Genome-wide differential expression analysis of cell-free microRNAs in amniotic fluid of fetus with Down syndrome

Background: The biological pathways related to the phenotypic development of trisomy 21 (Down syndrome, DS) have not been fully clarified. Cell-free microRNAs (miRNAs) in amniotic fluid are a valuable source of biological information for better understanding the pathogenesis of DS.Methods: In the present study, small RNA sequencing was used to detect the genome-wide expression profile of cell-free miRNAs in amniotic fluid of standard DS versus normal karyotype (each n = 3). Unsupervised hierar-chical clustering, differential expression analysis and KEGG pathway enrichment were performed using bioin-formatics online tools. The differentially detected miRNAs were selectively validated by quantitative RT-PCR in another case-control cohort (each n = 6).Results: A total of 75 miRNAs were detected in the amniotic fluid supernatants of the two study groups. Compared with normal karyotype, 33 miRNAs are significantly differentially expressed in DS, among which 9 are upre-gulated and 24 are downregulated. There are 329 coding genes predicted to be targeted by the differential miRNAs. The predicted target genes are mainly involved in cancer pathways, Cushing's syndrome, P13K-Akt, MAPK and AMPK signaling pathways, longevity regulating pathway and cellular senescence. Validation assay shows that miR-22-3p is significantly downregulated in the DS group compared to the normal group (Student's t -test, P < 0.05).Conclusion: Our results provide new insights into the differential expression of cell-free miRNAs in amniotic fluid of fetus with Down syndrome.

Automated summary

This study used small RNA sequencing to detect the expression profile of cell-free miRNAs in amniotic fluid of Down syndrome (DS) and normal karyotype. The findings revealed 33 differentially expressed miRNAs in DS, including 9 upregulated and 24 downregulated miRNAs. These differentially expressed miRNAs were predicted to target genes involved in various pathways such as cancer, Cushing's syndrome, P13K-Akt, MAPK and AMPK signaling pathways, longevity regulating pathway, and cellular senescence. Furthermore, validation assays confirmed the significant downregulation of miR-22-3p in the DS group. These results provide new insights into the differential expression of cell-free miRNAs in amniotic fluid of DS fetuses.