bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional response of Candida auris to the Mrr1 inducers methylglyoxal and benomyl
Authors: Biermann Amy R. , Hogan Deborah A. 
Published: March 2022

AbstractCandida auris is an urgent threat to human health due to its rapid spread in healthcare settings and its repeated development of multidrug resistance. Diseases that put individuals at a higher risk for C. auris infection, such as diabetes, kidney failure, or immunocompromising conditions, are associated with elevated levels of methylglyoxal (MG), a reactive dicarbonyl compound derived from several metabolic processes. In other Candida species, expression of MG reductase enzymes that catabolize and detoxify MG are controlled by Mrr1, a multidrug resistance-associated transcription factor, and MG induces Mrr1 activity. Here, we used transcriptomics and genetic assays to determine that C. auris MRR1a contributes to MG resistance, and that the main Mrr1a targets are an MG reductase and MDR1, which encodes an drug efflux protein. The C. auris Mrr1a regulon is smaller than Mrr1 regulons described in other species. In addition to MG, benomyl (BEN), a known Mrr1 stimulus, induces C. auris Mrr1 activity, and characterization of the MRR1a-dependent and independent transcriptional responses revealed substantial overlap in genes that were differentially expressed in response to each compound. Additionally, we found that an MRR1 allele specific to one C. auris phylogenetic clade, clade III, encodes a hyperactive Mrr1 variant, and this activity correlated with higher MG resistance. C. auris MRR1a alleles were functional in Candida lusitaniae and were inducible by BEN, but not by MG, suggesting that the two Mrr1 inducers act via different mechanisms. Together, the data presented in this work contribute to the understanding Mrr1 activity and MG resistance in C. auris.ImportanceCandida auris is a fungal pathogen that has spread since its identification in 2009 and is of concern due to its high incidence of resistance against multiple classes of antifungal drugs. In other Candida species, the transcription factor Mrr1 plays a major role in resistance against azole antifungals and other toxins. More recently, Mrr1 has been recognized to contribute to resistance to methylglyoxal (MG), a toxic metabolic byproduct. Here, we show that C. auris MRR1a, the closest ortholog to MRR1 in other species, contributes to resistance to MG, and that Mrr1a strongly co-regulates expression of MGD1, encoding a methylglyoxal reductase enzyme and MDR1, encoding an efflux protein involved in resistance to azole drugs, antimicrobial peptides and bacterial products. We found that one major clade of C. auris has a constitutively active Mrr1 despite high azole resistance due to other mutations, and that this high Mrr1a activity correlates with higher MG resistance. Finally, we gain insights into the activities of MG and another Mrr1 inducer, benomyl, to better understand C. auris regulation of phenotypes relevant in vivo.
Process evaluation protocol for the SLEEP study: a hybrid digital CBT-I intervention for working people with insomnia
Authors: Hurley-Wallace A. , Moukhtarian T. , Patel K. , Toro C. , Russel S. , Daley G. , Walasek L. , Tang N. K. Y. , Meyer C. 
Published: March 2022

AbstractIntroductionThe Supporting Employees with Insomnia and Emotional Regulation Problems (SLEEP) pilot uses hybrid digital Cognitive Behavioural Therapy for Insomnia (CBT-I) to help working people address their sleep and emotion regulation problems, using cognitive, behavioural, and psychoeducation techniques. A process evaluation within this trial will improve our understanding of how the intervention brought about change, including identifying barriers and facilitators to engagement and subsequent change, and the extent to which contextual factors played a role.Methods and analysisThis qualitative process evaluation will use semi-structured interviews, conducted via online videoconferencing, to explore participant experiences of the SLEEP intervention. Twenty-five participants who completed the SLEEP intervention (16 %) will be randomly sampled. Interviews will be analysed using a thematic and framework analytic approach. A codebook style thematic analysis will be used, and a framework focusing on the research questions will be applied to the codebook. The final report will present themes generated, alongside the finalised codebook. The report resulting from this research will adhere to CORE-Q quality guidelines.Ethics and disseminationFull approval for the SLEEP study was given by the University of Warwick Biomedical and Research Ethics Committee (BSREC 45/20-21). All data collection adheres to data collection guidelines. Participants provided written informed consent for the main trial, and all interviewees provided additional written and verbal (audio-recorded) consent. The results of the process evaluation will be published in a peer-reviewed journal and presented at conferences. A lay report will be provided to all participants.Trial registrationISRCTN13596153; Pre-results.
Clonality and timing of relapsing colorectal cancer metastasis revealed through whole-genome single-cell sequencing
Authors: Alves Joao M. , Prado-López Sonia , Tomás Laura , Valecha Monica , Estévez-Gómez Nuria , Alvariño Pilar , Geissel Dominik , Modest Dominik Paul , Sauer Igor M. , Pratschke Johann , Raschzok Nathanael , Sers Christine , Mamlouk Soulafa , Posada David 
Published: March 2022

AbstractBACKGROUNDRecurrence of tumor cells following local and systemic therapy is a significant hurdle in cancer. Most patients with metastatic colorectal cancer (mCRC) will relapse, despite resection of the metastatic lesions. A better understanding of the evolutionary history of recurrent lesions is thus required to identify the spatial and temporal patterns of metastatic progression and expose the genetic determinants of therapeutic resistance.METHODSUtilizing a robust Bayesian phylogenetic approach, we analyzed a unique single-cell whole-genome sequencing dataset comprising 60 cells sampled from metastatic and recurrent hepatic lesions of a patient with a long-term disease course to investigate the origin, timing, and clonality of a colorectal metastatic relapse. We further tracked the changes in the size of the malignant cell population and evaluated the impact of the treatment strategy on the mutational landscape of this tumor.RESULTSOur results suggest that the recurrent lesion originated from the clonal expansion of a single drug-resistant metastatic lineage, which began to expand around one year before surgical resection of the relapse. We additionally observed substantial variability in the substitution rates along the tumor cell phylogeny and found a large number of mutations specific to the ancestral lineage that gave rise to the relapse, including non-silent mutations in CRC genes. Moreover, our results point to a substantial contribution of chemotherapy exposure to the overall mutational burden.CONCLUSIONSOur study suggests that resistant colorectal metastatic clones can quickly grow, even under strong drug-imposed pressure, highlighting the importance of profiling the genomic landscape of tumor lesions to identify mutations potentially contributing to treatment failure.
Sex-specific genetic and transcriptomic liability to neuroticism
Authors: Wendt Frank R , Pathak Gita A , Singh Kritika , Stein Murray B , Koenen Karestan C , Krystal John H , Gelernter Joel , Davis Lea K , Polimanti Renato 
Published: March 2022

ABSTRACTBackgroundThe presentation, etiology, and relative risk of psychiatric disorders are strongly influenced by biological sex. Neuroticism is a transdiagnostic feature of psychiatric disorders displaying prominent sex differences. We performed genome-wide association studies (GWAS) of neuroticism separately in males and females to identify sex-specific genetic and transcriptomic profiles.MethodsNeuroticism scores were derived from the Eysenck Personality Inventory Neuroticism scale. GWAS were performed in 145,669 females and 129,229 males from the UK Biobank considering autosomal and X-chromosomal variation. Two-sided Z-tests were used to test for sex-specific effects of discovered loci, genetic correlates (N=673 traits), tissue and gene transcriptomic profiles, and polygenic associations across health outcomes in the Vanderbilt University Biobank (BioVu, 39,692 females and 31,268 males).ResultsThe SNP-heritability of neuroticism was not statistically different between males (h2=10.6%) and females (h2=11.85%). Four female-specific (rs10736549-CNTN5, rs6507056-ASXL3, rs2087182-MMS22L, and rs72995548-HSPB2) and two male-specific (rs10507274-MED13L and rs7984597) neuroticism risk loci reached genome-wide significance. Male- and female-specific neuroticism polygenic scores were most significantly associated with “mood disorders” (male OR=1.11, P=1.40×10−9; female OR=1.14, P=6.05×10−22). They also associated with sex-specific laboratory measures related to erythrocyte count, distribution, and hemoglobin concentration. Gene expression variation in the pituitary was enriched for neuroticism loci in males (males β=0.026, P=0.002) and genetically-regulated transcriptomic changes highlighted the effect of RAB7L1, TEX26, and PLOT1.ConclusionsThrough a comprehensive assessment of genetic risk for neuroticism and the associated biological processes, this study identified several molecular pathways that can partially explain the known sex differences in neurotic symptoms and their psychiatric comorbidities.
The role of alternative splicing in CEP290-related disease pathogenesis
Authors: Taylor Rowan D. , Poulter James A. , Cockburn Joseph , Ladbury John E. , Peckham Michelle , Johnson Colin A 
Published: March 2022

AbstractPrimary ciliopathies are a group of inherited developmental disorders resulting from defects in the primary cilium. Mutations in CEP290 (Centrosomal protein of 290kDa) are the most frequent cause of recessive ciliopathies (incidence up to 1:15,000). Pathogenic variants span the full length of this large (93.2kb) 54 exon gene, causing phenotypes ranging from isolated inherited retinal dystrophies (IRDs; Leber Congenital Amaurosis, LCA) to a pleiotropic range of severe syndromic multi-organ ciliopathies affecting retina, kidney and brain. Most pathogenic CEP290 variants are predicted null (37% nonsense, 42% frameshift), but there is no clear genotype-phenotype association. Almost half (26/53) of the coding exons in CEP290 are in-phase “skiptic” (or skippable) exons. Variants located in skiptic exons could be removed from CEP290 transcripts by skipping the exon, and nonsense-associated altered splicing (NAS) has been proposed as a mechanism that attenuates the pathogenicity of nonsense or frameshift CEP290 variants. Here, we have used in silico bioinformatic techniques to study the propensity of CEP290 skiptic exons for NAS. We then used CRISPR-Cas9 technology to model CEP290 frameshift mutations in induced pluripotent stem cells (iPSCs) and analysed their effects on splicing and ciliogenesis. We identified exon 36, a hotspot for LCA mutations, as a strong candidate for NAS that we confirmed in mutant iPSCs that exhibited sequence-specific exon skipping. Exon 36 skipping did not affect ciliogenesis, in contrast to a larger frameshift mutant that significantly decreased cilia size and incidence in iPSCs. We suggest that sequence-specific NAS provides the molecular basis of genetic pleiotropy for CEP290-related disorders.
Acute and long-term impacts of COVID-19 on economic vulnerability: a population-based longitudinal study (COVIDENCE UK)
Authors: Williamson Anne E , Tydeman Florence , Miners Alec , Pyper Kate , Martineau Adrian R 
Published: March 2022

AbstractBackgroundSocio-economic deprivation is well recognised as a risk factor for developing COVID-19. However, the impact of COVID-19 on economic vulnerability has not previously been characterised.ObjectiveTo determine whether COVID-19 has a significant impact on adequacy of household income to meet basic needs (primary outcome) and work absence due to sickness (secondary outcome), both at the onset of illness (acutely) and subsequently (long-term).DesignMultivariate mixed regression analysis of self-reported data from monthly on-line questionnaires, completed 1st May 2020 to 28th October 2021, adjusting for baseline characteristics including age, sex, socioeconomic status and self-rated health.Setting and ParticipantsParticipants (n=16,910) were UK residents aged 16 years or over participating in a national longitudinal study of COVID-19 (COVIDENCE UK).ResultsIncident COVID-19 was independently associated with increased odds of participants reporting household income as being inadequate to meet their basic needs, both acutely (adjusted odds ratio [aOR) 1.39, 95% confidence interval [CI] 1.12 to 1.73) and in the long-term (aOR 1.15, 95% CI 1.00 to 1.33). Exploratory analysis revealed the long-term association to be restricted to those who reported ‘long COVID’, defined as the presence of symptoms lasting more than 4 weeks after the acute episode (aOR 1.39, 95% CI 1.10 to 1.77). Incident COVID-19 associated with increased odds of reporting sickness absence from work in the long-term (aOR 5.29, 95% CI 2.76 to 10.10) but not acutely (aOR 1.34, 95% CI 0.52 to 3.49).ConclusionsWe demonstrate an independent association between COVID-19 and increased risk of economic vulnerability, both acutely and in the long-term. Taking these findings together with pre-existing research showing that socio-economic disadvantage increases the risk of developing COVID-19, this may generate a ‘vicious cycle’ of impaired health and poor economic outcomes.Trial registrationNCT04330599Summary BoxWhat is already known on this topicSocioeconomic deprivation is recognised as a major risk factor for incidence and severity of COVID-19 disease, mediated via factors including increased occupational and household exposure to SARS-CoV-2 and greater physical vulnerability due to comorbiditiesThe potential for COVID-19 to act as a cause, rather than a consequence, of economic vulnerability has not previously been characterised.What this study addsWe demonstrate an independent association between incident COVID-19 and subsequent self-report of household income being inadequate to meet basic needs, both acutely and in the long termIncident COVID-19 was also associated with increased odds of subsequent self-report of sickness absence from work in the long-term.
Roles of the second-shell amino acid R266 in other members of the MLE subgroup of the enolase superfamily
Authors: Truong Dat P. , Fults Susan , Davila Cristian , Huddleston Jamison , Brock Dakota , Zhu Mingzhao , Pellois Jean-Phillipe , Hull Kenneth G. , Romo Daniel , Raushel Frank M. , Glasner Margaret E. 
Published: March 2022

AbstractCatalytic promiscuity is the coincidental ability to catalyze non-biological reactions in the same active site as the native biological reaction. Several lines of evidence show that catalytic promiscuity plays a role in the evolution of new enzyme functions. Thus, studying catalytic promiscuity can help identify structural features that predispose an enzyme to evolve new functions. This study identifies such a pre-adaptive residue in an N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) enzymes from the NSAR/OSBS subfamily. Previously, we identified a point mutation, R266Q, in the catalytically promiscuous Amycolatopsis sp. T-1-60 NSAR/OSBS that has a deleterious effect on NSAR activity with a lesser effect on OSBS activity (Truong et al., in preparation). We demonstrated that R266 was a pre-adaptive feature that enabled the emergence and evolution of NSAR activity in AmyNSAR/OSBS. We examined the role of the residue R266 in the evolution of NSAR activity by examining the effects of the single substitution R266Q in other members of the NSAR/OSBS subfamily including Enterococcus faecalis NSAR/OSBS, Roseiflexus castenholzii NSAR/OSBS, Lysinibacillus varians NSAR/OSBS, and Listeria innocua NSAR/OSBS, which have been previously characterized to carry out both OSBS and NSAR activities efficiently. RcNSAR/OSBS, LvNSAR/OSBS, EfNSAR/OSBS, and LiNSAR/OSBS are 49, 48, 32, and 28% identical, respectively, to AmyNSAR/OSBS. We found that while the R266Q mutation decreases NSAR activity more than OSBS activity, as expected, in most NSAR/OSBS members, the differential effects of the R266Q substitution on NSAR and OSBS activities are not as striking as observed in AmyNSAR/OSBS. In some homologs, the R266Q mutation has very deleterious effects on both OSBS and NSAR activities. Furthermore, the mutation unexpectedly decreases OSBS activity more than NSAR activity in LiNSAR/OSBS. Thus, the effects of R266Q on NSAR and OSBS activities depend on differences in sequence context between members of the NSAR/OSBS subfamily, demonstrating the complex role of epistasis in the evolution of NSAR activity in the NSAR/OSBS subfamily.
Validation of carbon isotopologue distribution measurements by GC-MS and application to13C-metabolic flux analysis of the tricarboxylic acid cycle inBrassica napusleaves
Authors: Dellero Younès , Berardocco Solenne , Berges Cécilia , Filangi Olivier , Bouchereau Alain 
Published: March 2022

AbstractThe estimation of metabolic fluxes in photosynthetic organisms represents an important challenge that has gained interest over the last decade with the development of13C-Metabolic Flux Analysis at isotopically non-stationary steady-state. This approach requires a high level of accuracy for the measurement of Carbon Isotopologue Distribution in plant metabolites. But this accuracy has still not been evaluated at the isotopologue level for GC-MS, leading to uncertainties for the metabolic fluxes calculated based on these fragments. Here, we developed a workflow to validate the measurements of CIDs from plant metabolites with GC-MS by producing tailor-madeE. colistandard extracts harboring a predictable binomial CID for some organic and amino acids. Overall, most of our TMS-derivatives mass fragments were validated with these standards and at natural isotope abundance in plant matrices. Then, we applied this validated MS method to investigate the light/dark regulation of plant TCA cycle by incorporating U-13C-pyruvate toBrassica napusleaf discs. We took advantage of pathway-specific isotopologues/isotopomers observed between two and six hours of labeling to show that the TCA cycle can operate in a cyclic manner under both light and dark conditions. Interestingly, this forward cyclic flux mode has a nearly four-fold higher contribution for pyruvate-to-citrate and pyruvate-to-malate fluxes than the phosphoenolpyruvate carboxylase (PEPc) flux reassimilating carbon derived from some mitochondrial enzymes. The contribution of stored citrate to the mitochondrial TCA cycle activity was also questioned based on dynamics of13C-enrichment in citrate, glutamate and succinate and variations of citrate total amounts under light and dark conditions. Interestingly, there was a light-dependent13C-incorporation into glycine and serine showing that decarboxylations from pyruvate dehydrogenase complex and TCA cycle enzymes were actively reassimilated and could represent up to 5% to net photosynthesis.
Oxidative stress profiles of lymphoblasts from Amyotrophic Lateral Sclerosis patients with or without known SOD1 mutations
Authors: Cunha-Oliveira Teresa , Franco Silva Daniela , Segura Luis , Baldeiras Inês , Marques Ricardo , Rosenstock Tatiana , Oliveira Paulo J. , Silva Filomena S.G. 
Published: March 2022

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal and rapidly progressing neurodegenerative disease that affects motor neurons. This disease is associated with oxidative stress especially in mutant superoxide dismutase 1 (mutSOD1) patients. However, less is known for the most prevalent sporadic ALS due to a lack of disease models. Here, we studied oxidative the stress profiles in lymphoblasts from ALS patients with mutSOD1 or unknown (undSOD1) mutations.mutSOD1 and undSOD1 lymphoblasts, as well as sex/age-matched controls (3/group) were obtained from Coriell and divided in 46 years-old-men (C1), 46 years-old-women (C2) or 26/27 years-old-men (C3) cohorts. Growth curves were performed, and several parameters associated with redox homeostasis were evaluated, including SOD activity and expression, general oxidative stress levels, lipid peroxidation, response to oxidative stimulus, glutathione redox cycle, catalase expression, and activity, and Nrf2 transcripts. Pooled (all cohorts) and paired (intra-cohort) statistical analyses were performed, followed by clustering and principal component analyses (PCA).Although a high heterogeneity among lymphoblast redox profiles was found between cohorts, clustering analysis based on 7 parameters with high chi-square ranking (total SOD activity, oxidative stress levels, catalase transcripts, SOD1 protein levels, metabolic response to mM concentrations of tert-butyl hydroperoxide, glutathione reductase activity, and Nrf2 transcript levels) provided a perfect separation between samples from healthy controls and ALS (undSOD1 and mutSOD1), also visualized in the PCA analysis.Our results show distinct redox signatures in lymphoblasts from mutSOD1, undSOD1, and healthy controls that can be used as therapeutic targets for ALS drug development.Highlights⍰ Lymphoblasts from ALS patients present altered redox properties⍰ Redox profiling evidenced total SOD and glutathione reductase activities, SOD1 protein levels, DCF fluorescence, catalase and Nrf2 transcripts, and tert-butyl hydroperoxide cytotoxicity, as discriminant features for experimental groups.⍰ Lymphoblast redox profiles may be helpful for patient stratification and precision medicine
An innovative hematopoietic stem cell gene therapy approach benefits CLN1 disease in the mouse model
Authors: Peviani Marco , Das Sabyasachi , Patel Janki , Jno-Charles Odella , Kumar Rajesh , Zguro Ana , Mathews Tyler D. , Milazzo Rita , Cavalca Eleonora , Poletti Valentina , Biffi Alessandra 
Published: March 2022

AbstractHematopoietic stem and progenitor cells (HSPCs) can lead to the establishment of a long-lasting microglia-like progeny in the brain of properly myeloablated hosts. We exploited this approach to treat the severe CLN1 neurodegenerative disorder, which is the most aggressive form of neuronal ceroid lipofuscinoses, due to deficiency of palmitoyl-protein thioesterase 1 (hPPT1). We here provide first evidence that: i) transplantation of wild type HSPCs exerts a partial but long-lasting mitigation of the symptoms; ii) transplantation of HSPCs over-expressing hPPT1 by lentiviral gene transfer enhances therapeutic benefit as compared to wild type cell transplant, with first demonstration of such a dose-effect benefit for a purely neurodegenerative condition like CLN1 disease; iii) transplantation of hPPT1 over-expressing HSPCs by a novel intracerebroventricular (ICV) approach is sufficient to transiently ameliorate CLN1 disease symptomatology in the absence of hematopoietic tissue engraftment of the transduced cells; and iv) the combinatorial transplantation of transduced HSPCs intravenously and ICV results in the most robust therapeutic benefit among the tested approaches on both pre-symptomatic as well as symptomatic animals. Overall, these findings provide first evidence of the efficacy and feasibility of this novel approach to treat CLN1 disease and possibly other neurodegenerative conditions, paving the way for its future clinical application.