Cancer Antigen Discovery Is Enabled by RNA Sequencing of Highly Purified Malignant and Nonmalignant Cells

Area of Science:

• Oncology
• Immunology
• Genomics

Background:

• Broadly expressed tumor-associated antigens (TAAs) can induce antitumor immunity, but vaccine development has faced challenges due to poor antigen selection and immunosuppressive tumor microenvironments.
• Previous methods for TAA identification often involved sequencing whole tumor samples, potentially obscuring crucial tumor-specific antigens.

Purpose of the Study:

• To identify novel, broadly expressed colorectal TAAs by employing highly purified tumor cells for RNA sequencing.
• To evaluate the protein expression and T-cell immunogenicity of candidate TAAs.
• To identify promising TAAs for future cancer immunotherapy development.

Main Methods:

• RNA sequencing was performed on highly purified colorectal tumor cells and patient-matched colonic epithelial cells.
• Immunohistochemistry (IHC) was used to confirm candidate TAA protein expression.
• Preexisting T-cell responses to candidate TAAs were assessed in patients with cancer.

Main Results:

• A panel of novel, widely expressed colorectal TAAs was identified through purification and sequencing of tumor cells.
• DNAJB7 (DnaJ heat shock protein family (Hsp40) member B7) was identified as a novel cancer-testis antigen with broad tumor expression and strong immunogenicity.
• DNAJB7-specific T cells demonstrated in vitro killing of colorectal tumor lines, with enhanced responses when immunosuppression was controlled.

Conclusions:

• Purification of tumor cells before genetic sequencing is crucial for identifying novel TAAs, overcoming limitations of whole-tumor fraction analysis.
• DNAJB7 represents a promising candidate for the development of novel immunotherapies targeting a variety of cancers.
• Targeting identified TAAs, particularly DNAJB7, holds potential for advancing cancer vaccine strategies.