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ABSTRACT: Transcriptional Signatures and Network-Based Approaches identified Master Regulators Transcription Factors involved in Periodontitis Pathogenesis

PROVIDER: PRJNA1010977 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25823256_1.fastq.gz	Fastqsanger.gz
	SRR25823256_2.fastq.gz	Fastqsanger.gz
	SRR25823257_1.fastq.gz	Fastqsanger.gz
	SRR25823257_2.fastq.gz	Fastqsanger.gz
	SRR25823258_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

Project description:Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

2016-09-15 | GSE81984 | GEO

An ectopic network of transcription factors regulated by Hippo signaling drives growth and invasion of a malignant tumor model [larval imaginal discs (eye, wing and leg)]

Project description:Cancer cells have abnormal gene expression patterns, however, the transcription factors and the architecture of the regulatory network that drive cancer specific gene expression profiles is often not known. Here we studied a model of Ras-driven invasive tumorigenesis in Drosophila larval epithelial tissues and combined in vivo genetic analyses with high-throughput sequencing and computational modeling to decipher the regulatory logic of tumor cells. Surprisingly, we discovered that tumor specific gene expression is driven by a highly interconnected network composed of few transcription factors. These are: Stat, Mef2, the AP-4 homolog Cropped, the nuclear receptor Ftz-f1, the bHLH factors Myc and Taiman, and the AP-1 transcription factors Kayak, ATF-3, Pdp1, and dCEBPG. Many of these transcription factors are ectopically expressed and/or hyperactivated in human tumors. The members of this tumor master regulatory network are predicted to directly regulate the majority of the tumor specific gene expression profile. Similar to networks of master regulators that control organ development and cellular differentiation, there is a predicted high degree of co-regulation of target genes, and these network members are required in multiple eptihelia for tumor growth and invasiveness. We further found that Yki/Sd and bZIP/AP-1 factors, the downstream transcription factors of the Hippo and JNK pathways, initiate cellular reprogramming by activating several transcription factors of this network. Thus, modeling regulatory networks identified an ectopic yet highly ordered network of master regulators that control cancer cell specific gene expression. RNA-seq gene expression profiling across Drosophila 3rd instar larval imaginal discs (eye-antenna, wing and leg) in a hh driven tumor model, perturbations and controls.

2016-06-10 | E-GEOD-81272 | biostudies-arrayexpress

Homo sapiens

Project description:Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis.

| PRJNA322829 | ENA

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

Project description:Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

| PRJNA323558 | ENA

Chromatin immunoprecipitation analysis of human hepatocyte regulatory circuitry

Project description:We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network motifs created by regulator-gene interactions. Auto-regulation was a prominent theme among these regulators. We found that hepatocyte master regulators tend to bind promoter regions combinatorially and that the number of transcription factors bound to a promoter corresponds with observed gene expression. Our studies reveal portions of the core circuitry of human hepatocytes.

2006-05-09 | E-WMIT-9 | biostudies-arrayexpress

An ectopic network of transcription factors regulated by Hippo signaling drives growth and invasion of a malignant tumor model [larval imaginal discs (eye, wing and leg)]

2016-06-10 | GSE81272 | GEO

Comparison of mRNA expression levels in peri-implantitis and periodontitis within the same host environment

Project description:Purpose: The aim of this study was to explore whether differences exist and to what an extent of the immune-mediated inflammatory reactions between periodontitis and peri-implantitis at the transcriptional level in the same susceptible host. Methods: Ligature-induced experimental peri-implantitis and periodontitis in the same mice were established. Gingival tissues of healthy, periodontitis and peri-implantitis sites from the same oral cavity were collected and used for RNA-sequencing. Differentially expressed genes (DEGs) were screened between periodontitis/peri-implantitis sites and healthy sites. The enrichment analysis of DEGs were analyzed. Comprehensive immune landscape was annotated by seq-ImmuCC. Results: The results showed that 137 and 353 up-regulated DEGs as well as and 670 and 174 down-regulated DEGs were specifically expressed periodontitis/peri-implantitis group compared to the healthy control group, respectively. The pathways of complement and coagulation cascade and osteoclast differentiation were dominating in the peri-implantitis sites. Moreover, peri-implantitis sites exhibited elevated macrophage proportions and relatively enriched macrophage activation and bone loss compared with periodontitis. Conclusions: Results indicated that peri-implantitis and periodontitis exhibited significantly distinct transcriptional signatures. Additionally, the study suggests that the interplay between macrophages and bone resorption are comparatively more active in peri-implantitis compared with periodontitis. These biological processes may be factors contributing to the pathogenesis of peri-implantitis being distinct from that of periodontitis.

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scRNA-seq of two triple knockout SCLC mouse models for subtyping

Project description:Adopting a systems approach, we devise a general workflow to define actionable subtypes in human cancers. Applied to small cell lung cancer (SCLC), the workflow identifies four subtypes based on global gene expression patterns and ontologies. Three correspond to known subtypes, while the fourth is a previously undescribed neuroendocrine variant (NEv2). Tumor deconvolution with subtype gene signatures shows that all of the subtypes are detectable in varying proportions in human and mouse tumors. To understand how multiple stable subtypes can arise within a tumor, we infer a network of transcription factors and develop BooleaBayes, a minimally-constrained Boolean rule-fitting approach. In silico perturbations of the network identify master regulators and destabilizers of its attractors. Specific to NEv2, BooleaBayes predicts ELF3 and NR0B1 as master regulators of the subtype, and TCF3 as a master destabilizer. Since the four subtypes exhibit differential drug sensitivity, with NEv2 consistently least sensitive, these findings may lead to actionable therapeutic strategies that consider SCLC intratumoral heterogeneity. Our systems-level approach should generalize to other cancer types.

2019-09-20 | GSE137749 | GEO

Metaproteomics characterizes human gingival crevicular fluid microbiome function in periodontitis

Project description:The human gingival crevicular fluid proteome and metaproteome of periodontitis are investigated, to shed light on the factors that mediate the host-microbiota interactions in the pathogenesis of periodontitis.

2023-05-06 | PXD042037 |

Altered gene expressions of leukocyte transendothelial migration and cell communication pathways in periodontitis-affected gingival tissues

Project description:Gene expressions relate to the pathogenesis of periodontitis and have a crucial role in local tissue destruction and susceptibility to the disease. The aims of the present study were to explore comprehensive gene expressions/transcriptomes in periodontitis-affected gingival tissues, and to identify specific biological processes. The purpose of the present study was 1) to compare comprehensive gene expression/transcriptomes of periodontitis-affected gingival tissues with those of healthy tissues by using microarray and data mining technologies, and 2) to analyze significantly differentially expressed genes which belong to pathological pathways in periodontitis by qRT-PCR. Two distinct gingival samples including healthy and periodontal-affected gingiva were taken from 3 patients with severe chronic periodontitis. Total RNAs from 6 gingival tissue samples were used for microarray and data-mining analyses. Comparisons, gene ontology, and pathway frequency analyses were performed and identified significant biological pathways in periodontitis. Quantitative reverse transcription real-time polymerase chain reaction (qRT-PCR) analyse using 14 chronic periodontitis patients including 3 patients listed above and 14 healthy individuals showed 9 differentially expressed genes in leukocyte migration and cell communication pathways.

2010-08-13 | E-GEOD-23586 | biostudies-arrayexpress

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