scholarly journals Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yan Kou ◽  
Xiaomin Xu ◽  
Zhengnong Zhu ◽  
Lei Dai ◽  
Yan Tan
Keyword(s):  
Statistical Significance ◽  
Functional Characterization ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Functional Interpretation ◽  
Useful Knowledge ◽  
Knowledge Based ◽  
Disease Associations ◽  
Differential Abundance Analysis ◽  
Microbiome Profiling

AbstractThe commensal microbiome is known to influence a variety of host phenotypes. Microbiome profiling followed by differential abundance analysis has been established as an effective approach to study the mechanisms of host-microbiome interactions. However, it is challenging to interpret the collective functions of the resultant microbe-sets due to the lack of well-organized functional characterization of commensal microbiome. We developed microbe-set enrichment analysis (MSEA) to enable the functional interpretation of microbe-sets by examining the statistical significance of their overlaps with annotated groups of microbes that share common attributes such as biological function or phylogenetic similarity. We then constructed microbe-set libraries by query PubMed to find microbe-mammalian gene associations and disease associations by parsing the Disbiome database. To demonstrate the utility of our novel MSEA methodology, we carried out three case studies using publicly available curated knowledge resource and microbiome profiling datasets focusing on human diseases. We found MSEA not only yields consistent findings with the original studies, but also recovers insights about disease mechanisms that are supported by the literature. Overall, MSEA is a useful knowledge-based computational approach to interpret the functions of microbes, which can be integrated with microbiome profiling pipelines to help reveal the underlying mechanism of host-microbiome interactions.

scholarly journals Cancer-associated fibroblasts promote the survival of irradiated nasopharyngeal carcinoma cells via the NF-κB pathway

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Weiqiang Huang ◽  
Longshan Zhang ◽  
Mi Yang ◽  
Xixi Wu ◽  
Xiaoqing Wang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Nasopharyngeal Carcinoma ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Gene Set Enrichment Analysis ◽  
Cancer Associated Fibroblasts ◽  
Western Blot Assay ◽  
Damage Level ◽  
Radiation Resistant

Abstract Background Irradiation has emerged as a valid tool for nasopharyngeal carcinoma (NPC) in situ treatment; however, NPC derived from tissues treated with irradiation is a main cause cancer-related death. The purpose of this study is to uncover the underlying mechanism regarding tumor growth after irradiation and provided potential therapeutic strategy. Methods Fibroblasts were extracted from fresh NPC tissue and normal nasopharyngeal mucosa. Immunohistochemistry was conducted to measure the expression of α-SMA and FAP. Cytokines were detected by protein array chip and identified by real-time PCR. CCK-8 assay was used to detect cell proliferation. Radiation-resistant (IRR) 5-8F cell line was established and colony assay was performed to evaluate tumor cell growth after irradiation. Signaling pathways were acquired via gene set enrichment analysis (GSEA). Comet assay and γ-H2AX foci assay were used to measure DNA damage level. Protein expression was detected by western blot assay. In vivo experiment was performed subcutaneously. Results We found that radiation-resistant NPC tissues were constantly infiltrated with a greater number of cancer-associated fibroblasts (CAFs) compared to radiosensitive NPC tissues. Further research revealed that CAFs induced the formation of radioresistance and promoted NPC cell survival following irradiation via the IL-8/NF-κB pathway to reduce irradiation-induced DNA damage. Treatment with Tranilast, a CAF inhibitor, restricted the survival of CAF-induced NPC cells and attenuated the of radioresistance properties. Conclusions Together, these data demonstrate that CAFs can promote the survival of irradiated NPC cells via the NF-κB pathway and induce radioresistance that can be interrupted by Tranilast, suggesting the potential value of Tranilast in sensitizing NPC cells to irradiation.

scholarly journals Melanoma is associated with an increased risk of bullous pemphigoid: a large population-based longitudinal study

2021 ◽  
Author(s):  
Khalaf Kridin ◽  
Jennifer E. Hundt ◽  
Ralf J. Ludwig ◽  
Kyle T. Amber ◽  
Dana Tzur Bitan ◽  
...  
Keyword(s):  
Bullous Pemphigoid ◽  
Statistical Significance ◽  
Large Population ◽  
Underlying Mechanism ◽  
Population Based ◽  
Control Subjects ◽  
Increased Risk ◽  
Bidirectional Association ◽  
History Of ◽  
Incident Cases

AbstractThe association between bullous pemphigoid (BP) and melanoma is yet to be investigated. We aimed to assess assess the bidirectional association between BP and melanoma and to delineate the epidemiological features of patients with both diagnoses. A population-based cohort study was performed comparing BP patients (n = 3924) with age-, sex- and ethnicity-matched control subjects (n = 19,280) with regard to incident cases of melanoma. A case–control design was additionally adopted to estimate the risk of BP in individuals with a preexisting diagnosis of melanoma. The prevalence of preexisting melanoma was higher in patients with BP than in control subjects (1.5% vs. 1.0%, respectively; P = 0.004). A history of melanoma confers a 50% increase in the risk of subsequent BP (OR 1.53; 95% CI 1.14–2.06). This risk was higher among males (OR 1.66; 95% CI 1.09–2.54) and individuals older than 80 years (OR 1.63; 95% CI 1.11–2.38), and persisted after adjustment for multiple putative confounders including PD-1/PDL-1 antagonists (adjusted OR 1.53; 95% CI 1.14–2.06). Conversely, the risk of melanoma among patients with BP was slightly elevated, but did not reach the level of statistical significance (adjusted HR 1.13; 95% CI 0.73–1.74). Patients with a dual diagnosis of BP and melanoma were older at the onset of BP and had lower body mass index. A history of melanoma is associated with a 50% increase in the incidence of subsequent BP. Physicians managing patients with both conditions should be aware of this association. Further research is warranted to reveal the underlying mechanism of these findings.

scholarly journals Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

2021 ◽  
Author(s):  
Nestor Timonidis ◽  
Alberto Llera ◽  
Paul H. E. Tiesinga
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
Structural Connectivity ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Synaptic Function ◽  
Reticular Nucleus ◽  
Sources Of Information ◽  
Independent Components ◽  
Brain Connectome

AbstractFinding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.

scholarly journals MicroRNA-8 targets the Wingless signaling pathway in the female mosquito fat body to regulate reproductive processes

2015 ◽  
Vol 112 (5) ◽  
pp. 1440-1445 ◽  
Author(s):  
Keira J. Lucas ◽  
Sourav Roy ◽  
Jisu Ha ◽  
Amanda L. Gervaise ◽  
Vladimir A. Kokoza ◽  
...  
Keyword(s):  
Blood Meal ◽  
Molecular Mechanisms ◽  
Fat Body ◽  
Control Strategies ◽  
Functional Characterization ◽  
Target Prediction ◽  
Underlying Mechanism ◽  
Female Mosquito ◽  
Reproductive Events

Female mosquitoes require a blood meal for reproduction, and this blood meal provides the underlying mechanism for the spread of many important vector-borne diseases in humans. A deeper understanding of the molecular mechanisms linked to mosquito blood meal processes and reproductive events is of particular importance for devising innovative vector control strategies. We found that the conserved microRNA miR-8 is an essential regulator of mosquito reproductive events. Two strategies to inhibit miR-8 function in vivo were used for functional characterization: systemic antagomir depletion and spatiotemporal inhibition using the miRNA sponge transgenic method in combination with the yeast transcriptional activator gal4 protein/upstream activating sequence system. Depletion of miR-8 in the female mosquito results in defects related to egg development and deposition. We used a multialgorithm approach for miRNA target prediction in mosquito 3′ UTRs and experimentally verified secreted wingless-interacting molecule (swim) as an authentic target of miR-8. Our findings demonstrate that miR-8 controls the activity of the long-range Wingless (Wg) signaling by regulating Swim expression in the female fat body. We discovered that the miR-8/Wg axis is critical for the proper secretion of lipophorin and vitellogenin by the fat body and subsequent accumulation of these yolk protein precursors by developing oocytes.

scholarly journals Rare variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations

2018 ◽  
Author(s):  
Ridge Dershem ◽  
Raghu P.R. Metpally ◽  
Kirk Jeffreys ◽  
Sarathbabu Krishnamurthy ◽  
Diane T. Smelser ◽  
...  
Keyword(s):  
Rare Variant ◽  
Functional Characterization ◽  
Data Sets ◽  
Common Variants ◽  
Loss Of Function ◽  
Altered Expression ◽  
Missense Variants ◽  
Association Testing ◽  
Disease Associations ◽  
Causes Of Disease

AbstractMany G protein-coupled receptors (GPCRs) lack common variants that lead to reproducible genome-wide disease associations. Here we used rare variant approaches to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants were used as independent data sets for sequence kernel association testing (SKAT). Strong, phenome-wide disease associations shared by two or more variant categories were found for 39% of the GPCRs. Validating the bioinformatics and SKAT analyses, functional characterization of rare missense and synonymous variants of GPR39, a Family A GPCR, showed altered expression and/or Zn2+-mediated signaling for members of both variant classes. Results support the utility of rare variant analyses for identifying disease associations for genes that lack common variants, while also highlighting the functional importance of rare synonymous variants.Author summaryRare variant approaches have emerged as a viable way to identify disease associations for genes without clinically important common variants. Rare synonymous variants are generally considered benign. We demonstrate that rare synonymous variants represent a potentially important dataset for deriving disease associations, here applied to analysis of a set of orphan or understudied GPCRs. Synonymous variants yielded disease associations in common with loss-of-function or missense variants in the same gene. We rationalize their associations with disease by confirming their impact on expression and agonist activation of a representative example, GPR39. This study highlights the importance of rare synonymous variants in human physiology, and argues for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.

scholarly journals Network Pharmacology-Based Strategy for the Investigation of the Anti-Osteoporosis Effects and Underlying Mechanism of Zhuangguguanjie Formulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Wang Gong ◽  
Xingren Chen ◽  
Tianshu Shi ◽  
Xiaoyan Shao ◽  
Xueying An ◽  
...  
Keyword(s):  
Bone Resorption ◽  
Bone Formation ◽  
Bone Mass ◽  
Signaling Pathway ◽  
Osteoclast Differentiation ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Network Pharmacology ◽  
Biological Processes

As the society is aging, the increasing prevalence of osteoporosis has generated huge social and economic impact, while the drug therapy for osteoporosis is limited due to multiple targets involved in this disease. Zhuangguguanjie formulation (ZG) is extensively used in the clinical treatment of bone and joint diseases, but the underlying mechanism has not been fully described. This study aimed to examine the therapeutic effect and potential mechanism of ZG on postmenopausal osteoporosis. The ovariectomized (OVX) mice were treated with normal saline or ZG for 4 weeks after ovariectomy following a series of analyses. The bone mass density (BMD) and trabecular parameters were examined by micro-CT. Bone remodeling was evaluated by the bone histomorphometry analysis and ELISA assay of bone turnover biomarkers in serum. The possible drug–disease common targets were analyzed by network pharmacology. To predict the potential biological processes and related pathways, GO/KEGG enrichment analysis was performed. The effects of ZG on the differentiation phenotype of osteoclasts and osteoblasts and the predicted pathway were verified in vitro. The results showed that ZG significantly improved the bone mass and micro-trabecular architecture in OVX mice compared with untreated OVX mice. ZG could promote bone formation and inhibit bone resorption to ameliorate ovariectomy-induced osteoporosis as evidenced by increased number of osteoblast (N.Ob/Tb.Pm) and decreased number of osteoclast (N.Oc/Tb.Pm) in treated group compared with untreated OVX mice. After identifying potential drug–disease common targets by network pharmacology, GO enrichment analysis predicted that ZG might affect various biological processes including osteoblastic differentiation and osteoclast differentiation. The KEGG enrichment analysis suggested that PI3K/Akt and mTOR signaling pathways could be the possible pathways. Furthermore, the experiments in vitro validated our findings. ZG significantly down-regulated the expression of osteoclast differentiation markers, reduced osteoclastic resorption, and inhibited the phosphorylation of PI3K/Akt, while ZG obviously up-regulated the expression of osteogenic biomarkers, promoted the formation of calcium nodules, and hampered the phosphorylation of 70S6K1/mTOR, which can be reversed by the corresponding pathway activator. Thus, our study suggested that ZG could inhibit the PI3K/Akt signaling pathway to reduce osteoclastic bone resorption as well as hamper the mTORC1/S6K1 signaling pathway to promote osteoblastic bone formation.

scholarly journals The Theoretical Embedding Of Born Globals: Challenging Existing Internationalization Theories

2014 ◽  
Vol 14 (1) ◽  
pp. 39
Author(s):  
Ricarda B. Bouncken ◽  
Felix Schuessler ◽  
Sascha Kraus
Keyword(s):  
Competitive Advantage ◽  
Underlying Mechanism ◽  
Learning Processes ◽  
Sustainable Competitive Advantage ◽  
Born Globals ◽  
Resource Based View ◽  
Knowledge Based ◽  
A Company

This article examines the embedding of the phenomenon of Born Globals into three existing theories of the firm. The model of Born Globals deals with young companies that begin shortly after their foundation to internationalize. The Uppsala Internationalization Model helps to delimit the concept of Born Globals from existing internationalization models and to highlight their special features. The resource-based view takes up the integration of knowledge as the key resource of Born Globals and explains the underlying mechanism with which a company achieves a sustainable competitive advantage from a bundle of resources. The knowledge-based view is concerned with the generation of knowledge and explains the learning processes that are performed by the entrepreneur. A recurring theme could be identified and contains the following elements which interconnect the three theories of the firm with the concept of Born Globals - knowledge as a key resource, learning, and integration of knowledge into organizations.

scholarly journals NPF genes excavation and their expression response to vernalization and nitrogen deficiency in allotetraploid rapeseed

2021 ◽  
Author(s):  
Hongbo Chao ◽  
Jianjie He ◽  
Weiguo Zhao ◽  
Hong Fu ◽  
Yingpeng Hua ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Nitrogen Deficiency ◽  
Enrichment Analysis ◽  
Functional Differentiation ◽  
Peptide Transporter ◽  
Peptide Transporters ◽  
Transporter Family ◽  
Expression Response ◽  
Metabolite Content

Abstract Background The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY (NPF) genes, initially characterized as nitrate or peptide transporters in plants, involve in the transport of a large variety of substrates including amino acids, nitrate, auxin (IAA), jasmonates (JAs), abscisic acid (ABA) and gibberellins (GAs) and glucosinolates. The evolution and expression diversification of genes determine their functional differentiation in polyploid species. Results Among 169 NPF genes excavated in Brassica napus, 97 B. napus NPF (BnaNPF) genes evolved from B. rapa, and 72 BnaNPF genes from B. olereaca. They unevenly distributed on B. napus genome and exhibited obvious synteny with NPF genes in Arabidopsis thaliana, B. rapa and B. olereaca. BnaNPF genes were identified to show diversified expression patterns in 90 different organs or tissues based on transcriptome profile data. Besides, they exhibited complex expression changes in the development process of leaves, silique wall and seeds, which indicated that the expression of BnaNPF genes maybe respond to altered phytohormone and secondary metabolite content through combining with promoter elements enrichment analysis. Furthermore, many BnaNPF genes were detected to response to vernalization with two different patterns and 20 BnaNPF genes responded to nitrate deficiency. Conclusion The evolution of BnaNPF genes and their expression pattern including response to vernalization and nitrogen deficiency were characterized and provide valuable information for further functional characterization in rapeseed.

scholarly journals The Underlying Mechanism of Chinese Herb of Regulating Marrow in the Treatment of  Osteonecrosis of the Femoral Head Based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xiaojian Wang ◽  
Rui Wang ◽  
Ting Xu ◽  
Hongting Jin ◽  
Peijian Tong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Active Components ◽  
Pathway Enrichment

Abstract Background The lesion of marrow is a crucial factor in orthopedic diseases, which is recognized by orthopedics-traumatology expert from "Zhe-School of Chinese Medicine". The Chinese herbs of regulating marrow has been widely used to treat osteonecrosis of the femoral head (ONFH) in China, while the interaction mechanisms were still elucidated. Thus, we conducted this study to explore the underlying mechanism of the five highest-frequency Chinese herbs of regulating marrow(HF-CHRM) in the treatment of ONFH with the aid of network pharmacology(NP) and molecular docking(MD). Methods The active components and potential targets of HF-CHRM were obtained through several online databases, such as Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), UniProt database. The gene targets related to ONFH were collected with the help of the OMIM and GeneCards disease-related databases. The "drug- component-target-disease" network and protein-protein interaction(PPI) network of the drug and disease intersecting targets were constructed by using Cytoscape software and the STRING database. R software was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The MD of critical components and targets was carried out using Autodock Vina and Pymol to validate the binding affinity. Results A total of 54 active components, 1074 drug targets and 195 gene targets were obtained. There were 1219 ONFH related targets. 39 drug and disease intersection targets(representative genes: IL6, TP53, VEGFA, ESR1, IL1B) were obtained and considered potential therapeutic targets. 1619 items were obtained by the GO enrichment analysis, including 1517 biological processes, 10 cellular components and 92 molecular functions, which is mainly related to angiogenesis, bone and lipid metabolism and inflammatory reaction. The KEGG pathway enrichment analysis revealed 119 pathways, including AGE-RAGE signaling pathway, PI3K-Akt signaling pathway and IL-17 signaling pathway. MD results showed that quercetin, wogonin, and kaempferol active components had good affinity with IL6, TP53, and VEGFA core proteins. Conclusion The HF-CHRM can treat ONFH by multi-component, multi-target, and multi-pathway comprehensive action.

Features and prognosis of cytomegalovirus-associated biliary atresia: a retrospective study

2020 ◽  
Author(s):  
Zhe Wang ◽  
Xi-Si Guan ◽  
Yue Wu ◽  
Qiu-Ming He ◽  
Le Li ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Biliary Atresia ◽  
Statistical Significance ◽  
Underlying Mechanism ◽  
Gamma Glutamyl Transferase ◽  
Cmv Infection ◽  
Short Term ◽  
Term Outcome ◽  
Dna Test ◽  
Glutamyl Transferase

Abstract Purpose To investigate the relationship between cytomegalovirus (CMV) infection and biliary atresia (BA) onset, development and short-term prognosis after Kasai operation. Methods A retrospective study was conducted. BA Patients with obstructive jaundice and tested for CMV infection were included and grouped by CMV-IgM and CMV-DNA test results, between-group differences of preoperative blood tests and short-term prognosis indicators were investigated for the statistical significance. Results the CMV infection rate was higher in BA patients compared with non-BA jaundiced patients. Higher preoperative gamma-glutamyl transferase (GGT) level and lymphocyte percentage (Lym%) were significantly corelated with the CMV infection in BA patients. CMV(+) BA Patients had similar short-term outcome comparing with CMV(-) patients. IgM(+)DNA(+) group had highest GGT, total bilirubin (TBiL) and direct bilirubin (DBiL) level. IgM(-)DNA(+) group had the lowest GGT and the highest alkaline phosphatase (ALP) level. IgM(+)DNA(-) group had the highest bodyweight and lymphocyte percentage. The IgM (+)DNA (-) group had more patient achieved complete jaundice clearance than other groups. Conclusion CMV infection may associate to BA development and progression. Perioperative antivirus treatments may be necessary for improving outcome. Better elucidation of the underlying mechanism will require further investigation.

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