MSc Thesis Presentation by Asimenia Giagli titled: “A Reproducible Pipeline for Prioritizing Antibody-Accessible Cell-Surface Targets from Single-Cell Transcriptomic Data”

Abstract:
Cell-surface proteins are promising candidates for antibody-based therapies, but their prioritization from transcriptomic data requires more than differential expression alone. This thesis developed a reproducible computational workflow to identify biologically plausible, antibody-accessible surface proteins from single-cell RNA-sequencing data. The workflow was implemented as a modular Nextflow pipeline integrating single-cell preprocessing, cell-type annotation, donor-level pseudobulk differential expression, UniProt protein mapping, transmembrane-topology prediction, GTEx-based normal-tissue filtering, and external validation. It was evaluated using a human cutaneous squamous cell carcinoma dataset containing tumour and matched normal skin samples. Differential expression was performed within annotated cell populations to retain cellular context. Tumour-upregulated genes were mapped to human membrane proteins, filtered for predicted single-pass Type I or Type II topology with sufficient extracellular domains, and screened for low expression in selected vital tissues using GTEx. This progressively reduced the candidate space to a smaller set of cell-type-specific proteins. Validation included comparison with antibody-related IEDB antigens, therapeutic-target annotations, and extracellular-domain BepiPred predictions. The final candidates represent computational priorities rather than validated therapeutic targets and require experimental confirmation of protein expression, surface localization, antibody binding, functional relevance, and normal-tissue safety. Overall, the framework provides a transparent approach for narrowing transcriptomic data toward experimentally testable cell-surface therapeutic candidates.

Date/Time: 16/10/2026 – 13:30 PM
Examination Committee:
Theodore Dalamagas, Research Director, ATHENA Research Center
Dimitrios Stravopodis, Associate Professor, Department of Biology, National and Kapodistrian University of Athens
Eleni Christodoulou, Scientific Associate, ATHENA Research Center

Teams link: https://teams.microsoft.com/meet/362275300616504?p=SX5AkcQxcBxmfu4aOl