Homologous recombination deficiency (HRD) in non-small cell lung cancer: Genomic analysis using an RNA-based HRD algorithm.

Authors

null

Stephanie Thiede

Tempus Labs, Inc., Chicago, IL

Stephanie Thiede , Matthew Berginski , Akash Mitra , Timothy J. Taxter , Michelle M. Stein , Rotem Ben-Shachar , Halla Nimeiri , Charu Aggarwal , Jyoti D. Patel

Organizations

Tempus Labs, Inc., Chicago, IL, University of Pennsylvania, Philadelphia, PA, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL

Research Funding

Pharmaceutical/Biotech Company
Tempus Labs

Background: Recent evidence has suggested that some patients with non-small cell lung cancer (NSCLC) harbor a HRD signature that represents a distinct genomic subtype that could be targeted by PARP inhibitors (PARPi). However, there is little data on HRD prevalence in NSCLC or its genomic associations. Here, we evaluated the co-occurrence of driver mutations and established immune biomarkers with an RNA-based HRD signature in a large, real-world NSCLC cohort. Methods: We analyzed data from 5119 NSCLC patients that underwent sequencing via the Tempus xT test (DNA-seq of 648 genes; RNA-seq with whole exome capture). HRD status was predicted by the Tempus HRD-RNA test, a pan-cancer logistic regression classifier that uses an RNA gene expression signature optimized to distinguish between BRCA-biallelic loss and homologous recombination repair (HRR)-WT samples (Leibowitz et al, 2022). Cohort samples were excluded from model training. All comparisons were tested via chi-squared or Fisher’s exact tests. Results: An RNA-derived signature of HRD (HRD-RNA+) was observed in 3.53% (n=181/5119) of patients. HRD-RNA+ prevalence was higher in squamous cell carcinoma (84/1331, 6.3%) relative to adenocarcinoma (68/3015, 2.3%; p < 0.001). The prevalence of select alterations by HRD-RNA status are shown in Table. Alterations in BRCA1/2 and HRR genes (inclusive of BRCA1/2) were enriched in HRD-RNA+ vs. HRD-RNA- cases (8.8% vs. 2.5%, p < 0.001; 22% vs. 15%, p = 0.008 respectively). Notably, 141 (78%) HRD-RNA+ patients had no alterations in HRR genes. Of all NCCN targetable driver mutations assessed, KRAS G12C and ALK fusions were the only targetable drivers with significantly different prevalence in HRD-RNA+ vs. HRD-RNA- patients. Across the entire cohort, NCCN driver mutations were depleted in HRD RNA+ patients (18% in HRD-RNA+ vs. 30% in HRD-RNA-, p < 0.001). Immune biomarkers (TMB, PD-L1) did not vary by HRD-RNA status. Conclusions: Compared to HRD-RNA- NSCLC, HRD-RNA+ NSCLC represents a unique, molecularly defined subset that has a decreased prevalence of NCCN-driver mutations and is not enriched for TMB-H or PD-L1 expression. Further, this signature increases the number of patients classified as HRD-RNA+ compared to HRR gene alterations alone. Functional characterization (e.g. RAD51 foci immunofluorescence assay) and clinical benefit of targeted HRD therapies such as PARPi should be explored in this HRD-RNA+ population.

HRD-RNA+, N = 181HRD-RNA-, N = 4,938p-value
BRCA1/2 loss or mutation, n (%)16 (8.8%)122 (2.5%)<0.001
HRR gene(s) loss or mutation, n (%)40 (22%)736 (15%)0.008
KRAS G12C, n (%)8 (4.4%)529 (11%)0.007
ALK Fusion, n (%)0 (0%)112 (2.3%)0.034
BRAF V600E, n (%)0 (0%)60 (1.2%)0.3
EGFR mutation, n (%)22 (12%)761 (15%)0.2
ROS1/NTRK1/2/3/RET Fusion, n (%)1 (0.6%)45 (0.9%)>0.9
MET Exon 14 skipping, n (%)1 (0.6%)47 (1.0%)>0.9
NCCN Driver(s), n (%)33 (18%)1,617 (33%)<0.001

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Abstract Details

Meeting

2023 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Developmental Therapeutics—Molecularly Targeted Agents and Tumor Biology

Track

Developmental Therapeutics—Molecularly Targeted Agents and Tumor Biology

Sub Track

Tissue-Based Biomarkers

Citation

J Clin Oncol 41, 2023 (suppl 16; abstr 3123)

DOI

10.1200/JCO.2023.41.16_suppl.3123

Abstract #

3123

Poster Bd #

321

Abstract Disclosures