Gene and cell therapy fields have experienced remarkable growth during the past decade. Demands for preclinical and clinical safety assessments of these cell and gene therapy test articles (TAs) have ...effectively increased the necessity for regulated biodistribution, vector shedding, gene expression, and/or pharmacokinetics bioanalysis studies. Guidance documents issued from numerous international regulatory authorities recommend the use of quantitative polymerase chain reaction (qPCR) and/or quantitative reverse transcriptase PCR (qRT-PCR) assays due to their highly sensitive and robust target-specific detection. However, only preclinical biodistribution assay sensitivity is specified in these documents. Criteria such as accuracy, precision, and repeatability are not yet defined. This guidance void has resulted in several conflicting institutional interpretations of essential parameters necessary for the development and validation of robust assays to support safety assessments of gene and cell therapy TAs. There is an urgent need for an ongoing discussion among bioanalytical scientists in this field to generate a “best practice” consensus around preclinical and clinical qPCR/qRT-PCR assay design. With regard to this need, we offer critical points to consider when developing, validating, running sample analysis, and reporting qPCR/qRT-PCR assays.
Display omitted
Ma and colleagues offer critical points to consider when developing and validating qPCR/qRT-PCR assays and analyzing the biodistribution and vector shedding samples to support the preclinical and clinical safety assessments of the gene and cell therapy test articles. Assay acceptance criteria are recommended to the scientific community.
Abstract
Summary
Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of ...assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads.
Availability and implementation
WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/).
Supplementary information
Supplementary data are available at Bioinformatics online.
Adenosine diphosphate (ADP)‐ribosylation is a post‐translational protein modification implicated in the regulation of a range of cellular processes. A family of proteins that catalyse ...ADP‐ribosylation reactions are the poly(ADP‐ribose) (PAR) polymerases (PARPs). PARPs covalently attach an ADP‐ribose nucleotide to target proteins and some PARP family members can subsequently add additional ADP‐ribose units to generate a PAR chain. The hydrolysis of PAR chains is catalysed by PAR glycohydrolase (PARG). PARG is unable to cleave the mono(ADP‐ribose) unit directly linked to the protein and although the enzymatic activity that catalyses this reaction has been detected in mammalian cell extracts, the protein(s) responsible remain unknown. Here, we report the homozygous mutation of the c6orf130 gene in patients with severe neurodegeneration, and identify C6orf130 as a PARP‐interacting protein that removes mono(ADP‐ribosyl)ation on glutamate amino acid residues in PARP‐modified proteins. X‐ray structures and biochemical analysis of C6orf130 suggest a mechanism of catalytic reversal involving a transient C6orf130 lysyl‐(ADP‐ribose) intermediate. Furthermore, depletion of C6orf130 protein in cells leads to proliferation and DNA repair defects. Collectively, our data suggest that C6orf130 enzymatic activity has a role in the turnover and recycling of protein ADP‐ribosylation, and we have implicated the importance of this protein in supporting normal cellular function in humans.
Crystal structure and biochemical data reveal a gene mutated in patients with severe neurodegeneration to encode an elusive enzyme for removing ADP‐ribose from proteins.
Smouldering multiple sclerosis: the ‘real MS’ Giovannoni, Gavin; Popescu, Veronica; Wuerfel, Jens ...
Therapeutic Advances in Neurological Disorders,
01/2022, Letnik:
15
Book Review, Journal Article
Recenzirano
Odprti dostop
Using a philosophical approach or deductive reasoning, we challenge the dominant clinico-radiological worldview that defines multiple sclerosis (MS) as a focal inflammatory disease of the central ...nervous system (CNS). We provide a range of evidence to argue that the ‘real MS’ is in fact driven primarily by a smouldering pathological disease process. In natural history studies and clinical trials, relapses and focal activity revealed by magnetic resonance imaging (MRI) in MS patients on placebo or on disease-modifying therapies (DMTs) were found to be poor predictors of long-term disease evolution and were dissociated from disability outcomes. In addition, the progressive accumulation of disability in MS can occur independently of relapse activity from early in the disease course. This scenario is underpinned by a more diffuse smouldering pathological process that may affect the entire CNS. Many putative pathological drivers of smouldering MS can be potentially modified by specific therapeutic strategies, an approach that may have major implications for the management of MS patients. We hypothesise that therapeutically targeting a state of ‘no evident inflammatory disease activity’ (NEIDA) cannot sufficiently prevent disability accumulation in MS, meaning that treatment should also focus on other brain and spinal cord pathological processes contributing to the slow loss of neurological function. This should also be complemented with a holistic approach to the management of other systemic disease processes that have been shown to worsen MS outcomes.
Aim of this study was to investigate the activation of the IFNγ pathway in the affected liver and in the blood of patients with secondary hemophagocytic lymphohistiocytosis (sHLH). To this purpose, ...the mRNA expression levels of IFNG and IFNγ-inducible genes as well as Tyrosine (701)-phosphorylated signal transducer and activator of transcription 1 (STAT1) protein levels were evaluated in the liver and in peripheral blood mononuclear cells (PBMCs) of three patients with sHLH with predominant liver involvement. The mRNA expression levels of IFNG and IFNγ-inducible genes were markedly higher in patient livers compared to control livers and to one disease control liver. Conversely, slight differences in the expression levels of Type I IFN-inducible genes and other classical inflammatory cytokine genes were found. Further supporting the activation of the IFNγ pathway, higher protein levels of phosphorylated and total STAT1 were detected in patient livers compared to control livers. When the expression of the same genes analysed in liver tissues was evaluated in PBMCs collected from 2 out of 3 patients before the liver biopsy, we found that mRNA levels of IFNγ-inducible genes were markedly increased. Accordingly, high circulating levels of IFNγ-inducible CXCL9 were observed in patients. Altogether, these data demonstrate the selective and marked up-regulation of the IFNγ pathway in the liver tissue and blood of patients with active sHLH. Finally, we show that measurement of circulating CXCL9 levels and evaluation of IFNγ-inducible gene expression levels in PBMCs may represent a new valid tool to better identify patients with suspected HLH with predominant liver involvement.
Poly(ADP-ribose)polymerase-1 (PARP-1) is a predominantly nuclear enzyme that exerts numerous functions in cellular physiology and pathology, from maintenance of DNA stability to transcriptional ...regulation. Through a proteomic analysis of PARP-1 co-immunoprecipitation complexes, we identified Mitofilin, a mitochondrial protein, as a new PARP-1 interactor. This result prompted us to further investigate the presence and the role of the enzyme in mitochondria. Using laser confocal microscopy and Western blot analysis of purified mitochondria, we demonstrated the mitochondrial localization of a fraction of PARP-1. Further, the effects of overexpressing or down-regulating Mitofilin showed that this protein promotes and is required for PARP-1 mitochondrial localization. We also report several lines of evidence suggesting that intramitochondrial PARP-1 plays a role in mitochondrial DNA (mtDNA) damage signaling and/or repair. First, we show that PARP-1 binds to different regions throughout the mtDNA. Moreover, we demonstrated that the depletion of either PARP-1 or Mitofilin, which abrogates the mitochondrial localization of the enzyme, leads to the accumulation of mtDNA damage. Finally, we show that DNA ligase III, known to be required for mtDNA repair, participates in a PARP-1-containing complex bound to mtDNA. This work highlights a new environment for PARP-1, opening the possibility that at least some of the nuclear functions of the enzyme can be also extended to mtDNA metabolism.
Background
Williams syndrome (WS) phenotype is described as unique and intriguing. The aim of this study was to investigate the associations between speech–language abilities, general cognitive ...functioning and behavioural problems in individuals with WS, considering age effects and speech–language characteristics of WS sub‐groups.
Methods
The study's participants were 26 individuals with WS and their parents. General cognitive functioning was assessed with the Wechsler Intelligence Scale. Peabody Picture Vocabulary Test, Token Test and the Cookie Theft Picture test were used as speech–language measures. Five speech–language characteristics were evaluated from a 30‐min conversation (clichés, echolalia, perseverative speech, exaggerated prosody and monotone intonation). The Child Behaviour Checklist (CBCL 6‐18) was used to assess behavioural problems.
Results
Higher single‐word receptive vocabulary and narrative vocabulary were negatively associated with CBCL T‐scores for Social Problems, Aggressive Behaviour and Total Problems. Speech rate was negatively associated with the CBCL Withdrawn/Depressed T‐score. Monotone intonation was associated with shy behaviour, as well as exaggerated prosody with talkative behaviour. WS with perseverative speech and exaggerated prosody presented higher scores on Thought Problems. Echolalia was significantly associated with lower Verbal IQ. No significant association was found between IQ and behaviour problems. Age‐associated effects were observed only for the Aggressive Behaviour scale.
Conclusions
Associations reported in the present study may represent an insightful background for future predictive studies of speech–language, cognition and behaviour problems in WS.
PDF
