Related Regulatory Networks Research Articles

Comprehensive analysis of m6A reader YTHDF2 prognosis, immune infiltration, and related regulatory networks in hepatocellular carcinoma

BackgroundN6-Methyladenosine (m6A) RNA modification is the most prevalent internal modification pattern in eukaryotic mRNAs and plays critical roles in diverse physiological and pathological processes. However, the expression of m6A regulator YTHDF2, its prognostic value, its biological function, its correlation with tumor microenvironment (TME) immune infiltrates, and related regulatory networks in hepatocellular carcinoma (HCC) remain determined. MethodsTCGA, GTEx, and GEO databases were used to investigate the expression profile of YTHDF2 in HCC. We performed differentially expressed genes (DEGs) analysis and constructed a PPI network to explore the biological processes of YTHDF2 in HCC. Kaplan-Meier curves and Cox regression analysis were used to assess the prognostic value of YTHDF2 and then a clinical prognostic nomogram was constructed. Additionally, ssGSEA was performed to assess the correlation between YTHDF2 and immune infiltration levels. The TISIDB database was applied to explore the expression of YTHDF2 in immune and molecular subtypes of HCC. GSEA identifies the YTHDF2-related signaling pathways. Finally, we utilized miRNet and starBase database to construct regulatory networks for HCC based on lncRNA-miRNA and miRNA-YTHDF2 interactions. ResultsYTHDF2 was significantly upregulated in HCC tumor tissues compared with the adjacent normal tissues. HCC patients in the high YTHDF2 expression group had poorer survival. Multivariate Cox analysis suggested that YTHDF2 may be a new independent prognostic indicator for HCC patients, with the prognostic nomogram exhibiting satisfactory results. YTHDF2 expression was significantly correlated with TME immune cell-infiltrating characteristics. Strong correlations were also shown in immune subtypes, molecular subtypes and immune checkpoints. Further analysis revealed that the combination of YTHDF2 expression and immune cell score was considerably associated with survival outcome in HCC patients. GESA analysis demonstrated that high YTHDF2 expression is associated with multiple biological processes and oncogenic pathways. Moreover, 14 possible regulatory networks were constructed, which are associated with HCC progression. ConclusionOur findings revealed that YTHDF2 may serve as a promising prognostic biomarker for HCC and may regulate the tumor immune microenvironment to provide effective therapeutic strategies.

Developmental Mapping of Hair Follicles in the Embryonic Stages of Cashmere Goats Using Proteomic and Metabolomic Construction.

The hair follicle (HF) is the fundamental unit for fleece and cashmere production in cashmere goats and is crucial in determining cashmere yield and quality. The mechanisms regulating HF development in cashmere goats during the embryonic period remain unclear. Growing evidence suggests that HF development involves complex developmental stages and critical events, and identifying the underlying factors can improve our understanding of HF development. In this study, samples were collected from embryonic day 75 (E75) to E125, the major HF developmental stages. The embryonic HFs of cashmere goats were subjected to proteomic and metabolomic analyses, which revealed dynamic changes in the key factors and signalling pathways controlling HF development at the protein and metabolic levels. Gene ontology and the Kyoto Encyclopaedia of Genes and Genomes were used to functionally annotate 1784 significantly differentially expressed proteins and 454 significantly differentially expressed metabolites enriched in different HF developmental stages. A joint analysis revealed that the oxytocin signalling pathway plays a sustained role in embryonic HF development by activating the MAPK and Ca2+ signalling pathways, and a related regulatory network map was constructed. This study provides a global perspective on the mechanism of HF development in cashmere goats and enriches our understanding of embryonic HF development.

The effect of plant growth-promoting bacteria application on rhizospheric microbial community and cadmium related regulatory network of Chrysopogon zizanioides in mining soil

The effect of plant growth-promoting bacteria application on rhizospheric microbial community and cadmium related regulatory network of Chrysopogon zizanioides in mining soil

Specific Gibberellin 2-Oxidase 3 (SbGA2ox3) Mutants Promote Yield and Stress Tolerance in Sorghum bicolor

Sorghum (Sorghum bicolor (L.) Moench) is a raw material that can be used as food, feed, bioenergy, and wine; it is also a gramineous crop with drought, salt, waterlogging, and high temperature resistance. However, liquor-making sorghum faces the disadvantages of having a narrow genetic basis, poor resources, and few high-quality varieties. Ethyl methane sulfonate (EMS) is a common alkylating agent that can react with one or more bases to alkylate and cause changes in the molecular structure of DNA, thereby causing mutations. It has a minimum effect on organisms and the highest efficiency. The obtained mutant populations are of great significance for cultivating new plant varieties and enriching plant germplasm resources. Therefore, in this study, ‘Hongyingzi’ a liquor-making sorghum variety, was studied using seeds treated with 0.5% EMS and 415 M3 generation plants were obtained. (1) Investigation and statistical analysis of agronomic traits in mutant libraries showed that in the M3 generation, nine important phenotypic mutant lines were obtained, including plant type, leaf blade, spike, glume, growth period, fertility, plant height, and drought resistance. The variation frequency from high to low was as follows: glume color (75.42%) > spike type (54.70%) > spike shape (47.23%) > chaff coating degree (28%) > plant growth period (23.86%) > plant height (23.61%) > absorption degree (16.14%) > branchiness (10.84%) > leaf color (4.58%) > tillering (2.16%). (2) The PCR sequencing of SbGA2ox3 from 415 sorghum M3 plants revealed that the mutation frequency of SbGA2ox3 was 1/99.02 kb. Eight plants underwent mutations, but only one line experienced missense mutations of different amino acid types, changing Ser/Ala/Val/Leu/Gln/Ser/Pro/Ala to Asn/Thr/Gly/Val/Gln/Ala/Ser. The mutant line also had shorter plant height, reduced glume coating degree, and enhanced drought resistance. The constructions of the sorghum mutant library widened the sorghum germplasm library and provided a method for sorghum breeding with a molecular basis for the functional verification of related genes and the analysis of related regulatory networks.

Genome-Wide Analysis of Long Non-Coding RNAs Related to UV-B Radiation in the Antarctic Moss Pohlia nutans

Antarctic organisms are consistently suffering from multiple environmental pressures, especially the strong UV radiation caused by the loss of the ozone layer. The mosses and lichens dominate the vegetation of the Antarctic continent, which grow and propagate in these harsh environments. However, the molecular mechanisms and related regulatory networks of these Antarctic plants against UV-B radiation are largely unknown. Here, we used an integrated multi-omics approach to study the regulatory mechanism of long non-coding RNAs (lncRNAs) of an Antarctic moss (Pohlia nutans) in response to UV-B radiation. We identified a total of 5729 lncRNA sequences by transcriptome sequencing, including 1459 differentially expressed lncRNAs (DELs). Through functional annotation, we found that the target genes of DELs were significantly enriched in plant-pathogen interaction and the flavonoid synthesis pathway. In addition, a total of 451 metabolites were detected by metabonomic analysis, and 97 differentially change metabolites (DCMs) were found. Flavonoids account for 20% of the total significantly up-regulated metabolites. In addition, the comprehensive transcriptome and metabolome analyses revealed the co-expression pattern of DELs and DCMs of flavonoids. Our results provide insights into the regulatory network of lncRNA under UV-B radiation and the adaptation of Antarctic moss to the polar environments.

New insights on the regulatory network of drought-responsive key genes in Arabidopsis thaliana.

Drought stress is complex abiotic stress that seriously affects crop productivity and yield. Many genes with various functions are induced in response to drought stress. The present study aimed to identify drought-responsive hub genes and their related regulation network in Arabidopsis thaliana under drought stress. In this study, RNA-sequencing data of well-watered and drought treatment samples of Arabidopsis were analyzed, and differential expression genes were identified. The gene ontology enrichment and protein-protein interaction network analyses were performed for differential expression genes. Then, the most important hub genes, gene ontology enrichment, co-expression network, and prediction of related miRNAs of hub genes were investigated by in silico approaches. A total of 2462 genes were expressed differentially, of which 1926 transcripts were up-regulated under drought stress, and the rest were down-regulated. WRKY33, WRKY40, AT1G19020, STZ, SYP122, CNI1, CML37, BCS1, AT3G02840, and AT5G54490 were identified as hub genes in drought stress. The gene ontology analysis showed that hub genes significantly enriched in response to hypoxia, chitin, wounding, and salicylic acid-mediated signaling pathway. The hub genes were co-expressed with important drought-responsive genes such as WRKY46, WRKY60, CML38, ERF6, ERF104, and ERF1A. They were regulated by many stress-responsive miRNAs, such as ath-miR5021, miR413, miR5998, and miR162, that could be used as candidate miRNAs for regulating key genes under drought stress. It seems that the regulation network was involved in signaling pathways and protein degradation under drought stress, and it consists of several important genes and miRNAs that are potential candidates for plant improvement and breeding programs.

Comprehensive analysis of chemokines family and related regulatory ceRNA network in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is one of the world's commonest malignancies with a high fatality rate. Chemokines not only regulate immune response but also participate in tumor development and metastasis and yet the mechanism of chemokines in LUAD remains unclear. In this study, transcriptional expression profiles, mutation data, and copy number variation data were downloaded from The Cancer Genome Atlas (TCGA). Risk gene protein expression was assessed by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Human Protein Atlas (HPA). Gene Expression Omnibus (GEO) data was used to validate the prognostic model. We summarized the genetic mutation variation landscape of chemokines. The risk prognosis model was developed based on differentially expressed chemokines, and patients in the high-risk score (RS) group had lower survival rates. Gene Set Enrichment Analysis (GSEA) revealed that high-RS patients were associated with metabolic transformation pathways, while low-RS patients were associated with immune-related pathways. Compared with the high-RS group, the low-RS group had higher immune/stromal/estimate scores calculated by the ESTIMATE package. The proportion of immune cells obtained using the CIBERSORT package was significantly different between the two groups. Most of the immune checkpoints were highly expressed in low-RS samples. Finally, we discovered that the lncRNA MIR17HG/AC009299.3/miR-21–5p/CCL20 regulatory network might be crucial in the pathogenesis of LUAD. In conclusion, we developed a risk signature and chemokine-related competing endogenous RNA (ceRNA) network.

Integrated analysis of competitive endogenous ribose nucleic acids (ceRNAs)-related regulatory networks in invasive and non-invasive non-functioning pituitary adenomas (NFPAs).

BackgroundThis study aims to identify the differentially expressed (DE) non-coding ribose nucleic acids (ncRNAs), messenger RNA (mRNA) expression profiles, and competitive endogenous RNA (ceRNA)-related regulatory networks in invasive and non-invasive nonfunctioning pituitary adenomas (NFPAs).MethodsA full-transcriptome sequencing of invasive and non-invasive NFPAs is carried out to evaluate the expression profiles of circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNA expression profiles.ResultsThe screening criteria resulted in 118 DEcircRNAs (88 up-regulated and 30 down-regulated), 105 DElncRNAs (68 up-regulated and 37 down-regulated), 43 DEmiRNAs (22 up-regulated and 21 down-regulated), and 268 DEmRNAs (194 up-regulated and 74 down-regulated). Accordingly, a ceRNA regulatory network related to invasive NFPA is constructed. Further, the Gene Ontology and Kyoto Encylopedia of Genes and Genomes analyses showed that circRNAs and lncRNAs in the network are related to chromatin remodeling, participating in the Janus kinase/signal transducer and activator of transcription (JAK-STAT) and calcium signaling pathways. Hsa-miR-1248 showed exceptional connectivity in the ceRNA regulatory network, which could be closely related to the invasiveness of NFPAs.ConclusionsTogether, these findings clarified the regulatory mechanisms of invasive and non-invasive NFPAs, providing innovative research avenues and therapeutic targets for invasive NFPAs.

Investigation on the differentially expressed circular RNAs in myocardium of mice with diabetic cardiomyopathy

Objective: To identify the differentially expressed circular RNA (circRNA) in the myocardium of diabetic cardiomyopathy (DCM) mice, and analyze their possible biological functions and related regulatory network. Methods: C57BL/6 mice, aged 8 weeks, and weighing were 21-27 g. Eight mice were selected as the control group and 15 mice were selected as the experimental group. The diabetic mice model was established by intraperitoneal injection of streptozotocin in the experimental group. One week after injection, the fasting blood glucose level of mice was measured, and 12 diabetic mice were included in the final experimental group. All mice were fed for 12 weeks under the same laboratory conditions. The cardiac structure and function were detected by echocardiography. Diabetic mice with the left ventricular ejection fraction less than 60% and the E/A less than 1.6 were selected as DCM group (n=3). Mice in DCM group and control group were then sacrificed under deep anesthesia. RNA was extracted from myocardial tissue. High-throughput RNA sequencing technology was used to sequence and identify the RNA in the myocardial tissue of DCM group and normal control group, and the difference was analyzed by DeSeq2. The analysis results were verified at the tissue level by RT-qPCR, and the differential circRNA were analyzed by GO and KEGG pathway analysis. The differentially expressed circRNA-microRNA(miRNA) interaction was predicted by the miRNA target gene prediction software. Results: A total of 63 differentially expressed circRNAs were found in the myocardium of DCM mice. The results of RT-qPCR showed that the tissue level expression of 8 differentially expressed circRNAs was consistent with the sequencing results, of which 7 were up-regulated and 1 was down-regulated. KEGG pathway analysis showed that the up-regulated circRNAs was mainly related to AMPK signal pathway and intercellular adhesion junction pathway, and the down-regulated circRNA was mainly related to cardiomyopathy. Go analysis showed that the up-regulated circRNA was mainly related to the binding process of ions, proteins, kinases and other factors in terms of molecular function, and was involved in regulating the intracellular structure, especially the composition of organelles in terms of cell components. The functional analysis of molecular function and cell components showed that the up-regulated circRNA were related to the cell component origin, recruitment and tissue, and thus participated in the regulation of cell biological process. The down regulated circRNA was related to catalytic activity in terms of molecular function, protein kinase binding process, transferase and calmodulin activity, and was closely related to the components of contractile fibers and the composition of myofibrils. These differentially expressed circRNAs were also related to biological processes such as lysine peptide modification, sarcomere composition, myofibril assembly, morphological development of myocardial tissue, myocardial hypertrophy and so on. Conclusions: In this study, we detected the novel differentially expressed circRNAs in the myocardium of DCM mice, and bioinformatics analysis confirmed that these circRNAs are related to oxidative stress, fibrosis and death of cardiomyocytes, and finally participate in the pathophysiological process of DCM.

Whole Transcriptome Sequencing Identified CircRNA Profiles and the Related Networks in Schizophrenia

Schizophrenia (SCZ) is a complex psychiatric syndrome with uncertain etiology. This study aimed to uncover the expression profiles and related regulatory networks of circular RNA (circRNA) in SCZ. Whole transcriptome sequencing was performed to assess the expression profiles of circRNAs and microRNAs (miRNAs) in the peripheral blood of three patients with SCZ and three healthy controls. Five circRNAs were validated by quantitative real-time PCR (RT-qPCR). TargetScan, RNAhybrid, and miRanda were performed to predict the target miRNAs of the top 10 dysregulated circRNAs. MiRTarBase was applied to predict the target mRNAs of miRNAs to construct circRNA-miRNA-mRNA (ceRNA) networks. CatRAPID and StarBase were used to predict the target RNA-binding proteins (RBPs) of circRNAs to construct circRNA-RBP networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the potential functions of the maternal genes of circRNAs and target mRNAs. In total, 450 circRNAs and 160 miRNAs were found to be significantly differentially expressed, with hsa_circ_0003999 and hsa_circ_0030042 being significantly different between patients with SCZ and healthy controls (P < 0.05). The PI3K-AKT, MAPK, and cell cycle pathways were predicted to be associated with SCZ. GO analysis showed that focal adhesion was related to SCZ. The ceRNA networks, especially hsa_circ_0006151/hsa-miR-4685-3p/ZBTB16, hsa_circ_0000008/hsa-miR-1976/ZBTB16, and the hsa_circ_0007963/hsa-miR-3127-3p/UBE2K axes have the greatest probability of being involved in the pathophysiology of SCZ. The RBP networks, FXR1, FXR2, DGCR8, XRN2, FMR1, and QKI were the RBPs associated with SCZ. In conclusion, the circRNAs, ceRNAs, and RBP network expression patterns and related pathways indicate the potential role of circRNAs in the pathogenesis and development of SCZ.

Utilisation of semiconductor sequencing for the detection of predictive biomarkers in glioblastoma.

The standard treatment for glioblastoma involves a combination of surgery, radiation and chemotherapy but have limited impact on survival. The exponential increase in targeted agents directed at pivotal oncogenic pathways now provide new therapeutic opportunities for this tumour type. However, lack of comprehensive precision oncology testing at diagnosis means such therapeutic opportunities are potentially overlooked. To investigate the role of semiconductor sequencing for detection of predictive biomarkers in routine glioblastoma samples we have undertaken analysis of test trending data generated by a clinically validated next generation sequencing platform designed to capture actionable genomic variants distributed across 505 genes. Analysis was performed across a cohort of 55 glioblastoma patients. Analysis of trending data has revealed a complex and rich actionable mutational landscape in which 166 actionable mutations were detected across 36 genes linked to 17 off label targeted therapy protocols and 111 clinical trials. The majority of patients harboured three or more actionable mutations affecting key cancer related regulatory networks including the PI3K/AKT/MTOR and RAS/RAF/MEK/MAPK signalling pathways, DNA-damage repair pathways and cell cycle checkpoints. Linkage with immunotherapy and PARP inhibitors was identified in 44% of glioblastoma patients as a consequence of alterations in DNA-damage repair genes. Taken together our data indicates that precision oncology testing utilising semiconductor sequencing can be used to identify a broad therapeutic armamentarium of targeted therapies and immunotherapies that can be potentially employed for the improved clinical management of glioblastoma patients.

Posttranscriptional Regulation of Insulin Resistance: Implications for Metabolic Diseases.

Insulin resistance defines an impairment in the biologic response to insulin action in target tissues, primarily the liver, muscle, adipose tissue, and brain. Insulin resistance affects physiology in many ways, causing hyperglycemia, hypertension, dyslipidemia, visceral adiposity, hyperinsulinemia, elevated inflammatory markers, and endothelial dysfunction, and its persistence leads to the development metabolic disease, including diabetes, obesity, cardiovascular disease, or nonalcoholic fatty liver disease (NAFLD), as well as neurological disorders such as Alzheimer’s disease. In addition to classical transcriptional factors, posttranscriptional control of gene expression exerted by microRNAs and RNA-binding proteins constitutes a new level of regulation with important implications in metabolic homeostasis. In this review, we describe miRNAs and RBPs that control key genes involved in the insulin signaling pathway and related regulatory networks, and their impact on human metabolic diseases at the molecular level, as well as their potential use for diagnosis and future therapeutics.

Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response

Drought is one of the most common environmental stresses affecting crops yield and quality. Plants’ responses to drought are controlled by regulatory mechanisms. Sesame is an important oilseed crop that most likely faces drought during its growth due to growing in semi-arid and arid areas. Despite this importance, there is little information about sesame regulatory mechanisms against drought stress. In this study, highly differentially expressed genes were identified using in-silico transcriptome analysis of two sesame genotypes (one sensitive and one tolerant) under drought stress. Interactions between identified genes and regulators including Transcription Factors (TF) and microRNAs (miRNA) were predicted using bioinformatics tools and then related regulatory networks were constructed. A total of 117 TFs and 133 miRNAs that might be involved in drought stress were identified with this approach. Key regulators of sesame under drought stress were detected by network analysis. Regulatory modules involved in drought response were extracted from the integrated networks using the MCODE algorithm, to explore important relationships. Finally, some of the identified drought-tolerance-related genes were examined using qRT-PCR analysis in two contrasting sesame genotypes under drought conditions. Interestingly, the studied genes showed a different expression pattern in the tolerant genotype compared to the sensitive. Taken together, our results suggest that miR530/TGA1/CER1, miR319/NAC29L, and miR171/SUC2L modules might play key roles in sesame drought tolerance by regulating wax biosynthesis, leaf senescence, and sugar transport during drought, respectively. Overall, the identified drought-related genes including TFs and miRNAs along with their relationships could be valuable candidates for future studies and breeding programs on enhancing sesame tolerance under drought stress.

Identification of Candidate Gene Signatures and Regulatory Networks in Endometriosis and its Related Infertility by Integrated Analysis.

Endometriosis is a common gynecological disease associated with infertility, and it represents an economic burden worldwide. However, the molecular mechanisms underlying endometriosis development have not yet been fully elucidated. Here, we aimed to identify reliable key genes and the related regulatory network that may be involved in endometriosis. Differentially expressed genes (DEGs) were identified through integrated analysis of four expression datasets of endometriosis from Gene Expression Omnibus. Gene functional analysis and protein-protein interaction network construction were performed to reveal the potential function of DEGs. Subsequently, candidate hub genes were defined and validated in GSE105764 dataset, and the associated regulatory networks were constructed. Additionally, GSE120103 dataset was applied to identify the differential expression between the infertile and fertile groups of patients with stage IV endometriosis. Finally, real-time quantitative polymerase chain reaction analysis was performed to identify the differential expression of hub genes in the collected clinical specimens. Robust rank aggregation integrated analysis determined 158 DEGs. Epithelial cell differentiation was the most significantly enriched biological process, and leukocyte transendothelial migration was the most significantly enriched pathway. Eight hub genes including CLDN3, CLDN5, CLDN7, CLDN11, HOXC8, HOXC6, HOXB6, and HOXB7 were identified, and most of these were validated as abnormally expressed genes in both the infertile group and patients with endometriosis. Transcriptional factors and microRNAs related to these genes were identified. Altogether, our integrated analysis identified critical gene signatures, involved pathways, and regulatory networks, which could provide clinically significant insights into the molecular mechanisms underlying endometriosis and its related infertility.

Cell signaling during drought and/or cold stress in cassava

Cassava (<italic>Manihot esculenta</italic> Crantz) is a root crop significant in food security and various bio-industrial applications such as animal feed, modified starch, and biofuels. Drought and cold stress are two major factors limiting cassava production qualitatively and quantitatively, for which plants have evolved mechanisms to overcome the impact of these two stressors. In recent years, significant progress has been achieved in understanding the response mechanism of cassava plants to stress signals to tolerate the above stresses. In this review, core stress-signaling pathways, including transcription factor (TF)-related regulatory networks, plant hormone signaling, reactive oxygen species (ROS) scavenging, and non-coding RNA (ncRNA) and alternative splicing (AS) that modify gene expression levels in response to drought and/or cold stress in cassava, are summarized. Understanding these stress signaling and responses will increase our ability to improve the crops tolerance to multiple stresses for agricultural sustainability and food security for the growing world population.

PaPYL9 is involved in the regulation of apricot fruit ripening through ABA signaling pathway

Abscisic acid (ABA) is a major regulator of non-climacteric fruit ripening; however, the role of ABA in the ripening of climacteric fruit is not clear. Here, as a typical climacteric fruit, apricots were used to investigate the role of ABA in fruit ripening. Based on weighted gene co-expression network analysis (WGCNA) of our previous transcriptome data, we treated ‘Danxing’ fruit with exogenous ABA and obtained ABA receptor genes, genes related to ABA biosynthesis and signal transduction, and analyzed the response of these candidate genes to exogenous ABA during fruit ripening. Subsequently, the full length of candidate PYLs genes were cloned, and their putative function were analyzed by phylogenetic analysis and protein structure domain analysis. And then the function of one candidate gene PaPYL9 was verified by using transgenic tomato. Furthermore, the response genes in transgenic tomato were screened by transcriptome sequencing, and ultimately the related regulatory network was proposed. The results showed that the injection of exogenous 1.89 mmol·L-1 ABA remarkably promoted fruit coloration, and increased the color index for red grapes (CIRG) and the total soluble solids (TSS) content, but significantly decreased the firmness and titratable acid (TA) content (p < 0.01). Nordihydroguaiaretic acid (NDGA), the inhibitor of ABA, appeared to have the converse role in TA, TSS, CIRG and firmness, during the ripening process. One NCED (9-cis-epoxycarotenoiddioxygenase) and five ABA receptor genes related to signal transduction were mined from the transcriptome data of apricot fruit through WGCNA. Compared with the control, the expression levels of NCED1, PYL9 (PYR/PYL/RCAR), SnRK2 (SUCROSE NON-FERMENTING1 (SNF1)-RELATED PROTEIN KINASE 2S), and ABF2 (ABRE-binding bZIP transcription) were induced dramatically by ABA treatment (p < 0.01), while NDGA treatment significantly inhibited their expression. Based on gene expression and protein domain analysis, we inferred that PaPYL9 is putatively involved in apricot fruit ripening. Overexpression of PaPYL9 in Micro-TOM tomatoes resulted in the promotion of early ripening. Simultaneously, the expression levels of genes related ethylene biosynthesis, chlorophyll degradation, fruit softening, flavor formation, pigment synthesis, and metabolism were all significantly induced in overexpression of PaPYL9 tomatoes. This indicates the central role of ABA in climacteric fruit ripening. A regulatory network was tentatively proposed, laying the foundation to unveil the molecular mechanism of the regulatory role of PaPYL9 in fruit ripening.

A Risk Score Model Incorporating Three m6A RNA Methylation Regulators and a Related Network of miRNAs-m6A Regulators-m6A Target Genes to Predict the Prognosis of Patients With Ovarian Cancer.

Ovarian cancer (OC) is the leading cause of cancer-related death among all gynecological tumors. N6-methyladenosine (m6A)-related regulators play essential roles in various tumors, including OC. However, the expression of m6A RNA methylation regulators and the related regulatory network in OC and their correlations with prognosis remain largely unknown. In the current study, we obtained the genome datasets of OC from GDC and GTEx database and analyzed the mRNA levels of 21 key m6A regulators in OC and normal human ovarian tissues. The expression levels of 7 m6A regulators were lower in both the OC tissues and the high-stage group. Notably, the 5-year survival rate of patients with OC presenting low VIRMA expression or high HNRNPA2B1 expression was higher than that of the controls. Next, a risk score model based on the three selected m6A regulators (VIRMA, IGF2BP1, and HNRNPA2B1) was built by performing a LASSO regression analysis, and the moderate accuracy of the risk score model to predict the prognosis of patients with OC was examined by performing ROC curve, nomogram, and univariate and multivariate Cox regression analyses. In addition, a regulatory network of miRNAs-m6A regulators-m6A target genes, including 2 miRNAs, 3 m6A regulators, and 47 mRNAs, was constructed, and one of the pathways, namely, miR-196b-5p-IGF2BP1-PTEN, was initially validated based on bioinformatic analysis and assay verification. These results demonstrated that the risk score model composed of three m6A RNA methylation regulators and the related network of miRNAs-m6A regulators-m6A target genes is valuable for predicting the prognosis of patients with OC, and these molecules may serve as potential biomarkers or therapeutic targets in the future.

English

Chlorogenic acid (CGA), as a kind of depside in plants, has a variety of beneficial effects on human health, which also plays an important role in helping plants resist a variety of stresses. Therefore, the biosynthetic pathway of CGA has been studied in many plants, however, the synthesis of CGA has not been well elucidated in Camellia sinensis. In our research, different CGA levels were detected between triploid tea variety „Qianfu 4‟ and diplont tea variety „Qianmei 419‟ using HPLC and the CGA content in triploid Camellia sinensis was greater than that in diploid Camellia sinensis. Transcriptome sequencing for diploid and triploid Camellia sinensis was employed to explore genes associated with CGA biosynthesis. Finally, 154,097 unigenes were obtained in total, of which 891 may be related to the biosynthesis of CGA. Furthermore, differentially expressed genes (DEGs) were screened between diploid and triploid Camellia sinensis, 32 DEGs were discovered to be related to CGA biosynthesis, including sixteen phenylalanine ammonia lyase (PAL) genes, three 4-coumarate coenzyme A ligase (4CL) genes, nine cinnamate 4-Hydroxylase (C4H) genes, four Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HQT/HCT), and two hundred and twenty-one TFs including eighty-eight ERFs, forty-one bZIPs, forty-two MYBs and fifty WRKYs, which may also play an important role in the biosynthesis of CGA. Our results will lay the foundation for further exploration of the biosynthesis of CGA and revealing the related regulatory network in Camellia sinensis. © 2021 Friends Science Publishers

Gamma-interferon inducible lysosomal thiolreductase (GILT) effect on breast tumor microenvironment through regulating CXCR6/CXCL16 axis.

e15081 Background: Gamma-interferon Inducible Lysosomal Thiolreductase (GILT) is constitutively expressed in most antigens endocytosed by antigen presenting cells (APCs), and its function is to catalyze the reduction of disulfide (S-S) bonds in protein substrates. The cytokine CXCL16 is one of the only two known plasma membrane chemokines which induces chemotaxis of activated T cells and bone marrow plasma cells in tumor microenvironment. It contains a free end folded by two sulfur bonds and therefore could also be a zymolyte of GILT. Previous studies found that specific receptor of CXCL16, CXCR6, was significantly overexpressed in breast cancer tissues and metastatic axillary lymph nodes. We suppose whether CXCR6/CXCL16 axis is regulated by GILT and affect tumor microenvironment, thereby eliciting specific anti-tumor immune responses in breast cancer (BC). Methods: GILT expression in BC was evaluated using publicly available data from The Cancer Genome Atlas (TCGA). GILT gene was analyzed in UALCAN ( http://ualcan.path.uab.edu/analysis-prot.html ) . In vitro, Immunohistochemistry (IHC) was conducted to examine the location and relation of GILT and CXCR6. Gene Set Enrichment Analysis (GSEA) was performed to mine the biological pathways involved in BC related GILT regulatory network. The expression of GILT at protein and RNA levels were detected by Western Blot and RT-PCR assay. Overexpression and knockdown of GILT in BC cell lines was carried out to further analyzed the correlation between GILT and CXCL16/CXCR6. Results: TCGA database showed that GILT expression was increased in the stroma of BC compared with normal, and was correlated to shorter BC overall survival. GSEA suggested that the expression of GILT was associated with chemotactic factors. Pearson analysis and IHC showed GILT had a strong correlation with CXCL16/CXCR6 axis in the aspect of angiogenesis and immunity. qRT-PCR and Western Blot assay also revealed that GILT had high expression in BC. Besides, patients with high expression of GILT in IHC simultaneously showed high immunoreactive to macrophage markers, which was related to neovascularization and anti-tumor immune responses. Compared with the normal breast cell line MCF-10A, GILT protein had high expression in Hs578T and low expression in MDA-MB-231 cell line. GILT was overexpressed in MDA-MB-231 and knockdown in Hs578T. Result showed that high level GILT promoted the production of CXCL16/CXCR6,while GILT siRNA knockdown inhibited the production of CXCL16/CXCR6. Conclusions: GILT could catalyze CXCL16 in BC, function as a key mechanism to affect tumor microenvironment through CXCR6/CXCL16 pathway. GILT-activated CXCL16 levels showed a strong connection with unfavorable outcomes in BC, which could be a potential biomarker of prognosis and a novel therapeutic target.

SGK1 regulated apoptosis in invasive breast carcinoma.

e13061 Background: Worldwide, breast cancer is the most common type of cancers and the presentation of drug resistance is often associated with poor prognosis. Previous studies have shown the mechanism of drug resistance was affected by apoptosis at different levels in the signaling cascades. This article is aimed to explore the relationship between the serum and glucocorticoid-regulated kinase 1 (SGK1) and apoptosis in invasive breast cancer (IBC). Methods: We evaluated the expression of SGK1 in IBC using publicly available data from The Cancer Genome Atlas (TCGA) and Curtis Breast program. TaqMan probe-based qRT-PCR assay and Western Blot analysis were performed to quantitatively detect the expression of SGK1 at RNA and protein levels in the IBC specimens. Clinicopathologic characteristics associated with overall survival were tested by Cox regression. Gene Set Enrichment Analysis (GSEA) was performed to mine the biological pathways involved in IBC pathogenesis related SGK1 regulatory network using MSigDB database. Immunohistochemistry staining (IHC) was used to detect apoptotic markers Fas, Bcl2 and SGK1 in the IBC specimens. Results: Totally 1109 IBC samples with SGK1 expression data were downloaded from TCGA databases for analyzed. SGK1 expression was elevated in normal breast tissues compared with both invasive ductal carcinoma and invasive lobular carcinoma (p &lt; 0.0001). Among them, SKG expression in 112 tumor tissues was significantly lower than that in paracancerous tissues, especially in advanced patients with TNM stage IV. Western Blot and qRT-PCR assay confirmed that SGK1 expression in IBC was distinctly lower than normal. The Kaplan-Meier survival analysis showed that decreased expression of SGK1 was significantly correlated with the clinical stage (p = 0.036). In Curtis Breast program, we further verified SGK1 gene expression was reduced in stage IV than stage I. The univariate analysis demonstrated that clinicopathologic variables associated with poor survival include age, advanced stage, lymph nodes, distant metastasis and deep myometrial invasion. GSEA revealed that apoptosis was differentially enriched when SGK1 was highly expressed. Similarly, TCGA data indicated that the positive rate of SGK1 was higher in Fas positive IBCs, and the same result was also obtained by IHC in the IBC specimens. Conclusions: Expression of SGK1 regulated apoptosis in invasive breast carcinoma, which might be a potential therapeutic target to overcome refractory and drug-resistant breast cancer.