Identification of New Potential LncRNA Biomarkers in Hirschsprung Disease

Abstract

Hirschsprung disease (HSCR) is a neurocristopathy defined by intestinal aganglionosis due to alterations during the development of the Enteric Nervous System (ENS). A wide spectrum of molecules involved in different signaling pathways and mechanisms have been described in HSCR onset. Among them, epigenetic mechanisms are gaining increasing relevance. In an effort to better understand the epigenetic basis of HSCR, we have performed an analysis for the identification of long non-coding RNAs (lncRNAs) by qRT-PCR in enteric precursor cells (EPCs) from controls and HSCR patients. We aimed to test the presence of a set lncRNAs among 84 lncRNAs in human EPCs, which were previously related with crucial cellular processes for ENS development, as well as to identify the possible differences between HSCR patients and controls. As a result, we have determined a set of lncRNAs with positive expression in human EPCs that were screened for mutations using the exome data from our cohort of HSCR patients to identify possible variants related to this pathology. Interestingly, we identified three lncRNAs with different levels of their transcripts (SOCS2-AS, MEG3 and NEAT1) between HSCR patients and controls. We propose such lncRNAs as possible regulatory elements implicated in the onset of HSCR as well as potential biomarkers of this pathology.

Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

“…In recent years, a growing number of studies have shown that non-coding RNAs (ncRNAs) play a significant role in HSCR onset [ 29 ]. Since the main goal of this study is to further clarify the epigenetic basis of HSCR, we decided to further examine the DMRs associated with ncRNAs.…”

“…Moreover, it should be noted that these ncRNAs ( MEG3 , AFAP1-AS and MIR195 ) were included in the gene list of promising candidates according to the enrichment analysis. It should be mentioned that two differentially methylated genes encoded for lncRNAs previously described as potential genes with a role during ENS based on their expression in human EPCs ( IPW and NR2F1-AS1 ) [ 29 ]. It has been reported an aberrant expression level of MEG3 , AFAP1-AS and MIR195 in gut tissues from HSCR patients, which suppressed cell migration and proliferation [ 30 – 32 ].…”

“…It has been reported an aberrant expression level of MEG3 , AFAP1-AS and MIR195 in gut tissues from HSCR patients, which suppressed cell migration and proliferation [ 30 – 32 ]. In addition, MEG3 was also reported as potential susceptibility factor for HSCR by our group based on an increase at transcript level of MEG3 in HSCR EPCs and potential pathogenic rare variants in its sequence carried by HSCR patients [ 29 ]. In the current study, an aberrant hypomethylation level was detected in MEG3 and AFAP1-AS , IPW and NR2F1-AS1 , whereas MIR195 was detected as hypermethylated gene in HSCR EPCs.…”

Biomarkers in Rare Diseases

“…Two contributions from Borrego’s group focus on Hirschsprung disease, a disorder caused by a defective proliferation, differentiation, survival, and/or migration of enteric precursor cells originating from the neural crest [ 5 , 6 ]. Current tests employed for the diagnosis of Hirschsprung disease are burdensome, and thus the availability of a simple disease biomarker would provide immense benefit to the patient and clinician.…”

“…Using a combined experimental and computational approach, Villalba-Benito et al report the dysregulation of five candidate genes related to PAX , which are potentially involved in the development of the enteric nervous system and implicated as the cause of disease onset [ 5 ]. In the group’s commentary, Torroglosa et al report the dysregulation of three long non-coding RNAs (lncRNAs) in the enteric precursor cells of patients with Hirschsprung disease, compared to healthy controls [ 6 ]. lncRNAs are transcripts with a length greater than 200 nucleotides and have regulatory roles in gene expression at the epigenetic, transcriptional, translational, post-transcriptional, and post-translational levels in many biological processes.…”