Východiska: Signální dráha UPR (unfolded protein response, tj. odpověď na chybně složené proteiny) pomáhá myelomovým buňkám vyrovnat se se stresovými podmínkami vzniklými v důsledku nadměrné proteosyntézy, a představuje tak pro myelomové buňky prostředek umožňující jejich přežití. Extramedulární onemocnění je agresivnější forma mnohočetného myelomu, při které myelomové buňky ztrácí svoji závislost na mikroprostředí kostní dřeně a mohou infiltrovat jiné tkáně a orgány. Patogeneze vzniku extramedulárního onemocnění není dosud zcela objasněna. Cílem této studie bylo zjistit, zda existuje rozdíl v expresi genů spjatých s UPR mezi plazmatickými buňkami kostní dřeně od pacientů s mnohočetným myelomem a extramedulárním onemocněním. Materiál a metody: Pomocí reverzní transkripce ve spojení s kvantitativní polymerázovou řetězovou reakcí byla analyzována exprese šesti genů spjatých s UPR (ERN1, DDIT3, EIF2AK3, TUSC3, XBP1, HSPA5). Použito bylo celkem 76 vzorků plazmatických buněk kostní dřeně, z toho 44 bylo od pacientů s mnohočetným myelomem a 32 od pacientů s extramedulárním onemocněním. Výsledky: Byl pozorován statisticky významný rozdíl v expresi genů HSPA5, DDIT3, EIF2AK3 a ERN1 mezi skupinou mnohočetného myelomu a extramedulárního onemocnění; exprese byla ve všech případech vyšší u vzorků od pacientů s extramedulárním onemocněním. V případě genů XBP1 a TUSC3 nebyl pozorován statisticky významný rozdíl. Prokázáno bylo také několik statisticky významných korelací mezi hladinou exprese analyzovaných genů a klinickými daty pacientů. Závěr: Výsledky poukazují na možný význam signální dráhy UPR v patogenezi extramedulárního onemocnění. UPR se jeví jako vhodný směr dalšího výzkumu.
Background: The unfolded protein response (UPR) enables myeloma cells to overcome the stress conditions arising from excessive proteosynthesis and thus provides a survival advantage for myeloma cells. Extramedullary disease is a more aggressive form of multiple myeloma in which myeloma cells lose their dependence on the bone marrow microenvironment and are able to infiltrate other tissues and organs. The pathogenesis of extramedullary disease is not fully elucidated yet. The aim of this study was to determine whether there is a difference in the expression of UPR-related genes between bone marrow plasma cells from multiple myeloma and extramedullary disease patients. Materials and methods: Gene expression of six genes involved in UPR (ERN1, DDIT3, EIF2AK3, TUSC3, XBP1, HSPA5) was analyzed by quantitative reverse transcription polymerase chain reaction. In total, 76 bone marrow plasma cell samples were used, of which 44 were from patients with multiple myeloma and 32 from patients with extramedullary disease. Results: A statistically significant difference was observed between the multiple myeloma and extramedullary disease groups regarding the expression of HSPA5, DDIT3, EIF2AK3, and ERN1 genes. However, in the case of XBP1 and TUSC3 genes, no statistically significant difference in the expression was found. Several statistically significant correlations between the expression levels of the analyzed genes and the clinical data of the patients were observed as well. Conclusion: Our results suggest the importance of UPR in the pathogenesis of extramedullary disease. UPR appears to be a promising avenue for further research.
The secondary structure of nucleic acids containing quartets of guanines, termed G-quadruplexes, is known to regulate the transcription of many genes. Several G-quadruplexes can be formed in the HIV-1 long terminal repeat promoter region and their stabilization results in the inhibition of HIV-1 replication. Here, we identified helquat-based compounds as a new class of anti-HIV-1 inhibitors that inhibit HIV-1 replication at the stage of reverse transcription and provirus expression. Using Taq polymerase stop and FRET melting assays, we have demonstrated their ability to stabilize G-quadruplexes in the HIV-1 long-terminal repeat sequence. Moreover, these compounds were not binding to the general G-rich region, but rather to G-quadruplex-forming regions. Finally, docking and molecular dynamics calculations indicate that the structure of the helquat core greatly affects the binding mode to the individual G-quadruplexes. Our findings can provide useful information for the further rational design of inhibitors targeting G-quadruplexes in HIV-1.
Use of blood RNA sequencing (RNA-seq) as a splicing analysis tool for clinical interpretation of variants of uncertain significance (VUSs) found via whole-genome and exome sequencing can be difficult for genes that have low expression in the blood due to insufficient read count coverage aligned to specific genes of interest. Here, we present a short amplicon reverse transcription-polymerase chain reaction(RT-PCR) for the detection of genes with low blood expression. Short amplicon RT-PCR, is designed to span three exons where an exon harboring a variant is flanked by one upstream and one downstream exon. We tested short amplicon RT-PCRs for genes that have median transcripts per million (TPM) values less than one according to the genotype-tissue expression database. Median TPM values of genes analyzed in this study are SYN1 = 0.8549, COL1A1 = 0.6275, TCF4 = 0.4009, DSP = .2894, TTN = 0.2851, COL5A2 = 0.1036, TERT = 0.04452, NTRK2 = 0.0344, ABCA4 = 0.00744, PRPH = 0, and WT1 = 0. All these genes show insufficient exon-spanning read coverage in our RNA-seq data to allow splicing analysis. We successfully detected all genes tested except PRPH and WT1. Aberrant splicing was detected in SYN1, TCF4, NTRK2, TTN, and TERT VUSs. Therefore, our results show short amplicon RT-PCR is a useful alternative for the analysis of splicing events in genes with low TPM in blood RNA for clinical diagnostics.
- MeSH
- ATP-Binding Cassette Transporters genetics MeSH
- Alternative Splicing * MeSH
- Humans MeSH
- Reverse Transcriptase Polymerase Chain Reaction MeSH
- Reverse Transcription MeSH
- RNA * genetics MeSH
- RNA Splicing genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Fullerene derivatives with hydrophilic substituents have been shown to exhibit a range of biological activities, including antiviral ones. For a long time, the anti-HIV activity of fullerene derivatives was believed to be due to their binding into the hydrophobic pocket of HIV-1 protease, thereby blocking its activity. Recent work, however, brought new evidence of a novel, protease-independent mechanism of fullerene derivatives' action. We studied in more detail the mechanism of the anti-HIV-1 activity of N,N-dimethyl[70]fulleropyrrolidinium iodide fullerene derivatives. By using a combination of in vitro and cell-based approaches, we showed that these C70 derivatives inhibited neither HIV-1 protease nor HIV-1 maturation. Instead, our data indicate effects of fullerene C70 derivatives on viral genomic RNA packaging and HIV-1 cDNA synthesis during reverse transcription-without impairing reverse transcriptase activity though. Molecularly, this could be explained by a strong binding affinity of these fullerene derivatives to HIV-1 nucleocapsid domain, preventing its proper interaction with viral genomic RNA, thereby blocking reverse transcription and HIV-1 infectivity. Moreover, the fullerene derivatives' oxidative activity and fluorescence quenching, which could be one of the reasons for the inconsistency among reported anti-HIV-1 mechanisms, are discussed herein.
- MeSH
- Fullerenes metabolism pharmacology MeSH
- Genome, Viral drug effects MeSH
- gag Gene Products, Human Immunodeficiency Virus metabolism MeSH
- HEK293 Cells MeSH
- HIV-1 drug effects genetics metabolism physiology MeSH
- Anti-HIV Agents metabolism pharmacology MeSH
- Humans MeSH
- Nucleocapsid Proteins metabolism MeSH
- Reverse Transcription MeSH
- RNA, Viral metabolism MeSH
- Virus Uncoating drug effects MeSH
- Protein Binding MeSH
- Virion metabolism MeSH
- Viral Genome Packaging drug effects MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Reverse transcription quantitative PCR (RT-qPCR) has delivered significant insights in understanding the gene expression landscape. Thanks to its precision, sensitivity, flexibility, and cost effectiveness, RT-qPCR has also found utility in advanced single-cell analysis. Single-cell RT-qPCR now represents a well-established method, suitable for an efficient screening prior to single-cell RNA sequencing (scRNA-Seq) experiments, or, oppositely, for validation of hypotheses formulated from high-throughput approaches. Here, we aim to provide a comprehensive summary of the scRT-qPCR method by discussing the limitations of single-cell collection methods, describing the importance of reverse transcription, providing recommendations for the preamplification and primer design, and summarizing essential data processing steps. With the detailed protocol attached in the appendix, this tutorial provides a set of guidelines that allow any researcher to perform scRT-qPCR measurements of the highest standard.
- MeSH
- Single-Cell Analysis methods standards MeSH
- Real-Time Polymerase Chain Reaction methods standards MeSH
- Humans MeSH
- Reverse Transcription genetics MeSH
- Sensitivity and Specificity MeSH
- Gene Expression Profiling methods standards MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
RNA triplexes are significant tertiary structure motifs that are found in many functional RNAs. Hence, small molecules capable of recognition, binding, and stabilization of the triple-helical RNA structures are emerging as attractive potential molecular biology tools and therapeutic agents. Here, we utilize methods of molecular biology and biophysics to study the interactions of a series of antitumor substitution-inert polynuclear platinum complexes (SI-PPCs) with triple-helical RNA structures. We show that SI-PPCs recognize and stabilize RNA triplexes and inhibit reverse transcription preferentially in the RNA template prone to the triplex formation. These so far unexplored properties of SI-PPCs suggest that the targeting of triple-stranded regions in RNA might contribute to the biological effects of SI-PPCs.
The single-celled parasite Giardia intestinalis (Diplomonadida) has two equally sized nuclei in one cell. The nuclei have been considered identical. We have previously shown that they contain different chromosomal sets and proceed through the cell cycle with some asynchrony. Here, we demonstrate by fluorescence in situ hybridization that several genes from chromosome 5 are lost in one of the two nuclei of the WBc6 Giardia line. The missing segment stretches over at least 50kb near the 5' chromosome end. In both WB and WBc6 Giardia cell lines, chromosome 5 is trisomic in one nucleus and monosomic in the other nucleus. The described chromosomal deletion has always been observed at the monosomic chromosome in WBc6; however, the deletion was not detected in the parent line WB. The chromosomal segment was thus initially lost after biological cloning of WB, which gave rise to clone WBc6. We show that Giardia is capable of carrying out gene expression from only one nucleus. The two nuclei display a certain level of diversity, making each of them irreplaceable. The doubled karyomastigonts of diplomonads likely have separate functions both in the mastigont/flagellar organization and in chromosomal and gene content. To our knowledge, our results offer the first methodical approach to differentiating the two, so far indistinguishable nuclei.
- MeSH
- Cell Nucleus genetics MeSH
- Time Factors MeSH
- Chromosome Deletion MeSH
- Gene Deletion MeSH
- Giardia lamblia * genetics ultrastructure MeSH
- In Situ Hybridization, Fluorescence standards MeSH
- DNA, Complementary MeSH
- Real-Time Polymerase Chain Reaction methods MeSH
- Mitosis MeSH
- Monosomy * MeSH
- Reverse Transcriptase Polymerase Chain Reaction MeSH
- Gene Expression Regulation physiology MeSH
- Reverse Transcription MeSH
- RNA, Protozoan genetics isolation & purification MeSH
- Signal Transduction MeSH
- Trisomy genetics MeSH
The single-celled parasite Giardia intestinalis (Diplomonadida) has two equally sized nuclei in one cell. The nuclei have been considered identical. We have previously shown that they contain different chromosomal sets and proceed through the cell cycle with some asynchrony. Here, we demonstrate by fluorescence in situ hybridization that several genes from chromosome 5 are lost in one of the two nuclei of the WBc6 Giardia line. The missing segment stretches over at least 50 kb near the 5' chromosome end. In both WB and WBc6 Giardia cell lines, chromosome 5 is trisomic in one nucleus and monosomic in the other nucleus. The described chromosomal deletion has always been observed at the monosomic chromosome in WBc6; however, the deletion was not detected in the parent line WB. The chromosomal segment was thus initially lost after biological cloning of WB, which gave rise to clone WBc6. We show that Giardia is capable of carrying out gene expression from only one nucleus. The two nuclei display a certain level of diversity, making each of them irreplaceable. The doubled karyomastigonts of diplomonads likely have separate functions both in the mastigont/flagellar organization and in chromosomal and gene content. To our knowledge, our results offer the first methodical approach to differentiating the two, so far indistinguishable nuclei.
- MeSH
- Cell Nucleus genetics MeSH
- Time Factors MeSH
- Chromosome Deletion MeSH
- Gene Deletion MeSH
- Giardia lamblia genetics ultrastructure MeSH
- In Situ Hybridization, Fluorescence standards MeSH
- DNA, Complementary genetics MeSH
- Real-Time Polymerase Chain Reaction methods MeSH
- Mitosis MeSH
- Monosomy * genetics MeSH
- Reverse Transcriptase Polymerase Chain Reaction MeSH
- Gene Expression Regulation physiology MeSH
- Reverse Transcription MeSH
- RNA, Protozoan genetics isolation & purification MeSH
- Signal Transduction MeSH
- Trisomy * genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
In addition to specific RNA-binding zinc finger domains, the retroviral Gag polyprotein contains clusters of basic amino acid residues that are thought to support Gag-viral genomic RNA (gRNA) interactions. One of these clusters is the basic K16NK18EK20 region, located upstream of the first zinc finger of the Mason-Pfizer monkey virus (M-PMV) nucleocapsid (NC) protein. To investigate the role of this basic region in the M-PMV life cycle, we used a combination of in vivo and in vitro methods to study a series of mutants in which the overall charge of this region was more positive (RNRER), more negative (AEAEA), or neutral (AAAAA). The mutations markedly affected gRNA incorporation and the onset of reverse transcription. The introduction of a more negative charge (AEAEA) significantly reduced the incorporation of M-PMV gRNA into nascent particles. Moreover, the assembly of immature particles of the AEAEA Gag mutant was relocated from the perinuclear region to the plasma membrane. In contrast, an enhancement of the basicity of this region of M-PMV NC (RNRER) caused a substantially more efficient incorporation of gRNA, subsequently resulting in an increase in M-PMV RNRER infectivity. Nevertheless, despite the larger amount of gRNA packaged by the RNRER mutant, the onset of reverse transcription was delayed in comparison to that of the wild type. Our data clearly show the requirement for certain positively charged amino acid residues upstream of the first zinc finger for proper gRNA incorporation, assembly of immature particles, and proceeding of reverse transcription.IMPORTANCE We identified a short sequence within the Gag polyprotein that, together with the zinc finger domains and the previously identified RKK motif, contributes to the packaging of genomic RNA (gRNA) of Mason-Pfizer monkey virus (M-PMV). Importantly, in addition to gRNA incorporation, this basic region (KNKEK) at the N terminus of the nucleocapsid protein is crucial for the onset of reverse transcription. Mutations that change the positive charge of the region to a negative one significantly reduced specific gRNA packaging. The assembly of immature particles of this mutant was reoriented from the perinuclear region to the plasma membrane. On the contrary, an enhancement of the basic character of this region increased both the efficiency of gRNA packaging and the infectivity of the virus. However, the onset of reverse transcription was delayed even in this mutant. In summary, the basic region in M-PMV Gag plays a key role in the packaging of genomic RNA and, consequently, in assembly and reverse transcription.
- MeSH
- Cell Line MeSH
- Gene Products, gag genetics MeSH
- HEK293 Cells MeSH
- Humans MeSH
- Mason-Pfizer monkey virus genetics physiology MeSH
- Mutation genetics MeSH
- Nucleocapsid Proteins genetics MeSH
- Reverse Transcription genetics MeSH
- RNA, Viral genetics MeSH
- Amino Acid Sequence genetics MeSH
- Virus Assembly genetics MeSH
- Zinc Fingers genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
