Integrated analysis of genome-wide DNA methylation and gene expression data provide a regulatory network in intrauterine growth restriction

Redefining cerebral palsies as a diverse group of neurodevelopmental disorders with genetic aetiology

Cerebral palsy is a clinical descriptor covering a diverse group of permanent, non-degenerative disorders of motor function. Around one-third of cases have now been shown to have an underlying genetic aetiology, with the genetic landscape overlapping with those of neurodevelopmental disorders including intellectual disability, epilepsy, speech and language disorders and autism. Here we review the current state of genomic testing in cerebral palsy, highlighting the benefits for personalized medicine and the imperative to consider aetiology during clinical diagnosis. With earlier clinical diagnosis now possible, we emphasize the opportunity for comprehensive and early genomic testing as a crucial component of the routine diagnostic work-up in people with cerebral palsy.

Epigenetic Mechanisms Responsible for the Transgenerational Inheritance of Intrauterine Growth Restriction Phenotypes

A poorly functioning placenta results in impaired exchanges of oxygen, nutrition, wastes and hormones between the mother and her fetus. This can lead to restriction of fetal growth. These growth restricted babies are at increased risk of developing chronic diseases, such as type-2 diabetes, hypertension, and kidney disease, later in life. Animal studies have shown that growth restricted phenotypes are sex-dependent and can be transmitted to subsequent generations through both the paternal and maternal lineages. Altered epigenetic mechanisms, specifically changes in DNA methylation, histone modifications, and non-coding RNAs that regulate expression of genes that are important for fetal development have been shown to be associated with the transmission pattern of growth restricted phenotypes. This review will discuss the subsequent health outcomes in the offspring after growth restriction and the transmission patterns of these diseases. Evidence of altered epigenetic mechanisms in association with fetal growth restriction will also be reviewed.

Fetal growth restriction impairs hippocampal neurogenesis and cognition via Tet1 in offspring

Fetal growth restriction (FGR) increases the risk for impaired cognitive function later in life. However, the precise mechanisms remain elusive. Using dexamethasone-induced FGR and protein restriction-influenced FGR mouse models, we observe learning and memory deficits in adult FGR offspring. FGR induces decreased hippocampal neurogenesis from the early post-natal period to adulthood by reducing the proliferation of neural stem cells (NSCs). We further find a persistent decrease of Tet1 expression in hippocampal NSCs of FGR mice. Mechanistically, Tet1 downregulation results in hypermethylation of the Dll3 and Notch1 promoters and inhibition of Notch signaling, leading to reduced NSC proliferation. Overexpression of Tet1 activates Notch signaling, offsets the decline in neurogenesis, and enhances learning and memory abilities in FGR offspring. Our data indicate that a long-term decrease in Tet1/Notch signaling in hippocampal NSCs contributes to impaired neurogenesis following FGR and could serve as potential targets for the intervention of FGR-related cognitive disorders.

Integrated Analysis of Key Genes and Pathways Involved in Fetal Growth Restriction and Their Associations With the Dysregulation of the Maternal Immune System

Fetal growth restriction (FGR) is a common pregnancy complication and a risk factor for infant death. Most patients with FGR have preeclampsia, gestational diabetes mellitus, or other etiologies, making it difficult to determine the specific molecular mechanisms underlying FGR. In this study, an integrated analysis was performed using gene expression profiles obtained from Gene Expression Omnibus. Differentially expressed genes (DEGs) between healthy and FGR groups were screened and evaluated by functional enrichment and network analyses. In total, 80 common DEGs (FDR < 0.05) and 17 significant DEGs (FDR < 0.005) were screened. These genes were enriched for functions in immune system dysregulation in the placenta based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Among hub genes identified as candidates for FGR and fetal reprogramming, LEP, GBP5, HLA–DQA1, and CTGF were checked by quantitative polymerase chain reaction, immunohistochemistry, and western blot assays in placental tissues. Immune imbalance could cause hypoxia environment in placenta tissues, thus regulating the fetal-reprogramming. A significant association between CTGF and HIF-1α levels was confirmed in placenta tissues and HTR8 cells under hypoxia. Our results suggest that an immune imbalance in the placenta causes FGR without other complications. We provide the first evidence for roles of CTGF in FGR and show that CTGF may function via HIF-1α-related pathways. Our findings elucidate the pathogenesis of FGR and provide new therapeutic targets.

The role of chromosomal microarray analysis among fetuses with normal karyotype and single system anomaly or nonspecific sonographic findings

INTRODUCTION

Chromosomal microarray analysis is recommended as the first-tier test for the evaluation of fetuses with structural anomalies. This study aims to investigate the incremental diagnostic yield of chromosomal microarray over conventional karyotyping analysis in fetuses with anomalies restricted to one anatomic system and those with nonspecific anomalies detected by sonography.

MATERIAL AND METHODS

This is a retrospective cohort analysis of 749 fetuses undergoing prenatal diagnosis for abnormal ultrasound findings isolated to one anatomic system and normal karyotype, utilizing chromosomal microarray. Overall, 495 (66%) fetuses had anomalies confined to one anatomic system and 254 (34%) had other nonspecific anomalies including increased nuchal translucency (≥3.5 mm), cystic hygroma, intrauterine growth restriction and hydrops fetalis.

RESULTS

Fetuses with ultrasound anomalies restricted to one anatomic system had a 3.0% risk of carrying a pathogenic copy number variant; the risk varied dependent on the anatomic system affected. Fetuses with confined anomalies of the cardiac system had the highest diagnostic yield at 4.6%, but there were none in the urogenital system. Fetuses with nonspecific ultrasound anomalies had the highest diagnostic yield in fetuses with an intrauterine growth restriction at 5.9%. Overall, fetuses with a nonspecific ultrasound anomaly were affected with pathogenic copy number variants in 1.6% in the cases.

CONCLUSIONS

The diagnostic yield of chromosomal microarray in fetuses with normal karyotype and ultrasound abnormality confined to a single anatomic system was highest if it involved cardiac defects or intrauterine growth restriction. This diagnostic yield ranges from 0% to 4.6% depending on the anatomic system involved. Chromosomal microarray has considerable diagnostic value in these pregnancies.

Data-Mining Approach on Transcriptomics and Methylomics Placental Analysis Highlights Genes in Fetal Growth Restriction

Intrauterine Growth Restriction (IUGR) affects 8% of newborns and increases morbidity and mortality for the offspring even during later stages of life. Single omics studies have evidenced epigenetic, genetic, and metabolic alterations in IUGR, but pathogenic mechanisms as a whole are not being fully understood. An in-depth strategy combining methylomics and transcriptomics analyses was performed on 36 placenta samples in a case-control study. Data-mining algorithms were used to combine the analysis of more than 1,200 genes found to be significantly expressed and/or methylated. We used an automated text-mining approach, using the bulk textual gene annotations of the discriminant genes. Machine learning models were then used to explore the phenotypic subgroups (premature birth, birth weight, and head circumference) associated with IUGR. Gene annotation clustering highlighted the alteration of cell signaling and proliferation, cytoskeleton and cellular structures, oxidative stress, protein turnover, muscle development, energy, and lipid metabolism with insulin resistance. Machine learning models showed a high capacity for predicting the sub-phenotypes associated with IUGR, allowing a better description of the IUGR pathophysiology as well as key genes involved.

Small intestinal transcriptome analysis revealed changes of genes involved in nutrition metabolism and immune responses in growth retardation piglets1

Postnatal growth retardation (PGR) is common in piglets. Abnormal development in small intestine was casually implicated in impaired growth, but the exact mechanism is still implausible. The present study unveiled transcriptome profile of jejunal mucosa, the major site of nutrient absorption, in PGR and healthy piglets using RNA-sequencing (RNA-seq). The middle segments of jejunum and ileum, and jejunal mucosa were obtained from healthy and PGR piglets at 42 d of age. Total RNA samples extracted from jejunal mucosa of healthy and PGR piglets were submitted for RNA-seq. Lower villus height was observed in both jejunum and ileum from PGR piglets suggesting structural impairment in small intestine (P < 0.05). RNA-seq libraries were constructed and sequenced, and produced average 4.8 × 107 clean reads. Analysis revealed a total of 499 differently expressed genes (DEGs), of which 320 DEGs were downregulated in PGR piglets as compared to healthy piglets. The functional annotation based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted that most DEGs were involved in nutrient metabolism and immune responses. Our results further indicated decreased gene expression associated with glucose, lipid, protein, mineral, and vitamin metabolic process, detoxication ability, oxidoreductase activity, and mucosal barrier function; as well as the increased insulin resistance and inflammatory response in the jejunal mucosa of PGR piglets. These results characterized the transcriptomic profile of the jejunal mucosa in PGR piglets, and could provide valuable information with respect to better understanding the nutrition metabolism and immune responses in the small intestine of piglets.

A novel CpG-based signature for survival prediction of lung adenocarcinoma patients

Lung adenocarcinoma (LACA) is the leading cause of cancer-associated death worldwide. The present study intended to identify DNA methylation patterns that may serve as diagnostic and prognostic biomarkers for LACA. Data on DNA methylation and the survival data of the patients of LACA were obtained from The Cancer Genome Atlas. Kaplan-Meier curves and receiver operating characteristic curve analysis were utilized to build diagnostic and prognostic models. A total of 13 CpG sites were identified and validated as the optimal diagnostic and prognostic signature for overall survival. It was concluded that the CpG-based signature is a reliable predictor for the diagnosis and prognosis of patients with LACA.

Microtia epigenetics: An overview of review and new viewpoint

INTRODUCTION

Microtia is a congenital malformation of the external and middle ear caused by the abnormal development of the first and second zygomatic arch and the first sulcus. There is currently no consensus concerning the pathogenesis and etiology of microtia; genetic and environmental factors may play a role. Gene-based studies have focused on finding the genes that cause microtia and on gene function defects. However, no clear pathogenic genes have so far been identified. Microtia is multifactorial; gene function defects cannot completely explain its pathogenesis. In recent years, the epigenetic aspects of microtia have begun to receive attention.

CONCLUSIONS

Analysis of the existing data suggests that certain key genes and pathways may be the underlying cause of congenital microtia. However, further exploration is needed.

Fetal Growth Restriction Prediction: How to Move beyond

The actual burden and future burden of the small-for-gestational-age (SGA) babies turn their screening in pregnancy a question of major concern for clinicians and policymakers. Half of stillbirths are due to growth restriction in utero, and possibly, a quarter of livebirths of low- and middle-income countries are SGA. Growing body of evidence shows their higher risk of adverse outcomes at any period of life, including increased rates of neurologic delay, noncommunicable chronic diseases (central obesity and metabolic syndrome), and mortality. Although there is no consensus regarding its definition, birthweight centile threshold, or follow-up, we believe birthweight <10th centile is the most suitable cutoff for clinical and epidemiological purposes. Maternal clinical factors have modest predictive accuracy; being born SGA appears to be of transgenerational heredity. Addition of ultrasound parameters improves prediction models, especially using estimated fetal weight and abdominal circumference in the 3rd trimester of pregnancy. Placental growth factor levels are decreased in SGA pregnancies, and it is the most promising biomarker in differentiating angiogenesis-related SGA from other causes. Unfortunately, however, only few societies recommend universal screening. SGA evaluation is the first step of a multidimensional approach, which includes adequate management and long-term follow-up of these newborns. Apart from only meliorating perinatal outcomes, we hypothesize SGA screening is a key for socioeconomic progress.

The brain development of infants with intrauterine growth restriction: role of glucocorticoids

Brain injury is a serious complication of intrauterine growth restriction (IUGR), but the exact mechanism remains unclear. While glucocorticoids (GCs) play an important role in intrauterine growth and development, GCs also have a damaging effect on microvascular endothelial cells. Moreover, intrauterine adverse environments lead to fetal growth restriction and the hypothalamus-pituitary-adrenal (HPA) axis resetting. In addition, chronic stress can cause a decrease in the number and volume of astrocytes in the hippocampus and glial cells play an important role in neuronal differentiation. Therefore, it is speculated that the effect of GCs on cerebral neurovascular units under chronic intrauterine stimulation is an important mechanism leading to brain injury in infants with growth restrictions.

New Insights into the Pathogenesis and Treatment of Malnutrition

The volume of research into the pathogenesis and treatment of malnutrition has increased markedly over the past ten years, providing mechanistic insights that can be leveraged into more effective treatment options. These discoveries have been driven by several landmark studies employing metabolomics, metagenomics, and new preclinical models. This review highlights some of the most important recent findings, focusing in particular on the emerging roles of prenatal and perinatal factors, protein deficiency, impaired gut barrier function, immune deficiency, and the intestinal microbiome.

Carotid body removal normalizes arterial blood pressure and respiratory frequency in offspring of protein-restricted mothers

The aim of this study is to evaluate the short-term and long-term effects elicited by carotid body removal (CBR) on ventilatory function and the development of hypertension in the offspring of malnourished rats. Wistar rats were fed a normo-protein (NP, 17% casein) or low-protein (LP, 8% casein) diet during pregnancy and lactation. At 29 days of age, the animals were submitted to CBR or a sham surgery, according to the following groups: NP-cbr, LP-cbr, NP-sham, or LP-sham. In the short-term, at 30 days of age, the respiratory frequency (RF) and immunoreactivity for Fos on the retrotrapezoid nucleus (RTN; brainstem site containing CO₂ sensitive neurons) after exposure to CO₂ were evaluated. In the long term, at 90 days of age, arterial pressure (AP), heart rate (HR), and cardiovascular variability were evaluated. In the short term, an increase in the baseline RF (~6%), response to CO₂ (~8%), and Fos in the RTN (~27%) occurred in the LP-sham group compared with the NP-sham group. Interestingly, the CBR in the LP group normalized the RF in response to CO₂ as well as RTN cell activation. In the long term, CBR reduced the mean AP by ~20 mmHg in malnourished rats. The normalization of the arterial pressure was associated with a decrease in the low-frequency (LF) oscillatory component of AP (~58%) and in the sympathetic tonus to the cardiovascular system (~29%). In conclusion, carotid body inputs in malnourished offspring may be responsible for the following: (i) enhanced respiratory frequency and CO₂ chemosensitivity in early life and (ii) the production of autonomic imbalance and the development of hypertension.

Long-term cardiovascular consequences of fetal growth restriction: biology, clinical implications, and opportunities for prevention of adult disease

In the modern world, cardiovascular disease is a leading cause of death for both men and women. Epidemiologic studies consistently have suggested an association between low birthweight and/or fetal growth restriction and increased rate of cardiovascular mortality in adulthood. Furthermore, experimental and clinical studies have demonstrated that sustained nutrient and oxygen restriction that are associated with fetal growth restriction activate adaptive cardiovascular changes that might explain this association. Fetal growth restriction results in metabolic programming that may increase the risk of metabolic syndrome and, consequently, of cardiovascular morbidity in the adult. In addition, fetal growth restriction is strongly associated with fetal cardiac and arterial remodeling and a subclinical state of cardiovascular dysfunction. The cardiovascular effects ocurring in fetal life, includes cardiac morphology changes, subclinical myocardial dysfunction, arterial remodeling, and impaired endothelial function, persist into childhood and adolescence. Importantly, these changes have been described in all clinical presentations of fetal growth restriction, from severe early- to milder late-onset forms. In this review we summarize the current evidence on the cardiovascular effects of fetal growth restriction, from subcellular to organ structure and function as well as from fetal to early postnatal life. Future research needs to elucidate whether and how early life cardiovascular remodeling persists into adulthood and determines the increased cardiovascular mortality rate described in epidemiologic studies.