Transcriptional Regulatory Network Analysis Research Articles

The Critical Role of Phenylpropanoid Biosynthesis Pathway in Lily Resistance Against Gray Mold

Gray mold caused by Botrytis elliptica is one of the most determinative factors of lily growth and has become a major threat to lily productivity. However, the nature of the lily B. elliptica interaction remains largely unknown. Here, comparative transcriptomic and metabolomic were used to investigate the defense responses of resistant (‘Sorbonne’) and susceptible (‘Tresor’) lily cultivars to B. elliptica infection at 24 hpi. In total, 1326 metabolites were identified in ‘Sorbonne’ and ‘Tresor’ after infection, including a large number of phenylpropanoids. Specifically, the accumulation of four phenylpropanes, including eriodictyol, hesperetin, ferulic acid, and sinapyl alcohol, was significantly upregulated in the B. elliptica-infected ‘Sorbonne’ compared with the infected ‘Tresor’, and these phenylpropanes could significantly inhibit B. elliptica growth. At the transcript level, higher expression levels of F3′M, COMT, and CAD led to a higher content of resistance-related phenylpropanes (eriodictyol, ferulic acid, and sinapyl alcohol) in ‘Sorbonne’ following B. elliptica infection. It can be assumed that these phenylpropanes cause the resistance difference between ‘Sorbonne’ and ‘Tresor’, and could be the potential marker metabolites for gray mold resistance in the lily. Further transcriptional regulatory network analysis suggested that members of the AP2/ERF, WRKY, Trihelix, and MADS-M-type families positively regulated the biosynthesis of resistance-related phenylpropanes. Additionally, the expression patterns of genes involved in phenylpropanoid biosynthesis were confirmed using qRT-PCR. Therefore, we speculate that the degree of gray mold resistance in the lily is closely related to the contents of phenylpropanes and the transcript levels of the genes in the phenylpropanoid biosynthesis pathway. Our results not only improve our understanding of the lily’s resistance mechanisms against B. elliptica, but also facilitate the genetic improvement of lily cultivars with gray mold resistance.

Integrated multi-omics investigation revealed the importance of phenylpropanoid metabolism in the defense response of Lilium regale Wilson to fusarium wilt.

Lilies (genus Lilium) play a significant role in the global cut-flower industry, but they are highly susceptible to fusarium wilt caused by Fusarium oxysporum. However, Lilium regale, a wild lily species, exhibits remarkable resistance to F. oxysporum. To investigate the quantitative resistance of L. regale to fusarium wilt, a comprehensive multi-omics analysis was conducted. Upon inoculation with F. oxysporum, L. regale roots showed a significant accumulation of phenylpropane metabolites, including lignin precursors, flavonoids, and hydroxycinnamic acids. These findings were consistent with the upregulated expression of phenylpropanoid biosynthesis-related genes encoding various enzymes, as revealed by transcriptomics and proteomics analyses. Furthermore, metabolomics and proteomics data demonstrated differential activation of monoterpenoid and isoquinoline alkaloid biosynthesis. Colorimetry and high-performance liquid chromatography analyses revealed significantly higher levels of total flavonoids, lignin, ferulic acid, phlorizin, and quercetin contents in L. regale scales compared with susceptible lily 'Siberia' scales during F. oxysporum infection. These phenylpropanes exhibited inhibitory effects on F. oxysporum growth and suppressed the expression of pathogenicity-related genes. Transcriptional regulatory network analysis suggested that ethylene-responsive transcription factors (ERFs) may positively regulate phenylpropanoid biosynthesis. Therefore, LrERF4 was cloned and transiently overexpressed in the fusarium wilt-susceptible Oriental hybrid lily 'Siberia'. The overexpression of LrERF4 resulted in increased levels of total flavonoids, lignin, ferulic acid, phlorizin, and quercetin, while the silencing of LrERF4 in L. regale through RNAi had the opposite effect. In conclusion, phenylpropanoid metabolism plays a crucial role in the defense response of L. regale against fusarium wilt, with LrERF4 acting as a positive regulator of phenylpropane biosynthesis.

Abstract 6883: Investigation of tumor-immune interactions in pediatric sarcomas using single-cell multi-omics

Abstract Background: Pediatric sarcoma represents the second most common solid tumor in children. Despite advances in multimodal therapies, one-third of sarcoma patients do not survive the disease. Over the past few decades, the development of novel therapeutic strategies for sarcoma has been impeded by an insufficient understanding of the tumor microenvironment (TME). In particular, the potential of immunotherapy remains constrained by the gap of knowledge about the molecular and functional phenotypes of the immune cells in the sarcoma TME. Methods: To address this knowledge gap, we collected treatment-naïve tumor samples from 32 patients with five pediatric sarcoma subtypes. We employed a single-nuclei RNA+ATAC-Seq multi-omics assay to comprehensively characterize the transcriptomic and epigenomic heterogeneity of tumor and immune cells within the sarcoma TME. Results: Our analysis revealed that tumor-associated macrophages (TAMs) were the most abundant immune cell type in the sarcoma TME. We identified seven distinct TAM subpopulations, each exhibiting unique gene expression and chromatin accessibility patterns. Among these, TAM subsets with higher expression of SPP1 and C1QC genes displayed the strongest immunosuppressive potential. Transcriptional regulatory network (TRN) analysis identified transcription factors that were most likely to drive the phenotypes of SPP1+ and C1QC+ TAMs, including ELF2, JUND and RUNX1. Through cell-cell communication analysis, we discovered that SPP1+ TAMs interact with T cells via SPP1-CD44 signaling, while C1QC+ TAMs interact with NK cells through HLA-E-KLRC1 signaling, suggesting the potential involvement of these signaling pathways in TAM-mediated suppression of these cytotoxic lymphocytes. We prioritized ligand-receptor gene pairs, such as SEMA3D-NRP1 and LTBP3-ITGB5, which likely mediate the interaction between malignant sarcoma cells and SPP1+/C1QC+ TAMs based on their dominance across sarcoma subtypes and association with poorer clinical outcomes. On the other hand, our analysis revealed that sarcoma subtype-specific interactions between TAMs and malignant cells are common, highlighting the heterogeneity of signaling events across sarcoma subtypes. Conclusion and Significance: Our study presents a comprehensive single-cell multi-omics characterization of pediatric sarcomas and sheds light on its tumor microenvironment. By identifying unique markers for immunosuppressive TAM subpopulations and elucidating intercellular interactions promoting tumor development, this study proposes potential therapeutic targets for sarcoma treatment based on the role of TAMs in sarcoma TME. Citation Format: Zhan Zhang, Kyung Jin Ahn, Changya Chen, Rumeysa Biyik Sit, Hesham Mohei, Brian Lockhart, Malay Haldar, Kathrin Bernt, Vinodh Pillai, Kai Tan. Investigation of tumor-immune interactions in pediatric sarcomas using single-cell multi-omics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6883.

Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration

Lung epithelial regeneration after acute injury requires coordination cellular coordination to pattern the morphologically complex alveolar gas exchange surface. During adult lung regeneration, Wnt-responsive alveolar epithelial progenitor (AEP) cells, a subset of alveolar type 2 (AT2) cells, proliferate and transition to alveolar type 1 (AT1) cells. Here, we report a refined primary murine alveolar organoid, which recapitulates critical aspects of in vivo regeneration. Paired scRNAseq and scATACseq followed by transcriptional regulatory network (TRN) analysis identified two AT1 transition states driven by distinct regulatory networks controlled in part by differential activity of Nkx2-1. Genetic ablation of Nkx2-1 in AEP-derived organoids was sufficient to cause transition to a proliferative stressed Krt8+ state, and AEP-specific deletion of Nkx2-1 in adult mice led to rapid loss of progenitor state and uncontrolled growth of Krt8+ cells. Together, these data implicate dynamic epigenetic maintenance via Nkx2-1 as central to the control of facultative progenitor activity in AEPs.

Research on radiotherapy related genes and prognostic target identification of rectal cancer based on multi-omics

BackgroundRadiosensitivity of rectal cancer is related to the radiotherapy efficacy and prognosis of patients with rectal cancer, and the genes and molecular mechanisms related to radiosensitivity of rectal cancer have not been clarified. We explored the radiosensitivity related genes of rectal cancer at a multi omics level.MethodsmRNA expression data and rectum adenocarcinoma (READ) data were obtained from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus Database (GEO) (GSE150082, GSE60331, GSE46862, GSE46862). Differentially expressed genes between radiotherapy sensitive group and radiotherapy insensitive group were screened. GO analysis and KEGG pathway analysis were performed for differentially expressed genes. Among the differentially expressed genes, five core genes associated with rectal cancer prognosis were selected using random survival forest analysis. For these five core genes, drug sensitivity analysis, immune cell infiltration analysis, TISIDB database immune gene correlation analysis, GSEA enrichment analysis, construction of Nomogram prediction model, transcriptional regulatory network analysis, and qRT-PCR validation was performed on human rectal adenocarcinoma tissue.ResultsWe found that 600 up-regulated genes and 553 down-regulated genes were significantly different between radiotherapy sensitive group and radiotherapy insensitive group in rectal cancer. Five key genes, TOP2A, MATR3, APOL6, JOSD1, and HOXC6, were finally screened by random survival forest analysis. These five key genes were associated with different immune cell infiltration, immune-related genes, and chemosensitivity. A comprehensive transcriptional regulatory network was constructed based on these five core genes. qRT-PCR revealed that MATR3 expression was different in rectal cancer tissues and adjacent non-cancerous tissues, while APOL6, HOXC6, JOSD1, and TOP2A expression was not different.ConclusionFive radiosensitivity-related genes related to the prognosis of rectal cancer: TOP2A, MATR3, APOL6, JOSD1, HOXC6, are involved in multiple processes such as immune cell infiltration, immune-related genes, chemosensitivity, signaling pathways and transcriptional regulatory networks and may be potential biomarkers for radiotherapy of rectal cancer.

Multi-omics network analysis on samples from sequential biopsies reveals vital role of proliferation arrest for Macrosteatosis related graft failure in rats after liver transplantation

To investigate the molecular impact of graft MaS on post-transplant prognosis, based on multi-omics integrative analysis. Rats were fed by methionine-choline deficient diet (MCD) for MaS grafts. Samples were collected from grafts by sequential biopsies. Transcriptomic and metabolomic profilings were assayed. Post-transplant MaS status showed a close association with graft failure. Differentially expressed genes (DEGs) for in-vivo MaS were mainly enriched on pathways of cell cycle and DNA replication. Post-transplant MaS caused arrests of graft regeneration via inhibiting the E2F1 centered network, which was confirmed by an in vitro experiment. Data from metabolomics assays found insufficient serine/creatine which is located on one‑carbon metabolism was responsible for MaS-related GF. Pre-transplant MaS caused severe fibrosis in long-term survivors. DEGs for grafts from long-term survivors with pre-transplant MaS were mainly enriched in pathways of ECM-receptor interaction and focal adhesion. Transcriptional regulatory network analysis confirmed SOX9 as a key transcription factor (TF) for MaS-related fibrosis. Metabolomic assays found elevation of aromatic amino acid (AAA) was a major feature of fibrosis in long-term survivors. Graft MaS in vivo increased post-transplant GF via negative regulations on graft regeneration. Pre-transplant MaS induced severe fibrosis in long-term survivors via activations on ECM-receptor interaction and AAA metabolism.

Canagliflozin mediates tumor suppression alone and in combination with radiotherapy in non-small cell lung cancer (NSCLC) through inhibition of HIF-1α.

Non-small cell lung cancer (NSCLC) has a poor prognosis and effective therapeutic strategies are lacking. The diabetes drug canagliflozin inhibits NSCLC cell proliferation and the mammalian target of rapamycin (mTOR) pathway, which mediates cell growth and survival, but it is unclear whether this drug can enhance response rates when combined with cytotoxic therapy. Here, we evaluated the effects of canagliflozin on human NSCLC response to cytotoxic therapy in tissue cultures and xenografts. Ribonucleic acid sequencing (RNA-seq), real-time quantitative PCR (RT-qPCR), metabolic function, small interfering ribonucleic acid (siRNA) knockdown and protein expression assays were used in mechanistic analyses. We found that canagliflozin inhibited proliferation and clonogenic survival of NSCLC cells, and augmented the efficacy of radiotherapy to mediate these effects and inhibit NSCLC xenograft growth. Canagliflozin treatment alone moderately inhibited mitochondrial oxidative phosphorylation and exhibited greater anti-proliferative capacity than specific mitochondrial complex-I inhibitors. The treament downregulated genes mediating hypoxia-inducible factor (HIF)-1α stability, metabolism and survival, activated adenosine monophosphate-activated protein kinase (AMPK) and inhibited mTOR, a critical activator of HIF-1α signaling. HIF-1α knockdown and stabilization experiments suggested that canagliflozin mediates anti-proliferative effects, in part, through suppression of HIF-1α. Transcriptional regulatory network analysis pinpointed histone deacetylase 2 (HDAC2), a gene suppressed by canagliflozin, as a key mediator of canagliflozin's transcriptional reprogramming. HDAC2 knockdown eliminated HIF-1α levels and enhanced the anti-proliferative effects of canagliflozin. HDAC2-regulated genes suppressed by canagliflozin are associated with poor prognosis in several clinical NSCLC datasets. In addition, we include evidence that canagliflozin also improves NSCLC response to chemotherapy. In summary, canagliflozin may be a promising therapy to develop in combination with cytotoxic therapy in NSCLC.

Pien-Tze-Huang prevents hepatocellular carcinoma by inducing ferroptosis via inhibiting SLC7A11-GSH-GPX4 axis

BackgroundMalignant transformation from hepatic fibrosis to carcinogenesis may be a therapeutic target for hepatocellular carcinoma (HCC). The aim of this study was to evaluate anti-cancer efficacy of Pien-Tze-Huang (PZH), and to investigate the underlying mechanisms by integrating transcriptional regulatory network analysis and experimental validation.MethodsA diethylnitrosamine (DEN)-induced HCC model in rats was established and used to evaluate the anti-cancer efficacy of PZH. After detecting a transcriptomic profiling, the “disease-related gene–drug effective target” interaction network was constructed, and the candidate targets of PZH against malignant transformation from hepatic fibrosis to HCC were identified and verified in vitro.ResultsPZH effectively alleviated the pathological changes of hepatic fibrosis and cirrhosis, and inhibited tumor formation and growth in DEN-induced HCC rats. Additionally, the administration of PZH reduced the levels of various hepatic function-related serological indicators significantly. Mechanically, a ferroptosis-related SLC7A11-GSH-GPX4 axis might be one of potential targets of PZH against malignant transformation from hepatic fibrosis to HCC. Especially, high SLC7A11 expression may be associated with poor prognosis of HCC patients. Experimentally, the administration of PZH markedly increased the trivalent iron and ferrous ion, suppressed the expression levels of SLC7A11 and GPX4 proteins, and reduced the GSH/GSSG ratio in the liver tissues of DEN-induced HCC rats.ConclusionsOur data offer an evidence that PZH may effectively improve the hepatic fibrosis microenvironment and prevent the occurrence of HCC through promoting ferroptosis in tumor cells via inhibiting the SLC7A11-GSH-GPX4 axis, implying that PZH may be a potential candidate drug for prevention and treatment of HCC at an early stage.

Single-cell transcriptional profiling of hearts during cardiac hypertrophy reveals the role of MAMs in cardiomyocyte subtype switching

Pathological cardiac hypertrophy is the main predecessor of heart failure. Its pathology is sophisticated, and its progression is associated with multiple cellular processes. To explore new therapeutic approaches, more precise examination of cardiomyocyte subtypes and involved biological processes is required in response to hypertrophic stimuli. Mitochondria and the endoplasmic reticulum (ER) are two crucial organelles associated with the progression of cardiac hypertrophy and are connected through junctions known as mitochondria-associated endoplasmic reticulum membranes (MAMs). Although MAM genes are altered in cardiac hypertrophy, the importance of MAMs in cardiac hypertrophy and the expression pattern of MAMs in certain cardiac cell types require a comprehensive analysis. In this study, we analyzed the temporal expression of MAM proteins in the process of cardiac hypertrophy and observed that MAM-related proteins preferentially accumulated in cardiomyocytes at the initial stage of cardiac hypertrophy and underwent a gradual decline, which was synchronized with the proportion of two cardiomyocyte subtypes (CM2 and CM3). Meanwhile, these subtypes went through a functional switch during cardiac hypertrophy. Trajectory analysis suggested that there was a differentiation trajectory of cardiomyocyte subtypes from high to low MAM protein expression. Distinct regulon modules across different cardiomyocyte cell types were revealed by transcriptional regulatory network analysis. Furthermore, scWGCNA revealed that MAM-related genes were clustered into a module that correlated with diabetic cardiomyopathy. Altogether, we identified cardiomyocyte subtype transformation and the potential critical transcription factors involved, which may serve as therapeutic targets in combating cardiac hypertrophy.

Single-cell transcriptomics uncovers the differentiation of a subset of murine esophageal progenitors into taste buds in vivo

Mouse esophagus is lined with a stratified epithelium, which is maintained by the constant renewal of unipotent progenitors. In this study, we profiled mouse esophagus by single-cell RNA sequencing and found taste buds specifically in the cervical segment of the esophagus. These taste buds have the same cellular composition as the ones from the tongue but express fewer taste receptor types. State-of-the-art transcriptional regulatory network analysis allowed the identification of specific transcription factors associated to the differentiation of immature progenitors into the three different taste bud cell types. Lineage tracing experiments revealed that esophageal taste buds arise from squamous bipotent progenitor, thus demonstrating that all esophageal progenitors are not unipotent. Our cell resolution characterization of cervical esophagus epithelium will enable a better understanding of esophageal progenitor potency and insights into the mechanisms involved in the development of taste buds.

TEAD4 is a master regulator of high-risk nasopharyngeal carcinoma

The molecular basis underlying nasopharyngeal carcinoma (NPC) remains unclear. Recent progress in transcriptional regulatory network analysis helps identify the master regulator (MR) proteins that transcriptionally define malignant tumor phenotypes. Here, we investigated transcription factor-target interactions and identified TEA domain transcription factor 4 (TEAD4) as an MR of high-risk NPC. Precisely, TEAD4 promoted NPC migration, invasion and cisplatin resistance, depending on its autopalmitoylation. Mechanistically, YTHDF2 (YTH domain family 2) recognized WTAP (Wilms tumor 1-associating protein)-mediated TEAD4 m6A methylation to facilitate its stability and led to aberrant up-regulation of TEAD4. Up-regulated TEAD4 further drove NPC progression by transcriptionally activating BZW2 (basic leucine zipper and W2 domains 2) to induce the oncogenic AKT pathway. Moreover, the transcriptional activity of TEAD4 was independent of its canonical coactivators YAP/TAZ. Clinically, TEAD4 serves as an independent predictor of unfavorable prognosis and cisplatin response in NPC. Our data revealed the crucial role of TEAD4 in driving tumor malignancy, thus, may provide therapeutic vulnerability in NPC.

Nuclear Receptor Subfamily 4A Signaling as a Key Disease Pathway of CD1c+ Dendritic Cell Dysregulation in Systemic Sclerosis.

This study was undertaken to identify key disease pathways driving conventional dendritic cell (cDC) alterations in systemic sclerosis (SSc). Transcriptomic profiling was performed on peripheral blood CD1c+ cDCs (cDC2s) isolated from 12 healthy donors and 48 patients with SSc, including all major disease subtypes. We performed differential expression analysis for the different SSc subtypes and healthy donors to uncover genes dysregulated in SSc. To identify biologically relevant pathways, we built a gene coexpression network using weighted gene correlation network analysis. We validated the role of key transcriptional regulators using chromatin immunoprecipitation (ChIP) sequencing and in vitro functional assays. We identified 17 modules of coexpressed genes in cDCs that correlated with SSc subtypes and key clinical traits, including autoantibodies, skin score, and occurrence of interstitial lung disease. A module of immunoregulatory genes was markedly down-regulated in patients with the diffuse SSc subtype characterized by severe fibrosis. Transcriptional regulatory network analysis performed on this module predicted nuclear receptor 4A (NR4A) subfamily genes (NR4A1, NR4A2, NR4A3) as the key transcriptional regulators of inflammation. Indeed, ChIP-sequencing analysis indicated that these NR4A members target numerous differentially expressed genes in SSc cDC2s. Inclusion of NR4A receptor agonists in culture-based experiments provided functional proof that dysregulation of NR4As affects cytokine production by cDC2s and modulates downstream T cell activation. NR4A1, NR4A2, and NR4A3 are important regulators of immunosuppressive and fibrosis-associated pathways in SSc cDCs. Thus, the NR4A family represents novel potential targets to restore cDC homeostasis in SSc.

Uncovering Transcriptome Characteristics in Bone Marrow Hematopoiesis in Immune Thrombocytopenia at Single-Cell Resolution

Immune thrombocytopenia (ITP) is an autoimmune disorder, in which megakaryocyte dysfunction caused by an autoimmune reaction can lead to thrombocytopenia, although the underlying mechanisms remain unclear. Here, we hypothesized that bone marrow (BM) CD34+ hematopoietic stem and progenitor cells (HSPCs) participated in the defective megakaryogenesis in ITP patients, and we performed single-cell RNA-seq (scRNA-seq) of BM CD34+ HSPCs to reveal the overall transcriptome alterations in HSPCs in ITP. Dimensional reduction using uniform manifold approximation and projection (UMAP) showed the effective integration of the datasets from different samples. We manually annotated the cell clusters into 17 different cell types with distinct gene expression patterns. By performing differential expression analysis, enrichment analysis, trajectory analysis, transcriptional regulatory network analysis and cell-cell interaction analysis, we found that gene expression, transcriptional regulatory networks and cell-cell interactions varied in HSPCs of ITP, particularly in a pre-B cell population and natural killer/T cell progenitors, highlighting the selective immune aberration associated with defective megakaryopoiesis in ITP. Differentially expressed gene (DEG) analysis indicated that the top upregulated genes in a megakaryocytic progenitors (MkP) population of ITP were associated with erythropoiesis, suggesting a bias toward erythrocytes in megakaryopoiesis in ITP. Moreover, Flow cytometry confirmed that the number of CD9+ cells from CD34+ HSPCs decreased in ITP. Liquid culture assays demonstrated that CD9+ CD34+ HSPCs from healthy controls tended to differentiate into megakaryocytes; however, this tendency was not observed in ITP patients. The percentage of megakaryocytes differentiated from CD9+CD34+ HSPCs was higher than that of the CD9- counterparts from healthy controls, whereas in ITP patients, the percentage decreased to only 1/4th of that in the healthy controls and was comparable to that from the CD9- HSPCs, indicating that differentiation of CD9+ HSPCs toward the megakaryopoietic lineage was impaired in ITP. Further analysis revealed the universality of their heterogeneity and provided an analytical basis for the study of megakaryocyte-related diseases, including ITP. Enrichment analysis confirmed the definition of MkP in our ITP integrated dataset. To further analyze the transcriptional difference between ITP and HC, we pooled MkP from all samples. The expression of several molecular features of MkP was visualized, and seven transcriptionally heterogeneous subpopulations of MkP were identified. We then assessed the expression of marker genes in each subpopulation and characterized the gene sets enriched in different clusters, which showed pronounced heterogeneity within MkP, consistent with the results of previous analyses of MkP/Mk from multi-hematopoietic tissues. We evaluated ITP-associated DEGs in each MkP subcluster, and we found that most of these DEGs were subtype-specific, indicative of the subtype-specific effects of the disorder. In summary, this study dissects the significant heterogeneity and disease characteristics of BM CD34+ HSPCs from ITP patients at single-cell resolution, revealing new insights regarding the pathophysiology of ITP.

A joint transcriptional regulatory network and protein activity inference analysis identifies clinically associated master regulators for biliary atresia.

Biliary atresia (BA) is a devastating cholangiopathy in neonate. Transcription factors (TFs), a type of master regulators in biological processes and diseases, have been implicated in pathogenesis of BA. However, a global view of TFs and how they link to clinical presentations remain explored. Here, we perform a joint transcriptional regulatory network and protein activity inference analysis in order to investigate transcription factor activity in BA. By integration of three independent human BA liver transcriptome datasets, we identify 22 common master regulators, with 14 activated- and 8 repressed TFs. Gene targets of activated TFs are enriched in biological processes of SMAD, NF-kappaB and TGF-beta, while those of repressed TFs are related to lipid metabolism. Mining the clinical association of TFs, we identify inflammation-, fibrosis- and survival associated TFs. In particular, ZNF14 is predictive of poor survival and advanced live fibrosis. Supporting this observation, ZNF14 is positively correlated with T helper cells, cholangiocytes and hepatic stellate cells. In sum, our analysis reveals key clinically associated master regulators for BA.

Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells

BackgroundThe application of cell-specific construction of transcription regulatory networks (TRNs) to identify their master regulators (MRs) in EMP2 induced vascular proliferation disorders has been largely unexplored.MethodsDifferent expression gene (DEGs) analyses was processed with DESeq2 R package, for public RNA-seq transcriptome data of EMP2-treated hRPECs versus vector control (VC) or wild type (WT) hRPECs. Virtual Inference of protein activity by Enriched Regulon analysis (VIPER) was used for inferring regulator activity and ARACNE algorithm was conducted to construct TRNs and identify some MRs with DEGs from comparisons.ResultsFunctional analysis of DEGs and the module analysis of TRNs demonstrated that over-expressed EMP2 leads to a significant induction in the activity of regulators next to transcription factors and other genes implicated in vasculature development, cell proliferation, and protein kinase B signaling, whereas regulators near several genes of platelet activation vascular proliferation were repressed. Among these, PDGFA, ALDH1L2, BA1AP3, ANGPT1 and ST3GAL5 were found differentially expressed and significantly activitve in EMP2-over-expressed hRPECs versus vector control under hypoxia and may thus identified as MRs for EMP2-induced lesion under hypoxia.ConclusionsMRs obtained in this study might serve as potential biomarkers for EMP2 induced lesion under hypoxia, illustrating gene expression landscapes which might be specific for diabetic retinopathy and might provide improved understanding of the disease.

COMBINED EXOSOMAL AND PLASMA NON-CODING RNA SIGNATURE ASSOCIATED WITH URINARY ALBUMIN EXCRETION IN HYPERTENSION

Objective: Non-coding RNA (ncRNA), released into circulation or packaged into exosomes, play important roles in many biological processes in the kidney. The purpose of the present study is to identify a common ncRNA signature associated with early renal damage and its related molecular pathways by constructing a RNA-based transcriptional network. Design and method: This is an observational case-control study which included 43 hypertensives, twenty-one patients with essential hypertension and twenty-two without persistent elevated urinary albuminuria (UAE) (higher or equal to 30 mg/g urinary creatinine). Three individual libraries (plasma and urinary exosomes and total plasma) were prepared from each hypertensive patient for ncRNA sequencing analysis. Next, a RNA-based transcriptional regulatory network was constructed. Results: The three RNA biotypes with the greatest number of differentially expressed transcripts were long-ncRNA (lncRNA), microRNA (miRNA) and piwi-interacting RNA (piRNA). We identified a common 24 ncRNA molecular signature related to hypertension-associated albuminuria, of which lncRNA was the most representative. In addition, the transcriptional regulatory network analysis showed five lncRNA (LINC02614, BAALC-AS1, FAM230B, LOC100505824 and LINC01484), and the miR-301a-3p to play a significant role in network organization and to target critical pathways regulating filtration barrier integrity, tubule reabsorption and systemic endothelial dysfunction. Conclusions: Our study found a combined ncRNA signature associated with albuminuria, independently of biofluid origin (urine or plasma, circulating or in exosomes) that identifies a handful of potential targets involved in filtration barrier, tubule reabsorption and endothelial function that may be utilized to treating hypertension-associated albuminuria and cardiovascular damage progression.

A promising drug combination of mangiferin and glycyrrhizic acid ameliorates disease severity of rheumatoid arthritis by reversing the disturbance of thermogenesis and energy metabolism

BackgroundActivation of immune system in rheumatoid arthritis (RA) consumes amount of energy, and the energy metabolic signals may be a potential target for RA therapy. Baihu-Guizhi decoction (BHGZD) achieves satisfactory therapeutic effects in RA in clinics by recovering the adjacent articular cartilage and bone destruction, and abnormal articular temperature. However, its pharmacological material basis and molecular mechanisms have not been fully elucidated. PurposeThis study focused on exploring the potential acting mechanism of BHGZD against RA, and identifying its main bioactive compounds (BACs) of the combination of mangiferin and glycyrrhizic acid. MethodsKey putative targets of BHGZD acting on adjuvant-induced arthritis (AIA)-M rats were screened by the transcriptomic profiling of the whole blood cells and synovium tissues collected from rats in normal control, AIA-M model and AIA-M-BHGZD treatment groups. Then, BACs of BHGZD against RA were identified using Ultra Performance Liquid Chromatography-Mass spectrum/Mass spectrum, molecular docking, surface plasmon resonance and pharmacokinetic analysis. In vivo experiments based on AIA-M rats and in vitro experiments based on 3T3-L1 preadipocytes were performed to verify the pharmacological effects of BACs against RA and the corresponding mechanisms. ResultsPKA-ADCY5-PPARγ-PGC 1α-UCP1-PRDM16 signal axis was demonstrated to be the candidate targets of BHGZD against RA and was involved in maintaining the balance of thermogenesis and energy metabolism, according to the transcriptional regulatory network analysis based on “herbs-putative targets-disease interaction network”. Then, mangiferin from Rhizoma Anemarrhenae and glycyrrhizic acid from Radix Glycytthizae were identified as the main BACs of BHGZD against RA due to their highly accumulation in the blood in vivo, strong binding affinities with the two candidate targets of BHGZD against RA-ADCY5 and PPARγ, as well as the in vivo and in vitro strong regulation effects on energy metabolism disturbance. ConclusionsThese findings offer evidence that the combination of mangiferin and glycyrrhizic acid from BHGZD may be a promising candidate drug for RA therapy, and also provide an important reference for the development and modernization of traditional Chinese formulae.

Single-Cell Analysis Reveals Transcriptomic Reprogramming in Aging Cardiovascular Endothelial Cells.

The senescence of cardiovascular endothelial cells (ECs) is a major risk factor in the development of aging-related cardiovascular diseases. However, the molecular dynamics in cardiovascular EC aging are poorly understood. Here, we characterized the transcriptomic landscape of cardiovascular ECs during aging and observed that ribosome biogenesis, inflammation, apoptosis and angiogenesis-related genes and pathways changed with age. We also highlighted the importance of collagen genes in the crosstalk between ECs and other cell types in cardiovascular aging. Moreover, transcriptional regulatory network analysis revealed Jun as a candidate transcription factor involved in murine cardiovascular senescence and we validated the upregulation of Jun in aged cardiovascular ECs both in vitro and in vivo. Altogether, our study reveals the transcriptomic reprogramming in the aging murine cardiovascular ECs, which deepens the understanding of the molecular mechanisms of cardiovascular aging and provides new insights into potential therapeutic targets against age-related cardiovascular diseases.

A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is one of the most common and malignant cancer types. Abnormal cell proliferation, exemplified by cell cycle and cell division dysregulation, is one of the most prominent hallmarks of cancer and is responsible for recurrence, metastasis, and resistance to cancer therapy. However, LUAD-specific gene regulation and clinical significance remain obscure. Here, by using both tissues and cells from LUAD and normal lung samples, 434 increased and 828 decreased genes of biological significance were detected, including 127 cell cycle-associated genes (95 increased and 32 decreased), 66 cell division-associated genes (56 increased and 10 decreased), and 81 cell proliferation-associated genes (34 increased and 47 decreased). Among them, 12 increased genes (TPX2, CENPF, BUB1, PLK1, KIF2C, AURKB, CDKN3, BUB1B, HMGA2, CDK1, ASPM, and CKS1B) and 2 decreased genes (TACC1 and MYH10) were associated with all the three above processes. Importantly, 2 (CDKN3 and CKS1B) out of the 11 increased genes (except HMGA2) are previously uncharacterized ones in LUAD and can potentially be prognostic markers. Moreover, PLK1 could be a promising therapeutic target for LUAD. Besides, protein–protein interaction network analysis showed that CDK1 and CDC20 were the hub genes, which might play crucial roles in cell proliferation of LUAD. Furthermore, transcriptional regulatory network analysis suggested that the transcription factor E2F1 could be a key regulator in controlling cell proliferation of LUAD via expression modulation of most cell cycle-, cell division-, and cell proliferation-related DEGs. Finally, trichostatin A, hycanthone, vorinostat, and mebeverine were identified as four potential therapeutic agents for LUAD. This work revealed key regulators contributing to cell proliferation in human LUAD and identified four potential therapeutic agents for treatment strategy.

An Integrative Systems Biology Approach Identifies Molecular Signatures Associated with Gallbladder Cancer Pathogenesis

Gallbladder cancer (GBC) has a lower incidence rate among the population relative to other cancer types but is a major contributor to the total number of biliary tract system cancer cases. GBC is distinguished from other malignancies by its high mortality, marked geographical variation and poor prognosis. To date no systemic targeted therapy is available for GBC. The main objective of this study is to determine the molecular signatures correlated with GBC development using integrative systems level approaches. We performed analysis of publicly available transcriptomic data to identify differentially regulated genes and pathways. Differential co-expression network analysis and transcriptional regulatory network analysis was performed to identify hub genes and hub transcription factors (TFs) associated with GBC pathogenesis and progression. Subsequently, we assessed the epithelial-mesenchymal transition (EMT) status of the hub genes using a combination of three scoring methods. The identified hub genes including, CDC6, MAPK15, CCNB2, BIRC7, L3MBTL1 were found to be regulators of cell cycle components which suggested their potential role in GBC pathogenesis and progression.