bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction of Cystatin B results in increased cathepsin B activity in disomic but not Trisomy21 human cellular and mouse models
Authors: Wu Yixing , Cleverley Karen , Wiseman Frances K. 
Published: April 2024

AbstractDown syndrome, resulting from trisomy of human chromosome 21, is a common form of chromosomal disorder that results in intellectual disability and altered risk of several medical conditions. Individuals with Down syndrome have a greatly increased risk of Alzheimer’s disease (DSAD), due to the presence of theAPPgene on chromosome 21 that encodes the amyloid-β precursor protein (APP). APP can be processed to generate amyloid-β, which accumulates in plaques in the brains of people who have Alzheimer’s disease and is the upstream trigger of disease. Cathepsin B has potential roles in both APP processing and amyloid-β degradation and has been suggested to contribute to amyloid-β accumulation. An endogenous inhibitor of Cathepsin B, Cystatin B (CSTB), is encoded on chromosome 21. The abundance of this protein is increased in the brains of individuals with DSAD, which may be associated with a decrease in Cathepsin B activity compared to individuals who have Alzheimer’s disease in the general population. Whether targetingCSTBcan modulate Cathepsin B activity in the context of trisomy of chromosome 21 is unclear. Here we test if reducing CSTB can alter Cathepsin B activity in a mouse and a cellular model of trisomy of chromosome 21. We find that reducing CSTB abundance increases Cathepsin B activity in disomic controls but not in the presence of trisomy of chromosome 21. These findings offer new insights into the role of CSTB in regulating Cathepsin B activity.
Seed sequences mediate off-target activity in the CRISPR-interference (CRISPRi) system
Authors: Rohatgi Neha , Fortin JP , Lau Ted , Ying Yi , Zhang Yue , Costa Mike , Reja Rohit 
Published: April 2024

AbstractThe CRISPR interference (CRISPRi) system is a powerful tool that is widely used to selectively and efficiently silence genes in functional genomics research applications. However, the extent of off-target activity associated with the CRISPRi system has not been systematically investigated. Here, we utilized a genome-wide CRISPRi Cas9 single guide RNA (sgRNA) library to investigate the presence of off-target activity and its effects on gene expression. Our findings suggest that off-target effects in CRISPRi are quite pervasive and have direct and indirect impact on gene expression. Most of the identified off-target activities can be accounted for by complementarity of the PAM-proximal genomic sequence with the 3’ half of the sgRNA spacer sequence, the seed sequence. We also report that not all PAM proximal positions are equally important for binding of sgRNA to the DNA and that mismatches in the PAM-proximal regions can be tolerated depending on the sequence context.
Antiviral RNA interference targets viral transcripts but not genomes of RNA viruses inDrosophila melanogaster
Authors: Silva Emanuele G. , Ferreira Álvaro G. A. , Jiran Thiago Henrique L. , de Faria Isaque João S. , Armache Juliana N. , Amadou Siad C. G. , Haas Gabrielle , Martin Franck , Luc-Imler Jean , Marques João T. 
Published: April 2024

AbstractRNA interference (RNAi) mediated by the small interfering RNA (siRNA) pathway is a major antiviral mechanism in insects. This pathway is triggered when double-stranded RNA (dsRNA) produced during virus replication is recognized by Dicer-2, leading to the formation of virus-derived siRNA duplexes. These siRNAs are loaded onto the programmable nuclease Argonaute-2 (AGO2), with one strand serving as a guide to target and cleave fully complementary sequences of viral RNAs. While siRNAs are generated from viral dsRNA, the specific viral RNA species targeted for silencing during RNA virus replication remains unclear. In this study, we characterized the primary viral RNA targets of theDrosophilasiRNA pathway during infections caused by negative and positive RNA viruses, namely Vesicular stomatitis virus (VSV) and Sindbis virus (SINV). Our findings reveal that polyadenylated transcripts of VSV and SINV are the major targets of silencing by the siRNA pathway during infection, likely when they are poised for translation. Consistent with earlier findings, we confirmed that AGO2 copurifies with ribosomes, and this is not affected by virus infection. Therefore, we propose that the inhibition of the replication of RNA viruses inDrosophilaresults from the silencing of incoming viral transcripts, facilitated by the association of AGO2 with ribosomes.Author SummaryThe small interfering RNA (siRNA) pathway mediates major antiviral immune response in insects, functioning to cleave viral RNA. While this pathway has been extensively studied in the fruit flyDrosophila melanogaster, the specific molecular targets of inhibition by the siRNA pathway have remained unclear. In this study, we aimed to elucidate these targets. Our findings demonstrate that polyadenylated transcripts produced during viral infection are the primary targets of the Drosophila siRNA pathway, in the case of both negative and positive single-stranded RNA viruses. The silencing of these transcripts accounts for the antiviral effect of the siRNA pathway, suggesting that direct targeting of viral RNA genomes is unlikely to occur. We confirmed that Argonaute-2 (AGO2), the core component of the silencing complex, co-purifies with ribosomes and also show that this association is not affected by viral infection. This suggests that AGO2 is in permanent association with ribosomes where it can efficiently scan viral transcripts before they undergo translation by the cellular machinery, thereby preventing viral replication. These results provide valuable insights into the mechanism of gene silencing the siRNA pathway.
The landscape of regional missense mutational intolerance quantified from 125,748 exomes
Authors: Chao Katherine R. , Wang Lily , Panchal Ruchit , Liao Calwing , Abderrazzaq Haneen , Ye Robert , Schultz Patrick , Compitello John , Grant Riley H. , Kosmicki Jack A. , Weisburd Ben , Phu William , Wilson Michael W. , Laricchia Kristen M. , Goodrich Julia K. , Goldstein Daniel , Goldstein Jacqueline I. , Vittal Christopher , Poterba Timothy , Baxter Samantha , Watts Nicholas A. , Solomonson Matthew ,   gnomAD Consortium, Tiao Grace , Rehm Heidi L. , Neale Benjamin M. , Talkowski Michael E. , MacArthur Daniel G. , O’Donnell-Luria Anne , Karczewski Konrad J. , Radivojac Predrag , Daly Mark J. , Samocha Kaitlin E. 
Published: April 2024

AbstractMissense variants can have a range of functional impacts depending on factors such as the specific amino acid substitution and location within the gene. To interpret their deleteriousness, studies have sought to identify regions within genes that are specifically intolerant of missense variation1–12. Here, we leverage the patterns of rare missense variation in 125,748 individuals in the Genome Aggregation Database (gnomAD)13against a null mutational model to identify transcripts that display regional differences in missense constraint. Missense-depleted regions are enriched for ClinVar14pathogenic variants,de novomissense variants from individuals with neurodevelopmental disorders (NDDs)15,16, and complex trait heritability. Following ClinGen calibration recommendations for the ACMG/AMP guidelines, we establish that regions with less than 20% of their expected missense variation achieve moderate support for pathogenicity. We create a missense deleteriousness metric (MPC) that incorporates regional constraint and outperforms other deleteriousness scores at stratifying case and controlde novomissense variation, with a strong enrichment in NDDs. These results provide additional tools to aid in missense variant interpretation.
Comparative genomics and transcriptomics reveal differences in effector complement and expression between races ofFusarium oxysporumf.sp.lactucae
Authors: Bates Helen J. , Pike Jamie , Price R. Jordan , Jenkins Sascha , Connell John , Legg Andrew , Armitage Andrew , Harrison Richard J. , Clarkson John P. 
Published: April 2024

AbstractThis study presents the first genome and transcriptome analyses forFusarium oxysporumf.sp.lactucae(Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with otherF. oxysporumf.spp. followingmimp-based bioinformatic analyses. Notably, homologues ofSecreted in Xylem(SIX) genes, also present in many otherF. oxysporumf.spp, were identified in Fola, with bothSIX9andSIX14(multiple copies with sequence variants) present in both Fola1 and Fola4. All Fola4 isolates also contained an additional single copy ofSIX8. RNAseq of lettuce following infection with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in otherF. oxysporumf.spp. including several inF. oxysporumf.sp.apii. AlthoughSIX8,SIX9andSIX14were all highly expressed in Fola4, of the twoSIXgenes present in Fola1, onlySIX9was expressed as further analysis revealed that copies ofSIX14gene copies were disrupted by insertion of a transposable element. Two variants of Fola4 were also identified based on different genome and effector-based analyses. This included two differentSIX8sequence variants which were divergently transcribed from a shared promoter with eitherPSE1orPSL1respectively. In addition there was evidence of two independent instances of HCT in the different Fola4 variants. The involvement of helitrons in Fola genome rearrangement and gene expression is discussed.
Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations
Authors: Li Wei-Ping , Su Jia-Ying , Chang Yu-Chi , Wang Yun-Lin , Chiang Hung-Lun , Hsieh Yu-Tung , Chiang Yi-Hsuan , Ko Yen-Ling , Chiang Bing-Jen , Yang Cheng-Han , Huang Yen-Tsung , Lin Chien-Ling 
Published: April 2024

ABSTRACTThe untranslated regions (UTRs) of mRNAs harbor regulatory elements influencing translation efficiency. Although 3.7% of disease-relevant human mutations occur in UTRs, their exact role in pathogenesis remains unclear. Through metagene analysis, we mapped pathogenic UTR mutations to regions near coding sequences, with a focus on the upstream open reading frame (uORF) initiation site. Subsequently, we utilized massively parallel poly(ribo)some profiling to compare the ribosome associations of 6,555 pairs of wildtype and mutant UTR fragments. We identified 46 UTR variants that altered polysome profiles, with enrichment in pathogenic mutations. Both univariate analysis and the elastic model highlighted the significance of motifs of short repeated sequences, including SRSF2 binding sites, as mutation hotspots that lead to aberrant translation. Furthermore, these polysome-shifting mutations exhibited considerable impact on RNA secondary structures, particularly for upstream AUG-containing 5’ UTRs. Integrating these features, our model achieved high accuracy (AUROC > 0.8) in predicting polysome-shifting mutations in the test dataset. Additionally, several lines of evidence indicate that changes in uORF usage underlie the translation deficiency arising from these mutations. Illustrating this, we demonstrate that a pathogenic mutation in the IRF6 5’ UTR suppresses translation of the primary open reading frame by creating a uORF. Remarkably, site-directed ADAR editing of the mutant mRNA rescued this translation deficiency. Overall, our study provides insights into the molecular mechanisms of UTR mutations and their links to clinical impacts through translation defects.
Mutations in the IgG B cell receptor associated with class-switched B cell lymphomas
Authors: Wasim Laabiah , Chu Sin Wah Tooki , Sale Ben , Pickard Lucy , Léonard Simon , Zhang Lingling , Tolarová Helena , Tean Zhang Sung , Engels Niklas , Calado Dinis P. , Tarte Karin , Okosun Jessica , Forconi Francesco , Tolar Pavel 
Published: April 2024

SummaryImmunoglobulin class-switching from IgM to IgG enhances B cell receptor (BCR) signalling1,2and promotes germinal centre (GC) B cell responses to antigens3,4. In contrast, non-Hodgkin lymphomas derived from GC B cells typically avoid IgG BCR expression and retain the unswitched IgM BCR, suggesting that the IgG BCR may protect B cells from malignant transformation5,6. However, the mechanism of this phenomenon and its significance for the pathogenicity of IgG-expressing lymphomas remains unclear. Here, we report that IgG-positive follicular lymphoma (FL) and the related EZB subset of diffuse large B cell lymphoma (DLBCL) acquire mutations in the IgG heavy chain, disrupting its unique intracellular tail. Enforced class switching of IgM-expressing EZB DLBCL cell lines to IgG reduces BCR surface levels, signalling via phosphoinositide-3 kinase (PI3K), levels of MYC, cell proliferation and in vivo growth. Inhibiting GSK3, a target of BCR-PI3K signalling, or stimulating the BCR rescues IgG+cell proliferation. In contrast, IgG tail-truncating mutations enhance BCR surface expression, intracellular signalling and competitive growth. These findings suggest that the expansion of IgG-switched GC-like B lymphoma cells is limited by low tonic PI3K activity of the wild-type IgG BCR, but a subset of these cancers acquires mutations of the IgG intracellular tail that reverse this effect, promoting the oncogenicity of their BCRs. The presence of IgG tail mutations underscores the importance of isotype-specific BCR signalling in the pathogenesis of FL and EZB DLBCL and can potentially inform therapeutic targeting with BCR signalling inhibitors or antibody-drug conjugates.
Colour preference in juvenile European lobster (Homarus gammarus)
Authors: Bell Matt E. , Kuvaldin Nicholas , Frontaura Erik Romero , Kuebutornye Felix K.A. , Domech Paula Costa , Wan Alex H. L. 
Published: April 2024

AbstractLobsters are high-value marine-fished species, and re-stocking efforts are essential for replenishing depleted wild populations and ensuring the longevity of these valuable marine species. The need for stock enhancement and hatcheries for aquaculture is vital to reduce the strain on wild populations. Therefore, environmental colours should be acknowledged when rearing lobsters in terms of behaviour, growth, movement, and survival. However, the behavioural effects the surrounding colour poses are virtually unknown. To better understand this behaviour, the movement of juvenile European lobsters (Homarus gammarus) was analysed through videos in two sub-trials. Lobsters were acclimated to custom-made alternating colour chambers, allowing for colour preferences based on individual movement. Sub-trial one alternated between black, red, blue, green, white, and yellow. The study identified that there was a significant preference for black (1 hour and 51 minutes) and red (1 hour and 33 minutes), indicating a potential underlying benefit for juvenileH. gammarusdevelopment. Despite this, little is known about the overall association of colour and lobster perception. A better understanding of environmental colour preference may guide the construction of aquaculture units to suit colour preference and enhance acclimation into newly released environments. This experiment aims to determine the preferred colours of stage four juvenileH. gammarusin a controlled laboratory setting and inspire further research to explore this unfamiliar field.
Conformational dynamics associated with remote residues regulate the kinetic properties of homologous glutamate dehydrogenases (GDHs)
Authors: Godsora Barsa Kanchan Jyotshna , Das Parijat , Sairaman Anjali , Mishra Prasoon Kumar , Kaledhonkar Sandip , Punekar Narayan S. , Bhaumik Prasenjit 
Published: April 2024

AbstractGlutamate dehydrogenase (GDH) is a key enzyme in all living organisms and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs,Aspergillus nigerGDH (AnGDH) andAspergillus terreusGDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. The crystal structures and first-ever cryo-EM structures of apo-AtGDH captured arrays of conformational ensembles. Comparative structural analysis has revealed a wider mouth opening in allosteric AnGDH (∼ 21 Å) compared to non-allosteric AtGDH (∼17 Å) in their apo states. A network of interaction related to the amino acid substitutions in Domain II is responsible for differential structural dynamics in these GDHs. Remarkably, we identified one remotely located substitution in Domain II, i.e., R246 to S, a part of the network, which reversed the kinetic properties of AtGDH into an allosteric one and controls the mouth opening. Our data also indicate that dynamic discrepancy influences the substrate binding affinity and catalytic activity in AnGDH and AtGDH. We have successfully demonstrated for the first time, that remotely located residues and the conformational dynamics regulate the kinetic properties in homologous GDHs.
The cochlear hook region detects harmonics beyond the canonical hearing range
Authors: Horii Kazuhiro , Ogawa Bakushi , Nagase Noriko , Morimoto Iori , Abe Chikara , Ogawa Takenori , Choi Samuel , Nin Fumiaki 
Published: April 2024

AbstractUltrasound, or sound at frequencies exceeding the conventional range of human hearing, is not only audible to mice, microbats, and dolphins, but also creates an auditory sensation when delivered through bone conduction in humans. Although ultrasound is utilized for brain activation and in hearing aids, the physiological mechanism of ultrasonic hearing remains unknown. In guinea pigs, we found that ultrasound above the hearing range delivered through ossicles of the middle ear evokes an auditory brainstem response and a mechano-electrical transduction current through hair cells, as shown by the local field potential called the cochlear microphonic potential (CM). The CM synchronizes with ultrasound, and like the response to audible sounds is actively and nonlinearly amplified. In vivo optical nano-vibration analysis revealed that the sensory epithelium in the hook region, the basal extreme of the cochlear turns, resonates in response both to ultrasound within the hearing range and to harmonics beyond the hearing range. The results indicate that hair cells can respond to stimulation at the optimal frequency and its harmonics, and the hook region detects ultrasound stimuli with frequencies more than two octaves higher than the upper limit of the ordinary hearing range.
Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction
Authors: Xiang Ruidong , Liu Yang , Ben-Eghan Chief , Ritchie Scott , Lambert Samuel A. , Xu Yu , Takeuchi Fumihiko , Inouye Michael 
Published: April 2024

AbstractBlood cell phenotypes are routinely tested in healthcare to inform clinical decisions. Genetic variants influencing mean blood cell phenotypes have been used to understand disease aetiology and improve prediction; however, additional information may be captured by genetic effects on observed variance. Here, we mapped variance quantitative trait loci (vQTL), i.e. genetic loci associated with trait variance, for 29 blood cell phenotypes from the UK Biobank (N∼408,111). We discovered 176 independent blood cell vQTLs, of which 147 were not found by additive QTL mapping. vQTLs displayed on average 1.8-fold stronger negative selection than additive QTL, highlighting that selection acts to reduce extreme blood cell phenotypes. Variance polygenic scores (vPGSs) were constructed to stratify individuals in the INTERVAL cohort (N∼40,466), where genetically less variable individuals (low vPGS) had increased conventional PGS accuracy (by ∼19%) than genetically more variable individuals. Genetic prediction of blood cell traits improved by ∼10% on average combining PGS with vPGS. Using Mendelian randomisation and vPGS association analyses, we found that alcohol consumption significantly increased blood cell trait variances highlighting the utility of blood cell vQTLs and vPGSs to provide novel insight into phenotype aetiology as well as improve prediction.
The Impacts of Oral Anticoagulants on Clinical Outcomes in Patients with Atrial Fibrillation Across Five Stages of Renal Function
Authors: Liao Jo-Nan , Chan Yi-Hsin , Lee Hsin-Fu , Yeh Yung-Hsin , Chang Shang-Hung , Chen Shih-Ann , Chao Tze-Fan 
Published: April 2024

AbstractBackgroundTo analyze the impact of using different renal function equations and stroke prevention strategy in atrial fibrillation (AF) across all chronic kidney disease (CKD) stages.MethodsWe used the Cockcroft-Gault (CG), Modified Diet in Renal Disease (MDRD), and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations to classify 39,217 patients into stage 1 to 5 CKD during July 1st, 2001, and September 30st, 2018. The endpoint is a composite outcome including ischemic stroke or major bleeding or mortality.ResultsMore patients belonged to stage 1 and 2 CKD using the MDRD and CKD-EPI equations. In subgroups of patients with eGFR-MDRD or eGFR-CKD-EPI ≥ 60 mL/min, a 17-18% increase of event was observed in patients with eGFR-CG < 60 mL/min compared to those ≥ 60 mL/min. Compared to no oral anticoagulant (OAC), OAC use was associated with a significantly lower risk of event across stage 1 to 4 CKD but not in stage 5 CKD. Both warfarin and NOACs exhibited better outcome compared to no OAC across stage 1 to 4 CKD while NOACs was associated with more risk reduction compared to warfarin. Among patients on OACs, there was a trend toward better outcome with NOAC than warfarin across stage 2-4 CKD but not in stage 1 and 5 CKD.ConclusionsOAC should be used in stage 1 to 4 CKD with NOAC exhibiting the trend of better outcome through stage 2 to 4 CKD than warfarin. For stage 5 CKD, optimal strategy remains undetermined.Clinical PerspectiveWhat Is New?The stages of renal function of AF patients varied significantly with different renal equations, and tthe CG equation remained effective in differentiating clnical outcomes for patients with eGFR-MDRD ≥ 60 mL/min or eGFR-CKD-EPI ≥ 60 mL/minWhat Are the Clinical Implications?OAC should be used in stage 1 to 4 CKD with NOAC exhibiting the trend of better outcome through stage 2 to 4 CKD than warfarin.