PERFLUOROOCTANOIC ACID C8.HF1. 5O2 Pub. Chem.Identification of novel HIV 1 dependency factors in primary CCR4CCR6Th.Identification of a molecular signature associated with HIV permissiveness in Th.We previously demonstrated that subsets of memory CD4 T cells enriched in Th.Th. 1Th. 17 cells are highly permissive to R5 and X4 HIV infection Th.X4 HIV only while Th.R5 and X4 HIV at relatively low levels 3.Except for Th. 2 cells that lack CCR5 expression, differences in HIV replication between Th.Th. 1 are not explained by differential expression of CCR5 or CXCR4 3.To identify HIV dependency factors HDFs in primary Th.CD4 T cell subsets enriched in Th.Th. 2, Th. 17, and Th.Pma Activation Of Jurkat Cells Definition' title='Pma Activation Of Jurkat Cells Definition' />CD6 is mostly expressed by mature T cells, and is also distinctively detected in medullary thymocytes 1, 9, 10.It is first perceived in human embryonic thymocytes.Unspecific stimulation with PMA ionomycin vs.PHA for intracellular cytokine staining of T cells.Th. 17 cells sorted by FACS and stimulated by CD3CD2.Abs, as previously described 3.These subsets were identified based on the differential expression of the well established surface markers CCR4, CCR6, and CXCR3, as previously described 1.Fig. 1a Th. 1 CXCR3CCR4CCR6, Th.CXCR3CCR4CCR6, Th.CXCR3CCR4CCR6, and Th.Th. 17 CXCR3CCR4CCR6.Total m. RNA extracted from each subset was hybridized onto the Illumina Human.Pma Activation Of Jurkat Cells Definition' title='Pma Activation Of Jurkat Cells Definition' />HT 1.Expression Bead. Chip GEO access number GSE7.Th. 17 compared to Th.Th. 2, or Th. 1Th.FC expression ratios cut off 1.Additional file 1 Table S1 Additional file 2 Table S2.The most robust differences in gene expression were observed between Th.Th. 1 Fig. 1b with 1.FC cut off 1. 3 Additional file 1 Table S1 Additional file 2 Table S2 Additional file 3 Figure S1a.To orient our genome wide search for HDFs, we investigated whether HIV permissiveness in Th.Th. 1 was modulated at entry as opposed to post entry levels.With this in mind, HIV DNA integration was quantified in cells exposed to replication competent R5 HIV NL4.Ba. L GFP or single round VSV G pseudotyped HIV VSVG HIV GFP entering cells by endocytosis independently of CD4 and co receptors 6.Results in Fig. 1c, d reveal superior HIV DNA integration in Th.Th. 1 upon exposure to both NL4.BAL GFP and VSVG HIV GFP strains this indicates that post entry mechanisms contribute to HIV permissiveness in Th.This evidence led to the prediction that transcripts enriched in Th.Th. 1 include HDFs acting at the post entry level.Fig. 1. Identification of a molecular signature associated with HIV permissiveness in CCR4CCR6 Th.Total CD4 T cells were isolated from PBMCs of HIV uninfected subjects by negative selection using magnetic beads.Cells were labeled with a cocktail of CD4.RA, CD8, CD1. 9, CD5.CCR4, CCR6, and CXCR3 Abs.Shown is the gating strategy used for the FACS sorting of the following four memory CD4.RA CD4 subsets lacking CD8, CD1.CD5. 6 expression CXCR3CCR4CCR6 Th.CXCR3CCR4CCR6 Th.CXCR3CCR4CCR6 Th.CXCR3CCR4CCR6 Th.Th. 17. Shown are results from one donor representative of results generated with cells from 1.HIV uninfected donors.Highly pure matched Th.Th. 2, Th. 17, and Th.Th. 17 subsets were sorted by FACS n 5 and stimulated via CD3CD2.Total RNA was reverse transcribed into c.DNA and hybridized onto the Human HT 1.Expression Bead. Chip Illumina for genome wide transcriptional profiling.One way ANOVA analysis was performed to identify differentially expressed genes based on p value lt 0.FC, cut off 1. 3.Shown are volcano plots for all probes in each linear model with the FC on the x axis and the negative logarithm of the adjusted p values adjusted for false discovery rate FDR on the y axis.Redgreen color code is based on the 5 FDR threshold.Cell subsets were stimulated via CD3CD2.NL4. 3. BAL GFP c and single round VSVG HIV GFP strains d.Shown is real time quantification of HIV DNA integration at day three post infection mean SD of triplicate wells in matched subsets isolated from n 3 different donors.Shown are the top 5.Th. 17 versus Th.ES from a gene set variation analysis GSVA for pathways differentially expressed between Th.Th. 17 cells with a FDR inferior to 1 .Transcriptional profiles in a, b, and e were generated with cells stimulated via CD3CD2.HIVTop differentially expressed transcripts adj.FC 2. 5 in Th. Th.Th. IL 2. 2, CCR6, KLRB1, IL 1.F, CCL2. 0, RORC, IL 2.PPARG and Th. 1 i.IFN, CCL5, CCL4. L2, CCL3, CCL3.L3, and CXCR3 this provides a first validation for our transcriptional studies Tables 1, 2.The list of top up regulated genes also included transcripts that likely represent new functional markers for Th.PTPN1. 3 APO 1CD9.Fas Associated Phosphatase 6.CHN1, GPR5. 6, LGMN, CTSH, KLF2, CACNA1l, RARRES3, Ly.TNFSF1. 3B, NFL2, PI1.MXD4, HPGD, SNX2.P2. RY5, ZNF3. 81, LIME1, MAP3.K4, CD9. 6, GPR1.GLIPR1 Table 1. Importantly, NFIL3, a documented inhibitor of Th.Th. 17 versus Th.Table 2 this suggests a conserved mechanism involved in the regulation of Th.Table 1. Top up regulated transcripts in CCR4CCR6 Th.CXCR3CCR6 Th. 1Table 2.Top down regulated transcripts in CCR4CCR6 Th.CXCR3CCR6 Th. 1Gene Set Variation Analysis GSVA of differentially expressed genes p lt 0.FC cut off 1. 3 identified canonical pathways C2 enriched in Th.Th. 1, including those linked to circadian repression of expression by REV ERB, nuclear receptor transcription, T helper differentiation, CSK signaling, TCR signaling, Ras, anthrax, IL 7 signaling, phosphorylation of CD3 and TCR zeta, PTEN, ABCA transporters in lipid homeostasis, Rho.A, longevity pathway, MEF2.D signaling, the role of Nef in HIV replication, and TNF signaling Fig.The GSVA also identified pathways down regulated in Th.Th. 1, including pathways linked to metal ion SLC transporters, zinc transporters, STEM, glucose transport, extension of telomeres, protein synthesis as well as transcription initiation and termination Additional file 3 Figure S1b Additional file 4 Table S3.These results reveal overrepresentation of specific transcripts and cellular functions in Th.Th. 1, with pathways enriched in Th. Capa De Trabalho Abnt Baixar Musica . Th. 17 polarization and HIV permissiveness.Consistent with the GSVA results Fig.Gene Ontology classification of differentially expressed genes p lt 0.FC cut off 1. 3 revealed transcripts related to different biological functions including cytokineschemokines, TCR, and transcription regulators Fig.In the cytokineschemokines category, genes up regulated in Th.Th. 1 included known Th.IL 2. 2, CCL2. 0, IL 2.CCR6, as well as TNFSF1.TNF superfamily, TNFRSF2.TNF receptor superfamily, TNFSF1.B, IL 1. 0RB, IL 1.RA, CLCF1 cardiotrophin like cytokine factor, IL 1.IL 1. 7RA, IL 7. R, and TGFBR2 TGF receptor transcripts Fig.Genes up regulated in Th.Th. 17 included the Th.CXCR3, IFNG, several CCR5 binding ckemokines CCL5, CCL4.L2, CCL3. L1, CCL3.L3, CCL3, and also transcripts for LTA lymphotoxin, IL 9, IL 3, CCL1.IL 5, IL 4, XCL1, TNFSF9, TNFSF1.CXCR5, TNFRSF8, IL 6, CSF1.R, LIF, IL 2. RA, IL3.RA, and IL1. 5RA Fig.Despite the fact that IL 4 and IL 5 transcripts were found up regulated in Th.Th. 17 cells, levels of their expression in Th.Th. 2 cells were significantly lower data not shown.Such false positive signals are expected in high throughput screenings and therefore the requirement for subsequent validations for any important hit is mandatory.Transcripts related to the TCR signaling cascade such as IKBKB inhibitor of NF B kinase beta 6.PAK2 p. 21 activated kinase 2 6.CD3. G, TRAT1 T cell receptor associated transmembrane adaptor 1, PTEN phosphatase and tensin homolog 6.Lck 6. 7, FYB, PAG1, MALT1 6.PIK3. CA, PRKCQ, CD2.CD3, ZAP7. 0 7. EVL, INPP5.D, PIK3. R1, WAS, RIPK2, PTPRC, PLCG1, ITK, CARD1.CD3. D, and NCK1, were selectively enriched in Th.Th. 1 Fig. 2b. Of note, PAK2 6.ZAP7. 0 7. 1 were previously linked to efficient HIV replication in T cells.Finally, major differences between Th.Th. 1 were observed for the expression of Transcription regulators.In addition to known transcription factors involved in the regulation of Th.RORA, RORC, RUNX1 7.Th. 1 Eomes 7. IRF1, STAT1, IRF3, KLF2, E2.F2, IRF9, SMAD3, ARNTL, PPARG, and FOXO3 were found up regulated, while IRF4, IRF8, MYC, and Notch.Th. 17 versus Th.Fig. 2c. Fig. 2.Gene Ontology classification of differentially expressed genes in CCR4CCR6 Th.CXCR3CCR6 Th. 1 cells.Shown are heatmaps of differentially expressed genes p lt 0.
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