18q12.3-q21.1 microdeletion detected in the prenatally alcohol-exposed dizygotic twin with discordant fetal alcohol syndrome phenotype

Abstract Background A pair of dizygotic twins discordantly affected by heavy prenatal alcohol exposure (PAE) was reported previously by Riikonen, suggesting the role of genetic risk or protective factors in the etiology of alcohol-induced developmental disorders. Now, we have re-examined these 25-year-old twins and explored genetic origin of the phenotypic discordancy reminiscent with fetal alcohol syndrome (FAS). Furthermore, we explored alterations in DNA methylation profile of imprinting control region at growth-related insulin-like growth factor 2 (IGF2)/H19 locus in twins' white blood cells (WBC), which have been associated earlier with alcohol-induced genotype-specific changes in placental tissue. Methods Microarray-based comparative genomic hybridization (aCGH) was used to detect potential submicroscopic chromosomal abnormalities, and developmental as well as phenotypic information about twins were collected. Traditional bisulfite sequencing was used for DNA methylation analysis. Results Microarray-based comparative genomic hybridization revealed a microdeletion 18q12.3-q21.1. in affected twin, residing in a known 18q deletion syndrome region. This syndrome has been associated with growth restriction, developmental delay or intellectual deficiency, and abnormal facial features in previous studies, and thus likely explains the phenotypic discordancy between the twins. We did not observe association between WBCs? DNA methylation profile and PAE, but interestingly, a trend of decreased DNA methylation at the imprinting control region was seen in the twin with prenatal growth retardation at birth. Conclusions The microdeletion emphasizes the importance of adequate chromosomal testing in examining the etiology of complex alcohol-induced developmental disorders. Furthermore, the genotype-specific decreased DNA methylation at the IGF2/H19 locus cannot be considered as a biological mark for PAE in adult WBCs.Peer reviewe

Early prenatal alcohol exposure alters imprinted gene expression in placenta and embryo in a mouse model

Prenatal alcohol exposure (PAE) can harm the embryonic development and cause life-long consequences in offspring's health. To clarify the molecular mechanisms of PAE we have used a mouse model of early alcohol exposure, which is based on maternal ad libitum ingestion of 10% (v/v) ethanol for the first eight days of gestation (GD 0.5-8.5). Owing to the detected postnatal growth-restricted phenotype in the offspring of this mouse model and both prenatal and postnatal growth restriction in alcohol-exposed humans, we focused on imprinted genes Insulin-like growth factor 2 (Igf2), H19, Small Nuclear Ribonucleoprotein Polypeptide N (Snrpn) and Paternally expressed gene 3 (Peg3), which all are known to be involved in embryonic and placental growth and development. We studied the effects of alcohol on DNA methylation level at the Igf2/H19 imprinting control region (ICR), Igf2 differentially methylated region 1, Snrpn ICR and Peg3 ICR in 9.5 embryonic days old (E9.5) embryos and placentas by using MassARRAY EpiTYPER. To determine alcohol-induced alterations globally, we also examined methylation in long interspersed nuclear elements (Line-1) in E9.5 placentas. We did not observe any significant alcohol-induced changes in DNA methylation levels. We explored effects of PAE on gene expression of E9.5 embryos as well as E9.5 and E16.5 placentas by using quantitative PCR. The expression of growth promoter gene Igf2 was decreased in the alcohol-exposed E9.5 and E16.5 placentas. The expression of negative growth controller H19 was significantly increased in the alcohol exposed E9.5 embryos compared to controls, and conversely, a trend of decreased expression in alcohol-exposed E9.5 and E16.5 placentas were observed. Furthermore, increased Snrpn expression in alcohol-exposed E9.5 embryos was also detected. Our study indicates that albeit no alterations in the DNA methylation levels of studied sequences were detected by EpiTYPER, early PAE can affect the expression of imprinted genes in both developing embryo and placenta.Peer reviewe

P5-lääketiede jalkautuu Suomeen

Teema : biopankki. English summaryPeer reviewe

Economic evaluation of using polygenic risk score to guide risk screening and interventions for the prevention of type 2 diabetes in individuals with high overall baseline risk

Type 2 diabetes (T2D) with increasing prevalence is a significant global public health challenge. Obesity, unhealthy diet, and low physical activity are one of the major determinants of the rise in T2D prevalence. In addition, family history and genetic risk of diabetes also play a role in the process of developing T2D. Therefore, solutions for the early identification of individuals at high risk for T2D for early targeted detection of T2D, prevention, and intervention are highly preferred. Recently, novel genomic-based polygenic risk scores (PRSs) have been suggested to improve the accuracy of risk prediction supporting the targeting of preventive interventions to those at highest risk for T2D. Therefore, the aim of the present study was to assess the cost-utility of an additional PRS testing information (as a part of overall risk assessment) followed by a lifestyle intervention and an additional medical therapy when estimated 10-year overall risk for T2D exceeded 20% among Finnish individuals screened as at the high-risk category (i.e., 10%-20% 10-year overall risk of T2D) based on traditional risk factors only. For a cost-utility analysis, an individual-level state-transition model with probabilistic sensitivity analysis was constructed. A 1-year cycle length and a lifetime time horizon were applied in the base-case. A 3% discount rate was used for costs and QALYs. Cost-effectiveness acceptability curve (CEAC) and estimates for the expected value of perfect information (EVPI) were calculated to assist decision makers. The use of the targeted PRS strategy reclassified 12.4 percentage points of individuals to be very high-risk individuals who would have been originally classified as high risk using the usual strategy only. Over a lifetime horizon, the targeted PRS was a dominant strategy (i.e., less costly, more effective). One-way and scenario sensitivity analyses showed that results remained dominant in almost all simulations. However, there is uncertainty, since the probability (EVPI) of cost-effectiveness at a WTP of 0(sic)/QALY was 63.0% (243(sic)) indicating the probability that the PRS strategy is a dominant option. In conclusion, the results demonstrated that the PRS provides moderate additional value in Finnish population in risk screening leading to potential cost savings and better quality of life when compared with the current screening methods for T2D risk.Peer reviewe

Annotation and curation of human genomic variations: an ELIXIR Implementation Study

Background: ELIXIR is an intergovernmental organization, primarily based around European countries, established to host life science resources, including databases, software tools, training material and cloud storage for the scientific community under a single infrastructure. Methods: In 2018, ELIXIR commissioned an international survey on the usage of databases and tools for annotating and curating human genomic variants with the aim of improving ELIXIR resources. The 27-question survey was made available on-line between September and December 2018 to rank the importance and explore the usage and limitations of a wide range of databases and tools for annotating and curating human genomic variants, including resources specific for next generation sequencing, research into mitochondria and protein structure. Results: Eighteen countries participated in the survey and a total of 92 questionnaires were collected and analysed. Most respondents (89%, n=82) were from academia or a research environment. 51% (n=47) of respondents gave answers on behalf of a small research group (10 people). The survey showed that the scientific community considers several resources supported by ELIXIR crucial or very important. Moreover, it showed that the work done by ELIXIR is greatly valued. In particular, most respondents acknowledged the importance of key features and benefits promoted by ELIXIR, such as the verified scientific quality and maintenance of ELIXIR-approved resources. Conclusions ELIXIR is a "one-stop-shop" that helps researchers identify the most suitable, robust and well-maintained bioinformatics resources for delivering their research tasks

Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model

The adverse effects of alcohol consumption during pregnancy are known, but the molecular events that lead to the phenotypic characteristics are unclear. To unravel the molecular mechanisms, we have used a mouse model of gestational ethanol exposure, which is based on maternal ad libitum ingestion of 10% (v/v) ethanol for the first 8 days of gestation (GD 0.5-8.5). Early neurulation takes place by the end of this period, which is equivalent to the developmental stage early in the fourth week post-fertilization in human. During this exposure period, dynamic epigenetic reprogramming takes place and the embryo is vulnerable to the effects of environmental factors. Thus, we hypothesize that early ethanol exposure disrupts the epigenetic reprogramming of the embryo, which leads to alterations in gene regulation and life-long changes in brain structure and function. Genome-wide analysis of gene expression in the mouse hippocampus revealed altered expression of 23 genes and three miRNAs in ethanol-exposed, adolescent offspring at postnatal day (P) 28. We confirmed this result by using two other tissues, where three candidate genes are known to express actively. Interestingly, we found a similar trend of upregulated gene expression in bone marrow and main olfactory epithelium. In addition, we observed altered DNA methylation in the CpG islands upstream of the candidate genes in the hippocampus. Our MRI study revealed asymmetry of brain structures in ethanol-exposed adult offspring (P60): we detected ethanol-induced enlargement of the left hippocampus and decreased volume of the left olfactory bulb. Our study indicates that ethanol exposure in early gestation can cause changes in DNA methylation, gene expression, and brain structure of offspring. Furthermore, the results support our hypothesis of early epigenetic origin of alcohol-induced disorders: changes in gene regulation may have already taken place in embryonic stem cells and therefore can be seen in different tissue types later in life.Peer reviewe

In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages

Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)1,2,3, its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos4. Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis5,6, a high number of embryos containing abnormal cells can pass this strong selection barrier7,8. However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages

Effects of prenatal alcohol exposure on the epigenome, gene expression and development

Prenatal alcohol exposure affects the developing fetus and causes a wide range of physical and neurological abnormalities. The phenotype is generally described as fetal alcohol spectrum disorders (FASD) which is used as an umbrella term for all disorders caused by prenatal alcohol exposure. To date, the prevalence of FASD ranges from 1-5% in Finland. Even though, a wide range of the phenotypic characteristics have been identified, the underlying molecular mechanisms of FASD have remained unclear. Previous studies have suggested that epigenetic mechanisms represent a link between adverse early-life conditions and health consequences. Since the epigenome has a critical role during embryonic development by mediating the gene-environment interactions, this has raised interest in exploring the epigenetic changes behind FASD. The aim of this thesis was to approach the subject of prenatal alcohol exposure from the epigenetic point of view by exploring the associations between the molecular changes and the phenotypic characteristics. In our investigations of prenatal alcohol exposure, we exploited both a mouse model and human samples. The results obtained with the mouse model underline the vulnerability of the early embryo to alcohol-induced effects. Genome-wide gene expression analysis of adolescent male hippocampi revealed altered expression of several genes. Moreover, an MRI study of adult male brains in mice revealed asymmetry in the volume of the hippocampi: the left hippocampus was significantly larger than the right in alcohol-exposed offspring. Furthermore, we observed expression changes in growth-related imprinted genes in mouse embryos and placentas. Our human results highlight the importance of taking into account individual’s genetic characteristics when examining the background behind the alcohol disorder phenotype. We detected a single nucleotide polymorphism rs10732516G/A within the imprinting control region of the Insulin-like growth factor 2 (IGF2)/H19 imprinted locus and investigated the locus in a new way. As a result, we detected genotype-specific DNA methylation changes in the imprinting control region in alcohol-exposed placentas. Furthermore, the most significant finding was genotype-specific changes in the head circumference of the alcohol-exposed newborns.Raskaudenaikainen alkoholialtistus vaikuttaa sikiön kehitykseen aiheuttaen laajan kirjon niin fyysisiä kuin neurologisia kehityshäiriöitä. Yleisesti sikiövaurioiden kirjoa kuvataan termillä sikiöaikaisen alkoholialtistuksen aiheuttamat oireyhtymät (Fetal Alcohol Spectrum Disorders, FASD). FASD-oireyhtymän esiintyvyydeksi Suomessa on arvioitu 1-5%. Vaikka alkoholi aiheuttaa muutoksia sikiön normaalissa kehityksessä, niin itse taustalla oleva mekanismi on suurelta osin yhä tuntematon. Tämän hetkisten tutkimustulosten mukaan ympäristö vaikuttaisi geenien toimintaan epigeneettisten muutosten kautta jotka näkyisivät muutoksina sikiön kehityksessä. Koska epigenomilla tiedetään olevan merkittävä rooli alkionkehityksen aikana, ja se toimii myös ympäristön ja geenien välisenä säätelijänä, on epigeneettisiä mekanismeja tutkittu myös FASD-oireyhtymän taustalla. Väitöskirjassani tarkastelin raskaudenaikaisen alkoholialtistuksen vaikutuksia epigeneettisestä näkökulmasta. Pyrin selvittämään mitä muutoksia alkoholi sikiön epigenomissa ja genomissa aiheuttaa ja löytämään yhtäläisyyksiä näiden muutosten ja oireyhtymän ilmiasun välillä. Tutkimuksissani käytin apunani hiirimallia ja ihmisiltä kerättyä aineistoa. Tutkimustulokset hiirimallilla osoittavat, että alkoholialtistus aivan raskauden alussa vaikuttaa merkittävästi sikiön kehitykseen. Alkoholialtistus muutti hippokampuksessa useiden geenien toimintaa ja aiheutti epäsymmetrisyyttä oikean ja vasemman aivopuoliskon välillä: vasen hippokampus oli merkittävästi oikeaa suurempi. Lisäksi alkoholialtistus muutti epigeneettisesti säädeltyjen ja kasvuun vaikuttavien leimautuneiden geenien ilmenemistä alkiossa ja istukassa. Ihmisillä tehty tutkimus puolestaan korostaa erityisesti geneettisen variaation merkitystä alkoholivaurioiden taustalla. Tutkimuksessa havaitsimme yhden emäksen variaation rs10732516G/A Insuliinikaltainen kasvutekijä 2 (IGF2) /H19 -leimatun geenilokuksen säätelyalueella, ja tutkimme geenilokusta uudesta näkökulmasta jakamalla lapset ryhmiin genotyypin perusteella. Tarkastelemalla alkoholin vaikutusta lokuksen DNA metylaatioihin, havaitsimme, että alkoholin aiheuttamat muutokset säätelyalueen metylaatioprofiilissa riippuivat yksilön genotyypistä. Tämän lisäksi alkoholille altistuneiden vastasyntyneiden päänympärykset poikkesivat merkittävästi toisistaan riippuen geneettisestä variaatioista

rs10732516 polymorphism at the IGF2/H19 locus associates with a genotype-specific trend in placental DNA methylation and head circumference of prenatally alcohol-exposed newborns

STUDY QUESTION: Does prenatal alcohol exposure (PAE) affect regulation of the insulin-like growth factor 2 (IGF2)/H19 locus in placenta and the growth-restricted phenotype of newborns? SUMMARY ANSWER: PAE results in genotype-specific trends in both placental DNA methylation at the IGF2/H19 locus and head circumference (HC) of newborns. WHAT IS KNOWN ALREADY: PAE can disturb development of the nervous system and lead to restricted growth of the head, even microcephaly. To clarify the etiology of alcohol-induced growth restriction, we focused on the imprinted IGF2/H19 locus known to be important for normal placental and embryonic growth. The expression of IGF2 and a negative growth controller H19 are regulated by the H19 imprinting control region (H19 ICR) with seven-binding sites for the methylation-sensitive zinc-finger regulatory protein CTCF. A single nucleotide polymorphism rs10732516 G/A in the sixth-binding site has shown to associate with genotype-specific DNA methylation profiles at the H19 ICR. STUDY DESIGN, SIZE, DURATION: By grouping 39 alcohol-exposed and 100 control samples according to rs10732516 polymorphism we explored alcohol-induced, genotype-specific changes in DNA methylation at the H19 ICR and the promoter region of H19 (H19 differentially methylated region). Also, IGF2 and H19 mRNA expression level in placenta as well as the phenotypes of newborns were examined. PARTICIPANTS/MATERIALS, SETTING, METHODS: We explored alcohol-induced, genotype-specific changes in placental DNA methylation by MassARRAY EpiTYPER and allele-specific changes by bisulphite sequencing. IGF2 and H19 expression in placenta were analyzed by quantitative PCR and the HC, birthweight and birth length of newborns were examined using national growth charts. MAIN RESULTS AND THE ROLE OF CHANCE: We observed a consistent trend in genotype-specific changes in DNA methylation at H19 ICR in alcohol-exposed placentas. DNA methylation level in the normally highly methylated paternal allele of rs10732516 paternal A/ maternal G genotype was decreased in alcohol-exposed placentas. In addition to decreased IGF2 mRNA expression in alcohol-exposed placentas of this specific genotype (P = 0.03), we observed significantly increased expression of H19 in relation to IGF2 when comparing all alcohol-exposed placentas to unexposed controls (P = 0.006). Furthermore, phenotypic examination showed a significant genotype-specific association between the alcohol exposure and HC of newborns (P = 0.001).Peer reviewe