Decoction mediates spinal cord repair in vitro and in vivo through the PI3K-AKT signaling pathway
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PROVIDER: PRJNA730520 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to find the potential molecular mechanism of traditional Chinese medicine in the treatment of spinal cord injury Methods: Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 . The RNA integrity was assessed by Bioanalyzer 2100 with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase , which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution . An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results:In this study, we obtained: chromosome: 23, Genes (G): 32623, Transcripts (T): 40808, GO Annoated: 20795, KEGG Annoated: 8299; in further pathway analysis, it was shown that PI3K-AKT signaling pathway may be the underlying molecular mechanism. Conclusions: Our study represents the first detailed analysis of the spinal cord transcriptome generated by RNA-seq technology with biological replicates. Our results suggest that Modified Erxian decoction may mediate spinal cord repair through the PI3K-AKT pathway.
2021-05-17 | GSE174549 | GEO
Project description:Airway remodeling is a main pathological feature of asthma. The current therapy for asthma is mainly targeted for reducing inflammation, not particularly for airway remodeling. Herein, developing alternative and more effective therapy to attenuate remodeling is worthy of further study. Gu-Ben-Fang-Xiao Decoction (GBFXD) has been used to treat asthma for decades effectively and safely. In present study, GBFXD significantly regulated the airway inflammation, collagen deposition and the molecules relevant to airway remodeling such as Vimentin, α-SMA, hydroxyproline (HYP), and E-cadherin in chronic remission asthma (CRA) murine model. Subsequently, we found the overlapping differentially expressed proteins (DEPs) between Model/Control and GBFXD/Model mainly belonged to Collagen and Laminin which were extracellular matrix (ECM) proteins by iTRAQ proteomics. In addition, the KEGG analysis showed GBFXD could regulate pathways related to airway remodeling, such as ECM-receptor interaction, Focal adhesion, and PI3K/AKT signaling pathway which were top three pathways of most DEPs (Model/Control and GBFXD/Model) significantly enriched simultaneously. Further validation research showed GBFXD regulated Reticulon-4 (RTN4), thus suppressing the activation of PI3K/AKT pathway to alleviate the ECM proteins deposition. Thus, our findings indicate GBFXD regulate the PI3K/AKT pathway via RTN4 to improve airway remodeling and provide a new insight into the molecular mechanism of GBFXD for treating CRA.
2021-09-09 | PXD020711 | Pride
Project description:Insufficient osteogenesis is greatly essential to osteoporosis. Bugu Shengsui Decoction, a compound formula for osteoporosis, has significant clinical effects in the treatment of osteoporosis. Yet the detailed mechanisms are unclear. In this study, we first evaluated the pharmacological effects of Bugu Shengsui Decoction on bone metabolism, bone mineral density, bone morphology and biomechanics in ovariectomized rats. It also clarified the promoting effect of Bugu Shengsui Decoction on the proliferation and differentiation of osteoblasts. Based on the above results, we conducted quantitative proteomics research and a series of validation experiments, the results showed that PI3K-AKT signaling pathway and targets, such as Fn1, Col1a1, Col1a2, Col6a1, Col6a2, Col6a3, Rac1, Hsp90ab1, Hsp90b1, Ywhaz and Gnb2, were most relevant to the anti-osteoporosis efficacy of BGSSD. Summarily, our discoveries certify that Bugu Shengsui Decoction is an effective treatment for osteoporosis via PI3K-AKT.
2022-01-28 | PXD030275 | Pride
Project description:The metastasis of nasopharyngeal carcinoma (NPC) is a complex process associated with oncogenic dysfunction, the deciphering of which remains a challenge and requires more in-depth studies. Y-box protein 3 (YBX3) is a DNA/RNA binding protein associated with gene transcription, DNA repair and the progression of various diseases. However, whether and how YBX3 affects the metastasis of NPC remains unknown. Thus, in this study, we aimed to investigate the role of YBX3 in the metastasis of NPC and determine its underlying mechanism. Interestingly, it was found that the expression of YBX3, which was associated with NPC metastasis, was upregulated in the clinical NPC tissues and cell lines using solid experimental evidences. Moreover, we found that knockdown of YBX3 expression by lentivirus shRNA significantly suppressed NPC cells migration in vitro and metastasis in vivo. Mechanistically, RNA sequencing results suggested that the genes regulated by YBX3 were significantly enriched in cell adhesion molecules, cAMP signaling pathway, calcium signaling pathway, focal adhesion, PI3K-Akt signaling pathway, Ras signaling pathway, Rap1 signaling pathway, NF-κB signaling pathway, and Chemokine signaling pathway. Of these, PI3K-Akt signaling pathway contained the most genes. Accordingly, YBX3 knockdown decreased the activation of PI3K/AKT signaling, thereby inhibit epithelial-to-mesenchymal transition and MMP1. These results have demonstrated that YBX3 are involved in the metastasis of NPC through regulating PI3K/AKT signaling pathway, and serve as a potential therapeutic target for patients with NPC.
2021-04-07 | GSE160245 | GEO
Project description:Diabetic peripheral neuropathy (DPN) is the most common neurological complication of diabetes. More than 500 differentially expressed genes (DEGs) belonging to multiple functional pathways were identified in diabetic spinal cord and of those the most enriched was RAGE-Diaph1 related PI3K-Akt pathway.
2022-10-16 | E-MTAB-12252 | biostudies-arrayexpress
Project description:Hyperactivation of the phosphatydil-inositol-3' phosphate kinase (PI3K)/AKT pathway is observed in most NSCLCs, promoting proliferation, migration, invasion and resistance to therapy. AKT can be activated through several mechanisms that include loss of the negative regulator PTEN, activating mutations of the catalytic subunit of PI3K (PIK3CA) and/or mutations of AKT1 itself. However, number and identity of downstream targets of activated PI3K/AKT pathway are poorly defined. To identify the genes that are targets of constitutive PI3K/AKT signalling in lung cancer cells, we performed a comparative transcriptomic analysis of human lung epithelial cells (BEAS-2B) expressing active mutant AKT1 (AKT1-E17K), active mutant PIK3CA (PIK3CA-E545K) or that are silenced for PTEN. For each sample, 500 ng of total RNA were used to synthesize biotinylated cRNA with Illumina RNA Amplification Kit (Ambion, Austin, TX). Synthesis was carried out according to the manufacturersâ instructions. From each sample, technical triplicates were produced and 750 ng cRNA were hybridized for 18h to Human HT-12_V3_0_R1 Expression BeadChips (Illumina, San Diego, CA). Hybridized chips were washed and stained with streptavidin-conjugated Cy3 (GE Healthcare, Milan, Italy). BeadChips were dried and scanned with an Illumina Bead Array Reader (Illumina).
2016-12-01 | E-MTAB-5286 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE35701: CP001: Modulation of glutamine metabolism by the PI3K-PKB/c-akt-FOXO network regulates autophagy GSE35703: CP003: Modulation of glutamine metabolism by the PI3K-PKB/c-akt-FOXO network regulates autophagy Refer to individual Series
2012-07-21 | E-GEOD-35705 | biostudies-arrayexpress
Project description:Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system with a highly variable prognosis. Activation of the PI3K/AKT pathway in neuroblastoma is correlated with poor patient prognosis, but the precise downstream effectors mediating this effect have not been determined. Here, we identify the forkhead transcription factor FOXO3a as a key target of the PI3K/AKT pathway in neuroblastoma. FOXO3a expression was elevated in low stage neuroblastoma tumors and normal embryonal neuroblasts, but reduced in late stage neuroblastoma. Inactivation of FOXO3a by AKT was essential for neuroblastoma cell survival. Treatment of neuroblastoma cells with the dual PI3K/mTOR inhibitor PI-103 activated FOXO3a and triggered apoptosis. This effect was rescued by FOXO3a silencing. Conversely, apoptosis induced by PI-103 or the AKT inhibitor MK-2206 was potentiated by FOXO3a overexpression. Further, levels of total or phosphorylated FOXO3a correlated closely with apoptotic sensitivity to MK-2206. In clinical specimens, there was an inverse relationship between gene expression signatures regulated by PI3K signaling and FOXO3a transcriptional activity. Moreover, high PI3K activity and low FOXO3a activity were each associated with an extremely poor prognosis. Our work indicates that expression of FOXO3a and its targets offer useful prognostic markers as well as biomarkers for PI3K/AKT inhibitor efficacy in neuroblastoma. Affymetrix U133 Plus 2.0 profiling of SY5Y-TetR-FOXO3A cells treated with doxycycline and/or the PI3K/mTOR inhibitor PI-103. Each condition profiled in triplicate.
2013-05-01 | E-GEOD-42762 | biostudies-arrayexpress
Project description:Yinchenzhufu decoction (YCZFD) is a traditional Chinese medicine formula with hepatoprotective effects. In this study, the protective effects of YCZFD against cholestatic liver fibrosis and its mechanisms of action were evaluated in a mouse model of 3,5-diethoxycarbonyl-1,4-dihydro-collidine (DDC)-induced cholestasis. YCZFD significantly decreased levels of serum biochemical, liver injury, and fibrosis indicators. Data-independent acquisition-based mass spectrometry (MS) was used to investigate proteomic changes in the livers of mice in three groups: control, model, and model treated by high-dose YCZFD. In total, 460 differentially expressed proteins (DEPs) were identified. Enrichment analyses of these DEPs uncovered that YCZFD influences multiple pathways, including PI3K-Akt, focal adhesion, ECM-receptor interaction, glutathione metabolism, and steroid biosynthesis pathways. PDGFRβ, a receptor associated with the PI3K/AKT and focal adhesion pathways, was significantly upregulated in the livers of cholestatic mice but downregulated by YCZFD. The effects of YCZFD on the expression levels of key proteins in the PDGFRβ/PI3K/AKT pathway were further confirmed in TGFβ-induced hepatic stellate cells. Finally, we uncovered six components (i.e., chlorogenic acid, scoparone, isoliquiritigenin, glycyrrhetinic acid, formononetin, atractylenolide I, and benzoylaconitine) of YCZFD that may regulate PDGFRβ expression. Overall, YCZFD exerts a substantial protective effect against DDC-induced cholestatic liver fibrosis mainly through regulating the PDGFRβ/PI3K/AKT signaling pathway.
2023-10-13 | PXD046101 | iProX
Project description:YBX3 mediates the metastasis of nasopharyngeal carcinoma via PI3K/AKT signaling
| PRJNA672705 | ENA