Biomarkers in Breast Cancer: An Integrated Analysis of Comprehensive Genomic Profiling and PD-L1 Immunohistochemistry Biomarkers in 312 Patients with Breast Cancer

Abstract

Background: We examined the current biomarker landscape in breast cancer when programmed death-ligand 1 (PD-L1) testing is integrated with comprehensive genomic profiling (CGP).

Material and methods: We analyzed data from samples of 312 consecutive patients with breast carcinoma tested with both CGP and PD-L1 (SP142) immunohistochemistry (IHC) during routine clinical care. These samples were stratified into hormone receptor positive (HR+)/human epidermal growth factor receptor negative (HER2-; n = 159), HER2-positive (n = 32), and triple-negative breast cancer (TNBC) cohorts (n = 121).

Results: We found that in the TNBC cohort, 43% (52/121) were immunocyte PD-L1-positive, and in the HR+/HER2- cohort, 30% (48/159) had PIK3CA companion diagnostics mutations, and hence were potentially eligible for atezolizumab plus nab-paclitaxel or alpelisib plus fulvestrant, respectively. Of the remaining 212 patients, 10.4% (22/212) had a BRCA1/2 mutation, which, if confirmed by germline testing, would allow olaparib plus talazoparib therapy. Of the remaining 190 patients, 169 (88.9%) were positive for another therapy-associated marker or a marker that would potentially qualify the patient for a clinical trial. In addition, we examined the relationship between immunocyte PD-L1 positivity and different tumor mutation burden (TMB) cutoffs and found that when a TMB cutoff of ≥9 mutations per Mb was applied (cutoff determined based on prior publication), 11.6% (14/121) patients were TMB ≥9 mutations/Mb and of these, TMB ≥9 mutations per Mb, 71.4% (10/14) were also positive for PD-L1 IHC.

Conclusion: Our integrated PD-L1 and CGP methodology identified 32% of the tested patients as potentially eligible for at least one of the two new Food and Drug Administration approved therapies, atezolizumab or alpelisib, and an additional 61.2% (191/312) had other biomarker-guided potential therapeutic options.

Implications for practice: This integrated programmed death-ligand 1 immunohistochemistry and comprehensive genomic profiling methodology identified 32% of the tested patients as eligible for at least one of the two new Food and Drug Administration-approved therapies, atezolizumab or alpelisib, and an additional 61.2% (191/312) had other biomarker-guided potential therapeutic options. These findings suggest new research opportunities to evaluate the predictive utility of other commonly seen PIK3CA mutations in hormone receptor-positive breast cancers and to standardize tumor mutation burden cutoffs to evaluate its potentially predictive role in triple-negative breast cancer.

Keywords: Biomarkers; Breast carcinoma; Comprehensive genomic profiling; PD-L1 immunohistochemistry.

Figure 1

Represents patients with breast carcinoma eligible for therapy based on biomarker status. Patients with breast carcinoma were stratified into HR+/HER2−, HER2+, and triple‐negative breast cancer (TNBC) groups and tested with standard of care diagnostics. Next, in the HR+/HER2− cohort, patients were stratified into PIK3CA+ versus PIK3CA− groups, and patients with TNBC were stratified into programmed death‐ligand 1 (PD‐L1) + versus PD‐L1− groups. The remaining patients that were not positive for PIK3CA and/or PD‐L1 were stratified into whether they had a BRCA1/2 mutation. Last, the patients without positivity in one of the above‐mentioned biomarkers were examined for positivity in a biomarker that was clinically actionable or potentially clinically actionable. Abbreviations: −, negative; +, positive; CDx, companion diagnostics; HR, hormone receptor.

Figure 2

Comutation plots of the top 20 genes for each breast carcinoma cohort stratified based on biomarker status of HR and HER2. Here, we see that although there was some overlap in the top 20 genes in each cohort (HR+/HER2−, HER2+, and TNBC) there were some differences. For the HR+/HER2− cohort, the top 5 genes in descending order were PIK3CA, TP53, RAD21, NBN, and CCND1; for the HER2⁺ cohort, they were TP53, CDK12, PIK3CA, MYC, and RAD21; and for the TNBC cohort, they were TP53, RAD21, MYC, PIK3CA, and NBN. Abbreviations: −, negative; +, positive; HR, hormone receptor; TNBC, triple‐negative breast cancer.

Figure 3

Comutation plots of the top 20 genes for the TNBC PD‐L1+ and TNBC PD‐L1− breast carcinoma cohort. Here, we see that although there was some overlap in the top 20 genes, in each cohort there were some differences. In the TNBC breast carcinoma cases, the top five genes in the PD‐L1+ cohort in descending order were TP53, RAD21, MYC, DDR2, and FH; and for the PD‐L1− cohort, they were TP53, RAD21, MYC, NBN, and RB1. Abbreviations: −, negative; +, positive; PD‐L1, programmed death‐ligand 1; TNBC, triple‐negative breast cancer.

Figure 4

Mutational prevalence of different breast carcinoma patient cohorts based on HR, HER2, and PD‐L1 status. (A): Mutation prevalence of top 20 genes in HR+/HER2−, TNBC, and HER2+ cohorts. Mutation prevalence was determined for each cohort, and Fisher's exact test was performed to compare HR+/HER2− versus HER2+, HR+/HER2− versus TNBC, and HER2+ versus TNBC cohorts (supplemental online Table 1). The p value was adjusted for multiple comparisons using the Bonferroni method, and p < .05 was considered significant. It was found that there was a significantly higher TP53 (p < .001) rate of mutation in the TNBC disease subset vs the HR+/HER2− disease subset and that there were significantly higher PIK3CA (p = .020), CCND1(p = .015), ZNF703 (p = .003), and ESR1 (p < .001) rates of mutation in the HR+/HER2− disease subset when compared with the TNBC disease subset. (B): The top 20 genes in the TNBC cohort were also extracted and no significant difference was discovered using the Fisher's exact test when comparing the programmed death‐ligand 1 (PD‐L1) + and PD‐L1− cohort (supplemental online Table 2). Bars represent genes with significant differences in rate of mutation. Abbreviations: −, negative; +, positive; HR, hormone receptor; TNBC, triple‐negative breast cancer.

Figure 5

Figure of relationship between PD‐L1 status using the SP142 companion diagnostics immunohistochemistry assay and different exploratory TMB cutoffs (≥5, ≥9, ≥10, and ≥ 20 mutations per Mb). PD‐L1+ was defined as tumor‐infiltrating immune cell% ≥1% as per U.S. Food and Drug Administration companion diagnostic approval for atezolizumab plus nab‐pacitaxel. Abbreviations: +, positive; HR, hormone receptor; mut, mutation; TMB, tumor mutation burden; TNBC, triple‐negative breast cancer; PD‐L1, programmed death‐ligand 1.