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Transcriptome sequencing analysis of Mesenchymal Stem Cells derived from the Human Placenta and Umbilical Cord

ABSTRACT: Based on transcriptome sequencing analysis, umbilical cord mesenchymal stem cells and placental mesenchymal stem cells share a total of 10529 common genes (called hpcCS consensus genes), which are umbilical cord-placental-consistent DEGs. The UC-MSC-specific region (referred to as the UC-specific gene) has most of the DEG (383 genes). The AM-MSC specific region (referred to as the AM specific gene) has 311 DEGs. The CM-MSC specific region (referred to as the CM specific gene) has 182 DEGs. The CV-MSC specific region (referred to as a CV-specific gene) has 169 DEGs. These results suggest that hMSCs from the umbilical cord and placenta have similar gene expression patterns, but have their own specific genes. The specific genes are not only involved in cell cycle, cell division, cell death, cell growth and development, transcriptional regulation, DNA repair, DNA. Replication plays an important role in chromosomal stability and is also involved in the movement of cellular or subcellular components, cellular communication and cell projection tissue, cytokine secretion and hormonal metabolism. The results of transcriptome sequencing analysis explain to some extent the differences in the biological characteristics of MSCs from different sources at the gene level.

ORGANISM(S): Homo sapiens

PROVIDER: GSE131355 | GEO | 2019/05/17

REPOSITORIES: GEO

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Project description:BACKGROUND: Ischemia/reperfusion injury (IRI) is the leading cause of acute kidney injury (AKI). The current standard of care focuses on supporting kidney function, stating the need for more efficient and targeted therapies to enhance repair. Mesenchymal Stromal Cells (MSCs) and their secretome, either as conditioned medium (CM) or extracellular vesicles (EVs), have emerged as promising options for regenerative therapy, however, their full potential in treating AKI remains unknown.METHODS: In this study, we employed an in vitro model of chemically-induced ischemia using antimycin A combined with 2-deoxy-D-glucose to induce ischemic injury in proximal tubule epithelial cells. Afterwards, we evaluated the effects of MSC secretome, CM or EVs obtained from adipose tissue, bone marrow and umbilical cord, on ameliorating the detrimental effects of ischemia. To assess the damage and treatment outcomes, we analyzed cell morphology, mitochondrial health parameters (mitochondrial activity, ATP production, mass and membrane potential) and overall cell metabolism by metabolomics.RESULTS: Our findings show that ischemic injury caused cytoskeletal changes confirmed by disruption of the F-actin network, energetic imbalance as revealed by a 50% decrease in the oxygen consumption rate, increased oxidative stress, mitochondrial dysfunction and reduced cell metabolism. Upon treatment with MSC secretome, the morphological derangements were partly restored and ATP production increased by 40-50%, with umbilical cord-derived EVs being most effective. Furthermore, MSC treatment led to phenotype restoration as indicated by an increase in cell bioenergetics, including increased levels of glycolysis intermediates, as well as an accumulation of antioxidant metabolites.CONCLUSION: Our in vitro model effectively replicated the in vivo-like morphological and molecular changes observed during ischemic injury. Additionally, treatment with MSC secretome ameliorated proximal tubule damage, highlighting its potential as a viable therapeutic option for targeting AKI.

Project description:Mesenchymal stem cells (MSC) are multipotent cells which can be obtained from several adult and fetal tissues including human umbilical cord units. We have recently shown that umbilical cord tissue (UC) is richer in MSC than umbilical cord blood (UCB) but their origin and characteristics in blood as compared to the cord remains unknown. Here we compared, for the first time, the exonic protein-coding and intronic noncoding RNA (ncRNA) expression profiles of MSC from match-paired UC and UCB samples, harvested from the same donors, processed simultaneously and under the same culture conditions. The patterns of intronic ncRNA expression in MSC from UC and UCB paired units were highly similar, indicative of their common donor origin. The respective exonic protein-coding transcript expression profiles, however, were significantly different. Hierarchical clustering based on protein-coding expression similarities grouped MSC according to their tissue location rather than original donor. Genes related to systems development, osteogenesis and immune system were expressed at higher levels in UCB, whereas genes related to cell adhesion, morphogenesis, secretion, angiogenesis and neurogenesis were more expressed in UC cells. These molecular differences verified in tissue-specific MSC gene expression may reflect functional activities influenced by distinct niches and should be considered when developing clinical protocols involving MSC from different sources. In addition, these findings reinforce our previous suggestion on the importance of banking the whole umbilical cord unit for research or future therapeutic use. Cy5- and Cy3-labeled cRNAs were obtained using 300 ng total RNA as template for amplification of poly(A) RNA by T7-RNA polymerase with the Agilent Low RNA Input Fluorescent Linear Amplification kit. The T7-polymerase amplified cRNA labeling approach advantageously replaces the reverse-transcriptase cDNA labeling used in early microarray experiments, because T7-RNA polymerase labeling of cRNA preserves the strand orientation of the original mRNA template. Reverse-transcriptase labeling can eventually generate a complementary cDNA second strand and cause artifactual labeling of a target with the opposite sense to that of the original message. Hybridization of 825 ng of Cy3- or Cy5-labeled RNA (dye swap technical replicate) from each UC sample with its paired UCB sample was performed with Agilent in situ Hybridization kit-plus, as recommended by the manufacturer, using a total of 4 intron-exon 44K expression oligoarrays. This array comprises a total of 13,699 exonic probes representing different protein-coding genes, along with custom-designed intronic probes for the antisense or sense strand. Slides were washed and processed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Version 5.5) and scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Fluorescence intensities were extracted using Feature Extraction (FE) software (version 9.0; Agilent). A gene was considered expressed if its probe intensity was significantly higher than the local background intensity, as calculated by the FE software. Then, the software applies local background subtraction and corrects for unequal dye incorporation using the default LOWESS (locally weighted linear regression) method.

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Transcriptome sequencing analysis of Mesenchymal Stem Cells derived from the Human Placenta and Umbilical Cord

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