Investigations of HIV Latency Through Transcriptomic and Proteomic Profiling

The human immunodeficiency virus (HIV) has been a global threat for over three decades despite treatments, preventative measures, and public awareness. HIV hides from the immune system by entering a latent state within CD4 T-cells and removal of therapy results in a resurgence of infection. Therapies to combat HIV were designed to shock the virus from latency and kill infected cells, i.e. "Shock and Kill", and are often studied in cell models due to the paucity of infected cells and no method to isolate them from HIV infected individuals. Transcriptomic and proteomic methods have proven key to studying HIV latency and demonstrate methods by which the "Shock and Kill" strategy may be improved for HIV eradication. First, two RNA-Seq studies of models of HIV latency are presented (Chapters 2 and 3). Through host transcriptome analysis in the "Bosque and Planelles TCM model of HIV latency", it was demonstrated that host gene expression was reflective of the response to active instead of latent infection. It was shown that fully infectious virus was reconstituted through recombination between the deficient HIV construct and pLET-LAI plasmid. Analysis of host and virus transcripts in the refined "Martins et al." model, demonstrated it represented a form of latency. Furthermore, genes relating to p53 signaling were dysregulated and inhibition of p53 resulted in reduction of the total percentage of latently infected cells. Next, the effect of the histone deacetylase inhibitor SAHA, a latency reversing agent, was analyzed (Chapters 4 and 5). This revealed SAHA dysregulated genes in a way that was counterproductive to HIV reactivation. Furthermore, analysis of HERV elements dysregulated by SAHA demonstrated elements from multiple families were upregulated with a specificity for those from LTR12. In summary, this work demonstrated the importance of transcriptomic and proteomic analysis to the study of HIV latency models, led to a revision of the first model, and the importance of the p53 signaling in latency for the second. This work also demonstrated the effect of SAHA treatment on CD4 T-cells, which may potentially explain why SAHA has proven somewhat ineffective in clinical trials to reactivate HIV from latency

Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

BACKGROUND: Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. METHODS: We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N?=?9358) and in children aged 1-11 years (12 cohorts, N?=?3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. RESULTS: We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values?<?0.05) at two CpGs at birth (winter-born) and four in the childhood (summer-born) analyses when compared to children born in autumn. Furthermore, we identified twenty-six differentially methylated regions (DMR) at birth (winter-born: 8, spring-born: 15, summer-born: 3) and thirty-two in childhood (winter-born: 12, spring and summer: 10 each) meta-analyses with few overlapping DMRs between the birth seasons or the two time points. The DMRs were associated with genes of known functions in tumorigenesis, psychiatric/neurological disorders, inflammation, or immunity, amongst others. Latitude-stratified meta-analyses [higher (=?50°N), lower (<?50°N, northern hemisphere only)] revealed differences in associations between birth season and DNAm by birth latitude. DMR analysis implicated genes with previously reported links to schizophrenia (LAX1), skin disorders (PSORS1C, LTB4R), and airway inflammation including asthma (LTB4R), present only at birth in the higher latitudes (=?50°N). CONCLUSIONS: In this large epigenome-wide meta-analysis study, we provide evidence for (i) associations between DNAm and season of birth that are unique for the seasons of the year (temporal effect) and (ii) latitude-dependent variations in the seasonal associations (spatial effect). DNAm could play a role in the molecular mechanisms underlying the effect of birth season on adult health outcomes

Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

BACKGROUND: Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear.METHODS: We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1-11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points.RESULTS: We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values &lt; 0.05) at two CpGs at birth (winter-born) and four in the childhood (summer-born) analyses when compared to children born in autumn. Furthermore, we identified twenty-six differentially methylated regions (DMR) at birth (winter-born: 8, spring-born: 15, summer-born: 3) and thirty-two in childhood (winter-born: 12, spring and summer: 10 each) meta-analyses with few overlapping DMRs between the birth seasons or the two time points. The DMRs were associated with genes of known functions in tumorigenesis, psychiatric/neurological disorders, inflammation, or immunity, amongst others. Latitude-stratified meta-analyses [higher (≥ 50°N), lower (&lt; 50°N, northern hemisphere only)] revealed differences in associations between birth season and DNAm by birth latitude. DMR analysis implicated genes with previously reported links to schizophrenia (LAX1), skin disorders (PSORS1C, LTB4R), and airway inflammation including asthma (LTB4R), present only at birth in the higher latitudes (≥ 50°N).CONCLUSIONS: In this large epigenome-wide meta-analysis study, we provide evidence for (i) associations between DNAm and season of birth that are unique for the seasons of the year (temporal effect) and (ii) latitude-dependent variations in the seasonal associations (spatial effect). DNAm could play a role in the molecular mechanisms underlying the effect of birth season on adult health outcomes.</p

Additional file 8 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 8. Table S8: “Genes mapped to DMR identified in the childhood samples of children born in the latitude ≥ 50°N and some examples of their associations with biological functions”. Provides examples of known functional associations of genes mapped to significant differentially methylated regions identified in this study

Additional file 9 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 9. “Trait Enrichment Analysis (EWAS Atlas)”. Trait names and the odds ratios for their association with CpG sites for all the models meta-analysed in this study

Additional file 6 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 6. Table S5: “Genes mapped to DMP/DMR identified in at-birth samples of babies born in the latitude ≥ 50°N and some examples of their associations with biological functions”. Provides examples of known functional associations of genes mapped to significant CpG sites or differentially methylated regions identified in this study

Additional file 5 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 5. Table S4: “Direction of differential methylation of CpGs in DMRs of the at-birth and childhood analyses (preliminary analysis”)

Additional file 4 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 4. Table S2: “Models used in this meta-analysis study”. Inflation (lambda) and bias information of the models. Table S3: “Comparison of magnitude and direction of the FDR-significant DNA methylation signals identified in the at-birth and childhood meta-analyses”

Additional file 7 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 7. Table S6: “Season of birth-associated differentially methylated regions (DMRs) at birth in babies born in latitudes < 50°N”. Differentially methylated regions and mapped genes identified in the at-birth samples of babies born in latitudes < 50°N (lower latitude subgroup analysis). Table S7: “Season of birth associated with differentially methylated regions (DMRs) in children born in latitudes ≥ 50°N”

Additional file 3 of Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude

Additional file 3. “PACE analysis plan for Season of Birth and methylation profiles in children (6 June 2018)”. Analysis plan that was circulated amongst the participant cohorts for the Season of Birth study