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Understanding molecular mechanisms of Rhodiola rosea for the treatment of acute mountain sickness through computational approaches (a STROBE-compliant article).

ABSTRACT: Rhodiola rosea has been used in the treatment of acute mountain sickness (AMS) for a long time, but the mechanism of its action is not still completely clear. In this paper, the therapeutic mechanism of R rosea for AMS was investigated by analysis of the relationship between R rosea compositions and hypoxia-inducible factor 1 (HIF-1) degradation pathway.System biology and network biology, computational approaches were used to explore the molecular mechanisms of traditional Chinese medicine (TCM).Our results showed that chemical compositions of R rosea could inhibit the targets of HIF-1 degradation pathway in multi-composition/multi-target ways.We conclude that the 18 components with more than 2 targets and 5 targets (arrest-defective-1 [ARD1], forkhead transcription factor [FOXO4], osteosarcoma-9 [OS-9], prolyl hydroxylase 2 [PHD2], human double minute 2 [Hdm2]) deserve to be noticed, and PHD2, receptor for activated C-kinase1 (RACK1) and spermidine/spermine-N1-acetyltransferase-1 (SSAT1) may be the targets of active ingredients of rhodionin, rhodiosin, and rhodiolatuntoside, respectively.

SUBMITTER: Liang ZL

PROVIDER: S-EPMC6181534 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Understanding molecular mechanisms of Rhodiola rosea for the treatment of acute mountain sickness through computational approaches (a STROBE-compliant article).

Liang Zi-Liang ZL Zhang Xu-Yi XY Wang Fan F Zhang Kai K Liu Hai-Feng HF Liu Hui-Liang HL

Medicine 20180901 39

Rhodiola rosea has been used in the treatment of acute mountain sickness (AMS) for a long time, but the mechanism of its action is not still completely clear. In this paper, the therapeutic mechanism of R rosea for AMS was investigated by analysis of the relationship between R rosea compositions and hypoxia-inducible factor 1 (HIF-1) degradation pathway.System biology and network biology, computational approaches were used to explore the molecular mechanisms of traditional Chinese medicine (TCM) ...[more]

PMID: 30278484

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Project description:The potential association between the prognosis of the pancreatic adenocarcinoma (PAAD) and its microenvironment is unclear. This study aims to construct a prognostic index (PI) model of the PAAD microenvironment to predict PAAD patient survival outcomes.The mRNA sequencing and the clinical parameters data were obtained from The Cancer Genome Atlas. Immune and stromal scores were computed using the expression data algorithm to capture infiltration of immune and stromal cells in the PAAD tissue, where patients were categorized as high and low score groups according to these scores. Differentially expressed genes were identified using the R package LIMMA. Univariate and multivariate Cox regression analysis were conducted to select candidate survival-correlated gene signatures from the tumor microenvironment for constructing a model. The Kaplan-Meier method was used to access overall survival of the primary and validation cohorts. The immunological features of the PI model was explored using the Tumor Immune Estimation Resource (TIMER) database. Bioinformatic analyses were conducted based on the DAVID database.A total of 1266 overlapping differentially expressed genes and 49 prognosis-associated genes were identified. A 7-mRNA signature (GBP5, BICC1, SLC7A14, CYSLTR1, P2RY6, VENTX, and RAB39B) was screened for the construction of a PI model (area under the curve = 0.791). In both the primary and validation cohorts, Kaplan Meier analysis revealed that the overall survival of the high-risk group was significantly worse compared to the low-risk group (P?<?.0001, P?=?.0028 respectively). The TIMER database described that the 7 signature genes were correlated with immune infiltrating cells and tumor purity. Bioinformatic analyses revealed that these prognosis-associated genes were significantly enriched during inflammation, the defense response, would response, calcium ion transport, and plasma membrane part.A list of the prognosis-correlated genes was generated based on the PAAD microenvironment. A 7-mRNA PI model may be used for predicting the prognosis of PAAD patients.

Dataset Information

Understanding molecular mechanisms of Rhodiola rosea for the treatment of acute mountain sickness through computational approaches (a STROBE-compliant article).

Publications

Understanding molecular mechanisms of Rhodiola rosea for the treatment of acute mountain sickness through computational approaches (a STROBE-compliant article).

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