing the bioinformatic results. For in vivo experiments, mice were divided into the sham and NP groups. The expressions of DEGs were validated to screen out the NP hub genes. For in vitro experiments, the hub genes in resting M0-BV2 and polarized M1-BV2 microglia were examined by immunofluorescence, flow cytometry, and qRT-PCR. DEGs in the NP microarray and sequencing data shared five candidate genes, CD244, MEGF9, PCGF2, PLSCR1, and NECAB2. The results of the in vivo experiment showed that the NP model group exhibited higher expression of PLSCR1 and MEGF9 compared to the sham group. The enrichment results of the DEGs revealed the biological processes of “response to lipopolysaccharide”. PLSCR1 was highly expressed in the lipopolysaccharide-induced M1-BV2 microglia. PLSCR1 is a potential gene associated with microglial polarization in NP. These findings provide a new view on understanding the pathogenesis mechanism of NP.

MME and PTPRC: key renal biomarkers in lupus nephritis

Background Lupus nephritis (LN) is an autoimmune-related kidney disease with a poor prognosis, however the potential pathogenic mechanism remains unclear and there is a lack of precise biomarkers. Therefore, a thorough screening and identification of renal markers in LN are immensely beneficial to the research on its pathogenic mechanisms and treatment strategies. Methods We utilized bioinformatics to analyze the differentially expressed genes (DEGs) at the transcriptome level of three clusters: total renal, glomeruli, and renal tubulointerstitium in the GEO database to discover potential renal biomarkers of LN. We utilized NephroSeq datasets and measured mRNA and protein levels in the kidneys of MRL/lpr mice to confirm the expression of key DEGs. Results Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis. The seven hot differential genes were verified to have consistent change trends using three datasets from NephroSeq database. The receiver operating characteristic (ROC) curve indicated that five DEGs (PTPRC, MX1, EGR1, MME and RORC) exhibited a higher diagnostic ROC value in both the glomerulus and tubulointerstitium group. Validation of core genes using MRL/lpr mice showed that MME and PTPRC exhibit significantly differential mRNA and protein expression patterns in mouse kidneys like the datasets. Conclusions This study identified seven key renal biomarkers through bioinformatics analysis using the GEO and NephroSeq databases. It was identified that MME and PTPRC may have a high predictive value as renal biomarkers in the pathogenesis of LN, as confirmed by animal validation.

Transcriptomic analysis unveils alterations in the genetic expression profile of tree peony (Paeonia suffruticosa Andrews) infected by Alternaria alternata

BackgroundBlack spot disease in tree peony caused by the fungal necrotroph A. alternata, is a primary limiting factor in the production of the tree peony. The intricate molecular mechanisms underlying the tree peony resistance to A. alternata have not been thoroughly investigated.ResultsThe present study utilized high-throughput RNA sequencing (RNA-seq) technology to conduct global expression profiling, revealing an intricate network of genes implicated in the interaction between tree peony and A. alternata. RNA-Seq libraries were constructed from leaf samples and high-throughput sequenced using the BGISEQ-500 sequencing platform. Six distinct libraries were characterized. M1, M2 and M3 were derived from leaves that had undergone mock inoculation, while I1, I2 and I3 originated from leaves that had been inoculated with the pathogen. A range of 10.22–11.80 gigabases (Gb) of clean bases were generated, comprising 68,131,232 − 78,633,602 clean bases and 56,677 − 68,996 Unigenes. A grand total of 99,721 Unigenes were acquired, boasting a mean length of 1,266 base pairs. All these 99,721 Unigenes were annotated in various databases, including NR (Non-Redundant, 61.99%), NT (Nucleotide, 45.50%), SwissProt (46.32%), KEGG (Kyoto Encyclopedia of Genes and Genomes, 49.33%), KOG (clusters of euKaryotic Orthologous Groups, 50.18%), Pfam (Protein family, 47.16%), and GO (Gene Ontology, 34.86%). In total, 66,641 (66.83%) Unigenes had matches in at least one database. By conducting a comparative transcriptome analysis of the mock- and A. alternata-infected sample libraries, we found differentially expressed genes (DEGs) that are related to phytohormone signalling, pathogen recognition, active oxygen generation, and circadian rhythm regulation. Furthermore, multiple different kinds of transcription factors were identified. The expression levels of 10 selected genes were validated employing qRT-PCR (quantitative real-time PCR) to confirm RNA-Seq data.ConclusionsA multitude of transcriptome sequences have been generated, thus offering a valuable genetic repository for further scholarly exploration on the immune mechanisms underlying the tree peony infected by A. alternata. While the expression of most DEGs increased, a few DEGs showed decreased expression.

The consistently up-regulated expression of NLRP3 in severe asthma patients from mRNA microarray and ovalbumin-induced mouse model of asthma.

Severe asthma (SA) is a chronic lung disease, resistant to current treatments, symbolized by repeated symptoms of reversible airflow obstruction, airway hyper-responsiveness, and inflammation. The aim of this study was to identify genes exhibiting differential expression in individuals without asthma and SA patients. We aimed to pinpoint hub differentially expressed genes (DEGs) by utilizing a mouse model of asthma sensitized to ovalbumin (OVA). Microarray data for SA were acquired from the Gene Expression Omnibus (GEO) databases. DEGs were identified, and functional enrichment analyses were carried out. STRING and Cytoscape were utilized to design a protein-protein interaction (PPI) network and conduct module analysis. An OVA-induced asthma mice model was established. Lung tissue from the mice was collected for quantitative reverse transcription polymerase chain reaction (qRT-PCR), Western blot, and immunohistochemistry (IHC) to assess the expression of DEGs. A total of 545 DEGs were identified, among which 172 genes were upregulated in SA patients compared to healthy controls. The nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) was significantly up-regulated in SA patients [adjusted P value (Padj) =0.001]. Analysis of lung tissue using qRT-PCR, western blot, and IHC revealed higher expression of NLRP3 in OVA-induced asthma mice compared to the control group. Enrichment analysis suggests the involvement of NLRP3 in pathways related to pyroptosis, c-type lectin receptor signaling, and NOD-like receptor signaling. Through bioinformatics analysis, we identified a multitude of DEGs that could potentially contribute significantly to the development of SA. Notably, our findings highlight NLRP3 as a potential pivotal player in asthma pathogenesis, underscoring its prospective utility as a biomarker for SA.