Genoomi struktuursed varieeruvused platsenta ja raseduse mõjutajatena

Väitekirja elektrooniline versioon ei sisalda publikatsiooneEma ja loote vaheline suhtlus loob aluse raseduse edukaks kulgemiseks. Rasedus on naise jaoks füsioloogiline väljakutse, mida kinnitab nii varaste (korduv raseduse katkemine, KRK) kui hiliste (preeklampsia, gestatsioonidiabeet, raseduskestuse kohta suur/väike sünnikaal) rasedustüsistuste rohkus. Rasedusaegseid komplikatsioone on sageli seostatud puuduliku platsenta invasiooni ning funktsiooniga, seetõttu on äärmiselt oluline täielik arusaam platsenta bioloogiast. Platsenta geenide avaldumise tase ja dünaamika reguleerib platsenta funktsiooni ja seeläbi raseduse kulgemist. Inimese platsenta RNA molekulide profiili moduleerib geneetiline varieeruvus, millest kõige enam on uuritud ühenukleotiidseid muutusi. Käesolevas doktoritöös uuriti esmakordselt DNA koopiaarvu muutuste (copy number variation, CNV) mõju teadmata põhjusega KRK (=>3 järjestikust raseduse katkemist) tekkes. CNV-d põhjustavad nähtust, kus teatud genoomi osad on kustutatud ja teistest on tehtud lisakoopiaid. CNV-sid on seostatud mitmete erinevate haigustega, kuid vähe on uuringuid rasedustüsistuste vallas. Kogu genoomi CNV piirkondade uuring Eesti ja Taani valimites tuvastas lisakoopia ehk duplikatsiooni 5. kromosoomil, mis suurendab KRK riski naistel ligi viis korda. Antud duplikatsioon hõlmab kahte platsentas kõrgelt avaldunud geeni (PDZD2 ja GOLPH3), mida pole varasemalt rasedusega seostatud. Lisauuringus leiti, et KRK vanemate genoomides leidub enam pikki kromosoomide otste ja keskmete läheduses asuvaid muutusi, mis võivad soosida vigu kromosoomide normaalsel jagunemisel. Lisaks võrreldi kogu genoomi CNV-de profiili vanemate verest ja platsentast eraldatud DNA-s nii normaalse raseduse erinevatel trimestritel kui rasedustüsistuste korral. Tulemused näitavad, et raseduse edukaks kulgemiseks ajab platsenta oma rakkude genoomi sassi justkui vähkkasvaja. Seetõttu esineb platsenta genoomis suurel hulgal muutusi, eelkõige duplikatsioone: ligi kuus korda enam kui vanematel genoomis. Kui aga ümberkorraldusi on liiga vähe, võivad tekkida mitmed rasedusaegsed komplikatsioonid. Duplikatsioonid hõlmasid geene, mis on seotud embrüonaalse arenguga ja platsenta rakkude invasiooni toetava protsessiga. See viitab sellele, et platsenta genoomis toimunud muutused soodustavad organi tööd ja raseduse edukat kulgemist.The establishment and maintenance of pregnancy relies on the well-coordinated crosstalk between the mother and the embryo. Pregnancy is an enormous physiological challenge a woman can experience and can cause early (recurrent pregnancy loss, RPL) as well as late (preeclampsia, gestational diabetes mellitus and fetal growth abnormalities) gestational complications. As these complications are often associated with poor trophoblast invasion and placental function, there is an urgent need for complete understanding of placental biology. Placental gene expression levels and dynamics regulate the function of placenta and therefore pregnancy maintenance. Transcriptome of the human placenta is modulated by genetic variation of which single nucleotide variants have been investigated the most. The experimental part of the thesis explored the role of DNA copy number variation (CNV) in idiopathic RPL (=>3 consecutive pregnancy losses). CNVs represent a phenomenon where parts of the genome are missing or duplicated. CNVs have been implicated in various human diseases; however, studies are lacking in reproductive disorders. Genome-wide CNV profiling of parental genomes of Estonian and Danish couples with recurrent pregnancy loss discovered a duplication on chromosome 5 increasing maternal risk of RPL up to 5 times. The duplication encompasses two genes (PDZD2 and GOLPH3) with enhanced expression in placenta and associated with pregnancy maintenance for the first time. Further research detected overrepresentation of large pericentromeric and subtelomeric CNVs in RPL parental genomes that may promote errors in normal chromosome segregation. Additionally, a comparison of genome-wide CNV profiles of parental and placental genomes of three trimesters of normal gestations as well as pregnancy complications was conducted. Similarly to cancer genomes, an extensive load of CNVs was detected as a hallmark of normal placental development. The load was mostly caused by the number of duplications, which were enriched in genes relevant to embryonic development. Early as well as late pregnancy complications showed reduced capacity to promote somatic genomic rearrangements in the placenta. The results indicate that the extensive amount of changes in the placental genome contributes to placental function and successful maintenance of pregnancy

Sekkumistõhusad teisesed leiud geneetikas

Kliinilises praktikas kasutatakse üha enam haigusseoseliste geenivariantide tuvastamiseks eksoomi (1–2% genoomist) sekveneerimist, sest selle diagnostiline saagis on suur (ligikaudu 30%). See suur andmestik (üle 80 000 geenivariandi) võib sisaldada ka teiseseid leide – kliiniliselt olulisi geenivariante, mis ei ole seotud patsiendi esmase kliinilise näidustusega. Teiseste leidude alla kuuluvad sekkumistõhusad monogeensed ehk ühe geeni muutusestpõhjustatud haigused, mis on eraldiseisvalt harvad, kuid mõjutavad kokku umbes 1–3% inimestest. Need haigused avalduvad elu jooksul ja on mõningatel juhtudel kiiresti areneva sümptomaatikaga. Päriliku riski varane hindamine on oluline, sest mitmete haiguste puhul on juba enne sümptomite teket võimalik meditsiiniline sekkumine (nt ravidieet, ennetavad ravimid, kirurgia), mis aitab vähendada tüsistusi ja enneaegset suremust. Artiklis on antud ülevaade eksoomi andmetest tuvastatavatest sekkumistõhusatest pärilikest haigustest, nende esinemissagedusest ja võimalikest ennetusmeetmetest ning teisestest leidudest tagasiside andmise rahvusvahelistest seisukohtadest

Enneaegne munasarjapuudulikkus: geneetika kasvav roll diagnostikas ja kliinilises käsitluses

Enneaegne munasarjapuudulikkus on sündroom, mis põhjustab munasarjade funktsiooni häiret enne 40. eluaastat. Haigus mõjutab paljusid naisi (levimus ligikaudu 1%), kahjuks ei leita seitsmel patsiendil kümnest haiguse põhjust.Teadaolevatest põhjustest moodustavad geneetilised tegurid 20–25%. Nendest levinuimad on kromosomaalsed häired ja FMR1 geeni premutatsioon. Nüüdseks on teada 20 geeni, mille haigusseoselised variandid põhjustavad isoleeritud enneaegset munasarjapuudulikkust ja viljatust. Täiendavaid uuringuid vajavad veel kümned eksoomi sekveneerimise meetodil tuvastatud kandidaatgeenid, mis vastutavad munasarja arengu ja funktsiooni, meioosi ja DNA parandusprotsesside eest.Kliinilises praktikas on enneaegse munasarjapuudulikkuse geneetiliste põhjuste selgitamine muutumas aina olulisemaks, sest arvestatav hulk naisi soovib tänapäeval sünnitada pigem 30. eluaastates. Konkreetne geneetiline leid on oluline patsiendi käsitluses ja ravis, samuti on see hädavajalik perekondlikus nõustamises. Ka uute ravitaktikate väljatöötamisel on geneetilise etioloogia tundmisel lisandväärtus

Structural Genomic Variation as Risk Factor for Idiopathic Recurrent Miscarriage

Peer reviewe

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.The wetland soil microbiome has a major impact on greenhouse gas emissions. Here the authors characterize how a group of archaea contribute to N2O emissions and find that climate and land use changes could promote these organisms

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O

Undiagnosed RASopathies in infertile men

RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failure (SPGF; total sperm count per ejaculate 0–39 million), we hypothesized that men seeking infertility management include cases with undiagnosed RASopathies. Likely pathogenic or pathogenic (LP/P) variants in 22 RASopathy-linked genes were screened in 521 idiopathic SPGF patients (including 155 CR cases) and 323 normozoospermic controls using exome sequencing. All 844 men were recruited to the ESTonian ANDrology (ESTAND) cohort and underwent identical andrological phenotyping. RASopathy-specific variant interpretation guidelines were used for pathogenicity assessment. LP/P variants were identified in PTPN11 (two), SOS1 (three), SOS2 (one), LZTR1 (one), SPRED1 (one), NF1 (one), and MAP2K1 (one). The findings affected six of 155 cases with CR and SPGF, three of 366 men with SPGF only, and one (of 323) normozoospermic subfertile man. The subgroup “CR and SPGF” had over 13-fold enrichment of findings compared to controls (3.9% vs. 0.3%; Fisher’s exact test, p = 5.5 × 10−3). All ESTAND subjects with LP/P variants in the Ras/MAPK pathway genes presented congenital genitourinary anomalies, skeletal and joint conditions, and other RASopathy-linked health concerns. Rare forms of malignancies (schwannomatosis and pancreatic and testicular cancer) were reported on four occasions. The Genetics of Male Infertility Initiative (GEMINI) cohort (1,416 SPGF cases and 317 fertile men) was used to validate the outcome. LP/P variants in PTPN11 (three), LZTR1 (three), and MRAS (one) were identified in six SPGF cases (including 4/31 GEMINI cases with CR) and one normozoospermic man. Undiagnosed RASopathies were detected in total for 17 ESTAND and GEMINI subjects, 15 SPGF patients (10 with CR), and two fertile men. Affected RASopathy genes showed high expression in spermatogenic and testicular somatic cells. In conclusion, congenital defects in the Ras/MAPK pathway genes represent a new congenital etiology of syndromic male infertility. Undiagnosed RASopathies were especially enriched among patients with a history of cryptorchidism. Given the relationship between RASopathies and other conditions, infertile men found to have this molecular diagnosis should be evaluated for known RASopathy-linked health concerns, including specific rare malignancies