Analysis of microRNA expression profile by small RNA sequencing in Down syndrome fetuses

Abstract

Down syndrome (DS) is caused by trisomy of human chromosome 21 (Hsa21) and is associated with numerous deleterious phenotypes, including cognitive impairment, childhood leukemia and immune defects. Five Hsa21‑derived microRNAs (i.e., hsa-miR-99a, let-7c, miR-125b-2, miR-155 and miR-802) are involved in variable phenotypes of DS. However, the changes involved in the genome-wide microRNA expression of DS fetuses under the influence of trisomy 21 have yet to be determined. To investigate the expression characteristic of microRNAs during the development of DS fetuses and identify whether another microRNA gene resides in the Hsa21, Illumina high-throughput sequencing technology was employed to comprehensively characterize the microRNA expression profiles of the DS and normal fetal cord blood mononuclear cells (CBMCs). In total, 149 of 395 identified microRNAs were significantly differentially expressed (fold change >2.0 and P<0.001) and 2 of 181 candidate novel microRNAs were identified as residing within the ̔DS critical region̓ of human chromosome 21 (chr21q22.2‑22.3). Additionally, 7 of 14 Hsa21-derived microRNAs were detected, although not all seven were overexpressed in DS CBMCs compared with the control. Gene ontology enrichment analyses revealed that a set of abnormally expressed microRNAs were involved in the regulation of transcription, gene expression, cellular biosynthetic process and nucleic acid metabolic process. Significantly, most of the mRNA targets in these categories were associated with immune modulation (i.e., SOD1, MXD4, PBX1, BCLAF1 and FOXO1). Findings of the present study provided a considerable insight into understanding the expression characteristic of microRNAs in the DS fetal CBMCs. To the best of our knowledge, this is the first study to examine genome-wide microRNA expression profiles in the DS fetus. Differentially expressed microRNAs may be involved in hemopoietic abnormalities and the immune defects of DS fetuses and newborns.

MicroRNAs as potential biomarkers for noninvasive detection of fetal trisomy 21

“…Therefore, analysis of the genome-wide expression of miRNAs is indispensable to understanding their molecular regulating mechanisms. Recently, genome-wide miRNAs expression profiles of the T21 fetal cord blood mononuclear cells were reported, and found six up-regulated and 143 down-regulated miRNAs to be differentially expressed in T21 [8]. Among them, four hsa21-derived miRNAs including mir-99a, let-7c, mir-125b-2, and mir-155 were down-regulated in T21, while mir-802, mir-3648, and mir-3687 were up-regulated in T21.…”

“…Many studies of miRNAs in T21 have been reported [6][7][8][22][23][24], with most studies focused the correlation of hsa21-derived miRNAs with T21 phenotypes. Recently, Kotlabova et al reported hsa21-derived miRNAs in plasma samples from pregnancies bearing euploid and T21 fetuses [24].…”

“…In previous studies, hsa21-derived miRNAs have been proven to be correlated with the complex and variable phenotypes of T21 [6][7][8][21][22][23][24]. However, changes in miRNA expression that affect phenotypes can occur in the entire genome, i.e., an miRNA can potentially regulate a large number of protein-coding genes, and multiple miRNAs can regulate a single target gene [25].…”

“…Therefore, the genome-wide expression patterns of miRNAs must be investigated to identify miRNAs that are differentially expressed in T21. Moreover, miRNAs have disease specific characteristics [4][5][6][7][8][9][10]21] and exhibit different expression pattern according to tissue type and the presence or absence of pregnancy [12,26,27]. Therefore, all of disease, tissue, and pregnancyspecific characteristics having miRNAs should be considered for identification of miRNAs as potential biomarkers for NIPT of fetal diseases using maternal blood.…”

“…They have emerged as key posttranscriptional regulators that inhibit gene expression by perfect complementary binding to target mRNA degradation or imperfect binding in the 3′ untranslated region (UTR) to inhibit translation [2,3]. Moreover, abnormal miRNA expression has been reported to be involved in the occurrence and development of various diseases, such as cancer, cardiovascular disease, mental retardation, fetal growth restriction, and trisomy 21 (T21) [4][5][6][7][8][9][10].…”