Human U90926 orthologous long non-coding RNA as a novel biomarker for visual prognosis in herpes simplex virus type-1 induced acute retinal necrosis

Noncanonical microprotein regulation of immunity

The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.

Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein

Thousands of long noncoding RNAs are encoded in mammalian genomes, yet most remain uncharacterized. In this study, we functionally characterized a mouse long noncoding RNA named U90926. Analysis of U90926 RNA levels revealed minimal expression across multiple tissues at steady state. However, the expression of this gene was highly induced in macrophages and dendritic cells by TLR activation, in a p38 MAPK- and MyD88-dependent manner. To study the function of U90926, we generated U90926-deficient (U9-KO) mice. Surprisingly, we found minimal effects of U90926 deficiency in cultured macrophages. Given the lack of macrophage-intrinsic effect, we investigated the subcellular localization of U90926 transcript and its protein-coding potential. We found that U90926 RNA localizes to the cytosol, associates with ribosomes, and contains an open reading frame that encodes a novel glycosylated protein (termed U9-ORF), which is secreted from the cell. An in vivo model of endotoxic shock revealed that, in comparison with wild type mice, U9-KO mice exhibited increased sickness responses and mortality. Mechanistically, serum levels of IL-6 were elevated in U9-KO mice, and IL-6 neutralization improved endotoxemia outcomes in U9-KO mice. Taken together, these results suggest that U90926 expression is protective during endotoxic shock, potentially mediated by the paracrine and/or endocrine actions of the novel U9-ORF protein secreted by activated myeloid cells.

The impact of non-coding RNAs in the pathobiology of eye disorders

Eye disorders are common disorders with significant effects on personal, economic, and social aspects of life. These disorders have a genetic background and are associated with dysregulation of non-coding RNAs. Three classes of these transcripts, namely long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) have established roles in the regulation of gene expression and pathoetiology of ocular disorders. H19, MEG3, BANCR, UCA1, HOTAIR, ANRIL, XIST and MIAT are among important lncRNAs in ocular disorders. CircRNAs from ZBTB44, HIPK3, circ-PSEN1, COL1A2, ZNF532 and FAM158A loci have also been found to affect pathoetiology of ocular disorders. Both lncRNAs and circRNAs can serve as molecular sponges for miRNAs. In this review, we searched PubMed and Google Scholar databases to find the research articles summarizing the impact of non-coding RNAs in ocular disorders. The results of these studies would help in identification of suitable targets for treatment of ocular disorders.

Comprehensive LncRNA and Potential Molecular Mechanism Analysis in Noninfectious Uveitis

Purpose

Long noncoding RNA (lncRNA) is noncoding RNA and have played a key role or be treated as a biomarker in a variety of diseases such as tumors. However, extensive lncRNA analysis for uveitis has not been explored completely. In this study, we analyzed the lncRNAs with altered expression in peripheral blood comprehensively for three major autoimmune diseases (ankylosing spondylitis [AS], Behҫet's disease [BD], and sarcoidosis) to search potential hub gene and molecular mechanism for noninfectious uveitis.

Methods

In total, we included 18 patients with AS and 12 patients with sarcoidosis versus 25 controls for GSE18781; we also included 15 patients with BD versus 14 controls for GSE17114 in this study. The lncRNA and messenger RNA (mRNA) expression levels were determined by microarray using serum samples from patients and healthy controls.

Results

Twenty-one lncRNAs and 1073 mRNAs were detected in patients with AS, 4 lncRNAs and 62 mRNAs in patients with BD, and 196 lncRNAs and 5376 mRNAs in patients with sarcoidosis. Thus, we suspected lncRNA XIST and MIAT, mRNA FCGBP, CD247, CTSW, AES, NCR3, TIGIT, CASP5, DUSP2, and TBX21 may be the most possible hub genes for AS, BD, and sarcoidosis. These RNAs were involved in the mitogen-activated protein kinase signaling pathway and inflammatory cytokine pathways.

Conclusions

In this study, comprehensive bioinformatics analysis identified lncRNAs with altered expression in three major autoimmune diseases that may combine with noninfectious uveitis. This study provides novel insights into the molecular pathogenetic mechanisms and key information toward developing new diagnostic biomarkers and special therapeutic targets for noninfectious uveitis in AS, BD, and sarcoidosis.

Translational Relevance

LncRNAs and their potential mechanisms provide new strategies for prevention and treatment for noninfectious uveitis in patients with AS, BD, and sarcoidosis.

The Host Non-Coding RNA Response to Alphavirus Infection

Alphaviruses are important human and animal pathogens that can cause a range of debilitating symptoms and are found worldwide. These include arthralgic diseases caused by Old-World viruses and encephalitis induced by infection with New-World alphaviruses. Non-coding RNAs do not encode for proteins, but can modulate cellular response pathways in a myriad of ways. There are several classes of non-coding RNAs, some more well-studied than others. Much research has focused on the mRNA response to infection against alphaviruses, but analysis of non-coding RNA responses has been more limited until recently. This review covers what is known regarding host cell non-coding RNA responses in alphavirus infections and highlights gaps in the knowledge that future research should address.