The Dynamics of β-Amyloid Proteoforms Accumulation in the Brain of a 5xFAD Mouse Model of Alzheimer’s Disease

Alzheimer’s disease (AD) is the leading cause of dementia among the elderly. Neuropathologically, AD is characterized by the deposition of a 39- to 42-amino acid long β-amyloid (Aβ) peptide in the form of senile plaques. Several post-translational modifications (PTMs) in the N-terminal domain have been shown to increase the aggregation and cytotoxicity of Aβ, and specific Aβ proteoforms (e.g., Aβ with isomerized D7 (isoD7-Aβ)) are abundant in the senile plaques of AD patients. Animal models are indispensable tools for the study of disease pathogenesis, as well as preclinical testing. In the presented work, the accumulation dynamics of Aβ proteoforms in the brain of one of the most widely used amyloid-based mouse models (the 5xFAD line) was monitored. Mass spectrometry (MS) approaches, based on ion mobility separation and the characteristic fragment ion formation, were applied. The results indicated a gradual increase in the Aβ fraction of isoD7-Aβ, starting from approximately 8% at 7 months to approximately 30% by 23 months of age. Other specific PTMs, in particular, pyroglutamylation, deamidation, and oxidation, as well as phosphorylation, were also monitored. The results for mice of different ages demonstrated that the accumulation of Aβ proteoforms correlate with the formation of Aβ deposits. Although the mouse model cannot be a complete analogue of the processes occurring in the human brain in AD, and several of the observed parameters differ significantly from human values supposedly due to the limited lifespan of the model animals, this dynamic study provides evidence on at least one of the possible mechanisms that can trigger amyloidosis in AD, i.e., the hypothesis on the relationship between the accumulation of isoD7-Aβ and the progression of AD-like pathology.

TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats

Advances in mass spectrometry instrumentation have led to the development of mass spectrometers with ion mobility separation (IMS) capabilities and dual source instrumentation, but the current software ecosystem lacks interoperability with downstream data analysis using open-source software/pipelines. Here, we present TIMSCONVERT, a data conversion workflow from timsTOF fleX MS raw data files to size conscious mzML and imzML formats with minimal preprocessing to allow for compatibility with downstream data analysis tools, which we showcase with several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX. Availability and Implementation: TIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command line interface, Nextflow workflow, and online in the Global Natural Products Social (GNPS) platform (https://proteomics2.ucsd.edu/ProteoSAFe/index.jsp?params={%22workflow%22%3A%20%22T IMSCONVERT%22}).

Immature Persimmon Suppresses Amyloid Beta (Aβ) Mediated Cognitive Dysfunction via Tau Pathology in ICR Mice

This study confirmed the ameliorating effect of immature persimmon (Diospyros kaki) ethanolic extract (IPEE) on neuronal cytotoxicity in amyloid beta (Aβ)1–42-induced ICR mice. The administration of IPEE ameliorated the cognitive dysfunction in Aβ1–42-induced mice by improving the spatial working memory, the short-term and long-term memory functions. IPEE protected the cerebral cholinergic system, such as the acetylcholine (ACh) level and acetylcholinesterase (AChE) activity, and antioxidant system, such as the superoxide dismutase (SOD), reduced glutathione (GSH) and malondialdehyde (MDA) contents. In addition, mitochondrial dysfunction against Aβ1–42-induced toxicity was reduced by regulating the reactive oxygen species (ROS), mitochondrial membrane potential and ATP contents. In addition, IPEE regulated the expression levels of tau signaling, such as TNF-α, p-JNK, p-Akt, p-GSK3β, p-tau, p-NF-κB, BAX and caspase 3. Finally, gallic acid, ellagic acid and quercetin 3-O-(6″-acetyl-glucoside) were identified as the physiological compounds of IPEE using ultra-performance liquid chromatography ion mobility separation quadrupole time-of-flight/tandem mass spectrometry (UPLC IMS Q-TOF/MS2).

A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Unlike cohesin, in vivo regulators of condensin binding dynamics remain unclear. Here we addressed this question using C. elegans condensin DC, which specifically binds to and represses transcription of both X chromosomes in hermaphrodites for dosage compensation. Mutants of several chromatin modifiers that regulate H4K20me and H4K16ac cause varying degrees of X chromosome derepression. We used fluorescence recovery after photobleaching (FRAP) to analyze how these modifiers regulate condensin DC binding dynamics in vivo. We established FRAP using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. The greatest effect on condensin DC dynamics was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of the complex reduced from ~30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Separation of catalytic and non-catalytic activity is also supported by Hi-C data in the dpy-21 null mutant. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.