RUNX1 overlapping RNA (RUNXOR) is a long noncoding RNA and a key regulator of myeloid-derived suppressor cells (MDSCs) via targeting runt-related transcription factor 1 (RUNX1). We and others have previously reported MDSC expansion and inhibition of host immune responses during viral infections; however, the mechanisms regulating MDSC differentiation and suppressive functions, especially the role of RUNXOR-RUNX1 in the regulation of MDSCs in people living with HIV (PLHIV), remain unknown. In this study, we demonstrate that RUNXOR and RUNX1 expressions are upregulated in MDSCs that expand and accumulate in human PBMCs derived from PLHIV. We found that the upregulation of RUNXOR and RUNX1 is associated with the expressions of several key immunosuppressive molecules, including arginase 1, inducible NO synthase, STAT3, IL-6, and reactive oxygen species. RUNXOR and RUNX1 could positively regulate each other's expression and control the expressions of these suppressive mediators. Specifically, silencing RUNXOR or RUNX1 expression in MDSCs from PLHIV attenuated MDSC expansion and immunosuppressive mediator expressions, whereas overexpressing RUNXOR in CD33+ myeloid precursors from healthy subjects promoted their differentiation into MDSCs and enhanced the expression of these mediators. Moreover, loss of RUNXOR-RUNX1 function in MDSCs improved IFN-γ production from cocultured autologous CD4 T cells derived from PLHIV. These results suggest that the RUNXOR-RUNX1 axis promotes the differentiation and suppressive functions of MDSCs via regulating multiple immunosuppressive signaling molecules and may represent a potential target for immunotherapy in conjunction with antiviral therapy in PLHIV.

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Efficient targeting of genes to either inhibit or increase their expression in specific tissues in vivo remains a challenge. Adeno-Associated Virus (AAV) has emerged as an efficacious delivery method in both humans and murine model systems. AAV is a non-enveloped, single-stranded DNA virus that is non-integrating with long-term expression. Due to its low immunogenicity and various serotypes with specific tissue tropisms, AAV is a preferred choice for organ specific-gene delivery in many experimental settings. This project focused on protocol optimization for high-volume production of AAV plasmids, improved transfection efficiency, and increased viral yield and purity to specifically target noncoding RNAs (ncRNAs) expressed from the imprinted Dlk1-Dio3 locus. Five AAV9 viruses were produced, each containing one of the following transgenes: 1) human Meg3 cDNA for overexpression of this long noncoding RNA, 2) Meg3-specific short hairpin RNA for knockdown analysis, 3) eGFP cDNA to demonstrate AAV9 tissue tropism, 4) Cas9 cDNA, and 5) gene-specific guide RNAs to target the Meg3 proximal promoter. The AAV9 virus production protocol optimized in this project expands the tools available for in vivo study of the Dlk1-Dio3 ncRNA locus.

O timo é um órgão linfoide primário essencial para a manutenção da tolerância central através da seleção e eliminação de células T autoreativas. Precursores de células T, oriundas da medula óssea, chegam ao timo e migram do córtex para região da medula. As células epiteliais medulares tímicas (mTECs) expressam em sua superfície antígenos de tecidos periféricos (em inglês tissue-restricted antigens ou TRAs) que representam autoantígenos de todos os tecidos do corpo. Atuando como um fator de transcrição não clássico em células mTEC, o gene Autoimmune Regulator (Aire) desempenha um papel na expressão dos TRAs, cuja proteína codificada libera a RNA polimerase II (RNA Pol II) ancorada na cromatina e regula a expressão de mRNAs na glândula timo. A função biológica deste gene está ligada à indução de tolerância imunológica central impedindo o aparecimento de doenças autoimunes. Isso é resultado da seleção negativa de timócitos (precursores de células T) autoreativos que interagem fisicamente com as mTECs. Os timócitos autoreativos que reconhecem os TRAs como elementos estranhos são eliminados por apoptose. O co-cultivo de mTECs com timócitos representa um sistema-modelo in vitro adequado para se aproximar da interação celular que ocorre dentro do timo. Os resultados anteriores do nosso laboratório demonstraram que além do controle de mRNA de TRAs, o gene Aire também participa da modulação de miRNAs em mTECs uma vez que estas espécies de RNA são transcritas pela RNA Pol II. Continuando com essa linha de estudos, neste trabalho nós demonstramos pela primeira vez que Aire também modula a expressão de long noncoding RNAs (lncRNAs) em mTECs. Para isto fizemos uso da estratégia da perda de função analisando a expressão dessa espécie de RNA, assim como de mRNAs, em células mTEC Aire +/+ e mTEC Aire nocautes (KO Aire -/-) obtidas pela edição gênica por Crispr-Cas9. O transcriptoma dessas células que passaram ou não por adesão com timócitos, foi então analisado por hibridizações com microarrays. Isso evidenciou que Aire e adesão celular influenciam a expressão tanto de mRNAs como de lncRNAs. A reconstrução de redes de interação lncRNAs-mRNAs possibilitou evidenciar uma nova via de regulação pós-transcricional em células mTEC. / The thymus is a primary lymphoid organ essential for the maintenance of central tolerance through the selection and elimination of autoreactive T cells. Precursors of T cells, originating from the bone marrow, reach the thymus and migrate from the thymic cortex to the medullary region. Thymic medullary epithelial cells (mTECs) express on their surface tissue-restricted antigens (TRAs) that represent autoantigens of all tissues in the body. Acting as a non-classical transcription factor in mTEC cells, the Autoimmune regulator (Aire) gene plays a role in the expression of TRAs, whose encoded protein releases the RNA polymerase II (RNA Pol II) anchored in the chromatin and regulates the expression of mRNAs in the thymus gland. The biological function of this gene is associated to the induction of central immune tolerance preventing the onset of autoimmune diseases. This is a result of negative selection of autoreactive thymocytes (T cell precursors) that interact physically with mTECs. Self-reactive thymocytes that recognize TRAs as foreign elements are eliminated by apoptosis. The co-culture of mTECs with thymocytes represents an appropriate in vitro model system to approximate the cellular interaction that occurs within the thymus. Previous results from our laboratory demonstrated that in addition to the control of TRA mRNAs, Aire also participates in the modulation of miRNAs in mTECs since these RNA species are transcribed by RNA Pol II. Continuing with this line of studies, in this study we demonstrate for the first time that Aire also modulates the expression of long non-coding RNAs (lncRNAs) in mTECs. For this, we used the loss-of-function strategy to analyze the expression of this RNA species, as well as mRNAs in mTEC Aire + / + or Aire knockout mTEC cells (KO Aire - / -) obtained by the gene editing by Crispr-Cas9. The transcriptome of these cells, whether or not adhered to thymocytes, was then analyzed by microarray hybridizations. This demonstrated that Aire and cell adhesion influence the expression of both mRNAs and lncRNAs. The reconstruction of lncRNAs-mRNAs interaction networks made possible to evidence a new post-transcriptional regulation pathway in mTEC cells.

Recent genome-wide sequencing projects revealed the pervasive transcription of intergenic long noncoding RNAs (lincRNAs) in eukaryotic genomes (reviewed in Ponting et al. 2009). For the vast majority of lincRNAs, their mechanisms of function remain largely unrecognized. However, the genome-wide signatures of functionality associated with many lincRNAs, including apparent evolutionary sequence conservation, spatial and temporal-restricted expression patterns, strong associations with epigenetic marks, and reported molecular and cellular functions, reinforce their biological relevance. My work investigates lincRNAs that post-transcriptionally regulate gene abundance by competing for the binding of common microRNAs (miRNAs) with protein-coding transcripts, termed competitive endogenous RNAs (ceRNAs) acting lincRNAs (lnceRNAs). First, I examine the biological relevance of this post-transcriptional regulation of gene abundance by ceRNAs. Next, I estimate the genome-wide prevalence of lnceRNAs in mouse embryonic stem cells (mESCs) and characterize their properties. Finally, using two specific examples of lnceRNAs, I show the contributions of lnceRNAs to human monogenic and complex trait diseases. Collectively, these results illustrate that lnceRNAs provide a novel layer of post-transcriptional regulation via a miRNA-mediated mechanism that contributes to organismal and cellular biology.

Short ORF-encoded peptides (SEPs) are increasingly being identified as functional elements in various cellular processes. The current computational methods and experimental molecular biochemistry allow us to discover putative SEPs or micropeptides from proteogenomic datasets and experimentally validate them. Here, we identified a micropeptide produced from a putative long noncoding RNA (lncRNA) 1810058I24Rik which is downregulated in both human and murine myeloid cells exposed to lipopolysaccharide (LPS), as well as other TLR ligands and inflammatory cytokines. Analysis of lncRNA 1810058I24Rik subcellular localization revealed this transcript is localized in the cytosol, prompting us to evaluate its coding potential. In vitro translation with 35S-labeled methionine resulted in translation of a 47 amino acid micropeptide. Microscopy and subcellular fractionation studies in macrophages demonstrated endogenous expression of this peptide on the mitochondrion. We thus named this gene ‘Mitochondrial micropeptide-47 (Mm47)’. Functional studies using siRNA and Cripsr-cas9-mediated deletion in primary cells, showed that the transcriptional response downstream of TLR4 was not affected by Mm47 loss of function. In contrast, both the Crispr-cas9- and siRNA-targeted BMDM cells were compromised for Nlrp3 inflammasome responses. However, the primary macrophages derived from the Mm47 knockout mice do not require Mm47 for Nlrp3 activation, likely due to basal downregulation of a negative regulator microRNA of Nlrp3 called Mir-223. Notably, the Mm47-deficient mice are susceptible to influenza virus infection and succumb despite comparable antiviral and inflammatory response to wildtype mice. We hypothesize that the Mm47 deficiency may affect the antiviral resilience of mice due to secondary mitochondria dependent immunometabolic defect or failure of recovery from immune pathology, which warrants further investigation. This study therefore identifies a novel mitochondrial micropeptide Mm47 that is required for activation of the Nlrp3 inflammasome in cells and resistance to influenza virus infection. Broadly, this work highlights the presence of translatable ORFs is annotated noncoding RNA transcripts and underscores their importance in innate immunity and virus infection.

O splicing alternativo do pré-mRNA de BCL-X produz duas isoformas de mRNAs com funções antagônicas, a pró-apoptótica BCL-XS e a anti-apoptótica BCL-XL, cujo balanço regula a homeostasia celular. Entretanto, o mecanismo que regula esse processamento ainda é desconhecido. Nesse trabalho, nós identificamos e caracterizamos um longo RNA não codificador de proteínas (lncRNA) nomeado INXS, que é transcrito a partir da fita oposta do locus genômico de BCL-X, sendo menos abundante em linhagens celulares tumorais e tecidos tumorais de pacientes quando comparados com os respectivos pares não tumorais. INXS é um RNA unspliced de 1903 nts, é transcrito pela RNA Polimerase II, possui cap 5\', está enriquecido na fração nuclear das células e se liga à proteína Sam68 do complexo modulador de splicing. O tratamento de células tumorais 786-O com cada um de três agentes indutores de apoptose aumentou a expressão endógena do INXS, levando ao aumento expressivo da proporção entre os mRNAs de BCL-XS / BCL-XL, e ativação das caspases 3, 7 e 9. Estes efeitos foram anulados na presença do knockdown do INXS. Da mesma forma, a superexpressão ectópica do INXS causou uma mudança no splicing favorecendo a isoforma BCL-XS e ativação das caspases, aumentando os níveis da proteína BCL-XS e conduzindo as células à apoptose. Utilizando um modelo in vivo, cinco injeções intra-tumorais do INXS durante 15 dias causaram uma regressão acentuada no volume dos xenotumores. Portanto, INXS é um lncRNA que induz a apoptose, sugerindo que essa molécula seja um possível alvo a ser explorado na terapia contra o câncer. / BCL-X mRNA alternative splicing generates pro-apoptotic BCL-XS or anti-apoptotic BCL-XL, whose balance regulates cell homeostasis. However, the mechanism that regulates the splice shifting is incompletely understood. Here, we identified and characterized a long noncoding RNA (lncRNA) named INXS, transcribed from the opposite genomic strand of BCL-X, that was less abundant in tumor cell lines and patient tumor tissues compared with non-tumors. INXS is an unspliced 1903 nt-long RNA, is transcribed by RNA Polymerase II, 5\'-capped, nuclear enriched and binds Sam68 splicing-modulator. The treatment of tumor cell line 786-O with each of three apoptosis-inducing agents increased endogenous INXS lncRNA, increased BCL-XS / BCL-XL mRNA ratio, and activated caspases 3, 7 and 9. These effects were abrogated in the presence of INXS knockdown. Similarly, ectopic INXS overexpression caused a shift in splicing towards BCL-XS and activation of caspases, increasing the levels of BCL-XS protein and then leading the cells to apoptosis. In a mouse xenograft model, five intra-tumor injections of INXS along 15 days caused a marked regression in tumor volume. INXS is an lncRNA that induces apoptosis, suggesting that INXS is a possible target to be explored in cancer therapies.

Cada vez mais, RNAs longos não codificadores (lncRNAs) surgem como importantes reguladores da biologia celular, principalmente em processos de diferenciação durante o desenvolvimento. O interesse no estudo das funções e mecanismos de atuação dessa classe de transcritos durante esses processos é crescente, e mostra-se bastante relevante no processo de diferenciação neural, pelo qual são gerados neurônios e células da glia. A linhagem celular P19, uma célula pluripotente advinda de um tipo de carcinoma embrionário murino, é bem consolidada como modelo in vitro de diferenciação neural. Após tratamento com ácido retinóico, ela é capaz de se diferenciar em neurônios e células da glia (astrócitos e oligodendrócitos). Em busca de evidências que indiquem a atuação de lncRNAs durante o processo de diferenciação neural, nosso grupo realizou experimentos utilizando microarranjos para averiguar os níveis de expressão gênica de lncRNAs e genes codificadores de proteínas (mRNAs) durante a diferenciação de células P19 em neurônios (predominância após 10 dias de diferenciação) e glia (predominância em 14 dias de diferenciação). Em um primeiro momento foi realizada a reanotação das sondas referentes a esses lncRNAs da plataforma de microarranjo, visto que as informações presentes nos arquivos de anotação da mesma eram muito escassas e desatualizadas. Registros de lncRNAs e mRNAs foram obtidos a partir de bancos de dados públicos para esse fim, e ao final dessa etapa aproximadamente 25,0% das sondas que não tinham uma anotação foram reanotadas com identificadores advindos desses bancos de dados. A partir dos dados de expressão, foram identificados todos os lncRNAs e mRNAs que apresentaram expressão diferencial entre as diferentes condições estudadas. As informações dos mRNAs diferencialmente expressos foram então utilizadas para a realização de análises de enriquecimento de categorias gênicas do Gene Ontology, nas ontologias de processo biológico e função molecular. A partir das sondas reanotadas, foram realizadas análises de coexpressão entre lncRNAs e mRNAs. A partir do cruzamento das informações obtidas, foram selecionados lncRNAs que através dos princípios de guilt by association se mostraram propensos a desempenharem um papel regulatório na diferenciação neural. Assim, as informações geradas nesse trabalho servirão como base para estudos futuros de validação funcional desses lncRNAs. / Increasingly, long noncoding RNAs (lncRNAs) emerge as important regulators of cell biology, especially in differentiation processes during development. The interest in the study of functions and mechanisms of action of this class of transcripts during these processes is growing, and shows quite relevant in the neural differentiation process by which neurons and glia are generated. The P19 cell line, pluripotent cells arising from a type of murine embryonal carcinoma, is well established as an in vitro model of neural differentiation. After treatment with retinoic acid, it is capable of differentiating into neurons and glial cells (astrocytes and oligodendrocytes). In search of evidence that indicate the action of lncRNAs during the neural differentiation process, our group conducted experiments using microarrays to assess gene expression levels of lncRNAs and protein coding genes (mRNAs) during differentiation of P19 cells into neurons (mainly after 10 days of differentiation) and glial cells (mainly after 14 days of differentiation). At first was performed the reannotation of the probes relating to these microarrays lncRNAs, as the information provided in the annotation files were very scarce or outdated. LncRNAs and mRNAs records were obtained from public databases for this purpose, and at the end of this stage approximately 25.0% of the probes without annotation were reannotated with identifiers arising from these databases. From the expression data, we identified all lncRNAs and mRNAs that showed differential expression between the different studied conditions. The information of differentially expressed mRNAs were then used to perform Gene Ontology enrichment, in the ontologies biological process and molecular function. From the reannotated probes, coexpression analyses were performed for lncRNAs and mRNAs. From the crosscheck of information obtained, we selected those lncRNAs that by the principles of guilt by association proved likely to play a regulatory role in neural differentiation. Thus, the information generated in this study will serve as a basis for future studies of functional validation of these lncRNAs.

Ctcf is a "master regulator" of the genome that plays a role in a variety of gene regulatory functions as well as in genome architecture. Evidence from studying the epigenetic process of X-chromosome inactivation suggests that, in certain cases, Ctcf might carry out its functions through interacting with RNA. Using mouse embryonic stem (ES) cells and a modified protocol for UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), Ctcf is found to interact with a multitude of transcripts genome-wide, both protein-coding mRNA (or noncoding transcripts therein) as well as many long-noncoding RNA (lncRNA). Examples of the latter include both well-characterized species from imprinted loci and previously unannotated transcripts from intergenic space. RNA binding targets of Ctcf are validated by a variety of biochemical methods, and Ctcf is found to interact with RNA through its C-terminal domain, distinct from its DNA-binding zinc-finger domain. Ctcf chromatin immunoprecipitation (ChIP)-seq done in parallel reveals distinct but correlated binding of Ctcf to DNA and RNA. In addition, allelic analysis of Ctcf ChIP pattern reveals significant differences between Ctcf binding to the presumptive inactive and active X chromosomes. Together, the current work reveals a further layer of complexity to Ctcf biology by implicating a role for Ctcf-RNA interactions in its recruitment to genomic binding sites.