Evidence for GALNT12 as a moderate penetrance gene for colorectal cancer

Abstract

Characterizing moderate penetrance susceptibility genes is an emerging frontier in colorectal cancer (CRC) research. GALNT12 is a strong candidate CRC-susceptibility gene given previous linkage and association studies, and inactivating somatic and germline alleles in CRC patients. Previously, we found rare segregating germline GALNT12 variants in a clinic-based cohort (N = 118) with predisposition for CRC. Here, we screened a new population-based cohort of incident CRC cases (N = 479) for rare (MAF ≤1%) deleterious germline GALNT12 variants. GALNT12 screening revealed eight rare variants. Two variants were previously described (p.Asp303Asn, p.Arg297Trp), and additionally, we found six other rare variants: five missense (p.His101Gln, p.Ile142Thr, p.Glu239Gln, p.Thr286Met, p.Val290Phe) and one putative splice-altering variant (c.732-8 G>T). Sequencing of population-matched controls (N = 400) revealed higher burden of these variants in CRC cases compared with healthy controls (P = 0.0381). We then functionally characterized the impact of substitutions on GALNT12 enzyme activity using in vitro-derived peptide substrates. Three of the newly identified GALNT12 missense variants (p.His101Gln, p.Ile142Thr, p.Val290Phe) demonstrated a marked loss (>2-fold reduction) of enzymatic activity compared with wild-type (P ≤ 0.05), whereas p.Glu239Gln exhibited a ∼2-fold reduction in activity (P = 0.077). These findings provide strong, independent evidence for the association of GALNT12 defects with CRC-susceptibility; underscoring implications for glycosylation pathway defects in CRC.

New Pathogenic Germline Variants in Very Early Onset and Familial Colorectal Cancer Patients

“…#112;80). This variant has been described several times, and although the role of GALNT12 in familial cancer is controversial, this particular variant most likely confers a moderate risk (Guda et al, 2009;Clarke et al, 2012;Seguí et al, 2014;Lorca et al, 2017;Evans et al, 2018). In EXO1 we identified the c.2212-1G>C variant in two individuals (no.…”

Cosmc overexpression enhances malignancies in human colon cancer

“…We selected 5 types of ppGalNac-Ts (GALNT2, GALNT3, GALNT6, GALNT12, GALNT14), as these ppGalNac-Ts have been reported to be closely associated with CRC. [27][28][29][30][31] Our analysis did not detect obvious differences in the mRNA levels of these ppGalNAc-Ts between Cosmc-overexpressing cells and the control cells ( Figure 4C). Collectively, these results suggested that aberrant O-glycosylation is unlikely the cause for Cosmc overexpression-mediated oncogenic alterations.…”

The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function

“…The di-glycosylated peptide sequence (Fig. 1 B ) is based on a previously optimized GalNAc-T12 peptide, T12_Pep (17), containing residues that uniquely enhance GalNAc-T12 activity, including Tyr at positions −3 and −2 (Y11 and Y12) N-terminal to the acceptor Thr at position 14 (T14) ( SI Appendix , Fig. S1 A ) and Arg at position +2 (R16) C-terminal to T14 (20, 23).…”

“…However, its expression is diminished in colon cancer cell lines and tissues from patients with CRC (15). Over the last decade, several studies in patients with CRC have led to the characterization of somatic and germ line mutations that reduce the in vitro enzymatic activity of GalNAc-T12 (16–18). Many mutations occur in conserved residues, while a distinct subset alters nonconserved residues, suggesting the presence of GalNAc-T12–specific features ( SI Appendix , Table S1).…”