Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome

Abstract

The extracellular matrix (ECM) protein SNED1 has been shown to promote breast cancer metastasis and control neural crest cell-specific craniofacial development, but the cellular and molecular mechanisms by which it does so remain unknown. ECM proteins exert their functions by binding to cell surface receptors, sequestering growth factors, and interacting with other ECM proteins, actions that can be predicted using knowledge of protein’s sequence, structure and post-translational modifications. Here, we combined in-silico and in-vitro approaches to characterize the physico-chemical properties of SNED1 and infer its putative functions. To do so, we established a mammalian cell system to produce and purify SNED1 and its N-terminal fragment, which contains a NIDO domain. We have determined experimentally SNED1’s potential to be glycosylated, phosphorylated, and incorporated into insoluble ECM produced by cells. In addition, we used biophysical and computational methods to determine the secondary and tertiary structures of SNED1 and its N-terminal fragment. The tentative ab-initio model we built of SNED1 suggests that it is an elongated protein presumably able to bind multiple partners. Using computational predictions, we identified 114 proteins as putative SNED1 interactors. Pathway analysis of the newly-predicted SNED1 interactome further revealed that binding partners of SNED1 contribute to signaling through cell surface receptors, such as integrins, and participate in the regulation of ECM organization and developmental processes. Altogether, we provide a wealth of information on an understudied yet important ECM protein with the potential to decipher its functions in physiology and diseases.

A pan-cancer analysis of matrisome proteins reveals CTHRC1and LOXL2 as major ECM regulators across cancers

“…SNED1 was recently discovered as a ECM glycoprotein whose exact function remains unknown [22,27]. SNED1 knockout mice die perinatally showing significant growth defects [22].…”

“…Our stringent DEG analysis to identify genes that could be potentially regulated by SNED1 in three or more cancers did not yield any candidates of interest. In silico studies predicting possible binding partners of SNED1 have suggested the presence of an RGD and LDV motif in SNED1 could potentially support integrin binding [27]. Interactome studies predict multiple forms of collagen to also be possible binding partners for SNED1 [27], raising the possibility that it could be involved in regulating the assembly and organization of collagen.…”