SLITRK6 (SLIT and NTRK-like protein 6) is a monomeric transmembrane protein
belonging to the SLITRK family, members of which are characterized by leucine-rich repeat
(LRR) domains and are predominantly associated with nervous system function. SLITRK6
plays a key role in synaptogenesis and is primarily expressed in the central nervous system.
In addition to its neurological role, SLITRK6 has been implicated in carcinogenesis.
Elevated mRNA expression has been reported in colorectal cancer, and a similar
upregulation at both the mRNA and protein levels has been observed in bladder cancer. In
hepatocellular carcinoma, SLITRK6 has been shown to promote carcinogenesis, with its
function modulated by acquired nucleotide variants. An association between SLITRK6
expression and the development of lung adenocarcinoma has also been described. Based on
unpublished deglycosylation data, we established that SLITRK6 is a glycoprotein. This
prompted us to investigate whether glycosylation plays a functional role in SLITRK6-
associated carcinogenesis, and whether the glycosylation pattern is influenced by variants
frequently occurring in cancer tissue. Potential N- and O-glycosylation sites were predicted
across the SLITRK6 amino acid sequence using multiple tools and further evaluated based
on the local quality of the protein structural model. Using Sanger sequencing, we determined
SLITRK6 sequences from formalin-fixed, paraffin-embedded (FFPE) tissue samples from 42
colorectal cancer patients and 8 prostate cancer patients. A total of 21 candidate variants
potentially affecting SLITRK6 structure and glycosylation were identified. Subsequent
analysis using alignment and pathogenicity prediction tools, together with cross-referencing
against the Ensembl, COSMIC, ClinVar, and TCGA databases, yielded 10 candidate
missense variants, three of which were predicted to be pathogenic: c.1670T>A, c.665G>T,
and c.485T>C. The impact of these variants on protein structure and glycosylation patterns
was assessed. Although no direct effect on glycosylation was confirmed, analysis of the
SLITRK6 model revealed that several variants introduce steric clashes within the protein
structure or lead to the formation of a premature stop codon. Variant c.665G>T, previously
reported in lung adenocarcinoma tissue, was validated and subsequently submitted to the
COSMIC database. Additionally, we identified variants in other cancer types from the
COSMIC database that may potentially influence the glycosylation status of SLITRK6.
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