Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum–host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

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Gene Expression Response ofTrichophyton rubrumduring Coculture on Keratinocytes Exposed to Antifungal Agents

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2015/180535 ◽

2015 ◽

Vol 2015 ◽

pp. 1-7 ◽

Cited By ~ 15

Author(s):

Tatiana Takahasi Komoto ◽

Tamires Aparecida Bitencourt ◽

Gabriel Silva ◽

Rene Oliveira Beleboni ◽

Mozart Marins ◽

...

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Citrate Synthase ◽

Isocitrate Lyase ◽

Glyoxylate Cycle ◽

Serine Proteinase ◽

Gene Expression Response ◽

Fungal Host ◽

Host Interaction ◽

Genes Encoding

Trichophyton rubrumis the most common causative agent of dermatomycoses worldwide, causing infection in the stratum corneum, nails, and hair. Despite the high prevalence of these infections, little is known about the molecular mechanisms involved in the fungal-host interaction, particularly during antifungal treatment. The aim of this work was to evaluate the gene expression ofT. rubrumcocultured with keratinocytes and treated with the flavonoidtrans-chalcone and the glycoalkaloidα-solanine. Both substances showed a marked antifungal activity againstT. rubrumstrain CBS (MIC = 1.15 and 17.8 µg/mL, resp.). Cytotoxicity assay against HaCaT cells produced IC50values of 44.18 totrans-chalcone and 61.60 µM toα-solanine. The interaction of keratinocytes withT. rubrumconidia upregulated the expression of genes involved in the glyoxylate cycle, ergosterol synthesis, and genes encoding proteases but downregulated the ABC transporterTruMDR2 gene. However, both antifungals downregulated the ERG1 and ERG11, metalloprotease 4, serine proteinase, andTruMDR2 genes. Furthermore, thetrans-chalcone downregulated the genes involved in the glyoxylate pathway, isocitrate lyase, and citrate synthase. Considering the urgent need for more efficient and safer antifungals, these results contribute to a better understanding of fungal-host interactions and to the discovery of new antifungal targets.

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The Transcriptional Profile of Trichophyton rubrum Co-Cultured with Human Keratinocytes Shows New Insights about Gene Modulation by Terbinafine

Pathogens ◽

10.3390/pathogens8040274 ◽

2019 ◽

Vol 8 (4) ◽

pp. 274 ◽

Cited By ~ 1

Author(s):

Monise Fazolin Petrucelli ◽

Josie Budag Matsuda ◽

Kamila Peroni ◽

Pablo Rodrigo Sanches ◽

Wilson Araújo Silva ◽

...

Keyword(s):

Trichophyton Rubrum ◽

Human Keratinocytes ◽

Major Facilitator Superfamily ◽

Ergosterol Biosynthesis ◽

Rna Seq ◽

Host Interaction ◽

Culture Model ◽

Superficial Mycosis ◽

Genes Encoding ◽

Major Facilitator

The dermatophyte Trichophyton rubrum is the main causative agent of dermatophytoses worldwide. Although a superficial mycosis, its incidence has been increasing especially among diabetic and immunocompromised patients. Terbinafine is commonly used for the treatment of infections caused by dermatophytes. However, cases of resistance of T. rubrum to this allylamine were reported even with the efficacy of this drug. The present study is the first to evaluate the effect of terbinafine using a co-culture model of T. rubrum and human keratinocytes, mimicking a fungus-host interaction, in conjunction with RNA-seq technique. Our data showed the repression of several genes involved in the ergosterol biosynthesis cascade and the induction of genes encoding major facilitator superfamily (MFS)- and ATP-binding cassette superfamily (ABC)-type membrane transporter which may be involved in T. rubrum mechanisms of resistance to this drug. We observed that some genes reported in the scientific literature as candidates of new antifungal targets were also modulated. In addition, we found the modulation of several genes that are hypothetical in T. rubrum but that possess known orthologs in other dermatophytes. Taken together, the results indicate that terbinafine can act on various targets related to the physiology of T. rubrum other than its main target of ergosterol biosynthetic pathway.

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Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

Archives of Microbiology ◽

10.1007/s00203-021-02502-4 ◽

2021 ◽

Author(s):

Guohong Zeng ◽

Jin Li ◽

Yuxiu Ma ◽

Qian Pu ◽

Tian Xiao ◽

...

Keyword(s):

Root Rot ◽

Molecular Mechanisms ◽

Management Strategies ◽

Panax Notoginseng ◽

Glycoside Hydrolases ◽

Rna Seq ◽

Host Interaction ◽

Excellent Starting Point ◽

Starting Point ◽

Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

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Identification of saponins detoxification genes in I. mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

10.21203/rs.3.rs-212506/v1 ◽

2021 ◽

Author(s):

Guohong Zeng ◽

Jin Li ◽

Yuxiu Ma ◽

Qian Pu ◽

Tian Xiao ◽

...

Keyword(s):

Root Rot ◽

Molecular Mechanisms ◽

Management Strategies ◽

Panax Notoginseng ◽

Glycoside Hydrolases ◽

Rna Seq ◽

Host Interaction ◽

Excellent Starting Point ◽

Starting Point ◽

Genes Encoding

Abstract Saponins are kinds of antifungal compounds produced by P. notoginseng to resist invasion by pathogens. I. mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4 H and 12 H compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4 H and 12 H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation-reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen-Host Interaction) genes out of those 93 up-regulated genes. In this report, we identified virulence associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

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Cyclophilin a as a Mediator of Tissue Injure and Nephrotoxicity

Nephrology Research & Reviews ◽

10.4081/nr.2012.e9 ◽

2012 ◽

Vol 4 (2) ◽

pp. 42-44

Author(s):

Grace Moscoso-Solorzano ◽

Gianna Mastroianni-Kirsztajn

Keyword(s):

Molecular Mechanisms ◽

Tissue Injury ◽

Cyclophilin A ◽

Common Mechanism ◽

Ppiase Activity ◽

Expression Of Genes ◽

Inflammatory Stimuli ◽

Genes Encoding ◽

Inflammatory Processes

Cyclophilin A (CypA) belongs to the peptidyl-prolil isomerase (PPlase) family of proteins and it is also known as the cellular receptor for cyclosporine A (CsA). CsA binds to CypA and inhibits the PPIase activity, but the CypA-CsA complex also binds to calcineurin that promotes the expression of genes encoding cytokines and other proteins required for immune response. In addition, the polymorphism variation of CypA promoter seems to have an influence on the expression of CypA in in vitro studies. CypA was also implicated in inflammatory processes (such as, among others, those observed in rheumatoid arthritis, atherosclerotic disease, nephrotoxicity) and it can be secreted by cells in response to inflammatory stimuli. CypA can also have a role in the molecular mechanisms by which CsA induces nephroxicity but these remain poorly understood. Recent studies suggest that CsA inhibition of CypA PPlase activity is a possible mechanism of this drug toxicity. In addition, CypA overexpression could be protective against CsA nephrotoxicity. Finally, the putative common mechanism by which CypA could be involved in CsA nephrotoxicity and tissue injury is related to its proinflammatory effects in cells.

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Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma

Scientific Reports ◽

10.1038/s41598-019-52559-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 14

Author(s):

Xia Tang ◽

Delong Feng ◽

Min Li ◽

Jinxue Zhou ◽

Xiaoyuan Li ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Rna Seq ◽

Pairwise Interactions ◽

Micro Rnas ◽

Non Coding Rnas ◽

First Time

Abstract Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.

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Comparative RNA-seq-Based Transcriptome Analysis of the Virulence Characteristics of Methicillin-Resistant and -Susceptible Staphylococcus pseudintermedius Strains Isolated from Small Animals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01907-15 ◽

2015 ◽

Vol 60 (2) ◽

pp. 962-967 ◽

Cited By ~ 15

Author(s):

Natacha Couto ◽

Adriana Belas ◽

Manuela Oliveira ◽

Paulo Almeida ◽

Carla Clemente ◽

...

Keyword(s):

Virulence Genes ◽

Expression Profiles ◽

Brain Heart Infusion ◽

Surface Proteins ◽

Rna Seq ◽

Staphylococcus Pseudintermedius ◽

Methicillin Resistant ◽

Content Type ◽

Genes Encoding

ABSTRACTStaphylococcus pseudintermediusis often associated with pyoderma, which can turn into a life-threatening disease. The dissemination of highly resistant isolates has occurred in the last 10 years and has challenged antimicrobial treatment of these infections considerably. We have compared the carriage of virulence genes and biofilm formation between methicillin-resistant and methicillin-susceptibleS. pseudintermedius(MRSP and MSSP, respectively) isolates and theirin vitrogene expression profiles by transcriptome sequencing (RNA-seq). Isolates were relatively unevenly distributed among the fouragrgroups, andagrtype III predominated in MRSP. Five virulence genes were detected in all isolates. Only thespsOgene was significantly associated with MSSP isolates (P= 0.04). All isolates produced biofilm in brain heart infusion broth (BHIB)–4% NaCl. MSSP isolates produced more biofilm on BHIB and BHIB–1% glucose media than MRSP isolates (P= 0.03 andP= 0.02, respectively). Virulence genes encoding surface proteins and toxins (spsA,spsB,spsD,spsK,spsL,spsN,nucC,coa, andluk-I) and also prophage genes (encoding phage capsid protein, phage infection protein, two phage portal proteins, and a phage-like protein) were highly expressed in the MRSP isolate (compared with the MSSP isolate), suggesting they may play a role in the rapid and widespread dissemination of MRSP. This study indicates that MRSP may upregulate surface proteins, which may increase the adherence of MRSP isolates (especially sequence type 71 [ST71]) to corneocytes. MSSP isolates may have an increased ability to form biofilm under acidic circumstances, through upregulation of the entirearcoperon. Complete understanding ofS. pseudintermediuspathogenesis and host-pathogen signal interaction during infections is critical for the treatment and prevention ofS. pseudintermediusinfections.

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Chondrodysplasias With Multiple Dislocations Caused by Defects in Glycosaminoglycan Synthesis

Frontiers in Genetics ◽

10.3389/fgene.2021.642097 ◽

2021 ◽

Vol 12 ◽

Author(s):

Johanne Dubail ◽

Valérie Cormier-Daire

Keyword(s):

Molecular Mechanisms ◽

Glycosaminoglycan Synthesis ◽

Genes Encoding ◽

Vertebral Anomalies ◽

A Cell ◽

Novel Biomarkers ◽

Severe Short Stature ◽

Hand Anomalies

Chondrodysplasias with multiple dislocations form a group of severe disorders characterized by joint laxity and multiple dislocations, severe short stature of pre- and post-natal onset, hand anomalies, and/or vertebral anomalies. The majority of chondrodysplasias with multiple dislocations have been associated with mutations in genes encoding glycosyltransferases, sulfotransferases, and transporters implicated in the synthesis or sulfation of glycosaminoglycans, long and unbranched polysaccharides composed of repeated disaccharide bond to protein core of proteoglycan. Glycosaminoglycan biosynthesis is a tightly regulated process that occurs mainly in the Golgi and that requires the coordinated action of numerous enzymes and transporters as well as an adequate Golgi environment. Any disturbances of this chain of reactions will lead to the incapacity of a cell to construct correct glycanic chains. This review focuses on genetic and glycobiological studies of chondrodysplasias with multiple dislocations associated with glycosaminoglycan biosynthesis defects and related animal models. Strong comprehension of the molecular mechanisms leading to those disorders, mostly through extensive phenotypic analyses of in vitro and/or in vivo models, is essential for the development of novel biomarkers for clinical screenings and innovative therapeutics for these diseases.

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Genes encoding proteins regulating fatty acid metabolism and cellular response to lipids are differentially expressed in porcine luminal epithelium during long-term culture

Medical Journal of Cell Biology ◽

10.2478/acb-2019-0008 ◽

2019 ◽

Vol 7 (2) ◽

pp. 58-65

Author(s):

Magdalena Kulus ◽

Blanka Borowiec ◽

Małgorzata Popis ◽

Piotr Celichowski ◽

Michal Jeseta ◽

...

Keyword(s):

Fatty Acid ◽

Epithelial Cells ◽

Cellular Response ◽

Molecular Mechanisms ◽

In Vitro Cultivation ◽

Beta Oxidation ◽

Physiological Processes ◽

Genes Encoding ◽

Fatty Acid Beta Oxidation

AbstractAmong many factors, the epithelium lining the oviductal lumenis very important for the development of the oocyte and its subsequent fertilization. The oviductal epithelium is characterized by the presence of ciliary cells, supporting the movement of cumulus-oocyte complexes towards the uterus. By interacting with the semen, the epithelium of the fallopian tube makes the sperm acquire the ability to fertilize. So far, the exact molecular mechanisms of these changes have not been known. Hence, understanding the metabolism of oviduct epithelial cells and the level of expression of individual groups of genes seems to be a way to deepen the knowledge about the broadly understood reproduction.In our research, we decided to culture oviductal epithelial cells (OECs) in vitro for a long period of time. After 24h, 7, 15 and 30 days, the OECs were harvested, with their RNA isolated. Transcriptomic changes were analyzed using microarrays. The “cellular response to lipid” group was represented by the following genes: MUC1, CYP24A1, KLF4, IL24, SNAI2, CXCL10, PPARD, TNC, ABCA10, while the genes belonging to the “cellular lipid metabolic processes” were: LIPG, ARSK, ACADL, FADS3, P2RX7, ACSS2, PPARD, KITLG, SPTLC3, ERBB3, KLF4, CRABP2. Additionally, PPARD and ACADL were members of the “fatty acid beta-oxidation” ontology group. Our study describes genes that are not directly related to fertility processes. However, significant changes in their expression in in vitro cultured OECs may indicate their usefulness as markers of OECs’ physiological processes.Running title: Fatty acids changes in porcine oviductal epithelial cells in in vitro cultivation

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