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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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- Vogel, G. F., et al.
(författare)
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Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants
- 2023
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Ingår i: Genetics in Medicine. - : Elsevier BV. - 1098-3600. ; 25:6
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: This study aimed to define the genotypic and phenotypic spectrum of reversible acute liver failure (ALF) of infancy resulting from biallelic pathogenic TRMU variants and determine the role of cysteine supplementation in its treatment. Methods: Individuals with biallelic (likely) pathogenic variants in TRMU were studied within an international retrospective collection of de-identified patient data. Results: In 62 individuals, including 30 previously unreported cases, we described 47 (likely) pathogenic TRMU variants, of which 17 were novel, and 1 intragenic deletion. Of these 62 individuals, 42 were alive at a median age of 6.8 (0.6-22) years after a median follow-up of 3.6 (0.1-22) years. The most frequent finding, occurring in all but 2 individuals, was liver involvement. ALF occurred only in the first year of life and was reported in 43 of 62 individuals; 11 of whom received liver transplantation. Loss-of-function TRMU variants were associated with poor survival. Supplementation with at least 1 cysteine source, typically N-acetylcysteine, improved survival significantly. Neurodevelopmental delay was observed in 11 individuals and persisted in 4 of the survivors, but we were unable to determine whether this was a primary or a secondary consequence of TRMU deficiency. Conclusion: In most patients, TRMU-associated ALF was a transient, reversible disease and cysteine supplementation improved survival.
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- Euro, L., et al.
(författare)
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Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2) defects predicts differential effects on aminoacylation
- 2015
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 5:FEB
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Tidskriftsartikel (refereegranskat)abstract
- The accuracy of mitochondrial protein synthesis is dependent on the coordinated action of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mtARSs) and the mitochondrial DNA-encoded tRNAs. The recent advances in whole-exome sequencing have revealed the importance of the mtARS proteins for mitochondrial pathophysiology since nearly every nuclear gene for mtARS (out of 19) is now recognized as a disease gene for mitochondrial disease. Typically, defects in each mtARS have been identified in one tissue-specific disease, most commonly affecting the brain, or in one syndrome. However, mutations in the AARS2 gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS) have been reported both in patients with infantile-onset cardiomyopathy and in patients with childhood to adulthood-onset leukoencephalopathy. We present here an investigation of the effects of the described mutations on the structure of the synthetase, in an effort to understand the tissue-specific outcomes of the different mutations. The mtAlaRS differs from the other mtARSs because in addition to the aminoacylation domain, it has a conserved editing domain for deacylating tRNAs that have been mischarged with incorrect amino acids. We show that the cardiomyopathy phenotype results from a single allele, causing an amino acid change R592W in the editing domain of AARS2, whereas the leukodystrophy mutations are located in other domains of the synthetase. Nevertheless, our structural analysis predicts that all mutations reduce the aminoacylation activity of the synthetase, because all mtAlaRS domains contribute to tRNA binding for aminoacylation. According to our model, the cardiomyopathy mutations severely compromise aminoacylation whereas partial activity is retained by the mutation combinations found in the leukodystrophy patients. These predictions provide a hypothesis for the molecular basis of the distinct tissue-specific phenotypic outcomes.
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- Hedin, Charlotte Rose Hawkey, et al.
(författare)
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Effects of Tumor Necrosis Factor Antagonists in Patients With Primary Sclerosing Cholangitis
- 2020
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Ingår i: Clinical Gastroenterology and Hepatology. - : Elsevier BV. - 1542-3565 .- 1542-7714. ; 18:10, s. 2-2304
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Tidskriftsartikel (refereegranskat)abstract
- Background & Aims: Few patients with primary sclerosing cholangitis (PSC) and inflammatory bowel diseases (IBDs) are exposed to tumor necrosis factor (TNF) antagonists because of the often mild symptoms of IBD. We assessed the effects of anti-TNF agents on liver function in patients with PSC and IBD, and their efficacy in treatment of IBD. Methods: We performed a retrospective analysis of 141 patients with PSC and IBD receiving treatment with anti-TNF agents (infliximab or adalimumab) at 20 sites (mostly tertiary-care centers) in Europe and North America. We collected data on the serum level of alkaline phosphatase (ALP). IBD response was defined as either endoscopic response or, if no endoscopic data were available, clinical response, as determined by the treating clinician or measurements of fecal calprotectin. Remission was defined more stringently as endoscopic mucosal healing. We used linear regression analysis to identify factors associated significantly with level of ALP during anti-TNF therapy. Results: Anti-TNF treatment produced a response of IBD in 48% of patients and remission of IBD in 23%. There was no difference in PSC symptom frequency before or after drug exposure. The most common reasons for anti-TNF discontinuation were primary nonresponse of IBD (17%) and side effects (18%). At 3 months, infliximab-treated patients had a median reduction in serum level of ALP of 4% (interquartile range, reduction of 25% to increase of 19%) compared with a median 15% reduction in ALP in adalimumab-treated patients (interquartile range, reduction of 29% to reduction of 4%; P =.035). Factors associated with lower ALP were normal ALP at baseline (P <.01), treatment with adalimumab (P =.090), and treatment in Europe (P =.083). Conclusions: In a retrospective analysis of 141 patients with PSC and IBD, anti-TNF agents were moderately effective and were not associated with exacerbation of PSC symptoms or specific side effects. Prospective studies are needed to investigate the association between use of adalimumab and reduced serum levels of ALP further.
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- Lundstrom, M, et al.
(författare)
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Strategy to reduce the number of patients perceiving impaired visual function after cataract surgery
- 2002
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Ingår i: Journal of Cataract and Refractive Surgery. - 1873-4502. ; 28:6, s. 971-976
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To reduce the number of patients who perceive more difficulties performing daily life activities 6 months after cataract extraction than before surgery. Setting: Surgeons at 4 surgical units participating in the yearly outcome studies organized by the Swedish National Cataract Register. Methods: This study comprised surgical outcomes data and completed Catquest results before and after surgery collected from consecutive patients during a 1-month period yearly since 1995. The reasons for a no-benefit outcome from 1995 to 1997 were identified. During the 1-month study period in 1999, a strategy was launched to reduce postoperative anisometropia and disturbances from cataract in the fellow eye through better surgical planning. Results: The percentage of patients with a no-benefit outcome who had anisometropia or cataract in the fellow eye as a probable reason for the outcome decreased from 27.3% and 13.0%, respectively, in the 1995 to 1997 study to 10.5% and 10.5%, respectively, in the 1999 study. Other reasons for a no-benefit outcome such as ocular co-morbidity or few preoperative problems increased in frequency, presumably as a result of a change in case mix. Conclusions: A strategy to reduce the number of patients perceiving more difficulties in performing daily life activities after cataract extraction than before surgery was tested, The number of patients with reasons for a poor outcome that the study focused on was reduced. Patients who gave reasons for a poor outcome other than anisometropia or cataract in the fellow eye increased in frequency, probably as a result of a change in case mix.
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- Lundström, M, et al.
(författare)
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Cataract surgery and quality of life in patients with age related macular degeneration
- 2002
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Ingår i: British Journal of Ophthalmology. - : BMJ. - 0007-1161 .- 1468-2079. ; 86:12, s. 1330-1335
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Tidskriftsartikel (refereegranskat)abstract
- Background: The coexistence of cataract and age related macular degeneration (AMD) is not unusual, especially in the very elderly. The outcome of cataract surgery in these cases depends on the effect of AMD on vision. In this study the authors have compared the outcome of cataract patients with AMD to that of cataract patients with no vision threatening ocular comorbidity, and analysed possible predictors of good or poor outcome. Methods: An observational prospective study on consecutive cases operated for cataract during 1 month at six surgical departments affiliated to the Swedish National Cataract Register (NCR). Data were collected according to the protocol of NCR and subjects completed the Catquest questionnaire before and 6 months after surgery. 90 subjects with AMD were compared to 335 subjects with no sight threatening ocular comorbidity. Results: Difficulties in performing various daily life activities improved significantly for AMD subjects after surgery (p<0.001, Wilcoxon signed rank test). Satisfaction with vision also improved significantly after surgery (p<0.001, Wilcoxon signed rank test). Activity level and independence were unchanged. Subjects with no ocular comorbidity had a still better outcome. The most important variable related to a good self assessed functional outcome was postoperative visual acuity irrespective of the presence of AMD. AMD subjects scheduled for second eye surgery and AMD subjects dissatisfied with their vision before surgery had a poorer outcome. Conclusion: Subjects with various stages of dry AMD and cataract improved their self assessed visual function and satisfaction with vision significantly after cataract extraction.
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