NGS-based multiplex gene assay for molecular profiling analysis and variant annotation in a CRC patient
The patient, a 57-year-old man, was diagnosed with colorectal adenocarcinoma with liver metastasis (Fig. 1A). After resection of the primary lesion, eight courses of chemotherapy with mFOLFOX6 plus cetuximab (anti-EGFR antibody) were performed. Subsequently, a right hepatic lobectomy was performed, but recurrence occurred in the liver, lung and brain, and the patient was referred to Kyoto University Hospital for clinical NGS examination .
As shown in Fig. 1B, three somatic mutations, HER2 G776S mutation, APC nonsense mutation, and TP53 missense mutation, were detected from his liver metastasis specimen by the NGS-based multiplex gene assay. Other mutations related to the HER2 signaling pathway (KRAS, NRAS, BRAF, and PIK3CA) were not detected. We also confirmed the HER2 G776S mutation in this specimen using Sanger sequencing (Fig. 1C). HER2 copy number amplification was not detected by real-time quantitative PCR (Supplementary Fig. 1).
According to the COSMIC database (v91; http://cancer.sanger.ac.uk/cosmic/), the amino acid position G776 is in the kinase domain of HER2, and several mutations in this region, such as G776 > VC, have been registered as oncogenic genes (Fig. 1D). G776S is a rare mutation that has been detected in three cases: two cases of gastric cancer and one case of urothelial tract cancer. However, its significance has not been elucidated.
Effect of HER2 G776S mutation on kinase activity and phosphorylation and its evaluation in classical cell-based transfection assays
We established plasmid expression vectors containing human cDNA encoding full-length HER2 WT (Supplementary Fig. 2A), mutant HER2 G776S, and G776 > VC as a positive control (Supplementary Fig. 2B). To evaluate the effect of HER2 G776S on kinase activity, we transiently transfected the HER2 WT or HER2 mutant expression vectors into HeLa cells, which do not have oncogenic variants in RTK-RAS-ERK pathway or Wnt/β-actin pathway. (Supplementary Table 3). We confirmed by immunoprecipitation that HER2 proteins were successfully generated in the transfected cells (Fig. 2A).
We measured their kinase activity toward peptide substrates. The kinase activity was significantly higher for HER2 G776S protein than WT protein but was less than that of HER2 G776 > VC (Fig. 2B). We assessed the phosphorylation of HER2 and EGFR, which is one of the dimerization partners of HER2, in WT-, G776S- and G776 > VC-transfected HeLa cells. As shown in Fig. 2C, G776S and G776 > VC transfection increased the phosphorylation of both HER2 and EGFR. However, similar to the results for kinase activity, the degree of HER2 and EGFR phosphorylation was weaker for G776S transfection than for G776 > VC transfection.
Next, we evaluated the oncogenic potential of HER2 G776S using classical cell-based transfection assay using murine cell lines, NIH/3T3 focus formation assay [24], and Ba/F3 transformation assay [4, 25]. NIH/3T3 cells acquired the focus-forming ability by transfection with G776 > VC but not with G776S (Fig. 2D). Similarly, Ba/F3 cells exhibited IL3-independent proliferation upon transfection with G776 > VC but not G776S (Fig. 2E). These findings suggest that HER2 G776S had weaker phosphorylation capacity and kinase activity than the known HER2 mutation and did not promote the transformed phenotype in the transfection assays using murine cells.
Differences in the effects of HER2 G776S mutation on activation of the HER2 signaling pathway between APC-intact and APC-mutant cells
To assess the effect of the HER2 G776S mutation on the HER2 downstream signaling pathway in human cancer cells, we transfected HER2 WT or HER2 G776S expression vectors into several human cell lines: HeLa, FHC, CACO-2 and COLO-320 cells. As described in the Materials and methods section, these cell lines have no HER2 mutations or amplifications and no mutation in the HER2 downstream signals genes, KRAS, NRAS, BRAF or PIK3CA (Supplementary Table 3). HeLa and FHC cells are APC WT, and CACO-2 and COLO-320 harbor APC mutations. Using Western blotting, we consistently detected full-length APC in HeLa and FHC cells, and truncated APC in CACO-2 and COLO-320 cells (Fig. 3A). Using the TCF/LEF reporter assay, we confirmed that the Wnt activity was relatively higher in CACO-2 and COLO-320 cells than in the other two cell lines (HeLa and FHC cells) (Fig. 3B).
As shown in Fig. 3C, G776S transfection increased the amount of phosphorylated HER2 compared with WT transfection in all cell lines. Of note, G776S transfection increased the phosphorylation of the HER2 downstream signaling proteins, AKT and ERK1/2, in CACO-2 and COLO-320 cells (with mutant APC) but not in HeLa and FHC cells (with WT APC). Next, we established stably transfected FHC and COLO-320 cells and examined the effects of HER2 G776S transfection on cell proliferation and anchorage-independent cell growth activity. Transfection with HER2 WT or G776S did not affect cell proliferation in FHC or COLO-320 cells (Supplementary Fig. 3). By contrast, G776S transfection significantly increased anchorage-independent cell growth activity in COLO-320 cells (mutant APC) but not in FHC cells (WT APC). WT transfection did not alter anchorage-independent growth in either cell line (Fig. 3D).
To evaluate the effects of loss of APC function on the HER2 signaling pathway, we used CRISPR-Cas9 to establish APC-KO HeLa cells. As described in Supplementary Table 3, we used HeLa cells in this experiment because they have no oncogenic variant in RTK-RAS-ERK pathway or Wnt/β-actin pathway. As shown in Fig. 4A, we confirmed the loss of full-length APC protein in APC-KO cells. We used the TCF/LEF reporter assay to confirm that the Wnt/β-catenin signaling pathway was significantly activated in APC-KO cells compared with nontargeting control (NTC) cells (Fig. 4B).
To examine the effects of APC deficiency on the HER2 signaling pathway, we assessed the amount and phosphorylation of HER2 and downstream signal proteins, including detection of RAS–GTP (activated RAS), in APC-KO cells and NTC cells. APC KO significantly increased the amount of RAS–GTP (Fig. 4C) and slightly increased phosphorylated ERK 1/2 (Fig. 4A), whereas there was no apparent change in the amount or phosphorylation of other proteins of the HER2 signaling pathway (HER2, CRAF, MEK and AKT) (Fig. 4A and Supplementary Fig. 4A). These results suggest that APC KO increases RAS–GTP as well as the activity of the Wnt pathway without affecting phosphorylation of HER2 and other downstream signals.
To assess the effects of activation of the HER2 signaling pathway in G776S-transfected APC-KO cells, we next transiently transfected the HER2 WT or HER2 G776S expression plasmid vector into APC-KO and NTC cells. As shown in Fig. 3D, HER2 G776S transfection massively increased the phosphorylation of downstream proteins in the HER2 pathway, especially ERK1/2, in APC-KO cells. By contrast, G776S transfection did not affect AKT or ERK1/2 phosphorylation in NTC cells (Fig. 4D). G776S transfection and KO of APC synergistically increased RAS-GTP. (Interaction P < 0.01, two-way ANOVA) (Fig. 4E). Moreover, G776S transfection in APC-KO cells significantly increased anchorage-independent growth, whereas growth was not affected by mock or HER2 WT transfection in APC-KO cells (Fig. 4F).
Next, we cotransfected the APC WT expression vector with the HER2 WT or HER2 G776S expression vector into COLO-320 cells. HER2 G776S transfection increased the phosphorylation of AKT and ERK1/2 in cells without APC transfection, whereas their phosphorylation was not increased in cells with APC transfection (Fig. 5D). In COLO-320 cells, the amount of RAS–GTP was significantly increased by HER2 G776S transfection, but was not increased when APC was cotransfected (Fig. 5E).
To elucidate further the effect of Wnt/β-catenin pathway activity on RAS–GTP, we cultured COLO-320 cells with ICG-001, a Wnt pathway inhibitor that antagonizes β-catenin/TCF-mediated transcription [26]. As shown in Fig. 5F, ICG-001 dose-dependently suppressed Wnt pathway activity in COLO-320 (APC mutant) cells but did not change the amount of RAS–GTP (Fig. 5G). These results indicate that inhibition of transcription downstream of the Wnt pathway dose not suppress the amount of RAS–GTP.
Inhibition by afatinib of the proliferation and tumor growth of colon cancer cells harboring HER2 G776S and APC mutations
To investigate the efficacy of HER2-targeted therapy in colon cancer cells harboring HER2 G776S, we examined the cytotoxic effect of afatinib, an irreversible pan-HER tyrosine kinase inhibitor (TKI), on COLO-320 cells (mutant APC) stably transfected with HER2 WT or HER2 G776S. Cells were also treated with gefitinib (EGFR TKI) for comparison. As shown in Fig. 6A, HER2 WT or G776S transfection increased EGFR and HER2 phosphorylation in COLO-320 cells, and afatinib inhibited both EGFR and HER2 phosphorylation. By contrast, gefitinib did not inhibit phosphorylation of either protein. Afatinib strongly suppressed AKT and ERK1/2 phosphorylation in HER2 G776S-transfected cells. Similarly, afatinib inhibited the cell viability of HER2 G776S-transfected COLO-320 cells compared with HER2 WT-transfected cells, but gefitinib did not alter their viability (Fig. 6B and Supplementary Fig. 5). In addition, as shown in Fig. 6C, afatinib significantly inhibited the anchorage-independent growth acquired by HER2 G776S transfection, but gefitinib did not. By contrast, gefitinib and afatinib did not alter the anchorage-independent growth of HER2 WT-transfected cells.
Next, we investigated the antitumor effects of afatinib using COLO-320 cells stably transfected with HER2 WT or HER2 G776S in a xenograft mouse model. Afatinib did not inhibit the growth of xenograft tumors in WT-transfected cells, but it significantly suppressed the growth of HER2 G776S-transfected cells compared with the vehicle (DMSO) control group (Fig. 6D). Evaluation of the pathology revealed that HER2 G776S-transfected tumors treated with afatinib had a sparse cell density compared with those in the vehicle control group (Fig. 6E). We confirmed that Ki-67 expression was significantly suppressed by afatinib treatment in HER2 G776S-transfected xenograft tumors but not in HER2 WT-transfected tumors (Fig. 6F).