Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis

Abstract

Highlights d Proteomics define the NSC niche-specific extracellular matrix d Detergent-solubility profiling reveals extracellular matrix architecture d Transglutaminase 2 regulates neurogenesis d Stiffness is increased in the neurogenic niches of the brain

Filling the Gaps – A Call for Comprehensive Analysis of Extracellular Matrix of the Glial Scar in Region- and Injury-Specific Contexts

“…In our investigation of the adult neurogenic niche (Kjell et al, 2020), also using the QDSP protocol, we found that ECM proteins, such as Tn-C, are more soluble compared to the brain parenchyma. Tn-C is also highly soluble in the scar region analyzed by QDSP at 28 dpi here, which is opposite to its insoluble nature in lung injury and atherosclerotic plaques (Schiller et al, 2015;Wierer et al, 2018).…”

“…We also see changes in the solubility of synaptic proteins (e.g., Gria2-3, Olfm3, Glgap1, and Vamp1), while we did not see an obvious change in the solubility of PNN proteins in the scar stage between the genotypes. Our previous QDSP analysis of PNN proteins in the uninjured cerebral cortex had revealed that they are typically not insoluble (in fraction 4), but rather belong to a less detergent resistant category (fractions 2-3; Kjell et al, 2020). Taken together, lack of monocyte invasion affects ECM proteins in a long-term manner toward a state closer to the un-injured contralateral site, thus normalizing the scar ECM.…”

“…We used state-of the-art proteomics (Cox and Mann, 2008;Mann et al, 2013;Cox et al, 2014;Kulak et al, 2014;Tyanova et al, 2016) and the quantitative detergent solubility profile (QDSP) method, in order to also investigate the architecture and composition of the ECM. The QDSP method analyses all the tissue lysates fractions after the tissue has been sequentially processed in increasing strength of detergent (see Supplementary Material or Kjell et al, 2020), with the most detergent-insoluble proteins in a separate fraction (fraction 4 -see Figure 1A). Basically, it is a tissue decellularization that also provides information regarding the intermediates solubilities as proteins are identified and quantified in all (four) fractions using labelfree mass spectrometry.…”

“…However, there may be further aspects of the ECM to be resolved with other sample-separation protocols, including investigations concerning the sugar-chain composition with glycomics or glycoproteomics. Comparative proteome-totranscriptome analysis may yield further insights (Schiller et al, 2015;Angelidis et al, 2019;Kjell et al, 2020), specifically with single-cell RNA sequencing data that may allow identification of the cellular source of specific ECM proteins. For example, our analysis of the adult neurogenic niche shows that quiescent NSCs are by large the main contributor to the ECM composition of this niche (Kjell et al, 2020).…”

The irradiated brain microenvironment supports glioma stemness and survival via astrocyte-derived Transglutaminase 2

“…45 It cross-links fibronectin and has scaffolding functions with integrin β1, both of which are associated with radiation resistance and stemness, 46,47 and has recently been proposed to promote neurogensis from neural stem cells in the adult brain. 48 Its inhibition improved survival in a glioma xenograft model 49 and it has been shown to be a prognostic indicator of shorter time to relapse after chemoradiotherapy. 50 We first confirmed increased expression of TGM2 in matrix from multiple batches of astrocytes from different individuals by western blot (Fig 5B).…”