Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy

Abstract

The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirus-type-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.

Modeling biological and genetic diversity in upper tract urothelial carcinoma with patient derived xenografts

“…Consistent with the poor response of HER2-mutant UC patients to the HER kinase inhibitor neratinib as compared to HER2mutant breast and cervical cancer patients 36 , the HER2 S310Fmutant cell line UCC14-PDC was significantly less sensitive to neratinib than the HER2-amplified BT-474 breast cancer and HER2 S310F-mutant CVX-4 cervical cancer cell lines. The relative lack of neratinib sensitivity of the UCC14 cell line was consistent with the higher doses of neratinib required to inhibit downstream ERK signaling in this cell line model as compared to BT-474 and CVX-4 cells 37 . This result suggests that the variable sensitivity of different tumor lineages to HER2-directed therapies as reported in a recent basket trial 36 , is likely due, at least in part, to differences among cancers in their dependence on HER2 signaling for tumor growth and survival.…”

“…For western blot studies, cells were seeded into 60 mm dishes. At 75% confluence in log phase growth, cells were treated with neratinib at 0-250 nM for 1 h and then lysed in 1% NP-40 lysis buffer or RIPA buffer and processed for immunoblotting 37,52 . For primary antibodies, phospho-antibodies were used at 1:500 in TBST/5%BSA and totals were used at 1:1000 TBST/5% BSA with incubation overnight at 4°C.…”

“…We thus generated a cell line from an early passage UCC14-PDX (UCC14-PDC) and assessed its sensitivity to neratinib, a HER2 kinase inhibitor. Both UCC14-PDC (IC50 508.3 nM) and MGHU3 (an ERBB2 wildtype bladder cancer line, IC50 245.9 nM) were significantly less sensitive to neratinib as compared to CVX-4 37 (a HER2 S310F-mutant cervical cancer line, IC50 56.8 nM) and BT-474 (an ERBB2 amplified breast cancer cell line, IC50 0.1 nM) (Fig. 5c).…”

Pharmacological Treatment of Patients with Metastatic, Recurrent or Persistent Cervical Cancer Not Amenable by Surgery or Radiotherapy: State of Art and Perspectives of Clinical Research

“…An international randomized double-blind clinical trial of BCD-100 (Prolgolimab anti-PD-1 antibody) plus platinum-based chemotherapy with and without Bevacizumab versus placebo plus platinum-based chemotherapy with and without Bevacizumab as first-line treatment of subjects with advanced cervical cancer [126][127][128][129]. PIK3catalytic subunit α (PI3KCA) mutations have been found in 14-25% of adenocarcinomas and in 37.5-48% of squamous cell carcinomas of the uterine cervix [126,128].…”

Neratinib in patients with HER2-mutant, metastatic cervical cancer: Findings from the phase 2 SUMMIT basket trial

“…Somatic activating HER2 mutations are a recently identified class of oncogenic drivers that are present in a variety of solid tumor malignancies including bladder, colorectal, lung, breast, and cervical cancers [11][12][13][14]. Sequencing studies indicate that HER2 mutations are present in 3-6% of cervical cancers [15][16][17][18] and may be associated with a poor prognosis [16]. Given the clinical utility of HER2targeted therapies in patients with breast, esophagogastric, endometrial, and lung cancers, the subset of patients with cervical cancers harboring HER2 mutations could potentially benefit from HER2targeted therapies, such as irreversible pan-HER kinase inhibitors [15][16][17]19].…”