Abstract
Immune-based cancer therapies such as checkpoint inhibitors (CPI) and vaccines have been increasingly studied across different cancer types. Response to such therapies depends on a number of factors such as mutational burden, neoantigen load, presence of tumor infiltrating lymphocytes, among others. Next-generation sequencing (NGS) technologies are particularly attractive to interrogate the immune response compared to traditional assays such as qRT-PCR and immunohistochemistry (IHC) because they enable the discovery of neoantigens and simultaneous profiling of immune infiltration using gene expression on a large scale. Current approaches in immune profiling utilizes whole-exome sequencing (WES) for human leukocyte allele (HLA) typing and neoantigen predictions, and RNA sequencing (RNA-seq) for filtering unexpressed neoantigens and inferring immune infiltration. They have been successfully applied to the tumor setting as there is abundant sample material to perform both experiments. However, premalignant specimens are often much smaller compared to tumors. Therefore, there is a need to explore the viability of adopting a single approach for immune, neoantigen, and mutation profiling. Here, we describe our workflow of using RNA-seq to analyze mutational burden, neoantigen load, and immune expression profile.
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Abbreviations
- CPI:
-
Checkpoint inhibitors
- CRC:
-
Colorectal cancer
- FAP:
-
Familial Adenomatous Polyposis
- FSP:
-
Frameshift peptides
- GEO:
-
Gene Expression Omnibus
- HLA:
-
Human leukocyte typing
- IHC:
-
Immunohistochemistry
- LS:
-
Lynch syndrome
- MHC:
-
Major histocompatibility complex
- MMR:
-
Mismatch repair
- MS:
-
Microsatellite
- MSigDB:
-
Molecular Signatures Database
- NGS:
-
Next-generation sequencing
- RNA-seq:
-
RNA sequencing
- TCGA:
-
The Cancer Genome Atlas
- TCR:
-
T-cell receptor
- TPM:
-
Transcripts per million
- WES:
-
Whole-exome sequencing
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Acknowledgments
This work was supported by grants R21 CA208461 and R01 CA219463 (US National Institutes of Health/National Cancer Institute), The University of Texas MD Anderson Cancer Center Colorectal Cancer Moonshot Program, and a gift from the Feinberg Family to E.V.; Cancer Prevention Educational Award R25T CA057730 (U.S. National Institutes of Health/National Cancer Institute) to K.C.; and P30 CA016672 (US National Institutes of Health/National Cancer Institute) to the University of Texas Anderson Cancer Center Core Support Grant.
Conflict of Interest: Dr. Vilar has a consulting or advisory role with Janssen Research and Development and Recursion Pharma. He has received research support from Janssen Research and Development.
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Chang, K., McAllister, F., Vilar, E. (2022). Transcriptomic-Assisted Immune and Neoantigen Profiling in Premalignancy. In: McAllister, F. (eds) Cancer Immunoprevention. Methods in Molecular Biology, vol 2435. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2014-4_7
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DOI: https://doi.org/10.1007/978-1-0716-2014-4_7
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