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Evaluation of global gene expression in regenerate tissues during Masquelet treatment.

ABSTRACT: The Masquelet induced-membrane (IM) technique is indicated for large segmental bone defects. Attributes of the IM and local milieu that contribute to graft-to-bone union are unknown. Using a rat model, we compared global gene expression profiles in critically sized femoral osteotomies managed using a cement spacer as per Masquelet to those left empty. At the end of the experiment, IM and bone adjacent to the spacer were collected from the Masquelet side. Nonunion tissue in the defect and bone next to the empty defect were collected from the contralateral side. Tissues were subjected to RNA isolation, sequencing, and differential expression analysis. Cell type enrichment analysis suggested the IM and the bone next to the polymethylmethacrylate (PMMA) spacer were comparatively enriched for osteoblastic genes. The nonunion environment was comparatively enriched for innate and adaptive immune cell markers, but only macrophages were evident in the Masquelet context. iPathwayGuide was utilized to identify cell signaling pathways and protein interaction networks enriched in the Masquelet environment. For IM vs nonunion false-discovery rate correction of P values rendered overall pathway differences nonsignificant, and so only protein interaction networks are presented. For the bone comparison, substantial enrichment of pathways and networks known to contribute to osteogenic mechanisms was revealed. Our results suggest that the PMMA spacer affects the cut bone ends that are in contact with it and at the same time induces the foreign body reaction and formation of the IM. B cells in the empty defect suggest a chronic inflammatory response to a large segmental osteotomy.

SUBMITTER: Gohel N

PROVIDER: S-EPMC7494657 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS:To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. CONCLUSION:A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.

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Evaluation of global gene expression in regenerate tissues during Masquelet treatment.

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