scholarly journals The Interactions of Small Proline-rich Proteins With Late Cornified Envelope Proteins Are Involved in the Pathogenesis of Psoriasis

Author(s):  
Siyu Tian ◽  
Shuming Chen ◽  
Yongyi Feng ◽  
Yong Li

Abstract Background: Psoriasis is a common cutaneous disease with many characteristics including inflammation and aberrant keratinocyte proliferation. However, the pathogenesis of psoriasis is not completely clear. Methods: We explore the differentially expressed genes (DEGs) in psoriasis by analyzing the gene expression profile obtained from the Gene Expression Omnibus (GEO) database. The DEGs were examined by gene ontology (GO) functional enrichment analysis and protein-protein interactions (PPI) network. Correlation analysis in R studio software analyzed the association of SPRR and LCE genes. The potential direct protein-protein interactions between SPRR proteins and LCE3D was further verified by co-localization observed in 293T cells and co-immunoprecipitation (CO-IP). The expression levels of SPRR and LCE genes were detected in the IMQ-induced psoriasiform dermatitis mice. Results: The small proline-rich (SPRR) and late cornified envelope (LCE) genes were identified as a module in constructed PPI network. The gene expression profile GSE63684 analysis showed that both SPRR family and LCE family genes were significantly upregulated in imiquimod (IMQ) induced psoriasiform dermatitis mice. Correlation analysis in R studio software recognized the association of SPRR and LCE genes, in which the potential direct protein-protein interactions between SPRR proteins and LCE3D was further verified by co-localization observed in 293T cells and co-immunoprecipitation (CO-IP) results that suggest direct interaction between SPRR2 and LCE3D. Notably, we found that the expression levels of SPRR and LCE genes were significantly increased in the IMQ-induced psoriasiform dermatitis mice while tazarotene cream treatment specifically decreased the mRNA expression of these genes, which indicated that the SPRR and LCEs were regulated simultaneously in psoriasis. Conclusion: Our studies found the interactions of SPRR proteins with LCE proteins, which may provide new insights into the pathogenesis of psoriasis.

2021 ◽  
Vol 11 ◽  
Author(s):  
Chun Yang ◽  
Si-Jia Chen ◽  
Bo-Wen Chen ◽  
Kai-Wen Zhang ◽  
Jing-Jie Zhang ◽  
...  

Sporamin, a proteinase inhibitor isolated from the sweet potato (Ipomoea batatas), has shown promising anticancer effect against colorectal cancer (CRC) in vitro and in vivo but its mechanisms of action are poorly understood. In the present study, high throughput RNA sequencing (RNA-seq) technology was applied to explore the transcriptomic changes induced by sporamin in the presence of thapsigargin (TG), a non-12-O-tetradecanolphorbol-13-acetate type cancer promoter, in the LoVo human CRC cells. Cellular total RNA was extracted from the cells after they were treated with vehicle (CTL), 1 μM of thapsigargin (TG), or 1 μM of TG plus 30 μM of sporamin (TGSP) for 24 h. The migratory capacity of the cells was determined by wound healing assay. The gene expression profiles of the cells were determined by RNA-seq on an Illumina platform. GO enrichment analysis, KEGG pathway analysis, protein-protein interaction (PPI) network construction, and transcription factors (TF) prediction were all performed based on the differentially expressed genes (DEGs) across groups with a series of bioinformatics tools. Finally, the effect and potential molecular targets of the sporamin at the transcriptome level were evaluated. Sporamin significantly inhibited the migration of cells induced by TG. Among the 17915 genes detected in RNA-seq, 46 DEGs were attributable to the effect of sporamin. RT-PCR experiment validated that the expression of RGPD2, SULT1A3, and BIVM-ERCC5 were up-regulated while NYP4R, FOXN1, PAK6, and CEACAM20 were down-regulated. Sporamin enhanced the mineral absorption pathway, worm longevity regulating pathway, and pyrimidine metabolism pathway. Two TFs (SMIM11A and ATOH8) were down-regulated by sporamin. HMOX1 (up-regulated) and NME1-NME2 (down-regulated) were the main nodes in a PPI network consisting of 16 DEGs that were modulated by sporamin in the presence of TG. Sporamin could favorably alter the gene expression profile of CRC cells, up-regulating the genes that contribute to the homeostasis of intracellular metal ions and the activities of essential enzymes and DNA damage repairment. More studies are warranted to verify its effect on specific genes and delineate the mechanism of action implicated in the process.


2020 ◽  
Vol 9 (6) ◽  
pp. 385-391
Author(s):  
T Poongodi ◽  
◽  
TH Nazeema ◽  

The Multi-targeted action of Polyherbal formulation is responsible for enhanced therapeutic efficacy in combating various diseases. But, understanding the mode of action of herbal medicine remains a challenge because of its complex metabolomics. Network pharmacology-based approach enables to explore the mechanism of action of polyherbal formulation in biological system. In present investigation, we have explored the molecular mechanism of action of the Polyherbal formulation MKA comprising of three botanicals Mimusops elengi L., Kedrostis foetidissima (Jacq.) Cogn. and Artemisia vulgaris L. in treating respiratory diseases by network pharmacology-based approach. The protein targets were mined from Binding database for the bioactive present in MKA. The disease associated targets were identified using Open target Platform. Based on ligand-target interactions, it was interpreted that MKA could alleviate the symptoms of respiratory disease by multiple mechanisms like EGFR inhibition by Quercetin and Quercetin-3-O-rhamnoside, KDR inhibition by Quercetin, STAT-3 inhibition by β-sitosterol- β-Dglucoside, TRPV1 inhibition by phytol acetate, etc. The Protein-protein interaction (PPI) network was constructed using STRING database. KEGG pathway based functional enrichment was also predicted for the PPI network. It was found that multiple ligand-target interactions and protein-protein interactions is responsible for pharmacological activity of MKA in respiratory diseases.


2014 ◽  
Vol 2014 ◽  
pp. 1-12
Author(s):  
Jun Ren ◽  
Wei Zhou ◽  
Jianxin Wang

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based onλ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to aλ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameterλ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value ofλ_th. Experimental results ofS. cerevisiaeshow that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.


2021 ◽  
Vol 22 (15) ◽  
pp. 8160
Author(s):  
Katarzyna Zielniok ◽  
Anna Burdzinska ◽  
Victor Murcia Pienkowski ◽  
Agnieszka Koppolu ◽  
Malgorzata Rydzanicz ◽  
...  

Mesenchymal stromal cell (MSC) therapy is making its way into clinical practice, accompanied by research into strategies improving their therapeutic potential. Preconditioning MSCs with hypoxia-inducible factors-α (HIFα) stabilizers is an alternative to hypoxic priming, but there remains insufficient data evaluating its transcriptomic effect. Herein, we determined the gene expression profile of 6 human bone marrow-derived MSCs preconditioned for 6 h in 2% O2 (hypoxia) or with 40 μM Vadadustat, compared to control cells and each other. RNA-Sequencing was performed using the Illumina platform, quality control with FastQC and adapter-trimming with BBDUK2. Transcripts were mapped to the Homo_sapiens. GRCh37 genome and converted to relative expression using Salmon. Differentially expressed genes (DEGs) were generated using DESeq2 while functional enrichment was performed in GSEA and g:Profiler. Comparison of hypoxia versus control resulted in 250 DEGs, Vadadustat versus control 1071, and Vadadustat versus hypoxia 1770. The terms enriched in both phenotypes referred mainly to metabolism, in Vadadustat additionally to vesicular transport, chromatin modifications and interaction with extracellular matrix. Compared with hypoxia, Vadadustat upregulated autophagic, phospholipid metabolism, and TLR cascade genes, downregulated those of cytoskeleton and GG-NER pathway and regulated 74 secretory factor genes. Our results provide valuable insight into the transcriptomic effects of these two methods of MSCs preconditioning.


2021 ◽  
Author(s):  
Jiawen Xu ◽  
Haibo Si ◽  
Yi Zeng ◽  
Yuangang Wu ◽  
Shaoyun Zhang ◽  
...  

Abstract Background Spondyloarthritis(SpA) is a group of multi-factorial bone diseases influenced by genetic factors, environment and lifestyles. However, the genetic and pathogenic mechanism of SpA is still elusive. Methods Firstly, the tissue-specific transcriptome-wide association study (TWAS) of SpA was performed by utilizing the genome-wide association study (GWAS, including 3966 SpA patients and 452264 controls) summary data and gene expression weights of the whole blood and skeletal muscle. Secondly, the SpA-associated genes identified by TWAS were further compared with the differentially expressed genes(DEGs) detected by gene expression profile of SpA acquired from the Gene Expression Omnibus database (GEO, accession number:GSE58667). Finally, FUMA and Metascape tools were used to conduct gene functional enrichment and annotation analysis. Results TWAS detected 28 significant genes associated with SpA both in the whole blood and skeletal muscle, such as CTNNAL1 (PSM=0.0304, PWB=0.0096). Further comparing with gene expression profile of SpA, we identified 20 candidate genes which overlapped in TWAS, such as MCM4 (PTWAS=0.0132, PDEG=0.0275), KIAA1109 (PTWAS=0.0371,PDEG=0.0467). The enrichment analysis of the genes identified by TWAS detected 93 significant GO terms 33 and KEGG pathways, such as mitochondrion organization (GO:0007005, log10(P)= -4.29) and axon guidance(hsa04360, log10(P)= -4.26). Conclusion We identified multiple candidate genes genetically related to SpA. Our study may provide some novel clues for the further study of the genetic mechanism, diagnosis and treatment of SpA.


2021 ◽  
Author(s):  
Chunyang Wang ◽  
Shiwei Liao ◽  
jing xu

Abstract In this study, we developed a computational method to identify Guillain–Barré syndrome (GBS) related genes based on (i) a gene expression profile, and (ii) the shortest path analysis in a protein-protein interaction (PPI) network. The mRMR (Maximum Relevance Minimum Redundancy) method was employed to select significant genes from an mRNA profile dataset of GBS patients and healthy controls. The protein products of the significant genes were then mapped to a PPI network generated from the STRING database. Shortest paths were computed and all shortest path proteins were picked out and were ranked according to their betweenness. Related genes of the top-most proteins in the ordered list were then retrieved and were regarded as potential GBS related genes in this study. As a result, totally 30 GBS related genes were screened out, in which 20 were retrieved from PPI analysis of up-regulated expressed genes and 23 were from down-regulated expressed genes (13 overlap genes). GO enrichment and KEGG enrichment analysis were performed respectively. Results showed that there were some overlap GO terms and KEGG pathway terms in both up-regulated and down-regulated analysis, which indicated these terms may play critical role during GBS process. These results could shed some light on the understanding of the Genetic and molecular pathogenesis of GBS disease, providing basis for future experimental biology studies and for the development of effective genetic strategies for GBS clinical therapies.


2019 ◽  
Author(s):  
Jing Luo ◽  
Zhenwei Liu ◽  
Chenlu Li ◽  
Ruochen Wang ◽  
Jinxia Fang ◽  
...  

Abstract Background: Pulmonary arterial hypertension (PAH) is a life-threatening condition that gets worse over time. Despite advances in the development of strategies for treating PAH, prognosis of the disease remains unsatisfactory, especially for advanced PAH. The aim of this study was to explore potential crucial genes and pathways associated with PAH that can be used as potential biomarkers for early diagnosis.Results: Gene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). A total of 521 differentially expressed genes (DEGs), including 432 up-regulated DEGs and 89 down-regulated DEGs were identified using “limma” package in R. Functional enrichment analysis showed that these DEGs were mainly enriched in mitotic cell cycle process, mitotic cell cycle and microtubule cytoskeleton organization. Moreover, five key genes (CDK1, SMC2, SMC4, KIF23, and CENPE) were identified based on the comprehensive evaluation of PPI analysis, modular analysis and cytohubba’s analysis, then further validated in another transcriptomic data set associated with PAH from public database (GSE33463). Furthermore, these hub genes were mainly enriched in promoting mitotic cell cycle process, which may be closely associated with the pathogenesis of PAH. We also found that the predicted miRNAs targeting these hub genes were found to be enriched in TGF-β and Hippo signaling pathway.Conclusion: These findings are expected to gain a further insight into the development of PAH and provide a promising index for the detection of PAH.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3458-3458
Author(s):  
Ebru Coskun ◽  
Martin Neumann ◽  
Cornelia Schlee ◽  
Nicola Goekbuget ◽  
Dieter Hoelzer ◽  
...  

Abstract Abstract 3458 Introduction: Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) has been identified as high-risk subgroup in pediatric acute T-lymphoblastic leukemia (T-ALL). ETP-ALLs originate from early thymic progenitors that retain stem cell features and are characterized by a specific immunophenotype and by a specific gene expression profile. Recently, we have characterized ETP-ALL as subgroup of early T-ALL in adults. To unravel the underlying mechanisms for the aberrant and distinct gene expression profile in ETP-ALL we now explored the expression of microRNAs (miRNAs) as gene regulators in ETP-ALL and further investigated their functional role in acute leukemia. Patients and methods: We screened expression levels of 667 miRNAs in newly diagnosed T-ALL patients (n=14: ETP-ALL n=8, non-ETP early T-ALL n=3, thymic T-ALL n=3) and 2 healthy controls (CD3 selected T cells) using a Taqman Low Density Array (TLDA; Applied Biosystems). The expression levels of miR-221 and miR-222 were validated in a large cohort of adult T-ALL (n=178: ETP-ALL n=66 and typical T-ALL n=112 including early-, thymic-, and mature T-ALLs) and healthy controls (n=6) by real-time-PCR (Taqman microRNA assays; Applied Biosystems). These patients were enrolled on the GMALL study 07/03. Functional analysis was performed by AMAXA transfection of pSUPER vector containing the miR-221 and miR-222 DNA sequences in Jurkat (T-lineage ALL) and KG1a (AML) cells. Viability was determined by cell proliferation reagent WST-1, and BrdU ELISA. Apoptosis was measured by annexin-V/7AAD staining with subsequent flow cytometric analysis. Results: In our screen 229 (34%) of the 667 miRNAs represented by the TLDA were expressed at detectable levels in at least two-thirds of the T-ALL samples and the controls. Of these we identified 55 miRNAs to be differentially expressed in T-ALL samples compared to healthy controls: 49 miRNAs were upregulated and 6 miRNAs were downregulated in the patient samples. Of these, miR-221 and miR-222 were the only miRNAs significantly upregulated in the ETP-ALL compared to the combined early and thymic T-ALL subgroups (8.0-fold, P<0.01; 5.0-fold, P<0.01, respectively). Therefore, we further validated miR-221 and miR-222 expression in a larger set of 178 T-ALL samples and observed a 3.3-fold higher expression of miR-221 (P<0.0001) and 3.9-fold higher expression of miR-222 (P<0.0001) in ETP-ALL (n=66) compared to typical T-ALL (n=112). For the correlation of miR-221 and miR-222 expression with molecular features, samples were divided into groups (low and high) according to the median of the miRNA expression levels. High miR-222 expression was associated with an immature phenotype of early T-ALL (P<0.01) and cell surface expression of CD34 (mean: 32%) compared to low miR-222 expressers (mean: 8%; P<0.01). Moreover, high miR-222 expression was associated with expression of myeloid markers CD33 (mean: 23% compared to 4% in low miRNA expressers, P<0.01) and CD13 (mean: 18% vs. 4%, P<0.01). Similar results were obtained for miR-221. In vitro studies revealed that overexpression of miR-222 inhibited proliferation of Jurkat (58% reduction of proliferation compared to cells transfected with the empty vector, P<0.001) and KG1a cells (50% reduction of proliferation compared to control cells, P<0.01) determined by WST-1. A reduction of the DNA synthesis was detected by BrdU incorporation after miR-222 overexpression in Jurkat (37% reduction compared to control cells) and in KG1a cells (54% reduction compared to control cells). Overexpression of miR-222 induced a 1.3- (P=0.02) and 3.0-fold (P<0.01) increase in apoptosis in Jurkat and KG1a cells, respectively. No significant changes were observed for miR-221 transfected cells in these functional assays. Conclusion: In summary, our study revealed aberrant expression of miRNAs in ETP-ALL, with miR-221 and miR-222 as the most overexpressed miRNAs. Functional analysis demonstrated that miR-222 impaired the proliferation and induced apoptosis, indicating a potential role for miR-222 in acute leukemia. Importantly, miR-222 targets such as the proto-oncogene c-KIT and the ETS1oncogene are contained in the gene expression profile of ETP-ALL. Thus, aberrant expression of miR-222 may directly impact leukemogenesis by altering expression of key oncogenes in acute leukemia. Disclosures: Goekbuget: Micromet: Consultancy.


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