Title: Investigation of Novel lincRNAs SIMALR and RP11-184M15.1 Functions in Inflammatory and Resolving Human Macrophage
Description: Long noncoding RNAs (lncRNAs) are emerging as novel regulators of macrophage biology and related inflammatory cardiovascular diseases. However, studies focused on lncRNAs in human macrophage subtypes, particularly human-specific lncRNAs that are not conserved in rodents, are limited. Through deep RNA-seq of human monocyte-derived macrophages, we identified SIMALR (suppressor of inflammatory macrophage apoptosis lincRNA), a human macrophage-specific long intergenic noncoding RNA (lincRNA), to be highly induced in the nucleus of LPS/IFNγ-stimulated macrophages. Treatment of LPS/IFNγ-stimulated THP1 human macrophages with SIMALR antisense oligonucleotides induced apoptosis of inflammatory macrophages, as shown by increased Annexin V+ macrophages, and increased protein expression of cleaved PARP, caspase 9, and caspase 3. Differential expression analysis of RNA-seq data from SIMALR knockdown versus control in human macrophages revealed Netrin 1 (NTN1), a known regulator of macrophage apoptosis, to be one of the top downregulated genes.

NTN1 knockdown in LPS/IFNγ-stimulated THP1 macrophages induced apoptosis. This apoptotic phenotype was attenuated by treating LPS/IFNγ-stimulated macrophages with recombinant human NTN1 after SIMALR knockdown. Furthermore, NTN1 promoter-luciferase reporter activity was increased in HEK293T cells treated with lentiviral overexpression of SIMALR. NTN1 promoter activity is known to require HIF1α and RNA immunoprecipitation (RIP) showed that SIMALR binds HIF1α, suggesting that SIMALR may modulate HIF1α binding at the NTN1 promoter to regulate apoptosis of macrophages. In human translational studies, SIMALR was found to be upregulated in macrophages in unstable human atherosclerotic plaques, suggesting a possible mechanistic link between inflammation and cardiovascular diseases. In addition to SIMALR, through deep RNA-seq of human monocyte-derived macrophages, we identified RP11-184M15.1, a human macrophage-specific lincRNA, to be highly induced in the cytoplasm of IL-4-stimulated macrophage.

Preliminary data showed that treatment of IL-4-stimulated THP1 human macrophages with RP11-184M15.1 small interfering RNA (siRNA) repressed apoptosis of resolving macrophages, as shown by decreased Annexin V+ macrophages, and reduced protein expression of cleaved PARP. Biotinylated RP11-184M15.1 pulldown coupled with mass spectrometry indicated an interaction between RP11-184M15.1 and zinc finger RNA-binding protein (ZFR). RIP corroborated the proposed interaction between RP11-184M15.1 and ZFR. RNAInter revealed mRNAs predicted to interact with ZFR, and some of those genes (e.g., ALYREF, CCNYL1) were also differentially expressed in RNA-seq data of control versus RP11-184M15.1 knockdown in IL-4-stimulated THP1 macrophages. qPCR validated that ALYREF and CCNYL1 expression are reduced with RP11-184M15.1 knockdown. In contrast, with ZFR siRNA, ALYREF and CCNYL1 mRNA expressions were elevated. Thus, a hypothesis to be further tested is that RP11-184M15.1 interacts with ZFR to regulate mRNA stability in IL-4-stimulated macrophages.

Nuclear RNA export factor 1 (NXF1) was also validated by RIP to interact with RP11-184M15.1. NXF1 is a known interacting partner of ALYREF in the transcription-export (TREX) complex. With RP11-184M15.1 knockdown, the protein level of ALYREF decreased, and Ingenuity Pathway Analysis (IPA) of RNA-seq data of control versus RP11-184M15.1 knockdown revealed that THO complex subunit 5 homolog (THOC5), another component of the TREX complex, may be an upstream regulator. In addition, past studies have revealed that ALYREF and NXF1 are involved in nuclear export of inflammatory mRNAs and proinflammatory macrophage phenotype, respectively. With RP11-184M15.1 knockdown, there was decreased expression of inflammatory macrophage-associated genes. It may be possible that RP11-184M15.1 functions in mRNA export, along with NXF1 and ALYREF. In human translational studies, RP11-184M15.1 was found to be upregulated in macrophages in unstable human atherosclerotic plaques. Further work is needed to better understand the functions and molecular mechanism of RP11-184M15.1.

In summary, we found that SIMALR may interact with HIF1α to regulate macrophage apoptosis via NTN1. Our preliminary work also revealed that RP11-184M15.1 may regulate apoptosis, mRNA stability and mRNA export in anti-inflammatory macrophages. Both lincRNAs may be upregulated in unstable human atherosclerotic plaques. By studying SIMALR and RP11-184M15.1, we were able to illustrate the importance of interrogating the functions of human-specific lincRNAs despite the lack of rodent models, and demonstrated roles in macrophage inflammation that may be relevant to human cardiovascular disease.