Inimese endomeetriumi normaalne ja patoloogiline profiil proteoomika vaatevinklist

Väitekirja elektrooniline versioon ei sisalda publikatsiooneDNA ja RNA-põhiste meetodite kasutamine on reproduktiivmeditsiini arengut märkimisväärselt mõjutanud, suurendades arusaamist haiguste pärilikest tagamaadest ja tuues kliinilisse praktikasse uusi diagnostilisi meetodeid. Geenide peamiseks funktsionaalseks väljundiks on aga valgud ning nende uurimine on ainus viis haiguslikest protsessidest vahetu ja detailsema pildi saamiseks. Seda enam, et esmase geeniekspressiooni seos valkude tasemetega rakkudes, kudedes ja kehavedelikes on tihtilugu piiratud. Valkude uurimiseks kasutatav massispektromeetrial põhinev proteoomika on kiirelt arenev teadusharu, mis võimaldab bioloogilisest materjalist, st. nii kudedest, rakkudest kui kehavedelikest kõrge tundlikkusega määrata nende valgulist koostist ehk proteoomi. Antud uurimistöö eesmärgiks oligi rakendada kaasaegseid massispektromeetria-põhiseid proteoomika meetodeid, et leida täpsemaid vastuseid naiste reproduktiivtervisega seotud probleemide molekulaarsete mehhanismide selgitamiseks ja välja pakkuda uusi markerikandidaate diagnostikaks. Täpsemalt keskendus meie töö endometrioosile ja kehavälise viljastamise (IVF) efektiivsusega seotud biomarkerite otsingule. Meie tööst selgus, et endometrioosi korral on haiguskolde rakkudes toimunud mitmeid muutusi, mis sarnanevad vähi- ja tüvirakkudes kirjeldatud ainevahetuslike kohastumustega. Meie tulemused näitavad, et endometrioosikolde rakud kasutavad sõltumata hapniku juuresolust suurenenud määral anaeroobset ainevahetust. Samuti on kolderakkudes muutunud valkude avaldumine, mis on seotud rakkude levimise ja ellujäämisega. Meie tulemused pakuvad küll välja potentsiaalseid sihtmärk-valke haiguskulu mõjutamiseks, kuid rõhutavad ka vajadust edasisteks uuringuteks suuremates kohortides. Töö teises osas uurisime emakaõõne sekreedi valke, et leida biomarkereid kehavälise viljastamise optimeerimiseks. Selle töö tulemusena leidsime, et emakaõõne sekreet sisaldab valke, mida on võimalik rakendada embrüosiirdamise efektiivsemaks ajastamiseks. Samuti viitavad meie tulemused, et naistel, kellel on IVF korduvalt ebaõnnestunud, esineb häireid emaka limaskesta vastuvõtlikkuses embrüotele ehk retseptiivsuses. Leitud valguliste biomarkerite paneeli on võimalik arendada diagnostiliseks testiks, mis tõstaks IVFi tõhusust ja aitaks paremini tuvastada retseptiivsushäirega naisi.The impact of genomics and transcriptomics methods for reproductive medicine has been substantial by increasing the understanding behind heritable factors of diseases and by enabling new avenues for diagnostic testing. Nevertheless, the main functional output of genes are proteins, and, studying proteins is essential for providing further detail into the understanding of pathogenetic mechanisms. Furthermore, the correlation between early gene expression and the levels of proteins in cells, tissues and bodily fluids has been shown to be limited. Mass spectrometry-based proteomics is a progressively developing field that has finally reached to a point where measurement of proteomes or the full protein complement is now becoming feasible. The main objective of the current work was to apply modern proteomics methods to enhance the understanding behind reproductive diseases and to propose new biomarkers for diagnostics. More specifically, our work focused on endometriosis and the search for markers that could improve the in vitro fertilization (IVF) process. By analyzing cells from the uterine lining and endometriosis lesions, we found evidence for altered energy metabolism in endometriotic stromal cells and these changes are akin to changes previously seen in tumor and stem cells. In addition, lesion stromal cells appear to have changes in the expression of proteins that are associated with increased invasiveness and survival of cells. Our results propose novel candidates for future studies to see whether targeting these proteins could affect the course of the illness. In the second part of our work, we analyzed secreted proteins from uterine cells to find biomarkers for improving the success rates of IVF. As a result of our study, we found that the uterine secretome contains proteins that reflect the embryo receptivity status of the endometrium. Our results also underlined that women with recurrent implantation failure in IVF have altered uterine secretomes. The proposed biomarker panel of our study can be developed into a diagnostic test that would increase the effectiveness of the IVF procedure and would help to screen for women with pathological uterine receptivity.https://www.ester.ee/record=b534053

Differential phosphorylation determines the repressor and activator potencies of GLI1 proteins and their efficiency in modulating the HPV life cycle

The Sonic Hedgehog (Shh) signalling pathway plays multiple roles during embryonic development and under pathological conditions. Although the core components of the Shh pathway are conserved, the regulation of signal transduction varies significantly among species and cell types. Protein kinases Ulk3 and Pka are involved in the Shh pathway as modulators of the activities of Gli transcription factors, which are the nuclear mediators of the signal. Here, we investigate the regulation and activities of two GLI1 isoforms, full-length GLI1 (GLI1FL) and GLI1ΔN. The latter protein lacks the first 128 amino acids including the conserved phosphorylation cluster and the binding motif for SUFU, the key regulator of GLI activity. Both GLI1 isoforms are co-expressed in all human cell lines analysed and possess similar DNA binding activity. ULK3 potentiates the transcriptional activity of both GLI1 proteins, whereas PKA inhibits the activity of GLI1ΔN, but not GLI1FL. In addition to its well-established role as a transcriptional activator, GLI1FL acts as a repressor by inhibiting transcription from the early promoters of human papillomavirus type 18 (HPV18). Additionally, compared to GLI1ΔN, GLI1FL is a more potent suppressor of replication of several HPV types. Altogether, our data show that the N-terminal part of GLI1FL is crucial for the realization of its full potential as a transcriptional regulator

Stanniocalcin-1 expression in normal human endometrium and dysregulation in endometriosis

Objective To determine expression of stanniocalcin-1 (STC1) in human endometrium with and without endometriosis and its regulation by steroid hormones. Design Laboratory study. Setting University. Patient(s) Nineteen women with endometriosis and 33 control women. Intervention(s) Endometrial biopsy and fluid sampling. Main Outcome Measure(s) Analysis of early secretory (ESE) and midsecretory (MSE) endometrial secretomes from fertile women with the use of nano–liquid chromatography–dual mass spectrometry; real-time quantitative polymerase chain reaction, and immunohistochemistry for STC1 and its receptor calcium-sensing receptor (CASR) mRNA and proteins in endometrium with and without endometriosis; evaluation of STC1 and CASR mRNA expression in endometrial stromal fibroblasts (eSF) from women with and without endometriosis decidualized with the use of E2P or 8-bromo-cyclic adenosine monophosphate (cAMP). Result(s) STC1 protein was strongly up-regulated in MSE versus ESE in endometrial fluid of fertile women. STC1 mRNA significantly increased in MSE from women with, but not from those without, endometriosis, compared with proliferative endometrium or ESE, with no significant difference throughout the menstrual cycle between groups. STC1 mRNA in eSF from control women increased >230-fold on decidualization with the use of cAMP versus 45-fold from women with endometriosis, which was not seen on decidualization with E2/P. CASR mRNA did not exhibit significant differences in any condition and was not expressed in isolated eSF. STC1 protein immunoexpression in eSF was significantly lower in women with endometriosis compared with control women. Conclusion(s) STC1 protein is significantly up-regulated in MSE endometrial fluid and is dysregulated in eutopic endometrial tissue from women with endometriosis. It is likely regulated by cAMP and may be involved in the pathogenesis of decidualization defects

Target prediction and validation of microRNAs expressed from FSHR and aromatase genes in human ovarian granulosa cells

MicroRNAs (miRNAs) are known post-transcriptional regulators of various biological processes including ovarian follicle development. We have previously identified miRNAs from human preovulatory ovarian granulosa cells that are expressed from the intronic regions of two key genes in normal follicular development: FSH receptor (FSHR) and CYP19A1, the latter encoding the aromatase enzyme. The present study aims to identify the target genes regulated by these miRNAs: hsa-miR-548ba and hsa-miR-7973, respectively. The miRNAs of interest were transfected into KGN cell line and the gene expression changes were analyzed by Affymetrix microarray. Potential miRNA-regulated genes were further filtered by bioinformatic target prediction algorithms and validated for direct miRNA:mRNA binding by luciferase reporter assay. LIFR, PTEN, NEO1 and SP110 were confirmed as targets for hsa-miR-548ba. Hsa-miR-7973 target genes ADAM19, PXDN and FMNL3 also passed all verification steps. Additionally, the expression pattern of the miRNAs was studied in human primary cumulus granulosa cell culture in relation to the expression of their host genes and FSH stimulation. Based on our findings we propose the involvement of hsa-miR-548ba in the regulation of follicle growth and activation via LIFR and PTEN. Hsa-miR-7973 may be implicated in the modulation of extracellular matrix and cell-cell interactions by regulating the expression of its identified targets.Peer reviewe

Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake

Naturally competent bacteria acquire DNA from their surroundings to survive in nutrient-poor environments and incorporate DNA into their genomes as new genes for improved survival. The secretin HofQ from the oral pathogen Aggregatibacter actinomycetemcomitans has been associated with DNA uptake. Cytokine sequestering is a potential virulence mechanism in various bacteria and may modulate both host defense and bacterial physiology. The objective of this study was to elucidate a possible connection between natural competence and cytokine uptake in A. actinomycetemcomitans. The extramembranous domain of HofQ (emHofQ) was shown to interact with various cytokines, of which IL-8 exhibited the strongest interaction. The dissociation constant between emHofQ and IL-8 was 43nM in static settings and 2.4M in dynamic settings. The moderate binding affinity is consistent with the hypothesis that emHofQ recognizes cytokines before transporting them into the cells. The interaction site was identified via crosslinking and mutational analysis. By structural comparison, relateda type I KH domain with a similar interaction site was detected in the Neisseria meningitidis secretin PilQ, which has been shown to participate in IL-8 uptake. Deletion of hofQ from the A. actinomycetemcomitans genome decreased the overall biofilm formation of this organism, abolished the response to cytokines, i.e., decreased eDNA levels in the presence of cytokines, and increased the susceptibility of the biofilm to tested -lactams. Moreover, we showed that recombinant IL-8 interacted with DNA. These results can be used in further studies on the specific role of cytokine uptake in bacterial virulence without interfering with natural-competence-related DNA uptake.Peer reviewe

Mutation of CD2AP and SH3KBP1 binding motif in alphavirus nsP3 hypervariable domain results in attenuated virus

Infection by Chikungunya virus (CHIKV) of the Old World alphaviruses (family Togaviridae) in humans can cause arthritis and arthralgia. The virus encodes four non-structural proteins (nsP) (nsP1, nsp2, nsP3 and nsP4) that act as subunits of the virus replicase. These proteins also interact with numerous host proteins and some crucial interactions are mediated by the unstructured C-terminal hypervariable domain (HVD) of nsP3. In this study, a human cell line expressing EGFP tagged with CHIKV nsP3 HVD was established. Using quantitative proteomics, it was found that CHIKV nsP3 HVD can bind cytoskeletal proteins, including CD2AP, SH3KBP1, CAPZA1, CAPZA2 and CAPZB. The interaction with CD2AP was found to be most evident; its binding site was mapped to the second SH3 ligand-like element in nsP3 HVD. Further assessment indicated that CD2AP can bind to nsP3 HVDs of many different New and Old World alphaviruses. Mutation of the short binding element hampered the ability of the virus to establish infection. The mutation also abolished ability of CD2AP to co-localise with nsP3 and replication complexes of CHIKV; the same was observed for Semliki Forest virus (SFV) harbouring a similar mutation. Similar to CD2AP, its homolog SH3KBP1 also bound the identified motif in CHIKV and SFV nsP3

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in GeneSpecific Translation Efficiency in Yeast

Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology

Compartmentalized gene expression profiling of receptive endometrium reveals progesterone regulated ENPP3 is differentially expressed and secreted in glycosylated form

The complexity of endometrial receptivity at the molecular level needs to be explored in detail to improve the management of infertility. Here, differential expression of transcriptomes in receptive endometrial glands and stroma revealed Ectonucleotide Pyrophosphatase/Phosphodiesterase 3 (ENPP3) as a progesterone regulated factor and confirmed by various methods, both at mRNA and protein level. The involvement of ENPP3 in embryo attachment was tested in an in vitro model for human embryo implantation. Interestingly, there was high expression of ENPP3 mRNA in stroma but not protein. Presence of N-glycosylated ENPP3 in receptive phase uterine fluid in women confirms its regulation by progesterone and makes it possible to use in a non-invasive test of endometrial receptivity.Peer reviewe

Proteomic dataset of wolframin-deficient mouse heart and skeletal muscles.

The data presented in this article are related to the research article entitled "Increased Mitochondrial Protein Levels and Bioenergetics in the musculus rectus femoris of Wfs1-Deficient mice" (Eimre et al., accepted for publication). This dataset reports the analysis of Wfs1-deficient mouse heart, musculus soleus, and white part of musculus rectus femoris by liquid chromatography/tandem mass spectrometry. Label-free quantitative analysis of the mass spectrometry data identified 4056 proteins, with 114, 212, and 1290 proteins differentially expressed (t-test; p m. soleus, and m. rectus femoris, respectively, between the Wfs1-deficient and wild-type groups. Eight proteins were found to be differentially expressed in all mentioned muscles, with 1 protein differently expressed in oxidative (m. soleus and heart) and 88 in skeletal muscles. This dataset supports the cited study and can be used to extend additional analyses. Data are available via ProteomeXchange with identifier PXD011019