Abstract P4-10-34: Plasma sequencing demonstrates that breast cancer patients have a higher prevalence of clonal and multiple PIK3CA mutations than other solid tumor patients
Authors: Chen Christopher , Sahu Avinash , Price Kristin , Pinto Christopher , Allen Read , Wang Xiaoman , Szabolcs Annamaria , Goyal Lipika , Ting David , Liu Shirley , Juric Dejan 
Published: March 2020

Background: Alpelisib, a PI3Kα inhibitor, was recently approved by the FDA for the treatment of metastatic PIK3CA-mutated HR+ breast cancer in combination with fulvestrant. This therapeutic breakthrough came after years of disappointing efforts to develop solid tumor drugs targeting PIK3CA, one of the most commonly altered oncogenes in cancer, including 40% of HR+ breast and 30% of head and neck squamous cell cancer. The limited success of PI3Kinhibitors outside of breast cancer may be partly because cancers may harbor heterogeneous PIK3CA mutations and/or co-occurring mutations that confer varying degrees of sensitivity to PI3Kα inhibition.

Methods: To identify biomarkers of sensitivity and resistance to PI3Kinhibitors, we assessed all plasma samples sent to a CLIA-certified commercial laboratory (Guardant Health) for a targeted NGS assay (Guardant360) from November 2016 to March 2019. The assay included 73 genes for single-nucleotide variants, 23 genes for insertions / deletions, 18 genes for amplifications, and 6 genes for fusions. In total, 53,118 cancer patients were sequenced, of whom 8,464 patients (15.9%) had a PIK3CA point mutation or amplification. This PIK3CA-mutated subset served as our analysis cohort.

Results: The four most common tumor types in our PIK3CA-mutated cohort were breast (n=2060), non-small cell lung (n=2667), colorectal (n=999), and prostate cancer (n=713); head and neck cancer patients (n=129) were also included given the high frequency of PIK3CA mutations in this disease. Breast cancer patients had a median of 6 plasma mutations detected (range 1-92) and median maximum variant allele frequency (VAF) of 7.6% (range 0.05-96.5%). PIK3CA mutations were clonal in 68.2% of breast cancer patients (as defined by a VAF&gt;50% of the maximum VAF), compared to 18-44% in patients of other tumor types (p&lt;0.05). Co-altered genes were generally similar between patients with clonal vs subclonal PIK3CA mutations by tumor type; the five most common co-altered genes among breast cancer patients with clonal PIK3CA mutations were TP53 (50.7%), ESR1 (31.6%), EGFR (24.7%), ERBB2 (20.8%), and FGFR1 (18.7%). Breast and head and neck patients were significantly more likely to have more than one mutation in the PIK3CA gene or in the PI3K pathway (AKT1, PIK3CA, PTEN). 36.8% of breast cancer patients had kinase domain mutations as compared to 10.7-19.9% of patients with other tumor types. Lung and colorectal cancer patients more commonly had concurrent KRAS mutations.

Conclusions: PIK3CA-mutated breast cancer patients were more likely to have clonal PIK3CA mutations and multiple PIK3CA and PI3K pathway mutations compared to patients with other tumor types, which may suggest greater PI3Kpathway dependency and sensitivity to treatment with PI3Kα inhibitors. Ongoing whole exome and RNA sequencing of 21 pairs of pre- and post-treatment tissue biopsies of breast cancer patients treated with PI3Kα inhibitors will provide additional genomic and transcriptomic context to these plasma-based results.

Breast (n=2060)NSCLC (n=2667)Colorectal (n=999)Prostate (n=713)Head and neck (n=129)Median age (range)60 (25-101)68 (25-97)62 (17-94)71 (39-97)60 (21-88)% male0%49%56%100%72.7%Median # mutations (range)6 (1-92)6 (1-51)8 (1-207)7 (1-76)6 (1-66)Median max VAF (range)7.6% (0.05-96.5)9.2% (0.04-96.1)17.7% (0.08-90.1)12.2% (0.01-94.5)3.7% (0.08-84.5)% PIK3CA clonal mutation a68.2% (1404)27.1% (724)44.1% (441)18.2% (130)40.3% (52)5 most frequent co-mutated genes, among patients with clonal PIK3CA mutationsTP53 (50.7%)TP53 (66.3%)APC (81.0%)AR (48.5%)TP53 (36.6%)ESR1 (31.6%)EGFR (34.9%)TP53 (70.5%)TP53 (40%)ARID1A (25%)EGFR (24.7%)KRAS (21.7%) bKRAS (67.3%) bEGFR (21.5%)NF1 (21.2%)ERBB2 (20.8%)NF1 (18.0%)EGFR (31.1%)MYC (19.2%)EGFR (21.2%)FGFR1 (18.7%)ARID1A(15.0%)BRAF (23.4%)CDK6 (18.5%)TERT (17.3%)5 most frequent co-mutated genes, among patients with subclonal PIK3CA mutationsTP53 (60.7%)TP53 (80.6%)APC (81.6%)TP53 (63.9%)TP53 (60%)ESR1 (28.1%)EGFR (43.3%)TP53 (76.2%)AR (63.0%)NOTCH1 (36.7%)ERBB2 (24.7%)KRAS (24.0%)KRAS (64.7%)EGFR (30.3%)EGFR 33.3%)NF1 (24.0%)NF1 (18.3%)EGFR (41.3%)BRAF (26.9%)MTOR (26.7%)EGFR (23.0%)MET (18.3%)BRAF (32.0%)APC (26.0%)ERBB2 (26.7%)&gt;1 PIK3CA mutation c 29.7% (612)14.2% (378)17.3% (173)10.8% (77)31.0% (40)&gt;1 PI3K pathway mutation c38.2% (787)21.0% (561)26.6% (266)20.9% (149)36.4% (47)% helical mutations36.8% (1079)16.1% (504)19.9% (245)10.7% (87)12.9% (25)% kinase mutations a15.1% (444)16.0% (501)24.1% (296)9.5% (77)16.0% (31)% other point mutations15.1% (444)16.0% (501)24.1% (296)9.5% (77)16.0% (31)% amplifications18.4% (538)37.7% (1182)14.6% (180)64.9% (526)37.6% (73)a p&lt;0.05 vs NSCLC, colorectal, prostate, HNb p&lt;0.05 vs breast, prostate, HNc p&lt;0.05 vs NSCLC, colorectal, prostate

Citation Format: Christopher Chen, Avinash Sahu, Kristin Price, Christopher Pinto, Read Allen, Xiaoman Wang, Annamaria Szabolcs, Lipika Goyal, David Ting, Shirley Liu, Dejan Juric. Plasma sequencing demonstrates that breast cancer patients have a higher prevalence of clonal and multiple PIK3CA mutations than other solid tumor patients [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-34.