Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis of PkARF members in different tissues.

BACKGROUND: Polygonatum kingianum holds significant importance in Traditional Chinese Medicine due to its medicinal properties, characterized by its diverse chemical constituents including polysaccharides, terpenoids, flavonoids, phenols, and phenylpropanoids. The Auxin Response Factor (ARF) is a pivotal transcription factor known for its regulatory role in both primary and secondary metabolite synthesis. However, our understanding of the ARF gene family in P. kingianum remains limited. METHODS AND RESULTS: We employed RNA-Seq to sequence three distinct tissues (leaf, root, and stem) of P. kingianum. The analysis revealed a total of 31,558 differentially expressed genes (DEGs), with 43 species of transcription factors annotated among them. Analyses via gene ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that these DEGs were predominantly enriched in metabolic pathways and secondary metabolite biosynthesis. The proposed temporal expression analysis categorized the DEGs into nine clusters, suggesting the same expression trends that may be coordinated in multiple biological processes across the three tissues. Additionally, we conducted screening and expression pattern analysis of the ARF gene family, identifying 12 significantly expressed PkARF genes in P. kingianum roots. This discovery lays the groundwork for investigations into the role of PkARF genes in root growth, development, and secondary metabolism regulation. CONCLUSION: The obtained data and insights serve as a focal point for further research studies, centred on genetic manipulation of growth and secondary metabolism in P. kingianum. Furthermore, these findings contribute to the understanding of functional genomics in P. kingianum, offering valuable genetic resources.

Visfatin Affects the Transcriptome of Porcine Luteal Cells during Early Pregnancy.

Visfatin/NAMPT (VIS), the hormone exerting a pleiotropic effect, is also perceived as an important factor in the regulation of reproductive processes and pregnancy maintenance. Previous studies confirmed its involvement in the control of porcine pituitary and ovary function. In this study, we hypothesized that VIS may affect the global transcriptome of luteal cells and thus regulate the functioning of the ovaries. Illumina's NovaSeq 6000 RNA sequencing was performed to investigate the differentially expressed genes (DEGs) and long non-coding RNAs (DELs) as well as the occurrence of differential alternative splicing events (DASs) in the porcine luteal cells exposed to VIS (100 ng/mL) during the implantation period. The obtained results revealed 170 DEGs (99 up- and 71 downregulated) assigned to 45 functional annotations. Moreover, we revealed 40 DELs, of which 3 were known and 37 were described for the first time. We identified 169 DASs events. The obtained results confirmed a significant effect of VIS on the transcriptome and spliceosome of luteal cells, including the genes involved in the processes crucial for successful implantation and pregnancy maintenance as angiogenesis, steroidogenesis, inflammation, cell development, migration, and proliferation.

Genome-Wide Identification of Candidate Genes Associated with Heat Stress in Mulberry (Morus alba L.).

Mulberry (Morus alba L.) is an economically important plant for the silk industry and has the possibility of contributing immensely to Chinese pharmacopeia because of its health benefits. Domesticated silkworms feed only on mulberry leaves, meaning that the worms' survival depends on the mulberry tree. Mulberry production is threatened by climate change and global warming. However, the regulatory mechanisms of mulberry responses to heat are poorly understood. We performed transcriptome analysis of high-temperature-stressed (42 °C) M. alba seedlings using RNA-Seq technologies. A total of 703 differentially expressed genes (DEGs) were discovered from 18,989 unigenes. Among these, 356 were up-regulated, and 347 were down-regulated. KEGG analysis revealed that most DEGs were enriched in valine, leucine and isoleucine degradation, and in starch and sucrose metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis and galactose metabolism, among others. In addition, TFs such as the NAC, HSF, IAA1, MYB, AP2, GATA, WRKY, HLH and TCP families were actively involved in response to high temperatures. Moreover, we used RT-qPCR to confirm the expression changes of eight genes under heat stress observed in the RNA-Seq analysis. This study provides M. alba transcriptome profiles under heat stress and provides theoretical bases to researchers for better understanding mulberry heat response mechanisms and breeding heat-tolerant mulberry plants.

Transcriptomic analysis the mechanisms of anti-osteoporosis of desert-living Cistanche herb in ovariectomized rats of postmenopausal osteoporosis.

Desert-living Cistanche herb (DC), as a traditional Chinese medicine for tonifying kidney yang, is often used to treat postmenopausal osteoporosis (PMOP). Total phenylethanoid glycosides are instruction ingredients for discrimination and assay according to the China pharmacopoeia for DC. This research aimed to reveal the anti-osteoporosis mechanism of total phenylethanoid glycosides of DC (PGC) by transcriptomic analysis of ovariectomized rats. Serum levels of BGP were evaluated by ELISA, the bone weight was measured, and transmission electron microscopy was used to examine the ultrastructure of osteoblasts in rats. In addition, micro-CT was used to detect the bone volume (Tb.BS/BV), bone mineral density (Tb.BMD), and bone mineral content (Tb.BMC) in trabecular bone, and the ratio of cortical bone area to total area (Ct.ar/Tt.ar), and the level of bone mineral content (Ct.BMC) in cortical bone. Differential expressed genes (DEGs) after PGC treatment were analyzed by transcriptomics. Then, a bioinformatics analysis of DEGs was carried out through GO enrichment, KEGG enrichment, and selection of the nucleus gene through the protein-protein interaction network. Through qRT-PCR analysis, the DEGs were verified. The analysis results indicated that PGC increased the secretion of osteogenic markers, and ultrastructural characterization of osteoblasts and bone morphology were improved in ovariectomized rats. A total of 269 genes were differentially expressed, including 201 genes that were downregulated and 68 genes that were upregulated between the model group and the PGC group. Bioinformation analysis results prompt the conclusion that PGC could promote the bone metabolism by muscle cell development, myofibril assembly, etc. In addition, our study also found that PGC has a good effect on osteoporosis complicated with cardiomyopathy, and it also provided evidence for the correlation between sarcopenia and osteoporosis.

Estrogen-related genes for thyroid cancer prognosis, immune infiltration, staging, and drug sensitivity.

BACKGROUND: Thyroid cancer (THCA) has become increasingly common in recent decades, and women are three to four times more likely to develop it than men. Evidence shows that estrogen has a significant impact on THCA proliferation and growth. Nevertheless, the effects of estrogen-related genes (ERGs) on THCA stages, immunological infiltration, and treatment susceptibility have not been well explored. METHODS: Clinicopathological and transcriptome data of patients with THCA from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were cleaned before consensus clustering. Differential expression analysis was performed on the genes expressed between THCA and paraneoplastic tissues in TCGA, and Wayne analysis was performed on the ERGs obtained from the Gene Set Enrichment Analysis MsigDB and differentially expressed genes (DEGs). Univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses were used to identify the set of estrogen-related differentially expressed genes (ERDEGs) associated with progression-free intervals (PFI) and to establish a prediction model. Receiver operating characteristic curves were plotted to calculate the risk scores and PFI status to validate the predictive effect of the model. Enrichment analyses and immune infiltration analyses were performed to analyze DEGs between the high- and low-risk groups, and a nomogram plot was used in the risk model to predict the PFI of THCA. RESULTS: The expression of 120 ERDEGs differed significantly between the two groups (P < 0.05). Five (CD24, CAV1, TACC1, TIPARP, and HSD17B10) of the eight ERDEGs identified using univariate Cox and LASSO regression were validated via RT-qPCR and immunohistochemistry analysis of clinical tissue samples and were used for clinical staging and drug sensitivity analysis. Risk-DEGs were shown to be associated with immune modulation and tumor immune evasion, as well as defense systems, signal transduction, the tumor microenvironment, and immunoregulation. In 19 of the 28 immune cells, infiltration levels differed between the high- and low-risk groups. High-risk patients in the immunotherapy dataset had considerably shorter survival times than low-risk patients. CONCLUSION: We identified and confirmed eight ERDEGs using a systematic analysis and screened sensitive drugs for ERDEGs. These results provide molecular evidence for the involvement of ERGs in controlling the immunological microenvironment and treatment response in THCA.

Inoculation of Freund's adjuvant in European eel (Anguilla anguilla) revealed key KEGG pathways and DEGs of host anti-Edwardsiella anguillarum infection.

Freund's complete (FCA) and incomplete adjuvants (FIA), generally applied in subunit fishery vaccine, have not been explored on the molecular mechanism of the nonspecific immune enhancement. In this study, we examined the RNA-seq in the spleen of European eel (Anguilla anguilla) inoculated with FCA and FIA (FCIA group) to elucidate the key KEGG pathways and differential expressed genes (DEGs) in the process of Edwardsiella anguillarum infection and A. anguilla anti-E. anguillarum infection using genome-wide transcriptome. After eels were challenged by E. anguillarum at 28 d post the first inoculation (dpi), compared to the control uninfected eels (Con group), the control infected eels (Con_inf group) showed severe pathological changes in the liver, kidney and spleen, although infected eels post the inoculation of FCIA (FCIA_inf group) also formed slight bleeding. Compared to the FCIA_inf group, there was more than 10 times colony forming unit (cfu) in the Con_inf group per 100 µg spleen, kidney or blood, and the relative percent survival (RPS) of eels was 44.4% in FCIA_inf vs Con_inf. Compared to the Con group, the SOD activity in the FCIA group increased significantly in the liver and spleen. Using high-throughput transcriptomics, DEGs were identified and 29 genes were verified using fluorescence real-time polymerase chain reaction (qRT-PCR). The result of DEGs clustering showed 9 samples in 3 groups of Con, FCIA and FCIA_inf were similar, contrast to distinct differences of 3 samples in the Con_inf group. We found 3795 up and 3548 down regulated DEGs in the compare of FCIA_inf vs Con_inf, of which 5 enriched KEGG pathways of "Lysosome", "Autophagy", "Apoptosis", "C-type lectin receptor signaling" and "Insulin signaling" were ascertained, and 26 of 30 top GO terms in the compare were significantly enriched. Finally, protein-protein interactions between the DEGs of the 5 KEGG pathways and other DEGs were explored using Cytoscape 3.9.1. The compare of FCIA_inf vs Con_inf showed 110 DEGs from the 5 pathways and 718 DEGs from other pathways formed total of 9747° in a network, of which 9 hub DEGs play vital roles in anti-infection or apoptosis. Together, the interaction networks revealed that 9 DEGs involved in the 5 pathways underlies the key process of A. anguilla anti-E. anguillarum infection or host cell apoptosis.

A statistical network pre-processing method to improve relevance and significance of gene lists in microarray gene expression studies.

BACKGROUND: Microarrays can perform large scale studies of differential expressed gene (DEGs) and even single nucleotide polymorphisms (SNPs), thereby screening thousands of genes for single experiment simultaneously. However, DEGs and SNPs are still just as enigmatic as the first sequence of the genome. Because they are independent from the affected biological context. Pathway enrichment analysis (PEA) can overcome this obstacle by linking both DEGs and SNPs to the affected biological pathways and consequently to the underlying biological functions and processes. RESULTS: To improve the enrichment analysis results, we present a new statistical network pre-processing method by mapping DEGs and SNPs on a biological network that can improve the relevance and significance of the DEGs or SNPs of interest to incorporate pathway topology information into the PEA. The proposed methodology improves the statistical significance of the PEA analysis in terms of computed p value for each enriched pathways and limit the number of enriched pathways. This helps reduce the number of relevant biological pathways with respect to a non-specific list of genes. CONCLUSION: The proposed method provides two-fold enhancements. Network analysis reveals fewer DEGs, by selecting only relevant DEGs and the detected DEGs improve the enriched pathways' statistical significance, rather than simply using a general list of genes.

Transcriptome and co-expression network analyses of key genes and pathways associated with differential abscisic acid accumulation during maize seed maturation.

BACKGROUND: Currently, mechanical maize kernel harvesting has not been fully utilized in developing countries including China, partly due to the absence of suitable cultivars capable of rapid desiccation during seed maturation. The initiation of rapid desiccation during seed maturation is regulated by abscisic acid (ABA). For further characterization of ABA-regulated key genes and cellular events, it is necessary to perform transcriptome analysis of maize developing embryos. The ABA synthesis-deficient mutant (vp5) and normal maize (Vp5) seeds are suitable materials for such purpose. RESULTS: In the present work, developing vp5 and Vp5 embryos were compared by ABA content and transcriptome analyses. Quantitative analysis revealed the significant difference in ABA synthesis between both genotypes. From 29 days after pollination (DAP), ABA content increased rapidly in Vp5 embryos, but decreased gradually in vp5 embryos. At 36 DAP, ABA level in vp5 decreased to 1/4 that of Vp5, suggesting that the differential ABA levels would affect seed maturation. Comparative transcriptomic analysis has found 1019 differentially expressed genes (DEGs) between both genotypes, with the most DEGs (818) at 36 DAP. Further, weighted correlation network analysis (WGCNA) revealed eight DEGs co-expression modules. Particularly, a module was negatively correlated with ABA content in vp5 embryos. The module was mainly involved in metabolic and cellular processes, and its hub genes encoded thiamine, NPF proteins, calmodulin, metallothionein etc. Moreover, the expression of a set of key genes regulated by ABA was further verified by RT-qPCR. The results of the present work suggested that because of ABA deficiency, the vp5 seeds maintained strong metabolic activities and lacked dormancy initiation during seed maturation. CONCLUSION: Transcriptome and WGCNA analyses revealed significant ABA-related changes in metabolic pathways and DEGs between vp5 and Vp5 during seed maturation. The results would provide insights for elucidating the molecular mechanism of ABA signaling and developing high dehydration tolerance maize suitable for mechanical harvesting.

Developing a 5-gene prognostic signature for cervical cancer by integrating mRNA and copy number variations.

BACKGROUND: Cervical cancer is frequently detected gynecological cancer all over the world. This study was designed to develop a prognostic signature for an effective prediction of cervical cancer prognosis. METHODS: Differentially expressed genes (DEGs) were identified based on copy number variation (CNV) data and expression profiles from different databases. A prognostic model was constructed and further optimized by stepwise Akaike information criterion (stepAIC). The model was then evaluated in three groups (training group, test group and validation group). Functional analysis and immune analysis were used to assess the difference between high-risk and low-risk groups. RESULTS: The study developed a 5-gene prognostic model that could accurately classify cervical cancer samples into high-risk and low-risk groups with distinctly different prognosis. Low-risk group exhibited more favorable prognosis and higher immune infiltration than high-risk group. Both univariate and multivariate Cox regression analysis showed that the risk score was an independent risk factor for cervical cancer. CONCLUSIONS: The 5-gene prognostic signature could serve as a predictor for identifying high-risk cervical cancer patients, and provided potential direction for studying the mechanism or drug targets of cervical cancer. The integrated analysis of CNV and mRNA expanded a new perspective for exploring prognostic signatures in cervical cancer.

Transcriptional, secondary metabolic, and antioxidative investigations elucidate the rapid response mechanism of Pontederia cordata to cadmium.

Pontederia cordata is previously demonstrated a cadmium (Cd) tolerant plant, and also a candidate for the phytoremediation of heavy-metal-contaminated wetlands. A hydroponic experiment was used to investigate variations in photosynthetic gas exchange parameters, antioxidative activities, chlorophyll and secondary metabolite contents, and transcriptome in leaves of the plant exposed to 0.44 mM Cd2+ for 0 h, 24 h, and 48 h. Under Cd2+ exposure for 24 h, the plant presented a favorable photosynthesis by maintaining relatively higher antioxidant activity. Cd2+ exposure for 48 h accelerated membrane peroxidation, declined photosynthetic pigment content, and increased polyphenol oxidase activity, thus interfering with photosynthesis. The phenylpropane pathway served as a chemical rather than physical defense against Cd2+ in the plant leaves. A total of 20,998, 4743, and 4413 differentially expressed genes (DEGs) were identified in the groups of 0 h vs 24 h, 0 h vs 48 h, and 24 h vs 48 h, respectively. The primary metabolic pathways of the DEGs were mainly enriched in nitrogen metabolism, starch and sucrose metabolism, fructose and mannose metabolism, as well as pentose-phosphate pathway, contributing to a stable cell structure and function. Flavonoid biosynthesis directly or indirectly played an antioxidative role against Cd2+ in the leaves. Forty-nine transcription factor (TF) families were identified, and 8 TF families were shared among the three groups. The present study provides a theoretical foundation for investigating tolerance mechanisms of wetland plants to Cd stress in terms of secondary metabolism and transcriptional regulation.

Transcriptional Responses for Biosynthesis of Triterpenoids in Exogenous Inducers Treated Inonotus Hispidus Using RNA-Seq.

Inonotus hispidus is a traditional medicinal that grows in Northeast China and produces various economically important compounds, including polysaccharide compounds and terpenoids; triterpenoid saponins is the main bioactive component. Our research group has found that the accumulation of triterpenoid was affected by exogenous inducers. Experimental results showed that treatment with methyl jasmonate (MeJA) and oleic acid significantly increased the triterpenoid content of I. hispidus. However, how exogenous inducers enhance production of secondary metabolites in I. hispidus is not well understood. In this study, metabolite changes were further investigated with UPLC-TOF/MS following exogenous inducer treatment. As a result, a total of eight types of triterpenoids in I. hispidus were identified. The RNA-seq analysis was used to evaluate the effects of exogenous inducers on the expression of triterpenoid-synthesis-related genes in I. hispidus in liquid fermentation. This study is the first exploration to profile the transcriptome of I. hispidus after adding exogenous inducers; the generated data and gene will facilitate further molecular studies on the physiology and metabolism in this fungi. By comparative transcriptomic analysis, a series of candidate genes involved in the biosynthetic pathway of triterpenoids are identified, providing new insights into their biosynthesis at the transcriptome level.

Bioinformatics screening of biomarkers related to liver cancer.

BACKGROUND: Liver cancer is a common malignant tumor in China, with high mortality. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abundant data on gene expression, mRNA quantification and the clinical data of liver cancer. However, the hub genes, which can be served as biomarkers for diagnosis and treatment of early liver cancer, are not well screened. RESULTS: Here we present a new method for getting 6 key genes, aiming to diagnose and treat the early liver cancer. We firstly analyzed the different expression microarrays based on TCGA database, and a total of 1564 differentially expressed genes were obtained, of which 1400 were up-regulated and 164 were down-regulated. Furthermore, these differentially expressed genes were studied by using GO and KEGG enrichment analysis, a PPI network was constructed based on the STRING database, and 15 hub genes were obtained. Finally, 15 hub genes were verified by applying the survival analysis method on Oncomine database, and 6 key genes were ultimately identified, including PLK1, CDC20, CCNB2, BUB1, MAD2L1 and CCNA2. The robustness analysis of four independent data sets verifies the accuracy of the key gene's classification of the data set. CONCLUSIONS: Although there are complicated differences between cancer and normal cells in gene functions, cancer cells could be differentiated in case that a group of special genes expresses abnormally. Here we presented a new method to identify the 6 key genes for diagnosis and treatment of early liver cancer, and these key genes can help us understand the pathogenesis of liver cancer more deeply.

Transcriptomics analysis of differentially expressed genes in subcutaneous and perirenal adipose tissue of sheep as affected by their pre- and early postnatal malnutrition histories.

BACKGROUND: Early life malnutrition is known to target adipose tissue with varying impact depending on timing of the insult. This study aimed to identify differentially expressed genes in subcutaneous (SUB) and perirenal (PER) adipose tissue of 2.5-years old sheep to elucidate the biology underlying differential impacts of late gestation versus early postnatal malnutrition on functional development of adipose tissues. Adipose tissues were obtained from 37 adult sheep born as twins to dams fed either NORM (fulfilling energy and protein requirements), LOW (50% of NORM) or HIGH (110% of protein and 150% of energy requirements) diets in the last 6-weeks of gestation. From day 3 to 6 months of age, lambs were fed high-carbohydrate-high-fat (HCHF) or moderate low-fat (CONV) diets, and thereafter the same moderate low-fat diet. RESULTS: The gene expression profile of SUB in the adult sheep was not affected by the pre- or early postnatal nutrition history. In PER, 993 and 186 differentially expressed genes (DEGs) were identified in LOW versus HIGH and NORM, respectively, but no DEG was found between HIGH and NORM. DEGs identified in the mismatched pre- and postnatal nutrition groups LOW-HCHF (101) and HIGH-HCHF (192) were largely downregulated compared to NORM-CONV. Out of 831 DEGs, 595 and 236 were up- and downregulated in HCHF versus CONV, respectively. The functional enrichment analyses revealed that transmembrane (ion) transport activities, motor activities related to cytoskeletal and spermatozoa function (microtubules and the cytoskeletal motor protein, dynein), and responsiveness to the (micro) environmental extracellular conditions, including endocrine and nervous stimuli were enriched in the DEGs of LOW versus HIGH and NORM. We confirmed that mismatched pre- and postnatal feeding was associated with long-term programming of adipose tissue remodeling and immunity-related pathways. In agreement with phenotypic measurements, early postnatal HCHF feeding targeted pathways involved in kidney cell differentiation, and mismatched LOW-HCHF sheep had specific impairments in cholesterol metabolism pathways. CONCLUSIONS: Both pre- and postnatal malnutrition differentially programmed (patho-) physiological pathways with implications for adipose functional development associated with metabolic dysfunctions, and PER was a major target.

Transcriptomic analyses of Pinus koraiensis under different cold stresses.

BACKGROUND: Pinus koraiensis is an evergreen tree species with strong cold resistance. However, the transcriptomic patterns in response to cold stress are poorly understood for P. koraiensis. In this study, global transcriptome profiles were generated for P. koraiensis under cold stress (- 20 °C) over time by high-throughput sequencing. RESULTS: More than 763 million clean reads were produced, which assembled into a nonredundant data set of 123,445 unigenes. Among them, 38,905 unigenes had homology with known genes, 18,239 were assigned to 54 gene ontology (GO) categories and 18,909 were assigned to 25 clusters of orthologous groups (COG) categories. Comparison of transcriptomes of P. koraiensis seedlings grown at room temperature (20 °C) and low temperature (- 20 °C) revealed 9842 differential expressed genes (DEGs) in the 6 h sample, 9250 in the 24 h sample, and 9697 in the 48 h sample. The number of DEGs in the pairwise comparisons of 6 h, 24 h and 48 h was relatively small. The accuracy of the RNA-seq was validated by analyzing the expression patterns of 12 DEGs by quantitative real-time PCR (qRT-PCR). In this study, 34 DEGs (22 upregulated and 12 downregulated) were involved in the perception and transmission of cold signals, 96 DEGs (41 upregulated and 55 downregulated) encoding 8 transcription factors that regulated cold-related genes expression, and 27 DEGs (17 upregulated and 10 downregulated) were involved in antioxidant mechanisms in response to cold stress. Among them, the expression levels of c63631_g1 (annexin D1), c65620_g1 (alpha-amylase isozyme 3C), c61970_g1 (calcium-binding protein KIC), c51736_g1 (ABA), c58408_g1 (DREB3), c66599_g1 (DREB3), c67548_g2 (SOD), c55044_g1 (CAT), c71938_g2 (CAT) and c11358_g1 (GPX) first increased significantly and then decreased significantly with the extension of stress time. CONCLUSIONS: A large number of DEGs were identified in P. koraiensis under cold stress, especially the DEGs involved in the perception and transmission of cold signals, the DEGs encoding TFs related to cold regulation and the DEGs removing ROS in antioxidation mechanisms. The transcriptome and digital expression profiling of P. koraiensis could facilitate the understanding of the molecular control mechanism related to cold responses and provide the basis for the molecular breeding of conifers.

AKT3 Is a Pivotal Molecule of Cadherin-22 and GDNF Family Receptor-α1 Signal Pathways Regulating Self-Renewal in Female Germline Stem Cells.

Female germline stem cells (FGSCs) are rare population residing in cortex of ovary, with the potential to rescue female infertility caused by ovary failure. Recently, we reported that cadherin-22 (CDH22), a member of cadherin family, regulates self-renewal of mouse FGSCs via interaction with JAK-STAT signal pathway and ß-catenin. In this study, the expression profiles of FGSCs and spermatogonial stem cells (SSCs) were analyzed to further reveal their similarity and difference, and AKT3 was predicted as a pivotal molecule for FGSCs self-renewal. Then, we demonstrated that CDH22 interacted with PI3K to phosphorylate AKT3 and subsequently enhanced the expression levels of N-myc and cyclin family in FGSCs to promote self-renewal. Moreover, glial cell line-derived neurotrophic factor (GDNF) was identified as an essential factor for FGSCs self-renewal with a more complicated mechanism: GDNF-GFRA1 activates AKT3 via PI3K or Src family kinase (SFK), and SFK upregulates its target genes, Bcl6b, Etv5, and Lhx1, to promote self-renewal of FGSCs. However, Src, the key intermediate factor for SSCs, was not the functional molecule of SFK family in the GDNF signal network of FGSCs. Based on the observations of bioinformatics analysis and molecular evidence, we demonstrate the underlying links of potential factors which are critical to the self-renewal in FGSC and imply the therapeutic potentials of FGSCs in cure of female infertility. Stem Cells 2019;37:1095-1107.

Comparative transcriptomic analysis reveal the regulation mechanism underlying MeJA-induced accumulation of alkaloids in Dendrobium officinale.

Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale.

Genome-Wide Analysis of Coding and Long Non-Coding RNAs Involved in Cuticular Wax Biosynthesis in Cabbage (Brassica oleracea L. var. capitata).

Cuticular wax is a mixture of very long chain fatty acids (VLCFAs) and their derivatives, which determines vital roles for plant growth. In cabbage, the cuticular wax content of leaf blades is an important trait influencing morphological features of the head. Understanding the molecular basis of cuticular wax biosynthesis can help breeders develop high quality cabbage varieties. Here, we characterize a cabbage non-wax glossy (nwgl) plant, which exhibits glossy green phenotype. Cryo-scanning electron microscope analysis showed abnormal wax crystals on the leaf surfaces of nwgl plants. Cuticular wax composition analyzed by GC-MS displayed severely decreased in total wax loads, and individual wax components in nwgl leaves. We delimited the NWGL locus into a 99-kb interval between the at004 marker and the end of chromosome C08 through fine mapping. By high-throughput RNA sequencing, we identified 1247 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs in nwgl leaves relative to the wild-type. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DEGs and cis-regulated target genes for differentially expressed lncRNAs were significantly enriched in wax and lipid biosynthetic or metabolic processes. Our results provide the novel foundation to explore the complex molecular basis of cuticular wax biosynthesis.

In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma.

Understanding the gene regulatory network governing cancer initiation and progression is necessary, although it remains largely unexplored. Enhancer elements represent the center of this regulatory circuit. The study aims to identify the gene expression change driven by copy number variation in enhancer elements of pancreatic adenocarcinoma (PAAD). The pancreatic tissue specific enhancer and target gene data were taken from EnhancerAtlas. The gene expression and copy number data were taken from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) and copy number variations (CNVs) were identified between matched tumor-normal samples of PAAD. Significant CNVs were matched onto enhancer coordinates by using genomic intersection functionality from BEDTools. By combining the gene expression and CNV data, we identified 169 genes whose expression shows a positive correlation with the CNV of enhancers. We further identified 16 genes which are regulated by a super enhancer and 15 genes which have high prognostic potential (Z-score > 1.96). Cox proportional hazard analysis of these genes indicates that these are better predictors of survival. Taken together, our integrative analytical approach identifies enhancer CNV-driven gene expression change in PAAD, which could lead to better understanding of PAAD pathogenesis and to the design of enhancer-based cancer treatment strategies.

A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies.

The advancement of high-throughput RNA sequencing has uncovered the profound truth in biology, ranging from the study of differential expressed genes to the identification of different genomic phenotype across multiple conditions. However, lack of biological replicates and low expressed data are still obstacles to measuring differentially expressed genes effectively. We present an algorithm based on differential entropy-like function (DEF) to test for the differential expression across time-course data or multi-sample data with few biological replicates. Compared with limma, edgeR, DESeq2, and baySeq, DEF maintains equivalent or better performance on the real data of two conditions. Moreover, DEF is well suited for predicting the genes that show the greatest differences across multiple conditions such as time-course data and identifies various biologically relevant genes.

A systemic study of lipid metabolism regulation in salmon fingerlings and early juveniles fed plant oil.

In salmon farming, the scarcity of fish oil has driven a shift towards the use of plant-based oil from vegetable or seed, leading to fish feed low in long-chain PUFA (LC-PUFA) and cholesterol. Atlantic salmon has the capacity to synthesise both LC-PUFA and cholesterol, but little is known about the regulation of synthesis and how it varies throughout salmon life span. Here, we present a systemic view of lipid metabolism pathways based on lipid analyses and transcriptomic data from salmon fed contrasting diets of plant or fish oil from first feeding. We analysed four tissues (stomach, pyloric caeca, hindgut and liver) at three life stages (initial feeding 0·16 g, 2·5 g fingerlings and 10 g juveniles). The strongest response to diets higher in plant oil was seen in pyloric caeca of fingerlings, with up-regulation of thirty genes in pathways for cholesterol uptake, transport and biosynthesis. In juveniles, only eleven genes showed differential expression in pyloric caeca. This indicates a higher requirement of dietary cholesterol in fingerlings, which could result in a more sensitive response to plant oil. The LC-PUFA elongation and desaturation pathway was down-regulated in pyloric caeca, probably regulated by srebp1 genes. In liver, cholesterol metabolism and elongation and desaturation genes were both higher on plant oil. Stomach and hindgut were not notably affected by dietary treatment. Plant oil also had a higher impact on fatty acid composition of fingerlings compared with juveniles, suggesting that fingerlings have less metabolic regulatory control when primed with plant oil diet compared with juveniles.