Transcriptomic Analysis of Long Non-Coding RNA during Candida albicans Infection

Abstract

Candida albicans is one of the most commonly found species in fungal infections. Due to its clinical importance, molecular aspects of the host immune defense against the fungus are of interest to biomedical sciences. Long non-coding RNAs (lncRNAs) have been investigated in different pathologies and gained widespread attention regarding their role as gene regulators. However, the biological processes in which most lncRNAs perform their function are still unclear. This study investigates the association between lncRNAs with host response to C. albicans using a public RNA-Seq dataset from lung samples of female C57BL/6J wild-type Mus musculus with induced C. albicans infection. The animals were exposed to the fungus for 24 h before sample collection. We selected lncRNAs and protein-coding genes related to the host immune response by combining the results from different computational approaches used for gene selection: differential expression gene analysis, co-expression genes network analysis, and machine learning-based gene selection. Using a guilt by association strategy, we inferred connections between 41 lncRNAs and 25 biological processes. Our results indicated that nine up-regulated lncRNAs were associated with biological processes derived from the response to wounding: 1200007C13Rik, 4833418N02Rik, Gm12840, Gm15832, Gm20186, Gm38037, Gm45774, Gm4610, Mir22hg, and Mirt1. Additionally, 29 lncRNAs were related to genes involved in immune response, while 22 lncRNAs were associated with processes related to reactive species production. These results support the participation of lncRNAs during C. albicans infection, and may contribute to new studies investigating lncRNA functions in the immune response.

Fungal extracellular vesicle-mediated regulation: from virulence factor to clinical application

“…In invasive fungi like Candida albicans , Aspergillus fumigatus , and Paracoccidioides brasiliensis , different intraspecific cells exhibit varied gene regulation induced by EVs. Goncalves et al identified 10 up-regulated lncRNAs, including 1200007C13Rik, 4833418N02Rik, Gm12840, Gm15832, Gm20186, Gm38037, Gm45774, Gm4610, Mir22hg, and Mirt1, associated with biological processes during Candida albicans infection, particularly the response to injury ( Goncalves et al, 2023 ). In addition, Rosenblad et al discovered three novel ncRNA genes, namely nuclear RNase P RNA, RNase MRP RNA, and a potential snoRNA U14, originating from the ribosomal region of fungi, highlighting the important role of ncRNA genes in fungal EVs genetics ( Rosenblad et al, 2022 ).…”

lncRNA-Gm5532 regulates osteoclast differentiation through the miR-125a-3p/TRAF6 axis

“…The identification of novel lncRNAs involved in osteoclast differentiation is of great importance for understanding the mechanism of bone homeostasis. The present study focused on lncRNA-Gm5532, which has been found to be altered in developing retinas, spermatogenesis, and Candida albicans infection [ 6 – 8 ]. However, whether lncRNA-Gm5532 regulates osteoclastogenesis and its regulatory mechanism remain elusive.…”