Temporal and spacial control of RNA stability in the early embryo of Drosophila melanogaster

Early embryogenesis in metazoa is controlled by maternally synthesized products. Among these products, the mature egg is loaded with transcripts representing approximately two thirds of the genome. A subset of this maternal RNA pool is degraded prior to the transition to zygotic control of development. This transfer of control of development from maternal to zygotic products is referred to as the midblastula transition (or MBT). It is believed that the degradation of maternal transcripts is required to terminate maternal control of development and to allow zygotic control of development to begin. Until now this process of maternal transcript degradation and the subsequent timing of the MBT has been poorly understood. I have demonstrated that in the early embryo there are two independent RNA degradation pathways, either of which is sufficient for transcript elimination. However, only the concerted action of both pathways leads to elimination of transcripts with the correct timing, at the MBT. The first pathway is maternally encoded, is triggered by egg activation, and is targeted to specific classes of mRNAs through cis-acting elements in the 3' untranslated region (UTR}. The second pathway is activated 2 hr after fertilization and functions together with the maternal pathway to ensure that transcripts are degraded by the MBT. In addition, some transcripts fail to degrade at select subcellular locations adding an element of spatial control to RNA degradation. The spatial control of RNA degradation is achieved by protecting, or masking, transcripts from the degradation machinery. The RNA degradation and protection events are regulated by distinct cis-elements in the 3' untranslated region (UTR). These results provide the first systematic dissection of this highly conserved process in development and demonstrate that RNA degradation is a novel mechanism used for both temporal and spatial control of development.

Regulation of cyclin D1 RNA stability by SNIP1

Cyclin D1 expression represents one of the key mitogen-regulated events during the G1 phase of the cell cycle, whereas Cyclin D1 overexpression is frequently associated with human malignancy. Here, we describe a novel mechanism regulating Cyclin D1 levels. We find that SNIP1, previously identified as a regulator of Cyclin D1 expression, does not, as previously thought, primarily function as a transcriptional coactivator for this gene. Rather, SNIP1 plays a critical role in cotranscriptional or posttranscriptional Cyclin D1 mRNA stability. Moreover, we show that the majority of nucleoplasmic SNIP1 is present within a previously undescribed complex containing SkIP, THRAP3, BCLAF1, and Pinin, all proteins with reported roles in RNA processing and transcriptional regulation. We find that this complex, which we have termed the SNIP1/SkIP–associated RNA-processing complex, is coordinately recruited to both the 3' end of the Cyclin D1 gene and Cyclin D1 RNA. Significantly, SNIP1 is required for the further recruitment of the RNA processing factor U2AF65 to both the Cyclin D1 gene and RNA. This study shows a novel mechanism regulating Cyclin D1 expression and offers new insight into the role of SNIP1 and associated proteins as regulators of proliferation and cancer.

Spatial and temporal control of RNA stability

Maternally encoded RNAs and proteins program the early development of all animals. A subset of the maternal transcripts is eliminated from the embryo before the midblastula transition. In certain cases, transcripts are protected from degradation in a subregion of the embryonic cytoplasm, thus resulting in transcript localization. Maternal factors are sufficient for both the degradation and protection components of transcript localization. Cis-acting elements in the RNAs convert transcripts progressively (i) from inherently stable to unstable and (ii) from uniformly degraded to locally protected. Similar mechanisms are likely to act later in development to restrict certain classes of transcripts to particular cell types within somatic cell lineages. Functions of transcript degradation and protection are discussed.

The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes

In Arabidopsis thaliana (Arabidopsis), DICER-LIKE1 (DCL1) functions together with the double-stranded RNA binding protein (dsRBP), DRB1, to process microRNAs (miRNAs) from their precursor transcripts prior to their transfer to the RNA-induced silencing complex (RISC). miRNA-loaded RISC directs RNA silencing of cognate mRNAs via ARGONAUTE1 (AGO1)-catalyzed cleavage. Short interefering RNAs (siRNAs) are processed from viral-derived or transgene-encoded molecules of doublestranded RNA (dsRNA) by the DCL/dsRBP partnership, DCL4/DRB4, and are also loaded to AGO1-catalyzed RISC for cleavage of complementary mRNAs. Here, we use an artificial miRNA (amiRNA) technology, transiently expressed in Nicotiana benthamiana, to produce a series of amiRNA duplexes with differing intermolecular thermostabilities at the 5′ end of duplex strands. Analyses of amiRNA duplex strand accumulation and target transcript expression revealed that strand selection (amiRNA and amiRNA*) is directed by asymmetric thermostability of the duplex termini. The duplex strand possessing a lower 59 thermostability was preferentially retained by RISC to guide mRNA cleavage of the corresponding target transgene. In addition, analysis of endogenous miRNA duplex strand accumulation in Arabidopsis drb1 and drb2345 mutant plants revealed that DRB1 dictates strand selection, presumably by directional loading of the miRNA duplex onto RISC for passenger strand degradation. Bioinformatic and Northern blot analyses of DCL4/DRB4-dependent small RNAs (miRNAs and siRNAs) revealed that small RNAs produced by this DCL/dsRBP combination do not conform to the same terminal thermostability rules as those governing DCL1/DRB1-processed miRNAs. This suggests that small RNA processing in the DCL1/DRB1-directed miRNA and DCL4/DRB4-directed sRNA biogenesis pathways operates via different mechanisms.

The DLK-1 kinase promotes mRNA stability and local translation in C. elegans synapses and axon regeneration.

Growth cone guidance and synaptic plasticity involve dynamic local changes in proteins at axons and dendrites. The Dual-Leucine zipper Kinase MAPKKK (DLK) has been previously implicated in synaptogenesis and axon outgrowth in C. elegans and other animals. Here we show that in C. elegans DLK-1 regulates not only proper synapse formation and axon morphology but also axon regeneration by influencing mRNA stability. DLK-1 kinase signals via a MAPKAP kinase, MAK-2, to stabilize the mRNA encoding CEBP-1, a bZip protein related to CCAAT/enhancer-binding proteins, via its 3'UTR. Inappropriate upregulation of cebp-1 in adult neurons disrupts synapses and axon morphology. CEBP-1 and the DLK-1 pathway are essential for axon regeneration after laser axotomy in adult neurons, and axotomy induces translation of CEBP-1 in axons. Our findings identify the DLK-1 pathway as a regulator of mRNA stability in synapse formation and maintenance and also in adult axon regeneration.

p38 MAPK regulates IL-1β induced IL-6 expression through mRNA stability in osteoblasts

Osteoblast-derived IL-6 functions in coupled bone turnover by supporting osteoclastogenesis favoring bone resorption instead of bone deposition. Gene regulation of IL-6 is complex occurring both at transcription and post-transcription levels. The focus of this paper is at the level of mRNA stability, which is important in IL-6 gene regulation. Using the MC3T3-E1 as an osteoblastic model, IL-6 secretion was dose dependently decreased by SB203580, a p38 MAPK inhibitor. Steady state IL-6 mRNA was decreased with SB203580 (2 μM) ca. 85% when stimulated by IL-1β (1-5 ng/ ml). These effects require de novo protein synthesis as they were inhibited by cycloheximide. p38 MAPK had minor effects on proximal IL-6 promoter activity in reporter gene assays. A more significant effect on IL-6 mRNA stability was observed in the presence of SB203580. Western blot analysis confirmed that SB203580 inhibited p38 MAP kinase, in response to IL-1β in a dose dependent manner in MC3T3-E1 cells. Stably transfected MC3T3-E1 reporter cell lines (MC6) containing green fluorescent protein (GFP) with the 3′untranslated region of IL-6 were constructed. Results indicated that IL-1β, TNFα, LPS but not parathyroid hormone (PTH) could increase GFP expression of these reporter cell lines. Endogenous IL-6 and reporter gene eGFP-IL-6 3′UTR mRNA was regulated by p38 in MC6 cells. In addition, transient transfection of IL-6 3′UTR reporter cells with immediate upstream MAP kinase kinase-3 and -6 increased GFP expression compared to mock transfected controls. These results indicate that p38 MAPK regulates IL-1β-stimulated IL-6 at a post transcriptional mechanism and one of the primary targets of IL-6 gene regulation is the 3′UTR of IL-6.

RNA-Strukturen im Hepatitis-C-Virus und ihre Bedeutung für Translation und Replikation

Das Hepatitis C Virus (HCV) ist ein umhülltes Virus aus der Familie der Flaviviridae. Es besitzt ein Plusstrang-RNA Genom von ca. 9600 Nukleotiden Länge, das nur ein kodierendes Leseraster besitzt. Das Genom wird am 5’ und 3’ Ende von nicht-translatierten Sequenzen (NTRs) flankiert, welche für die Translation und vermutlich auch Replikation von Bedeutung sind. Die 5’ NTR besitzt eine interne Ribosomeneintrittsstelle (IRES), die eine cap-unabhängige Translation des ca. 3000 Aminosäure langen viralen Polyproteins erlaubt. Dieses wird ko- und posttranslational von zellulären und viralen Proteasen in 10 funktionelle Komponenten gespalten. Inwieweit die 5’ NTR auch für die Replikation der HCV RNA benötigt wird, war zu Beginn der Arbeit nicht bekannt. Die 3’ NTR besitzt eine dreigeteilte Struktur, bestehend aus einer variablen Region, dem polyU/UC-Bereich und der sogenannten X-Sequenz, eine hochkonservierte 98 Nukleotide lange Region, die vermutlich für die RNA-Replikation und möglicherweise auch für die Translation benötigt wird. Die genuae Rolle der 3’ NTR für diese beiden Prozesse war zu Beginn der Arbeit jedoch nicht bekannt. Ziel der Dissertation war deshalb eine detaillierte genetische Untersuchung der NTRs hinsichtlich ihrer Bedeutung für die RNA-Translation und -Replikation. In die Analyse mit einbezogen wurden auch RNA-Strukturen innerhalb der kodierenden Region, die zwischen verschiedenen HCV-Genotypen hoch konserviert sind und die mit verschiedenen computer-basierten Modellen vorhergesagt wurden. Zur Kartierung der für RNA-Replikation benötigten Minimallänge der 5’ NTR wurde eine Reihe von Chimären hergestellt, in denen unterschiedlich lange Bereiche der HCV 5’ NTR 3’ terminal mit der IRES des Poliovirus fusioniert wurden. Mit diesem Ansatz konnten wir zeigen, dass die ersten 120 Nukleotide der HCV 5’ NTR als Minimaldomäne für Replikation ausreichen. Weiterhin ergab sich eine klare Korrelation zwischen der Länge der HCV 5’ NTR und der Replikationseffizienz. Mit steigender Länge der 5’ NTR nahm auch die Replikationseffizienz zu, die dann maximal war, wenn das vollständige 5’ Element mit der Poliovirus-IRES fusioniert wurde. Die hier gefundene Kopplung von Translation und Replikation in der HCV 5’ NTR könnte auf einen Mechanismus zur Regulation beider Funktionen hindeuten. Es konnte allerdings noch nicht geklärt werden, welche Bereiche innerhalb der Grenzen des IRES-Elements genau für die RNA-Replikation benötigt werden. Untersuchungen im Bereich der 3’ NTR ergaben, dass die variable Region für die Replikation entbehrlich, die X-Sequenz jedoch essentiell ist. Der polyU/UC-Bereich musste eine Länge von mindestens 11-30 Uridinen besitzen, wobei maximale Replikation ab einer Länge von 30-50 Uridinen beobachtet wurde. Die Addition von heterologen Sequenzen an das 3’ Ende der HCV-RNA führte zu einer starken Reduktion der Replikation. In den hier durchgeführten Untersuchungen zeigte keines der Elemente in der 3’ NTR einen signifikanten Einfluss auf die Translation. Ein weiteres cis aktives RNA-Element wurde im 3’ kodierenden Bereich für das NS5B Protein beschrieben. Wir fanden, dass Veränderungen dieser Struktur durch stille Punktmutationen die Replikation hemmten, welche durch die Insertion einer intakten Version dieses RNA-Elements in die variable Region der 3’ NTR wieder hergestellt werden konnte. Dieser Versuchsansatz erlaubte die genaue Untersuchung der für die Replikation kritischen Strukturelemente. Dadurch konnte gezeigt werden, dass die Struktur und die Primärsequenz der Loopbereiche essentiell sind. Darüber hinaus wurde eine Sequenzkomplementarität zwischen dem Element in der NS5B-kodierenden Region und einem RNA-Bereich in der X-Sequenz der 3’ NTR gefunden, die eine sog. „kissing loop“ Interaktion eingehen kann. Mit Hilfe von gezielten Mutationen konnten wir zeigen, dass diese RNA:RNA Interaktion zumindest transient stattfindet und für die Replikation des HCV essentiell ist.

RNA-basierte Impfstoffe zur Induktion optimaler Immunantworten

Antigen-kodierende RNA wird als eine sichere und effiziente Alternative zu traditionellen Impfstoff-Formulierungen, wie Peptid-, Protein-, rekombinanten viralen oder DNA basierten Impfstoffen betrachtet. Der endgültige klinische Nutzen RNA-basierter Impfstoffe wird von der Optimierung verschiedener Parameter abhängig sein, die zur Induktion und effizienten Expansion der humoralen und zellvermittelten Immunantwort beitragen. Vor diesem Hintergrund war die Zielsetzung der vorliegenden Arbeit, die Etablierung pharmakologischer und immunologischer Parameter für die Generierung effektiver Immunantworten durch RNA-Impfstoffe sowie deren Wirksamkeit in vitro und im Mausmodell unter Nutzung von Modellantigenen zu testen. Zur Untersuchung und Optimierung der RNA-Pharmakokinetik, als einem Schlüsselaspekt der klinischen Medikamentenentwicklung, wurde der Einfluss von strukturellen Modifikationen auf die Transkriptstabilität und Translationseffizienz von Reporter-Proteinen in einer zeitabhängigen Kinetik evaluiert. Es wurde gezeigt, dass ein poly(A) Schwanz von 120 Adenosinen, verglichen mit einem kürzeren, ein freies 3´ poly(A) Ende, verglichen mit einem verdeckten und eine doppelte β-globin 3´ UTR, unabhängig voneinander zu einer Erhöhung der IVT-RNA Stabilität und zu einer Verbesserung der Translationseffizienz beitrugen und dadurch insgesamt zu einer erhöhten Proteinexpression führten. Antigen-kodierende IVT-RNA mit diesen molekularen Merkmalen in Kombination führte, im Vergleich zur Standard IVT-RNA, zu einer erhöhten Dichte und Stabilität von Peptid/MHC-Komplexen auf der Zelloberfläche transfizierter DCs und dadurch zu einer verbesserten Stimulation von CD4+ und CD8+ T-Zellen im murinen und humanen System. Mit dem Ziel, die RNA kodierte Antigenform für die Induktion einer verstärkten Antikörperantwort zu modifizieren, wurde im zweiten Teil der Arbeit ein Antigen-IgM Fusionskonstrukt hergestellt und hinsichtlich seiner Eignung als neues Impfstoff-Format untersucht. Die Ausgangshypothese, dass die RNA kodierten Antigen-IgM Fusionsproteine polymerisieren, von transfizierten Zellen sezerniert werden und aufgrund der repetitiven Antigenstruktur im Vergleich mit dem monomeren Antigen zu einer Verstärkung der Antikörperantwort führen, wurde in vitro und in vivo im Mausmodell bestätigt. Die Entwicklung und Evaluierung von Zytokinfusionsproteinen zur selektiven Verstärkung der antigenspezifischen Immunantworten bildeten den dritten Schwerpunkt der vorliegenden Arbeit. Zur weiteren Verstärkung der Antikörperantwort wurde basierend auf den Resultaten aus dem zweiten Teil ein IL2-IgM Fusionskonstrukt hergestellt. Die Ko-Transfektion von Antigen-IgM und IL2-IgM kodierender IVT-RNA führte zu einer signifikant stärkeren Antikörperantwort als die Ko-Transfektion von Antigen-IgM und IL2. Für die Initiierung einer erfolgreichen anti-Tumor-Immunantwort ist das Priming antigenspezifischer T-Zellen essentiell. Um die Effizienz dieses Prozesses zu steigern, wurde ein bifunktionelles IL2-mCD40L Fusionskonstrukt hergestellt und sein Einfluss auf die Effektorfunktion von DCs in vitro und in vivo untersucht. Es wurde gezeigt, dass ein RNA kodiertes IL2-mCD40L Fusionsprotein als genetisches Adjuvanz zu einer Effizienzsteigerung des Priming zytotoxischer T-Zellen führt. Somit wurden in dieser Arbeit durch die Optimierung der Pharmakokinetik, die Modifikation der Antigenform und die Herstellung und Evaluierung von Zytokinfusionskonstrukten als genetische Adjuvantien, RNA-basierte Impfstoffe für eine optimierte Induktion von antigenspezifischen Immunantworten weiter verbessert.

Pabp binds to the osk 3'UTR and specifically contributes to osk mRNA stability and oocyte accumulation

RNA localization is tightly coordinated with RNA stability and translation control. Bicaudal-D (Bic-D), Egalitarian (Egl), microtubules and their motors are part of a Drosophila transport machinery that localizes mRNAs to specific cellular regions during oogenesis and embryogenesis. We identified the Poly(A)-binding protein (Pabp) as a protein that forms an RNA-dependent complex with Bic-D in embryos and ovaries. pabp also interacts genetically with Bic-D and, similar to Bic-D, pabp is essential in the germline for oocyte growth and accumulation of osk mRNA in the oocyte. In the absence of pabp, reduced stability of osk mRNA and possibly also defects in osk mRNA transport prevent normal oocyte localization of osk mRNA. pabp also interacts genetically with osk and lack of one copy of pabp(+) causes osk to become haploinsufficient. Moreover, pointing to a poly(A)-independent role, Pabp binds to A-rich sequences (ARS) in the osk 3'UTR and these turned out to be required in vivo for osk function during early oogenesis. This effect of pabp on osk mRNA is specific for this RNA and other tested mRNAs localizing to the oocyte are less and more indirectly affected by the lack of pabp

Coordinated changes in mRNA turnover, translation, and RNA processing bodies in bronchial epithelial cells following inflammatory stimulation.

Bronchial epithelial cells play a pivotal role in airway inflammation, but little is known about posttranscriptional regulation of mediator gene expression during the inflammatory response in these cells. Here, we show that activation of human bronchial epithelial BEAS-2B cells by proinflammatory cytokines interleukin-4 (IL-4) and tumor necrosis factor alpha (TNF-alpha) leads to an increase in the mRNA stability of the key chemokines monocyte chemotactic protein 1 and IL-8, an elevation of the global translation rate, an increase in the levels of several proteins critical for translation, and a reduction of microRNA-mediated translational repression. Moreover, using the BEAS-2B cell system and a mouse model, we found that RNA processing bodies (P bodies), cytoplasmic domains linked to storage and/or degradation of translationally silenced mRNAs, are significantly reduced in activated bronchial epithelial cells, suggesting a physiological role for P bodies in airway inflammation. Our study reveals an orchestrated change among posttranscriptional mechanisms, which help sustain high levels of inflammatory mediator production in bronchial epithelium during the pathogenesis of inflammatory airway diseases.

Messenger RNA half-life measurements in mammalian cells.

The recognition of the importance of mRNA turnover in regulating eukaryotic gene expression has mandated the development of reliable, rigorous, and "user-friendly" methods to accurately measure changes in mRNA stability in mammalian cells. Frequently, mRNA stability is studied indirectly by analyzing the steady-state level of mRNA in the cytoplasm; in this case, changes in mRNA abundance are assumed to reflect only mRNA degradation, an assumption that is not always correct. Although direct measurements of mRNA decay rate can be performed with kinetic labeling techniques and transcriptional inhibitors, these techniques often introduce significant changes in cell physiology. Furthermore, many critical mechanistic issues as to deadenylation kinetics, decay intermediates, and precursor-product relationships cannot be readily addressed by these methods. In light of these concerns, we have previously reported transcriptional pulsing methods based on the c-fos serum-inducible promoter and the tetracycline-regulated (Tet-off) promoter systems to better explain mechanisms of mRNA turnover in mammalian cells. In this chapter, we describe and discuss in detail different protocols that use these two transcriptional pulsing methods. The information described here also provides guidelines to help develop optimal protocols for studying mammalian mRNA turnover in different cell types under a wide range of physiologic conditions.

Exploring protein-RNA interactions with site-directed mutagenesis and phage display

The importance of RNA as a mediator of genetic information is widely appreciated. RNA molecules also participate in the regulation of various post-transcriptional activities, such as mRNA splicing, editing, RNA stability and transport. Their regulatory roles for these activities are highly dependent on finely tuned associations with cognate proteins. The RNA recognition motif (RRM) is an ancient RNA binding module that participates in hundreds of essential activities where specific RNA recognition is required. We have applied phage display and site-directed mutagenesis to dissect principles of RRM-controlled RNA recognition. The model systems we are investigating are U1A and CUG-BP1. In this dissertation, the molecular basis of the binding affinity of U1A-RNA beyond individual contacts was investigated. We have identified and evaluated the contributions of the local cooperativity formed by three neighboring residues (Asn15, Asn16 and Glu19) to the stability of the U1A-RNA complex. The localized cooperative network was mapped by double-mutant cycles and explored using phage display. We also showed that a cluster of these residues forms a “hot spot” on the surface of U1A; a single substitution at position 19 with Gln or His can alter the binding properties of U1A to recognize a non-cognate G4U RNA. Finally, we applied a deletion analysis of CUG-BP1 to define the contributions of individual RRMs and RRM combinations to the stability of the complex formed between CUG-BP1 and the GRE sequence. The preliminary results showed RRM3 of CUG-BP1 is a key domain for RNA binding. It possibly binds to the GRE sequence cooperatively with RRM2 of CUG-BP1. RRM1 of CUG-BP1 is not required for GRE recognition, but may be important for maintaining the stability of the full-length CUG-BP1.

Genetic, functional, and histopathological evaluation of two C-terminal BRCA1 missense variants

Background: The vast majority of BRCA1 missense sequence variants remain uncharacterised for their possible effect on protein expression and function, and therefore are unclassified in terms of their pathogenicity. BRCA1 plays diverse cellular roles and it is unlikely that any single functional assay will accurately reflect the total cellular implications of missense mutations in this gene. Objective: To elucidate the effect of two BRCA1 variants, 5236G>C (G1706A) and 5242C>A (A1708E) on BRCA1 function, and to survey the relative usefulness of several assays to direct the characterisation of other unclassified variants in BRCA genes. Methods and Results: Data from a range of bioinformatic, genetic, and histopathological analyses, and in vitro functional assays indicated that the 1708E variant was associated with the disruption of different cellular functions of BRCA1. In transient transfection experiments in T47D and 293T cells, the 1708E product was mislocalised to the cytoplasm and induced centrosome amplification in 293T cells. The 1708E variant also failed to transactivate transcription of reporter constructs in mammalian transcriptional transactivation assays. In contrast, the 1706A variant displayed a phenotype comparable to wildtype BRCA1 in these assays. Consistent with functional data, tumours from 1708E carriers showed typical BRCA1 pathology, while tumour material from 1706A carriers displayed few histopathological features associated with BRCA1 related tumours. Conclusions: A comprehensive range of genetic, bioinformatic, and functional analyses have been combined for the characterisation of BRCA1 unclassified sequence variants. Consistent with the functional analyses, the combined odds of causality calculated for the 1706A variant after multifactorial likelihood analysis (1:142) indicates a definitive classification of this variant as "benign". In contrast, functional assays of the 1708E variant indicate that it is pathogenic, possibly through subcellular mislocalisation. However, the combined odds of 262:1 in favour of causality of this variant does not meet the minimal ratio of 1000:1 for classification as pathogenic, and A1708E remains formally designated as unclassified. Our findings highlight the importance of comprehensive genetic information, together with detailed functional analysis for the definitive categorisation of unclassified sequence variants. This combination of analyses may have direct application to the characterisation of other unclassified variants in BRCA1 and BRCA2.

Base pairing interaction between 5′- and 3′-UTRs controls icaR mRNA translation in Staphylococcus aureus

UPNa. Instituto de Agrobiotecnología. Laboratorio de Biofilms Microbianos.

Mechanisms of CD8+ T Cell Mediated Virus Inhibition in HIV-1 Virus Controllers

CD8+ T cells are associated with long term control of virus replication to low or undetectable levels in a population of HIV+ therapy-naïve individuals known as virus controllers (VCs; <5000 RNA copies/ml and CD4+ lymphocyte counts >400 cells/µl). These subjects' ability to control viremia in the absence of therapy makes them the gold standard for the type of CD8+ T-cell response that should be induced with a vaccine. Studying the regulation of CD8+ T cells responses in these VCs provides the opportunity to discover mechanisms of durable control of HIV-1. Previous research has shown that the CD8+ T cell population in VCs is heterogeneous in its ability to inhibit virus replication and distinct T cells are responsible for virus inhibition. Further defining both the functional properties and regulation of the specific features of the select CD8+ T cells responsible for potent control of viremia the in VCs would enable better evaluation of T cell-directed vaccine strategies and may inform the design of new therapies.

Here we discuss the progress made in elucidating the features and regulation of CD8+ T cell response in virus controllers. We first detail the development of assays to quantify CD8+ T cells' ability to inhibit virus replication. This includes the use of a multi-clade HIV-1 panel which can subsequently be used as a tool for evaluation of T cell directed vaccines. We used these assays to evaluate the CD8+ response among cohorts of HIV-1 seronegative, HIV-1 acutely infected, and HIV-1 chronically infected (both VC and chronic viremic) patients. Contact and soluble CD8+ T cell virus inhibition assays (VIAs) are able to distinguish these patient groups based on the presence and magnitude of the responses. When employed in conjunction with peptide stimulation, the soluble assay reveals peptide stimulation induces CD8+ T cell responses with a prevalence of Gag p24 and Nef specificity among the virus controllers tested. Given this prevalence, we aimed to determine the gene expression profile of Gag p24-, Nef-, and unstimulated CD8+ T cells. RNA was isolated from CD8+ T-cells from two virus controllers with strong virus inhibition and one seronegative donor after a 5.5 hour stimulation period then analyzed using the Illumina Human BeadChip platform (Duke Center for Human Genome Variation). Analysis revealed that 565 (242 Nef and 323 Gag) genes were differentially expressed in CD8+ T-cells that were able to inhibit virus replication compared to those that could not. We compared the differentially expressed genes to published data sets from other CD8+ T-cell effector function experiments focusing our analysis on the most recurring genes with immunological, gene regulatory, apoptotic or unknown functions. The most commonly identified gene in these studies was TNFRSF9. Using PCR in a larger cohort of virus controllers we confirmed the up-regulation of TNFRSF9 in Gag p24 and Nef-specific CD8+ T cell mediated virus inhibition. We also observed increase in the mRNA encoding antiviral cytokines macrophage inflammatory proteins (MIP-1α, MIP-1αP, MIP-1β), interferon gamma (IFN-γ), granulocyte-macrophage colony-stimulating factor (GM-CSF), and recently identified lymphotactin (XCL1).

Our previous work suggests the CD8+ T-cell response to HIV-1 can be regulated at the level of gene regulation. Because RNA abundance is modulated by transcription of new mRNAs and decay of new and existing RNA we aimed to evaluate the net rate of transcription and mRNA decay for the cytokines we identified as differentially regulated. To estimate rate of mRNA synthesis and decay, we stimulated isolated CD8+ T-cells with Gag p24 and Nef peptides adding 4-thiouridine (4SU) during the final hour of stimulation, allowing for separation of RNA made during the final hour of stimulation. Subsequent PCR of RNA isolated from these cells, allowed us to determine how much mRNA was made for our genes of interest during the final hour which we used to calculate rate of transcription. To assess if stimulation caused a change in RNA stability, we calculated the decay rates of these mRNA over time. In Gag p24 and Nef stimulated T cells , the abundance of the mRNA of many of the cytokines examined was dependent on changes in both transcription and mRNA decay with evidence for potential differences in the regulation of mRNA between Nef and Gag specific CD8+ T cells. The results were highly reproducible in that in one subject that was measured in three independent experiments the results were concordant.

This data suggests that mRNA stability, in addition to transcription, is key in regulating the direct anti-HIV-1 function of antigen-specific memory CD8+ T cells by enabling rapid recall of anti-HIV-1 effector functions, namely the production and increased stability of antiviral cytokines. We have started to uncover the mechanisms employed by CD8+ T cell subsets with antigen-specific anti-HIV-1 activity, in turn, enhancing our ability to inhibit virus replication by informing both cure strategies and HIV-1 vaccine designs that aim to reduce transmission and can aid in blocking HIV-1 acquisition.