The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods - co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms - a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a double-stranded RNA (dsRNA)-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with high molecular weight poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.
- MeSH
- adenosindeaminasa * metabolismus genetika MeSH
- buněčné jádro * metabolismus MeSH
- cytoplazma * metabolismus MeSH
- dvouvláknová RNA metabolismus genetika MeSH
- editace RNA MeSH
- HEK293 buňky MeSH
- HeLa buňky MeSH
- interferony metabolismus genetika MeSH
- lidé MeSH
- mapy interakcí proteinů MeSH
- poly I-C farmakologie MeSH
- protein - isoformy * metabolismus genetika MeSH
- proteiny vázající RNA * metabolismus genetika MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Tick-borne encephalitis (TBE) is a neuroviral disease that ranges in severity from a mild febrile illness to a severe and life-threatening meningoencephalitis or encephalomyelitis. There is increasing evidence that susceptibility to tick-borne encephalitis virus (TBEV)-induced disease and its severity are largely influenced by host genetic factors, in addition to other virus- and host-related factors. In this study, we investigated the contribution of selected single nucleotide polymorphisms (SNPs) in innate immunity genes to predisposition to TBE in humans. More specifically, we investigated a possible association between SNPs rs304478 and rs303212 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 1 (IFIT1), rs7070001 and rs4934470 in the gene Interferon Induced Protein With Tetratricopeptide Repeats 2 (IFIT2), and RIG-I (Retinoic acid-inducible gene I) encoding gene DDX58 rs311795343, rs10813831, rs17217280 and rs3739674 SNPs with predisposition to TBE in population of the Czech Republic, where TBEV is highly endemic. Genotypic and allelic frequencies for these SNPs were analyzed in 247 nonimmunized TBE patients and compared with 204 control subjects. The analysis showed an association of IFIT1 rs304478 SNP and DDX58 rs3739674 and rs17217280 SNPs with predisposition to TBE in the Czech population indicating novel risk factors for clinical TBE but not for disease severity. These results also highlight the role of innate immunity genes in TBE pathogenesis.
- MeSH
- genotyp MeSH
- interferony genetika MeSH
- jednonukleotidový polymorfismus MeSH
- klíšťová encefalitida * genetika epidemiologie MeSH
- lidé MeSH
- přirozená imunita genetika MeSH
- viry klíšťové encefalitidy * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Lambda interferons mediate antiviral immunity by inducing interferon-stimulated genes (ISGs) in epithelial tissues. A common variant rs368234815TT/∆G creating functional gene from an IFNL4 pseudogene is associated with the expression of major ISGs in the liver but impaired clearance of hepatitis C. To explain this, we compared Halo-tagged and non-tagged IFNL3 and IFNL4 signaling in liver-derived cell lines. Transfection with non-tagged IFNL3, non-tagged IFNL4 and Halo-tagged IFNL4 led to a similar degree of JAK-STAT activation and ISG induction; however, the response to transfection with Halo-tagged IFNL3 was lower and delayed. Transfection with non-tagged IFNL3 or IFNL4 induced no transcriptome change in the cells lacking either IL10R2 or IFNLR1 receptor subunits. Cytosolic overexpression of signal peptide-lacking IFNL3 or IFNL4 in wild type cells did not interfere with JAK-STAT signaling triggered by interferons in the medium. Finally, expression profile changes induced by transfection with non-tagged IFNL3 and IFNL4 were highly similar. These data do not support the hypothesis about IFNL4-specific non-canonical signaling and point out that functional studies conducted with tagged interferons should be interpreted with caution.
- MeSH
- buněčné linie MeSH
- buňky Hep G2 MeSH
- exprese genu MeSH
- genový knockout MeSH
- hepatocyty imunologie metabolismus MeSH
- interferonové regulační faktory genetika metabolismus MeSH
- interferony nedostatek genetika metabolismus MeSH
- interleukiny nedostatek genetika metabolismus MeSH
- lidé MeSH
- messenger RNA genetika metabolismus MeSH
- receptor interleukinu-10 - beta-podjednotka nedostatek genetika metabolismus MeSH
- receptory interferonů nedostatek genetika metabolismus MeSH
- rekombinantní proteiny genetika metabolismus MeSH
- signální transdukce MeSH
- transfekce MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
OBJECTIVE: The TLR3/cGAS-STING-IFN signaling has recently been reported to be disturbed in colorectal cancer due to deregulated expression of the genes involved. Our study aimed to investigate the influence of potential regulatory variants in these genes on the risk of sporadic colorectal cancer (CRC) in a Czech cohort of 1424 CRC patients and 1114 healthy controls. METHODS: The variants in the TLR3, CGAS, TMEM173, IKBKE, and TBK1 genes were selected using various online bioinformatic tools, such as UCSC browser, HaploReg, Regulome DB, Gtex Portal, SIFT, PolyPhen2, and miRNA prediction tools. RESULTS: Logistic regression analysis adjusted for age and sex detected a nominal association between CRC risk and three variants, CGAS rs72960018 (OR: 1.68, 95% CI: 1.11-2.53, P-value = .01), CGAS rs9352000 (OR: 2.02, 95% CI: 1.07-3.84, P-value = .03) and TMEM173 rs13153461 (OR: 1.53, 95% CI: 1.03-2.27, P-value = .03). Their cumulative effect revealed a threefold increased CRC risk in carriers of 5-6 risk alleles compared to those with 0-2 risk alleles. Epistatic interactions between these genes and the previously genotyped IFNAR1, IFNAR2, IFNA, IFNB, IFNK, IFNW, IRF3, and IRF7 genes, were computed to test their effect on CRC risk. Overall, we obtained nine pair-wise interactions within and between the CGAS, TMEM173, IKBKE, and TBK1 genes. Two of them remained statistically significant after Bonferroni correction. Additional 52 interactions were observed when IFN variants were added to the analysis. CONCLUSIONS: Our data suggest that epistatic interactions and a high number of risk alleles may play an important role in CRC carcinogenesis, offering novel biological understanding for the CRC management.
- MeSH
- dospělí MeSH
- genetická epistáze * MeSH
- genotypizační techniky MeSH
- interferony genetika MeSH
- jednonukleotidový polymorfismus MeSH
- karcinogeneze genetika MeSH
- kinasa I-kappa B genetika MeSH
- kohortové studie MeSH
- kolon diagnostické zobrazování patologie MeSH
- kolonoskopie MeSH
- kolorektální nádory diagnóza genetika patologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- membránové proteiny genetika MeSH
- mladiství MeSH
- mladý dospělý MeSH
- nukleotidyltransferasy genetika MeSH
- protein-serin-threoninkinasy genetika MeSH
- regulace genové exprese u nádorů * MeSH
- rektum diagnostické zobrazování patologie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- signální transdukce genetika MeSH
- studie případů a kontrol MeSH
- toll-like receptor 3 genetika MeSH
- výpočetní biologie MeSH
- zdraví dobrovolníci pro lékařské studie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- práce podpořená grantem MeSH
BACKGROUND: Cytomegalovirus (CMV) disease represents a serious complication in liver transplant (OLT) recipients. CMV prophylaxis reduces incidence of CMV disease in the early post-transplant period (on-prophylaxis disease, OPD) but may postpone its manifestation after the completion of prophylaxis. Post-prophylaxis disease (PPD) incidence after prophylaxis cessation may be modified by genetic factors. METHODS: We analyzed impact of IL28B rs1297986 variants on CMV disease incidence in 743 adult OLT recipients receiving universal prophylaxis. RESULTS: One hundred and forty-four (19.4%) patients had at least one CMV disease episode. One hundred and two of them (70.8%) had at least one OPD and 36 (25%) patients had PPD, six (4.2%) patients had both. The rate of IL28B T allele carriers was lower in PPD group (38.9%) in comparison with OPD group (66.7%, P = 0.005) and group without CMV disease (61.4%, P = 0.009). The impact of IL28B genotype on the risk of CMV OPD was significant neither in the allelic (TT + CT vs CC, P = 0.32) nor in the recessive model (TT vs CT + CC, P = 0.79). Contrarily, in the PPD group, T allele (TT + CT vs CC) had a protective effect, OR 0.4 (95% CI 0.2-0.8, P = 0.008). Further risk factors of PPD were age <55 years and valganciclovir prophylaxis, whereas the risk factors of OPD were age <55 years, cyclosporine A therapy and pre-transplant CMV serostatus (donor +/recipient -). CONCLUSIONS: IL28B rs12979860 T allele carriers had a lower risk of CMV PPD.
- MeSH
- alely MeSH
- antivirové látky terapeutické užití MeSH
- cytomegalovirové infekce genetika prevence a kontrola MeSH
- dárci tkání MeSH
- dospělí MeSH
- ganciklovir terapeutické užití MeSH
- genotyp MeSH
- incidence MeSH
- interferony genetika MeSH
- jednonukleotidový polymorfismus MeSH
- kohortové studie MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- příjemce transplantátu MeSH
- senioři MeSH
- transplantace jater * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Tick-borne encephalitis virus (TBEV) is a member of the genus Flavivirus. It can cause serious infections in humans that may result in encephalitis/meningoencephalitis. Although several studies have described the involvement of specific genes in the host response to TBEV infection in the central nervous system (CNS), the overall network remains poorly characterized. Therefore, we investigated the response of DAOY cells (human medulloblastoma cells derived from cerebellar neurons) to TBEV (Neudoerfl strain, Western subtype) infection to characterize differentially expressed genes by transcriptome analysis. Our results revealed a wide panel of interferon-stimulated genes (ISGs) and pro-inflammatory cytokines, including type III but not type I (or II) interferons (IFNs), which are activated upon TBEV infection, as well as a number of non-coding RNAs, including long non-coding RNAs. To obtain a broader view of the pathways responsible for eliciting an antiviral state in DAOY cells we examined the effect of type I and III IFNs and found that only type I IFN pre-treatment inhibited TBEV production. The cellular response to TBEV showed only partial overlap with gene expression changes induced by IFN-β treatment - suggesting a virus-specific signature - and we identified a group of ISGs that were highly up-regulated following IFN-β treatment. Moreover, a high rate of down-regulation was observed for a wide panel of pro-inflammatory cytokines upon IFN-β treatment. These data can serve as the basis for further studies of host-TBEV interactions and the identification of ISGs and/or lncRNAs with potent antiviral effects in cases of TBEV infection in human neuronal cells.
- MeSH
- aktivace transkripce MeSH
- cytokiny genetika imunologie MeSH
- interakce hostitele a patogenu MeSH
- interferony genetika imunologie MeSH
- klíšťová encefalitida genetika imunologie virologie MeSH
- lidé MeSH
- neurony imunologie virologie MeSH
- viry klíšťové encefalitidy genetika fyziologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Interferon (IFN) signaling has been suggested to play an important role in colorectal carcinogenesis. Our study aimed to examine potentially functional genetic variants in interferon regulatory factor 3 (IRF3), IRF5, IRF7, type I and type II IFN and their receptor genes with respect to colorectal cancer (CRC) risk and clinical outcome. Altogether 74 single nucleotide polymorphisms (SNPs) were covered by the 34 SNPs genotyped in a hospital-based case-control study of 1327 CRC cases and 758 healthy controls from the Czech Republic. We also analyzed these SNPs in relation to overall survival and event-free survival in a subgroup of 483 patients. Seven SNPs in IFNA1, IFNA13, IFNA21, IFNK, IFNAR1 and IFNGR1 were associated with CRC risk. After multiple testing correction, the associations with the SNPs rs2856968 (IFNAR1) and rs2234711 (IFNGR1) remained formally significant (P = 0.0015 and P<0.0001, respectively). Multivariable survival analyses showed that the SNP rs6475526 (IFNA7/IFNA14) was associated with overall survival of the patients (P = 0.041 and event-free survival among patients without distant metastasis at the time of diagnosis, P = 0.034). The hazard ratios (HRs) for rs6475526 remained statistically significant even after adjustment for age, gender, grade and stage (P = 0.029 and P = 0.036, respectively), suggesting that rs6475526 is an independent prognostic marker for CRC. Our data suggest that genetic variation in the IFN signaling pathway genes may play a role in the etiology and survival of CRC and further studies are warranted.
- MeSH
- genetická predispozice k nemoci * MeSH
- genotyp MeSH
- interferony genetika metabolismus MeSH
- jednonukleotidový polymorfismus * MeSH
- kolorektální nádory genetika metabolismus MeSH
- lidé středního věku MeSH
- lidé MeSH
- multivariační analýza MeSH
- nemocnice MeSH
- přežití bez známek nemoci MeSH
- proporcionální rizikové modely MeSH
- rizikové faktory MeSH
- senioři MeSH
- signální transdukce MeSH
- studie případů a kontrol MeSH
- vazebná nerovnováha 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
The interferon (IFN) response, induced as a side effect after transfection of nucleic acids into mammalian cells, is known but inadequately described. We followed the IFN response, the fate of cells, and the possible mechanisms leading to this response in NIH3T3 mouse fibroblasts after DNA nucleofection. The gateway destination vector, phGf, and its derivatives encoding toxic and non-toxic variants of the minor structural proteins of polyomaviruses, VP2 and VP3, were used. DNA vector sequences induced in cells the production of high levels of IFN and the upregulation of the IFN-inducible genes, Mx-1, STAT1, IRF1, and IRF7. The IFN response was not restricted to phGf-derived plasmids. In nucleofected cells, upregulation of the modified γ-histone 2A.X indicating DNA damage and inhibition of cell proliferation were also observed. Although 3T3 cells expressed the Toll-like receptor-9 (TLR9) and vectors used for nucleofection contained unmethylated CpGs, signaling leading to IFN induction was found to be TLR9 independent. However, the early activation of nuclear factor-kappa B suggested the participation of this transcription factor in IFN induction. Surprisingly, in contrast to nucleofection, transfection using a cationic polymer induced only a poor IFN response. Together, the results point to a strong side effect of nucleofection.
- MeSH
- buňky NIH 3T3 MeSH
- CpG ostrůvky účinky léků genetika MeSH
- down regulace účinky léků genetika MeSH
- exprese genu MeSH
- genetické vektory genetika farmakologie fyziologie MeSH
- interferony genetika metabolismus MeSH
- kultivované buňky MeSH
- metylace DNA účinky léků MeSH
- myši MeSH
- plazmidy genetika farmakologie MeSH
- proliferace buněk * účinky léků MeSH
- regulace genové exprese účinky léků MeSH
- transfekce metody MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cellular senescence guards against cancer and modulates aging; however, the underlying mechanisms remain poorly understood. Here, we show that genotoxic drugs capable of inducing premature senescence in normal and cancer cells, such as 5-bromo-2'-deoxyuridine (BrdU), distamycin A (DMA), aphidicolin and hydroxyurea, persistently activate Janus kinase-signal transducer and activator of transcription (JAK/STAT) signaling and expression of interferon-stimulated genes (ISGs), such as MX1, OAS, ISG15, STAT1, PML, IRF1 and IRF7, in several human cancer cell lines. JAK1/STAT-activating ligands, interleukin 10 (IL10), IL20, IL24, interferon gamma (IFNgamma), IFNbeta and IL6, were also expressed by senescent cells, supporting autocrine/paracrine activation of JAK1/STAT. Furthermore, cytokine genes, including proinflammatory IL1, tumor necrosis factor and transforming growth factor families, were highly expressed. The strongest inducer of JAK/STAT signaling, cytokine production and senescence was BrdU combined with DMA. RNA interference-mediated knockdown of JAK1 abolished expression of ISGs, but not DNA damage signaling or senescence. Thus, although DNA damage signaling, p53 and RB activation, and the cytokine/chemokine secretory phenotype are apparently shared by all types of senescence, our data reveal so far unprecedented activation of the IFNbeta-STAT1-ISGs axis, and indicate a less prominent causative role of IL6-JAK/STAT signaling in genotoxic drug-induced senescence compared with reports on oncogene-induced or replicative senescence. These results highlight shared and unique features of drug-induced cellular senescence, and implicate induction of cancer secretory phenotype in chemotherapy.
- MeSH
- bromodeoxyuridin farmakologie MeSH
- cytokiny genetika metabolismus MeSH
- distamyciny farmakologie MeSH
- HeLa buňky MeSH
- interferony genetika metabolismus MeSH
- interleukin-10 genetika metabolismus MeSH
- interleukin-6 genetika metabolismus MeSH
- interleukin-8 genetika metabolismus MeSH
- interleukiny genetika metabolismus MeSH
- Janus kinasa 1 genetika metabolismus MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- RNA interference MeSH
- signální transdukce účinky léků MeSH
- stárnutí buněk účinky léků MeSH
- synergismus léků MeSH
- transkripční faktor STAT1 genetika metabolismus MeSH
- western blotting MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
The RNA interference (RNAi) approach is an efficient and widely used method for silencing plant and animal genes. However, numerous studies have highlighted several obstacles that need to be overcome in order to achieve a specific and efficient silencing effect. Among the major problems of using RNAi in mammalian systems are non-specific effects, such as an undesirable activation of the IFN response, and off-target effects, whereby partial complementarity of an RNAi trigger to non-targeted transcripts causes unwanted silencing effects. The causes of non-specific effects and possible approaches to minimize them are discussed in this review.
