Biology subjects

Potapenko, A.

Publications and source records attributed to Potapenko, A..

4 recordsLinked to original sources

bioRxiv2025

Mitochondrial dysfunction in Machado Joseph disease: insights from a multi-model system

Spinocerebellar ataxia type-3 (SCA3), also known as Machado Joseph disease, MJD) is a fatal, neurodegenerative disease belonging to the polyglutamine repeat disease family, caused by inheritance of an abnormal form of the ATXN3 gene, carrying a longer than usual trinucleotide repeat sequence. Within this study we explored mitochondrial function in a range of different experimental models of MJD, including transgenic zebrafish, mice and neuronal cells, to gain an understanding of mitochondrial function in the disease, and possible mechanisms of any dysfunction. Firstly, we examined the transgenic CMVMJD135 mouse model that develops impaired movement, neurodegeneration and decreased survival. We performed proteomic analysis on brain lysates extracted from a cohort of male and female WT and MJD mice, for analysis of differences in male and female mice separately. We identified that a major difference predicted by Ingenuity Pathway Analysis to be in both male and female MJD mice was related to impaired oxidative phosphorylation and mitochondrial dysfunction. We examined primary neuron cultures obtained from CMVMJD135 mice, validating the findings of the proteomic analysis, and finding changes to mitochondrial morphology, as well. We further examined a transgenic zebrafish model of MJD that expresses EGFP fused human ataxin-3 with short or long polyQ stretches (23 or 84Q, respectively) in neurons (expression driven under the elav/HuC promoter). The MJD zebrafish also exhibit altered mitochondrial electron transport chain complex protein levels, together with enhanced sensitivity to rotenone administration, which may be a valuable readout for treatment investigation studies in the future. Together, this study confirms, and extends on, the growing body of evidence suggesting that mitochondrial dysfunction plays a role in MJD, warranting investigation for therapeutic intervention.

neuroscience↗

bioRxiv2025

Gut transit and gut microbiome changes occur prior to the onset of motor impairment in a mouse model of Machado-Joseph disease

We previously identified microbial shifts prior to the onset of motor and neurological symptoms within a mouse model of the fatal neurodegenerative disease Machado-Joseph disease (MJD). Here, we aimed to explore possible mechanisms contributing to these changes within the microbiome-gut-brain axis, and whether it preceded or followed central neurodegeneration. Here, we report that pre-symptomatic male MJD mice present with significantly different microbiome communities as early as 5-weeks-old. Furthermore, we show that male MJD mice have faster total gut transit times by 9-weeks-old, prior to signs of impaired motor function by 11-weeks-old. To elucidate whether these microbial and colonic functional changes are due to the presence of pathological and morphological changes in the gut, we quantified the formation of ataxin-3 protein aggregates within the gut and examined morphological changes within the gut of pre- and early symptomatic MJD mice relative to proteinopathy in the brain. Interestingly, we observed ataxin-3 aggregates within the brains of pre-symptomatic MJD mice, with significantly more aggregates present in MJD than WT mice from 7-weeks-of-age, an earlier timepoint than previously reported, coinciding with changes within the microbiome. However, we observed no ataxin-3 protein aggregates and no changes in enteric neuron populations or morphology within the gut. Analysis of endocrine factors involved in gut motility and inflammatory markers within the small intestine of 13-week-old males revealed increased expression of genes encoding cholecystokinin (Cck), ghrelin (Ghrl), heme oxygenase (Ho1), interleukin-1 beta (Il1b), and decreased inducible nitric oxide synthase (Nos2). Together, we demonstrate for the first time that colonic dysfunction occurs after gut microbiome changes, but prior to the onset of motor impairments in male MJD mice. Our work suggests that whilst proteinopathy or morphological changes within the gut may not be involved in these changes, inflammation and related endocrine changes could have a role in the interplay between the gut and brain during MJD development, warranting further investigation.

neuroscience↗

bioRxiv2023

Mapping the dynamic cell surface interactome of high-density lipoprotein reveals Aminopeptidase N as modulator of its endothelial uptake

Heterogeneous high-density lipoprotein (HDL) particles, which can contain hundreds of proteins, affect human health and disease through dynamic molecular interactions with cell surface proteins. How HDL mediates its long-range signaling functions and interactions with various cell types is largely unknown. Due to the complexity of HDL, we hypothesize that multiple receptors engage with HDL particles resulting in condition-dependent receptor-HDL interaction clusters at the cell surface. Here we used the mass spectrometry-based and light-controlled proximity labeling strategy LUX-MS in a discovery-driven manner to decode HDL-receptor interactions. Surfaceome nanoscale organization analysis of hepatocytes and endothelial cells using LUX-MS revealed that the previously known HDL-binding protein scavenger receptor SCRB1 is embedded in a cell surface protein community, which we term HDL synapse. Modulating the endothelial HDL synapse, composed of 60 proteins, by silencing individual members showed that the HDL synapse can be assembled in the absence of SCRB1 and that the members are interlinked. The aminopeptidase AMPN (also known as CD13) was identified as an HDL synapse member that directly influences HDL uptake into the primary human aortic endothelial cells (HAECs). Our data indicate that preformed cell surface residing protein complexes modulate HDL function and suggest new theragnostic opportunities.

systems biology↗

bioRxiv2021

Protein complex prediction with AlphaFold-Multimer

While the vast majority of well-structured single protein chains can now be predicted to high accuracy due to the recent AlphaFold [1] model, the prediction of multi-chain protein complexes remains a challenge in many cases. In this work, we demonstrate that an AlphaFold model trained specifically for multimeric inputs of known stoichiometry, which we call AlphaFold-Multimer, significantly increases accuracy of predicted multimeric interfaces over input-adapted single-chain AlphaFold while maintaining high intra-chain accuracy. On a benchmark dataset of 17 heterodimer proteins without templates (introduced in [2]) we achieve at least medium accuracy (DockQ [3] [≥] 0.49) on 13 targets and high accuracy (DockQ [≥] 0.8) on 7 targets, compared to 9 targets of at least medium accuracy and 4 of high accuracy for the previous state of the art system (an AlphaFold-based system from [2]). We also predict structures for a large dataset of 4,446 recent protein complexes, from which we score all non-redundant interfaces with low template identity. For heteromeric interfaces we successfully predict the interface (DockQ [≥] 0.23) in 70% of cases, and produce high accuracy predictions (DockQ [≥] 0.8) in 26% of cases, an improvement of +27 and +14 percentage points over the flexible linker modification of AlphaFold [4] respectively. For homomeric inter-faces we successfully predict the interface in 72% of cases, and produce high accuracy predictions in 36% of cases, an improvement of +8 and +7 percentage points respectively.

bioinformatics↗