TGFβ prevents IgE-mediated allergic disease by restraining T follicular helper 2 differentiation

Allergic diseases are common, affecting more than 20% of the population. Genetic variants in the TGFβ pathway are strongly associated with atopy. To interrogate the mechanisms underlying this association, we examined patients and mice with Loeys-Dietz syndrome (LDS) who harbor missense mutations in the kinase domain of TGFΒR1/2. We demonstrate that LDS mutations lead to reduced TGFβ signaling and elevated total and allergen-specific IgE, despite the presence of wild-type T regulatory cells in a chimera model. Germinal center activity was enhanced in LDS and characterized by a selective increase in type 2 follicular helper T cells (TFH2). Expression of Pik3cg was increased in LDS TFH cells and associated with reduced levels of the transcriptional repressor SnoN. PI3Kγ/mTOR signaling in LDS naïve CD4+ T cells was elevated after T cell receptor cross-linking, and pharmacologic inhibition of PI3Kγ or mTOR prevented exaggerated TFH2 and antigen-specific IgE responses after oral antigen exposure in an adoptive transfer model. Naïve CD4+ T cells from nonsyndromic allergic individuals also displayed decreased TGFβ signaling, suggesting that our mechanistic discoveries may be broadly relevant to allergic patients in general. Thus, TGFβ plays a conserved, T cell-intrinsic, and nonredundant role in restraining TFH2 development via the PI3Kγ/mTOR pathway and thereby protects against allergic disease.

Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine

Protective immunity following vaccination is sustained by long-lived antibody-secreting cells and resting memory B cells (MBCs). Responses to two-dose SARS-CoV-2 mRNA-1273 vaccination are evaluated longitudinally by multimodal single-cell analysis in three infection-naïve individuals. Integrated surface protein, transcriptomics, and B cell receptor (BCR) repertoire analysis of sorted plasmablasts and spike+ (S-2P+) and S-2P- B cells reveal clonal expansion and accumulating mutations among S-2P+ cells. These cells are enriched in a cluster of immunoglobulin G-expressing MBCs and evolve along a bifurcated trajectory rooted in CXCR3+ MBCs. One branch leads to CD11c+ atypical MBCs while the other develops from CD71+ activated precursors to resting MBCs, the dominant population at month 6. Among 12 evolving S-2P+ clones, several are populated with plasmablasts at early timepoints as well as CD71+ activated and resting MBCs at later timepoints, and display intra- and/or inter-cohort BCR convergence. These relationships suggest a coordinated and predictable evolution of SARS-CoV-2 vaccine-generated MBCs.

Antigenic Determinants of SARS-CoV-2-Specific CD4+ T Cell Lines Reveals M Protein-Driven Dysregulation of Interferon Signaling

We generated CD4⁺ T cell lines (TCLs) reactive to either SARS-CoV-2 spike (S) or membrane (M) proteins from unexposed naïve T cells from six healthy donor volunteers to understand in fine detail whether the S and M structural proteins have intrinsic differences in driving antigen-specific CD4⁺ T cell responses. Having shown that each of the TCLs were antigen-specific and antigen-reactive, single cell mRNA analyses demonstrated that SARS-CoV-2 S and M proteins drive strikingly distinct molecular signatures. Whereas the S-specific CD4⁺ T cell transcriptional signature showed a marked upregulation of CCL1, CD44, IL17RB, TNFRSF18 (GITR) and IGLC3 genes, in general their overall transcriptome signature was more similar to CD4⁺ T cell responses induced by other viral antigens (e.g. CMV). However, the M protein-specific CD4⁺ TCLs have a transcriptomic signature that indicate a marked suppression of interferon signaling, characterized by a downregulation of the genes encoding ISG15, IFITM1, IFI6, MX1, STAT1, OAS1, IFI35, IFIT3 and IRF7 (a molecular signature which is not dissimilar to that found in severe COVID-19). Our study suggests a potential link between the antigen specificity of the SARS-CoV-2-reactive CD4⁺ T cells and the development of specific sets of adaptive immune responses. Moreover, the balance between T cells of significantly different specificities may be the key to understand how CD4⁺ T cell dysregulation can determine the clinical outcomes of COVID-19.

Genome-wide mapping of yeast RNA polymerase II termination

Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts.

Transcription termination is an important regulatory event for both non-coding and coding transcripts. Using high-throughput sequencing, we have mapped RNA Polymerase II's position in the genome after depletion of termination factors from the nucleus. We found that depletion of Ysh1 and Sen1 cause build up of polymerase directly downstream of coding and non-coding genes, respectively. Depletion of Nrd1 causes an increase in polymerase that is distributed up to 1,000 bases downstream of non-coding genes. The depletion of Nrd1 helped us to identify more than 250 unique termination regions for non-coding RNAs. Within this set of newly identified non-coding termination regions, we are further able to classify them based on sequence motif similarities, suggesting a functional role for different terminator motifs. The role of these factors in transcriptional termination of coding and/or non-coding transcripts can be inferred from the effect of polymerase's position downstream of given termination sites. This method of depletion and sequencing can be used to further elucidate other factors whose importance to transcription has yet to be determined.

Autoimmunity in interferon-gamma AU-rich element deleted-mice is associated with loss of marginal zone B cells and macrophages. (BA15P.217)

We generated a mouse model with a 162 nt AU-rich element (ARE) region deletion in the 3’ untranslated region (3’UTR) of the interferon (IFN)-gamma gene that results in chronic circulating serum IFN-gamma levels. Mice homozygous for the ARE deletion present both serologic and cellular abnormalities typical of patients with systemic lupus erythematosus (SLE). Marginal zone B (MZB) cells and marginal zone macrophages (MZMs) are absent in ARE-deleted (ARE-Del)-/- mice. ARE-Del+/- mice retain both MZB cells and MZMs and develop no or mild autoimmunity. However, low dose clodronate treatment in ARE-Del+/- mice specifically eliminates MZMs and promotes anti-DNA antibody development and glomerulonephritis. Our findings demonstrate the consequences of a chronic IFN-gamma milieu on MZB cell loss and MZM function in autoimmunity. Furthermore, similarities between disease states in ARE-Del-/- mice and SLE patients suggest that IFN-gamma may not only be a product of SLE but may be critical for disease onset and progression.

UK-1 and structural analogs are potent inhibitors of hepatitis C virus replication

The bacterial natural product UK-1 and several structural analogs inhibit replication of the hepatitis C virus in the replicon assay, with IC50 values as low as 0.50 μM. The NS3 helicase has been identified as a possible target of inhibition for several of these compounds, while the remaining inhibitors act via an undetermined mechanism. Gel shift assays suggest that helicase inhibition is a direct result of inhibitor-enzyme binding as opposed to direct RNA binding, and the ATPase activity of NS3 is not affected. The syntheses and biological results are presented herein.

Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing

RNA polymerase II transcribes both coding and noncoding genes, and termination of these different classes of transcripts is facilitated by different sets of termination factors. Pre-mRNAs are terminated through a process that is coupled to the cleavage/polyadenylation machinery, and noncoding RNAs in the yeast Saccharomyces cerevisiae are terminated through a pathway directed by the RNA-binding proteins Nrd1, Nab3, and the RNA helicase Sen1. We have used an in vivo cross-linking approach to map the binding sites of components of the yeast non-poly(A) termination pathway. We show here that Nrd1, Nab3, and Sen1 bind to a number of noncoding RNAs in an unexpected manner. Sen1 shows a preference for H/ACA over box C/D snoRNAs. Nrd1, which binds to snoRNA terminators, also binds to the upstream region of some snoRNA transcripts and to snoRNAs embedded in introns. We present results showing that several RNAs, including the telomerase RNA TLC1, require Nrd1 for proper processing. Binding of Nrd1 to transcripts from tRNA genes is another unexpected observation. We also observe RNA polymerase II binding to transcripts from RNA polymerase III genes, indicating a possible role for the Nrd1 pathway in surveillance of transcripts synthesized by the wrong polymerase. The binding targets of Nrd1 pathway components change in the absence of glucose, with Nrd1 and Nab3 showing a preference for binding to sites in the mature snoRNA and tRNAs. This suggests a novel role for Nrd1 and Nab3 in destruction of ncRNAs in response to nutrient limitation.

Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1

RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination.

Transcription in eukaryotes is widespread including both protein-coding transcripts and an increasing number of non-coding RNAs. Here we present the results of transcriptome-wide mapping of a set of yeast RNA–binding proteins that control expression of some protein-coding genes and a number of novel non-coding RNAs. The yeast Nrd1-Nab3-Sen1 pathway is required for termination and exosome-mediated processing of non-coding RNA polymerase II transcripts. Our data show that these components bind unexpected targets including a large number of antisense transcripts originating from the 3′ end of genes that are poorly expressed in the sense direction. We also show that Sen1 helicase, involved in termination of non-coding RNAs, is also present at the 3′ end of mRNAs, suggesting a more fundamental role in transcription termination. Mis-regulation of transcription is the underlying cause of many disease states. For example, mutation of the human Sen1 gene, senataxin, causes a range of neurodegenerative disorders. Understanding the roles of yeast RNA–binding proteins in controlling termination of coding and non-coding RNAs will be useful in deciphering the mechanism of these proteins in human cells.

Novel Gene Expression Patterns in IFN-γ 3’Untranslated Region AU-Rich Element-Deleted Mice (51.7)

Much research has focused on transcriptional control of interferon-gamma (IFN-γ); however, little is known about post-transcriptional control of this cytokine. Our studies focus on a highly conserved AU-rich region in the 3’untranslated region (UTR) of the IFN-γ mRNA. To study the impact of this sequence on IFN-γ gene expression and immune function, we created an IFN-γ 3’UTR ARE-deleted mouse. ARE elimination results in IFN-γ mRNA stabilization and chronic low levels of circulating IFN-γ protein that are not present in control mice. Upon stimulation, the ARE-deleted mice produce 3-5-fold more IFN-γ than wild-type mice, supporting the model that the ARE-region functions as a negative modulator of IFN-γ expression. Next, we conducted PCR array and Nanostring direct multiplexed assays on RNA from bone marrow, kidney, liver, lymph node, spleen, and thymus from ARE-deleted and WT mice. As expected, mRNA for IFN-γ and IFN-γ-responsive genes, CXCL9 and CXCL10, were elevated in all tissues from ARE-deleted mice. IFN-γ-induced tissue-specific gene expression patterns were associated with a variety of immune functions including chemotaxis, inflammation, Th1/Th2 development and B cell proliferation/antibody production. These results indicate that small changes in IFN-γ expression have far reaching effects on immune development and function. Thus, this mouse serves as a unique model for understanding the systems biology consequences of chronic IFN-γ expression.