Identification of EGFR mutations in type II papillary renal cell carcinoma

CASE SUMMARY History and examination A 32-year-old woman without a history of comorbidities, addictions, or past medical or surgical history, presented in February 2022 with abdominal pain. Her Eastern Cooperative Oncology Group (ECOG) performance status (PS) was 1. As part of the workup for the abdominal pain, a contrast-enhanced computed tomography (CECT) scan was performed. Investigations and diagnosis The CECT showed a lobulated hypodense mass in the upper pole of the left kidney measuring 4.9 × 4.4 × 5.4 cm [Figure 1a]. The lesion involved the anterior branch of the left renal artery and left renal vein. In addition, mild left hydroureteronephrosis was noted. Multiple lobulated variable-sized heterogeneously enhancing lesions with areas of necrosis were noted in both lobes of the liver, largest measuring 6.7 × 6.3 cm [Figure 1a]. A biopsy of the liver lesion revealed a metastatic deposit of renal cell carcinoma (RCC). The left renal mass biopsy showed oncocytic cells with low nuclear grade. Immunohistochemistry (IHC) revealed that the tumor cells were positive for AE1/AE3 (diffuse, strong), PAX8 (focal), and AMACR (diffuse, strong), whereas IHC was negative for CAIX, CK7, CK20, S100P, and c-Kit. The final histopathologic diagnosis was metastatic papillary renal cell carcinoma (pRCC) type II.Figure 1: (a) Contrast-enhanced computed tomography (CECT) shows 6.7 × 6.3 cm lobulated hypodense liver metastasis (*) and 4.9 × 4.4 × 5.4 cm lobulated hypodense left kidney mass (**). (b) Partial response on cabozantinib—CECT shows 5.8 × 4.6 cm tumor (*) and 3.4 × 3.0 × 3.5 cm tumor (**). (c) Stable response on cabozantinib—CECT shows 5.8 × 4.6 cm tumor (*) and 3.4 × 3.0 × 3.5 cm tumor shows a significant decrease in solid mass with the increase in internal necrosis. (d) Progression on cabozantinib—CECT shows new-onset liver metastasis (*) and 3.4 × 3.5 × 3.9 cm stable kidney mass (**). (e) Progression on bevacizumab + erlotinib treatment: interval increase in the size and density of multiple variable-sized heterogeneously enhancing lesions with areas of necrosis within noted in both lobes of liver, with the largest measuring 6.2 × 4.1 cm in segment VII (*), previously measured 3.6 × 2.6 (**). (f) Summary of patients’ history and treatment courseTreatment administered The patient was started on cabozantinib 40 mg orally, with a plan to escalate the dose based on tolerance [Figure 1f].[1] The patient tolerated the initial dose well, and hence, the dose was increased to 60 mg orally daily. Response evaluation CECT after three months in August 2022 showed partial response in the primary and liver lesions; however, the patient developed grade 3 hand-foot syndrome, and hence, cabozantinib was continued, but at the lower dose of 40 mg orally daily. The tumor continued to respond to cabozantinib therapy for approximately one year [Figure 1b and c]. In March 2023, a follow-up CECT showed a grossly stable hypodense cystic mass in the upper pole of the left kidney [Figure 1d], along with a new-onset tumor mass in the liver [Figure 1d]. In addition, stable and few new-onset suspicious skeletal lesions were observed. To help plan the next line of therapy, the patient was advised to undergo next-generation sequencing (NGS)-based molecular testing on the baseline biopsy. Next-generation sequencing Molecular testing was performed using amplicon-based NGS on the liver lesion biopsy (baseline formalin-fixed paraffin-embedded [FFPE] tissue). This NGS gene panel covered 50 genes and 3159 unique variants, including single nucleotide variants (SNVs)—indels (insertion and deletions), fusions, and copy number variations (CNV). The molecular test revealed classical EGFR exon 19 deletion (p.E746_A750del, variant allele frequency [VAF] = 5.3%) [Figure 2], along with EGFR L747P mutation (VAF = 15.4%). In addition, CTNNB1 mutation (p.S45F, VAF = 12.4%) was detected.Figure 2: Integrative genome viewer (IGV) shows the presence of EGFR exon 19 deletion mutation in formalin fixed paraffin embedded tissue sample with Variant Allele Frequency (VAF) = 5.3%EXCERPTS FROM THE DISCUSSION IN THE MOLECULAR TUMOR BOARD (MTB) The patient was diagnosed with type II pRCC. NGS-based molecular testing revealed the presence of classical EGFR exon-19 deletion (VAF = 5.3%) along with EGFR L747P (VAF = 15.4%) mutation and CTNNB1 mutation (VAF = 12.4%). The lower VAF of the EGFR exon 19 deletion was considered an indication that there were fewer clones in the patient’s tumor compared to other mutations. EGFR p.L747P mutation is a known rare EGFR mutation in exon 19, reported to occur in lung adenocarcinoma, with some case reports suggesting sensitivity to gefitinib and osimertinib,[2] while other case reports have suggested that this mutation confers resistance to EGFR tyrosine kinase inhibitors (TKI).[3] In addition, CTNNB1 mutations are known to confer resistance to EGFFR TKIs[4] in lung adenocarcinoma. All mutations belonged to tier IIC, and among these, only EGFR exon 19 deletion could be considered actionable, as Food and Drug Administration (FDA)-approved therapy was available for this variant. As per the guidelines, tier II indicates variants of potential clinical significance, wherein Level C evidence indicates FDA-approved therapy or practice guideline in other tumor type(s), evidence from multiple small published studies, or based on availability of investigational therapies.[5] Thus, all the mutations were considered to be tier IIC for RCC, as per the discussion in the MTB. In an earlier case report of a patient with clear-cell RCC with a classical EGFR exon 19 deletion, response to gefitinib treatment was oberved.[6] Our patient had received first-line treatment with cabozantinib, which led to an initial partial response, and progression after approximately a year; hence, as per the standard treatment protocol and the NGS report that showed classical EGFR exon 19 deletion, which was considered potentially actionable and responsive to EGFR TKIs, the patient was advised treatment with erlotinib in combination with bevacizumab. TREATMENT PLANNED AFTER THE MOLECULAR TUMOR BOARD DISCUSSION The MTB treatment recommendation of EGFR-directed therapy partially overlapped with the empirical treatment recommendation from the European Society for Medical Oncology (ESMO) and National Comprehensive Cancer Network (NCCN) of bevacizumab + erlotinib for metastatic pRCC [Figure 1f]. Hence, this patient was started on the combination of bevacizumab + erlotinib in May 2023, as a standard approach of treatment modulation following progression on cabozantinib. Following four cycles (approximately two months), the patient had improved clinically with reduced abdominal pain and increased appetite. However, response assessment CT scan showed unequivocal progressive disease [Figure 1e]. The treatment was then changed to lenvatinib + everolimus in August 2023. DISCUSSION Renal cell carcinoma (RCC) is a heterogenous and diverse disease with many subtypes, wherein pRCC accounts for approximately 10–20% of all the subtypes. pRCC further includes two subtypes: type I papillary and type II papillary.[7] The Tumor Cancer Genome Atlas (TCGA) group performed comprehensive genomic characterization of pRCC. This study characterized types I and II pRCC as molecularly distinct subtypes. Type I pRCC is associated with alterations in the MET pathway (MET gene), while activation of the nuclear factor erythroid 2-related factor 2-Antioxidant Response Element (NRF2-ARE) pathway is associated with type II pRCC. Additionally, CDKN2A loss and CpG island methylator phenotype (CIMP) in type II pRCC convey a poor prognosis. Type II pRCC is characterized by alterations in the NRF2 pathway, chromatin modifiers, and SWI/SNF complex genes.[8] Type II pRCC shows higher tumor grade, tumor necrosis, or lymphovascular invasion compared to type I. Type II pRCC has shown advanced tumor, nodal, and metastasis (TNM) stage and a higher pathological grade compared to type I pRCC. Type II pRCC has also been reported to result in poor outcomes, compared to type I pRCC.[7,9,10] Thus, it is clear that different treatment strategies should be implemented for the two subtypes of pRCC. Molecular characterization supplements histological classification and provides insights for precision oncology applications, personalized treatment, and clinical management of pRCC. There are several FDA-approved targeted therapies available for clear-cell RCC. These include bevacizumab, sorafenib, sunitinib, pazopanib, axitinib, tivozanib, cabozantinib, lenvatinib, temsirolimus, everolimus, and immunotherapies.[11,12] These drugs target various pathways involved in the regulation of vascular endothelial growth factor receptor (VEGFR), mechanistic target of rapamycin kinase C1 (mTORC1), mesenchymal–epithelial transition factor (c-MET), and fibroblast growth factor receptor (FGFR), cytokines, and anti-PD1/PD-L1 immune checkpoint inhibitors.[10,13] The literature suggests that molecularly directed treatment can be advantageous. Herewith, we report a unique case study of pRCC with EGFR exon 19 deletion, which has not been frequently reported in pRCC. EGFR overexpression in RCC cell lines and knockout of the same along with sunitinib treatment resulted in suppression of RCC proliferation.[14]EGFR alterations are significant therapeutic targets in many epithelial tumors such as lung cancer.[15] A difference in EGFR expression has been reported in clear-cell RCC tumors compared to normal tissue, with a higher expression in patients with metastatic disease, suggesting that EGFR could be a prognostic biomarker and novel therapeutic target for clear-cell RCC.[16] A case report showed EGFR codon 802 mutations and MET mutations at codons 969 and 991 in a female patient with pRCC.[14] There are studies that have described EGFR mutations in different cancer types including kidney cancers, indicating EGFR as a possible key target to evaluate for response to systemic therapy.[17] This suggests that EGFR-directed therapies could be a promising treatment for many other cancer types as have been successful in lung cancer.[18] However, it is important to recognize that although EGFR mutations are established drivers in lung cancer, they might not act similarly in other cancer types. In the present case report, we demonstrated the utility of NGS-based molecular testing, which revealed the EGFR mutations in the baseline tumor. However, the outcome of the testing was not beneficial in this present case (as the detected mutations were not known driver alterations) and a therapeutic trial was not beneficial, thus, the EGFR mutation did not prove to be tumor agnostic. Hence, the patient was given standard treatment for pRCC. Despite this, our patient’s tumor showed progression on the given treatment and therapy was revised accordingly. CONCLUSION The present case study describes the identification of rarely reported EGFR mutations in pRCC. It also gives the full spectrum of mutations that were present in the tumor, possibly playing a role in disease resistance mechanisms. The NGS findings opened a novel avenue to manage the patient’s cancer by prioritizing molecularly directed potentially actionable targets over alternative therapeutic options, which were limited by approved therapies and the types of alterations detected. Declaration of patient consent The authors certify that they have obtained all appropriate patient consent forms. In the form, the patient has given her consent for her radiological images and other clinical information to be reported in the journal. The patient understands that her name and initials will not be published, and due efforts will be made to conceal her identity, but absolute anonymity cannot be guaranteed. Financial support and sponsorship Nil. Conflicts of interest Vanita Noronha, Anuradha Chougule, and Kumar Prabhash are members of the editorial board of Cancer Research, Statistics and Treatment. As such, they may have had access to information and/or participated in decisions that could be perceived as influencing the publication of this manuscript. However, they had recused themselves from the peer review, editorial, and decision-making process for this manuscript, to ensure that the content is objective and unbiased.