A long non-coding RNA regulates in vitro and in vivo triazole antifungal susceptibility in <i>Aspergillus fumigatus</i>

Azole-resistant <i>Aspergillus</i> infections are a source of increasing concern with limited alternative therapeutic options. However, as most infections are still caused by azole-susceptible <i>Aspergillus</i> strains, there is a need to better understand fungal responses to azole antifungals. To this end, we discover that a long non-coding RNA, <i>afu-182</i>, is a major regulator of <i>cyp51</i>-independent azole recalcitrant colony growth (ARC). We observe that loss of <i>afu-182</i> leads to azole recalcitrant biofilms and poor treated disease outcomes in murine invasive pulmonary aspergillosis models. In contrast, overexpression of <i>afu-182</i> significantly reduces fungal burden in animals treated with azole drugs. Whole transcriptome analyses revealed that azole drug treatment leads to an increase in transcripts of genes encoding 7-transmembrane domain proteins of the RTA1 family, and these proteins are negatively regulated by <i>afu-182</i>. Two RTA1 family genes downstream of <i>afu-182</i> regulation have individual and combined effect in regulating fungal ARC. Taken together, our data show a trans-acting role of the long non-coding RNA <i>afu-182</i> in regulating <i>Aspergillus fumigatus</i> response to azole drugs both <i>in vitro</i> and <i>in vivo</i>. These data provide further support for investigating antifungal drug responses beyond minimum inhibitory concentration testing.