Browsing by Author "Jatsenko, Tatjana"

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A speculative outlook on embryonic aneuploidy: Can molecular pathways be involved?
(2018) Tšuiko, Olga; Jatsenko, Tatjana; Parameswaran Grace, Lalit Kumar; Kurg, Ants; Vermeesch, Joris Robert; Lanner, Fredrik; Altmäe, Signe; Salumets, Andres
The journey of embryonic development starts at oocyte fertilization, which triggers a complex cascade of events and cellular pathways that guide early embryogenesis. Recent technological advances have greatly expanded our knowledge of cleavage-stage embryo development, which is characterized by an increased rate of whole-chromosome losses and gains, mixoploidy, and atypical cleavage morphokinetics. Embryonic aneuploidy significantly contributes to implantation failure, spontaneous miscarriage, stillbirth or congenital birth defects in both natural and assisted human reproduction. Essentially, early embryo development is strongly determined by maternal factors. Owing to considerable limitations associated with human oocyte and embryo research, the use of animal models is inevitable. However, cellular and molecular mechanisms driving the error-prone early stages of development are still poorly described. In this review, we describe known events that lead to aneuploidy in mammalian oocytes and preimplantation embryos. As the processes of oocyte and embryo development are rigorously regulated by multiple signal-transduction pathways, we explore the putative role of signaling pathways in genomic integrity maintenance. Based on the existing evidence from human and animal data, we investigate whether critical early developmental pathways, like Wnt, Hippo and MAPK, together with distinct DNA damage response and DNA repair pathways can be associated with embryo genomic instability, a question that has, so far, remained largely unexplored.
Involvement of specialized DNA polymerases in mutagenic processes in Pseudomonas putida
(2010) Jatsenko, Tatjana
Karyotype of the blastocoel fluid demonstrates low concordance with both trophectoderm and inner cell mass
(2018-06) Tšuiko, Olga; Zhigalina, Daria I.; Jatsenko, Tatjana; Skryabin, Nikolay A.; Kanbekova, Olga R.; Artyukhova, Victoria G.; Svetlakov, Anatoly V.; Teearu, Katre; Trošin, Aleksander; Salumets, Andres; Kurg, Ants; Lebedev, Igor N.
Objective To compare the genomic profiles of blastocoel fluid (BF), inner cell mass (ICM), and trophectoderm (TE) cells derived from the same blastocyst. Design Prospective study. Setting Academic and in vitro fertilization units. Patient(s) Sixteen donated cryopreserved embryos at blastocyst stage. Intervention(s) BF, TE, and ICM cells were retrieved from each blastocyst for chromosome analysis by means of next-generation sequencing (NGS). Main Outcome Measure(s) Aneuploidy screening and assessment of mosaicism in BF, TE and ICM samples with subsequent comparison of genomic profiles between the three blastocyst compartments. Result(s) Out of 16 blastocysts, 10 BF samples and 14 TE and ICM samples provided reliable NGS data for comprehensive chromosome analysis. Only 40.0% of BF-DNA karyotypes were fully concordant with TE or ICM, compared with 85.7% concordance between TE and ICM. In addition, BF-DNA was burdened with mosaic aneuploidies and the total number of affected chromosomes in BF was significantly higher compared with the TE and ICM. Conclusion(s) BF-DNA can be successfully amplified and subjected to NGS, but owing to increased discordance with ICM and TE, BF does not adequately represent the status of the rest of the embryo. To overcome biologic and technical challenges associated with BF sampling and processing, blastocentesis would require improvement in both laboratory protocols and aneuploidy calling algorithms. Therefore, TE biopsy remains the most effective way to predict embryonic karyotype, and the use of BF as a single source of DNA for preimplantation genetic screening is not yet advised.
P. aeruginosa rifampitsiini resistentsusmehhanismide uurimine
(2008) Jatsenko, Tatjana
Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads
(2018-07-09) Jatsenko, Tatjana; Kivisaar, Maia, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond
Kahjustused DNA-s, mis tekivad kas rakkude normaalse elutegevuse käigus või erinevate keskonnategurite mõjul (näiteks UV-kiirgus, DNA-d kahjustavad kemikaalid), pärsivad genoomi replikatsiooni, takistades replikatiivse DNA polümeraasi edasiliikumist. Pikaajaline replikatsiooni seiskumine võib osutuda rakkudele letaalseks. Selleks, et DNA replikatsioon saaks jätkuda ka kahjustatud DNA-lt, on välja kujunenud DNA kahjustuste tolereerimise mehhanismid. Üheks neist on DNA kahjustustest ülesüntees (translesion DNA synthesis, TLS), mida viivad läbi spetsialiseeritud DNA polümeraasid. Need polümeraasid jätkavad DNA sünteesi kahjustatud nukleotiidi kohalt, tagades organismi ellujäämise DNA kahjustuste olemasolul. Samas võib vigaderohke süntees viia mutatsioonide tekkeni, mis on alusmaterjaliks evolutsioonile, kuid põhjustavad ka geneetilisi haigusi. Näiteks bakteritel on TLS polümeraaside toimel tekkinud geneetiline variantsus oluline antibiootikumide resistentsuse ja infektsioonivõime kujunemisel. TLS polümeraasid on potentsiaalseks märklauaks nii antibakteriaalses ravis kui ka vähiteraapias. Minu doktoritöö eesmärgiks oli selgitada TLS polümeraaside funktsioone, eeskätt nende võimalikku rolli mutatsiooniprotsessides ning DNA kahjustuste tolereerimisel perekonda Pseudomonas kuuluval mullabakteril P. putida ja inimese oportunistlikul patogeenil P. aeruginosa. Pseudomonaadidel on kolm TLS polümeraasi: Pol II, Pol IV ja ImuABC. Uurimistöö tulemused viitavad sellele, et bakteris P. putida võivad TLS polümeraasid osaleda DNA sünteesil DNA polümeraasi Pol I puudumisel. Lisaks selgus, et Pol IV ja ImuABC on olulised DNA alküülkahjustuste talumisel. Kui ImuC viib läbi vigaderohket sünteesi, suurendades mutatsioonide arvu, siis Pol IV ületab DNA alküülkahjustusi väga täpselt. Üllatuslikult selgus, et bakterite inkubeerimise temperatuur mõjutab DNA alküülkahjustuste tolereerimist ja/või reparatsiooni efektiivsust.
TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting
(2018) Teder, Hindrek; Koel, Mariann; Paluoja, Priit; Jatsenko, Tatjana; Rekker, Kadri; Laisk-Podar, Triin; Kukuškina, Viktorija; Velthut-Meikas, Agne; Fjodorova, Olga; Peters, Maire; Kere, Juha; Salumets, Andres; Palta, Priit; Krjutškov, Kaarel
Targeted next-generation sequencing (NGS) methods have become essential in medical research and diagnostics. In addition to NGS sensitivity and high-throughput capacity, precise biomolecule counting based on unique molecular identifier (UMI) has potential to increase biomolecule detection accuracy. Although UMIs are widely used in basic research its introduction to clinical assays is still in progress. Here, we present a robust and cost-effective TAC-seq (Targeted Allele Counting by sequencing) method that uses UMIs to estimate the original molecule counts of mRNAs, microRNAs, and cell-free DNA. We applied TAC-seq in three different clinical applications and compared the results with standard NGS. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX, +21) genomic DNA. TAC-seq mRNA profiling showed identical clustering results to transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard NGS. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p = 7.6 × 10−4) excess of chromosome 21 molecules at 10% fetal fraction level. Based on three proof-of-principle applications we demonstrate that TAC-seq is an accurate and highly potential biomarker profiling method for advanced medical research and diagnostics.