Our knowledge of the O-glycoproteome [N-acetylgalactosamine (GalNAc) type] is highly limited. The O-glycoproteome is differentially regulated in cells by dynamic expression of a subset of 20 polypeptide GalNAc-transferases (GalNAc-Ts), and methods to identify important functions of individual GalNAc-Ts are largely unavailable. We recently introduced SimpleCells, i.e., human cell lines made deficient in O-glycan extension by zinc finger nuclease targeting of a key gene in Oglycan elongation (Cosmc), which allows for proteome-wide discovery of O-glycoproteins. Here we have extended the SimpleCell concept to include proteome-wide discovery of unique functions of individual GalNAc-Ts. We used the GalNAc-T2 isoform implicated in dyslipidemia and the human HepG2 liver cell line to demonstrate unique functions of this isoform. We confirm that GalNAc-T2-directed site-specific Oglycosylation inhibits proprotein activation of the lipase inhibitor ANGPTL3 in HepG2 cells and further identify eight O-glycoproteins exclusively glycosylated by T2 of which one, ApoC-III, is implicated in dyslipidemia. Our study supports an essential role for GalNAc-T2 in lipid metabolism, provides serum biomarkers for GalNAc-T2 enzyme function, and validates the use of GALNT gene targeting with SimpleCells for broad discovery of disease-causing deficiencies in O-glycosylation. The presented glycoengineering strategy opens the way for proteome-wide discovery of functions of GalNAc-T isoforms and their role in congenital diseases and disorders.apolipoproteins | angiopoietin-like proteins | genetic engineering | glycoproteins T he GALNT2 gene involved in O-glycosylation has been associated with aberrant serum levels of triglyceride (TG) and highdensity lipoprotein cholesterol (HDL-C) by several genome-wide association studies (GWAS) (1, 2). A direct functional role of this gene was obtained by transient knockdown and overexpression of galnt2 in mouse liver, which resulted in increased and lowered plasma HDL-C, respectively (3). GALNT2 is a member of the largest family of homologous glycosyltransferase isoforms (up to 20) catalyzing the same glycosidic linkage (GalNAcα1-O-Ser/Thr) and initiating protein O-glycosylation (4, 5). These isoforms have overlapping but distinct peptide substrate specificities and identifying essential unique functions for individual GalNAc-T isoforms has been notoriously difficult. In search of putative functions of GALNT2 in lipid metabolism, we previously screened a number of known and predicted O-glycoproteins with roles in lipid metabolism for O-glycosylation by the encoded GalNAc-T2 enzyme and identified ANGPTL3 (6). We found that site-specific O-glycosylation of a Thr residue adjacent to the proprotein convertase (PC) processing site in ANGPTL3 that activates this lipase inhibitor was performed only by the GalNAc-T2 isoform. More recently, a heterozygous mutation in GALNT2 resulting in slightly reduced kinetic properties of the encoded GalNAc-T2 enzyme was found in two probands with elevated HDL and reduced TG (7). ...