Combined Transcriptome Research Articles

Integrated Transcriptomics and Metabolomics Analysis Reveals the Effects of Cutting on the Synthesis of Flavonoids and Saponins in Chinese Herbal Medicine Astragalus mongholious.

Astragali Radix, derived from the roots of Astragalus mongholicus, is a traditional Chinese medicine containing flavonoids and saponins as its key ingredients. With a shortage in the wild sources of the herbal plant, it is especially important to explore a cultivation mode for A. mongholicus for medicinal purposes. Cutting, a physical environmental stress method, was used in this study with the objective of improving the quality of this herbal legume. We found that cutting of the top 1/3 of the aboveground part of A. mongholicus during the fruiting period resulted in a significant increase in the content of flavonoids and saponins, as well as in root growth, including length, diameter, and dry weight. Furthermore, the leaves were sampled and analyzed using a combined transcriptome and metabolome analysis approach at five different time points after the treatment. Sixteen differentially expressed unigenes (DEGs) involved in the biosynthesis of flavonoids were identified; these were found to stimulate the synthesis of flavonoids such as formononetin and calycosin-7-O-β-D-glucoside. Moreover, we identified 10 DEGs that were associated with the biosynthesis of saponins, including astragaloside IV and soyasaponin I, and found that they only regulated the mevalonic acid (MVA) pathway. These findings provide new insights into cultivating high-quality A. mongholicus, which could potentially alleviate the scarcity of this valuable medicinal plant.

Single-cell N6-methyladenosine-related genes function within the tumor microenvironment to affect the prognosis and treatment sensitivity in patients with gastric cancer

BackgroundGastric cancer (GC) ranks fifth for morbidity and third for mortality worldwide. The N6-methyladenosine (m6A) mRNA methylation is crucial in cancer biology and progression. However, the relationship between m6A methylation and gastric tumor microenvironment (TME) remains to be elucidated.MethodsWe combined single-cell and bulk transcriptome analyses to explore the roles of m6A-related genes (MRG) in gastric TME.ResultsNine TME cell subtypes were identified from 23 samples. Fibroblasts were further grouped into four subclusters according to different cell markers. M6A-mediated fibroblasts may guide extensive intracellular communications in the gastric TME. The m6A-related genes score (MRGs) was output based on six differentially expressed single-cell m6A-related genes (SCMRDEGs), including GHRL, COL4A1, CAV1, GJA1, TIMP1, and IGFBP3. The protein expression level was assessed by immunohistochemistry. We identified the prognostic value of MRGs and constructed a nomogram model to predict GC patients’ overall survival. MRGs may affect treatment sensitivity in GC patients.ConclusionOur study visualized the cellular heterogeneity of TME at the single-cell level, revealed the association between m6A mRNA modification and intracellular communication, clarified MRGs as an independent risk factor of prognosis, and provided a reference for follow-up treatment.

MUCIN MRNA ISOFORM SIGNATURES AS POTENTIAL NOVEL BIOMARKERS TO EVALUATE DISEASE STATUS IN PATIENTS WITH INFLAMMATORY BOWEL DISEASES

Abstract Mucosal barrier dysfunction and aberrant mucin expression are major hallmarks in the pathophysiology of IBD. Mucins are highly polymorphic, and the presence of genetic differences can alter gene expression, resulting in several mRNA isoforms via alternative splicing. While most isoforms encode similar biological functions, others alter protein function, potentially resulting in progression towards disease. Currently, little attention has been given to the importance of mucin mRNA isoforms in IBD. The aim of our study is to investigate the potential of mucin mRNA isoforms as novel biomarkers for the evaluation of IBD activity and subtypes. To obtain this goal, RNA was extracted from colonic and terminal ileal biopsies of IBD patients that underwent an endoscopy at the Antwerp University Hospital (UZA). Additionally, patients without a history of IBD undergoing an endoscopy due to a positive iFOBT which show no endoscopic abnormalities, were included as controls. Library preparation was performed with the PacBio Iso-Seq multiplex protocol adapted for targeted transcriptome sequencing. Targeted capture was accomplished by using a custom-designed pool of probes, developed for the capture of all mucin gene transcripts. Samples were sequenced on the PacBio Sequel platform at the University of Antwerp. The data was analyzed by using the isoseq3-pipeline and additional filtering with SQANTI3 was performed. In total 106 biopsies were sequenced on the PacBio platform. The resulting intestinal mucin transcriptome was merged with the human reference transcriptome. On this combined mucin transcriptome Illumina bulk RNA sequencing data from over 2000 intestinal biopsies (GEO dataset GSE193677) were mapped to determine mucin isoform expression. An external dataset (GEO dataset GSE165512) was used for additional validation. A classification random forest was trained on this data to distinguish inflamed IBD from non-inflamed control patients based on the mucin isoform expression alone. The model performed well on train and test datasets but decreased in the external validation (Table 1). Dividing the samples based on disease phenotype greatly increases performance on the external validation dataset (Table 1). When only training on ileal biopsies, the model proved to be excellent in distinguishing Crohn’s disease patients from controls (Table 1). Classification of inflamed ulcerative colitis from control patients based on only the biopsies from the distal colon was similar to the latter (Table 1). Our machine learning model was able to distinguish Crohn’s disease from control patients and ulcerative colitis from control patients based on mucin mRNA isoform expression. In addition, our data suggests that the mucin isoform expression may vary between different regions within the colon. Table 1 Area under the receiver operator curve (AUCROC) from a random forest classifier trained on mucin isoform expression of inflamed biopsies of IBD and non-inflamed control patients.

Network Analysis of Metabolome and Transcriptome Revealed Regulation of Different Nitrogen Concentrations on Hybrid Poplar Cambium Development.

Secondary development is a key biological characteristic of woody plants and the basis of wood formation. Exogenous nitrogen can affect the secondary growth of poplar, and some regulatory mechanisms have been found in the secondary xylem. However, the effect of nitrogen on cambium has not been reported. Herein, we investigated the effects of different nitrogen concentrations on cambium development using combined transcriptome and metabolome analysis. The results show that, compared with 1 mM NH4NO3 (M), the layers of hybrid poplar cambium cells decreased under the 0.15 mM NH4NO3 (L) and 0.3 mM NH4NO3 (LM) treatments. However, there was no difference in the layers of hybrid poplar cambium cells under the 3 mM NH4NO3 (HM) and 5 mM NH4NO3 (H) treatments. Totals of 2365, 824, 649 and 398 DEGs were identified in the M versus (vs.) L, M vs. LM, M vs. HM and M vs. H groups, respectively. Expression profile analysis of the DEGs showed that exogenous nitrogen affected the gene expression involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the starch and sucrose metabolism pathway and the ubiquitin-mediated proteolysis pathway. In M vs. L, M vs. LM, M vs. HM and M vs. H, differential metabolites were enriched in flavonoids, lignans, coumarins and saccharides. The combined analysis of the transcriptome and metabolome showed that some genes and metabolites in plant hormone signal transduction, phenylpropanoid biosynthesis and starch and sucrose metabolism pathways may be involved in nitrogen regulation in cambium development, whose functions need to be verified. In this study, from the point of view that nitrogen influences cambium development to regulate wood formation, the network analysis of the transcriptome and metabolomics of cambium under different nitrogen supply levels was studied for the first time, revealing the potential regulatory and metabolic mechanisms involved in this process and providing new insights into the effects of nitrogen on wood development.

Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics

The consensus molecular subtypes (CMS) of colorectal cancer (CRC) is the most widely-used gene expression-based classification and has contributed to a better understanding of disease heterogeneity and prognosis. Nevertheless, CMS intratumoral heterogeneity restricts its clinical application, stressing the necessity of further characterizing the composition and architecture of CRC. Here, we used Spatial Transcriptomics (ST) in combination with single-cell RNA sequencing (scRNA-seq) to decipher the spatially resolved cellular and molecular composition of CRC. In addition to mapping the intratumoral heterogeneity of CMS and their microenvironment, we identified cell communication events in the tumor-stroma interface of CMS2 carcinomas. This includes tumor growth-inhibiting as well as -activating signals, such as the potential regulation of the ETV4 transcriptional activity by DCN or the PLAU-PLAUR ligand-receptor interaction. Our study illustrates the potential of ST to resolve CRC molecular heterogeneity and thereby help advance personalized therapy.

Characterization of yellow‐green leaf1 mutant for improved phosphorus use efficiency and rapid offspring screening in Tartary buckwheat

AbstractLeaf color mutations provide valuable genetic resources for elucidating the molecular regulatory mechanisms of plant growth and serve as efficient tools for screening offspring in crossbreeding. In this study, a Tartary buckwheat (Fagopyrum tataricum) mutant with yellow‐green leaves (yl1) was isolated from 60Co‐γ‐radiation mutation bank. Compared to wild type (WT), yl1 showed similar biomass and yield, despite a lower chlorophyll content and net photosynthetic rate. However, yl1 displayed significantly higher total phosphorus content after 14 days of medium and low phosphorus treatment. By using yl1 as the maternal parent, hybrid offspring could be visually distinguished at the cotyledon stage. Genetic analysis revealed that the yl1 phenotype was attributed to a single recessive mutation. Combined metabolome and transcriptome analysis identified 205 differential expressed metabolites (DEMs) and 123 differential expressed genes enriched in 30 pathways or metabolisms between yl1 and WT. Remarkably, the upregulation of SPX3, 5PTase2, PHO1, PAP3, PAP2, PAP7, and IPAP16, which are involved in enhancing phosphorus absorption, assimilation, transport, and remobilization, along with PLDζ1, GDPD1, MGD2, and NPC4L, which contribute to improving lipid metabolism, collectively resulted in high accumulation of 41 phosphorus‐containing DEMs (including 37 lipids) in yl1. This study emphasizes the potential of yl1 for effective screening of offspring and uncovers the interplay between photosynthesis and lipid metabolism, providing valuable insights to improve phosphorus use efficiency in Tartary buckwheat.

Characterization key genes of Arabidopsis seedlings in response to β-caryophyllene, eugenol using combined transcriptome and WGCN analysis.

Weeds present a significant challenge to high crop yield and quality. In our study, we investigated the phytotoxic activity of β-caryophyllene (BCP) and eugenol, which are natural allelopathic chemical compounds, on Arabidopsis seedlings. We found that these compounds inhibited the growth of Arabidopsis thaliana plants. When either BCP or eugenol was applied, it led to decrease in the content of cell wall components such as lignin, cellulose, hemicellulose, and pectin; and increase in the levels of endogenous hormones like ETH, ABA, SA, and JA in the seedlings. Through transcriptome profiling, we identified 7181 differentially expressed genes (DEGs) in the roots and shoots that were induced by BCP or eugenol. The genes involved in the synthesis of lignin, cellulose, hemicellulose, and pectin were down-regulated, whereas genes related to synthesis and signal transduction of ABA, ETH, SA, and JA were up-regulated. However, genes related to IAA synthesis and signal transduction were found to be down-regulated. Furthermore, we characterized 24 hub genes using Weighted Correlation Network Analysis (WGCNA). Among them, the identified 16 genes in response to BCP was primarily associated with hypoxia stress, while 8 genes induced by eugenol were linked to inhibition of cell division. Our results suggested that BCP and eugenol had ability to target multiple genes to inhibit growth and development of Arabidopsis plants. Therefore, they can serve as excellent candidates for natural biological herbicides.

T-Cell-Based Platform for Functional Screening of T-Cell Receptors Identified in Single-Cell RNA Sequencing Data Sets of Tumor-Infiltrating T-Cells.

The advent of single-cell RNA sequencing (scRNAseq) has enabled in-depth gene expression analysis of several thousand cells isolated from tissues. We recently reported the application of scRNAseq toward the dissection of the tumor-infiltrating T-cell repertoire in human pancreatic cancer samples. In this study, we demonstrated that combined whole transcriptome and T-cell receptor (TCR) sequencing provides an effective way to identify tumor-reactive TCR clonotypes on the basis of gene expression signatures. An important aspect in this respect was the experimental validation of TCR-mediated anti-tumor reactivity by means of an in vitro functional assay, which is the subject of the present protocol. This assay involves the transient transfection of mRNA gene constructs encoding TCRα/β pairs into a well-defined human T-cell line, followed by co-cultivation with the tumor cells of interest and detection of T-cell activation by flow cytometry. Due to the high transfectability and the low background reactivity of the mock-transfected T-cell line to a wide variety of tumor cells, this assay offers a highly robust and versatile platform for the functional screening of large numbers of TCR clonotypes as identified in scRNAseq data sets. Whereas the assay was initially developed to test TCRs of human origin, it was more recently also applied successfully for the screening of TCRs of murine origin. Key features • Efficient functional screening of-and discrimination between-TCRs isolated from tumor-reactive vs. bystander T-cell clones. • Applicable to TCRs from CD8+ and CD4+ tumor-infiltrating T-cells originating from patient-derived tumor samples and syngeneic mouse tumor models. • Rapid flow cytometric detection of T-cell activation by means of TNFα and CD107a expression after a 5 h T-cell/tumor cell co-cultivation.

Characterization of the Immune Microenvironment and Identification of Biomarkers in Chronic Rhinosinusitis with Nasal Polyps Using Single-Cell RNA Sequencing and Transcriptome Analysis.

Chronic rhinosinusitis is a prevalent condition in the field of otorhinolaryngology; however, its pathogenesis remains to be elucidated. The immunological defense of the nasal mucosa is significantly influenced by dendritic cells (DCs). We identified specific biological indicators linked to DCs and explored their significance in cases of chronic rhinosinusitis with nasal polyps (CRSwNP). We categorized cells using single-cell RNA (scRNA) sequencing, and combined transcriptome sequencing was used to identify potential candidate genes for CRSwNP. We selected three biomarkers based on two algorithms and performed enrichment and immune correlation analyses. Biomarkers were verified using training and validation sets, receiver operating characteristic curves, immunohistochemistry, and quantitative real-time reverse-transcription PCR (qRT-PCR). Variations in biomarker expression were validated using pseudotime analysis. The networks of competing transcription factor (TF)-mRNA and competing endogenous RNA (ceRNA) were established, and the protein drugs associated with these biomarkers were predicted. Both scRNA-seq and transcriptome data showed that DCs immune infiltration was higher in the CRSwNP group than in the control group. Three DC-related biomarkers (NR4A1, CLEC4G, and CD163) were identified. In CRSwNP, NR4A1 expression decreased, whereas CLEC4G and CD163 expression increased. All biomarkers were shown to be involved in immunological and metabolic pathways by enrichment analysis. These biomarkers were associated with γδ T cells, effector memory CD4 + T cells, regulatory T cells, and immature DCs. According to pseudotime analysis, NR4A1 and CD163 expression decreased from high to low, whereas CLEC4G expression remained low. We screened and identified potential DC-associated biomarkers of CRSwNP progression by integrating scRNA-seq with whole transcriptome sequencing. We analyzed the biological pathways in which they were involved, explored their molecular regulatory mechanisms and related drugs, and constructed ceRNA, TF-mRNA, and biomarker-drug networks to identify new CRSwNP treatment targets, laying the groundwork for the clinical management of CRSwNP.

Combining multiomics to analyze the molecular mechanism of hair follicle cycle change in cashmere goats from Inner Mongolia.

Sheep body size can directly reflect the growth rates and fattening rates of sheep and is also an important index for measuring the growth performance of meat sheep.Inner Mongolia Cashmere Goat is a local excellent breed of cashmere and meat dual-purpose, which is a typical heterogeneous indumentum. The hair follicles cycle through periods of vigorous growth (anagen), a regression caused by apoptosis (catagen), and relative rest (telogen). At present, it is not clear which genes affect the cycle transformation of hair follicles and unclear how proteins impact the creation and expansion of hair follicles.we using multi-omics joint analysis methodologies to investigated the possible pathways of transformation and apoptosis in goat hair follicles. The results showed that 917,1,187, and 716 proteins were specifically expressed in anagen, catagen andtelogen. The result of gene ontology (GO) annotation showed that differentially expressed proteins (DEPs) are in different growth cycle periods, and enriched GO items are mostly related to the transformation of cells and proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment result indicated that the apoptosis process has a great impact on hair follicle's growth cycle. The results of the protein interaction network of differential proteins showed that the ribosomal protein family (RPL4, RPL8, RPS16, RPS18, RPS2, RPS27A, RPS3) was the core protein in the network. The results of combined transcriptome and proteomics analysis showed that there were 16,34, and 26 overlapped DEGs and DEPs in the comparison of anagen VS catagen, catagen VS telogen and anagen VS telogen, of which API5 plays an important role in regulating protein and gene expression levels. We focused on API5 and Ribosomal protein and found that API5 affected the apoptosis process of hair follicles, and ribosomal protein was highly expressed in the resting stage of hair follicles. They are both useful as molecular marker candidate genes to study hair follicle growth and apoptosis,and they both have an essential function in the cycle transition process of hair follicles. The results of this study may provide a theoretical basis for further research on the growth and development of hair follicles in Inner Mongolian Cashmere goats.

Integrated Transcriptomic and Metabolomic Analyses Identify Critical Genes and Metabolites Associated with Seed Vigor of Common Wheat.

Seed aging is a common physiological phenomenon during storage which has a great impact on seed quality. An in-depth analysis of the physiological and molecular mechanisms of wheat seed aging is of great significance for cultivating high-vigor wheat varieties. This study reveals the physiological mechanisms of wheat seed aging in two cultivars differing in seed vigor, combining metabolome and transcriptome analyses. Differences between cultivars were examined based on metabolomic differential analysis. Artificial aging had a significant impact on the metabolism of wheat seeds. A total of 7470 (3641 upregulated and 3829 downregulated) DEGs were detected between non-aging HT and LT seeds; however, 10,648 (4506 up and 6142 down) were detected between the two cultivars after aging treatment. Eleven, eight, and four key metabolic-related gene families were identified in the glycolysis/gluconeogenesis and TCA cycle pathways, starch and sucrose metabolism pathways, and galactose metabolism pathways, respectively. In addition, 111 up-regulated transcription factor genes and 85 down-regulated transcription factor genes were identified in the LT 48h group. A total of 548 metabolites were detected across all samples. Cultivar comparisons between the non-aged groups and aged groups revealed 46 (30 upregulated and 16 downregulated) and 62 (38 upregulated and 24 downregulated) DIMs, respectively. Network analysis of the metabolites indicated that glucarate O-phosphoric acid, L-methionine sulfoxide, isocitric acid, and Gln-Gly might be the most crucial DIMs between HT and LT. The main related metabolites were enriched in pathways such as glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, fatty acid degradation, etc. However, metabolites that exhibited differences between cultivars were mainly enriched in carbon metabolism, the TCA cycle, etc. Through combined metabolome and transcriptome analyses, it was found that artificial aging significantly affected glycolysis/gluconeogenesis, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism, which involved key genes such as ACS, F16P2, and PPDK1. We thus speculate that these genes may be crucial in regulating physiological changes in seeds during artificial aging. In addition, an analysis of cultivar differences identified pathways related to amino acid and polypeptide metabolism, such as cysteine and methionine metabolism, glutathione metabolism, and amino sugar and nucleotide sugar metabolism, involving key genes such as BCAT3, CHI1, GAUT1, and GAUT4, which may play pivotal roles in vigor differences between cultivars.

Combined metabolome and transcriptome analyses of quality components and related molecular regulatory mechanisms during the ripening of Huangjin Peach

Huangjin Peach is highly nutritious with cinsiderable market potential. Flavonoids, sugars, and acids are among the key compounds affecting the quality of yellow peaches. In this study, we analyzed the metabolites and gene expression of Huangjin Peach to explain the quality formation mechanism during the ripening period (including the young fruit, color change, and mature stages). We explored the biosynthetic pathways of flavonoids, sugars, and organic acids through metabolomics (LC-MS/MS) and transcriptomics (RNA-seq) approaches. A total of 864 metabolites were identified during the ripening of Huangjin Peach. Flavonoids increased significantly mainly at the color change stage and accumulated at the mature stage. During the combined transcriptomic and metabolomic analyses, CHS, F3′H, DFR, and A3GT were identified as the main enzyme genes regulating flavonoid synthesis, as well as the key factors affecting fruit color. Sugar alcohols accumulated significantly in Huangjin Peach during the ripening period, and organic and phenolic acids decreased significantly during the color change stage, which affect the quality and taste of fruits. Most metabolites and genes changed dramatically during the color change stage, indicating that the color change stage is critical for fruit quality formation. The expression of key genes was verified by qRT-PCR. Our results explained some of the key fruit quality formation mechanisms of Huangjin Peach, which provide a valuable foundation for the improvement and development of functional foods.

Combined transcriptomics and proteomics studies on the effect of electrical stimulation on spinal cord injury in rats

Electrical stimulation (ES) of the spinal cord is a promising therapy for functional rehabilitation after spinal cord injury (SCI). However, the specific mechanism of action is poorly understood. We designed and applied an implanted ES device in the SCI area in rats and determined the effect of ES on the treatment of motor dysfunction after SCI using behavioral scores. Additionally, we examined the molecular characteristics of the samples using proteomic and transcriptomic sequencing. The differential molecules between groups were identified using statistical analyses. Molecular, network, and pathway-based analyses were used to identify group-specific biological features. ES (0.5 mA, 0.1 ms, 50 Hz) had a positive effect on motor dysfunction and neuronal regeneration in rats after SCI. Six samples (three independent replicates in each group) were used for transcriptome sequencing; we obtained 1026 differential genes, comprising 274 upregulated genes and 752 downregulated genes. A total of 10 samples were obtained: four samples in the ES group and six samples in the SCI group; for the proteome sequencing, 48 differential proteins were identified, including 45 up-regulated and three down-regulated proteins. Combined transcriptomic and proteomic studies have shown that the main enrichment pathway is the hedgehog signaling pathway. Western blot results showed that the expression levels of Sonic hedgehog (SHH) (P < 0.001), Smoothened (SMO) (P = 0.0338), and GLI-1 (P < 0.01) proteins in the ES treatment group were significantly higher than those in the SCI group. The immunofluorescence results showed significantly increased expression of SHH (P = 0.0181), SMO (P = 0.021), and GLI-1 (P = 0.0126) in the ES group compared with that in the SCI group. In conclusion, ES after SCI had a positive effect on motor dysfunction and anti-inflammatory effects in rats. Moreover, transcriptomic and proteomic sequencing also provided unique perspectives on the complex relationships between ES on SCI, where the SHH signaling pathway plays a critical role. Our study provides a significant theoretical foundation for the clinical implementation of ES therapy in patients with SCI.

Allantoin and jasmonic acid synergistically induce resistance response to powdery mildew in melon as revealed by combined hormone and transcriptome analysis

Powdery mildew is a major fungal disease affecting melon production, and analyzing the molecular regulatory mechanism of resistance in melon is a prerequisite for melon molecular breeding of powdery mildew resistance. In this study, a resistant melon material was selected for inoculation and sterile water control treatments, and four time points, 0 h, 24 h, 48 h and 72 h after treatment, were selected for transcriptome sequencing analysis. The content of disease resistance related hormones was also determined and WGCNA analysis was performed. The results showed that allantoin and jasmonic acid were related to the regulation of powdery mildew resistance in melon, and key genes responding to the disease resistance response were found. In this study, we found that powdery mildew infested melon leaves induced a rise in the content of allantoin, which in turn induced a rise in the content of jasmonic acid and induced the accumulation of reactive oxygen species and thus resistance through the signaling of Ca2+ and WRKY transcription factors. This study initially explored the molecular regulatory mechanism of powdery mildew resistance in melon and provided a theoretical basis for molecular breeding of powdery mildew resistance in melon.

Foeniculum vulgare essential oil nanoemulsion inhibits Fusarium oxysporum causing Panax notoginseng root-rot disease

BackgroundFusarium oxysporum (F. oxysporum) is the primary pathogenic fungus that causes Panax notoginseng (P. notoginseng) root rot disease. To control the disease, safe and efficient antifungal pesticides must currently be developed. MethodsIn this study, we prepared and characterized a nanoemulsion of Foeniculum vulgare essential oil (Ne-FvEO) using ultrasonic technology and evaluated its stability. Traditional Foeniculum vulgare essential oil (T-FvEO) was prepared simultaneously with 1/1000 Tween-80 and 20/1000 dimethyl sulfoxide (DMSO). The effects and inhibitory mechanism of Ne-FvEO and T-FvEO in F. oxysporum were investigated through combined transcriptome and metabolome analyses. ResultsResults showed that the minimum inhibitory concentration (MIC) of Ne-FvEO decreased from 3.65 mg/mL to 0.35 mg/mL, and its bioavailability increased by 10-fold. The results of gas chromatography/mass spectrometry (GC/MS) showed that T-FvEO did not contain a high content of estragole compared to Foeniculum vulgare essential oil (FvEO) and Ne-FvEO. Combined metabolome and transcriptome analysis showed that both emulsions inhibited the growth and development of F. oxysporum through the synthesis of the cell wall and cell membrane, energy metabolism, and genetic information of F. oxysporum mycelium. Ne-FvEO also inhibited the expression of 2-oxoglutarate dehydrogenase and isocitrate dehydrogenase and reduced the content of 2-oxoglutarate, which inhibited the germination of spores. ConclusionOur findings suggest that Ne-FvEO effectively inhibited the growth of F. oxysporum in P. notoginseng in vivo. The findings contribute to our comprehension of the antifungal mechanism of essential oils (EOs) and lay the groundwork for the creation of plant-derived antifungal medicines.

Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment

Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.

Integrated analysis of transcriptome and metabolome reveals the regulatory mechanism of largemouth bass (Micropterus salmoides) in response to Nocardia seriolae infection

Nocardia seriolae is a severe bacterial pathogen that has seriously affected the development of aquaculture industry. Largemouth bass (Micropterus salmoides) is a commercially significant freshwater fish that suffers a variety of environmental threats, including bacterial pathogens. However, the immune responses and metabolic alterations of largemouth bass to N. seriolae infection remain largely unclear. We discovered that N. seriolae caused pathological alterations in largemouth bass and shifted the transcript of immune-related and apoptotic genes in head kidney after infection. To answer the aforementioned question, a combined transcriptome and metabolome analysis was employed to explore the alterations in genes, metabolites, and metabolic pathways in largemouth bass following bacterial infection. A total of 3579 genes and 1929 metabolites are significant differentially changed in the head kidney post infection. In response to N. seriolae infection, host modifies the PI3K-Akt signaling pathway, TCA cycle, glycolysis, and amino acid metabolism. The integrated analysis of transcriptome and metabolome suggested that with the arginine metabolism pathway as the core, multiple biomarkers (arg gene, arginine) are involved in the antibacterial and immune functions of largemouth bass. Thus, we hypothesized that arginine plays a crucial role in the immune responses of largemouth bass against N. seriolae infection, and increasing arginine levels suitably is beneficial for the host against bacterial infection. Our results shed light on the regulatory mechanism of largemouth bass resistance to N. seriolae infection and contributed to the development of more effective N. seriolae resistance strategies.

Molecular genetic characterization and meat-use functional gene identification in Jianshui yellow-brown ducks through combined resequencing and transcriptome analysis.

The Jianshui yellow-brown duck is a unique country-specific waterfowl species in Yunnan Province, well known for its tender meat. However, there is a lack of comprehensive systematic research on the molecular genetic characteristics, especially germplasm resources and economic traits, of the Jianshui yellow-brown ducks. This study investigated the molecular genetic characteristics of Jianshui yellow-brown ducks, compared their selection signals with those of ancestral mallard and meat-type Pekin ducks, and identified genes specific to their meat-use performance. Furthermore, this study also evaluated the breeding potential for its meat performance. In this study, phylogenetic trees, PCA and Admixture analysis were used to investigate the population genetic structure among local duck breeds in China; population genetic differentiation index (Fst), nucleotide diversity and Tajima's D were used to detect selected loci and genes in the population of Jianshui yellow-brown ducks; and transcriptome technology was used to screen for differentially expressed genes in the liver, sebum and breast muscle tissues, and finally, the results of the genome selection signals and transcriptome data were integrated to excavate functional genes affecting the meat performance of the Jianshui yellow-brown ducks. The results of the genetic structure of the population showed that Jianshui yellow-brown ducks were clustered into a separate group. Selection signal analysis indicated significant selection pressure on certain genes related to meat characteristics (ELOVL2, ELOVL3, GDF10, VSTM2A, PHOSPHO1, and IGF2BP1) in both Jianshui yellow-brown ducks and mallards. Transcriptomic data analysis suggested that ELOVL3, PHOSPHO1, and GDF10 are vital candidate genes influencing meat production and quality in Jianshui yellow-brown ducks. A comparison of selection signals between Jianshui yellow-brown ducks and Pekin ducks revealed only 21 selected genes in the Jianshui yellow-brown duck population, and no significant genes were related to meat traits. Moreover, whole-genome resequencing data suggested that the Jianshui yellow-brown duck represents a unique category with distinct genetic mechanisms. Through selection signaling and transcriptomic approaches, we successfully screened and identified important candidate genes affecting meat traits in Jianshui yellow-brown ducks. Furthermore, the Jianshui yellow-brown duck has good potential for improved meat performance, highlighting the need for further improvement.

Combined transcriptomics and metabolomics analysis reveals the antifungal activity and mechanism of Enterococcus faecium cell-free supernatant against Alternaria alternata

Certain lactic acid bacteria have been utilized as bacteriostatic agents in the context of fruit and vegetable spoilage fungi. Although Enterococcus faecium is a member of the lactic acid bacteria group, its application in the prevention of post-harvest fruit spoilage remains largely unexplored. We investigated the activity of E. faecium cell-free supernatant (CFS) against fruit and vegetable spoilage fungi and probed the possible fungistatic mechanisms involved. The in vitro results showed that CFS possessed significant antifungal activity against Alternaria alternata with a MIC of 20%, which resulted in distorted rupture of A. alternata cell membranes and leakage of cellular components in a dose-dependent manner. In addition, transcriptomics and metabolomics results showed that CFS could also inhibit the growth of A. alternata by altering energy metabolism, impairing intracellular antioxidant function, reducing intracellular hormone biosynthesis, and slowing down or stopping asymmetric cell division. In summary, E. faecium CFS has been shown to effectively inhibit A. alternata.

Combined metabolomics and transcriptomics analysis of rats under neuropathic pain and pain-related depression.

Neuropathic pain often leads to negative emotions, which in turn can enhance the sensation of pain. This study aimed to investigate the molecular mechanisms mediating neuropathic pain and negative emotions. Chronic constriction injury (CCI) rats were used as model animals and behavioral tests were conducted to assess pain and negative emotions. Then, the rat anterior cingulate cortex (ACC) was analyzed using UPLC-MS/MS and subsequently integrated with our previously published transcriptome data. Metabolomics analysis revealed that 68 differentially expressed metabolites (DEMs) were identified, mainly in amino acid metabolites and fatty acyls. Combined with our previously published transcriptome data, we predicted two genes that potentially exhibited associations with these metabolites, respectively Apolipoprotein L domain containing 1 (Apold1) and WAP four-disulfide core domain 1 (Wfdc1). Taken together, our results indicated that peripheral nerve injury contributing to neuropathic pain and pain-related depression may be associated with these metabolites and genes. This research provides new insights into the molecular regulatory mechanism, which could serve as a reference for the treatment of neuropathic pain and pain-related depression.