Acquired MET D1228N Mutations Mediate Crizotinib Resistance in Lung Adenocarcinoma with ROS1 Fusion: A Case Report

Abstract

Patients with non‐small cell lung cancer (NSCLC) containing ROS1 fusions can have a marked response to the ROS1‐targeted tyrosine kinase inhibitors (TKIs), such as crizotinib. Common resistance mechanisms of ROS1‐fusion targeted therapy are acquired mutations in ROS1. Along with the use of next‐generation sequencing in the clinical management of patients with NSCLC during sequential targeted therapy, many mechanisms of acquired resistance have been discovered in patients with activated tyrosine kinase receptors. Besides acquired resistance mutations, bypass mechanisms of resistance to epidermal growth factor receptor (EGFR)‐TKI treatment are common in patients with EGFR mutations. Here we describe a patient with metastatic lung adenocarcinoma with CD74‐ROS1 fusion who initially responded to crizotinib and then developed resistance by the acquired mutation of D1228N in the MET kinase domain, which showed short‐term disease control for cabozantinib.

Key Points

• The D1228N point mutation of MET is an acquired mutation for crizotinib resistance.

• The patient obtained short‐term clinical benefit from cabozantinib therapy after resistance to crizotinib.

• The clinical use of next‐generation sequencing could maximize the benefits of precision medicine in patients with cancer.

Short abstract

Despite marked responses to tyrosine kinase inhibitors, patients with non‐small cell lung cancer eventually develop resistance to this treatment. This article reports a case of acquired mutation that caused crizotinib resistance in lung adenocarcinoma with CD74‐ROS1 fusion.

Introduction

Constitutive activations of tyrosine kinase, which is caused by genomic variations such as mutation and gene rearrangements and fusions, play a key role in the development and progression of non‐small cell lung cancer (NSCLC) [1]. Accordingly, tyrosine kinase inhibitors (TKIs) have significantly changed the treatment paradigm and improved the prognosis of NSCLC. Although ALK and ROS1 gene rearrangements and fusions are relatively rare, patients with these variations had a significant response to the corresponding TKIs. ROS1 and ALK have 77% similarity in amino acid sequence of their ATP‐binding domain and could be treated with shared TKIs [2]. ROS1 rearrangement is identified in approximately 1%–2% of NSCLC cases and is observed more often in patients with nonsmoking, younger age, and adenocarcinoma histology [3]. The patients with NSCLC containing ROS1 fusions can have marked responses to ROS1‐targeted inhibitors, such as crizotinib, with an overall response rate of 71% in east Asian patients [4].

Although kinase inhibitors are highly effective, patients ultimately develop resistance to the therapy. The most common mechanism of acquired resistance is the mutation in the kinase domain, such as T790M in epidermal growth factor receptor (EGFR), D2033N in ALK, and G2032R in ROS1 [5, 6]. The other resistance mechanism is bypass activation of other tyrosine kinases, such as mesenchymal‐epithelial transition factor (MET) amplification to EGFR‐TKI resistance [7]. The treatment strategies differ according to various mechanisms of resistance. These include switching drugs or combination therapy. Acquired resistance to TKIs targeted therapies is a major limitation to their long‐term therapeutic benefit. Along with the utility of next‐generation sequencing (NGS) in the clinical management of NSCLC during sequential targeted therapy, researchers have identified more mechanisms of acquired resistance. Herein, we report a case of a patient with metastatic lung adenocarcinoma containing a CD74‐ROS1 fusion gene. The patient achieved short‐term clinical benefit from cabozantinib treatment after acquired resistance to crizotinib.

Patient Story

A 30‐year‐old woman presented in October 2016 with cough complaints with expectoration and left shoulder blade pain of 1 month duration. A computed tomography (CT) scan of the chest and abdomen showed peripheral lung cancer in the left upper lobe with bilateral hilar lymphadenopathy, multiple lymph node metastases in the mediastinum and supraclavicular regions, and multiple nodules in the same lobe. Pathological examination of a needle biopsy of the tumor on the left lung revealed an adenocarcinoma, stage IIIC (T3N3M0). The neoplastic cells stained positive for CK7, napsin A, P40, TTF‐1, and p63 and negative for vertana ALK and CK5/6 (Fig. 1). An NGS‐based 123‐gene panel assay for common driver genes showed CD74‐ROS1 fusion and wild‐type EGFR/ALK (Table 1).

Figure 1.

Details of the imaging assessments, pathological images and treatments during the course of the disease. Abbreviatons: HE, hematoxylin and eosin; TTF1, thyroid transcription factor 1.

Table 1.

Results of the sequential next‐generation sequencing‐based genetic tests

Gene/TMB	Cervical lymph node	Lung node	Abdominal subcutaneous nodule
CD74‐ROS1	Fusion	Fusion	Fusion
MET	Negative	D1228N	D1228N/amplification
CDKN2A	Negative	D92_L97del	D92_L97del
TP53	Negative	c.376‐1G>A/ F134C	c.376‐1G>A
PIK3CB	Negative	D1067H	D1067H
RB1	Negative	E287*	Negative
TBX3	‐	T229M	Negative
NF1	Negative	W1314*	Negative
PPP2R1AA	Negative	Negative	A136T
LYN	Negative	Negative	Amplification
TMB	‐	10.1 Muts/Mb	3.8 Muts/Mb

Hyphen (‐) represents the missing detection.

Abbreviation: Mut, mutation.

The patient underwent one cycle of cisplatin and pemetrexed combination chemotherapy, and CT scan of the chest showed partial response with lung lesion shrinkage. The patient continued with four cycles of nedaplatin and pemetrexed combination chemotherapy. A second CT assessment showed an increase in primary lesions, suggesting disease progression. Based on the genetic analysis results, the patient began crizotinib treatment (250 mg, twice daily, oral) in February 2017 without obvious adverse effects. After 1 month, a chest CT scan showed a significant reduction in the size of the mass lesion (Fig. 1). Four months later, the patient underwent local radiotherapy for a single lymph node enlargement in the neck. Ten months after crizotinib treatment, the patient complained of intermittent headache with vomiting. Magnetic resonance imaging scans of the brain showed a metastatic tumor. The CT scan of the lungs also showed enlargement of the primary lesions (Fig. 1). The patient underwent whole‐brain radiotherapy (40 Gy/20 fractions).

To identify the mechanism underlying resistance to crizotinib, we performed a second needle biopsy of the left lung lesion, which pathologically confirmed invasive lung adenocarcinoma (Fig. 1) and a CD74‐ROS1 fusion. However, NGS‐based 450‐gene panel assay also identified the mutations in six other genes: MET, CDKN2A, TP53, NF1, PIK3CB, and TBX3. The tumor mutation burden (TMB) was 10.1 mutations (Muts)/Mb (Table 1). The D1228N variant was in the MET kinase domain, which can affect the binding of crizotinib to MET, leading to resistance to the MET inhibitor crizotinib [8, 9]. As a result, the patient was switched to cabozantinib (60 mg, daily) in March 2018 and experienced significant improvement with her headaches within 2 weeks, although her appetite was affected. After 1 month, an imaging assessment revealed shrinkage of both brain metastases and lung lesions (Fig. 1). However, 3 months later, the disease had progressed with increased pleural effusion, enlarged lung lesions, metastatic brain lesions, and extensive metastatic subcutaneous nodules. We performed an additional biopsy and genetic test on an abdominal subcutaneous nodule. Pathological examination revealed poorly differentiated cancer, whereas the NGS‐based 450‐gene panel analysis revealed an additional MET amplification, LYN amplification, and A136T mutation in PPP2R1AA. The TMB was 3.8 Muts/Mb this time (Table 1). In addition, the programmed death ligand‐1 (PD‐L1) expression of the subcutaneous nodule was 50% positive. The patient succumbed to the disease in July 2018. The time from diagnosis to death was 21 months.

Discussion

In this article, we describe an acquired mutation for crizotinib resistance in lung adenocarcinoma with CD74‐ROS1 fusion. CD74 is the most common fusion partner among several gene fusion partners of ROS1 fusions, and is identified in approximately 0.7% of patients with NSCLC [10]. The progression‐free survival with this tumor profile and crizotinib treatment is about 10 months, shorter than the reported median progression‐free survival of 19.2 months in an early phase study of crizotinib therapy in advanced ROS1‐rearranged NSCLC [4]. Crizotinib has poor central nervous system penetration [11], and pharmacokinetic disorders may be a factor of brain metastasis [12]. As with most kinase inhibitors, acquired resistance to targeted therapy is inevitable. The bypass activation of MET with D1228N was identified as the mechanism underlying resistance of crizotinib to CD74‐ROS1 fusion in this case. MET D1228N was reported to be an acquired resistance mutation to crizotinib in patients with NSCLC with MET exon 14 skipping [8] and in patients with MET‐amplified triple‐negative breast cancer [13]; MET D1228N was also reported to respond to cabozantinib in in vitro studies [9].

A study also reported that MET kinase activation by MET kinase domain duplication is a resistance mechanism to another ROS1 inhibitor, ceritinib [14]. As a result, this patient was treated with cabozantinib, and volumes of both brain metastases and lung lesions decreased 1 month later. It was hard to determine whether shrinkage of brain lesion was from the radiation treatment or the cabozantinib‐targeted therapy. However, the shrinkage of the lung lesions was considered to be a response to cabozantinib. Additional molecular testing after disease progression revealed new MET amplification in the metastases, which is not related to cabozantinib resistance. However, according to one case report, the gap between in vitro studies and clinical cases can lead to dissimilar drug responses. Therefore, MET D1228N could be the underlying mechanism for both crizotinib resistance and cabozantinib resistance [15]. Further investigations are needed to explain the resistance mechanism of acquired mutations to develop more efficacious ROS1 inhibitors.

Molecular testing of the lung nodules and abdominal subcutaneous nodule showed that TMBs were 10.1 Muts/Mb and 3.8 Muts/Mb, respectively. The variation of the genetic mutation profiles and TMB during the disease progression revealed the highly heterogeneous character of the patient's cancer. In addition, the abdominal subcutaneous nodule was positive for PD‐L1 (50%), suggesting that the patient may receive clinical benefits from a combination of immunotherapy and chemotherapy [16]. Unfortunately, the patient died suddenly before she was ready for immunotherapy. Because immunotherapy and targeted therapy are gradually becoming common as clinical treatments, it is very important to choose suitable treatments for patients without delay.

Disclosures

The authors indicated no financial relationships.