Unknown,Transcriptomics,Genomics,Proteomics

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Differential Gene Expression of Soluble CD8+ T-cell mediated suppression of HIV replication in three older children

ABSTRACT: Goal: To compare the gene expression profiles from pediatric patients with each other, with those reported in adults and in those related to exosomes. Background: Suppression of human immunodeficiency virus (HIV) replication by CD8+ T-cells (CD8 suppression) contributes to survival in adults and children < 1 year. Soluble CD8 suppression can also be seen in some older children with AIDS. The factor responsible, CD8-derived antiviral factor (CAF), acts at the level of HIV RNA transcription. Differential gene expression techniques have been used to define the gene(s) mediating this phenomenon in adults. Recently, CAF has been linked to exosomes secreted by CD8+ T-cells. Objective: To compare the gene expression profiles from pediatric patients with each other, with those reported in adults and in those reportedly related to exosomes. Design/Methods: We used differential gene expression to study 3 older children with HIV infection, 1 who did demonstrate soluble CD-8 suppression and 2 who did not, and compared our results with those reported in 2 previous studies in adults and their relatedness to exosome components secreted by CD8+ T-cells. Results: 18 differentially expressed genes were also seen in 1 adult study (p=0.002, Ï2 test), and 38 such genes (p < 0.0001, Ï2 test) in a second adult study. In addition, two exosome components and some RNAâs related to exosomal proteins were also differentially expressed. Conclusions: In children with HIV infection, we found significant differentially expressed genes that correlated to those previously reported in 2 studies in adults. Our data also lends some support to the recent identification of CAF with exosomes secreted by CD8+ T-cells. Differential gene expression was used to study 3 older children with HIV infection, 1 who did demonstrate soluble CD-8 suppression and 2 who did not, and compared our results with those reported in 2 previous studies in adults and their relatedness to exosome components secreted by CD8+ T-cells. Three vertically-HIV-1-infected adolescent boys were studied. This study was approved by the Childrenâs Memorial Institutional Review Board. After informed consent was obtained, 20 - 40 ml of heparinized peripheral blood was collected in association with regularly scheduled, clinically-indicated blood sampling. Keywords: differential gene expression; soluble CD8 suppression; gene array; pediatric HIV infection; CD8-derived antiviral factor

ORGANISM(S): Homo sapiens

SUBMITTER: Ben Katz

PROVIDER: E-GEOD-23183 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Purpose: Relationship between mesenchymal stem cells (MSCs) and cancer cells became mysterious because of having sufficient evidences regarding both stimulatory and inhibitory role of MSCs to cancer cells. Certainly, there is debate on customary role of MSCs (inhibitory/stimulatory), however, the notable involvement of MSCs in cancer biology is undoubtedly clear. MSCs might support tumor development through immune suppression, epithelial to mesenchymal transition (EMT), angiogenesis, and serving as cancer stromal cells. In contrast, MSCs are also reported to play role in suppression of cancer by downregulating the cancer survival signaling pathways such as Wnt/β-catenin and/or Akt3. Now, it is a rational demand to investigate the mechanism behind these completely contradictory roles of MSCs in cancer biology. Incidentally, cytokines and soluble factors secreted by MSCs have been scrutinized thoroughly and most of the reports with few exceptions concluded that MSCs-secreted cytokines and soluble factors have stimulatory effect in the progression of cancer. While, role of exosomes which is a type of micro-vesicles having 30-200 nm diameters, secreted by all cells, could be up-taken by neighboring cells, containing many important components including RNAs, proteins, DNA and lipids, serving as efficient vehicles for cancer-stromal communication, have been investigated very marginally and deserve to go for intensive investigation. Specially, cell-secreted miRNAs (18-22 nucleotides) are predominantly carried by exosomes and have been focused in recent years for its capacity in post-transcriptional regulation of gene expression through mRNA silencing. Hence, understating the functions of MSCs-derived secretome (particularly exosomes) in cancer is very much important to comprehend the cross-talk between MSCs and cancer cell biology. In this research, next generation sequencing (NGS) was performed for enrichment analysis of miRNAs in hAMSCs-CM derived exosomes. Methods: Exosomal-RNA was isolated from hAMSCs-CM derived exosomes, small RNA libraries were prepared through a series of processes such as adapter ligation, reverse transcription, PCR amplification, and pooled gel purification.Sequence quality was checked by FastQC experiment, unique sequences found for known miRNAs after clustering were verified with miRBase database (www.mirbase.org/) by blast, trimmed read might have considered as miRNA on condition of having 100% identical and whole length sequence of miRNA compare to the ones on miRBase database. Unmatched trimmed read excluded from miRBase were blast to ncRNA database Rfam (http://rfam.sanger.ac.uk/). Unmatched trimmed reads to any of non-miRNA on Rfam database were considered as a potential novel miRNA. Result: The exosomal-RNA sequencing explored that exosomes contains a rich population of miRNAs and many of the obtained miRNAs are reported to have anti-cancer properties through targeting different cancer survival pathways. Conclusion: Outwardly, we outlined that exosomal-miRNA is one of the conceivable reasons behind anti-proliferative effect of MSCs towards cancer cells.

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Differential Gene Expression of Soluble CD8+ T-cell mediated suppression of HIV replication in three older children

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