AUTHOR=Fernandes Juliane C. R. , Gonçalves André N. A. , Floeter-Winter Lucile M. , Nakaya Helder I. , Muxel Sandra M. 

TITLE=Comparative transcriptomic analysis of long noncoding RNAs in Leishmania-infected human macrophages

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1051568

DOI=10.3389/fgene.2022.1051568

ISSN=1664-8021

ABSTRACT=<p>It is well established that infection with <italic>Leishmania</italic> alters the host cell’s transcriptome. Since mammalian cells have multiple mechanisms to control gene expression, different molecules, such as noncoding RNAs, can be involved in this process. MicroRNAs have been extensively studied upon <italic>Leishmania</italic> infection, but whether long noncoding RNAs (lncRNAs) are also altered in macrophages is still unexplored. We performed RNA-seq from THP-1-derived macrophages infected with <italic>Leishmania amazonensis</italic> (<italic>La</italic>), <italic>L. braziliensis</italic> (<italic>Lb</italic>)<italic>,</italic> and <italic>L. infantum</italic> (<italic>Li</italic>)<italic>,</italic> investigating a previously unappreciated fraction of macrophage transcriptome. We found that more than 24% of the total annotated transcripts and 30% of differentially expressed (DE) RNAs in <italic>Leishmania</italic>-infected macrophage correspond to lncRNAs. LncRNAs and protein coding RNAs with altered expression are similar among macrophages infected with the <italic>Leishmania</italic> species. Still, some species-specific alterations could occur due to distinct pathophysiology in which <italic>Li</italic> infection led to a more significant number of exclusively DE RNAs. The most represented classes among DE lncRNAs were intergenic and antisense lncRNAs. We also found enrichment for immune response-related pathways in the DE protein coding RNAs, as well as putative targets of the lncRNAs. We performed a coexpression analysis to explore potential cis regulation of coding and antisense noncoding transcripts. We identified that antisense lncRNAs are similarly regulated as its neighbor protein coding genes, such as the BAALC/BAALC-AS1, BAALC/BAALC-AS2, HIF1A/HIF1A-AS1, HIF1A/HIF1A-AS3 and IRF1/IRF1-AS1 pairs, which can occur as a species-specific modulation. These findings are a novelty in the field because, to date, no study has focused on analyzing lncRNAs in <italic>Leishmania</italic>-infected macrophage. Our results suggest that lncRNAs may account for a novel mechanism by which <italic>Leishmania</italic> can control macrophage function. Further research must validate putative lncRNA targets and provide additional prospects in lncRNA function during <italic>Leishmania</italic> infection.</p>