EML4‐ALK Rearrangement and Its Therapeutic Implications in Inflammatory Myofibroblastic Tumors

A case of a patient who was successfully treated with crizotinib for a recurrent ALK‐rearranged pulmonary inflammatory myofibroblastic tumor is reported.

Abstract

With the advent of precision medicine, medical oncology is undergoing a transcendental change. These molecular studies have allowed us to learn about potential targeted therapies for patients with advanced cancers. Perhaps the best‐known example of success in precision medicine is chronic myeloid leukemia and its response to tyrosine kinase inhibitors targeting the BCR‐ABL kinase. Since that original discovery, the role of molecular therapeutics has expanded, and it now presents us with treatment options for common malignancies and rare atypical tumors. In this article, we present a case of a 61‐year‐old female with a recurrent pulmonary inflammatory myofibroblastic tumor. Subsequent molecular studies revealed an ALK rearrangement. The significance of this alteration in this tumor type and its therapeutic implications are discussed herein.

Key Points.

• This case exemplifies the heterogeneous behavior of inflammatory myofibroblastic tumors (IMTs) and the current role of targeted therapy in the therapeutic armamentarium of neoplastic processes.

• As evidenced by the different mutations found in IMTs, it is of great importance to perform next‐generation sequencing in uncommon neoplasms.

• These studies can find different potential targets and therapeutic options for patients devoid of standard effective therapies.

Introduction

Inflammatory myofibroblastic tumors (IMTs) are mesenchymal neoplasms with a heterogeneous clinical presentation, ranging from benign solitary tumors to aggressive neoplasms with metastatic potential. These tumors typically affect children and young adults but have been known to affect older adults in rare circumstances. Certain reports estimate that they comprise approximately 50% of benign lung lesions in children, with the most common sites of involvement being the lungs and the abdominopelvic region. [1]. They are characterized by a heterogeneous histology with variable degree of spindle, fibroblastic, myofibroblastic, and inflammatory cells.

More recently, cytogenetic and molecular sequencing has allowed the detection of rearrangements of the anaplastic lymphoma kinase (ALK) locus on chromosome 2 in these tumors. This discovery is of therapeutic relevance given our prior knowledge of ALK gene abnormalities as driver mutations in non‐small cell lung carcinoma (NSCLC) and its targetability through ALK inhibitors such as crizotinib. Here we describe a case of a patient with a recurrent ALK‐rearranged pulmonary IMT who was successfully treated with crizotinib. We also describe her exact molecular rearrangement partner and discuss potential relevance of determination of specific ALK molecular partners in prognosis and aggressiveness of disease.

Patient Story

The patient is a 61‐year‐old Hispanic female with history of congestive heart failure, chronic obstructive pulmonary disease, and a left‐sided breast cancer treated with lumpectomy, chemotherapy, and radiation. She initially presented in May 2016 with acute shortness of breath. The patient had been previously admitted in March 2016 for respiratory symptoms and fever and was diagnosed with a right lower lobe (RLL) community‐acquired pneumonia. At that time, she was treated with antibiotics and did improve until days prior to her current presentation.

In the emergency department, the patient underwent a chest computed tomography (CT) angiography to rule out a pulmonary embolism. Her imaging revealed improved aeration of the RLL, but there was now a more noticeable rounded area of airspace opacity measuring 3 × 2.8 cm; additionally, mediastinal and hilar adenopathies were appreciated. Subsequent positron emission tomography/CT revealed a highly fluorodeoxyglucose (FDG)‐avid lesion with an standardized uptake value (SUV) >20. Given these findings, the patient underwent a bronchoscopy, which revealed an endobronchial tumor that was completely occluding the basal posterior segment of the RLL. Biopsy of the lesion revealed a moderately cellular fascicular spindle cell neoplasm located in the submucosa. The neoplastic cells had palely eosinophilic cytoplasm and mildly atypical tapering nuclei (Fig. 1A). Immunohistochemical stains revealed cells that were negative for pan‐keratin, CK5, p63, SMA, and ROS1, focally positive for desmin, and strongly and diffusely positive for ALK (Fig. 1B). This tissue was sent for expert pathology review, and the patient was discharged home and planned for outpatient follow‐up.

Figure 1.

Biopsy findings. (A): Hematoxylin and eosin stain of inflammatory myofibroblastic tumor. Streaming fascicles of spindle cells admixed with few lymphocytes. (B): ALK antibody clone 5A4 from Leica Biosystems—at 1:100 with pressure cooker antigen retrieval. Diffuse cytoplasmic positivity. (C): Interphase fluorescence in situ hybridization (FISH) analysis was performed using the Abbott Molecular U.S. Food and Drug Administration‐approved ALK Break‐Apart FISH kit. For this case, 100 lung tumor nuclei were scored, and two abnormal break‐apart FISH signal patterns were seen in 21% of the cells. Normal cells show fused red and green signals (ALK 3′ is labeled with red fluorochromes and the 5′ is labeled with green fluorochromes). Abnormal cells show at least one single red and green signal apart indicating chromosomal break between the ALK 3’ and 5’.

Unfortunately, she developed hemoptysis, motivating an emergency department visit 3 weeks after discharge. By this time, further information from expert pathology review revealed that pathology was consistent with an inflammatory myofibroblastic tumor. During this admission, thoracic surgery was consulted for possible resection, but the patient was deemed not a surgical candidate. Given this, she underwent a bronchoscopy with laser therapy after porfimer sodium intravenous administration (photodynamic therapy). Forty‐eight hours later, debridement was done, followed by further laser light application and repeated debridement of the necrotic tissue. This led to gradual re‐expansion of the RLL and reduction in the size of the mass. However, the patient had early recurrence of the lesion with evidence of bronchial obstruction and required multiple interventions with laser therapy treatment and debridement. Given the rapid recurrence and findings of diffuse ALK staining by immunohistochemistry (IHC), additional studies were performed to further aid in management.

Molecular Tumor Board

Genotyping Results and Interpretation of the Molecular Results

First, fluorescence in situ hybridization (FISH) studies were performed and revealed an ALK gene rearrangement with an abnormal break‐apart signal pattern in 21% of nuclei (Fig. 1C). Of note was the concordance between initial ALK staining by IHC and FISH in our patient. It is important to mention that this is not always the case; thus, clinicians and pathologists should be aware of the possible discordance, and both studies should be performed in cases suspected to be IMTs [2]. Furthermore, we sought to determine the ALK fusion partner, and molecular profiling was performed at the Emory Medical Laboratory of Emory University Hospital, a Clinical Laboratory Improvement Amendments‐certified laboratory. After RNA preparation, The Archer FusionPlex Sarcoma Kit (ArcherDX, Boulder, CO) and next‐generation sequencing (on the Illumina MiSeq instrument [Illumina, San Diego, CA]) were performed. The Archer Sarcoma Fusion Panel 26 simultaneously detects fusions involving any of the 26 genes listed in Table 1. This test detects heterozygous fusions in tissue with 10% or greater tumor content or homozygous fusions in tissue with 5% or greater tumor content. In our patient's tumor, an EML4‐ALK fusion was detected. Further analysis to detect the exact variant of the fusion revealed that our patient had a Variant 5a, involving exon 2 of the EML4 gene and exon 20 of the ALK gene (Fig. 2). This variant has been previously described in NSCLC literature but is uncommon, having been reported in approximately 2% of cases with identified EML4‐ALK fusions [3]. With regard to IMTs, to our knowledge, it has been reported twice in the past, one in a toddler with an extremity IMT and another case in an adult female with a pulmonary IMT [2], [4]. To date, no prospective analysis to evaluate response rate in association with the different variants has been done. Nonetheless, retrospective studies evaluating this issue have shown discordant conclusions. It seems that the most sensitive variants to ALK inhibitors seem to be those that have a partial tandem atypical propeller (TAPE) domain, with less sensitivity to ALK inhibitors for variants with no TAPE domain (i.e., variants 3a/b and 5a) [3].

Table 1. Molecular characterization of inflammatory myofibroblastic tumors. Genes included in The Archer Sarcoma Fusion Panel 26.

Figure 2.

The EML4‐ALK fusion protein and its functional domains.

Abbreviations: CC, coiled coil; Gly‐rich, glycine rich; HELP, hydrophobic; MAM, extracellular; TKD, tyrosine kinase domain.

Functional and Clinical Significance of the ALK Translocation

From a historical perspective, IMTs were mostly described as inflammatory pseudo tumors, until the term plasma cell granuloma was coined by Bahadori and Liebow in 1973, based solely on histopathologic features [5]. Significant controversy as to the pathophysiology of this tumor followed, and it was largely felt to be a benign inflammatory and reactive process, as many of these lesions regressed with antibiotics and/or corticosteroids, rarely recurring after optimal local therapy. It wasn't until the 1990s when reports of possible clonality started to emerge from different case publications. Dr. Simon Treissman described the first such report in 1994. He described a case of a 3‐year‐old boy with an omental IMT with evidence of cytogenetic abnormality, specifically a t(2;9)(q1.3;p2.2) [6]. These findings in conjunction with subsequent investigations revealed that the majority of cases contained clonal rearrangements of the short arm of chromosome 2 [5], [6]. In 1999, Griffin et al. reported a case series of 11 patients with pulmonary and extra‐pulmonary IMTs that had documented cytogenetic abnormalities. In this series, three patients were shown to have abnormalities in chromosomal region 2p23, for the first time reporting a rearrangement in the ALK gene [7]. Subsequently, Lawrence et al. described the presence of TPM3/TPM4 as partner genes rearranged with ALK [8]. Several genetic rearrangements have been described and are shown in Table 2 [9].

Table 2. Molecular characterization of inflammatory myofibroblastic tumors (IMTs). Genetic rearrangements of IMTs described in the literature to date.

Specific to our case, the EML4‐ALK rearrangement has previously been described in different case reports, and these have predominantly been present in females, typically younger patients (age range: 6 months to 45 years) and most commonly have been described in pulmonary IMT, with only isolated cases in extrathoracic IMTs [4]. The prognostic significance of EML4 as a fusion partner in IMTs remains unclear; there have been cases describing very aggressive clinical course, but these have been isolated events [12].

Potential Strategies to Target the Pathway and Implications for Clinical Practice

Given the findings of ALK gene rearrangements as possible drivers of IMTs, targeted treatment options started to become evaluated. In 2010, Butrynski et al. enrolled two patients with locally and systemically recurrent unresectable IMTs in a phase I dose‐escalation trial of crizotinib (NCT00585195). One of these patients had an impressive response despite having had a very aggressive tumor, which promptly recurred after surgical excision and chemotherapy [22]. Experience with other ALK inhibitors has been limited, but Manfield et al. described a case of a patient with crizotinib‐resistant IMT that subsequently went on to have a prolonged partial response to ceritinib for approximately 24 months [12], [23]. Most recently, liquid biopsies have provided an important role in cancer therapeutics. Studies have shown that in patients with ALK‐rearranged malignancies who are on ALK inhibitors (especially NSCLC), these tests can provide information as to if mutations that confer resistance to particular ALK inhibitors (i.e., ALK^L1196M, ALK^G1202R) have developed, and assist in guiding the selection of further therapy, either next‐generation ALK inhibitors or systemic chemotherapy. The possibility of dynamic monitoring for response and resistance based on circulating tumor DNA next‐generation sequencing studies provides clinicians a noninvasive option for disease assessment. It is likely that such a strategy will also be highly valuable in a patient such as ours if the disease were to progress while on crizotinib.

In addition to ALK rearrangements, other actionable fusions found in the literature include ROS1 and NTRK3. ROS1 has been previously found as a driver in lung adenocarcinomas, and some ALK inhibitors have activity in such patients [24]. Another interesting finding was the previous report of an NTRK3 fusion in a patient with an IMT. Recently larotrectinib, a new pan‐tropomyosin receptor kinase (TRK) inhibitor, was evaluated in patients with TRK fusion‐driven cancers. This phase I trial revealed an unprecedented overall response rate of 78% [25].

Patient Update

Our patient had a very rapidly recurring tumor, which led to significant complications. Despite multiple interventions to attempt local control, she had frequent regrowth and complications secondary to endobronchial obstruction. Given the findings of an ALK rearrangement, the patient was started on systemic therapy with crizotinib 250 mg b.i.d. Respiratory symptoms improved initially, but approximately 3 months later, she developed diarrhea, which brought her into the hospital. An abdominopelvic CT was performed, which revealed improvement of the RLL mass. No infectious etiologies were found, and after improvement, she was able to resume crizotinib. The patient tolerated therapy well until symptoms of cough, mild hemoptysis, and shortness of breath concerning for disease progression developed 8 months from crizotinib initiation. Nonetheless, repeat chest CT demonstrated a continued response with significant tumor shrinkage (Fig. 3A, 3B). A repeat fiberoptic bronchoscopy to further evaluate the endobronchial lesion revealed a widely patent bronchus with no residual tumor (Fig. 3C, 3D). Her symptoms were attributed to exacerbation of congestive heart failure, with prompt improvement after aggressive diuresis. In summary, despite having an initial aggressive presentation with a rapidly recurring tumor, she has had a significant response to crizotinib that is still ongoing approximately 12 months after starting this therapy.

Figure 3.

Pulmonary mass before and after therapy. (A): Computed tomography (CT) chest reveals a mass in the subcarinal space measuring approximately 3 × 2.8 cm (arrow). (B): Repeat CT chest revealing tumor shrinkage, now measuring 2.1 × 2.2 cm (arrow). (C): Initial bronchoscopy revealed an obstructive mass in the posterior basilar segment of the right lower lobe. (D): Repeat bronchoscopy revealed a widely patent bronchus after therapy with crizotinib.

Glossary of Genomic Terms and Nomenclature

Sequencing: The process of determining the precise order of nucleotides within a DNA molecule

Locus: A locus (plural loci) is a fixed position on a chromosome

Fusion: A fusion gene is a hybrid gene formed from two previously separate genes

Translocations: Chromosome translocation is a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes

ALK gene: Anaplastic lymphoma kinase gene

Author Contributions

Conception/design: Fernando Vargas‐Madueno, Miguel A. Villalona‐Calero

Provision of study material or patients: Edwin Gould, Raul Valor

Collection and/or assembly of data: Fernando Vargas‐Madueno, Edwin Gould, Raul Valor, Miguel A. Villalona‐Calero

Data analysis and interpretation: Fernando Vargas‐Madueno, Edwin Gould, Miguel A. Villalona‐Calero, Nhu Ngo, Linsheng Zhang

Manuscript writing: Fernando Vargas‐Madueno, Miguel A. Villalona‐Calero

Final approval of manuscript: Fernando Vargas‐Madueno, Edwin Gould, Raul Valor, Miguel A. Villalona‐Calero

Disclosures

The authors indicated no financial relationships.