Boyle, Sean M.

Abstract Background: Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of patients with deficient DNA mismatch repair (d-MMR) cancers, yet less than half of patients with metastatic colorectal cancer (mCRC) receive clinical benefit. We analyzed heterogeneity within d-MMR tumors using a multi-omics approach inclusive of percent unstable microsatellite loci (MS). Methods: We studied consecutive patients with d-MMR mCRC with available primary tumors (N=32) that were treated with an anti-PD-1 antibody at Mayo Clinic (2015-2022). Tumors were profiled using a whole exome and transcriptome platform (ImmunoID NeXT®). MSIsensor was used to calculate percent unstable microsatellite loci from whole exome sequencing data. CIBERSORT and ssGSEA were used to analyze immune gene expression in relationship to percent unstable microsatellite loci. An immune checkpoint gene expression signature was calculated as the mean expression of CD274, CTLA-4, HAVCR2, LAG-3, PDCD1, PDCD1LG2, TIGIT. Aforementioned variables were analyzed in relationship to objective tumor response (RECIST version 1.1). A Cox proportional hazards model was fit to predict progression-free survival (PFS). Results: Among 32 patients with d-MMR mCRC treated with PD-1 blockade, 16 (50%) received first-line anti-PD-1 therapy; others had > 1 prior chemotherapy regimen. Eighteen (56.3%) tumors harbored BRAFV600E, 4 (12.5%) had mutant KRAS, and median PFS was 24.6 months (95% CI: 8.4, NR) with 18 events. Neither tumor mutation burden (TMB) nor PD-L1 mRNA expression predicted PFS. Median percent unstable MS loci was 14.38 (IQR: 2.6-23.2). Patients whose tumors had higher percent unstable MS loci had significantly better PFS (Q2-4 vs Q1; HR: 0.22, 95%CI: 0.06, 0.62; P=0.003), and were associated with increased objective response (P=0.049). Tumors with higher unstable loci also had higher neoantigen clonality (R= 0.64; P= 0.0003) and increased M0 (resting) macrophages (P=0.02). Nonresponders (vs responders) to PD-1 blockade had an increased immune checkpoint expression signature (P= 0.005). Conclusion: A higher percentage of unstable microsatellite loci, associated with higher neoantigen clonality and resting macrophages, was predictive of anti-PD-1 efficacy. Furthermore, an immune checkpoint gene expression signature was associated with objective response. Citation Format: Bahar Saberzadeh-Ardestani, Oluwadunni E. Emiloju, Rondell P. Graham, Jason T. Lewis, Charles W. Abbott, Sean M. Boyle, Frank A. Sinicrope. Prediction of PD-1 treatment outcome in mismatch repair deficient metastatic colorectal cancer using a multi-omic approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 578.

Abstract Next-generation sequencing is now commonly applied to measure genomic modifications, providing the opportunity for a more accurate view of cancer progression. That being said, several challenges including tumor purity, heterogeneity and the broad set of cancer associated cellular functions, increase the difficulty of interpreting cancer genomes and make analyzing them distinct from analysis of germline diseases. The ability to detect low allelic mutations in the broad set of cancer-associated genes is critically important. To address these issues, we developed an extended cancer panel, a targeted enrichment sequencing platform that includes over 1,300 cancer genes and 200 miRNAs that improves coverage in traditionally difficult to sequence NGS regions. In this study, we apply an integrated RNA/DNA analysis approach as well as our extended cancer panel to explore mutations in metastatic renal cell carcinoma (RCC) tissue samples before and after treatment. Our goal with this study was to test the importance of integrating DNA and RNA analysis, which allows for detection of mutational events that cannot be observed by either method alone. With RNA analysis it is possible to detect gene fusion events, expression of small variants (SNVs/indels), and gene expression levels while DNA analysis allows for detection of loss of heterozygosity (LOH), copy number variants (CNVs), and small variants. By integrating both the RNA and DNA analysis, it is possible to identify unique variant classes, such as unexpressed variants, allele specific expression (ASE), effects of CNVs on gene expression levels, and how fusion gene integration sites affect CNVs. In our study, each variant class was interpreted pre- and post-treatment, allowing for optimal analysis of treatment effectiveness. By applying both our RNA/DNA integration approach and our extended cancer panel to investigate metastatic RCC samples, we were able to classify many genomic alterations that drive cancer progression. For example, we found that anywhere from 5% to 30% of small variant mutations in driver genes called in the DNA reside in genes that are unexpressed in the RNA. Likewise, we noted multiple cases of ASE, where high profile variants observed in DNA were entirely absent in the RNA despite high expression levels. Strong correlations between CNVs observed in DNA and gene expression changes found in RNA were also detected. We also observed that about half of the RCC samples we tested were biallelic for VHL mutations, suggesting inherited predisposition combined with second hit somatic mutations, facilitating cancer progression. This analysis demonstrates how combining an integrated RNA/DNA approach with a cancer focused augmented enrichment panel allows for detection of both low allelic representation variants and unique variant classes, both of which are critical for accurate interpretation of cancer samples. Citation Format: Sean M. Boyle, Michael J. Clark, Elena Helman, Alexander S. Parker, Thai Ho, Shujun Luo, Scott Kirk, Parin Sripakdeevong, Mirian Karbelashvili, Deanna M. Church, Michael Snyder, John West, Rich Chen. Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3899. doi:10.1158/1538-7445.AM2015-3899