INTRODUCTION: Amniotic Epithelial Cells (AEC) represent an emerging source in stem cells. However, AEC regenerative potential can be largely affected by the in vitro amplification. In order to standardize the AECs-based regenerative protocols, an advanced NGS approach of ovine cell characterization has been used to compare the transcriptome of 3 passages amplified oAEC obtained under standardized conditions (CTR) or by adding progesterone (P4) in order to preserve the epithelial native phenotype during expansion. METHODS: The transcriptome profile has been performed by RNA sequencing (NextSeq500 Illumina platform). Differentially Expressed Genes (DEGs), identified using Tophat2-Cufflink2 pipeline [2], were by in house developed scripts to obtain enriched Gene Ontology (GO) terms and pathways. RESULTS & DISCUSSION: The transcriptional landscape profiles showed 495 and 753 DEGs in CTR and P4, respectively, belonging to 3 main enriched GO-modules. In order to identify the mechanisms controlling biochemical pathways, we firstly derived a gene-gene network from DEGs. The networks were analyzed to detect both local and general hubs, which represent most connected nodes. They were compared to the bottleneck nodes that play a key role in controlling information throughout the networks. Integrating expression levels into the so obtained controlling structure (hubs, bottlenecks, DEGs), we identified a pattern of genes (listed in Figure1) characterizing the two oAECs transcriptomes. CONCLUSIONS: For the first time, we described the whole transcriptome portrait of oAECs by using RNA-seq. The results clearly defined most biological processes and molecular pathways having a key-role in the two morphologically different oAECs. We, also, provided useful information to understand essential mechanisms involved in tissue regeneration. This approach can suggest a research framework in sheep, considered a consolidated model organism in regenerative medicine [3] filling lacking of information about the ovine genome and gene sequences.
Ovine amniotic epithelial cells transcriptome portrait
Di Lollo V.;Bernabó N.;Canciello A.;Russo V.;Mattioli M.;Barboni B.
2019-01-01
Abstract
INTRODUCTION: Amniotic Epithelial Cells (AEC) represent an emerging source in stem cells. However, AEC regenerative potential can be largely affected by the in vitro amplification. In order to standardize the AECs-based regenerative protocols, an advanced NGS approach of ovine cell characterization has been used to compare the transcriptome of 3 passages amplified oAEC obtained under standardized conditions (CTR) or by adding progesterone (P4) in order to preserve the epithelial native phenotype during expansion. METHODS: The transcriptome profile has been performed by RNA sequencing (NextSeq500 Illumina platform). Differentially Expressed Genes (DEGs), identified using Tophat2-Cufflink2 pipeline [2], were by in house developed scripts to obtain enriched Gene Ontology (GO) terms and pathways. RESULTS & DISCUSSION: The transcriptional landscape profiles showed 495 and 753 DEGs in CTR and P4, respectively, belonging to 3 main enriched GO-modules. In order to identify the mechanisms controlling biochemical pathways, we firstly derived a gene-gene network from DEGs. The networks were analyzed to detect both local and general hubs, which represent most connected nodes. They were compared to the bottleneck nodes that play a key role in controlling information throughout the networks. Integrating expression levels into the so obtained controlling structure (hubs, bottlenecks, DEGs), we identified a pattern of genes (listed in Figure1) characterizing the two oAECs transcriptomes. CONCLUSIONS: For the first time, we described the whole transcriptome portrait of oAECs by using RNA-seq. The results clearly defined most biological processes and molecular pathways having a key-role in the two morphologically different oAECs. We, also, provided useful information to understand essential mechanisms involved in tissue regeneration. This approach can suggest a research framework in sheep, considered a consolidated model organism in regenerative medicine [3] filling lacking of information about the ovine genome and gene sequences.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
