Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long‐SAGE)

Abstract

Background Neural tube defects (NTDs) are common human birth defects with a complex etiology. To develop a comprehensive knowledge of the genes expressed during normal neurulation, we established transcriptomes from human neural tube fragments during and after neurulation using long Serial Analysis of Gene Expression (long-SAGE). Methods Rostral and caudal neural tubes were dissected from normal human embryos aged between 26 and 32 days of gestation. Tissues from the same region and Carnegie stage were pooled (n>=4) and total RNA extracted to construct four long-SAGE libraries. Tags were mapped using the UniGene Homo sapiens 17 bp tag-to-gene best mapping set. Differentially expressed genes were identified by chi-square or Fisher’s exact test and validation was performed for a subset of those transcripts using in situ hybridization. In silico analyses were performed with BinGO and EXPANDER. Results We observed most genes to be similarly regulated in rostral and caudal regions, but expression profiles differed during and after closure. In silico analysis found similar enrichments in both regions for biological process terms, transcription factor binding and miRNA target motifs. Twelve genes potentially expressing alternate isoforms by region or developmental stage, and the miRNAs miR-339-5p, miR-141/200a, miR-23ab, and miR-129/129-5p, are among several potential candidates identified here for future research. Conclusions Time appears to influence gene expression in the developing central nervous system more than location. These data provide a novel complement to traditional strategies of identifying genes associated with human NTDs, and offer unique insight into the genes associated with normal human neurulation.

Transcriptomic profile analysis of mouse neural tube development by RNA‐Seq

“…So, the DEGs involved in this pathway might help for interpreting the molecular mechanisms of diabetes‐associated NTDs. Compared with the previous study , many canonical signaling pathways, such as Wnt, Shh, Notch and TGF‐beta signaling, and cell adhesion molecules, axon guidance, also involved in human neural tube development, which confirmed the process in human and mouse is similar. In our study, we also found some DEGs enriched in cancer‐related, such as basal cell carcinoma, it indicates that some cancer‐related genes might also play the important role on neural tube development.…”

From sauropsids to mammals and back: New approaches to comparative cortical development

“…Hundreds of genes are differentially expressed between the anterior and posterior poles of the neural tube and correlate with different neurodevelopmental abnormalities with segmental preferences (Krupp et al, 2012). In the brain, transcriptomes from the whole cerebral cortex, and developing neocortical brain compartments (ventricular zone, subventricular zone, and cortical plate, CP), exhibit different sets of transcripts.…”

Neural tube defects, folate, and immune modulation

“…For example, C3aR was recently shown to play an important role in neutrophil mobilization from the bone marrow (Wu et al, ), and so it is not surprising that C3aR is also involved in cell migration of neurons in rat cerebellum (Benard et al, ), and chemotaxis of neural crest cells in Xenopus (Carmona‐Fontaine et al, ). Several studies have investigated gene expression in neural crest populations and revealed a range of immune factors to be expressed in these migratory cell populations, such as interleukin 2 receptor, NFkB2, RelA, genes relating to tumor necrosis factor signaling, and complement factors (Thomas et al, ; Makki and Capecchi, ; Krupp et al, ). The role for each of these factors in neurulation will need to be examined on a case‐by‐case basis.…”