3’ isomiR species and DNA contamination influence reliable quantification of microRNAs by stem-loop quantitative PCR

MicroRNAs (miRNAs) are ∼20-24 nucleotide-long regulatory RNAs that have been proven to play important roles in many cellular processes. Since their discovery, a number of different techniques have been developed to detect and accurately quantify them. For individual mature miRNA measurements, quantitative stem-loop real-time PCR represents a widely used method. Although there are some data on optimization of this technique, there are still many factors that have not been investigated yet. In this study, we have thoroughly optimized this technique and pointed out several important factors that influence reliable quantification. First, we found that total RNA input can affect the measurements. Second, our data showed that carryover DNA contamination could also mislead the detection in a sequence-specific manner. Additionally, we provided evidence that different 3' isomiR species of a particular miRNA can be reverse transcribed and cross-detected even by specifically targeted assays. Besides these, we have investigated the measurement of reaction efficiencies from total RNA samples and the accuracy of simultaneous reverse transcription reactions for increasing reliability and cost effectiveness without the loss of sensitivity and specificity. In summary, we provide a detailed, refined protocol for reliable detection of microRNA species by quantitative stem-loop PCR

Transcription activity of transposon sequence limits Sleeping Beauty transposition.

Sleeping Beauty (SB) transposon based technology has been extensively applied in basic research and biotechnology for routine cell culture gene delivery and vertebrate transgenesis, and it is also investigated in various gene therapy applications. Cell tolerance for the transgene is a key factor during transgenesis and is modulated not only through the type but by the dose of expression. Our experimental results exemplify that transgenes regulated with high activity promoters can reduce the overall success of gene delivery. Observations connected to transposon donors regulated by different promoters have also revealed inverse correlation between transcription activity and the hyperactive variant SB100X excision efficiency. This competition between transcription and transposition was independent of the transgene coding sequence and did not alter the transgenic efficiency in general. However, promoters applied in the transgene cassette can produce different average copy numbers depending on the transcriptional activity of the transposon. Unlike the piggyBac (PB) transposon system, this phenomenon allows a fine balance of expression using the high copy potential SB system that adjusts the copy number of lower activity promoter driven transgenes to a higher expression level. All this contributes to a well-tolerated and satisfactory transgenesis, and would be important to consider in gene therapy applications

A molekuláris onkogenezis mechanizmusai gyakori daganatokban = Mechanisms of molecular oncogenesis in common malignancies

Munkacsoportunk két évtizede megkezdett kutatási programját folytatta, amelynek fő célkitűzése új molekuláris rákgenetikai ismeretek szerzése a rák iránti fokozott genetikai fogékonyság molekuláris tényezőinek megismerésére. Vizsgálataink a Magyarországon gyakori daganatos megbetegedésekre (emlőrák, vastagbélrák, ivarszervi daganatok), elsősorban ezek familiáris formáira irányultak. Folytattuk, illetve megkezdtük a daganatszindrómák hajlamosító génjeinek elemzését örökletes emlő- és petefészekrákokban (BRCA1/2, CHEK2), familiáris adenomatozus polyposisban (APC), és herediter, nem a polyposis talaján kialakuló vastagbélrák szindróma (HNPCC) "mutátor gén"-jeiben (MSH2, MLH1). Az emlőrákos családokon, valamint kohorszokon nyert kutatási eredmények adatainak nemzetközi szintű összesítése, molekuláris epidemiológiai kiértékelése révén az örökletes daganatok kialakulására hajlamosító mutációt hordozók rákkockázatáról, a prevenciós tényezőkről és a betegség genetika-klinikai-pathológiai összefüggéseiről szereztünk további új ismereteket. Nemzetközi együttműködésben hozzájárultunk a csírasejtes hererákra hajlamosító első genetikai variánsok azonosításához. Daganatos megbetegedésre hajlamosító gének (BRCA1, STK11) esetében elemeztük az alternatív splicing szerepét a betegség kialakulásában. Újabban megkezdett génexpressziós profilvizsgálatok révén bepillantást nyertünk a molekuláris genetikai útvonalak és a metabolikus útvonalak kölcsönhatásába. | We have extended our molecular cancer genetic studies that were initiated in Hungary two decades ago and were aimed at providing new knowledge on molecular cancer genetics, with a focus on genetic susceptibility to cancer. The studies were conducted on common malignancies in Hungary (breast, colorectal and genitourinary cancers). Extended analysis of the predisposing genes of cancer syndromes was initiated or continued for hereditary breast- and/or ovarian cancer (BRCA1, BRCA2, CHEK2), for familial adenomatous polyposis (APC), for Peutz-Jeghers syndrome (STK11), and for hereditary non-polyposis colorectal carcinoma, HNPCC ("mutator genes" such as MSH2, MLH1). Forwarding the result and data of our molecular genetic analysis on breast cancer families and cancer cohorts for international data integration and molecular epidemiological analysis resulted in generation of new knowledge on cancer risk for the carriers of deleterious germ-line mutations, and on genetic-clinical and pathological correlations in development of breast cancer. Participating in international studies we have contributed to identification of new genetic variants predisposing to germ cell testicular cancer. The role of alternative splicing in development of cancer was investigated in cancer susceptibility genes BRCA1 and STK11. By recent introduction of gene-expression profiling we have gained preliminary insight into the interaction of metabolic and molecular pathways

Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications

There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the DeltaDeltaCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies

Excision efficiency is not strongly coupled to transgenic rate: cell type dependent transposition efficiency of Sleeping Beauty and piggyBac DNA transposons

The Sleeping Beauty (SB) and piggyBac (PB) DNA transposons represent an emerging new gene delivery technology, potentially suitable for human gene therapy applications. Previous studies pointed to important differences between these transposon systems, depending on the cell types examined and the methodologies applied. However, efficiencies cannot always be compared because of differences in applications. In addition, “overproduction inhibition,” a phenomenon believed to be a characteristic of DNA transposons, can remarkably reduce the overall transgenic rate, emphasizing the importance of transposase dose applied. Therefore, because of lack of comprehensive analysis, researchers are forced to optimize the technology for their own “in-house” platforms. In this study, we investigated the transposition of several SB (SB11, SB32, SB100X) and PB (mPB and hyPB) variants in various cell types at three levels: comparing the excision efficiency of the reaction by real-time PCR, testing the overall transgenic rate by detecting cells with stable integrations, and determining the average copy number when using different transposon systems and conditions. We concluded that high excision activity is not always followed by a higher transgenic rate, as exemplified by the hyperactive transposases, indicating that the excision and the integration steps of transposition are not strongly coupled as previously thought. In general, all levels of transposition show remarkable differences depending on the transposase used and cell lines examined, being the least efficient in human embryonic stem cells (hESCs). In spite of the comparably low activity in those special cell types, the hyperactive SB100X and hyPB systems could be used in hESCs with similar transgenic efficiency and with reasonably low (2–3) transgene copy numbers, indicating their potential applicability for gene therapy purposes in the future

Exosomal small RNA profiling in first-trimester maternal blood explores early molecular pathways of preterm preeclampsia

IntroductionPreeclampsia (PE) is a severe obstetrical syndrome characterized by new-onset hypertension and proteinuria and it is often associated with fetal intrauterine growth restriction (IUGR). PE leads to long-term health complications, so early diagnosis would be crucial for timely prevention. There are multiple etiologies and subtypes of PE, and this heterogeneity has hindered accurate identification in the presymptomatic phase. Recent investigations have pointed to the potential role of small regulatory RNAs in PE, and these species, which travel in extracellular vesicles (EVs) in the circulation, have raised the possibility of non-invasive diagnostics. The aim of this study was to investigate the behavior of exosomal regulatory small RNAs in the most severe subtype of PE with IUGR.MethodsWe isolated exosomal EVs from first-trimester peripheral blood plasma samples of women who later developed preterm PE with IUGR (n=6) and gestational age-matched healthy controls (n=14). The small RNA content of EVs and their differential expression were determined by next-generation sequencing and further validated by quantitative real-time PCR. We also applied the rigorous exceRpt bioinformatics pipeline for small RNA identification, followed by target verification and Gene Ontology analysis.ResultsOverall, >2700 small RNAs were identified in all samples and, of interest, the majority belonged to the RNA interference (RNAi) pathways. Among the RNAi species, 16 differentially expressed microRNAs were up-regulated in PE, whereas up-regulated and down-regulated members were equally found among the six identified Piwi-associated RNAs. Gene ontology analysis of the predicted small RNA targets showed enrichment of genes in pathways related to immune processes involved in decidualization, placentation and embryonic development, indicating that dysregulation of the induced small RNAs is connected to the impairment of immune pathways in preeclampsia development. Finally, the subsequent validation experiments revealed that the hsa_piR_016658 piRNA is a promising biomarker candidate for preterm PE associated with IUGR.DiscussionOur rigorously designed study in a homogeneous group of patients unraveled small RNAs in circulating maternal exosomes that act on physiological pathways dysregulated in preterm PE with IUGR. Therefore, our small RNA hits are not only suitable biomarker candidates, but the revealed biological pathways may further inform us about the complex pathology of this severe PE subtype

The importance of drug transporters in human pluripotent stem cells and in early tissue differentiation

Introduction: Drug transporters are large transmembrane proteins which catalyse the movement of a wide variety of chemicals, including drugs as well as xeno- and endobiotics through cellular membranes. The major groups of these proteins include the ATP-binding cassette transporters which in eukaryotes work as ATP-fuelled drug exporters and the Solute Carrier transporters, with various transport directions and mechanisms.Areas covered: In this review, we discuss the key ATP-binding cassette and Solute Carrier drug transporters which have been reported to contribute to the function and/or protection of undifferentiated human stem cells and during tissue differentiation. We review the various techniques for studying transporter expression and function in stem cells, and the role of drug transporters in foetal and placental tissues is also discussed. We especially focus on the regulation of transporter expression by factors modulating cell differentiation properties and on the function of the transporters in adjustment to environmental challenges.Expert opinion: The relatively new and as yet unexplored territory of transporters in stem cell biology may rapidly expand and bring important new information regarding the metabolic and epigenetic regulation of stemness and the early differentiation properties. Drug transporters are clearly important protective and regulatory components in stem cells and differentiation. © 2015 Taylor & Francis

ABC transzporterek vizsgálata emberi őssejtekben és a sejt-differenciálódás során = Expression and function of ABC transporters in human stem cells and during cell differentiation

A projektben az ABC (ATP-Binding Cassette) transzporterek kifejeződését és funkcióját vizsgáltuk emberi őssejtekben, valamint követtük a normális és daganatos sejtdifferenciálódás során bekövetkező molekuláris szintű változásokat. Elsősorban a gyógyszerek hatásában, anyagcseréjében, az ellenük kifejeződő rezisztenciában szereplő transzportereket, valamint a sejtmembrán lipid-anyagcseréjében szerepet játszó ABC transzportereket vizsgáltuk. A projekt fontos része volt az emberi embrionális őssejtek speciális tenyésztési és differenciálási módszereinek adaptálása, továbbfejlesztése. Az ABC transzporterek vizsgálata során igazoltuk, hogy a humán embrionális őssejtekben az ABCG2 a legjelentősebb xenobiotikum transzporter, a korai sejtdifferenciálódás során az ABCG2 kifejeződése először emelkedik, majd jelentősen csökken. Megállapítottuk, hogy az ABCG2 mRNS használata különbözik a tumorsejtekben, a differenciálódott szöveti sejtekben, illetve a nem-differenciálódott őssejtekben. Új, transzpozon-alapú módszereket dolgoztunk ki az őssejtek stabil genetikai módosítására, fluoreszcens riporter fehérjék bevitelére. Az ABCG2 és az ABCA1 fehérjék címkézett változatainak kifejezése lehetővé tette a transzporterek sejten belüli lokalizációjának követését. Részletesen elemeztük az ABCG2 multidrog transzporter szerkezet-funkció összefüggéseit, szubsztrátokkal jelentkező kölcsönhatásait, alkalmazásokat fejlesztettünk ki a gyógyszerhatások vizsgálatára. | In this project we have studied the expression and function of ABC (ATP-Binding Cassette) transporters in human embryonic and tumor stem cells and followed the changes during normal and tumor cell differentiation at a molecular level. We have focused on the investigation of ABC transporters involved in drug metabolism, cancer multidrug resistance and cellular lipid metabolism. An important part of the project was to establish and further develop proper laboratory conditions and methodologies for culturing and differentiating human pluripotent stem cells. When studying human ABC transporters in human embryonic stem cells we demonstrated the major role of the ABCG2 protein. We found that the expression of this transporter first increases, then greatly decreases during early stem cell differentiation. The use of mRNA was found to be different in the tumor cells, differentiated cells, and pluripotent stem cells, respectively. We have developed new, transposon-based methods for the stable genetic modification of pluripotent stem cells and for the expression of fluorescent reporter proteins. By using tagged versions of the ABCG2 and ABCA1 proteins we could follow the intracellular localization of these transporters. We have studied in detail the structure-function relationships and substrate interactions of the ABCG2 transporter and developed new assays for studying drug interactions