Molecule mechanisms of Ganoderma lucidum treated hepatocellular carcinoma based on the transcriptional profiles and miRNA-target network

Transcriptomics and systems network-based molecular mechanism of herbal formula Huosu-Yangwei inhibited gastric cancer in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

The efficacy of the herbal formula Huosu-Yangwei (HSYW) in the treatment of advanced gastric cancer and chronic atrophic gastritis with precancerous lesions has been reported in clinical trials. However, the molecular mechanisms underlying its inhibition of gastric tumor are not well-understood.

AIM OF THE STUDY

Combined with transcriptomics and systems network-based molecular mechanism to explore the potential circRNA-miRNA-mRNA network of HSYW in the treatment of gastric cancer.

MATERIALS AND METHODS

Animal experiments were conducted to investigate the effect of HSYW on tumor growth in vivo. RNA sequencing (RNA-seq) was implemented to identify the differentially expressed (DE) genes. Predictive miRNA targets and mRNA were used to construct circRNA-miRNA-mRNA networks and protein-protein interaction (PPI) networks. Quantitative real-time PCR (qRT-PCR) was utilized to verify the accuracy of the proposed circRNA-miRNA-mRNA networks. Additionally, the differentially expressed target proteins between gastric cancer (GC) and normal patients were assessed using data from the TCGA (The Cancer Genome Atlas) and HPA (The Human Protein Atlas) databases.

RESULTS

We demonstrate HSYW significantly inhibits tumor growth of N87 cell-bearing Balb/c mice. Transcriptomic analysis revealed the existence of 119 differentially expressed (DE) circRNAs and 200 DE mRNAs between HSYW-treated and model mice. By associating predicted circRNA-miRNA pairs and miRNA-mRNA pairs, we constructed a circRNA-miRNA-mRNA (CMM) network. Furthermore, a protein-protein interaction (PPI) network was developed using the differential expressed mRNAs. Consequently, the reconstructed core CMM network and qRT-PCR validation indicated that 4 circRNAs, 5 miRNAs and 6 mRNAs could potentially serve as biomarkers to assess the therapeutic effects of HSYW-treated N87-bearing Balb/c mice. The TCGA and HPA databases also demonstrated that mRNA KLF15 and PREX1 had substantial differences between gastric cancer (GC) and healthy controls.

CONCLUSIONS

By combining the experimental and bioinformatics analysis, this study confirms that the circRNA_00240/hsa-miR-642a-5p/KLF15 and circRNA_07980/hsa-miR-766-3p/PREX1 pathways play critical roles in HSYW-treated gastric cancer.

The molecular mechanism of γ-aminobutyric acid against AD: the role of CEBPα/circAPLP2/miR-671-5p in regulating CNTN1/2 expression

The expression levels of the synaptic-related proteins contactin 1/2 (CNTN1/2) are down-regulated in the brain of Alzheimer's disease (AD), but the mechanism has not been clarified. γ-Aminobutyric acid (GABA) is considered a biologically active ingredient in food. Our previous research revealed that GABA can regulate CEBPα expression in Aβ-treated U251 cells. However, it is uncertain whether GABA can antagonize the pathogenesis of AD. Whether GABA can inhibit the reduction in CNTN1/2 expression by regulating CEBPα/circAPLP2/miR-671-5p in the AD brain remains unclear yet. Here, we demonstrate that GABA could attenuate the deposition of Aβ in the brain and ameliorate cognitive impairments in AD model mice. The expressions of CEBPα, circAPLP2, and CNTN1/2 were decreased and that of miR-671-5p was increased in AD model mouse brains and Aβ-induced SH-SY5Y cells. These alterations were partly reversed by GABA. The CNTN1/2 expression was down-regulated and up-regulated in SH-SY5Y cells treated with miR-671-5p mimics and miR-671-5p inhibitors, respectively. The results from the luciferase reporter assay revealed that miR-671-5p could bind to the 3'-untranslated region of circAPLP2. The silencing of circAPLP2 with the siRNA duplex caused an up-regulation of miR-671-5p and a down-regulation of CNTN1/2 in SH-SY5Y cells. The silencing of CEBPα with the siRNA duplex caused a down-regulation of circAPLP2 or CNTN1/2 and an up-regulation of miR-671-5p. In conclusion, GABA may decrease the deposition of Aβ in the brain, inhibit the down-regulation of CNTN1/2 expression, and ameliorate the cognitive deficits of AD model mice. The CEBPα/circAPLP2/miR-671-5p pathway plays a role in regulating CNTN1/2 expression by GABA in AD.

Tanshinone IIA protects against chronic obstructive pulmonary disease via exosome‑shuttled miR‑486‑5p

Chronic obstructive pulmonary disease (COPD) is one of the major causes of death worldwide today, and its related morbidity has been predicted to show an increase in subsequent years. Recent studies have shown that Danshen, a Chinese herbal medicine, is a potential drug in the treatment of inflammation-related lung diseases. COPD was induced in this study using cigarette smoke (CS) exposure plus intranasal inhalation of lipopolysaccharide to ascertain whether the main pharmacological component from Danshen, tanshinone IIA (TIIA), and its water soluble form, sodium tanshinone IIA sulfonate (STS), protect against the development of COPD. The weight, lung function, hematoxylin and eosin staining, and Masson Trichrome determinations revealed that TIIA inhalation attenuated lung dysfunction in COPD mice induced by cigarette smoke and lipopolysaccharide exposure. In addition, exosomes derived from TIIA-treated COPD mice exerted similar protective effects against COPD, suggesting that TIIA may protect against COPD through exosome-shuttled signals. miR-486-5p was found to be a key molecule in mediating the protective effects of exosomes derived from TIIA-treated COPD mice using miRNA sequencing and cellular screening. Treatment of COPD mice with an agomiR of miR-486-5p protected lung function in COPD mice, and treatment of COPD mice with an antagomir of miR-486-5p abolished the protective effects of TIIA. Moreover, luciferase activity reporter assay, RT-qPCR, and western blot analyses showed that miR-486-5p exerted protective effects against COPD via targeting phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1). These results suggest that STS protects against COPD through upregulation of miR-486-5p, and that TIIA or miR-486-5p is a potential drug for the treatment of COPD.

Modular pharmacology-based approach to identify hub genes and kernel pathways of taodan granules treated psoriasis

ETHNOPHARMACOLOGICAL RELEVANCE

Taodan granules (TDG) have been observed to decrease interleukins, or psoriasis area and severity index (PASI) score for psoriasis vulgaris, without significant adverse events. However, the regulatory network remains elucidated.

AIM OF THE STUDY

The objective is to identify critical genes and kernel pathways of TDG treated psoriasis.

MATERIALS AND METHODS

Firstly, construct a network of components-targets of TDG using network pharmacology. Secondly, the ClusterONE algorithm was used to build a modular network and identify critical genes and corresponding pathways. Thirdly, the critical genes and kernel pathways were verified in imiquimod (IMQ) induced psoriasis-like mice model.

RESULTS

The results validated that TDG downregulated the mRNA expression of MMP2 (degree = 5, P < 0.05), IL6 (degree = 9, P < 0.05), TNF (degree = 14, P < 0.05), CCL2 (degree = 8, P < 0.05), CXCL2 (degree = 8, P < 0.05), IL1B (degree = 9, P < 0.05), and JUN (degree = 9, P < 0.05), while upregulated IL10 (degree = 8) expression. Besides, TDG were observed to regulate IL17 signaling pathway and TNF signaling pathway (size = 18), via the skin tissue homogenate of psoriasis-like mice.

CONCLUSION

In summary, this study identified the potential targets and pathways, providing additional evidence for the clinical application of TDG treated psoriasis.

Non-coding RNAs as biomarkers for hepatocellular carcinoma-A systematic review

Hepatocellular carcinoma (HCC) is the sixth most common malignancy in the world and the fourth leading cause of cancer-related death, and its incidence is increasing globally. Despite significant advances in treatment strategies for HCC, the prognosis is still poor due to its high recurrence rate. Therefore, there is an urgent need to understand the pathogenesis of HCC and further develop new therapies to improve the prognosis and quality of life of HCC patients. MicroRNAs (miRNAs, miRs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression that is abnormally expressed in cancer-associated genomic regions or vulnerable sites. More and more findings have shown that miRNAs are important regulatory factors of mRNA expression in HCC, and they are receiving more and more attention as a possible key biomarker of HCC. This review mainly summarizes the potential applied value on miRNAs as diagnostic, drug resistant, prognostic, and therapeutic biomarkers in the diagnosis, therapy, and prognosis of HCC. Also, we summarize the research value of long non-coding RNA (lncRNAs), circular RNAs (circRNAs), and miRNAs network in HCC as novel biomarkers, aiming at providing some references for the therapy of HCC.

Transcriptional profiling and circRNA-miRNA-mRNA network analysis identify the biomarkers in Sheng-ji Hua-yu formula treated diabetic wound healing

ETHNOPHARMACOLOGICAL RELEVANCE

Sheng-ji Hua-yu (SJHY) formula is a traditional Chinese herbal which is effective in treating diabetic ulcers. It has been indicated to accelerate re-epithelialization and healing time of cutaneous wounds in a Streptozotocin (STZ)-induced diabetic mouse model. However, its mechanisms remain undetermined.

AIM OF THE STUDY

To reveal the molecular mechanisms of SJHY formula in treating diabetic wounds through transcriptional profiling and circRNA-miRNA-mRNA network analysis clues.

MATERIALS AND METHODS

Protein expressions of tumor necrosis factor (TNF-α), interleukin (IL)-6, IL-1β in skin tissues of wounds from SJHY formula-treated and untreated mice were analyzed by Bio-Plex assay. Differentially expressed (DE) genes were detected by whole transcriptome sequencing (RNA-seq). Using predicted miRNA targets, circRNA-miRNA-mRNA networks were constructed. Furthermore, quantitative real-time PCR (qRT-PCR) was utilized to validate the circRNA-miRNA-mRNA networks.

RESULTS

Bio-Plex assay illustrated that the protein expressions of TNF-α, IL-1β, IL-6 were downregulated in SJHY formula-treated diabetic wounds compared with untreated wounds. RNA-seq identified 11 DE circRNAs and 476 DE mRNAs between SJHY formula-treated and diabetic mice, including 4 upregulated and 7 downregulated circRNAs, 311 upregulated and 165 downregulated mRNAs. CircRNA-Krt13/miR-665-3p/Itga3 and circRNA-Krt14/miR-706/Mylk4 pathways were built, which may contribute to the healing of SJHY formula-treated diabetic wounds.

CONCLUSIONS

Overall, this study suggests that these 2 circRNA-miRNA-mRNA networks are potential biomarkers for evaluation of SJHY formula efficacy in diabetic wound healing, which provides evidence to support its clinical applications.

Contactin 1: An Important and Emerging Oncogenic Protein Promoting Cancer Progression and Metastasis

Even with recent progress, cancer remains the second leading cause of death, outlining a need to widen the current understanding on oncogenic factors. Accumulating evidence from recent years suggest Contactin 1 (CNTN1)'s possession of multiple oncogenic activities in a variety of cancer types. CNTN1 is a cell adhesion molecule that is dysregulated in many human carcinomas and plays important roles in cancer progression and metastases. Abnormalities in CNTN1 expression associate with cancer progression and poor prognosis. Mechanistically, CNTN1 functions in various signaling pathways frequently altered in cancer, such as the vascular endothelial growth factor C (VEGFC)-VEGF receptor 3 (VEFGR3)/fms-related tyrosine kinase 4 (Flt4) axis, phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT), Notch signaling pathway and epithelial-mesenchymal transition (EMT) process. These oncogenic events are resulted via interactions between tumor and stroma, which can be contributed by CNTN1, an adhesion protein. CNTN1 expression in breast cancer correlates with the expression of genes functioning in cancer-stroma interactions and skeletal system development. Evidence supports that CNTN1 promotes cancer-stromal interaction, resulting in activation of a complex network required for cancer progression and metastasis (bone metastasis for breast cancer). CNTN1 inhibitions has been proven to be effective in experimental models to reduce oncogenesis. In this paper, we will review CNTN1's alterations in cancer, its main biochemical mechanisms and interactions with its relevant cancer pathways.