The precise and unambiguous detection and quantification of internal RNA modifications represents a critical step for understanding their physiological functions. The methods of direct RNA sequencing are quickly developing allowing for the precise location of internal RNA marks. This detection is, however, not quantitative and still presents detection limits. One of the biggest remaining challenges in the field is still the detection and quantification of m6A, m6Am, inosine, and m1A modifications of adenosine. The second intriguing and timely question remaining to be addressed is the extent to which individual marks are coregulated or potentially can affect each other. Here, we present a methodological approach to detect and quantify several key mRNA modifications in human total RNA and in mRNA, which is difficult to purify away from contaminating tRNA. We show that the adenosine demethylase FTO primarily targets m6Am marks in noncoding RNAs in HEK293T cells. Surprisingly, we observe little effect of FTO or ALKBH5 depletion on the m6A mRNA levels. Interestingly, the upregulation of ALKBH5 is accompanied by an increase in inosine level in overall mRNA.

• Klíčová slova
• ADAR, ALKBH5, FTO, RNA editing, adenosine methylation, inosine,
• MeSH
• adenosin * analogy a deriváty   metabolismus   genetika   analýza   MeSH
• alfa-ketoglutarát-dependentní dioxygenasa, AlkB homolog 5 * metabolismus   genetika   MeSH
• chromatografie kapalinová metody   MeSH
• gen pro FTO * metabolismus   genetika   MeSH
• HEK293 buňky MeSH
• inosin * metabolismus   genetika   MeSH
• kapalinová chromatografie-hmotnostní spektrometrie MeSH
• lidé MeSH
• messenger RNA * genetika   metabolismus   MeSH
• posttranskripční úpravy RNA MeSH
• tandemová hmotnostní spektrometrie * metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosin * MeSH
• alfa-ketoglutarát-dependentní dioxygenasa, AlkB homolog 5 * MeSH
• ALKBH5 protein, human MeSH Prohlížeč
• FTO protein, human MeSH Prohlížeč
• gen pro FTO * MeSH
• inosin * MeSH
• messenger RNA * MeSH
• N-methyladenosine MeSH Prohlížeč

Adar null mutant mouse embryos die with aberrant double-stranded RNA (dsRNA)-driven interferon induction, and Adar Mavs double mutants, in which interferon induction is prevented, die soon after birth. Protein kinase R (Pkr) is aberrantly activated in Adar Mavs mouse pup intestines before death, intestinal crypt cells die, and intestinal villi are lost. Adar Mavs Eifak2 (Pkr) triple mutant mice rescue all defects and have long-term survival. Adenosine deaminase acting on RNA 1 (ADAR1) and PKR co-immunoprecipitate from cells, suggesting PKR inhibition by direct interaction. AlphaFold studies on an inhibitory PKR dsRNA binding domain (dsRBD)-kinase domain interaction before dsRNA binding and on an inhibitory ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA provide a testable model of the inhibition. Wild-type or editing-inactive human ADAR1 expressed in A549 cells inhibits activation of endogenous PKR. ADAR1 dsRNA binding is required for, but is not sufficient for, PKR inhibition. Mutating the ADAR1 dsRBD3-PKR contact prevents co-immunoprecipitation, ADAR1 inhibition of PKR activity, and co-localization of ADAR1 and PKR in cells.

• Klíčová slova
• ADAR RNA editing, Adar mutant, Aicardi-Goutieres Syndrome (AGS), CP: Molecular biology, Mavs, dsRNA, dsRNA-binding protein, innate immune sensors, protein kinase R,
• MeSH
• adenosindeaminasa * metabolismus   genetika   MeSH
• aktivace enzymů MeSH
• buňky A549 MeSH
• dvouvláknová RNA * metabolismus   MeSH
• kinasa eIF-2 * metabolismus   MeSH
• lidé MeSH
• myši MeSH
• proteinové domény MeSH
• proteiny vázající RNA * metabolismus   genetika   MeSH
• vazba proteinů MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ADAR protein, human MeSH Prohlížeč
• adenosindeaminasa * MeSH
• dvouvláknová RNA * MeSH
• kinasa eIF-2 * MeSH
• proteiny vázající RNA * MeSH

The potential clinical applications of hematopoietic stem cells (HSCs) derived from human pluripotent stem cells (hPSCs) are limited by the difficulty of recapitulating embryoid hematopoiesis and by the unknown differentiation potential of hPSC lines. To evaluate their hematopoietic developmental potential, available hPSC lines were differentiated by an embryoid body (EB) suspension culture in serum-free medium supplemented with three different cytokine mixes (CMs). The hPSC differentiation status was investigated by the flow cytometry expression profiles of cell surface molecules, and the gene expression of pluripotency and differentiation markers over time was evaluated by real-time reverse transcription polymerase chain reaction (qRT-PCR). hPSC lines differed in several aspects of the differentiation process, including the absolute yield of hematopoietic progenitors, the proportion of hematopoietic progenitor populations, and the effect of various CMs. The ability to generate hematopoietic progenitors was then associated with the morphology of the developing EBs, the expression of the endodermal markers AFP and SOX17, and the hematopoietic transcription factor RUNX1. These findings deepen the knowledge about the hematopoietic propensity of hPSCs and identify its variability as an aspect that must be taken into account before the usage of hPSC-derived HSCs in downstream applications.

• Klíčová slova
• cytokines, embryoid bodies, hematopoietic differentiation, hematopoietic stem cells, pluripotent stem cells,
• MeSH
• buněčné linie MeSH
• diferenciační antigeny biosyntéza   MeSH
• embryoidní tělíska cytologie   metabolismus   MeSH
• endoderm cytologie   metabolismus   MeSH
• hematopoéza * MeSH
• lidé MeSH
• lidské embryonální kmenové buňky cytologie   metabolismus   MeSH
• regulace genové exprese * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• diferenciační antigeny MeSH

BACKGROUND: Human induced pluripotent stem cells (hiPSCs) play roles in both disease modelling and regenerative medicine. It is critical that the genomic integrity of the cells remains intact and that the DNA repair systems are fully functional. In this article, we focused on the detection of DNA double-strand breaks (DSBs) by phosphorylated histone H2AX (known as γH2AX) and p53-binding protein 1 (53BP1) in three distinct lines of hiPSCs, their source cells, and one line of human embryonic stem cells (hESCs). METHODS: We measured spontaneously occurring DSBs throughout the process of fibroblast reprogramming and during long-term in vitro culturing. To assess the variations in the functionality of the DNA repair system among the samples, the number of DSBs induced by γ-irradiation and the decrease over time was analysed. The foci number was detected by fluorescence microscopy separately for the G1 and S/G2 cell cycle phases. RESULTS: We demonstrated that fibroblasts contained a low number of non-replication-related DSBs, while this number increased after reprogramming into hiPSCs and then decreased again after long-term in vitro passaging. The artificial induction of DSBs revealed that the repair mechanisms function well in the source cells and hiPSCs at low passages, but fail to recognize a substantial proportion of DSBs at high passages. CONCLUSIONS: Our observations suggest that cellular reprogramming increases the DSB number but that the repair mechanism functions well. However, after prolonged in vitro culturing of hiPSCs, the repair capacity decreases.

• Klíčová slova
• 53BP1, DNA double-strand breaks, DNA repair, Human induced pluripotent stem cells, Long-term in vitro culture, γH2AX,
• MeSH
• 53BP1 genetika   metabolismus   MeSH
• buněčné linie MeSH
• DNA genetika   metabolismus   MeSH
• dvouřetězcové zlomy DNA * účinky záření   MeSH
• exprese genu MeSH
• fibroblasty cytologie   metabolismus   účinky záření   MeSH
• fosforylace účinky záření   MeSH
• histony genetika   metabolismus   MeSH
• indukované pluripotentní kmenové buňky cytologie   metabolismus   účinky záření   MeSH
• kontrolní body fáze G1 buněčného cyklu genetika   MeSH
• kontrolní body fáze G2 buněčného cyklu genetika   MeSH
• lidé MeSH
• lidské embryonální kmenové buňky cytologie   metabolismus   účinky záření   MeSH
• oprava DNA genetika   MeSH
• přeprogramování buněk MeSH
• stárnutí buněk genetika   účinky záření   MeSH
• záření gama MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 53BP1 MeSH
• DNA MeSH
• H2AX protein, human MeSH Prohlížeč
• histony MeSH
• TP53BP1 protein, human MeSH Prohlížeč

The potential clinical applications of human induced pluripotent stem cells (hiPSCs) are limited by genetic and epigenetic variations among hiPSC lines and the question of their equivalency with human embryonic stem cells (hESCs). We used MethylScreen technology to determine the DNA methylation profile of pluripotency and differentiation markers in hiPSC lines from different source cell types compared to hESCs and hiPSC source cells. After derivation, hiPSC lines compromised a heterogeneous population characterized by variable levels of aberrant DNA methylation. These aberrations were induced during somatic cell reprogramming and their levels were associated with the type of hiPSC source cells. hiPSC population heterogeneity was reduced during prolonged culture and hiPSCs acquired an hESC-like methylation profile. In contrast, the expression of differentiation marker genes in hiPSC lines remained distinguishable from that in hESCs. Taken together, in vitro culture facilitates hiPSC acquisition of hESC epigenetic characteristics. However, differences remain between both pluripotent stem cell types, which must be considered before their use in downstream applications.

• MeSH
• buněčná diferenciace genetika   MeSH
• buněčné linie MeSH
• fibroblasty cytologie   metabolismus   MeSH
• indukované pluripotentní kmenové buňky cytologie   metabolismus   MeSH
• kultivované buňky MeSH
• lidé MeSH
• lidské embryonální kmenové buňky cytologie   metabolismus   MeSH
• metylace DNA * MeSH
• přeprogramování buněk genetika   MeSH
• shluková analýza MeSH
• stanovení celkové genové exprese MeSH
• vývojová regulace genové exprese MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The molecular machinery of endoplasmic reticulum (ER) integrates various intracellular and extracellular cues to maintain homeostasis in diverse physiological or pathological scenarios. ER stress and the unfolded protein response (UPR) have been found to mediate molecular and biochemical mechanisms that affect cell proliferation, differentiation, and apoptosis. Although a number of reviews on the ER stress response have been published, comprehensive reviews that broadly summarize ER physiology in the context of pluripotency, embryonic development, and tissue homeostasis are lacking. This review complements the current ER literature and provides a summary of the important findings on the role of the ER stress and UPR in embryonic development and pluripotent stem cells.

• Klíčová slova
• Development, Embryonic stem cells, Endoplasmic reticulum stress, Pluripotency, Unfolded protein response,
• MeSH
• buněčná diferenciace * MeSH
• embryonální vývoj * MeSH
• homeostáza MeSH
• lidé MeSH
• pluripotentní kmenové buňky cytologie   metabolismus   MeSH
• stres endoplazmatického retikula * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.

• Klíčová slova
• Cell cycle, Chromatin, DNA replication, H3K56ac, Mammalian cells, Nucleosome,
• MeSH
• buněčný cyklus genetika   fyziologie   MeSH
• chromatin metabolismus   MeSH
• G2 fáze genetika   MeSH
• histony metabolismus   MeSH
• HL-60 buňky MeSH
• hmotnostní spektrometrie MeSH
• lidé MeSH
• nukleozomy metabolismus   MeSH
• replikace DNA genetika   fyziologie   MeSH
• S fáze genetika   MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chromatin MeSH
• histony MeSH
• nukleozomy MeSH
• Saccharomyces cerevisiae - proteiny MeSH

BACKGROUND: The surgical resection of lung disrupts glucose homeostasis and causes hyperglycemia, as in any other major surgery or critical illness. We performed a prospective study where we carefully lowered hyperglycemia by insulin administration during the surgery, and for the first time we monitored immediate insulin effects on lung physiology and gene transcription. METHODS: The levels of blood gases (pH, pCO2, pO2, HCO3-, HCO3- std, base excess, FiO2, and pO2/FiO2) were measured at the beginning of surgery, at the end of surgery, and two hours after. Samples of healthy lung tissue surrounding the tumour were obtained during the surgery, anonymized and sent for subsequent blinded qPCR analysis (mRNA levels of surfactant proteins A1, A2, B, C and D were measured). This study was done on a cohort of 64 patients who underwent lung resection. Patients were randomly divided, and half of them received insulin treatment during the surgery. RESULTS: We demonstrated for the first time that insulin administered intravenously during lung resection does not affect levels of blood gases. Furthermore, it does not induce immediate changes in the expression of surfactant proteins. CONCLUSION: According to our observations, short insulin treatment applied intravenously during resection does not affect the quality of breathing.

• MeSH
• analýza krevních plynů MeSH
• časové faktory MeSH
• dospělí MeSH
• exprese genu účinky léků   MeSH
• hydrogenuhličitany krev   MeSH
• hyperglykemie farmakoterapie   etiologie   MeSH
• hypoglykemika aplikace a dávkování   MeSH
• intravenózní podání MeSH
• inzulin aplikace a dávkování   MeSH
• koncentrace vodíkových iontů MeSH
• krevní glukóza účinky léků   MeSH
• kyslík krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• messenger RNA metabolismus   MeSH
• nádory plic chirurgie   MeSH
• oxid uhličitý krev   MeSH
• plíce účinky léků   patofyziologie   MeSH
• pneumektomie škodlivé účinky   MeSH
• poruchy acidobazické rovnováhy MeSH
• prospektivní studie MeSH
• proteiny asociované s plicním surfaktantem genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• randomizované kontrolované studie MeSH
• Názvy látek
• hydrogenuhličitany MeSH
• hypoglykemika MeSH
• inzulin MeSH
• krevní glukóza MeSH
• kyslík MeSH
• messenger RNA MeSH
• oxid uhličitý MeSH
• proteiny asociované s plicním surfaktantem MeSH

Hematopoietic progenitors derived from human embryonic stem cells (hESCs) present both a potential cell source for cell-replacement therapies and an in vitro model for hematopoietic stem cell (HSC) development. Current protocols for the hematopoietic differentiation of hESCs suffer from low efficiency and functional defects in the derived HSCs. Epigenetic mechanisms of HSC development should be addressed to overcome these imperfections. The focus of this review is to summarize the knowledge on the epigenetic regulation of pluripotency and lineage-specific genes with the emphasis on the hematopoietic cell lineage. The potential utilization of this knowledge to improve the generation of HSCs for clinical application is also discussed.

• MeSH
• buněčná diferenciace fyziologie   MeSH
• buněčný rodokmen genetika   MeSH
• embryonální kmenové buňky cytologie   MeSH
• epigeneze genetická * MeSH
• hematopoetické kmenové buňky cytologie   MeSH
• lidé MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

In this study, the effects of insulin and dexamethasone on the expression and mRNA transcription of 4 pulmonary surfactant-associated proteins [surfactant protein (SFTP)A, SFTPB, SFTPC and SFTPD] were examined. The commercially available cell lines, A549 and H441, were used as acceptable models of lung surfactant-producing cells. Subsequently, the effects of insulin on the expression of surfactant-associated proteins were examined in patients with lung adenocarcinoma during lung resection. Our results demonstrated the inhibitory effects of insulin on the transcription of the SFTPB, SFTPC and SFTPD genes in H441 cells and the SFTPB gene in A549 cells. Treatment with insulin significantly decreased the protein expression of SFTPA1 and SFTPA2 in the H441 cells and that of proSFTPB in the A549 cells. Dexamethasone promoted the transcription of the SFTPB, SFTPC and SFTPD genes in the A549 and H441 cells and reduced the transcription of the SFTPA1 and SFTPA2 genes in the H441 cells (SFTPA mRNA expression was not detected in A549 cells). Furthermore, we demonstrated that the mRNA levels of the selected genes were significantly lower in the cell lines compared to the lung tissue. A549 and H441 cells represent similar cell types. Yet, in our experiments, these cells reacted differently to insulin and/or dexamethasone treatment, and the mRNA levels of their main protein products, surfactant-associated proteins, were significantly lower than those in real tissue. Therefore, the results obtained in this study challenge the suitability of A549 and H441 cells as models of type II pneumocytes and Clara cells, respectively. However, we successfully demonstrate the possibility of studying the effects of insulin on pulmonary surfactant-associated genes and proteins in patients with lung adenocarcinoma.

• MeSH
• adenokarcinom plic MeSH
• adenokarcinom genetika   MeSH
• dexamethason farmakologie   MeSH
• inzulin farmakologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• nádory plic genetika   MeSH
• plíce účinky léků   metabolismus   MeSH
• protein A asociovaný s plicním surfaktantem genetika   metabolismus   MeSH
• protein B asociovaný s plicním surfaktantem genetika   metabolismus   MeSH
• protein C asociovaný s plicním surfaktantem genetika   metabolismus   MeSH
• protein D asociovaný s plicním surfaktantem genetika   metabolismus   MeSH
• proteiny asociované s plicním surfaktantem genetika   metabolismus   MeSH
• regulace genové exprese u nádorů účinky léků   MeSH
• regulace genové exprese účinky léků   MeSH
• senioři MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• dexamethason MeSH
• inzulin MeSH
• protein A asociovaný s plicním surfaktantem MeSH
• protein B asociovaný s plicním surfaktantem MeSH
• protein C asociovaný s plicním surfaktantem MeSH
• protein D asociovaný s plicním surfaktantem MeSH
• proteiny asociované s plicním surfaktantem MeSH