In advanced prostate cancer (PC), in particular after acquisition of resistance to androgen receptor (AR) signaling inhibitors (ARSI), upregulation of AR splice variants compromises endocrine therapy efficiency. Androgen receptor splice variant-7 (ARV7) is clinically the most relevant and has a distinct 3' untranslated region (3'UTR) compared to the AR full-length variant, suggesting a unique post-transcriptional regulation. Here, we set out to evaluate the applicability of the ARV7 3'UTR as a therapy target. A common single nucleotide polymorphism, rs5918762, was found to affect the splicing rate and thus the expression of ARV7 in cellular models and patient specimens. Serine/arginine-rich splicing factor 9 (SRSF9) was found to bind to and increase the inclusion of the cryptic exon 3 of ARV7 during the splicing process in the alternative C allele of rs5918762. The dual specificity protein kinase CLK2 interferes with the activity of SRSF9 by regulating its expression. Inhibition of the Cdc2-like kinase (CLK) family by the small molecules cirtuvivint or lorecivivint results in the decreased expression of ARV7. Both inhibitors show potent anti-proliferative effects in enzalutamide-treated or -naive PC models. Thus, targeting aberrant alternative splicing at the 3'UTR of ARV7 by disturbing the CLK2/SRSF9 axis might be a valuable therapeutic approach in late stage, ARSI-resistant PC.

• Klíčová slova
• 3′ untranslated region, allele‐specific regulation, androgen receptor splice variant 7, dual specificity protein kinase CLK2, serine/arginine‐family of splicing factors, splicing inhibitors,
• MeSH
• 3' nepřekládaná oblast genetika   MeSH
• alternativní sestřih genetika   účinky léků   MeSH
• androgenní receptory * metabolismus   genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• nádory prostaty * genetika   metabolismus   patologie   farmakoterapie   MeSH
• protein - isoformy genetika   metabolismus   MeSH
• protein-serin-threoninkinasy genetika   metabolismus   antagonisté a inhibitory   MeSH
• regulace genové exprese u nádorů * účinky léků   MeSH
• serin-arginin sestřihové faktory * metabolismus   genetika   MeSH
• sestřih RNA genetika   MeSH
• tyrosinkinasy * genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3' nepřekládaná oblast MeSH
• androgenní receptory * MeSH
• Clk dual-specificity kinases MeSH Prohlížeč
• protein - isoformy MeSH
• protein-serin-threoninkinasy MeSH
• serin-arginin sestřihové faktory * MeSH
• tyrosinkinasy * MeSH

Germline CHEK2 pathogenic variants confer an increased risk of female breast cancer (FBC). Here we describe a recurrent germline intronic variant c.1009-118_1009-87delinsC, which showed a splice acceptor shift in RNA analysis, introducing a premature stop codon (p.Tyr337PhefsTer37). The variant was found in 21/10,204 (0.21%) Czech FBC patients compared to 1/3250 (0.03%) controls (p = 0.04) and in 4/3639 (0.11%) FBC patients from an independent German dataset. In addition, we found this variant in 5/2966 (0.17%) Czech (but none of the 443 German) ovarian cancer patients, three of whom developed early-onset tumors. Based on these observations, we classified this variant as likely pathogenic.

• Klíčová slova
• Breast cancer, Deep intronic CHEK2 variant, Genetic testing, NGS, RNA analysis,
• MeSH
• checkpoint kinasa 2 * genetika   MeSH
• dospělí MeSH
• genetická predispozice k nemoci * genetika   MeSH
• introny * genetika   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádory prsu * genetika   MeSH
• nádory vaječníků genetika   MeSH
• prekurzory RNA genetika   MeSH
• sestřih RNA * genetika   MeSH
• zárodečné mutace * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Německo MeSH
• Názvy látek
• CHEK2 protein, human MeSH Prohlížeč

• MeSH
• 5' nepřekládaná oblast genetika   MeSH
• alternativní sestřih * MeSH
• proteosyntéza MeSH
• sestřih RNA * genetika   MeSH
• Publikační typ
• komentáře MeSH
• úvodníky MeSH
• Názvy látek
• 5' nepřekládaná oblast MeSH

SART3 is a multifunctional protein that acts in several steps of gene expression, including assembly and recycling of the spliceosomal U4/U6 small nuclear ribonucleoprotein particle (snRNP). In this work, we provide evidence that SART3 associates via its N-terminal HAT domain with the 12S U2 snRNP. Further analysis showed that SART3 associates with the post-splicing complex containing U2 and U5 snRNP components. In addition, we observed an interaction between SART3 and the RNA helicase DHX15, which disassembles post-splicing complexes. Based on our data, we propose a model that SART3 associates via its N-terminal HAT domain with the post-splicing complex, where it interacts with U6 snRNA to protect it and to initiate U6 snRNA recycling before a next round of splicing.

• Klíčová slova
• Recycling, Splicing, U2 snRNP, U6 snRNA,
• MeSH
• malý jaderný ribonukleoprotein U2 genetika   metabolismus   MeSH
• malý jaderný ribonukleoprotein U4-U6 genetika   metabolismus   MeSH
• malý jaderný ribonukleoprotein U5 genetika   metabolismus   MeSH
• ribonukleoproteiny malé jaderné genetika   metabolismus   MeSH
• RNA malá jaderná genetika   metabolismus   MeSH
• sestřih RNA * genetika   MeSH
• spliceozomy * genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malý jaderný ribonukleoprotein U2 MeSH
• malý jaderný ribonukleoprotein U4-U6 MeSH
• malý jaderný ribonukleoprotein U5 MeSH
• ribonukleoproteiny malé jaderné MeSH
• RNA malá jaderná MeSH

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.

• Klíčová slova
• RNA-seq, RT-PCR, VUS, aberrant splicing, blood RNA,
• MeSH
• ABC transportéry genetika   MeSH
• alternativní sestřih * MeSH
• lidé MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• reverzní transkripce MeSH
• RNA * genetika   MeSH
• sestřih RNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ABC transportéry MeSH
• ABCA4 protein, human MeSH Prohlížeč
• RNA * MeSH

Hepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor crucial for the development of several tissues, and a promising biomarker of certain solid tumours. Thus far, two HNF1B alternative splicing variants (ASVs) have been described, however, the complete spectrum, prevalence and role of HNF1B ASVs in tumorigenesis are unclear. Considering the equivocal data about HNF1B ASVs and expression presented in literature, our aim was to characterize the spectrum of HNF1B mRNA splicing variants across different tissues. Here, we characterize HNF1B ASVs with high sensitivity in carcinomas of the uterine corpus, large intestine, kidney, pancreas, and prostate, with selected paired healthy tissues, using the previously described multiplex PCR and NGS approach. We identified 45 ASVs, of which 43 were novel. The spectrum and relative quantity of expressed ASVs mRNA differed among the analysed tissue types. Two known (3p, Δ7_8) and two novel (Δ7, Δ8) ASVs with unknown biological functions were detected in all the analysed tissues in a higher proportion. Our study reveals the wide spectrum of HNF1B ASVs in selected tissues. Characterization of the HNF1B ASVs is an important prerequisite for further expression studies to delineate the HNF1B splicing pattern, potential ASVs functional impact, and eventual refinement of HNF1B's biomarker role.

• MeSH
• alternativní sestřih genetika   MeSH
• biologické markery metabolismus   MeSH
• hepatocytární jaderný faktor 1-beta genetika   metabolismus   MeSH
• ledviny metabolismus   patologie   MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• multiplexová polymerázová řetězová reakce MeSH
• pankreas metabolismus   patologie   MeSH
• sestřih RNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• biologické markery MeSH
• hepatocytární jaderný faktor 1-beta MeSH
• HNF1B protein, human MeSH Prohlížeč
• messenger RNA MeSH

The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.

• Klíčová slova
• ADAR2, RNA editing, epilepsy, intellectual disability, microcephaly, migrating focal seizures,
• MeSH
• adenosindeaminasa genetika   MeSH
• alely MeSH
• alternativní sestřih genetika   MeSH
• dítě MeSH
• genetická predispozice k nemoci genetika   MeSH
• genetická variace genetika   MeSH
• HEK293 buňky MeSH
• lidé MeSH
• mentální retardace genetika   MeSH
• mikrocefalie genetika   MeSH
• předškolní dítě MeSH
• proteiny vázající RNA genetika   MeSH
• sestřih RNA genetika   MeSH
• záchvaty genetika   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• ADARB1 protein, human MeSH Prohlížeč
• adenosindeaminasa MeSH
• proteiny vázající RNA MeSH

Single nucleotide polymorphisms located in 5' untranslated regions (5'UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5'UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5'UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5'UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5'UTRs, such as GC content variation, hairpin structure conservation or 5'UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.

• Klíčová slova
• 5′ untranslated region, ABCA1, bioinformatics, gene regulation, single nucleotide polymorphism,
• MeSH
• 5' nepřekládaná oblast genetika   MeSH
• ABCA1 protein chemie   genetika   MeSH
• anotace sekvence MeSH
• fylogeneze MeSH
• introny genetika   MeSH
• konformace nukleové kyseliny MeSH
• konzervovaná sekvence genetika   MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• nukleotidové motivy genetika   MeSH
• obratlovci genetika   MeSH
• otevřené čtecí rámce genetika   MeSH
• savci genetika   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sestřih RNA genetika   MeSH
• zastoupení bazí genetika   MeSH
• zesilovače transkripce genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• 5' nepřekládaná oblast MeSH
• ABCA1 protein MeSH
• messenger RNA MeSH

Pre-mRNA splicing is an essential step in gene expression, when introns are removed and exons joined by the complex of proteins called spliceosome. Correct splicing requires a precise exon/intron junction definition, which is determined by a consensual donor and acceptor splice site at the 5' and 3' end, respectively. An acceptor splice site (3'ss) consists of highly conserved AG nucleotides in positions E-2 and E-1. These nucleotides can appear in tandem, located 3 bp from each other. Then they are referred to as NAGNAG or tandem 3'ss, which can be alternatively spliced. NAG/TAG 3'ss motif abundance is extremely low and cannot be easily explained by just a nucleotide preference in this position. We tested artificial NAG/TAG motif's potential negative effect on exon recognition using a minigene assay. Introducing the NAG/TAG motif into seven different exons revealed no general negative effect on exon recognition. The only observed effect was the partial use of the newly formed distal 3'ss. We can conclude that this motif's extremely low preference in a natural 3'ss is not a consequence of the NAG/TAG motif's negative effect on exon recognition, but more likely the result of other RNA processing aspects, such as an alternative 3'ss choice, decreased 3'ss strength, or incorporating an amber stop codon.

• Klíčová slova
• Acceptor splice site, NAGNAG motif, Pre-mRNA splicing, Tandem acceptor splice site,
• MeSH
• alternativní sestřih MeSH
• exony * MeSH
• HeLa buňky MeSH
• introny MeSH
• lidé MeSH
• místa sestřihu RNA genetika   fyziologie   MeSH
• nukleotidy genetika   MeSH
• sekvence nukleotidů MeSH
• sestřih RNA genetika   MeSH
• tandemové repetitivní sekvence MeSH
• terminační kodon MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• místa sestřihu RNA MeSH
• nukleotidy MeSH
• terminační kodon MeSH

Calcium/calmodulin-dependent protein kinases (CaMKs) are key mediators of calcium signaling and underpin neuronal health. Although widely studied, the contribution of CaMKs to Mendelian disease is rather enigmatic. Here, we describe an unusual neurodevelopmental phenotype, characterized by milestone delay, intellectual disability, autism, ataxia, and mixed hyperkinetic movement disorder including severe generalized dystonia, in a proband who remained etiologically undiagnosed despite exhaustive testing. We performed trio whole-exome sequencing to identify a de novo essential splice-site variant (c.981+1G>A) in CAMK4, encoding CaMKIV. Through in silico evaluation and cDNA analyses, we demonstrated that c.981+1G>A alters CAMK4 pre-mRNA processing and results in a stable mRNA transcript containing a 77-nt out-of-frame deletion and a premature termination codon within the last exon. The expected protein, p.Lys303Serfs*28, exhibits selective loss of the carboxy-terminal regulatory domain of CaMKIV and bears striking structural resemblance to previously reported synthetic mutants that confer constitutive CaMKIV activity. Biochemical studies in proband-derived cells confirmed an activating effect of c.981+1G>A and indicated that variant-induced excessive CaMKIV signaling is sensitive to pharmacological manipulation. Additionally, we found that variants predicted to cause selective depletion of CaMKIV's regulatory domain are unobserved in diverse catalogs of human variation, thus revealing that c.981+1G>A is a unique molecular event. We propose that our proband's phenotype is explainable by a dominant CAMK4 splice-disrupting mutation that acts through a gain-of-function mechanism. Our findings highlight the importance of CAMK4 in human neurodevelopment, provide a foundation for future clinical research of CAMK4, and suggest the CaMKIV signaling pathway as a potential drug target in neurological disease.

• Klíčová slova
• athetoid cerebral palsy, language impairment, motor deterioration, psychomotor deterioration, torticollis,
• MeSH
• aktivační mutace genetika   MeSH
• cerebelární ataxie genetika   MeSH
• exom MeSH
• exony genetika   MeSH
• fenotyp MeSH
• hyperkineze genetika   MeSH
• lidé MeSH
• mentální retardace genetika   MeSH
• mutace MeSH
• nesmyslný kodon genetika   MeSH
• posunová mutace genetika   MeSH
• proteinkinasa závislá na vápníku a kalmodulinu typ 4 genetika   metabolismus   MeSH
• rodokmen MeSH
• sekvenování exomu MeSH
• sestřih RNA genetika   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• práce podpořená grantem MeSH
• Názvy látek
• CAMK4 protein, human MeSH Prohlížeč
• nesmyslný kodon MeSH
• proteinkinasa závislá na vápníku a kalmodulinu typ 4 MeSH