Early detection of colorectal cancer (CRC) is the key for prevention and the ability to impact long-term survival of CRC patients. Current CRC screening modalities are inadequate for global application because of low sensitivity and specificity in case of conventional stool-based screening tests, and high costs and a low participation compliance in colonoscopy. An accurate stool- or blood-based screening test with use of innovative biomarkers is an appealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher compliance rates. Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes, such as proliferation, differentiation, migration, angiogenesis and apoptosis. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various cancers, including CRC. The discovery that ncRNAs (mainly microRNAs) are stable in stool and in blood plasma and serum presents the opportunity to develop novel strategies taking advantage of circulating ncRNAs as early diagnostic biomarkers of CRC. This chapter is a comprehensive examination of aberrant ncRNAs expression levels in tumor tissue, stool and blood of CRC patients and a summary of the current findings on ncRNAs, including microRNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, circular RNAs and long ncRNAs in regards to their potential usage for screening or early detection of CRC.

• Klíčová slova
• Colorectal cancer, Early diagnosis, Non-coding RNA, Screening, lncRNA, microRNA, piRNAs, snRNAs, snoRNAs,
• MeSH
• adenokarcinom chemie   diagnóza   genetika   MeSH
• adenom chemie   diagnóza   genetika   MeSH
• časná detekce nádoru metody   MeSH
• feces chemie   MeSH
• kolorektální nádory chemie   diagnóza   genetika   MeSH
• krevní plazma MeSH
• lidé MeSH
• nádorové biomarkery analýza   krev   MeSH
• nekódující RNA analýza   krev   MeSH
• pacientův souhlas se zdravotní péčí MeSH
• polypy tlustého střeva chemie   diagnóza   genetika   MeSH
• regulace genové exprese u nádorů MeSH
• senzitivita a specificita MeSH
• sérum MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• nádorové biomarkery MeSH
• nekódující RNA MeSH

Multiple myeloma (MM) is a plasma cell malignancy whereby a single clone of plasma cells over-propagates in the bone marrow, resulting in the increased production of monoclonal immunoglobulin. While the complex genetic architecture of MM is well characterized, much less is known about germline variants predisposing to MM. Genome-wide sequencing approaches in MM families have started to identify rare high-penetrance coding risk alleles. In addition, genome-wide association studies have discovered several common low-penetrance risk alleles, which are mainly located in the non-coding genome. Here, we further explored the genetic basis in familial MM within the non-coding genome in whole-genome sequencing data. We prioritized and characterized 150 upstream, 5' untranslated region (UTR) and 3' UTR variants from 14 MM families, including 20 top-scoring variants. These variants confirmed previously implicated biological pathways in MM development. Most importantly, protein network and pathway enrichment analyses also identified 10 genes involved in mitogen-activated protein kinase (MAPK) signaling pathways, which have previously been established as important MM pathways.

• Klíčová slova
• MAPK pathway, familial multiple myeloma, non-coding genome, whole-genome sequencing,
• MeSH
• celogenomová asociační studie * MeSH
• lidé MeSH
• MAP kinasový signální systém MeSH
• mnohočetný myelom * genetika   MeSH
• sekvenování celého genomu MeSH
• zárodečné mutace MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes. The unifying features of most of these identified RNAs are aberrant processing and the presence of stable secondary structures. Most importantly, we demonstrate that uridylation mediates DIS3L2 degradation of short RNA polymerase II-derived RNAs. Our findings establish the role of DIS3L2 and oligouridylation as the cytoplasmic quality control for highly structured ncRNAs.

• Klíčová slova
• DIS3L2, RNA surveillance, TSSa, ncRNAs, uridylation,
• MeSH
• buněčné linie MeSH
• exoribonukleasy genetika   metabolismus   MeSH
• imunoprecipitace MeSH
• lidé MeSH
• nekódující RNA metabolismus   MeSH
• nukleotidyltransferasy metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DIS3L2 protein, human MeSH Prohlížeč
• exoribonukleasy MeSH
• nekódující RNA MeSH
• nukleotidyltransferasy MeSH

In a large family of Czech origin, we mapped a locus for an autosomal-dominant corneal endothelial dystrophy, posterior polymorphous corneal dystrophy 4 (PPCD4), to 8q22.3-q24.12. Whole-genome sequencing identified a unique variant (c.20+544G>T) in this locus, within an intronic regulatory region of GRHL2. Targeted sequencing identified the same variant in three additional previously unsolved PPCD-affected families, including a de novo occurrence that suggests this is a recurrent mutation. Two further unique variants were identified in intron 1 of GRHL2 (c.20+257delT and c.20+133delA) in unrelated PPCD-affected families. GRHL2 is a transcription factor that suppresses epithelial-to-mesenchymal transition (EMT) and is a direct transcriptional repressor of ZEB1. ZEB1 mutations leading to haploinsufficiency cause PPCD3. We previously identified promoter mutations in OVOL2, a gene not normally expressed in the corneal endothelium, as the cause of PPCD1. OVOL2 drives mesenchymal-to-epithelial transition (MET) by directly inhibiting EMT-inducing transcription factors, such as ZEB1. Here, we demonstrate that the GRHL2 regulatory variants identified in PPCD4-affected individuals induce increased transcriptional activity in vitro. Furthermore, although GRHL2 is not expressed in corneal endothelial cells in control tissue, we detected GRHL2 in the corneal "endothelium" in PPCD4 tissue. These cells were also positive for epithelial markers E-Cadherin and Cytokeratin 7, indicating they have transitioned to an epithelial-like cell type. We suggest that mutations inducing MET within the corneal endothelium are a convergent pathogenic mechanism leading to dysfunction of the endothelial barrier and disease.

• Klíčová slova
• GRHL2, PPCD, corneal dystrophy, corneal edema, corneal endothelium, ectopic expression, epithelial-to-mesenchymal transition, mesenchymal-to-epithelial transition, non-coding mutation, regulatory region,
• MeSH
• dědičné dystrofie rohovky genetika   MeSH
• DNA vazebné proteiny genetika   MeSH
• genetická transkripce MeSH
• genetické lokusy MeSH
• HEK293 buňky MeSH
• intergenová DNA genetika   MeSH
• introny genetika   MeSH
• lidé MeSH
• modely genetické MeSH
• mutace genetika   MeSH
• promotorové oblasti (genetika) genetika   MeSH
• rodina MeSH
• rodokmen MeSH
• rohovkový endotel patologie   MeSH
• sekvence nukleotidů MeSH
• sekvenování celého genomu MeSH
• transkripční faktory genetika   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• GRHL2 protein, human MeSH Prohlížeč
• intergenová DNA MeSH
• transkripční faktory MeSH

Clear cell tubulopapillary renal cell carcinoma (CCPRCC) is a recently described rare renal malignancy that displays characteristic gross, microscopic and immunohistochemical differences from other renal tumour types. However, CCPRCC remains a very poorly understood entity. We therefore sought to elucidate some of the molecular mechanisms involved in this neoplasm by carrying out targeted next-generation sequencing (NGS) to identify associated mutations, and in addition examined the expression of non-coding (nc) RNAs. We identified multiple somatic mutations in CCPRCC cases, including a recurrent [3/14 cases (21%)] non-synonymous T992I mutation in the MET proto-oncogene, a gene associated with epithelial-to-mesenchymal transition (EMT). Using a microarray approach, we found that the expression of mature (n = 1105) and pre-miRNAs (n = 1105), as well as snoRNA and scaRNAs (n = 2214), in CCPRCC cases differed from that of clear cell renal cell carcinoma (CCRCC) or papillary renal cell carcinoma (PRCC) tumours. Surprisingly, and unlike other renal tumour subtypes, we found that all five members of the miR-200 family were over-expressed in CCPRCC cases. As these miRNAs are intimately involved with EMT, we stained CCPRCC cases for E-cadherin, vimentin and β-catenin and found that the tumour cells of all cases were positive for all three markers, a combination rarely reported in other renal tumours that could have diagnostic implications. Taken together with the mutational analysis, these data suggest that EMT in CCPRCC tumour cells is incomplete or blocked, consistent with the indolent clinical course typical of this malignancy. In summary, as well as describing a novel pathological mechanism in renal carcinomas, this study adds to the mounting evidence that CCPRCC should be formally considered a distinct entity. Microarray data have been deposited in the GEO database [GEO accession number (GSE51554)].

• Klíčová slova
• EMT, clear cell papillary renal cell carcinoma, miRNA, non-coding RNA, renal carcinoma,
• MeSH
• DNA nádorová chemie   genetika   MeSH
• epitelo-mezenchymální tranzice MeSH
• karcinom z renálních buněk genetika   patologie   MeSH
• lidé MeSH
• mikro RNA chemie   genetika   izolace a purifikace   MeSH
• mutační analýza DNA MeSH
• nádorové biomarkery genetika   MeSH
• nádory ledvin genetika   patologie   MeSH
• následné studie MeSH
• nekódující RNA chemie   genetika   MeSH
• přežití bez známek nemoci MeSH
• protoonkogen Mas MeSH
• retrospektivní studie MeSH
• RNA nádorová genetika   izolace a purifikace   MeSH
• sekvenční analýza DNA MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• shluková analýza MeSH
• stanovení celkové genové exprese MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• DNA nádorová MeSH
• MAS1 protein, human MeSH Prohlížeč
• mikro RNA MeSH
• nádorové biomarkery MeSH
• nekódující RNA MeSH
• protoonkogen Mas MeSH
• RNA nádorová MeSH

Congenital hereditary endothelial dystrophy 1 (CHED1) and posterior polymorphous corneal dystrophy 1 (PPCD1) are autosomal-dominant corneal endothelial dystrophies that have been genetically mapped to overlapping loci on the short arm of chromosome 20. We combined genetic and genomic approaches to identify the cause of disease in extensive pedigrees comprising over 100 affected individuals. After exclusion of pathogenic coding, splice-site, and copy-number variations, a parallel approach using targeted and whole-genome sequencing facilitated the identification of pathogenic variants in a conserved region of the OVOL2 proximal promoter sequence in the index families (c.-339_361dup for CHED1 and c.-370T>C for PPCD1). Direct sequencing of the OVOL2 promoter in other unrelated affected individuals identified two additional mutations within the conserved proximal promoter sequence (c.-274T>G and c.-307T>C). OVOL2 encodes ovo-like zinc finger 2, a C2H2 zinc-finger transcription factor that regulates mesenchymal-to-epithelial transition and acts as a direct transcriptional repressor of the established PPCD-associated gene ZEB1. Interestingly, we did not detect OVOL2 expression in the normal corneal endothelium. Our in vitro data demonstrate that all four mutated OVOL2 promoters exhibited more transcriptional activity than the corresponding wild-type promoter, and we postulate that the mutations identified create cryptic cis-acting regulatory sequence binding sites that drive aberrant OVOL2 expression during endothelial cell development. Our data establish CHED1 and PPCD1 as allelic conditions and show that CHED1 represents the extreme of what can be considered a disease spectrum. They also implicate transcriptional dysregulation of OVOL2 as a common cause of dominantly inherited corneal endothelial dystrophies.

• MeSH
• alely * MeSH
• dědičné dystrofie rohovky genetika   MeSH
• DNA MeSH
• lidé MeSH
• mutace * MeSH
• promotorové oblasti (genetika) * MeSH
• rodokmen MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• transkripční faktory genetika   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• Ovol2 protein, human MeSH Prohlížeč
• transkripční faktory MeSH

Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network. Overall we detected 438 differentially expressed genes and 991 differentially expressed small non-coding RNAs in cortical tubers compared to autopsy control brain tissue. We observed increased expression of genes associated with inflammatory, innate and adaptive immune responses. In contrast, we observed a down-regulation of genes associated with neurogenesis and glutamate receptor signaling. MicroRNAs represented the largest class of over-expressed small non-coding RNA species in tubers. In particular, our analysis revealed that the miR-34 family (including miR-34a, miR-34b and miR-34c) was significantly over-expressed. Functional studies demonstrated the ability of miR-34b to modulate neurite outgrowth in mouse primary hippocampal neuronal cultures. This study provides new insights into the TSC transcriptomic network along with the identification of potential new treatment targets.

• MeSH
• dítě MeSH
• dospělí MeSH
• epilepsie genetika   MeSH
• genetická transkripce genetika   MeSH
• hamartin genetika   MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikro RNA genetika   MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mozková kůra fyziologie   MeSH
• mTORC1 genetika   MeSH
• mutace genetika   MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• neurony fyziologie   MeSH
• předškolní dítě MeSH
• signální transdukce genetika   MeSH
• tuberin genetika   MeSH
• tuberózní skleróza genetika   MeSH
• zvířata MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• myši MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hamartin MeSH
• mikro RNA MeSH
• MIRN34a microRNA, mouse MeSH Prohlížeč
• mTORC1 MeSH
• tuberin MeSH

Tuberous sclerosis complex (TSC) is an autosomal dominantly inherited neurocutaneous disorder caused by inactivating mutations in TSC1 or TSC2, key regulators of the mechanistic target of rapamycin complex 1 (mTORC1) pathway. In the CNS, TSC is characterized by cortical tubers, subependymal nodules and subependymal giant cell astrocytomas (SEGAs). SEGAs may lead to impaired circulation of CSF resulting in hydrocephalus and raised intracranial pressure in patients with TSC. Currently, surgical resection and mTORC1 inhibitors are the recommended treatment options for patients with SEGA. In the present study, high-throughput RNA-sequencing (SEGAs n = 19, periventricular control n = 8) was used in combination with computational approaches to unravel the complexity of SEGA development. We identified 9400 mRNAs and 94 microRNAs differentially expressed in SEGAs compared to control tissue. The SEGA transcriptome profile was enriched for the mitogen-activated protein kinase (MAPK) pathway, a major regulator of cell proliferation and survival. Analysis at the protein level confirmed that extracellular signal-regulated kinase (ERK) is activated in SEGAs. Subsequently, the inhibition of ERK independently of mTORC1 blockade decreased efficiently the proliferation of primary patient-derived SEGA cultures. Furthermore, we found that LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5 were overexpressed at both gene and protein levels in SEGA compared to control tissue. Taken together LAMTOR1-5 can form a complex, known as the 'Ragulator' complex, which is known to activate both mTORC1 and MAPK/ERK pathways. Overall, this study shows that the MAPK/ERK pathway could be used as a target for treatment independent of, or in combination with mTORC1 inhibitors for TSC patients. Moreover, our study provides initial evidence of a possible link between the constitutive activated mTORC1 pathway and a secondary driver pathway of tumour growth.

• Klíčová slova
• SEGA, TSC, low grade glioma, sequencing,
• MeSH
• adaptorové proteiny signální transdukční genetika   metabolismus   MeSH
• astrocytom etiologie   genetika   metabolismus   MeSH
• astrocyty účinky léků   metabolismus   MeSH
• butadieny farmakologie   MeSH
• dítě MeSH
• dospělí MeSH
• extracelulárním signálem regulované MAP kinasy antagonisté a inhibitory   genetika   metabolismus   MeSH
• hamartin genetika   MeSH
• inhibitory enzymů farmakologie   MeSH
• intracelulární signální peptidy a proteiny genetika   metabolismus   MeSH
• kojenec MeSH
• lidé MeSH
• MAP kinasový signální systém genetika   MeSH
• messenger RNA metabolismus   MeSH
• mikro RNA metabolismus   MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mTORC1 MeSH
• nádorové buňky kultivované MeSH
• nádory mozku komplikace   genetika   metabolismus   MeSH
• nitrily farmakologie   MeSH
• předškolní dítě MeSH
• sekvenční analýza RNA MeSH
• sekvenování transkriptomu MeSH
• stanovení celkové genové exprese MeSH
• tuberin genetika   MeSH
• tuberózní skleróza komplikace   genetika   MeSH
• výměnné faktory guaninnukleotidů genetika   metabolismus   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• adaptorové proteiny signální transdukční MeSH
• butadieny MeSH
• extracelulárním signálem regulované MAP kinasy MeSH
• hamartin MeSH
• inhibitory enzymů MeSH
• intracelulární signální peptidy a proteiny MeSH
• LAMTOR1 protein, human MeSH Prohlížeč
• LAMTOR2 protein, human MeSH Prohlížeč
• LAMTOR3 protein, human MeSH Prohlížeč
• LAMTOR4 protein, human MeSH Prohlížeč
• LAMTOR5 protein, human MeSH Prohlížeč
• messenger RNA MeSH
• mikro RNA MeSH
• mTORC1 MeSH
• nitrily MeSH
• TSC1 protein, human MeSH Prohlížeč
• TSC2 protein, human MeSH Prohlížeč
• tuberin MeSH
• U 0126 MeSH Prohlížeč
• výměnné faktory guaninnukleotidů MeSH

Haploinsufficiency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. In one case, the deletion of the maternal allele of the FOXF1 enhancer caused pulmonary hypertension and histopathologically diagnosed MPV without the typical ACD features. In the second case, the deletion of the paternal enhancer resulted in ACDMPV rather than the expected neonatal lethality. In both cases, FOXF1 expression in lung tissue was higher than usually seen or expected in patients with similar deletions, suggesting an increased activity of the remaining allele of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Moreover, in a family with three histopathologically-diagnosed ACDMPV siblings whose missense FOXF1 mutation was inherited from the healthy non-mosaic carrier mother, we have identified a rare SNV rs28571077-A within 2-kb of the above-mentioned non-coding SNVs in the FOXF1 enhancer in the mother, that was absent in the affected newborns and 13 unrelated ACDMPV patients with CNV deletions of this genomic region. Based on the low population frequencies of these three variants, their absence in ACDMPV patients, the results of reporter assay, RNAi and EMSA experiments, and in silico predictions, we propose that the described SNVs might have acted on FOXF1 enhancer as hypermorphs.

• MeSH
• dítě MeSH
• dospělí MeSH
• fenotyp MeSH
• forkhead transkripční faktory genetika   MeSH
• genomový imprinting MeSH
• jednonukleotidový polymorfismus * MeSH
• lidé MeSH
• missense mutace * MeSH
• novorozenec MeSH
• prognóza MeSH
• sekvenční delece * MeSH
• syndrom přetrvávajícího fetálního oběhu genetika   patologie   prevence a kontrola   MeSH
• zesilovače transkripce * MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé MeSH
• novorozenec MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• Názvy látek
• forkhead transkripční faktory MeSH
• FOXF1 protein, human MeSH Prohlížeč

Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.

• MeSH
• genetický kód genetika   MeSH
• kodon genetika   MeSH
• lidé MeSH
• messenger RNA chemie   genetika   MeSH
• modely genetické MeSH
• mutace * MeSH
• otevřené čtecí rámce genetika   MeSH
• proteiny chemie   genetika   metabolismus   MeSH
• proteosyntéza genetika   MeSH
• sbalování proteinů MeSH
• sbalování RNA MeSH
• stabilita RNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• kodon MeSH
• messenger RNA MeSH
• proteiny MeSH