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Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adapter ligation, to comprehensively interrogate the human transcriptome at single-molecule and -nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key component of RNA metabolism upon cellular stress that is dependent on stress granule formation., Competing Interests: SD, SM, VM, MP, CL, JM, AK, JM, CB, MM No competing interests declared

Background: RNA-binding proteins (RBPs) play a critical role in regulating gene expression by binding to specific sites on RNA molecules. Identifying these binding sites is crucial for understanding the many functions of RBPs in cellular function, development and disease. Current experimental methods for identifying RBP binding sites, such as ultra-violet (UV) crosslinking and immunoprecipitation (CLIP), and especially the enhanced CLIP (eCLIP) protocol, were developed to identify authentic RBP binding sites experimentally., Methods: To make this data more accessible to the scientific community, we have developed RBP-Tar ( https://ncbr.muni.cz/RBP-Tar ), a web server and database that utilises eCLIP data for 167 RBPs mapped on the human genome. The web server allows researchers to easily search and retrieve binding site information by genomic location and RBP name., Use Case: Researchers can produce lists of all known RBP binding sites on a gene of interest, or produce lists of binding sites for one RBP on different genomic loci., Conclusions: Our future goal is to continue to populate the web server with additional experimental datasets from CLIP experiments as they become available and processed, making it an increasingly valuable resource for the scientific community., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Gresova K et al.)

In eukaryotes, genes produce a variety of distinct RNA isoforms, each with potentially unique protein products, coding potential or regulatory signals such as poly(A) tail and nucleotide modifications. Assessing the kinetics of RNA isoform metabolism, such as transcription and decay rates, is essential for unraveling gene regulation. However, it is currently impeded by lack of methods that can differentiate between individual isoforms. Here, we introduce RNAkinet, a deep convolutional and recurrent neural network, to detect nascent RNA molecules following metabolic labeling with the nucleoside analog 5-ethynyl uridine and long-read, direct RNA sequencing with nanopores. RNAkinet processes electrical signals from nanopore sequencing directly and distinguishes nascent from pre-existing RNA molecules. Our results show that RNAkinet prediction performance generalizes in various cell types and organisms and can be used to quantify RNA isoform half-lives. RNAkinet is expected to enable the identification of the kinetic parameters of RNA isoforms and to facilitate studies of RNA metabolism and the regulatory elements that influence it., (Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics 2024.)

Quantification of the dynamics of RNA metabolism is essential for understanding gene regulation in health and disease. Existing methods rely on metabolic labeling of nascent RNAs and physical separation or inference of labeling through PCR-generated mutations, followed by short-read sequencing. However, these methods are limited in their ability to identify transient decay intermediates or co-analyze RNA decay with cis-regulatory elements of RNA stability such as poly(A) tail length and modification status, at single molecule resolution. Here we use 5-ethynyl uridine (5EU) to label nascent RNA followed by direct RNA sequencing with nanopores. We developed RNAkinet, a deep convolutional and recurrent neural network that processes the electrical signal produced by nanopore sequencing to identify 5EU-labeled nascent RNA molecules. RNAkinet demonstrates generalizability to distinct cell types and organisms and reproducibly quantifies RNA kinetic parameters allowing the combined interrogation of RNA metabolism and cis-acting RNA regulatory elements.

Background: Recently, deep neural networks have been successfully applied in many biological fields. In 2020, a deep learning model AlphaFold won the protein folding competition with predicted structures within the error tolerance of experimental methods. However, this solution to the most prominent bioinformatic challenge of the past 50 years has been possible only thanks to a carefully curated benchmark of experimentally predicted protein structures. In Genomics, we have similar challenges (annotation of genomes and identification of functional elements) but currently, we lack benchmarks similar to protein folding competition., Results: Here we present a collection of curated and easily accessible sequence classification datasets in the field of genomics. The proposed collection is based on a combination of novel datasets constructed from the mining of publicly available databases and existing datasets obtained from published articles. The collection currently contains nine datasets that focus on regulatory elements (promoters, enhancers, open chromatin region) from three model organisms: human, mouse, and roundworm. A simple convolution neural network is also included in a repository and can be used as a baseline model. Benchmarks and the baseline model are distributed as the Python package 'genomic-benchmarks', and the code is available at https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks ., Conclusions: Deep learning techniques revolutionized many biological fields but mainly thanks to the carefully curated benchmarks. For the field of Genomics, we propose a collection of benchmark datasets for the classification of genomic sequences with an interface for the most commonly used deep learning libraries, implementation of the simple neural network and a training framework that can be used as a starting point for future research. The main aim of this effort is to create a repository for shared datasets that will make machine learning for genomics more comparable and reproducible while reducing the overhead of researchers who want to enter the field, leading to healthy competition and new discoveries., (© 2023. The Author(s).)

The mitochondrial respiratory chain (MRC) complex III (CIII) associates with complexes I and IV (CI and CIV) into supercomplexes. We identified a novel homozygous missense mutation (c.665G>C; p.Gly222Ala) in UQCRC2 coding for structural subunit Core 2 in a patient with severe encephalomyopathy. The structural data suggest that the Gly222Ala exchange might result in an altered spatial arrangement in part of the UQCRC2 subunit, which could impact specific protein-protein interactions. Accordingly, we have found decreased levels of CIII and accumulation of CIII-specific subassemblies comprising MT-CYB, UQCRB, UQCRQ, UQCR10 and CYC1 subunits, but devoid of UQCRC1, UQCRC2, and UQCRFS1 in the patient's fibroblasts. The lack of UQCRC1 subunit-containing subassemblies could result from an impaired interaction with mutant UQCRC2 Gly222Ala and subsequent degradation of both subunits by mitochondrial proteases. Indeed, we show an elevated amount of matrix CLPP protease, suggesting the activation of the mitochondrial protein quality control machinery in UQCRC2 Gly222Ala fibroblasts. In line with growing evidence, we observed a rate-limiting character of CIII availability for the supercomplex formation, accompanied by a diminished amount of CI. Furthermore, we found impaired electron flux between CI and CIII in skeletal muscle and fibroblasts of the UQCRC2 Gly222Ala patient. The ectopic expression of wild-type UQCRC2 in patient cells rescued maximal respiration rate, demonstrating the deleterious effect of the mutation on MRC. Our study expands the phenotypic spectrum of human disease caused by CIII Core protein deficiency, provides insight into the assembly pathway of human CIII, and supports the requirement of assembled CIII for a proper accumulation of CI., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Atopic dermatitis is the most common chronic inflammatory skin disease. It is often the first indicator of allergic diseases, and a certain percentage of patients are affected by allergic rhinitis and/or asthma as a consequence. The study aimed to investigate the link between atopic dermatitis and comorbidity in family medicine. In the specialist family medicine practice Osijek, a retrospective study was conducted in the period from January 1, 2016 to July 1, 2017 on the percentage of patients with atopic dermatitis in the total number of patients, and their comorbid diseases. The data source was the E-chart. The results showed that 195 (10.53%) out of 2056 patients had atopic dermatitis, 80 (41%) patients had atopic dermatitis and allergic rhinitis, 34 (17.4%) asthma, 132 (67.7%) infections, 59 (30.3%) gastrointestinal disturbances, and 68 (34.3%) had mental disorders. Patients up to 18 years old were more likely to have infections, and adult patients were exposed to chronic stress. The most commonly used drug was loratadine (60.5%), while mometasone was the most commonly administered topical drug (40%). The result of this research showed the steps of the ˝atopic march˝. Atopic dermatitis is followed by changes in the skin and its progression to other organ systems in most of the patients., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Growth factors like BMP2 have been tested for osteochondral repair, but transfer methods used until now were insufficient. Therefore, the aim of this study was to analyse if stable BMP2 expression after retroviral vector (Bullet) transduction is able to regenerate osteochondral defects in rabbits. Fibrin clots colonized by control or BMP2-transduced chondrocytes were generated for in vitro experiments and implantation into standardized corresponding osteochondral defects (n=32) in the rabbit trochlea. After 4 and 12 weeks repair tissue was analysed by histology (HE, alcian-blue, toluidine-blue), immunohistochemistry (Col1, Col2, aggrecan, aggrecan-link protein), ELISA (BMP2), and quantitative RT-PCR (BMP2, Col1, Col2, Col10, Cbfa1, Sox9). In vitro clots were also analysed by BMP2-ELISA, histology (alcian-blue), quantitative RT-PCR and in addition by electron microscopy. BMP2 increased Col2 expression, proteoglycan production and cell size in vitro. BMP2 transduction by Bullet was efficient and gene expression was stable in vivo over at least 12 weeks. Proteoglycan content and ICRS-score of repair tissue were improved by BMP2 after 4 and 12 weeks and Col2 expression after 4 weeks compared to controls. However, in spite of stable BMP2 expression, a complete repair of osteochondral defects could not be demonstrated. Therefore, BMP2 is not suitable to regenerate osteochondral lesions completely.

Since efficient transfer of foreign genes into primary articular chondrocytes (CC) is difficult, a VSV.G pseudotyped retroviral vector (Bullet) was developed for marker and growth factor gene transfer. Transduction efficiency was analysed by FACS. BMP2 production was determined by specific hBMP2-ELISA. BMP2 effect on cells regarding proteoglycan production was measured by alcian blue staining and dye quantification. Alkaline phosphatase activity was determined by enzymatic reaction with p-nitrophenyl phosphate at OD 405nm and proliferation rate was analysed by MTT-assay. ATDC5 cells (98.3+/-0.6%SD) were transduced to express the reporter gene eGFP. After 52 weeks 94.7+/-0.6%SD of cells were positive. Retroviral transduction efficiency for nlslacZ exceeded 92.3+/-6.1%SD in rabbit CC and expression remained high after 15 weeks (75.7+/-14.2%SD). ATDC5 cells and CC expressed the growth factor gene hBMP2 after retroviral transduction at different time-points. BMP2 led to an increase in proteoglycan and alkaline phosphatase production. Initially, the proliferation rate detected by MTT-assay increased in both the cell types; afterwards the proliferation rate was similar to controls. The described retroviral vector system achieved high initial transduction rates in ATDC5 cells and CC. Gene transfer was very stable over the time period analysed, rendering it a useful tool for future in vitro and in vivo studies on cartilage remodelling.

To examine a retroviral gene transfer to chondrocytes in vitro and in vivo in tissue-engineered cell-collagen constructs articular chondrocytes from rabbits and humans were isolated and transduced with VSV.G pseudotyped murine leukemia virus-derived retroviral vectors. Viral supernatants were generated by transient transfection of 293T cells using the pBullet retroviral vector carrying the nlslacZ gene, a Moloney murine leukemia virus gag/pol plasmid and a VSV.G coding plasmid. Transduction efficiency was analyzed by fluorescence-activated-cell-sorter analysis and transduced autologous chondrocytes from rabbits were seeded on collagen-scaffolds and implanted into osteochondral defects in the patellar groove of the rabbit's femur (n=10). LacZ-expression was analyzed by X-gal staining on total knee explants and histological sections. Retroviral transduction efficiency exceeded 92.3% (SEM+/-3.5%) in rabbit articular chondrocytes, 74.7% (SEM+/-1.8%) in human articular chondrocytes and 52.7% (SEM+/-5.8%) in osteoarthritic human chondrocytes. Reporter gene expression remained high after 15 weeks in 75.7% (SEM+/-8.2%) of transduced rabbit articular chondrocytes. In vivo, intraarticular beta-galactosidase activity could be determined in the majority of implanted chondrocytes in the osteochondral defects after 4 weeks.

3-Nitrobenzanthrone (3-nitro-7H-benz[de]anthracen-7-one, 3-NBA) is a potent mutagen and suspected human carcinogen identified in diesel exhaust and air pollution. We compared the ability of human hepatic cytosolic samples to catalyze DNA adduct formation by 3-NBA. Using the (32)P-postlabeling method, we found that 12/12 hepatic cytosols activated 3-NBA to form multiple DNA adducts similar to those formed in vivo in rodents. By comparing 3-NBA-DNA adduct formation in the presence of cofactors of NAD(P)H:quinone oxidoreductase (NQO1) and xanthine oxidase, most of the reductive activation of 3-NBA in human hepatic cytosols was attributed to NQO1. Inhibition of adduct formation by dicoumarol, an NQO1 inhibitor, supported this finding and was confirmed with human recombinant NQO1. When cofactors of N,O-acetyltransferases (NAT) and sulfotransferases (SULT) were added to cytosolic samples, 3-NBA-DNA adduct formation increased 10- to 35-fold. Using human recombinant NQO1 and NATs or SULTs, we found that mainly NAT2, followed by SULT1A2, NAT1, and, to a lesser extent, SULT1A1 activate 3-NBA. We also evaluated the role of hepatic NADPH:cytochrome P450 oxidoreductase (POR) in the activation of 3-NBA in vivo by treating hepatic POR-null mice and wild-type littermates i.p. with 0.2 or 2 mg/kg body weight of 3-NBA. No difference in DNA binding was found in any tissue examined (liver, lung, kidney, bladder, and colon) between null and wild-type mice, indicating that 3-NBA is predominantly activated by cytosolic nitroreductases rather than microsomal POR. Collectively, these results show the role of human hepatic NQO1 to reduce 3-NBA to species being further activated by NATs and SULTs.

The aim of this study was to describe the indication, planning, technique, rehabilitation, and clinical results after cryopreserved allograft meniscus transplantation. Forty consecutive patients, 33 men and 7 women (mean, 37.3 years of age), were evaluated at 1-year follow-up post surgery. Symptoms, patient satisfaction, ROM (range of motion), surgical time, blood loss, and surgical history were evaluated. Thirty-eight (95%) patients had previous total or partial meniscectomy (mean, 11.4 years ago). Preoperatively, chief complaints were knee joint line pain and swelling. Mean surgical time and blood loss were 123 min and 87 g, respectively. At 12 months postsurgery, 5% and 10%, respectively, complained of pain and swelling; ROM was 0 degrees -132 degrees. Thirty-eight (95%) patients were satisfied. According to the results, meniscus transplantation can lead to significant pain relief and satisfaction in young symptomatic meniscectomized patients. However, long-term results must be obtained to prove the effectiveness of this technique in prevention of degenerative joint changes., (The Japanese Orthopaedic Association)