Browsing by Author "Saare, Merli"

Now showing 1 - 9 of 9

A molecular tool for menstrual cycle phase dating of endometrial samples in endometriosis transcriptome studies
(2019) Saare, Merli; Merli, Triin; Teder, Hindrek; Paluoja, Priit; Palta, Priit; Koel, Mariann; Kirss, Fred; Karro, Helle; Sõritsa, Deniss; Salumets, Andres; Krjutškov, Kaarel; Peters, Maire
Transcriptome profiling of 57 endometrial receptivity genes specifies the menstrual cycle phase of endometrial samples.
Aberrant expression of genes associated with stemness and cancer in endometria and endometrioma in a subset of women with endometriosis
(2018) Ponandai-Srinivasan, Sakthivignesh; Andersson, Karin L; Nister, Monica; Saare, Merli; Hassan, Halima A; Varghese, Suby J; Peters, Maire; Salumets, Andres; Gemzell-Danielsson, Kristina; Lalitkumar, Parameswaran Grace Luther
STUDY QUESTION Is there molecular evidence for a link between endometriosis and endometriosis-associated ovarian cancers (EAOC)? STUDY ANSWER We identified aberrant gene expression signatures associated with malignant transformation in a small subgroup of women with ovarian endometriosis. WHAT IS KNOWN ALREADY Epidemiological studies have shown an increased risk of EAOC in women with ovarian endometriosis. However, the cellular and molecular changes leading to EAOC are largely unexplored. STUDY DESIGN, SIZE, DURATION CD73+CD90+CD105+ multipotent stem cells/progenitors (SC cohort) were isolated from endometrium (n = 18) and endometrioma (n = 11) of endometriosis patients as well as from the endometrium of healthy women (n = 14). Extensive phenotypic and functional analyses were performed in vitro on expanded multipotent stem cells/progenitors to confirm their altered characteristics. Aberrant gene signatures were also validated in paired-endometrium and -endometrioma tissue samples from another cohort (Tissue cohort, n = 19) of endometriosis patients. PARTICIPANTS/MATERIALS, SETTINGS, METHODS Paired-endometrial and -endometriotic biopsies were obtained from women with endometriosis (ASRM stage III–IV) undergoing laparoscopic surgery. Control endometria were obtained from healthy volunteers. Isolated CD73+CD90+CD105+ SC were evaluated for the presence of known endometrial surface markers, colony forming efficiency, multi-lineage differentiation, cell cycle distribution and 3D-spheroid formation capacity. Targeted RT-PCR arrays, along with hierarchical and multivariate clustering tools, were used to determine both intergroup and intragroup gene expression variability for stem cell and cancer-associated markers, in both SC+ and tissue cohorts. MAIN RESULTS AND THE ROLE OF CHANCE Isolated and expanded SC+ from both control and patient groups showed significantly higher surface expression of W5C5+, clonal expansion and 3D-spheroid formation capacity (P < 0.05) compared with SC−. The SC+ cells also undergo mesenchymal lineage differentiation, unlike SC−. Gene expression from paired-endometriosis samples showed significant downregulation of PTEN, ARID1A and TNFα (P < 0.05) in endometrioma compared with paired-endometrium SC+ samples. Hierarchical and multivariate clustering from both SC+ and tissue cohorts together identified 4 out of 30 endometrioma samples with aberrant expression of stem cell and cancer-associated genes, such as KIT, HIF2α and E-cadherin, altered expression ratio of ER-β/ER-α and downregulation of tumour suppressor genes (PTEN and ARID1A). Thus, we speculate that above changes may be potentially relevant to the development of EAOC. LARGE-SCALE DATA N/A. LIMITATIONS, REASON FOR CAUTION As the reported frequency of EAOC is very low, we did not have access to those samples in our study. Moreover, by adopting a targeted gene array approach, we might have missed several other potentially-relevant genes associated with EAOC pathogenesis. The above panel of markers should be further validated in archived tissue samples from women with endometriosis who later in life developed EAOC. WIDER IMPLICATIONS OF THE FINDINGS Knowledge gained from this study, with further confirmation on EAOC cases, may help in developing screening methods to identify women with increased risk of EAOC. STUDY FUNDING/COMPETING INTEREST(S) The study is funded by the Swedish Research Council (2012-2844), a joint grant from Stockholm County and Karolinska Institutet (ALF), RGD network at Karolinska Institutet, Karolinska Institutet for doctoral education (KID), Estonian Ministry of Education and Research (IUT34-16), Enterprise Estonia (EU48695), Horizon 2020 innovation program (WIDENLIFE, 692065), European Union’s FP7 Marie Curie Industry-Academia Partnerships and Pathways funding (IAPP, SARM, EU324509) and MSCA-RISE-2015 project MOMENDO (691058). All authors have no competing interest.
Androgen receptor and 5α-reductase type2 gene polymorphisms in idiopathic male infertility
(2008-05-23T06:13:14Z) Saare, Merli
Androgen receptor and 5α-reductase type2 gene polymorphisms in idiopathic male infertility
(2008-05-26T06:27:06Z) Saare, Merli
Androgeenid, testosteroon ja dihüdrotestosteroon (DHT) toimivad seondumisel androgeeni retseptorile (AR), mõjutades seeläbi androgeen-sõltuvate geenide transkriptsiooni ning stimuleerides ja säilitades spermatogeneesi. AR geeni ühenukleotiidsed polümorfismid (SNP-d) ning CAG ja GGN mikrosatelliitsed variatsioonid võivad mõjutada AR aktiivsust ning seeläbi meeste viljakust. Ensüüm 5α-reduktaas (SRD5A) redutseerib testosterooni sihtmärkkudedes bioloogiliselt aktiivseks DHT-ks. 5α-reduktaasi tüüp 2 geeni (SRD5A2) polümorfismide mõju ensüümi aktiivsusele on vähe uuritud. Antud töös uuriti kuue AR geeni ühenukleotiidilise polümorfismi, kahe trinukleotiidse kordusjärjestuse (CAG ja GGN) ning viie SRD5A2 geeni polümorfismi võimalikke seoseid idiopaatilise mehepoolse viljatusega. AR geenis tuvastati 13 sagedasemat haplotüüpi, millest HAP4 osutus riskihaplotüübiks (OR = 5,15; 95% CI = 1,75–15,15; p = 0,003). Samuti leiti, et CAG/GGN mikrosatelliitsete kordusjärjestuste arv ei erinenud uuritavates gruppides. SRD5A2 geeni SNP-de analüüsil leiti, et SNP2 G alleel oli seotud riskiga oligozoospermia (OR = 2,98; 95% CI 1,26 – 7,05; p = 0,013) ja azoospermia (OR =2,87; 95% CI 1,01 – 8,19; p = 0,048) tekkimiseks. Samuti leiti, et SNP1 C alleel, SNP3 A alleel ja SNP4 C alleel suurendasid riski viljatuse kujunemiseks.
Challenges in endometriosis miRNA studies - From tissue heterogeneity to disease specific miRNAs.
(2017) Saare, Merli; Rekker, Kadri; Laisk-Podar, Triin; Rahmioglu, Nilufer; Zondervan, Krina; Salumets, Andres; Götte, Martin; Peters, Maire
In order to uncover miRNA changes in endometriosis pathogenesis, both endometriotic lesions and endometrial biopsies, as well as stromal and epithelial cells isolated from these tissues have been investigated and a large number of dysregulated miRNAs have been reported. However, the concordance between the result of different studies has remained small. One potential explanation for limited overlap between the proposed disease-related miRNAs could be the heterogeneity in tissue composition, as some studies have compared highly heterogeneous whole-lesion biopsies with endometrial tissue, some have compared the endometrium from patients and controls, and some have used pure cell fractions isolated from lesions and endometrium. This review focuses on the results of published miRNA studies in endometriosis to reveal the potential impact of tissue heterogeneity on the discovery of disease-specific miRNA alterations in endometriosis. Additionally, functional studies that explore the roles of endometriosis-involved miRNAs are discussed.
Differentially-Expressed miRNAs in Ectopic Stromal Cells Contribute to Endometriosis Development: The Plausible Role of miR-139-5p and miR-375
(2018) Rekker, Kadri; Tasa, Tõnis; Saare, Merli; Samuel, Külli; Kadastik, Ülle; Karro, Helle; Götte, Martin; Salumets, Andres; Peters, Maire
microRNA (miRNA) expression level alterations between endometrial tissue and endometriotic lesions indicate their involvement in endometriosis pathogenesis. However, as both endometrium and endometriotic lesions consist of different cell types in various proportions, it is not clear which cells contribute to variability in miRNA levels and the overall knowledge about cell-type specific miRNA expression in ectopic cells is scarce. Therefore, we utilized fluorescence-activated cell sorting to isolate endometrial stromal cells from paired endometrial and endometrioma biopsies and combined it with high-throughput sequencing to determine miRNA alterations in endometriotic stroma. The analysis revealed 149 abnormally expressed miRNAs in endometriotic lesions, including extensive upregulation of miR-139-5p and downregulation of miR-375 compared to eutopic cells. miRNA transfection experiments in the endometrial stromal cell line ST-T1b showed that the overexpression of miR-139-5p resulted in the downregulation of homeobox A9 (HOXA9) and HOXA10 expression, whereas the endothelin 1 (EDN1) gene was regulated by miR-375. The results of this study provide further insights into the complex molecular mechanisms involved in endometriosis pathogenesis and demonstrate the necessity for cell-type-specific analysis of ectopic tissues to understand the interactions between different cell populations in disease onset and progression.
High-throughput mRNA sequencing of stromal cells from endometriomas and endometrium
(2017) Rekker, Kadri; Saare, Merli; Eriste, Elo; Tasa, Tõnis; Kukuškina, Viktorija; Roost, Anne Mari; Anderson, Kristi; Samuel, Kadri; Karro, Helle; Salumets, Andres; Peters, Maire
The aetiology of endometriosis is still unclear and to find mechanisms behind the disease development, it is important to study each cell type from endometrium and ectopic lesions independently. The objective of this study was to uncover complete mRNA profiles in uncultured stromal cells from paired samples of endometriomas and eutopic endometrium. High-throughput mRNA sequencing revealed over 1300 dysregulated genes in stromal cells from ectopic lesions, including several novel genes in the context of endometriosis. Functional annotation analysis of differentially expressed genes highlighted pathways related to cell adhesion, extracellular matrix–receptor interaction and complement and coagulation cascade. Most importantly, we found a simultaneous upregulation of complement system components and inhibitors, indicating major imbalances in complement regulation in ectopic stromal cells. We also performed in vitro experiments to evaluate the effect of endometriosis patients’ peritoneal fluid (PF) on complement system gene expression levels, but no significant impact of PF on C3, CD55 and CFH levels was observed. In conclusion, the use of isolated stromal cells enables to determine gene expression levels without the background interference of other cell types. In the future, a new standard design studying all cell types from endometriotic lesions separately should be applied to reveal novel mechanisms behind endometriosis pathogenesis.
Molecular Profiling of Endometriotic Lesions and Endometria of Endometriosis Patients
(2016-04-15) Saare, Merli; Salumets, Andres, juhendaja; Peters, Maire, juhendaja; Karro, Helle, juhendaja; Tartu Ülikool. Meditsiiniteaduste valdkond.
Endometrioos on tõsine günekoloogiline haigus, mida iseloomustab emaka limaskesta ehk endomeetriumi koe kasvamine kolletena väljaspool emakaõõnt. Vaatamata intensiivsetele uuringutele on siiani ebaselge, miks endometrioosikolded moodustavad ja millised on need molekulaarsed muutused, mis haiguse kujunemisele kaasa aitavad. Endometrioosi tekkemehhanismide väljaselgitamist on oluliselt hõlbustanud mikrokiibi- ja sekveneerimistehnoloogiate kiire areng, mis võimaldavad ülevaatlikult kirjeldada molekulaarseid muutuseid endometrioosikolletes ja endomeetriumis. Varasemad suure läbilaskevõimega tehnoloogiatel põhinevad endometrioosi uuringud on paraku jõudnud vastukäivate tulemusteni, mis viitab suure tõenäosusega erinevustele katsete disainis ja seetõttu on väga oluline juba uuringut planeerides pöörata tähelepanu võimalikele kitsaskohtadele. Antud töö eesmärgiks oli leida endometrioosi kujunemist mõjutavaid geneetilisi, epigeneetilisi ja mikroRNAde tasemete muutuseid nii endometrioosikolletes kui ka endomeetriumis, kasutades selleks hoolikalt valitud katseskeemi ja mikrokiipidel ning süvasekveneerimisel põhinevaid tehnoloogiaid. Töö tulemuste põhjal võime järeldada, et kromosomaalsed ümberkorraldused endometrioosikolletes ja endomeetriumis ning muutused endomeetriumi DNA metülatsioonimustris ei ole endometrioosi kujunemise esmasteks põhjusteks. Leidsime viis endometrioosikolletes kõrgelt ekspresseeritud mikroRNAd, mille taseme määramine võimaldab ilma histoloogiliste uuringuteta koldeid tuvastada. See uuring tõi välja ka uuringudisaini olulisuse, näidates et kollete mikroRNA tasemete määramiseks tuleb arvesse võtta kollet ümbritseva koe normaalset mikroRNA profiili. Samuti näitasime, et menstruaaltükli jooksul toimuvad endomeetriumi DNA metülatsioonimustris olulised muutused, mida tuleb haigusseoseliste markerite otsimisel kindlasti arvestada.
The influence of menstrual cycle and endometriosis on endometrial methylome
(Clin Epigenetics, 2016-01) Saare, Merli; Modhukur, Vijayachitra; Suhorutshenko, Marina; Rajashekar, Balaji; Rekker, Kadri; Sõritsa, Deniss; Karro, Helle; Soplepmann, Pille; Sõritsa, Andrei; Lindgren, Cecilia M; Rahmioglu, Nilufer; Drong, Alexander; Becker, Christian M; Zondervan, Krina T; Salumets, Andres; Peters, Maire
BACKGROUND: Alterations in endometrial DNA methylation profile have been proposed as one potential mechanism initiating the development of endometriosis. However, the normal endometrial methylome is influenced by the cyclic hormonal changes, and the menstrual cycle phase-dependent epigenetic signature should be considered when studying endometrial disorders. So far, no studies have been performed to evaluate the menstrual cycle influences and endometriosis-specific endometrial methylation pattern at the same time. RESULTS: Infinium HumanMethylation 450K BeadChip arrays were used to explore DNA methylation profiles of endometrial tissues from various menstrual cycle phases from 31 patients with endometriosis and 24 healthy women. The DNA methylation profile of patients and controls was highly similar and only 28 differentially methylated regions (DMRs) between patients and controls were found. However, the overall magnitude of the methylation differences between patients and controls was rather small (Δβ ranging from -0.01 to -0.16 and from 0.01 to 0.08, respectively, for hypo- and hypermethylated CpGs). Unsupervised hierarchical clustering of the methylation data divided endometrial samples based on the menstrual cycle phase rather than diseased/non-diseased status. Further analysis revealed a number of menstrual cycle phase-specific epigenetic changes with largest changes occurring during the late-secretory and menstrual phases when substantial rearrangements of endometrial tissue take place. Comparison of cycle phase- and endometriosis-specific methylation profile changes revealed that 13 out of 28 endometriosis-specific DMRs were present in both datasets. CONCLUSIONS: The results of our study accentuate the importance of considering normal cyclic epigenetic changes in studies investigating endometrium-related disease-specific methylation patterns.