Novel human long noncoding RNA responses to Candida auris and its cell-wall components in peripheral blood mononuclear cells

Candida auris is an emerging multidrug-resistant fungal pathogen. However, little is known about the role of long noncoding RNAs (lncRNAs) in the human immune response to this fungus. We reanalyzed RNA-sequencing data from peripheral blood mononuclear cells obtained from three healthy donors. The cells were exposed to live C. auris, purified mannan, purified {beta} glucan, or RPMI control for 4 h and 24 h. We identified 607 putative novel polyadenylated lncRNA loci that were absent from GENCODE Release 48. Of the 449 novel loci tested for differential expression, 102 responded to at least one stimulus. Novel-lncRNA responses were limited at 4 h but increased markedly at 24 h. At 24 h, 78 novel lncRNAs responded to live C. auris, 34 to mannan, and 11 to {beta}-glucan. Many of these responses were specific to a particular stimulus. Among the 102 responsive lncRNAs, 94 were significantly co-expressed with protein coding genes. The coding-gene partners of the most highly connected lncRNAs were associated with innate immunity, defense responses, lysosomal functions, and signaling pathways. Temporal analysis identified 19 novel lncRNAs whose responses changed between 4 and 24 h. Fourteen were also differentially expressed and were selected for further analysis. Combining temporal response, co-expression, and genomic proximity identified 4 candidate cis-associated pairs: MSTRG.32011-TLR2, MSTRG.5763-DUSP5, MSTRG.25627-HCK, and MSTRG.18159 ITGB3.These findings reveal a predominantly late and stimulus-specific novel-lncRNA response to C. auris and provide prioritized candidates for experimental validation.