Circular RNAs Could Encode Unique Proteins and Affect Cancer Pathways

CircRNAs constitute a novel class of RNA, generally considered as non-coding RNAs; nonetheless, their coding potential has been under scrutiny. In this work, we systematically explored the predicted proteins of more than 160,000 circRNAs detected by exome capture RNA-sequencing and collected in the MiOncoCirc pan-cancer compendium, including normal and cancer samples from different types of tissues. For the functional evaluation, we compared their primary structure and domain composition with those derived from the same linear mRNAs. Among the 4362 circRNAs potentially encoding proteins with a unique primary structure and 1179 encoding proteins with a novel domain composition, 183 were differentially expressed in cancer. In particular, eight were associated with prognosis in acute myeloid leukemia. The functional classification of the dysregulated circRNA-encoded polypeptides showed an enrichment in the heme and cancer signaling, DNA-binding, and phosphorylation processes, and disclosed the roles of some circRNA-based effectors in cancer

HorTILLUS - a rich and renewable source of induced mutations for forward/reverse genetics and pre-breeding programs in barley (Hordeum vulgare L.)

TILLING (Targeting Induced Local Lesions IN Genomes) is a strategy used for functional analysis of genes that combines the classical mutagenesis and a rapid, high-throughput identification of mutations within a gene of interest. TILLING has been initially developed as a discovery platform for functional genomics, but soon it has become a valuable tool in development of desired alleles for crop breeding, alternative to transgenic approach. Here we present the HorTILLUS (Hordeum—TILLING—University of Silesia) population created for spring barley cultivar “Sebastian” after double-treatment of seeds with two chemical mutagens: sodium azide (NaN3) and N-methyl-N-nitrosourea (MNU). The population comprises more than 9,600 M2 plants from which DNA was isolated, seeds harvested, vacuum-packed, and deposited in seed bank. M3 progeny of 3,481 M2 individuals was grown in the field and phenotyped. The screening for mutations was performed for 32 genes related to different aspects of plant growth and development. For each gene fragment, 3,072–6,912 M2 plants were used for mutation identification using LI-COR sequencer. In total, 382 mutations were found in 182.2Mb screened. The average mutation density in the HorTILLUS, estimated as 1 mutation per 477 kb, is among the highest mutation densities reported for barley. The majority of mutations were G/C to A/T transitions, however about 8% transversions were also detected. Sixty-one percent of mutations found in coding regions were missense, 37.5% silent and 1.1% nonsense. In each gene, the missense mutations with a potential effect on protein function were identified. The HorTILLUS platformis the largest of the TILLING populations reported for barley and best characterized. The population proved to be a useful tool, both in functional genomic studies and in forward selection of barley mutants with required phenotypic changes. We are constantly renewing the HorTILLUS population, which makes it a permanent source of new mutations.We offer the usage of this valuable resource to the interested barley researchers on cooperative basis

A common cis-element in promoters of protein synthesis and cell cycle genes

Gene promoters contain several classes of functional sequence elements (cis elements) recognized by protein agents, e.g. transcription factors and essential components of the transcription machinery. Here we describe a common DNA regulatory element (tandem TCTCGCGAGA motif) of human TATA-less promoters. A combination of bioinformatic and experimental methodology suggests that the element can be critical for expression of genes involved in enhanced protein synthesis and the G1/S transition in the cell cycle. The motif was identified in a substantial fraction of promoters of cell cycle genes, like cyclins (CCNC, CCNG1), as well as transcription regulators (TAF7, TAF13, KLF7, NCOA2), chromatin structure modulators (HDAC2, TAF6L), translation initiation factors (EIF5, EIF2S1, EIF4G2, EIF3S8, EIF4) and previously reported 18 ribosomal protein genes. Since the motif can define a subset of promoters with a distinct mechanism of activation involved in regulation of expression of about 5% of human genes, further investigation of this regulatory element is an emerging task

Krioablacja balonowa w ujściach żył płucnych – ocena skuteczności i bezpieczeństwa u pacjentów z migotaniem przedsionków. Doniesienie wstępne

Background: Cryoballon isolation of the pulmonary veins has recently emerged as a promissing technique for ablation of atrial fibrillation (AF). Aim: To present our initial experience in cryoballon isolatin of the pulmonary veins in patients with AF. Methods: Eight patients (5 males; age 59 ± 2 years) with AF: 2 with persistent and 6 with paroxysmal (5 of them after unsuccessful RF ablation) with > 6 month follow-up after the procedure were included. One patient after myocardial infarction was treated with primary angioplasty with stent implantation. Another one had biatrial pacemaker. The procedure was performed with cryobaloon with 28 mm diameter (Arctic Front - Cryocath). After transseptal puncture mapping of the pulmonary vein ostia was performed with Lasso catheter (Johnson & Johnson). At each pulmonary vein ostium with pulmonary vein potentials 2 cryoapplications of 300 s duration was performed. Correct balloon placement before cryoapplication was checked using contrast injection into the pulmonary veins. During cryoapplication in the right pulmonary vein ostia permanent pacing of the phrenic nerve 30 beats per minute was performed to prevent its paralysis. After cryoapplications in all veins remapping with Lasso catheters was performed. In the absence of pulmonary vein potentials the procedure was finished, otherwise next cryoapplications were performed. During follow-up ECG was performed if any palpitations occurred, and 24-hour Holter monitoring was performed 1, 2 ,4, 6, 8, 10 and 12 months after the procedure. A 2-month blanking period after the procedure was used. The lack of symptomatic AF and the absence of AF > 30 s on Holter ECG monitoring were defined as successful procedure. An improvement was defined as reduction of frequency/duration of AF paroxysm and reduction of the EHRA index ≥ 1. Results: During 8 procedures isolation of 31 pulmonary vein was performed. Procedure duration was 3.5 ± 0.85 h, fluoroscopy time - 33.55 ± 15.44 min, and total cryoapplication time – 38.33 ± 4.1 min. There were no complications. After the follow-up of 8.5 ± 0.99 months 6 (75%) patients were free from arrhythmia, including the patient after myocardial infarction and one patient with permanent AF prior ablation. In another patient an improvement was observed (EHRA score II/III to I) whereas in one patient with permanent AF the procedure was unsuccessful. Conclusion: Cryoballoon ablation of pulmonary vein ostia is effective and safe, and can be an alternative to RF ablation. Easier procedure technique make possible shortening of the learning curve and increase the number of treated patients.Wstęp: Izolacja żył płucnych przy użyciu balonu do krioablacji jest nową metodą leczenia migotania przedsionków (AF). Wydaje się łatwiejsza technicznie, dzięki czemu stwarza szanse na skrócenie czasu nauki, a tym samym na zwiększenie dostępności leczenia zabiegowego AF. Cel: Ocena wstępnych doświadczeń z wykorzystaniem tej metody w zakresie skuteczności i bezpieczeństwa. Metody: Przy użyciu kriobalonów (Arctic Front-Cryocath) o średnicy 28 mm wykonano zabiegi u 8 pacjentów (5 mężczyzn, 3 kobiety; wiek 59 ± 2 lata) z objawowym AF, opornym na leki antyarytmiczne. W 2 przypadkach było to przetrwałe AF, a w 6 - napadowe (w 5 po nieskutecznej ablacji prądem o częstotliwości radiowej - RF). Jeden pacjent przebył zawał serca leczony angioplastyką z implantacją stentów, u innego wcześniej implantowano dwuprzedsionkowy resynchronizujący układ stymulujący. Przed zabiegiem u 8 pacjentów wykonano 16-rzędową tomografię komputerową, u 6 chorych również badanie echokardiograficzne przezprzełykowe. Leki przeciwzakrzepowe odstawiano 4 dni przed zabiegiem i zastępowano je heparyną drobnocząsteczkową. Poprzez żyły udowe wprowadzano elektrody diagnostyczne do zatoki wieńcowej i prawej komory. W trakcie ablacji pacjenci otrzymywali fentanyl i midazolam. Po nakłuciu transseptalnym podawano heparynę niefrakcjonowaną w dawce 6000 IU (następnie 1000 IU/godz.) oraz wprowadzano sterowalną koszulkę transseptalną do lewego przedsionka (płukana wolnym przepływem soli fizjologicznej z 1000 IU heparyny/500 ml). Ektrodą Lasso mapowano żyły płucne. Następnie wymieniano elektrodę na balon. Wykonywano dwie krioaplikacje po 300 s w ujściu każdej żyły płucnej, w której zarejestrowano potencjały żylne (PVP). W czasie krioaplikacji w żyłach prawych, elektrodą wprowadzoną do żyły głównej górnej (powyżej balonu) stymulowano nerw przeponowy z częstotliwością 30/min. W razie wystąpienia zaburzeń ruchu przepony konieczne jest natychmiastowe zaprzestanie krioaplikacji. Następnie ponownie wykonywano mapowanie ujść żylnych elektrodą Lasso. W przypadku utrzymywania się PVP wykonywano kolejne krioaplikacje weryfikowane mapowaniem Lasso. Pacjenci mieli zalecone wykonanie EKG przy każdej wizycie lekarskiej oraz EKG metodą Holtera 1, 2, 4 ,6, 8, 10 i 12 miesięcy po zabiegu w celu oceny rytmu serca. Okres 2 miesięcy po zabiegu przyjęto za czas tworzenia się blizny modyfikującej podłoże arytmii. Jeśli w tym okresie wystąpiły napady arytmii, zabieg uznawano za nieskuteczny. Do badania włączono pacjentów, których okres obserwacji wynosił > 6 miesięcy. Zabieg definiowano jako skuteczny, jeśli nie wystąpiły objawowe oraz nieme napady AF trwające > 30 s w monitorowaniu holterowskim. Jako poprawę definiowano rzadsze występowanie arytmii, krótszy czas jej trwania i mniejszą uciążliwość (zmniejszenie wskaźnika EHRA przynajmniej o 1 pkt). Przy utrzymywaniu się napadów na podobnym poziomie zabieg uznawano za nieskuteczny. Wyniki: Wykonano izolację 31 żył płucnych. Czas zabiegu wyniósł 3,5 ± 0,85 godz., czas krioaplikacji 38,33 ± 4,08 min, czas fluoroskopii 33,55 ± 15,44 min. Zabiegi przeprowadzono bez powikłań. W okresie 8,5 ± 0,99 miesiąca po zabiegu bez arytmii pozostało 6 pacjentów. W tej grupie u jednego pacjenta w okresie pierwszych 2 tygodni po ablacji wystąpiły 3 samoograniczające się napady AF. W grupie bez nawrotu arytmii znajduje się pacjent po zawale serca. U jednego pacjenta obserwowano zmniejszenie uporczywości arytmii (EHRA II/III na I), liczby napadów, czasu ich trwania oraz złagodzenie odczuwanych dolegliwości. U jednego pacjenta z przetrwałym AF zabieg był nieskuteczny. Wnioski: Krioablacja balonowa jest skuteczną i bezpieczną metoda leczenia napadowego i przetrwałego AF. Krioablacja balonowa wydaje się alternatywą dla ablacji RF

BMPR1B gene in brachydactyly type 2–A family with de novo R486W mutation and a disease phenotype

Abstract Background Brachydactylies are a group of inherited conditions, characterized mainly by the presence of shortened fingers and toes. Based on the patients’ phenotypes, brachydactylies have been subdivided into 10 subtypes. In this study, we have identified a family with two members affected by brachydactyly type A2 (BDA2). BDA2 is caused by mutations in three genes: BMPR1B, BMP2 or GDF5. So far only two studies have reported the BDA2 cases caused by mutations in the BMPR1B gene. Methods We employed next‐generation sequencing to identify mutations in culpable genes. Results and Conclusion In this paper, we report a case of BDA2 resulting from the presence of a heterozygous c.1456C>T, p.Arg486Trp variant in BMPR1B, which was previously associated with BDA2. The next generation sequencing analysis of the patients’ family revealed that the mutation occurred de novo in the proband and was transmitted to his 26‐month‐old son. Although the same variant was confirmed in both patients, their phenotypes were different with more severe manifestation of the disease in the adult

Cereblon (CRBN) gene polymorphisms predict clinical response and progression-free survival in relapsed/refractory multiple myeloma patients treated with lenalidomide: a pharmacogenetic study from the IMMEnSE consortium

Cereblon (CRBN) is crucial for antiproliferative and immunomodulatory properties of immunomodulatory drugs. The objective of this study was to verify whether germline single nucleotide polymorphisms (SNPs) in the CRBN gene may influence response to lenalidomide in multiple myeloma (MM). Fourteen tagging SNPs covering the genetic variability in the CRBN gene region were genotyped in 167 Polish patients with refractory/relapsed MM treated with lenalidomide-based regimens. We found that carriers of minor alleles of two studied CRBN SNPs rs1714327G > C (OR = 0.26; 95% CI = 0.1-0.67; p = .0055, Bonferroni corrected p = .033) and rs1705814T > C (OR = 0.22; 95% CI = 0.07-0.65; p = .0063, Bonferroni corrected p = .037) were significantly associated with lower probability of achievement at least partial remission while treated with lenalidomide-based regimens, using the dominant inheritance model. Moreover, one of these SNPs, namely rs1705814T > C, was correlated with shorter progression-free survival (HR = 2.49; 95%CI = 1.31-4.74, p = .0054, Bonferroni corrected p = .033). It is suggested that selected germline CRBN allelic variants (rs1714327G > C and rs1705814T > C) affect lenalidomide efficacy in patients with relapsed/refractory MM

Table3.DOCX

<p>TILLING (Targeting Induced Local Lesions IN Genomes) is a strategy used for functional analysis of genes that combines the classical mutagenesis and a rapid, high-throughput identification of mutations within a gene of interest. TILLING has been initially developed as a discovery platform for functional genomics, but soon it has become a valuable tool in development of desired alleles for crop breeding, alternative to transgenic approach. Here we present the HorTILLUS (Hordeum—TILLING—University of Silesia) population created for spring barley cultivar “Sebastian” after double-treatment of seeds with two chemical mutagens: sodium azide (NaN₃) and N-methyl-N-nitrosourea (MNU). The population comprises more than 9,600 M₂ plants from which DNA was isolated, seeds harvested, vacuum-packed, and deposited in seed bank. M₃ progeny of 3,481 M₂ individuals was grown in the field and phenotyped. The screening for mutations was performed for 32 genes related to different aspects of plant growth and development. For each gene fragment, 3,072–6,912 M₂ plants were used for mutation identification using LI-COR sequencer. In total, 382 mutations were found in 182.2 Mb screened. The average mutation density in the HorTILLUS, estimated as 1 mutation per 477 kb, is among the highest mutation densities reported for barley. The majority of mutations were G/C to A/T transitions, however about 8% transversions were also detected. Sixty-one percent of mutations found in coding regions were missense, 37.5% silent and 1.1% nonsense. In each gene, the missense mutations with a potential effect on protein function were identified. The HorTILLUS platform is the largest of the TILLING populations reported for barley and best characterized. The population proved to be a useful tool, both in functional genomic studies and in forward selection of barley mutants with required phenotypic changes. We are constantly renewing the HorTILLUS population, which makes it a permanent source of new mutations. We offer the usage of this valuable resource to the interested barley researchers on cooperative basis.</p