Integrated transcriptomic and proteomic validation identifies SLC35D3 as a tumor-selective surface antigen for colorectal and neuroendocrine carcinomas.

Antibody-drug conjugates (ADCs), bispecific T-cell engagers (TCEs), and chimeric antigen receptor (CAR)-T cells require truly tumor-restricted surface antigens to minimize on-target/off-tumor toxicity. To identify such antigens, we interrogated two complementary RNA-seq resources: (i) the Genotype-Tissue Expression (GTEx) atlas spanning diverse normal tissues and (ii) the Cancer Genome Atlas colon adenocarcinoma cohort (TCGA-COAD). Candidate membrane-protein transcripts were defined by low median GTEx expression (<1 RPKM across all normal tissues) and marked upregulation (≥10-fold) in TCGA colon tumors. Only two genes met these stringent criteria, with the little-studied nucleotide-sugar transporter SLC35D3 emerging as the leading candidate. Pan-cancer analysis of the TCGA datasets confirmed its selective enrichment in colorectal carcinoma and in pheochromocytoma/paraganglioma, while GTEx data showed near-background expression in essential organs including brain, heart, liver, lung, and kidney. Protein-level validation with immunohistochemistry on > 250 tissue-microarray cores revealed SLC35D3 positivity in 53% of colorectal cancers, 40% of small-cell lung cancers, and 24% of pancreatic neuroendocrine tumors, whereas vital normal organs were uniformly negative. Although SLC35D3 has been annotated as mainly localized to the endoplasmic reticulum and early endosomes, our analyses revealed its presence on the plasma membrane, which was corroborated by flow cytometry in SLC35D3 mRNA-positive cancer cell lines but not in negative control. Taken together, these transcriptomic and proteomic findings establish SLC35D3 as a tumor-selective surface antigen broadly represented in aggressive malignancies yet virtually absent from critical normal tissues, highlighting it as a promising new candidate for next-generation ADCs, TCEs, and CAR-T therapies in colorectal and neuroendocrine carcinomas.