Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR)

The Impact of SLC2A8 RNA Interference on Glucose Uptake and the Transcriptome of Human Trophoblast Cells

While glucose is the primary fuel for fetal growth, the placenta utilizes the majority of glucose taken up from the maternal circulation. Of the facilitative glucose transporters in the placenta, SLC2A8 (GLUT8) is thought to primarily function as an intracellular glucose transporter; however, its function in trophoblast cells has not been determined. To gain insight into the function of SLC2A8 in the placenta, lentiviral-mediated RNA interference (RNAi) was performed in the human first-trimester trophoblast cell line ACH-3P. Non-targeting sequence controls (NTS RNAi; n = 4) and SLC2A8 RNAi (n = 4) infected ACH-3P cells were compared. A 79% reduction in SLC2A8 mRNA concentration was associated with an 11% reduction (p ≤ 0.05) in ACH-3P glucose uptake. NTS RNAi and SLC2A8 RNAi ACH-3P mRNA were subjected to RNAseq, identifying 1525 transcripts that were differentially expressed (|log2FC| > 1 and adjusted p-value < 0.05), with 273 transcripts derived from protein-coding genes, and the change in 10 of these mRNAs was validated by real-time qPCR. Additionally, there were 147 differentially expressed long non-coding RNAs. Functional analyses revealed differentially expressed genes involved in various metabolic pathways associated with cellular respiration, oxidative phosphorylation, and ATP synthesis. Collectively, these data indicate that SLC2A8 deficiency may impact placental uptake of glucose, but that its likely primary function in trophoblast cells is to support cellular respiration. Since the placenta oxidizes the majority of the glucose it takes up to support its own metabolic needs, impairment of SLC2A8 function could set the stage for functional placental insufficiency.

IncRna: The R Package for Optimizing lncRNA Identification Processes

In silico identification of long noncoding RNAs (lncRNAs) is a multistage process including filtering of transcripts according to their physical characteristics (e.g., length, exon-intron structure) and determination of the coding potential of the sequence. A common issue within this process is the choice of the most suitable method of coding potential analysis for the conducted research. Selection of tools on the sole basis of their single performance may not provide the most effective choice for a specific problem. To overcome these limitations, we developed the R library lncRna, which provides functions to easily carry out the entire lncRNA identification process. For example, the package prepares the data files for coding potential analysis to perform error analysis. Moreover, the package gives the opportunity to analyze the effectiveness of various combinations of the lncRNA prediction methods to select the optimal configuration of the entire process.

Biomarker screening in fetal growth restriction based on multiple RNA-seq studies

Objective

Fetal growth restriction (FGR) is a severe pathological complication associated with compromised fetal development. The early diagnosis and prediction for FGR are still unclear. Sequencing technologies present a huge opportunity to identify novel biomarkers. However, limitation of individual studies (e.g., long lists of dysregulated genes, small sample size and conflicting results) hinders the selection of the best-matched ones.

Study design

A multi-step bioinformatics analysis was performed. We separately reanalyzed data from four public RNA-seq studies, followed by a combined analysis of individual results. The differentially expressed genes (DEGs) were identified based on DESeq2. Then, function enrichment analyses and protein-protein interaction network (PPI) were conducted to screen for hub genes. The results were further verified by using external microarray data.

Results

A total of 65 dysregulated genes (50 down and 15 upregulated) were identified in FGR compared to controls. Function enrichment and PPI analysis revealed ten hub genes closely related to FGR. Validation analysis found four downregulated candidate biomarkers (CEACAM6, SCUBE2, DEFA4, and MPO) for FGR.

Conclusions

The use of omics tools to explore mechanism of pregnancies disorders contributes to improvements in obstetric clinical practice.

Epigenetics Beyond Fetal Growth Restriction: A Comprehensive Overview

Fetal growth restriction is a pathological condition occurring when the fetus does not reach the genetically determined growth potential. The etiology of fetal growth restriction is expected to be multifactorial and include fetal, maternal, and placental factors, the latter being the most frequent cause of isolated fetal growth restriction. Severe fetal growth restriction has been related to both an increased risk of perinatal morbidity and mortality, and also a greater susceptibility to developing diseases (especially cardio-metabolic and neurological disorders) later in life. In the last decade, emerging evidence has supported the hypothesis of the Developmental Origin of Health and Disease, which states that individual developmental 'programming' takes place via a delicate fine tuning of fetal genetic and epigenetic marks in response to a large variety of 'stressor' exposures during pregnancy. As the placenta is the maternal-fetal interface, it has a crucial role in fetal programming, such that any perturbation altering placental function interferes with both in-utero fetal growth and also with the adult life phenotype. Several epigenetic mechanisms have been highlighted in modulating the dynamic placental epigenome, including alterations in DNA methylation status, post-translational modification of histones, and non-coding RNAs. This review aims to provide a comprehensive and critical overview of the available literature on the epigenetic background of fetal growth restriction. A targeted research strategy was performed using PubMed, MEDLINE, Embase, and The Cochrane Library up to January 2022. A detailed and fully referenced synthesis of available literature following the Scale for the Assessment of Narrative Review Articles guidelines is provided. A variety of epigenetic marks predominantly interfering with placental development, function, and metabolism were found to be potentially associated with fetal growth restriction. Available evidence on the role of environmental exposures in shaping the placental epigenome and the fetal phenotype were also critically discussed. Because of the highly dynamic crosstalk between epigenetic mechanisms and the extra level of complexity in interpreting the final placental transcriptome, a full comprehension of these phenomenon is still lacking and advances in multi-omics approaches are urgently needed. Elucidating the role of epigenetics in the developmental origins of health and disease represents a new challenge for the coming years, with the goal of providing early interventions and prevention strategies and, hopefully, new treatment opportunities.