A glycomics and proteomics study of aging and Parkinson’s disease in human brain

Abstract

previous studies on parkinson's disease mechanisms have shown dysregulated extracellular transport of α-synuclein and growth factors in the extracellular space. In the human brain these consist of perineuronal nets, interstitial matrices, and basement membranes, each composed of a set of collagens, non-collagenous glycoproteins, proteoglycans, and hyaluronan. The manner by which amyloidogenic proteins spread extracellularly, become seeded, oligomerize, and are taken up by cells, depends on intricate interactions with extracellular matrix molecules. We sought to assess the alterations to structure of glycosaminoglycans and proteins that occur in pD brain relative to controls of similar age. We found that PD differs markedly from normal brain in upregulation of extracellular matrix structural components including collagens, proteoglycans and glycosaminoglycan binding molecules. We also observed that levels of hemoglobin chains, possibly related to defects in iron metabolism, were enriched in PD brains. These findings shed important new light on disease processes that occur in association with pD. The volume of the extracellular space (~ 20%) that separates brain cell surfaces and through which molecules diffuse displays regional patterns that change during development, aging and neurodegeneration 1,2. The passage of protein molecules through the extracellular space depends on the geometries and chemical compositions of extracellular and cell surface molecular complexes, the specific binding domains thereof, and the fixed negative charges of glycosaminoglycan chains 3,4. Brain extracellular matrix (ECM) is composed of perineuronal nets (PNNs), interstitial matrices, and basement membranes (blood brain barrier), each consisting of a network of glycoproteins, proteoglycans, hyaluronan and collagens 5. Despite the obvious importance of the extracellular space to neural plasticity and neurodegeneration 6,7 , there is little information available on the alterations that occur to these molecules during Parkinson's disease (PD). Inflammation and disruption of the blood brain barrier can lead to infiltration of fibroblasts and trigger a fibrotic response in an attempt to restore normal function 8. Such fibrosis demolishes the structure of the ECM, and impedes healing by secreting inhibitory molecules and serves as a barrier to axons. Infiltration of fibroblasts leads to deposition of thrombin and fibrinogen and destruction of the integrity of the ECM. These inflammatory reactions lead to local neural degeneration and activation of glial cells. In PD, the activation of glial cells and recruitment of T-cells leads to increased pro-inflammatory cytokine release and increased levels of reactive oxygen and nitrogen species. While disruption is not believed to occur, activated microglia appear to induce blood brain barrier dysfunction in PD 9. Despite this, limited information is available concerning the changes in the distribution of ECM molecules in PD, with the exception of glycosaminoglycans (GAGs) found in senile plaques and...

Bioinformatic analysis of the human brain extracellular matrix proteome in neurodegenerative disorders

“…To overcome these difficulties, new methodological approaches should be developed. For example, Raghunathan and colleagues tested a new protocol for slicing brain tissue followed by digestion without prior homogenization, resulting in a ratio of ECM proteins to total identified proteins of 17%, which is closer to the 20% ECM ratio described on the central nervous system (Raghunathan et al, 2020). Similarly, a prior decellularization step to enrich samples for ECM components (Dequach et al, 2011;Lindsey et al, 2016), combined with improved and better tailored protocols for sample preparation toward F I G U R E 7 Network representation of the GO biological processes groups, built upon the ECM proteins altered in Parkinson's disease, exclusively.…”

“…samples (Ratovitski et al, 2016), whereas in Alzheimer's and Parkinson's diseases, it was upregulated (Minjarez et al, 2016;Raghunathan et al, 2020).…”

“…Their role in neuroprotection arises not only from the anti-apoptotic function exhibited by some components (Morawski et al 2004) but also because they can participate in ECM remodeling during tissue repair (i.e., tenascin C (Jones & Bouvier, 2014)). Tenascin C was found to be upregulated in Parkinson's disease in the studies collected (Raghunathan et al 2020). However, in the postmortem tissues of Alzheimer's disease patients, it has been found both upregulated (in the hippocampus, Hondius et al 2016, in the entorhinal cortex, caudate nucleus, amygdala, andthalamus, McKetney et al 2019) and downregulated (in the inferior parietal lobule, middle frontal gyrus, and superior temporal gyrus, McKetney et al 2019).…”

“…Noteworthy, the work published by Raghunathan et al (2020) showed the highest percentage of ECM-altered proteins relative to the total proteins identified (17%). Interestingly, they did not use common methods for protein extraction and solubilization.…”

“…region (Andreev et al, 2012;Bai et al, 2013;Hashimoto et al, 2012;Liao et al, 2004;Licker et al, 2014;McKetney et al, 2019;Raghunathan et al, 2020;Ratovitski et al, 2016). To better appreciate these findings, we created a Cytoscape network representing groups of proteins by brain region.…”