Abstract
Various pathologies result from disruptions to or stress of endoplasmic reticulum (ER) homeostasis, such as Parkinson's disease and most neurodegenerative illnesses, diabetes, pulmonary fibrosis, viral infections, and cancers. A critical process in maintaining ER homeostasis is the selection of misfolded proteins by the ER quality-control system for destruction via ER-associated degradation (ERAD). One key protein proposed to act during the first steps of misfolded glycoprotein degradation is the ER degradation–enhancing α-mannosidase-like protein 2 (EDEM2). Therefore, characterization of the EDEM2-associated proteome is of great interest. We took advantage of using melanoma cells overexpressing EDEM2 as a cancer model system, to start documenting at the deglycoproteome level (N-glycosites identification) the emerging link between ER homeostasis and cancer progression. The dataset created for identifying the EDEM2 glyco clients carrying high mannose/hybrid N-glycans provides a comprehensive N-glycosite analysis mapping over 1000 N-glycosites on more than 600 melanoma glycoproteins. To identify EDEM2-associated proteins, we used affinity proteomics and proteome-wide analysis of sucrose density fractionation in an integrative workflow. Using intensity and spectral count–based quantification, we identify seven new EDEM2 partners, all of which are involved in ER quality-control system and ERAD. Moreover, we defined novel endogenous candidates for EDEM2-dependent ERAD by combining deglycoproteomics, stable isotope labeling with amino acids in cell culture–based proteomics, and biochemical methods. These included tumor antigens and several ER-transiting endogenous melanoma proteins, including integrin alpha-1 and protocadherin 2, the expression of which was negatively correlated with that of EDEM2. Tumor antigens are key in the antigen presentation process, whereas integrin alpha-1 and protocadherin 2 are involved in melanoma metastasis and invasion. EDEM2 could therefore have a regulatory role in melanoma through the modulation of degradation and trafficking in these glycoproteins. The data presented herein suggest that EDEM2 is involved in ER homeostasis to a greater extent than previously suggested.
Highlights
IntroductionWe defined novel endogenous candidates for endoplasmic reticulum (ER) degradation–enhancing α-mannosidase-like protein 2 (EDEM2)-dependent ER-associated degradation (ERAD) by combining deglycoproteomics, stable isotope labeling with amino acids in cell culture–based proteomics, and biochemical methods
endoplasmic reticulum (ER) degradation–enhancing α-mannosidase-like protein 2 (EDEM2) affinity proteomics and proteome-wide analysis of sucrose density fractionation. New ER degradation–enhancing α-mannosidase-like protein 2 (EDEM2) partners involved in ER quality control and ER-associated degradation (ERAD). Soluble tyrosinase degradation is EDEM2 dependent in melanoma cells. Glycoproteomics and SILAC-based proteomics reveal novel EDEM2 potential substrates
Some of the candidates were validated using pulse stable isotope labeling with amino acids in cell culture proteomics, Western blot (WB), and confocal microscopy
Summary
We defined novel endogenous candidates for EDEM2-dependent ERAD by combining deglycoproteomics, stable isotope labeling with amino acids in cell culture–based proteomics, and biochemical methods. These included tumor antigens and several ER-transiting endogenous melanoma proteins, including integrin alpha-1 and protocadherin 2, the expression of which was negatively correlated with that of EDEM2. Initial investigations indicated that EDEM2 does not possess mannosidase activity and cannot recognize nonglycosylated versions of canonical ERAD substrates, subsequent reports challenged these aspects, suggesting that this protein is involved in gpERAD by trimming Man to Man glycoforms [9, 12, 13, 15] These point to a more complex landscape in EDEM2 partner recognition and selection.
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