Single-nucleus analysis of intact spinal cord and spared tissue after complete injury in rhesus monkey
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PROVIDER: PRJNA821161 | ENA |
REPOSITORIES: ENA
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Project description:The lumbar spinal cord is fundamental for hindlimb function and serves as spared tissue after spinal cord injury (SCI). However, our knowledge about cellular heterogeneity of the intact spinal cord and spared tissues is still scarce especially in primates. Here, we used single-nucleus RNA sequencing analysis in rhesus monkey to characterize the cellular heterogeneity of the spinal cord and profile the dynamic changes of cells in spared tissues after complete thoracic SCI. We found that rhesus monkey and mice shared a highly conserved pattern of cellular constitution but with divergent gene expression. After SCI, the cellular characteristics of spared tissue changed permanently and showed a regionally diverse response. We identified an emerging oligodendrocyte subtype that responded to interferon and a new permanently activated microglia subtype that was responsible for eliminating cell debris. Overall, our findings revealed dynamic changes of cells in spared tissue, providing comprehensive insights for SCI repair.
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Project description:Spinal cord injury (SCI) leads to severe sensory and motor dysfunction below the lesion. However, the cellular heterogeneity and dynamic responses in different regions below the lesion remain to be elusive. Here, we used single-cell transcriptomics to characterize the region-related cellular responses in complete thoracic SCI of rhesus monkeys from the acute to the chronic phase. We found that cells in the distal lumbar tissue were severely affected and generated a degenerative microenvironment dominated by sustained activation of phagocytic microglia, increased inhibitory interneurons, and demyelinated oligodendrocytes after SCI. Furthermore, we revealed scaffold implantation in the injury sites could improve the microenvironment of injury sites by regulating glial cells and fibroblasts, and remodel the spared lumbar tissues by decreasing the inhibitory neurons and enhancing phagocytosis and remyelination. Our findings provide comprehensive pathological insights into the spared distal tissues and proximal tissues after SCI, highlighting the importance of scaffold-based treatment strategies for targeting heterogeneous microenvironments.
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Project description:Embryonic stem cells (ESCs) may be able to cure or alleviate the symptoms of various degenerative diseases. However, unresolved issues regarding apoptosis, maintaining function and tumor formation mean a prudent approach should be taken towards advancing ESCs into human clinical trials. The rhesus monkey provides the ideal model organism for developing strategies to prevent immune rejection and test the feasibility, safety and efficacy of ESC-based medical treatments. Transcriptional profiling of rhesus ESCs provides a foundation for future pre-clinical ESC research using non-human primates as the model organism. In this research we use microarray, immunocytochemistry, real-time and standard RT-PCR to characterize and transcriptionally profile rhesus monkey embryonic stem cells. We identify 367 rhesus monkey stemness genes, we demonstrate the high level (>85%) of conservation of rhesus monkey stemness gene expression across five different rhesus monkey embryonic stem cell lines, we demonstrate that rhesus monkey ESC lines maintain a pluripotent undifferentiated state over a wide range of Pou5f1 (Oct-4) expression levels and we compare rhesus monkey, human and murine stemness genes to identify the key mammalian stemness genes. The supplementary tables list the genes that have been upregulated in each undifferentiated rhesus monkey embryonic stem cell line (GSM99998, GSM99999,GSM100000, GSM100001, GSM100002, GSM99965, GSM99966) in comparison analysis with the pooled differentiated embryonic stem cells (GSM99840). Supplemental Table 1 contains the comparison analysis for all 52,865 probe sets on the rhesus monkey gene chip, Supplemental Table 2 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the ORMES-6 biological replicates, Supplemental Table 3 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the pooled differentiated EBs and Supplemental Tables 4-8 represent genes that were significantly upregulated in ORMES 6A, 7, 9, 10 and 13 respectively. Supplemental Table 9 contains the RT-PCR primers used in this project. Keywords: Rhesus monkey embryonic stem cell microarray
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Project description:Rhesus Monkey is one of the important primate models widely used in the fields of disease mechanism study, pre-clinical test in drug discovery and molecular evolution. However, the majority of rhesus gene annotations were putatively mapped from human genome, with only 10% supported by rhesus EST data.So, to better study the transcriptome, paired-end, strand-specific, poly(A)-positive RNA-Seq were performed in 5 rhesus monkey tissues. 5 tissue samples examined: prefrontal cortex, liver, skeletal muscle, adipose, testis
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2007-08-29 | GSE7748 | GEO
Project description:We generated ChIP-Seq (H3K4me1, H3K4me3 and H3K27ac) data for term Rhesus monkey placenta. Together with RNA-Seq and epigenomic data generated for placentas of human and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.
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Project description:Induced pluripotent stem (iPS) cells can be generated from somatic cells by transduction with several transcription factors in both mouse and human. However, direct reprogramming in other species has not been reported. Here, we established an efficient method to generate monkey iPS cells from fibroblasts by retrovirus-mediated introduction of the four monkey transcription factors OCT4 (POU5F1), SOX2, KLF4, and c-MYC. The monkey iPS cells displayed ES-like morphology, expressed ES cell-marker genes, shared similar global gene profiles and methylation status in the OCT4 promoter to those of monkey ES cells, and possessed the ability to differentiate into three germ layers in vitro and in vivo. Our results suggest that the mechanism of direct reprogramming is conserved among species. The efficient generation of monkey iPS cells will allow investigation of the feasibility of therapeutic cloning in primate model with various diseases. Keywords: Induced pluripotent stem, iPS, Rhesus monkey We analysed each sample (Rhesus monkey fibroblast, embryonic stem cell (ES) and induced pluripotent stem cell (iPS)) for three replications and sought to see high similarty between iPS and ES.
2010-05-15 | E-GEOD-13146 | biostudies-arrayexpress