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BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qianyun Ge ◽  
Yongbo Guo ◽  
Wangshan Zheng ◽  
Yuan Cai ◽  
Xuebin Qi ◽  
...  

Abstract Background Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood. Results Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including ‘glycosaminoglycan degradation’, ‘pentose and glucuronate interconversions’ and ‘flavone and flavonol biosynthesis’, and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells. Conclusions This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases.


2021 ◽  
Vol 8 ◽  
Author(s):  
Hao-Yu Liu ◽  
Haotian Gu ◽  
Yanwei Li ◽  
Ping Hu ◽  
Yatian Yang ◽  
...  

Scope: Disruptions of circadian rhythm cause metabolic disorders and are closely related to dietary factors. In this study, we investigated the interplays between the dietary conjugated linoleic acid (CLA)-induced hepatic steatosis and the circadian clock regulation, in association with lipid homeostasis.Methods and Results: Exposure of mice to 1.5% dietary CLA for 28 days caused insulin resistance, enlarged livers, caused hepatic steatosis, and increased triglyceride levels. Transcriptional profiling showed that hepatic circadian clock genes were significantly downregulated with increased expression of the negative transcription factor, REV-ERBα. We uncovered that the nuclear receptor (NR) PPARα, as a major target of dietary CLA, drives REV-ERBα expression via its binding to key genes of the circadian clock, including Cry1 and Clock, and the recruitment of histone marks and cofactors. The PPARα or REV-ERBα inhibition blocked the physical connection of this NR pair, reduced the cobinding of PPARα and REV-ERBα to the genomic DNA response element, and abolished histone modifications in the CLA-hepatocytes. In addition, we demonstrated that CLA promotes PPARα driving REV-ERBα transcriptional activity by directly binding to the PPAR response element (PPRE) at the Nr1d1 gene.Conclusions: Our results add a layer to the understanding of the peripheral clock feedback loop, which involves the PPARα-REV-ERBα, and provide guidance for nutrients optimization in circadian physiology.


Marine Drugs ◽  
2021 ◽  
Vol 19 (10) ◽  
pp. 576
Author(s):  
Jichen Chen ◽  
Jianchao Yang ◽  
Hong Du ◽  
Muhmmad Aslam ◽  
Wanna Wang ◽  
...  

During the processes of primary and secondary endosymbiosis, different microalgae evolved to synthesis different storage polysaccharides. In stramenopiles, the main storage polysaccharides are β-1,3-glucan, or laminarin, in vacuoles. Currently, laminarin is gaining considerable attention due to its application in the food, cosmetic and pharmaceuticals industries, and also its importance in global biogeochemical cycles (especially in the ocean carbon cycle). In this review, the structures, composition, contents, and bioactivity of laminarin were summarized in different algae. It was shown that the general features of laminarin are species-dependence. Furthermore, the proposed biosynthesis and catabolism pathways of laminarin, functions of key genes, and diel regulation of laminarin were also depicted and comprehensively discussed for the first time. However, the complete pathways, functions of genes, and diel regulatory mechanisms of laminarin require more biomolecular studies. This review provides more useful information and identifies the knowledge gap regarding the future studies of laminarin and its applications.


2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Li Ou ◽  
Wenqian Kang ◽  
Ziyi Liang ◽  
Feng Gao ◽  
Taiwei Dong ◽  
...  

Abstract Background Rehmanniae Radix Preparata (RRP) can effectively improve the symptoms of osteoporosis, but its molecular mechanism for treating osteoporosis is still unclear. The objective of this study is to investigate the anti-osteoporosis mechanisms of RRP through network pharmacology. Methods The overlapping targets of RRP and osteoporosis were screened out using online platforms. A visual network diagram of PPI was constructed and analyzed by Cytoscape 3.7.2 software. Molecular docking was used to evaluate the binding activity of ligands and receptors, and some key genes were verified through pharmacological experiments. Results According to topological analysis results, AKT1, MAPK1, ESR1, and SRC are critical genes for RRP to treat osteoporosis, and they have high binding activity with stigmasterol and sitosterol. The main signal pathways of RRP in the treatment of osteoporosis, including the estrogen signaling pathway, HIF-1 signal pathway, MAPK signal pathway, PI3K-Akt signal pathway. Results of animal experiments showed that RRP could significantly increase the expression levels of Akt1, MAPK1, ESR1, and SRC1 mRNA in bone tissue to increase bone density. Conclusion This study explained the coordination between multiple components and multiple targets of RRP in the treatment of osteoporosis and provided new ideas for its clinical application and experimental research.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youfu Zhang ◽  
Jinran Yang ◽  
Xuyang Wang ◽  
Xinchang Li

AbstractPancreatic adenocarcinoma (PAAD) is one of the most lethal malignant tumors in the world. The GSE55643 and GSE15471 microarray datasets were downloaded to screen the diagnostic and prognostic biomarkers for PAAD. 143 downregulated genes and 118 upregulated genes were obtained. Next, we performed gene ontology (GO) and The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on these genes and constructed a protein–protein interaction (PPI) network. We screened out two important clusters of genes, including 13 upregulated and 5 downregulated genes. After the survival analysis, 3 downregulated genes and 10 upregulated genes were identified as the selected key genes. The KEGG analysis on 13 selected genes showed that GNG7 and ADCY1 enriched in the Pathway in Cancer. Next, the diagnostic and prognostic value of GNG7 and ADCY1 was investigated using independent cohort of the Cancer Genome Atlas (TCGA), GSE84129 and GSE62452. We observed that the expression of the GNG7 and ADCY1 was decreased in PAAD. The diagnostic receiver operating characteristic (ROC) analysis indicated that the GNG7 and ADCY1 could serve as sensitive diagnostic markers in PAAD. Survival analysis suggested that expression of GNG7, ADCY1 were significantly associated with PAAD overall survival (OS). The multivariate cox regression analysis showed that the expression of GNG7, ADCY1 were independent risk factors for PAAD OS. Our study indicated GNG7 and ADCY1 may be potential diagnostic and prognostic biomarkers in patients with PAAD.


Horticulturae ◽  
2021 ◽  
Vol 7 (10) ◽  
pp. 398
Author(s):  
Lu Tong ◽  
Shanhan Cheng ◽  
Honghao Lv ◽  
Chengzhi Zhao ◽  
Jie Zhu ◽  
...  

The content and component of glucosinolates in edible stems and leaves of eight Chinese kale varieties from Japan and eight varieties from China were determined by HPLC-MS. Simultaneously, the expression levels of glucosinolate biosynthesis pathway genes from four varieties with high and low total glucosinolate contents were analyzed by the qRT-PCR method. Four types of aliphatic glucosinolates (A-GLSs: GRA, SIN, GNA and GER) and indole glucosinolates (I-GLSs: 4-HGBS, GBS, 4-MGBS and NGBS) were detected in the stems and leaves of 16 varieties, and no aromatic glucosinolates (R-GLSs) were detected. A-GLSs account for more than 80.69% of the total content of total glucosinolates (T-GLSs), in which GNA and GRA are the main components of stems and leaves. Among Japanese varieties, QB1 has higher content of A- and T-GLSs, while that of XLB was lower; however, the corresponding varieties were ZH and DSHH in Chinese varieties. Among the above four varieties, the expression levels of SOT16, CYP83B1, SOT17, CYP83A1 and MAM1 genes were significantly higher in the varieties with higher GLSs; the expression levels of SOT16 and CYP83B1 were consistent with the content of I-GLSs; and SOT17, CYP83A1 and MAM1 expression levels were consistent with A-GLSs content. At the same time, the expression levels of SOT16 and CYP83B1 in the leaves were higher than those in the stems. CYP83A1 and MAM1 genes were less expressed in the leaves than in the stems of lower content varieties. It is speculated that these genes may be the key genes regulating GLS biosynthesis in Chinese kale.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Qingyuan Shi ◽  
Xiaojun Yan ◽  
Jiyun Wang ◽  
Xiangbao Zhang

Background. The safety of radiotherapy techniques in the treatment of vestibular schwannoma (VS) shows a high rate of tumor control with few side effects. Neuropeptide Y (NPY) may have a potential relevance to the recurrence of VS. Further research is still needed on the key genes that determine the sensitivity of VS to radiation therapy. Materials and Methods. Transcriptional microarray data and clinical information data from VS patients were downloaded from GSE141801, and vascular-related genes associated with recurrence after radiation therapy for VS were obtained by combining information from MSigDB. Logistics regression was applied to construct a column line graph prediction model for recurrence status after radiation therapy. Pan-cancer analysis was also performed to investigate the cooccurrence of these genes in tumorigenesis. Results. We identified eight VS recurrence-related genes from the GSE141801 dataset. All of these genes were highly expressed in the VS recurrence samples. Four collagen family genes (COL5A1, COL3A1, COL4A1, and COL15A1) were further screened, and a model was constructed to predict the risk of recurrence of VS. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these four collagen family genes play important roles in a variety of biological functions and cellular pathways. Pan-cancer analysis further revealed that the expression of these genes was significantly heterogeneous across immune phenotypes and significantly associated with immune infiltration. Finally, Neuropeptide Y (NPY) was found to be significantly and negatively correlated with the expression of COL5A1, COL3A1, and COL4A1. Conclusions. Four collagen family genes have been identified as possible predictors of recurrence after radiation therapy for VS. Pan-cancer analysis reveals potential associations between the pathogenesis of VS and other tumorigenic factors. The relevance of NPY to VS was also revealed for the first time.


2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Hongyan Huang ◽  
Youwen Hu ◽  
Li Guo ◽  
Zhili Wen

Author(s):  
Zhi-Zhou Shi ◽  
Hao Tao ◽  
Ze-Wen Fan ◽  
Sheng-Jie Song ◽  
Jie Bai

Solute carrier family 7 member 11 (SLC7A11), glutathione peroxidase 4 (GPX4), and apoptosis inducing factor mitochondria associated 2 (AIFM2) are the key regulators in ferroptosis. However, the expression patterns and prognostic roles of these genes in pan-cancer are still largely unclear. The expression patterns and prognostic roles of SLC7A11, GPX4, and AIFM2 and the relationships between the expression levels of these genes and immune infiltration levels in pan-cancer were analyzed by using TIMER, gene expression profiling interactive analysis (GEPIA), Oncomine, and Kaplan–Meier databases. Our results showed that both SLC7A11 and GPX4 were overexpressed in colorectal cancer, and SLC7A11 was overexpressed in lung cancer. High levels of SLC7A11 and AIFM2 were significantly linked with the shortened disease-free survival and overall survival (OS) in adrenocortical carcinoma (ACC), respectively. And high expression of SLC7A11, GPX4, and AIFM2 were significantly correlated with the shortened OS of acute myeloid leukemia patients. In esophageal carcinoma (ESCA), GPX4 expression was significantly associated with the infiltration of macrophage and myeloid dendritic cell, and AIFM2 expression was significantly associated with the infiltration of CD4+ T cell. Importantly, GPX4 expression was positively correlated with the expression levels of monocyte markers (CD14 and CD115) and M2 macrophage markers (VSIG4 and MS4A4A) both in ESCA and in head and neck squamous cell carcinoma (HNSC). In summary, SLC7A11, GPX4, and AIFM2 are dysregulated in many types of cancers, and are candidate prognostic biomarkers for many types of cancers, and can be used to evaluate the infiltration of immune cells in tumor tissues.


2021 ◽  
Author(s):  
Ming Li ◽  
Yiming Zhu ◽  
Qing Pei ◽  
Yuhao Deng ◽  
Tao Ni

Abstract Background The combination of low-level laser therapy (LLLT) and stem cell transplantation with tendon-derived stem cells (TDSCs) as seed cells provides a new treatment strategy for tendon injury. Nevertheless, the effect of LLLT on the biological behavior of TDSCs and its internal mechanisms remain unclear. The purpose of this study was to verify the effect of LLLT with a wavelength of 532 nm on the proliferation and differentiation of TDSCs of Sprague-Dawley (SD) rats. Methods TDSCs were isolated from Achilles tendons of SD rats and identified by cell morphology and flow cytometric analysis. Energy density gradient experiment was performed to determine the ideal energy. Then TDSCs were treated with LLLT using a wavelength of 532 nm at a fluence of 15J/cm2. Cell response after irradiation was observed at 6, 12 and 24 hours to ascertain cell morphology and cell proliferation. RT-PCR was used to detect the RNA expression levels of the key genes of TDSCs differentiation including Scx, Tnmd, Mkx and Dcn, PPARγ, Sox9 and Runx2. Then gene chip microarray was used to detect the expression of differential genes after 532 nm laser intervention in TDSCs, and the target genes were screened out to verify the role of target genes in this process. Results When the 532 nm laser energy density was 15 J/cm2, the proliferation capacity of TDSCs was improved (2.73 ± 0.24 vs. 1.81 ± 0.71, P < 0.05), and the expression of genes related to tenogenic differentiation of TDSCs was significantly increased (P < 0.01), showing the potential of tenogenic differentiation. After RNA-seq and bioinformatics analyses, we speculated that Nr4a1 was involved in the tenogenic differentiation process of TDSCs regulated by 532 nm laser treatment. Subsequent experiments confirmed that Nr4a1 regulated the expression of the tenogenic differentiation genes scleraxis (Scx) and tenomodulin (Tnmd) in TDSCs, affecting the process. Conclusion A 532 nm laser with 15J/cm2 regulated the process of TDSC proliferation and tenogenic differentiation by up-regulating Nr4a, which could accelerate tendon healing.


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