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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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- Kottyan, Leah C., et al.
(författare)
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The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share.
- 2015
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 24:2, s. 582-596
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Tidskriftsartikel (refereegranskat)abstract
- Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5-TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5-TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb (P-valuemeta = 6 × 10(-49); OR = 1.38-1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 (P-valuesEU = 10(-27)-10(-32), OR = 1.7-1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögrens syndrome and systemic sclerosis whereas only the IRF5-TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.
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- Birken, Sarah A., et al.
(författare)
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Toward a more comprehensive understanding of organizational influences on implementation: the organization theory for implementation science framework
- 2023
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Ingår i: Frontiers in Health Services. - : FRONTIERS MEDIA SA. - 2813-0146. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- IntroductionImplementation is influenced by factors beyond individual clinical settings. Nevertheless, implementation research often focuses on factors related to individual providers and practices, potentially due to limitations of available frameworks. Extant frameworks do not adequately capture the myriad organizational influences on implementation. Organization theories capture diverse organizational influences but remain underused in implementation science. To advance their use among implementation scientists, we distilled 70 constructs from nine organization theories identified in our previous work into theoretical domains in the Organization Theory for Implementation Science (OTIS) framework.MethodsThe process of distilling organization theory constructs into domains involved concept mapping and iterative consensus-building. First, we recruited organization and implementation scientists to participate in an online concept mapping exercise in which they sorted organization theory constructs into domains representing similar theoretical concepts. Multidimensional scaling and hierarchical cluster analyses were used to produce visual representations (clusters) of the relationships among constructs in concept maps. Second, to interpret concept maps, we engaged members of the Cancer Prevention and Control Research Network (CPCRN) OTIS workgroup in consensus-building discussions.ResultsTwenty-four experts participated in concept mapping. Based on resulting construct groupings coherence, OTIS workgroup members selected the 10-cluster solution (from options of 7-13 clusters) and then reorganized clusters in consensus-building discussions to increase coherence. This process yielded six final OTIS domains: organizational characteristics (e.g., size; age); governance and operations (e.g., organizational and social subsystems); tasks and processes (e.g., technology cycles; excess capacity); knowledge and learning (e.g., tacit knowledge; sense making); characteristics of a population of organizations (e.g., isomorphism; selection pressure); and interorganizational relationships (e.g., dominance; interdependence).DiscussionOrganizational influences on implementation are poorly understood, in part due to the limitations of extant frameworks. To improve understanding of organizational influences on implementation, we distilled 70 constructs from nine organization theories into six domains. Applications of the OTIS framework will enhance understanding of organizational influences on implementation, promote theory-driven strategies for organizational change, improve understanding of mechanisms underlying relationships between OTIS constructs and implementation, and allow for framework refinement. Next steps include testing the OTIS framework in implementation research and adapting it for use among policymakers and practitioners.
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- Klug, Matthew T., et al.
(författare)
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Tailoring metal halide perovskites through metal substitution: influence on photovoltaic and material properties
- 2017
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Ingår i: Energy & Environmental Science. - : ROYAL SOC CHEMISTRY. - 1754-5692 .- 1754-5706. ; 10:1, s. 236-246
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Tidskriftsartikel (refereegranskat)abstract
- We present herein an experimental screening study that assesses how partially replacing Pb in methylammonium lead triiodide perovskite films with nine different alternative, divalent metal species, B = {Co, Cu, Fe, Mg, Mn, Ni, Sn, Sr, and Zn}, influences photovoltaic performance and optical properties. Our findings indicate the perovskite film is tolerant to most of the considered homovalent metal species with lead-cobalt compositions yielding the highest power conversion efficiencies when less than 6% of the Pb2+ ions are replaced. Through subsequent materials characterisation, we demonstrate for the first time that partially substituting Pb2+ at the B-sites of the perovskite lattice is not restricted to Group IV elements but is also possible with at least Co2+. Moreover, adjusting the molar ratio of Pb: Co in the mixed-metal perovskite affords new opportunities to tailor the material properties while maintaining stabilised device efficiencies above 16% in optimised solar cells. Specifically, crystallographic analysis reveals that Co2+ incorporates into the perovskite lattice and increasing its concentration can mediate a crystal structure transition from the cubic to tetragonal phase at room-temperature. Likewise, Co2+ substitution continually modifies the perovskite work function and band edge energies without either changing the band gap or electronically doping the intrinsic material. By leveraging this orthogonal dimension of electronic tunability, we achieve remarkably high open-circuit voltages up to 1.08 V with an inverted device architecture by shifting the perovskite into a more favourable energetic alignment with the PEDOT: PSS hole transport material.
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| 6. |
- Upadhyay, Ranjan, et al.
(författare)
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A Critical Role for Fas-Mediated Off-Target Tumor Killing in T-cell Immunotherapy
- 2021
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Ingår i: Cancer Discovery. - : American Association For Cancer Research (AACR). - 2159-8274 .- 2159-8290. ; 11:3, s. 599-613
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Tidskriftsartikel (refereegranskat)abstract
- T cell-based therapies have induced cancer remissions, though most tumors ultimately progress, reflecting inherent or acquired resistance including antigen escape. Better understanding of how T cells eliminate tumors will help decipher resistance mechanisms. We used a CRISPR/Cas9 screen and identified a necessary role for Fas-FasL in antigen-specific T-cell killing. We also found that Fas-FasL mediated off-target "bystander" killing of antigen-negative tumor cells. This localized bystander cytotoxicity enhanced clearance of antigen-heterogeneous tumors in vivo, a finding that has not been shown previously. Fas-mediated on-target and bystander killing was reproduced in chimeric antigen receptor (CAR-T) and bispecific antibody T-cell models and was augmented by inhibiting regulators of Fas signaling. Tumoral FAS expression alone predicted survival of CAR-T-treated patients in a large clinical trial (NCT02348216). These data suggest strategies to prevent immune escape by targeting both the antigen expression of most tumor cells and the geography of antigen-loss variants. SIGNIFICANCE: This study demonstrates the first report of in vivo Fas-dependent bystander killing of antigen-negative tumors by T cells, a phenomenon that may be contributing to the high response rates of antigen-directed immunotherapies despite tumoral heterogeneity. Small molecules that target the Fas pathway may potentiate this mechanism to prevent cancer relapse.
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