PI3K/PTEN/Akt/mTOR pathway aberrations and co-incidence of hormone receptors and HER2 in 19,784 diverse solid tumors Sherri Z. Millis 1 , Sadakatsu Ikeda 2 , David Arguello 1 , Rebecca Feldman 1 , Joanne Xiu 1 , Todd Maney 1 , Sandeep Reddy 1 , and Razelle Kurzrock 2 1 Caris Life Sciences, Phoenix, AZ; 2 Center for Personalized Cancer Therapy, UC San Diego - Moores Cancer Center, La Jolla, CA Abstract Background: Molecular aberrations in the phosphatidylinositol 3-kinase (PI3K) pathway have been documented across cancers, especially PIK3CA mutations and mutation or loss of PTEN. These alterations may be relevant to therapies targeting the PI3K/PTEN/Akt/mTOR signaling pathway. Methods: Molecular profiling was performed on 19,784 tumors (>40 cancer types) at a CLIA-certified laboratory. Tests included next generation sequencing (NGS), protein expression (immunohistochemistry), and gene amplification (FISH or CISH). Results: Frequency and type of PIK3CA, AKT1 and PTEN mutations were collated across cancers. Aggregate gene mutation rates (47 genes), protein expression rates (18 proteins), and copy number (5 biomarkers) were measured. Comparison of frequencies and correlations across cancers identified lineage-specific differences, and co-incidences of associated biomarkers, which will be described. Of note, endometrial, breast, cervical, anal squamous cell, and bladder cancers had the highest PIK3CA mutation rate (37%, n=1600; 31%, n=2282; 29%, n=284; 28%, n=67, 22%, n=303, respectively). Patterns in AKT1 and PTEN mutation rates differed by cancer, as did PTEN loss - hepatocellular, 57%, prostate, 52%, and endometrial 50% loss. Co-mutation of PTEN and PIK3CA occurred in 1.5% of breast, 0% of prostate, and 12% of endometrial cancers. Of interest, PIK3CA mutations and PTEN loss co- occurred frequently, e.g. 31% of PIK3CA mutated patients also have a PTEN loss. PIK3CA mutations across cancers were distributed 43% in exon 9, 33% in exon 20, and 24% in other exons. Distribution of PIK3CA mutations by cancer type varied and occurred more frequently in the presence of HER2 protein expression or copy number increase (p=0.0001) and more frequently in the presence of hormone receptor overexpression (androgen receptor (AR), progesterone receptor (PR), and estrogen receptor (ER)) (p=0.0335). PTEN loss was seen in 27% of patients with and 30% without HER2 overexpression or amplification (p=0.004). Conclusions: Patterns of biomarker co-alterations across cancers may provide new insights relevant to targeted therapy and may be crucial to optimizing combination treatments. Frequency of PIK3CA, AKT1, and PTEN mutations or PTEN loss in presence/absence of hormone receptors or HER2 PIK3CA Mutations by Exon and Lineage PIK3CA, PTEN, AKT1 Mutation and PTEN Loss by Lineage Conclusions • 13.2% (2548/19356) of patients with diverse cancers have PIK3CA mutations; 33% of these mutations are found in the kinase domain and 43% in the helical domain. • 5.9% of tumors (1108/18885) have PTEN mutations; 30% (5510/18366) have PTEN loss. The total number of patients with any PI3K/AKT/mTOR pathway aberration is 39%. • Multiple aberrations, including but not limited to mutations in KRAS, BRAF, CTNNB1, TP53, and APC or altered expression of TS, MGMT, HER2, and hormone receptors may co-exist with PIK3CA or PTEN anomalies. • PIK3CA mutation, PTEN mutation and PTEN loss are found in an important subset of multiple tumor types and may be targeted by inhibitors. Optimization of the drug used may require determining the specific types of aberration seen, e.g., helical versus kinase domain (PIK3CA) versus PTEN aberration. • Since multiple anomalies may co-exist with PIK3CA or PTEN alterations, patients may require customized combinations of targeted agents to overcome resistance pathways. References 1. Dienstmann, R, et al. (2014) “Picking the point of inhibition: a comparative review of PI3K/AKT/mTOR pathway ihibitors.” Mol Cancer Ther; 13(5) 2014. 2. Janku, F et al. (2014) “Assessing PIK3CA and PTEN in early-phase trials with PI3K/AKT/mTOR inhibitors”. Cell Reports; 6, 2014. Coverage Gene Amino Acids Covered PIK3CA 75-118, 336-353, 418-555, 692-729, 979-1068 PTEN 1-27, 165-267, 280-342 AKT1 16-47 All differences are significant (p value<0.05), unless indicated with a #. A. Next Gen Seq, % Mutated IHC, % Protein Expression above threshold, unless noted ISH Biomarker TP53 BRAF KRAS HRAS FBXW7 FGFR2 HNF1A ATM CTNNB1 ERBB2 PTEN PIK3CA PTEN loss TOP2A AR ER PR MGMT PGP TS HER2 HER2 cMET PIK3CA WT 49 3.8 16 0.5 2 1 1 3 2 1 5 n/a 29 73 16 23 13 58 17 49 6 3.5 1.4 PIK3CA MT 35 2.1 21 1.0 6 3 2 # 4 7 2 16 n/a 31 86 29 44 33 54 12 52 11 6.4 0.2 PTEN WT 47 3.6 17 0.5 2 1 1 3 2 1 n/a 12 74 73 18 24 14 58 17 49 7 4.1 1.3 PTEN MT 34 4.1 # 19 # 0.4 # 6 7 5 5 12 2 n/a 33 27 84 23 49 42 42 10 60 4 0.9 0.2 Co-Incidence of Biomarker Aberrations in the presence or absence of PIK3CA or PTEN Mutations Table 1. A. Aggregate differences in gene mutation rates, protein expression rates, and copy number were measured and are shown between PIK3CA WT and PIK3CA MT patients and between PTEN WT and PTEN MT cases. B. Total mutations identified out of total cases tested, each, for PIK3CA or PTEN. B. PIK3CA PTEN MT/Total 2548/19784 1108/18885 % Total 13.2% 5.9% Figure 1. Percent PIK3CA, PTEN, AKT1 mutation and PTEN loss were compared across cancers. Total cases by lineage are indicated in parentheses. Total cases tested=19784. CNS-other =neuroblastoma, medulloblastoma, ependymoma, ganglioglioma; Head and neck cancers – Other= hypopharynx, nasopharynx, oropharynx Figure 4. Distribution of PIK3CA mutations in helical, kinase, or other regions differ by subtype. All non-exon 9 or 20 mutations are grouped as ‘Other’. Figure 2. 0% 20% 40% 60% 80% 100% Exon 20 Exon 9 Other Exons Incidence of any PI3K/AKT1/mTOR pathway aberrations, by lineage Figure 3. 0% 10% 20% 30% 40% 50% 60% All Composite (19784) Adenoid cystic carcinoma (67) Adrenocortical cancer (33) Ampullary cancer (41) Anal Cancer (71) Appendiceal cancer (188) Bladder cancer (313) Bone cancers (72) Breast Carcinoma (2333) Cervical Cancer (291) Cholangiocarcinoma (169) Extrahepatic Bile Duct Adenocarcinoma (30) Gallbladder cancer (72) Colorectal Adenocarcinoma (1991) Duodenal cancer (34) Endometrial cancer (1616) Esophageal, Esophagogastric Junction Cancers (208) Gastric Adenocarcinoma (221) Gastroesophageal Adenocarcinoma (92) Gastrointestinal Stromal Tumors (GIST) (71) Germ cell tumor (26) Glioblastoma (529) Low Grade Glioma (73) CNS-other (25) Head and neck Squamous Carcinoma (234) Head and neck cancers - Other (35) Salivary gland cancer (66) Kidney cancer, ccRCC (153) Kidney cancer, pRCC (17) Kidney cancer, sRCC (14) Liver Hepatocellular Carcinoma (116) Lung, NSCLC (2391) Lung Small Cell Cancer (SCLC) (157) Lung, BAC (25) Lymphoma (48) Melanoma (668) Non-Melanoma Skin Cancers (92) Uveal Melanoma (36) Meningioma (33) Mesothelioma (114) Neuroendocrine tumors (381) Non Epithelial Ovarian Cancer (non-EOC) (141) Ovarian Surface Epithelial Carcinomas (3539) Pancreatic Adenocarcinoma (761) Prostatic Adenocarcinoma (173) Rare, Other (126) Small Intestinal cancer (45) Soft Tissue cancers (679) Thymic Carcinoma (36) Thyroid Carcinoma (82) Unknown primary (638) Uterine Sarcomas (337) Vaginal cancer (26) Vulvar cancer (41) % Mutated, PIK3CA % Mutated, PTEN % Mutated, AKT1 % Loss, PTEN All Composite (19784) 0% 10% 20% 30% 40% 50% 60% 70% Gastrointestinal Stromal Tumors (GIST) (n=71) Meningioma (n=33) Low Grade Glioma (n=73) Thymic Carcinoma (n=36) Uveal Melanoma (n=36) Neuroendocrine tumors (n=381) CNS-other (neuroblastoma, medulloblastoma, ependymoma, ganglioglioma) (n=25) Mesothelioma (n=114) Adenoid cystic carcinoma (n=67) Thyroid Carcinoma (n=82) Uterine Sarcomas (n=337) Soft Tissue cancers (n=679) Bone cancers (n=72) Adrenocortical cancer (n=33) Melanoma (n=668) Lung, BAC (n=25) Glioblastoma (n=529) Kidney cancer, Wilms (n=4) Lung Small Cell Cancer (SCLC) (n=157) Ovarian Surface Epithelial Carcinomas (n=3539) Rare, Other (n=126) Salivary gland cancer (n=66) Lymphoma (n=48) Lung, NSCLC (n=2391) Vulvar cancer (n=41) Appendiceal cancer (n=188) Cholangiocarcinoma (n=169) Gastroesophageal Adenocarcinoma (n=92) Non-Melanoma Skin Cancers (n=92) Head and neck cancers - Other ( hypopharynx, nasopharynx, oropharynx) (n=35) Unknown primary (n=638) Pancreatic Adenocarcinoma (n=761) Duodenal cancer (n=34) Non Epithelial Ovarian Cancer (non-EOC) (n=141) Esophageal, Esophagogastric Junction Cancers (n=208) Extrahepatic Bile Duct Adenocarcinoma (n=30) Gastric Adenocarcinoma (n=221) Kidney cancer, medullary (n=5) Small Intestinal cancer (n=45) Kidney cancer, pRCC (n=17) Gallbladder cancer (n=72) Head and neck Squamous Carcinoma (n=234) Kidney cancer, sRCC (n=14) Bladder cancer (n=313) Kidney cancer, ccRCC (n=153) Germ cell tumor (n=26) Kidney cancer, chRCC (n=2) Cervical Cancer (n=291) Colorectal Adenocarcinoma (n=1991) Liver Hepatocellular Carcinoma (n=116) Anal Cancer (n=71) Prostatic Adenocarcinoma (n=173) Vaginal cancer (n=26) Ampullary cancer (n=41) Breast Carcinoma (n=2333) Endometrial cancer (n=1616) ALL, composite All Composite (39%)