The new computational platform could expand the range of targets for cancer immunotherapy

Researchers at the Children’s Hospital of Philadelphia (CHOP) and the University of California, Los Angeles (UCLA) have developed a computational platform capable of tumor detection. antigens It is derived from alternative RNA splicing, which expands the range of targets for cancer immunotherapy. The tool, called “Isoform peptides from RNA splicing for Immunotherapy target Screening” (IRIS), is described in research published today in Proceedings of the National Academy of Sciences.

Immunotherapy has revolutionized cancer treatment, but for many cancers including pediatric cancers, the antigen stock is incomplete, underlining the need to expand the stock of actionable immunotherapy targets. We know that aberrant alternative splicing of RNA is upregulated in cancer and generates a range of potential immunotherapy targets. In our study, we were able to show that our computational platform was able to identify immunotherapy targets that arise from alternative splicing, and provide a broadly applicable framework for the discovery of new targets for cancer immunotherapy that arise from this process. “

Yi Xing, PhD, co-author, director of the Center for Computational Medicine and Genomics at CHOP

Cancer immunotherapy has fundamentally changed the treatment of many blood cancers, harnessing the power of a patient’s immune system to fight the disease. Chimeric antigen receptor T-cell (CAR-T) and T-cell therapies engineered with T-cell receptor (TCR-T) modulate patient-specific therapies. T cells They attack known antigens on the surface of cancer cells and have often triggered lasting responses in cancers that were once considered incurable. However, the field has been challenged in the solid tumor space, in large part due to the lack of known, suitable targets for these cancers, highlighting the need for novel approaches to expand the range of immunotherapy targets.

Alternative splicing is a fundamental process that allows a single gene to encode several gene products, based on where the RNA is cut and joined, or spliced, before it is translated into proteins. However, the splicing process is unregulated in cancer cells, which often take advantage of this process to produce proteins that promote growth and survival, allowing them to multiply uncontrollably and spread. This occurs in many adult and pediatric cancers. Scientists have suggested that splicing irregularities could be a source of new tumor antigens for immunotherapy, but identifying these antigens has been challenging.

To address this difficulty, the researchers created IRIS to take advantage of extensive tumor sequencing data and normal RNA and integrate multiple screening approaches to discover tumor antigens that arise due to alternative splicing. By integrating RNA-sequencing-based transcriptome data and mass spectrometry-based proteomics data, the researchers showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules, a part of the human immune system that presents T-cell antigens. .

The researchers then applied IRIS to RNA-sequencing data from neuroendocrine prostate cancer (NEPC), a metastatic and highly lethal disease known to involve mutations in RNA splicing, as discovered in an earlier study by CHOP and UCLA researchers. Among the 2,939 alternative splicing events enriched in NEPC, IRIS predicted 1,651 peptides as potential TCR targets. The researchers then applied a more rigorous screening test, which prioritized 48 potential targets. Interestingly, the researchers found that these targets were very rich in peptides encoded by short sequences of less than 30 nucleotides in length – also known as ‘microexons’ – that may arise from a unique program of dysregulation in this type of cancer.

To check the immunogenicity of these targets, the researchers isolated T cells that interact with targets predicted by IRIS, and then used single-cell sequencing to determine the TCR sequence. The researchers modified human peripheral blood mononuclear cells with seven TCRs and found that they were highly reactive against targets predicted by IRIS to be good candidates for immunotherapy. One TCR was particularly effective in killing cancer cells that expressed the target peptide.

Owen N. Witt, MD, an undergraduate professor of microbiology, immunology and molecular genetics and a member of the Eli and Edythe Center for Regenerative Medicine and Stem Cell Research at UCLA, said Owen. “Discovering new antigenic targets that can be shared among different patients — and even different types of tumors — could be useful in expanding the value of cell-based therapies. Analyzing huge amounts of data about tumor and normal tissues, which requires sophisticated computational tools like the one developed by Xing Lab, providing actionable insights into targets that could one day be tested in the clinic.”

“This proof-of-concept study demonstrates that alternatively spliced ​​RNA transcripts are viable targets for cancer immunotherapy and provides a massive database and computational platform supported by multimodal science to find these targets,” added Dr. Xing. “We are applying IRIS for target discovery across a wide range of pediatric and adult cancers. We are also developing a next-generation IRIS platform that harnesses modern transcription technologies, such as long read and single-cell analysis.”

This research was supported in part by the Immuno-Oncology Translational Network (IOTN) of the National Cancer Institute’s Cancer Moonshot Initiative, funding from other National Institutes of Health, Parker Institute for Cancer Immunotherapy, Institute for Cancer Research, and Ressler Family Fund.