Cancer Res Treat.  2021 Jan;53(1):123-130. 10.4143/crt.2020.559.

Clinical Application of Targeted Deep Sequencing in Metastatic Colorectal Cancer Patients: Actionable Genomic Alteration in K-MASTER Project

• Lee Y
• Lee S
• Sung JS
• Chung HJ
• Lim Ar
• Kim JW
• Choi YJ
• Park KH
• Kim YH

• KMID: 2510654
• DOI: http://doi.org/10.4143/crt.2020.559

Abstract

Purpose
Next-generation sequencing (NGS) can facilitate precision medicine approaches in metastatic colorectal cancer (mCRC) patients. We investigated the molecular profiling of Korean mCRC patients under the K-MASTER project which was initiated in June 2017 as a nationwide precision medicine oncology clinical trial platform which used NGS assay to screen actionable mutations.
Materials and Methods
As of 22 January 2020, total of 994 mCRC patients were registered in K-MASTER project. Targeted sequencing was performed using three platforms which were composed of the K-MASTER cancer panel v1.1 and the SNUH FIRST Cancer Panel v3.01. If tumor tissue was not available, cell-free DNA was extracted and the targeted sequencing was performed by Axen Cancer Panel as a liquid biopsy.
Results
In 994 mCRC patients, we found 1,564 clinically meaningful pathogenic variants which mutated in 71 genes. Anti-EGFR therapy candidates were 467 patients (47.0%) and BRAF V600E mutation (n=47, 4.7%), deficient mismatch repair/microsatellite instability–high (n=15, 1.5%), HER2 amplifications (n=10, 1.0%) could be incorporated with recently approved drugs. The patients with high tumor mutation burden (n=101, 12.7%) and DNA damaging response and repair defect pathway alteration (n=42, 4.2%) could be enrolled clinical trials with immune checkpoint inhibitors. There were more colorectal cancer molecular alterations such as PIK3CA, KRAS G12C, atypical BRAF, and HER2 mutations and even rarer but actionable genes that approved or ongoing clinical trials in other solid tumors.
Conclusion
K-MASTER project provides an intriguing background to investigate new clinical trials with biomarkers and give therapeutic opportunity for mCRC patients.

Keyword

Colorectal neoplasms; Genomics; High-throughput nucleotide sequencing

Figure

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  Fig. 1. Top 20 pathogenic gene list. Among 71 genes with pathogenic variants, listed top 20 frequent mutated genes.

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  Fig. 2. Resistant to anti-EGFR therapy. Out of 994 patients, 527 patients (53.0%) were resistant to anti-EGFR therapy; having pathogenic variants in KRAS (n=433, 43.6%), BRAF (n=66, 6.6%), NRAS (n=32, 3.2%) or HER2 amplification (n=10, 1.0%). Others, 467 patients (47.0%) could be the candidate of anti-EGFR therapy with wild-type RAS.

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  Fig. 3. Current treatment landscape of metastatic colorectal cancer (mCRC). The current treatment landscape (n=534, 53.7%) will be KRAS/NRAS/BRAF mutants (resistant to anti-EGFR therapy) and several biomarkers that can help using targeted therapy or immunotherapy. For patients with BRAF V600E mutated mCRC, the combination of encorafenib and cetuximab or panitumumab was approved. The atypical BRAF mutated patients have pathogenic variants in BRAF other than V600E. Pembrolizumab and nivolumab (or ipilimumab combination) were approved for patients with microsatellite instability–high (MSI-H) mutations. Finally, dual blockade of anti-agents could be incorporated in HER2-amplified mCRC patients. Others (n=460, 46.3%), the remaining patients have unmet need of precision medicine approach.

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  Fig. 4. (A) Candidate for immune checkpoint inhibitors. Microsatellite instability–high (MSI-H) genes are MSH6, MSH2, MLH1, PMS2, and EPCAM (However, EPCAM was included only in FIRST Panel and not in Axen or K-MASTER panels. There was no pathogenic variant of EPCAM within FIRST Panel). Patients who have MSI-H pathogenic variants were approved for immune checkpoint inhibitors (n=15, 1.5%). One patient had two pathogenic variants with MSH2 deletion and MSH6 T1102fs simultaneously. Total 42 patients (4.2%) have pathogenic variants in defected DNA damage and repair pathway genes (homologous recombination deficiency genes, HRD genes) such as BRCA1/2, CHEK1/2, FANCA, ATM, POLE, RAD51B/C/D, RAD54L, ARID1A, BARD1, BRIP1, CDK1/2, PALB2, etc. (B) Tumor mutation burden. In 994 metastatic colorectal patients, 798 patients analyzed tumor mutation burden (TMB) with K-MASTER Panel (n=331) or FIRST Panel (n=467). Tumor mutational burden cut-off value defined as > 16 per 106 base pair in K-MASTER panel and as > 13 per 106 base pair in FIRST panel which were 59 patients (17.8%) and 42 (9.0%) patients irrespectively.

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  Fig. 5. Critical signaling pathways beyond metastatic colorectal cancer. Classifying pathogenic variants by critical signaling pathways: cell cycling pathway (CCND1, CDKN2A, CKD4, and CCNE1), receptor tyrosine kinase/growth factors (RTK/GFs) pathway (FGFR1/4, EGFR amplification, MET amplification, RET, and KIT), RAF/MAPK pathway (BRAF and MAP2K1), PI3K/mTOR pathway (PIK3CA, MTOR, AKT1, PTEN, and TSC2), p53 pathway (TP53 and MDM2), and RAS pathway (KRAS, NRAS, HRAS, and NF1).

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  Fig. 6. Maximize the therapeutic opportunity for metastatic colorectal cancer (mCRC) in precision medicine era. In this study, 534 patients (53.7%) have therapeutic options by current treatment landscape (Fig. 3). If all mCRC patients with ‘Potentially actionable’ variants would have challenged to get therapeutic opportunities, 294 patients (29.6%) would have tried to enroll the clinical trial. This group contains 180 (18.1%) patients with KRAS G12C/atypical BRAF/PIK3CA, HER2 mutations who could be participated in ongoing trials within mCRC and 137 patients (13.8%) who could take part in clinical trials with all solid tumors with novel variants. HRD, homologous recombination deficiency; RTK, receptor tyrosine kinase.

Reference

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