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Event: 889

Key Event Title

The KE title should describe a discrete biological change that can be measured. It should generally define the biological object or process being measured and whether it is increased, decreased, or otherwise definably altered relative to a control state. For example “enzyme activity, decreased”, “hormone concentration, increased”, or “growth rate, decreased”, where the specific enzyme or hormone being measured is defined. More help

Impaired, Proteostasis

Short name
The KE short name should be a reasonable abbreviation of the KE title and is used in labelling this object throughout the AOP-Wiki. The short name should be less than 80 characters in length. More help
Impaired, Proteostasis

Biological Context

Structured terms, selected from a drop-down menu, are used to identify the level of biological organization for each KE. Note, KEs should be defined within a particular level of biological organization. Only KERs should be used to transition from one level of organization to another. Selection of the level of biological organization defines which structured terms will be available to select when defining the Event Components (below). More help
Level of Biological Organization
Cellular

Cell term

Further information on Event Components and Biological Context may be viewed on the attached pdf.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable. More help
Cell term
eukaryotic cell

Organ term

Further information on Event Components and Biological Context may be viewed on the attached pdf.The biological context describes the location/biological environment in which the event takes place.  For molecular/cellular events this would include the cellular context (if known), organ context, and species/life stage/sex for which the event is relevant. For tissue/organ events cellular context is not applicable.  For individual/population events, the organ context is not applicable. More help

Key Event Components

Further information on Event Components and Biological Context may be viewed on the attached pdf.Because one of the aims of the AOP-KB is to facilitate de facto construction of AOP networks through the use of shared KE and KER elements, authors are also asked to define their KEs using a set of structured ontology terms (Event Components). In the absence of structured terms, the same KE can readily be defined using a number of synonymous titles (read by a computer as character strings). In order to make these synonymous KEs more machine-readable, KEs should also be defined by one or more “event components” consisting of a biological process, object, and action with each term originating from one of 22 biological ontologies (Ives, et al., 2017; See List). Biological process describes dynamics of the underlying biological system (e.g., receptor signalling). The biological object is the subject of the perturbation (e.g., a specific biological receptor that is activated or inhibited). Action represents the direction of perturbation of this system (generally increased or decreased; e.g., ‘decreased’ in the case of a receptor that is inhibited to indicate a decrease in the signalling by that receptor).Note that when editing Event Components, clicking an existing Event Component from the Suggestions menu will autopopulate these fields, along with their source ID and description. To clear any fields before submitting the event component, use the 'Clear process,' 'Clear object,' or 'Clear action' buttons. If a desired term does not exist, a new term request may be made via Term Requests. Event components may not be edited; to edit an event component, remove the existing event component and create a new one using the terms that you wish to add. More help
Process Object Action
Proteostasis deficiencies protein abnormal

Key Event Overview

AOPs Including This Key Event

All of the AOPs that are linked to this KE will automatically be listed in this subsection. This table can be particularly useful for derivation of AOP networks including the KE. Clicking on the name of the AOP will bring you to the individual page for that AOP. More help
AOP Name Role of event in AOP Point of Contact Author Status OECD Status
Mitochondrial dysfunction and Neurotoxicity KeyEvent Andrea Terron (send email) Open for citation & comment TFHA/WNT Endorsed
Mitochondrial complex inhibition leading to liver injury KeyEvent Wanda van der Stel (send email) Under development: Not open for comment. Do not cite

Stressors

This is a structured field used to identify specific agents (generally chemicals) that can trigger the KE. Stressors identified in this field will be linked to the KE in a machine-readable manner, such that, for example, a stressor search would identify this as an event the stressor can trigger. NOTE: intermediate or downstream KEs in one AOP may function as MIEs in other AOPs, meaning that stressor information may be added to the KE description, even if it is a downstream KE in the pathway currently under development.Information concerning the stressors that may trigger an MIE can be defined using a combination of structured and unstructured (free-text) fields. For example, structured fields may be used to indicate specific chemicals for which there is evidence of an interaction relevant to this MIE. By linking the KE description to a structured chemical name, it will be increasingly possible to link the MIE to other sources of chemical data and information, enhancing searchability and inter-operability among different data-sources and knowledgebases. The free-text section “Evidence for perturbation of this MIE by stressor” can be used both to identify the supporting evidence for specific stressors triggering the MIE as well as to define broad chemical categories or other properties that classify the stressors able to trigger the MIE for which specific structured terms may not exist. More help

Taxonomic Applicability

Latin or common names of a species or broader taxonomic grouping (e.g., class, order, family) can be selected from an ontology. In many cases, individual species identified in these structured fields will be those for which the strongest evidence used in constructing the AOP was available in relation to this KE. More help
Term Scientific Term Evidence Link
human Homo sapiens High NCBI
rat Rattus norvegicus High NCBI
mouse Mus musculus Moderate NCBI

Life Stages

The structured ontology terms for life-stage are more comprehensive than those for taxa, but may still require further description/development and explanation in the free text section. More help

Sex Applicability

The authors must select from one of the following: Male, female, mixed, asexual, third gender, hermaphrodite, or unspecific. More help

Key Event Description

A description of the biological state being observed or measured, the biological compartment in which it is measured, and its general role in the biology should be provided. For example, the biological state being measured could be the activity of an enzyme, the expression of a gene or abundance of an mRNA transcript, the concentration of a hormone or protein, neuronal activity, heart rate, etc. The biological compartment may be a particular cell type, tissue, organ, fluid (e.g., plasma, cerebrospinal fluid), etc. The role in the biology could describe the reaction that an enzyme catalyses and the role of that reaction within a given metabolic pathway; the protein that a gene or mRNA transcript codes for and the function of that protein; the function of a hormone in a given target tissue, physiological function of an organ, etc. Careful attention should be taken to avoid reference to other KEs, KERs or AOPs. Only describe this KE as a single isolated measurable event/state. This will ensure that the KE is modular and can be used by other AOPs, thereby facilitating construction of AOP networks. More help

The concept of proteostasis refers to the homeostasis of proteins in space and time, i.e. the correct balance between protein synthesis, modification, transport and degradation. Disturbance of proteostasis results in pathological changes either by loss of function events (lack of a pivotal protein/protein function) or by a gain of undesired functions (aggregation of a protein leading to the formation of inclusions and new structures in cells and disturbing turnover of many unrelated proteins).

Proteostasis regulation is the main defence mechanism against toxic proteins, whose accumulation could greatly compromise normal cellular function and viability. Therefore, the chaperone and degradation systems assuring the removal of misfolded and aggregated proteins, as well as damaged, dysfunctional cellular organelles (e.g. defective mitochondria) play a key role in cellular homeostasis (Lee et al., 2012). The two major degradation systems are the ubiquitin–proteasome system (UPS) and the autophagy–lysosome pathway (ALP) (Korolchuk et al., 2010; Kroemer et al., 2010; Ravikumar et al., 2010). The UPS works through the attachment of multiple ubiquitin molecules to a protein substrate, followed by the subsequent degradation of the tagged polyubiquitinated protein by the proteasome (Ciechanover, 1998; Ciechanover and Brundin, 2003). A compromised function of the UPS leads to the accumulation of ubiquitylated proteins, such as α-synuclein (Ii et al. 1997; Spillantini et al. 1997; Sulzer and Zecca 2000). The accumulation of polyubiquitinated proteins, as a consequence of a dysfunctional proteasome activity, is observed in some pathologies, and experimental inhibition of the proteasome has been shown to trigger parkinsonian neurodegeneration (McNaught and Jenner 2001; Hardy et al., 2001).

ALP involves the engulfment of cytoplasmic materials into autophagosomes, which are degraded by lysosomal enzymes after fusion of autophagosomes with lysosomes (Kuma et al., 2004) or direct import of proteins into lysosomes (Cuervo, 2004; Mizushima et al., 2008). Autophagy also plays an essential role for the removal of damaged organelles, such as mitochondria. Both, excessive autophagy or reduced autophagic flux can compromise cell survival (Rothermel and Hill, 2007), and several genetic forms of PD are linked to the autophagy-related genes Pink1, Parkin or Uchl1. Autophagy enables cell survival during mitochondrial stress by clearing the damaged organelles (Lee et al., 2012).

One of the main aggregated proteins found to accumulate in nigrostriatal cells during Parkinson's disease is α-synuclein. Aggregation of α-synuclein can obstruct normal cellular transport, leading to impaired intracellular trafficking and/or trapping of cellular organelles in inappropriate locations, this resulting in synaptic and cell dysfunctions (Bartels et al., 2011) (Bellucci A., et al., 2012; Cookson MR., 2005; Games D., et al., 2013; Hunn BH., et al., 2015). Importantly, accumulation of α-synuclein affects mitochondrial trafficking. The polarity and correct function of different types of cells depend on an efficient transport of mitochondria to areas of high energy consumption (Sheng, 2014). Therefore, the correct distribution of mitochondria to various parts of a cell is essential to preserve cell function (Schwarz, 2013; Zhu et al., 2012).

How It Is Measured or Detected

One of the primary considerations in evaluating AOPs is the relevance and reliability of the methods with which the KEs can be measured. The aim of this section of the KE description is not to provide detailed protocols, but rather to capture, in a sentence or two, per method, the type(s) of measurements that can be employed to evaluate the KE and the relative level of scientific confidence in those measurements. Methods that can be used to detect or measure the biological state represented in the KE should be briefly described and/or cited. These can range from citation of specific validated test guidelines, citation of specific methods published in the peer reviewed literature, or outlines of a general protocol or approach (e.g., a protein may be measured by ELISA).Key considerations regarding scientific confidence in the measurement approach include whether the assay is fit for purpose, whether it provides a direct or indirect measure of the biological state in question, whether it is repeatable and reproducible, and the extent to which it is accepted in the scientific and/or regulatory community. Information can be obtained from the OECD Test Guidelines website and the EURL ECVAM Database Service on Alternative Methods to Animal Experimentation (DB-ALM). ?

1. Evaluation of UPS function. General turnover assays: quantitative evaluation can be based on the detection of increased ubiquitin or ubiquinated proteins, as well as proteasomal subunits, either by immunocyto/histochemistry or by western blotting (Rideout et al., 2001; Ortega and Lucas, 2014). UPS activity can be continuously monitored by quantitating (by mean of flow cytometry or microscopy) the level of e.g. EGFP-degron fusion proteins (green fluorescent protein) that are selectively degraded by the proteasome (Bence et al., 2001).

Proteasome activity assay. Various fluorogenic substrates (e.g., Suc-Leu-Leu-Val-Tyr-AMC for the chymotrypsin-like activity) can be used for the determination of proteasomal activity in in vivo or in vitro applications. These substrates may be applied to tissue or cell homogenates, but specific measurements require partial purification of the proteasome (Kisselev and Goldberg, 2005).

Detection of α-synuclein (AS) aggregates. The most common methods to detect AS aggregates use immunostaining for AS (in cells or in tissues). In cell culture, AS may also be epitope-tagged or coupled to GFP to allow an indirect detection. The detection of small, not microscopically-visible AS aggregates is indicative of protease-resistance. Tissue slices may be exposed to proteases before immunostaining for AS. Alternatively, small or large aggregates may be biochemically enriched by differential centrifugation and proteolytic treatment, and then analyzed, e.g., by western blot, mass spectrometry or ELISA-like immunoquantification.

2. Evaluation of ALP function.

Quantification of lysosomes or autophagosomes. Disturbances of ALP often result in counter-regulations that can be visualized by staining of lysosomes or parts of the autophagy system. Several weakly basic dyes can be used to stain acidic organelles (lysosomes) in live cells. For example, the dye LysoTracker Red stains lysosomes and can be used to monitor autophagy (Klionsky et al., 2007; Klionsky et al., 2008). The autofluorescent drug monodansylcadaverine (MDC) has also been used as autophago-lysosome marker (Munafó and Colombo, 2002). A convenient way to stain lysosomes in tissue or fixed cells is the use of antibodies against the Lysosomal-Associated Membrane Protein 1 (LAMP-1) (Rajapakshe et al., 2015) or against cathepsins (Foghsgaard et al., 2001). For qualitative or semiquantitative estimates of lysosomes and related organelles, transmission electron microscopy has been frequently used (Barth et al., 2010).

Monitoring of autophagy-related molecules. The amount and the localization of autophagy-related proteins can change during disturbance of the ALP. Especially in cell culture, but also in transgenic mice, various techniques have been used to monitor autophagy by mean of fluorescence-tags or other substrates, e.g., ATG, autophagy-related protein or autophagy substrates, to monitor their fate in cells and thus provide information on disturbed ALP, or the over-expression of GFP–LC3, in which GFP (green fluorescent protein) is expressed as a fusion protein at the amino terminus of LC3 (microtubule-associated protein 1A/1B-light chain 3), which is the a mammalian homologue of S. cerevisiae ATG8 (Kadowaki and Karim, 2009).

Monitoring autophagic flux. The lysosomal degradation of the autophagic cargo constitutes the autophagic flux, which can be measured by assessing the rate of turnover of long-lived proteins that are normally turned over by autophagy (Bauvy et al., 2009). This is performed by labelling intracellular proteins with either [14C]-leucine or [14C]-valine, followed by a long culture period in standard medium. The release of radioactive leucin or valin into the culture medium corresponds to the protein degradation rate in cells, and it may be measured by liquid scintillation counting.

Monitoring the conversion of LC3-I to LC3-II. The progression of autophagy (autophagic flux) can be studied by the conversion of LC3-I into LC3-II (i.e. a post-translational modification specific for autophagy) by mean of Western blot analysis. The amount of LC3-II correlates with the number of autophagosomes. Conversion of LC3 can be used to examine autophagic activity in the presence or absence of lysosomal activity (Klionsky et al., 2007; Klionsky et al., 2008). The technology can also be used in vivo, e.g. by the use of transgenic mice that overexpress GFP–LC3 (Kuma et al., 2004).

3. Evaluation of intracellular transport of mitochondria and other organelles.

A range of technologies has been used to visualize mitochondrial dynamics in live cells (Jakobs, 2006; Grafstein and Forman, 1980). They usually employ a combination of mitochondrial labelling with fluorescent dyes (e.g. DiOC6 (3, 3′-Dihexyloxacarbocyanine iodide), JC-1 (5,5′,6,6′-Tetrachloro-1,1′,3,3′ tetraethylbenzimida-zolylcarbo-cyanine iodide), MitoTracker, MitoFluor probes, etc.), followed by video- or confocal microscopy for live cell imaging (Schwarz, 2013; Pool et al., 2006). Most frequently, mitochondrial mobility is observed along neurites, and measurable endpoints may be mitochondrial speed and direction with regard to the cell soma (Schildknecht et al. 2013). Additionally, also mitochondrial fusion and fission have been monitored by such methods (Exner et al., 2012). The transport of other organelles along neurites may be monitored using similar methods, and the microtubule structures that serve as transport scaffold may be co-stained.

Domain of Applicability

This free text section should be used to elaborate on the scientific basis for the indicated domains of applicability and the WoE calls (if provided). While structured terms may be selected to define the taxonomic, life stage and sex applicability (see structured applicability terms, above) of the KE, the structured terms may not adequately reflect or capture the overall biological applicability domain (particularly with regard to taxa). Likewise, the structured terms do not provide an explanation or rationale for the selection. The free-text section on evidence for taxonomic, life stage, and sex applicability can be used to elaborate on why the specific structured terms were selected, and provide supporting references and background information.  More help

The ubiquitin proteasome system is highly conserved in eukaryotes, from yeast to human. Ubiquitin is a small (8.5 kDa) regulatory protein that has been found in almost all tissues of eukaryotic organisms. For instance, drosophila has been used as PD model to study the role of ubiquitin in α-synuclein induced-toxicity (Lee et al., 2009). Human and yeast ubiquitin share 96% sequence identity. Neither ubiquitin nor the ubiquitination machinery are known to exist in prokaryotes. Autophagy is ubiquitous in eukaryotic cells and is the major mechanism involved in the clearance of oxidatively or otherwise damaged/worn-out macromolecules and organelles (Esteves et al., 2011). Due to the high degree of conservation, most of the knowledge on autophagy proteins in vertebrates is derived from studies in yeast (Klionsky et al., 2007). Autophagy is seen in all eukaryotic systems, including fungi, plants, slime mold, nematodes, fruit flies and insects, rodents (i.e., laboratory mice and rats), and humans. It is a fundamental and phylogenetically conserved self-degradation process that is characterized by the formation of double-layered vesicles (autophagosomes) around intracellular cargo for delivery to lysosomes and proteolytic degradation.

Evidence for Perturbation by Stressor

References

List of the literature that was cited for this KE description. Ideally, the list of references, should conform, to the extent possible, with the OECD Style Guide (https://www.oecd.org/about/publishing/OECD-Style-Guide-Third-Edition.pdf) (OECD, 2015). More help

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