Methods of Identifying Novel Proteins and Antigens in Cancer Cells

OVERVIEW

Neoantigens are mainly tumor-specific antigens generated by mutations in tumor cells and are only expressed in tumor cells. Despite the increasing interest in clinical interventions targeting neoantigens, substantial challenges remain to enable a more precise identification of neoantigens that are relevant for patient treatment. Georgetown researchers have developed novel methods of identifying neoantigens or potential neoantigens. The method involves sequencing of isolated long-read messenger RNA (mRNA) through Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing.

BACKGROUND

Neoantigens have become compelling targets for cancer immunotherapy due to high levels of immunogenicity and have also been shown to be effective in immune checkpoint blockade therapy. Therefore, neoantigens may serve as predictive biomarkers and synergistic treatment targets in cancer immunotherapy. Neoantigen candidate selection and identification usually rely on the spectra of somatic mutations identified by whole-exome sequencing (WES) coupled with RNA-seq. This approach suffers from a lack of direct experimental evidence of the real presence of predicted epitopes on the cell surface. Georgetown researchers developed methods of identifying neopeptides in abnormal cells, by sequencing isolated long-read messenger RNA (mRNA) through Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing.

Benefit

• Does not require sequencing of economic DNA
• Allows for the detection of mutations in RNA transcripts
• Uncovers neo-epitopes that would be missed by short-read RNA sequencing

Market Application

• Cancer therapies with immune checkpoint inhibitors
• Diagnostics in cancer
• Selection of patients for immune checkpoint inhibitor sensitivity and/or resistance

Publications

• US patent No. 16/322,824
• Full-length, single-cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity (DOI: https://doi.org/10.1101/2021.07.28.454226) (link: https://www.biorxiv.org/content/10.1101/2021.07.28.454226v2)
• Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations (DOI: https://doi.org/10.3390/genes10040253) (link: https://www.mdpi.com/2073-4425/10/4/253)