Long noncoding <scp>RNAs</scp> in bacterial infection

Schmerer, Nils; Schulte, Leon N.

doi:10.1002/wrna.1664

Cited by 11 publications

(7 citation statements)

References 133 publications

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“…ncRNAs can be at the crossroad of regulatory processes governing the interactions of the pathogens with their host during infection [20, 94, 95]. In the present study, many lncRNAs have been identified differentially expressed during CDI, but most of them have not yet been characterized.…”

Section: Resultsmentioning

confidence: 78%

“…ncRNAs can be at the crossroad of regulatory processes governing the interactions of the pathogens with their host during infection [20,94,95] Among the ncRNAs, the miRNAs have emerged as important players in host responses to bacterial pathogen infections [94,96]. We thus extracted the miRNAs differentially expressed in mice during CDI for each comparative analysis (Table 2).…”

Section: Differential Expression Of Host Ncrnas During CDImentioning

confidence: 99%

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Dual RNA-seq study of the dynamics of coding and non-coding RNAs expression duringClostridioides difficileinfection in a mouse model

Kreis,

Toffano-Nioche,

Denève-Larrazet

et al. 2024

Preprint

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Clostridioides difficileis the leading cause of healthcare associated diarrhoea in industrialized countries. Many questions remain to be answered about the mechanisms governing its interaction with the host during infection. Non-coding RNAs (ncRNAs) contribute to shaping virulence in many pathogens and modulate host responses, however, their role inC. difficileinfection (CDI) has not been explored. To better understand the dynamics of ncRNAs expression contributing toC. difficileinfectious cycle and host response, we used a dual RNA- seq approach in a conventional murine model. From the pathogen side, this transcriptomic analysis revealed the upregulation of virulence factors, metabolism and sporulation genes, as well as the identification of 61 ncRNAs differentially expressed during infection that correlated with the analysis of available raw RNA-seq datasets from two independent studies. From these data we identified 118 potential new transcripts inC. difficileincluding 106 new ncRNA genes. From the host side, we observed the induction of several pro-inflammatory pathways and, among the 185 differentially expressed ncRNAs, the overexpression of microRNAs (miRNAs) previously associated to inflammatory responses or unknown long ncRNAs and miRNAs. A particular host gene expression profile could be associated to the symptomatic infection. In accordance, the metatranscriptomic analysis revealed specific microbiota changes accompanying CDI and specific species associated with symptomatic infection in mice. This first adaptation ofin vivodual RNA-seq toC. difficilecontributes to unravelling the regulatory networks involved inC. difficileinfectious cycle and host response and provides valuable resources for further studies of RNA-based mechanisms during CDI.ImportanceClostridioides difficileis a major cause of nosocomial infections associated with antibiotic therapy classified as an urgent antibiotic resistance threat. This pathogen interacts with host and gut microbial communities during infection, but the mechanisms of these interactions remain largely to be uncovered. Noncoding RNAs contribute to bacterial virulence and host responses, but their expression has not been explored duringC. difficileinfection. We took advantage of the conventional mouse model ofC. difficileinfection to look simultaneously to the dynamics of gene expression in pathogen, its host and gut microbiota composition providing valuable resources for future studies. We identified a number of ncRNAs that could mediate the adaptation ofC. difficileinside the host and the crosstalk with the host immune response. Promising inflammation markers and potential therapeutic targets emerged from this work open new directions for RNA-based and microbiota-modulatory strategies to improve the efficiency ofC. difficileinfection treatments.

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Section: Resultsmentioning

confidence: 78%

Section: Differential Expression Of Host Ncrnas During CDImentioning

confidence: 99%

Dual RNA-seq study of the dynamics of coding and non-coding RNAs expression duringClostridioides difficileinfection in a mouse model

Kreis,

Toffano-Nioche,

Denève-Larrazet

et al. 2024

Preprint

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“…A recent study revealed the interaction of lncRNA NEAT 1 with an important regulator of Alzheimer's disease, PTEN‐induced putative kinase 1 (PINK1), promoting its degradation (Z. Huang et al, 2020). Furthermore, lncRNAs involvement has been stated in malaria or bacterial infection (Lodde et al, 2021; Schmerer & Schulte, 2021).…”

Section: Non‐coding Rnamentioning

confidence: 99%

Non‐coding RNAs in diseases with a focus on osteoarthritis

et al. 2022

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Osteoarthritis (OA) is a frequent musculoskeletal disorder affecting millions of people worldwide. Despite advances in understanding the pathogenesis of OA, prognostic biomarkers or effective targeted treatment are not currently available. Research on epigenetic factors has yielded some new insights as new technologies for their detection continue to emerge. In this context, noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, piwi-interacting RNAs, and small nucleolar RNAs, regulate intracellular signaling pathways and biological processes that have a crucial role in the development of several diseases. In this review, we present current knowledge on the role of epigenetic factors with a focus on non-coding RNAs in the development, prediction and treatment of OA.

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“…Several studies have shown that RNA sequencing analysis is helpful for understanding the overall host response to NTM infection ( 10 – 12 ), but analyses of the transcriptomes of host macrophages, which are thought to be the first cells to respond upon MAC infection, are limited. Furthermore, no published reports have examined the dynamics of long non-coding RNAs (lncRNAs) in MAC infection, although lncRNAs are known to be involved in diverse biological processes such as cell differentiation, oncogenesis, ontogeny, individual development, and disease, including bacterial infection, through regulation of transcription, translation, and epigenetics ( 13 , 14 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex–infected macrophages

Yoshida,

Kwon,

Qin

et al. 2024

Front. Immunol.

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Mycobacterium avium complex (MAC) is a non-tuberculous mycobacterium widely distributed in the environment. Even though MAC infection is increasing in older women and immunocompromised patients, to our knowledge there has been no comprehensive analysis of the MAC-infected host-cell transcriptome—and particularly of long non-coding RNAs (lncRNAs). By using in vitro-cultured primary mouse bone-marrow-derived macrophages (BMDMs) and Cap analysis of gene expression, we analyzed the transcriptional and kinetic landscape of macrophage genes, with a focus on lncRNAs, during MAC infection. MAC infection of macrophages induced the expression of immune/inflammatory response genes and other genes similar to those involved in M1 macrophage activation, consistent with previous reports, although Nos2 (M1 activation) and Arg1 (M2 activation) had distinct expression profiles. We identified 31 upregulated and 30 downregulated lncRNA promoters corresponding respectively to 18 and 26 lncRNAs. Upregulated lncRNAs were clustered into two groups—early and late upregulated—predicted to be associated with immune activation and the immune response to infection, respectively. Furthermore, an Ingenuity Pathway Analysis revealed canonical pathways and upstream transcription regulators associated with differentially expressed lncRNAs. Several differentially expressed lncRNAs reported elsewhere underwent expressional changes upon M1 or M2 preactivation and subsequent MAC infection. Finally, we showed that expressional change of lncRNAs in MAC-infected BMDMs was mediated by toll-like receptor 2, although there may be other mechanisms that sense MAC infection. We identified differentially expressed lncRNAs in MAC-infected BMDMs, revealing diverse features that imply the distinct roles of these lncRNAs in MAC infection and macrophage polarization.

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Long noncoding RNAs in bacterial infection

Cited by 11 publications

References 133 publications

Dual RNA-seq study of the dynamics of coding and non-coding RNAs expression duringClostridioides difficileinfection in a mouse model

Dual RNA-seq study of the dynamics of coding and non-coding RNAs expression duringClostridioides difficileinfection in a mouse model

Non‐coding RNAs in diseases with a focus on osteoarthritis

Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex–infected macrophages

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