Multi-database transcriptomic screening to identify subtype-selective cell surface targets for development of SNAP-tag based immunotherapeutics
*Correspondence to:
Stefan Barth, Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7700, Western Cape, South Africa; Centre for the Development of Cancer Therapeutics for Africa (CDCTA), Faculty of Health sciences, University of Cape Town 7700, Western Cape, South Africa.
E-mail: stefan.barth@uct.ac.za
Comput Biomed. 2026;1:202615. 10.70401/cbm.2026.0023
Received: April 23, 2026Accepted: August 06, 2026Published: August 06, 2026
This article belongs to the Special lssue Applications of Bioinformatics in Precision Medicine and Translational Healthcare
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Abstract
Aims: Cervical cancer is the second most common cancer globally in women of reproductive age. Current immunotherapies have been shown to provide a moderate improvement in overall patient survival for people with metastatic or refractory cervical cancer, demonstrating the need for patient-directed and efficacious immunotherapy methods for improving patient outcomes.
Methods: The described study uses a unified pipeline that reprocessed all the cancer genome atlas (TCGA) and genotype tissue expression (GTEx) samples from raw reads using identical alignment and quantification parameters to screen a curated set of 259 high-confidence surface protein genes. This analysis provided the foundation for selecting differentially overexpressed cell surface receptors as potential therapeutic targets for antibody-drug conjugates. Recombinant antibody fragment (single chain antibody fragment (scFv))-O6-alkylguanine-DNA alkyltransferase (SNAP) fusion proteins were expressed, then purified and characterised using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. The dose-dependent and selective cytotoxicity of an auristatin F-conjugated (scFv)-SNAP fusion protein was verified in vitro.
Results: Bioinformatic screening of high-confidence surface proteins revealed 30 potential targets overexpressed in cervical carcinoma (cervical adenocarcinoma and squamous carcinoma (CESC)) vs. healthy tissues. Tissue-of-origin analysis (endocervix vs. ectocervix) further refined priorities. These results, together with supporting evidence from the literature, justified drug production. The bioinformatic findings translated well in vitro. The (scFv)-SNAP fusion proteins exhibited strong surface binding across cervical cancer cell lines and, when conjugated to auristatin F, showed dose-dependent cytotoxicity at nanomolar concentrations, confirming the differences observed in transcriptomic analyses of endo- vs ectocervix profiling.
Conclusion: In conclusion, bioinformatics and in vitro validation synergize powerfully from initial screening through subtype refinement to iterative target confirmation, enabling a precision medicine approach for cervical cancer-specific immunotherapies. (scFv)-SNAP-auristatin F antibody-drug conjugate (ADC) conjugates have reproduced this refinement, showing highly promising potential.
Keywords
Cervical cancer, surfaceome screening, tissue-of-origin, SNAP-tag, immunotherapy, tumour heterogeneity, endocervix, ectocervix
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Matshoba T, Bolotnikov V, Henry M, Lekena N, Hunter R, Barth S. Multi-database transcriptomic screening to identify subtype-selective cell surface targets for development of SNAP-tag based immunotherapeutics. Comput Biomed. 2026;1:202615. https://doi.org/10.70401/cbm.2026.0023
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Matshoba T, Bolotnikov V, Henry M, Lekena N, Hunter R, Barth S. Multi-database transcriptomic screening to identify subtype-selective cell surface targets for development of SNAP-tag based immunotherapeutics. Comput Biomed. 2026;1:202615. https://doi.org/10.70401/cbm.2026.0023
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