Logistic regression was implemented with asthma transition status as the response variable, controlled for potential confounders including gender, family history of asthma, gestational maternal ...smoking, allergy, current smoking, birthweight, farm living, paracetamol use, social class, pet exposure, breast feeding, height and BMI changes. Results DNAm at 7 Cytosine-Phosphate-Guanine (CPG) sites was associated with negative transition, 17 with positive transition, and 3 with persistent asthma.
Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune ...system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in the disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies.
•SAHA induces HIV RNA expression, but does not reduce the size of the persistent cellular reservoir of HIV provirus.•We analyzed proteome and transcriptome changes induced by SAHA in human primary ...CD4+ T cells.•Positive and negative effects of SAHA on genes and proteins with a role in HIV reactivation from latency were identified.•These results may impact selection and modification of HDACis and prioritization of other compounds for future evaluations.
Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a “shock and kill” strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA (“shock”), treatment with SAHA did not result in a reduction of reservoir size (“kill”). We therefore utilized a combined analysis of effects of SAHA on the host transcriptome and proteome to dissect its mechanisms of action that may explain its limited success in “shock and kill” strategies. CD4+ T cells from HIV seronegative donors were treated with 1μM SAHA or its solvent dimethyl sulfoxide (DMSO) for 24h. Protein expression and post-translational modifications were measured with iTRAQ proteomics using ultra high-precision two-dimensional liquid chromatography–tandem mass spectrometry. Gene expression was assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the HIV transcriptional repressor HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFκB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, SAHA modulated numerous host cell transcripts, proteins and post-translational modifications of proteins, which would be expected to have very mixed effects on the induction of HIV-specific transcription and protein function. Proteome profiling highlighted a number of potential counter-regulatory effects of SAHA with respect to viral induction, which transcriptome profiling alone would not have identified. These observations could lead to a more informed selection and design of other HDACi with a more refined targeting profile, and prioritization of latency reversing agents of other classes to be used in combination with SAHA to achieve more potent induction of HIV expression.
Rationale Maternal age at birth has been associated with increased incidence of asthma, food allergy, and diabetes in children and young adults. Methods In peripheral blood samples from the Isle of ...Wight (IoW) Birth Cohort (10 (N=138) and 18 (N=367) years) and cord-blood samples from 200 subjects from the IoW 3rd Generation Cohort, methylation was assessed using Illumina HumanMethylation450 and EPIC Beadchips and analyzed with linear models.
Rationale Prior studies showed that DNA methylation (DNA-M) is associated with lung function and DNA-M at some cytosine-phosphate-guanine sites (CpGs) changes over time. Methods DNA-M was measured in ...peripheral blood samples collected at ages 10 (n = 329) and 18 years (n = 476) from the Isle of Wight birth cohort (UK) using Illumina Infinium HumanMethylation450 and EPIC Beadchips.
The growth and survival of neurofibromatosis type 2 (NF2)-deficient cells are enhanced by the activation of multiple signaling pathways including ErbBs/IGF-1R/Met, PI3K/Akt, and Ras/Raf/Mek/Erk1/2. ...The chaperone protein HSP90 is essential for the stabilization of these signaling molecules. The aim of the study was to characterize the effect of HSP90 inhibition in various NF2-deficient models.
We tested efficacy of the small-molecule NXD30001, which has been shown to be a potent HSP90 inhibitor. The antiproliferative activity of NXD30001 was tested in NF2-deficient cell lines and in human primary schwannoma and meningioma cultures in vitro. The antitumor efficacy of HSP90 inhibition in vivo was verified in two allograft models and in one NF2 transgenic model. The underlying molecular alteration was further characterized by a global transcriptome approach.
NXD30001 induced degradation of client proteins in and suppressed proliferation of NF2-deficient cells. Differential expression analysis identified subsets of genes implicated in cell proliferation, cell survival, vascularization, and Schwann cell differentiation whose expression was altered by NXD30001 treatment. The results showed that NXD30001 in NF2-deficient schwannoma suppressed multiple pathways necessary for tumorigenesis.
HSP90 inhibition showing significant antitumor activity against NF2-related tumor cells in vitro and in vivo represents a promising option for novel NF2 therapies.
Ménière's disease (MD) is a debilitating disorder of the inner ear characterized by cochlear and vestibular dysfunction. The cause of this disease is still unknown, and epidemiological data for MD ...are sparse. From the existing literature, women seem to be more susceptible than men, and Caucasians seem to be more susceptible than Asians.
In this article, we characterize a large definite MD cohort for sex and age of onset of disease and use molecular genetic methodologies to characterize ethnicity.
Medical record review for sex and age of onset. Ancestry analysis compared results from the principal component analysis of whole-genome genotype data from MD patients to self-identified ancestry in control samples.
House Clinic in Los Angeles.
Definitive MD patients.
Our review of medical records for definitive MD patients reveals that women are more susceptible than men. We also find that men and women have nearly identical age of onset for disease. Lastly, interrogation of molecular genetic data with principal component analysis allowed detailed observations about the ethnic ancestry of our patients. Comparison of the ethnicity of MD patients presenting to our tertiary care clinic with the self-recollected ethnicity of all patients visiting the clinic revealed an ethnic bias, with Caucasians presenting at a higher frequency than expected and the remaining major ethnicities populating Los Angeles (Hispanics, Blacks, and Asians) presenting at a lower frequency than expected.
To the best of our knowledge, this report is the first ethnic characterization of a large MD cohort from a large metropolitan region using molecular genetic data. Our data suggest that there is a bias in sex and ethnic susceptibility to this disease.
•The number of genes modulated following ART is an order of magnitude higher than previously recognized.•Well characterized drug metabolism genes not previously associated with ART appear upregulated ...by ART.•Droplet digital PCR (ddPCR) has been used to confirm gene expression for the first time in an infectious disease setting.
Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin’s lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.
The central memory T cell (TCM) model forms a unique HIV-1 latency model based on primary cells that closely resemble in vivo TCM. The virus employed in this model is based on an engineered vector ...incapable of replication after initial infection. We show that despite this strategy, replication competent viral particles are released into the culture medium due to recombination between overlapping sequences of the env deleted HIV genome that is co-transfected with intact env. This finding emphasizes the need for careful data analysis and interpretation if similar constructs are employed and urges for additional caution during laboratory work.
Noise-induced hearing loss (NIHL) is one of the more common sources of environmentally induced hearing loss in adults. In a mouse model, Castaneous (CAST/Ei) is an inbred strain that is resistant to ...NIHL, while the C57BL/6J strain is susceptible. We have used the genome-tagged mice (GTM) library of congenic strains, carrying defined segments of the CAST/Ei genome introgressed onto the C57BL/6J background, to search for loci modifying the noise-induced damage seen in the C57BL/6J strain. NIHL was induced by exposing 6-8-week old mice to 108 dB SPL intensity noise. We tested the hearing of each mouse strain up to 23 days after noise exposure using auditory brainstem response (ABR). This study identifies a number of genetic loci that modify the initial response to damaging noise, as well as long-term recovery. The data suggest that multiple alleles within the CAST/Ei genome modify the pathogenesis of NIHL and that screening congenic libraries for loci that underlie traits of interest can be easily carried out in a high-throughput fashion.
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