Maternal obesity and gestational diabetes reprogram the methylome of offspring beyond birth by inducing epigenetic signatures in metabolic and developmental pathways

Obesity is a negative health condition characterized by an excessive accumulation of fat that is diagnosed at a body mass index (BMI) equal to or greater than 30 kg/m² [1]. In recent decades, obesity has become a central public health concern due to its increasing prevalence, which has reached worldwide pandemic levels, and because it represents a leading risk factor for the development of cardiovascular, metabolic diseases (e.g., hypertension, myocardial infarction, stroke, diabetes mellitus) and certain types of cancer, amongst other illnesses [1, 2].

Interestingly, epidemiological studies have shown how maternal obesity during pregnancy constitutes an important risk factor related to the appearance of cardiometabolic diseases in the offspring [3], including obesity, elevated blood pressure, impaired insulin/glucose homoeostasis, increased inflammatory markers and altered lipid profiles [4‐8]. This is a serious concern since prevalence rates of obesity in pregnant women can exceed 30% [9]. Furthermore, a recent longitudinal girl study with a follow-up from birth to 10 years has found that birth weight and maternal obesity are the main risk factors responsible for the appearance of obesity at 5 years, while at 10 years the only significant related condition is maternal obesity [10].

The increased risk for these conditions is maintained not only in childhood, but also in terms of adulthood morbidity and mortality [11‐13], which evinces profound implications for the design of public health policies and interventions, especially in the case of cardiovascular diseases. Moreover, the most common medical complication of pregnancy, gestational diabetes mellitus (GDM, hyperglycaemia that develops during pregnancy and resolves after birth), represents another risk factor for the development of obesity and cardiovascular disease in both the mother and child [14]. A recent cohort study has evinced that previous GDM leads to a higher incidence of dyslipidemia in women [15]. What is more, maternal obesity is also correlated with metabolic complications in pregnancy such as GDM, gestational hypertension and pre-eclampsia, highlighting the fact that obesity and GDM are very intertwined [16].

However, due to obesity's multifactorial nature [17], little is known about the molecular mechanisms that underlie these strong epidemiological findings. Furthermore, it remains unclear whether childhood obesity is simply the result of the unhealthy eating behaviour instilled by parents during postnatal growth or whether the intrauterine environment may be capable of affecting children of obese mothers, predisposing them to the development of cardiometabolic diseases. In line with the theory of the developmental origins of health and disease, the intrauterine period is crucial to understand the adult risk to experience cardiovascular events [18], but at the same time, early postnatal development has gained relevance in recent decades. Longitudinal studies which trace a life course perspective are needed to address these questions, exploring the interrelations between the influence of the intrauterine environment and developmental processes [19].

To date, the mechanisms governing the influence of the intrauterine environment on the offspring’s health are still under discussion. For instance, extracellular vesicles are posited to play roles in the systemic regulation of physiological processes and pathologies [20]. In this line, we propose that epigenetic remodelling, which is especially sensitive to extrinsic and intrinsic influences during early life [21, 22], could constitute the molecular mechanism through which intrauterine stimuli can affect the biology of the cell. In fact, it is well known that DNA methylation patterns are key regulators of genes involved in pancreatic β-cell homeostasis, including insulin signalling and secretion [23]. At the same time, metabolic imbalance can disrupt epigenetic mechanisms through alterations in the levels of tricarboxylic acid cycle intermediates and the redox balance, which subsequently can have an impact on gene regulation and DNA damage and repair [24]. Ten-eleven translocation methylcytosine dioxygenases, responsible for DNA demethylation processes, are sensitive to these metabolic dysfunctions, such as obesity and diabetes mellitus, establishing a crosstalk between metabolism, epigenetics and genome stability [24]. In agreement with this, gestational diabetes [25, 26], maternal obesity [27] and hypertension [19] have been consistently associated with DNA methylation alterations in placenta, blood and tissue samples from offspring. To shed light on this issue, longitudinal studies are of great value for several reasons, among them: (a) in the field of developmental biology, they allow the definition of the key time frame when epigenetic alterations are most dynamic, and therefore, when external stimuli can have the greatest influence at the molecular level; (b) they can define epigenetic patterns that are acquired through uterine exposure but are maintained over time, acting as reliable childhood biomarkers.

This study presents, to the best of our knowledge, the first longitudinal genome-wide analysis of the methylome of whole blood samples from a paediatric cohort of children born to mothers suffering from obesity or obesity with GDM during pregnancy and healthy controls. We performed longitudinal measurements throughout the first year of life (0, 6 and 12 months) on 39 subjects (total N = 90) using Illumina Infinium MethylationEPIC BeadChip arrays to profile more than 770,000 CpG sites. The design allowed us to carry out both cross-sectional and longitudinal analyses in order to derive DNA methylation alterations associated with developmental and pathology-related epigenomics.

In this work, we have analysed the paediatric methylome across the first year of life in order to establish the existence of epigenetic signatures that reflect the maternal metabolic condition during pregnancy on the offspring beyond birth. To this end, we employed a cohort formed by longitudinal whole blood samples at 0, 6 and 12 months, whose methylome was profiled using Illumina Infinium MethylationEPIC BeadChip arrays. With this strategy, we first characterized those DNA methylation alterations produced during postnatal development, defining the first six months of life as the most dynamic for epigenetic remodelling. In addition, we observed that a significant proportion of the altered loci continued to experience changes until the age of 12 months, preserving the direction of the effect, which highlights their importance in achieving a correct postnatal development. Likewise, we performed cross-sectional studies to infer systemic DNA methylation alterations that allow to distinguish children born to mothers suffering from obesity or obesity with GDM during pregnancy from infants born to healthy controls. Our results revealed that there are DNA methylation biomarkers at both single CpG positions and genomic regions that track these maternal differences in pregnancy at least during the first year of infants’ lives. These DNA methylation alterations based on the maternal condition were concentrated at genes that recapitulated metabolic pathways of transport of fatty acids, mitochondrial bioenergetics and several developmental processes. Although an important part of these biomarkers experienced parallel alterations across the first year of life, the functionality of the involved genes remained in the same metabolic signatures, highlighting the consistency of these biomarkers during development. Interestingly, we found that maternal influence during pregnancy was able to alter postnatal development, especially those changes that implied gain of methylation. In addition, more subtle influences in development confirmed that maternal obesity tended to intensify development processes at the methylation level, in a global way, without apparently targeting any specific developmental process. Therefore, the results presented in this manuscript provide a systematic, comprehensive analysis of the epigenetic dynamics associated with the early postnatal development, the prenatal intrauterine conditioning and the interactions between both processes in a longitudinal fashion.

Regarding postnatal development, our results are in line with previous studies that establish the first 5 years of life [22] as the most critical for epigenetic remodelling, especially during the first 3 years [48]. The uncovering of the epigenetic relevance of the first six months of life could lead to new studies that point the importance of earlier lifestyle interventions on adult health, especially at the cardiovascular level. From a functional viewpoint, the genes that are involved in maturation processes of the hematopoietic compartment undergo a regulation programme mediated by hypomethylation changes, thus being a potential source of transcriptional activation, as has been previously reported [49]. On the other hand, loci involved in gene regulatory networks of embryonic development concentrate hypermethylation signatures in their promoter regions, consolidating Polycomb-mediated gene repression programmes once developmental processes have concluded [50, 51]. These results agree with previous longitudinal studies carried out from birth up to 10 years [22, 48]. All in all, early postnatal development is tightly regulated at the epigenetic level according to the direction of the methylation changes.

Using our longitudinal design, we performed a comprehensive epigenetic profiling at the single-CpG level to uncover reliable DNA methylation biomarkers of maternal obesity (with or without GDM) in infant blood samples. Importantly, these alterations were maintained beyond birth across the first year of life. Moreover, detecting DNA methylation changes at the regional level constituted a better option for discovering alterations enriched at regulatory sequences and thus with potential functional implications. Strikingly, our results revealed a clear enrichment of the alterations in functions important for the molecular physiopathology of obesity. For instance, hypermethylated regions affected important deregulated genes in cardiometabolic diseases, the majority related to the transport of organic molecules and fatty acids. In obese subjects, CPT1B promoter hypermethylation has been associated with diminished muscular expression in response to lipids leading to a reduced ability to oxidize fatty acids [52]. The SLC38A4 amino acid transporter, which is crucial for the placental nutrition of the embryo, is overexpressed in the placentas from human foetuses with macrosomia [53], while its knockout causes foetal weight reduction in mice [54]. Several polymorphisms in this transporter gene are also linked to the appearance of hyperglycaemia [55] even in the placenta of normal-weight newborns [56]. Similarly, Soranzo and colleagues have shown that ATP11A is significantly associated with the levels of HbA1c, which is used to monitor diabetes [57]. The SLC35F3 gene, a diabetes-specific biomarker, is a thiamine transporter that exhibits polymorphisms related to increased blood pressure and potential higher risk of hypertension [58, 59]. When we considered the hypomethylated regions, we found genes such as FN3K, which has been associated with HbA1clevels [57]. In addition, the RPH3AL and HOX genes are known to suffer DNA methylation alterations during adipogenesis in cells from obese patients with and without type II diabetes [60]. We also observed alterations in epigenetic modifiers such as HDAC4, whose mutation impairs β-cell function and insulin secretion, leading to a non-autoimmune paediatric diabetes [61].

In this work, we also seek to draw attention to the interplay between intrauterine conditioning and postnatal development. Importantly, obesity-mediated epigenetic alterations are maintained regardless of the developmental changes that can occur concurrently at those CpG sites. In fact, those DNA methylation biomarkers that are also modified during development are still related to the same metabolic functional pathways, providing robust evidence for the conservation of these epigenetic signatures with time. From a developmental viewpoint, we observed that maternal obesity with or without GDM tends to magnify the DNA methylation changes which occur with time, although opposite dynamics are also observed. Further longitudinal studies will be needed to ascertain if maternal metabolic condition causes an acceleration of developmental processes, at least from an epigenetic perspective. All in all, these results provide support for the notion that the maternal metabolic influence during pregnancy can affect the epigenetic features of early development, with hitherto unexplored consequences for future health. Ideally, public health interventions should focus on controlling the maternal metabolic status during pregnancy, but at the same time, our results point that the first six months of infant’s lives are crucial for an adequate postnatal development.

That said, our observations present limitations. First, individual genetic traits could explain why our obese-mediated DNA methylation changes are longitudinally maintained during the first year of life [62]. In addition, although our results support the existence of an obesity-mediated intrauterine effect on the childhood methylome, we cannot rule out that the maintenance of the DNA methylation changes across the first year of life is the result of early-life lifestyle factors. Nevertheless, our study clearly positions epigenetic mechanisms as the molecular link that explains the environmental maternal influence in the offspring. Other works that use methylation arrays also support this conclusion in a non-longitudinal fashion, showing that gestational diabetes is associated with methylation changes of metabolic genes in placenta [25, 26, 63, 64] and blood samples from newborns, children and adolescents [65‐70]. Fewer studies have addressed associations between DNA methylation alterations and maternal obesity, those that exist mainly using only cord blood samples from newborns [71‐74]. Finally, despite the fact that our study does not allow us to infer direct functional consequences, detecting these changes in blood indicates that maternal influence causes a systemic effect in the offspring through epigenetic footprints that are preserved beyond birth.

Altogether, in this work we have described DNA methylation alterations in whole blood cells of offspring born to mothers suffering from obesity (with or without GDM) during pregnancy, on the basis of a longitudinal follow-up. Importantly, this foetal reprogramming is maintained during the first year of life and displays epigenetic signatures enriched in metabolic pathways, thus suggesting a link between the maternal intrauterine environment and the offspring’s genome function. Moreover, some of these alterations are observed to interact with the epigenetic reprogramming occurring during early-life development. The definition of DNA methylation biomarkers in the offspring which are associated with maternal condition may be of value for estimating the risk for the development of cardiometabolic diseases, but further studies will be needed to assess their feasibility. From a paediatric perspective, we foresee that our results could pave the way to the design of earlier interventions that limit the appearance of cardiometabolic events in adult life. Thus, our longitudinal design could be a baseline for future studies aimed at exploring the potential functional implications of these epigenetic footprints on intergenerational health.