Analysis of the role of brome mosaic virus 1a protein domains in RNA replication, using linker insertion mutagenesis

Brome mosaic virus (BMV) belongs to a "superfamily" of plant and animal positive-strand RNA viruses that share, among other features, three large domains of conserved sequence in nonstructural proteins involved in RNA replication. Two of these domains reside in the 109-kDa BMV 1a protein. To examine the role of 1a, we used biologically active cDNA clones of BMV RNA1 to construct a series of linker insertion mutants bearing two-codon insertions dispersed throughout the 1a gene. The majority of these mutations blocked BMV RNA replication in protoplasts, indicating that both intervirally conserved domains function in RNA replication. Coinoculation tests with a large number of mutant combinations failed to reveal detectable complementation between mutations in the N- and C-terminal conserved domains, implying that these two domains either function in some directly interdependent fashion or must be present in the same protein. Four widely spaced mutations with temperature-sensitive (ts) defects in RNA replication were identified, including a strongly ts insertion near the nucleotide-binding consensus of the helicaselike C-terminal domain. Temperature shift experiments with this mutant show that 1a protein is required for continued accumulation of all classes of viral RNA (positive strand, negative strand, and subgenomic) and is required for at least the first 10 h of infection. ts mutations were also identified in the 3' noncoding region of RNA1, 5' to conserved sequences previously implicated in cis for replication. Under nonpermissive conditions, the cis-acting partial inhibition of RNA1 accumulation caused by these noncoding mutations was also associated with reduced levels of the other BMV genomic RNAs. Comparison with previous BMV mutant results suggests that RNA replication is more sensitive to reductions in expression of 1a than of 2a, the other BMV-encoded protein involved in replication.

Deletion analysis of brome mosaic virus 2a protein: effects on RNA replication and systemic spread

Brome mosaic virus (BMV) genomic RNA2 encodes the 94-kDa 2a protein, which is one of two BMV nonstructural proteins required for RNA replication and subgenomic mRNA transcription. 2a contains a central polymeraselike region, which has extensive sequence similarity with the Sindbis virus nsP4 and tobacco mosaic virus (TMV) 183-kDa replication proteins, and also contains N- and C-terminal flanking segments without counterparts in the Sindbis virus and TMV nonstructural proteins. To further investigate the roles of the central and flanking segments in 2a, we have constructed a series of deletion and frameshift mutants in a biologically active BMV RNA2 cDNA clone and tested their ability to support viral RNA replication in barley protoplasts and systemic infection in whole barley plants. The entire 125-amino-acid C-terminal segment following the polymeraselike region was dispensable for RNA replication and transcription. Within the 200-amino-acid N-terminal flanking segment, deletion of the first 50 residues dramatically reduced genomic and subgenomic RNA accumulation, and deletion of 100 or more residues abolished detectable RNA synthesis. All mutations removing residues from the central polymeraselike domain also blocked RNA replication in trans. Sequences required in cis for RNA2 replication or stability were found to occur within the first 300 nucleotides of the 2a coding region. In whole barley plants, systemic infection was inhibited even by 2a deletions that supported strong RNA replication in protoplasts. Some replication-competent 2a variants failed to spread to uninoculated leaves, while other showed 10- to 500-fold-reduced virus yield in both inoculated and uninoculated leaves. These reductions were not due to any defects in RNA2 encapsidation.

Identification of regions of Ail required for the invasion and serum resistance phenotypes

Yersinia enterocolitica is an enteric pathogen that has served as a model system for the study of microbial pathogenesis. Numerous virulence gene have been identified both on the virulence plasmid and on the chromosome. One of the chromosomal genes that is highly correlated with virulence is ail, a gene identified along with inv in a screen for Y. enterocolitica genes that could confer an invasive phenotype to Escherichia coli. Ail also promotes serum resistance in both E. coli and Y. enterocolitica. Several virulence factors homologous to Ail have been identified in other pathogens, yet very little is known about what constitutes the functional domain(s) of these proteins. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. We constructed and characterized a number of insertion, deletion and point mutations in the regions of ail predicted to encode the cell surface loops. The results from the analysis of these mutants indicate that cell surface loops one and four do not directly promote invasion or serum resistance, whereas mutations in loop three appear to modulate both phenotypes. Analysis of mutations in loop 2 suggests that this surface-exposed loop contains sequences required for serum resistance and invasion. In addition, a peptide derived from the sequence of loop 2 was able specifically to inhibit Ail-mediated invasion in a dose-dependent manner. These results suggest that Ail directly promotes invasion and that loop 2 contains an active site, perhaps a receptor-binding domain. Analyses of the mutations also suggest that the serum resistance and invasion phenotypes may be separable, because there are numerous mutations that affect one phenotype but not the other.

Novel mutations and a mutational hotspot in the MODY3 gene

Maturity-onset diabetes of the young 3 (MODY3) is a type of NIDDM caused by mutations in the transcription factor hepatocyte nuclear factor-1alpha (HNF-1alpha) located on chromosome 12q. We have identified four novel HNF-1alpha missense mutations in MODY3 families. In four additional and unrelated families, we observed an identical insertion mutation that had occurred in a polycytidine tract in exon 4. Among those families, one exhibited a de novo mutation at this location. We propose that instability of this sequence represents a general mutational mechanism in MODY3. We observed no HNF-1alpha mutations among 86 unrelated late-onset diabetic patients with relative insulin deficiency. Hence mutations in this gene appear to be most strongly associated with early-onset diabetes.

A recombinant Leishmania chagasi antigen that stimulates cellular immune responses in infected mice

Cellular immune mechanisms resulting in gamma interferon production are critical for protection against visceral leishmaniasis. Antigens stimulating T-cell responses are likely present in the intracellular amastigote form of the parasite, since this is the form found in a mammalian host. To identify T-cell antigens of Leishmania chagasi, the parasite causing South American visceral leishmaniasis, we used a double antibody-T-cell technique to screen an amastigote cDNA library. One cDNA selected (Lcr1) encodes an antigen that stimulated proliferation of splenic T lymphocytes from infected mice that were either resistant (C3H.HeJ) or susceptible (BALB/c) to L. chagasi infection. The Lcr1 cDNA contains four highly divergent 201-bp repeats homologous to the 204-bp repeat of a Trypanosoma cruzi flagellar antigen gene. Results are consistent with a single copy of the Lcr1 gene producing an mRNA of > 10 kb and a protein of > 200 kDa. Recombinant Lcr1, cloned adjacent to polyhistidine and purified on a nickel affinity column, stimulated gamma interferon but not interleukin-4 (IL-4), IL-5, or IL-10 secretion by T-cell-enriched splenocytes from either susceptible or resistant mice during L. chagasi infection. Immunization with Lcr1 partially protected BALB/c mice against challenge with L. chagasi, indicating the utility of the double screening approach in selecting relevant T-cell antigens.

Chronic ethanol induces inhibition of antigen-specific CD8+ but not CD4+ immunodominant T cell responses following Listeria monocytogenes inoculation

Chronic ethanol consumption results in immunodeficiency. Previous work with chronic ethanol-fed mice has shown reduced splenic weight and cellularity, including reduced numbers of CD8+ T cells. However, antigen-specific CD8+ and CD4+ T cell responses in chronic ethanol-fed mice have been studied relatively little. We have used an attenuated Listeria monocytogenes strain DPL 1942 (LM DeltaactA) to inoculate mice and subsequently used CD4+ and CD8+ immunodominant peptides of LM to measure the CD4+ and CD8+ T cell responses after chronic ethanol exposure. We found no major differences between control and ethanol-fed mice in the kinetics and persistence of antigen-specific CD4+ T cells in response to an immunodominant LM peptide, as measured by intracellular IFN-gamma staining. In contrast to CD4+ responses, three methods of in vitro antigen presentation indicated that the primary response of CD8+ T cells to several different epitopes was reduced significantly in mice chronically fed ethanol. Antigen-specific CD8+ T cells were also reduced in chronic ethanol-fed mice during the contraction phase of the primary response, and memory cells evaluated at 29 and 60 days after inoculation were reduced significantly. BrdU proliferation assays showed that in vivo proliferation of CD8+ T cells was reduced in ethanol-fed mice, and IL-2-dependent in vitro proliferation of naive CD8+ T cells was also reduced. In conclusion, these results suggest that antigen-specific CD4+ T cell responses to LM are affected little by chronic ethanol consumption; however, antigen-specific CD8+ T cell responses are reduced significantly, as are in vivo and in vitro proliferation. The reduction of antigen-specific CD8+ T cells may contribute strongly to the immunodeficiency caused by ethanol abuse.

The TGF-beta response to Leishmania chagasi in the absence of IL-12

Cure of leishmaniasis requires a type 1 immune response characterized by IFN-gamma production. Leishmania major infection leads to a type 2 response suppressing cure of susceptible BALB/c mice, and L. major causes an exacerbated type 2 response in mouse strains with a gene knockout (KO) such that they lack IL-12p40 (IL-12KO mice). In contrast, type 1 responses are inhibited by TGF-beta without Th2 cell expansion in BALB/c mice infected with L. chagasi. We questioned whether the type 2 or the TGF-beta response would dominate during L. chagasi infection of IL-12KO mice. C57BL/6 mice developed self-resolving L. chagasi infection with abundant IFN-gamma. In contrast, L. chagasi disease was exacerbated and IFN-gamma was low in IL-12KO mice. Total TGF-beta was significantly higher in IL-12KO than control C57BL/6 mice, but IL-4 and IL-10 levels were similar. TGF-beta was further augmented in IL-12/IFN-gamma double-KO mice. Thus, in contrast to L. major, the TGF-beta response was exacerbated whereas type 2 cells were not expanded during L. chagasi infection of IL-12KO mice. We conclude that L. chagasi has an inherent propensity to elicit a prominent TGF-beta response that either suppresses, or is suppressed by, a type 1 response. We propose this be termed a "type 3" immune response, which can antagonize a type 1 response.

Yersinia enterocolitica ClpB affects levels of invasin and motility

Expression of the Yersinia enterocolitica inv gene is dependent on growth phase and temperature. inv is maximally expressed at 23 degrees C in late-exponential- to early-stationary-phase cultures. We previously reported the isolation of a Y. enterocolitica mutant (JB1A8v) that shows a decrease in invasin levels yet is hypermotile when grown at 23 degrees C. JB1A8v has a transposon insertion within uvrC. Described here is the isolation and characterization of a clone that suppresses these mutant phenotypes of the uvrC mutant JB1A8v. This suppressing clone encodes ClpB (a Clp ATPase homologue). The Y. enterocolitica ClpB homologue is 30 to 40% identical to the ClpB proteins from various bacteria but is 80% identical to one of the two ClpB homologues of Yersinia pestis. A clpB::TnMax2 insertion mutant (JB69Qv) was constructed and determined to be deficient in invasin production and nonmotile when grown at 23 degrees C. Analysis of inv and fleB (flagellin gene) transcript levels in JB69Qv suggested that ClpB has both transcriptional and posttranscriptional effects. In contrast, a clpB null mutant, BY1v, had no effect on invasin levels or motility. A model accounting for these observations is presented.

A practical method of chronic ethanol administration in mice

Mice provide a useful model for the study of immune deficiency caused by chronic alcohol abuse. Their suitability is related to several factors, including in particular the extensive knowledge base in the immunology of mice already existing in the literature. Specific modeling of the immunodeficiency of the chronic human alcoholic requires that ethanol must be administered to the model for a significant portion of its life span. In mice, it has proven to be necessary to administer ethanol daily for up to 32 wk or longer to observe all the immune abnormalities that occur in middle-aged alcoholic humans. Such time spans are problematic with many of the common protocols for ethanol administration. It has been shown by others and confirmed by our group that the most practical way of accomplishing such long protocols is by administering ethanol in water as the only choice of water. Details of management of the chronic ethanol mouse colony are described here that are necessary for the success of such studies, including methods for initiating ethanol administration, maintenance of barrier protection, monitoring weight gain, strain differences and fetal alcohol exposure.

Research note: differences in major histocompatibility complex gene frequencies associated with feed efficiency and laying performance

Associations between egg production and feed efficiency and the genes of the major histocompatibility complex (MHC) of the chicken were investigated. Breeders were selected on the basis of indexes incorporating information on body weight and egg mass, with or without feed consumption information. Over 1,000 progeny were serotyped for the erythrocyte antigen B (Ea-B) after the 6th generation of selection. The B2 and B13 haplotypes accounted for over 75% of the Ea-B gene pool in all lines. Comparing each index-selected line with the control B2 significantly increased in frequency at the expense of B13. This study further implicates MHC-linked genes as important in the physiology of growth and reproduction in the chicken.

Preemptive analgesia in elective surgery in patients with complex regional pain syndrome: a case report

Complex regional pain syndrome (CRPS) can be a complication of injury or surgery or have an obscure etiology. Special precautions are indicated (i.e., preemptive analgesia) when surgery is required with a patient who has been diagnosed with CRPS. The complex case of a 44-year-old female diagnosed with reflex sympathetic dystrophy (RSD) is discussed, including current treatment options. A brief review of the literature as well as the features of complex regional pain syndrome (CRPS I/RSD and CRPS II/causalgia) are presented.

Polyclonal and antigen-specific responses of T cells and T cell subsets

Evaluation of the functional responses of T cells is of importance in determining the mechanism(s) of immunodeficiency resulting from chronic alcohol abuse and other conditions that lead to immune dysfunction. Mice that are chronically exposed to 20% (w/v) ethanol in water develop immunodeficiency and have T cells with abnormal activation profiles, reduced total numbers, increased CD4/CD8 ratios, and an increased memory/naïve phenotype ratio. These cells also have abnormal antigen-specific responses after inoculation of the ethanol mice with model infectious organisms. Study of the functional abnormalities of these cells requires a reliable system that can present appropriate activation stimuli in vitro for the generation of polyclonal or antigen-specific responses in enriched or purified T cells, free of the influence of previously ethanol exposed accessory cells. In this chapter, we describe protocols to assess the T cell response to polyclonal stimulation through the T cell receptor and the use of a model infectious disease bacterium, Listeria monocytogenes, that allows evaluation of the T-cell response to specific peptide epitopes of the bacterium after previous inoculation.

Fetal/neonatal ethanol exposure irreversibly alters immune parameters in young mice (36.28)

Chronic ethanol ingestion has been shown to impair immune defensive function of adult hosts to invading organisms. Children born to alcoholic mothers are known to have increased incidence and severity of infections, but EtOHÕs effect on the immune system in the fetus/neonate has not been well studied. We have developed a model of fetal/neonatal EtOH exposure in which female mice are maintained on 10% EtOH in the drinking water during breeding and gestation, and then on 12% EtOH during lactation. Pups have successfully been weaned and showed no significant difference in weights from controls through 42 days of age. These pups have been studied at 20 d (weaning) and 42 d (adolescence) for immunological cell numbers and function. Our data showed decreased splenic T and B cells in EtOH pups, but increased pulmonary leukocyte and dendritic cell (DC) numbers. Splenic DC and epidermal Langerhans cells numbers did not change. However, EtOH decreased baseline costimulatory molecule expression on splenic DC and the ability of these DC to stimulate allogeneic T cells, changes that persisted following cessation of EtOH exposure. These results indicate that mice born to EtOH-consuming mothers have immune deficiencies that are persistent following cessation of EtOH exposure. The dissection of T, B cell and DC dysfunction in EtOH pups is in progress.

Abstract P2-09-02: Blinded molecular subtyping analysis from RNA-Seq of FFPE samples in the GeparQuinto trial reveals predictive value of VEGFA metagene for bevacizumab treatment

Background:

RNA-Seq from total RNA in FFPE tissue can be more challenging due to limited capture of partially degraded RNA. Exome-capture based RNA-Seq may circumvent such problems and allow reproducible complete molecular characterization of low-quality RNA from small clinical samples.

Methods:

HER2 negative patients within the GeparQuinto trial were treated with neoadjuvant anthracycline-taxane-based chemotherapy +/- bevacizumab. Patients with bevacizumab therapy had a significantly higher pCR rate, especially within the triple negative subgroup. We performed exome-capture RNA-Seq on 5µm FFPE sections from pre-therapeutic cores of 400 HER2 negative samples from this trial. In a prospectively planned, blinded study we correlated molecular subtypes and metagenes for proliferation, stroma, MHC2, and VEGFA with clinical and histopathological data. Molecular subtypes were defined using the AIMS methods. Metagenes were calculated as mean values corresponding to previously described gene clusters after platform transfer (Rody et al. 2011 PMID 21978456, Hu et al. 2009 PMID 19291283) and then z-transformed.

Results:

296 samples with RNA-Seq data were classified as either of high (n=226) or of limited quality (n=70). For 22 samples RNA yield was insufficient and 82 did not pass initial QC. 121 (41%), 63 (21%), 34 (11.5%), 46 (15.5%), and 32 (11%) samples were defined as basal-like, HER2-enriched, luminal A, luminal B, and normal-like, respectively. Subtyping was robust with regard to gene filtering, normalization, and sample quality. ER and PR status from local IHC strongly correlated with gene expression (overall correctness 84% and 80% for ER, and 85% and 74% for PR, in samples with high and limited quality, respectively) and luminal subtypes (95% ER positive). Proliferation metagene correlated with histological grade (median -0.73, -0.39, and 0.53 in G1, G2, and G3, respectively; P<0.001) and MHC2 metagene correlated strongly with TIL counts (Rho=0.53, P<0.001). Among the high quality samples response rates (49.3% pCR overall) differed significantly by subtype, with higher pCR rates in basal-like (68.9%) and HER2-enriched (45.5%) than in luminal B (35.7%), luminal A (17.9%), and normal-like (20.0%). MHC2- (OR 1.60, 95%CI 1.21-2.12, P=0.001), proliferation- (OR 2.88, 95%CI 2.00-4.16, P<0.001), and VEGFA-metagenes (OR 1.92, 95%CI 1.41-2.60, P<0.001) were significant predictors for pCR. In a multivariate logistic regression (adjusted for bevacizumab treatment and hormone receptor status) both VEGFA metagene (OR 2.59, 95%CI 1.40-4.77, P=0.002) and the interaction between the VEGFA-metagene and bevacizumab treatment arm (P=0.023) significantly predicted pCR.

Conclusions:

Exome-capture RNA-Seq allows robust genomic characterization of clinical samples with limited FFPE material from core biopsies, and molecular subtypes and immune metagenes are predictive for pCR. The VEGFA metagene is a specific predictor for response to neoadjuvant bevacizumab treatment.

Citation Format: Karn T, Meissner T, Weber K, Sinn B, Denkert C, Budczies J, Nekljudova V, Fasching PA, Holtrich U, Schem C, Solbach C, Hartmann A, Röcken C, Untch M, Young BM, Willis S, Leyland-Jones B, von Minckwitz G, Loibl S. Blinded molecular subtyping analysis from RNA-Seq of FFPE samples in the GeparQuinto trial reveals predictive value of VEGFA metagene for bevacizumab treatment [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-02.

The Importance of TGF-β in Murine Visceral Leishmaniasis

IFN-γ is critical for the cure of leishmaniasis in humans and mice. BALB/c mice are genetically susceptible to infection with the visceralizing species of Leishmania, L. chagasi. We have evidence that a soluble factor(s) inhibits IFN-γ production by cultured liver granuloma cells from BALB/c mice during L. chagasi infection. In contrast, liver granulomas from C3H.HeJ mice, which are genetically resistant to L. chagasi infection, produce abundant IFN-γ. According to ELISAs and neutralization studies, there was not evidence that the Th2-type cytokines IL-10 or IL-4 contributed to IFN-γ suppression. However, both Ab neutralization and immunohistochemistry showed that granuloma-derived TGF-β was, at least in part, responsible for inhibiting IFN-γ release by CD4+ cells in BALB/c liver granuloma cultures. Consistently, TGF-β levels were high in liver granulomas from susceptible BALB/c mice but low in resistant C3H mice or in BALB/c mice that were immunized against L. chagasi disease. Administration of recombinant adenovirus expressing TGF-β (AdV-TGFβ) but not IL-10 (AdV-IL10) caused genetically resistant C3H mice to become significantly more susceptible to L. chagasi infection. In contrast, either AdV-TGFβ or AdV-IL10 could abrogate the protective immune response achieved by immunization of BALB/c mice. We conclude that locally secreted TGF-β inhibits Th1-associated cure of murine visceral leishmaniasis caused by L. chagasi, independently of Th2-type cytokines.

Reduced antigen-specific CD8+ T cell responses as a result of increased bacterial translocation in chronic ethanol consuming mice (129.17)

Chronic ethanol consumption leads to increased translocation of bacterial products such as LPS and PGN. Previously, we have shown that chronic ethanol consumption results in reduced antigen-specific CD8+ T cell responses following attenuated Listeria monocytogenes (actA-LM) inoculation. We hypothesized that reduced antigen-specific CD8+ T cell response in chronic ethanol mice can be modeled by treatment with bacterial products. Control water mice were pretreated with either LPS or TLR-2 agonist to mimic systemic bacterial product translocation and their response to actA-LM inoculation was evaluated. Antigen-specific CD8+ T cell responses to actA- LM were reduced in Pam3CSK4 or LPS treated mice, similar to ethanol mice. Further analyses showed that the reduction of antigen-specific CD8+ T cells in TLR agonist treated mice was due to an indirect effect on antigen presenting cells, as well as a direct effect on CD8+ T cells. None of the TLR agonist effects on CD8+ T cells was reversed by prior depletion of natural Treg cells, or by the depletion of all CD4+ T cells, nor was the reduction of IL2Rb reversed by several days in culture. Reduction of antigen-specific CD8+ T cells was also independent of IL-10. The data as a whole clearly indicate that TLR agonists resulting from bacterial translocation represent one potent mechanism for alteration of antigen-specific CD8+ T cell responses.