An epitranscriptomic approach to identify the methyl modifications of mature miRNASs in human placenta due to micronutrient deficiency promoting diabeses in pregnancy

Project ID: SST_SHiMR_6

Background: Globally micronutrient deficiency affects 2 billion people including children and young women leading to metabolic disease. B12 deficiency during pregnancy is associated with gestational diabetes (GDM) that contributes to long-term metabolic health of both mother and offspring. The placenta interposed between the mother and baby, generally tends to be less methylated to regulate fetal development. If placentae are subjected to further reduced methylated state in response to low B12 levels, this could lead to placental dysfunction. Increasing evidence demonstrates B12 deficiency regulates epigenetic mechanisms, however, regulation at epiptranscriptomic level particularly, methylation at miRNA is not explored. MicroRNA methylation affects their stability and interaction with mRNA targets, which subsequently alters target gene and protein expression, leading to disease progression. Our preliminary findings in low B12 placental trophoblasts showed decreased levels of methylation in total RNA.

Hypothesis: Therefore, we hypothesise that low B12 in the placenta could lead to aberrant methylation of mature miRNA and alter mRNA expression representing an unexplored layer of gene regulation that is likely to influence metabolic dysregulation resulting in GDM. The aim is to determine the changes in the level of methylation at N6-adenosine position (m6A) in mature miRNAs and study the epitranscriptomic interactions with transcriptome and cardiometabolic traits using integrated analysis in placenta of GDM with low B12.

Experimental approach: Placental tissue/blood samples will be obtained from a biobank (PRiDE) having 4750 pregnant women. The cohort is well-characterised with complete history of the mothers and metabolic parameters. Placental tissue samples will be chosen from mothers with circulating B12 levels (low<220pmol/L). Based on the rates of GDM with B12 deficiency in the PRiDE cohort, a sufficient sample size (n=30) will be selected to adequately power (90%) the study (α-0.05, two-tailed). A novel approach of comprehensive analysis of m6A-tagged mature miRs using small-RNA modification array will be performed (Arraystar). We will identify the differentially expressed mRNA, miRNA, and differentially methylated m6A miRNAs by analysing the omics data (mRNA-seq/miR-seq/snRNA-modification-array). We will then employ an integrated analysis of the omics/clinical data to identify the epitranscriptomic interactors between methylation-miRNA-gene network and its association with metabolic
pathway. Next, we will validate these targets using qRT-PCR/pyrosequencing.

Outcome: Identifying m6A at mature miRNAs with a particular focus on micronutrient will offer a potential modifiable target for intervention development to break the intergenerational cycle, an effective tool in early prediction of GDM and aid to develop methylated miRNA-targeting therapies.

Supervisory Team:

Dr Adaikala Antonysunil (DoS)

Dr Daniel D’Andrea

Professor Mark Christian

Entry qualifications

For the eligibility criteria, visit our studentship application page .

Fees and funding

This is part of NTU’s 2024 fully-funded PhD Studentship Scheme.