INI‐1 (SMARCB1)–Deficient Undifferentiated Sinonasal Carcinoma: Novel Paradigm of Molecular Testing in the Diagnosis and Management of Sinonasal Malignancies

Abstract

Sinonasal tumors consist of a group of rare heterogeneous malignancies, accounting for 3%–5% of all head and neck cancers. Although squamous cell carcinomas make up a significant portion of cancers arising in the sinonasal tract, there are a variety of aggressive tumor types that can present with a poorly differentiated morphology and continue to pose diagnostic challenges. Accurate classification of these unique malignancies has treatment implications for patients. Recent discoveries have allowed more detailed molecular characterization of subsets of these tumor types, and may lead to individualized treatments. INI‐1 (SMARCB1)–deficient sinonasal carcinoma is a recently identified subtype of sinonasal malignancy, which is characterized by deletion of the INI‐1 tumor suppressor gene. Loss of INI‐1 expression has emerged as an important diagnostic feature in several human malignancies including a subset of sinonasal carcinomas. In this article, we present a case of INI‐1 (SMARCB1)–deficient sinonasal carcinoma, provide an overview of recent advances in histological and molecular classification of sinonasal malignancies, and discuss challenges of caring for patients with these rare malignancies, as well as potential treatment implications.

Key Points

• Clinicians and pathologists should recognize that a variety of sinonasal tumors can present with a poorly differentiated morphology that warrants further workup and molecular classification.

• Routine workup of poorly or undifferentiated sinonasal tumors should include testing for INI‐1/SMARCB1, SMARCA4, and NUT.

• Patients with these molecularly defined subsets of tumors may benefit from clinical trials that seek to exploit these molecular alterations.

• The EZH2 inhibitor, tazemetostat, has demonstrated some antitumor activity in INI‐1–deficient tumors, and is currently under investigation.

Short abstract

Sinonasal tumors are a group of uncommon heterogeneous malignancies that account for 3% to 5% of all head and neck cancers. This article presents a case of INI‐1‐ (SMARCB1)‐deficient sinonasal carcinoma and discusses the challenges of caring for patients with these rare malignancies.

Patient Story

A 43‐year‐old Ukrainian man, lifelong nonsmoker, with a history of Graves’ disease status postradioactive iodine therapy, Gilbert's syndrome, and chronic sinusitis presented with 1 year of progressive right‐sided sinus pressure, headaches, and congestion. In the month leading up to presentation, he developed episodic right‐sided epistaxis and slight protuberance of the right eye.

Initial evaluation suggested sinusitis, however further workup was prompted by persistent symptoms despite a course of antibiotics. Magnetic resonance imaging (MRI) demonstrated a large mass arising from the right ethmoid sinus and obstructing the right frontal, maxillary, and sphenoid sinuses, with apparent involvement of the cribriform plate and possible involvement of the anterior cranial fossa. No lymphadenopathy was noted. Figure 1 shows representative MRI images.

Figure 1.

Magnetic resonance imaging of the brain with and without contrast. (A): Axial cut T1‐weighted with contrast demonstrating an enhancing mass within the right nasal cavity and paranasal sinuses with extension into the right extraconal orbit. (B): Coronal cut T2‐weighted image demonstrating dural involvement and mass effect on the inferior right frontal lobe.

Rigid nasal endoscopy revealed polypoid tissue filling the right nasal cavity, and several biopsy samples were taken. Pathological examination of the biopsy specimen demonstrated diffuse positivity for cytokeratin AE1/3, p63, p40, Ki67 (85%) and negativity for p16, CD56, synaptophysin, and Epstein‐Barr virus (EBV) by Epstein‐Barr encoding region in situ hybridization. Subsequent immunohistochemical analysis showed complete loss of INI‐1 (SMARCB1) expression in the tumor nuclei, no loss of expression of BRG1 (SMARCA4), and negative NUT antigen staining (Fig. 2).

Figure 2.

Histomorphology images from the patient's tumor. (A): Low power view of infiltrating poorly differentiated tumor with overlying sinonasal epithelium at bottom (H&E, original magnification ×40). (B): High power view shows nests of undifferentiated small round cell tumor (H&E, original magnification ×200). (C): The tumor shows complete loss of INI‐1 expression; background stromal cells are positive internal control with retained nuclear staining (immunohistochemistry, original magnification ×100). (D): Cytokeratin AE1/3 stain diffusely highlights tumor cells, establishing diagnosis of carcinoma (immunohistochemistry, original magnification ×100).

PET‐computed tomography (CT) confirmed a fluorodeoxyglucose (FDG) avid right ethmoid sinus mass extending medially into the nasal cavity, laterally into the right orbit and superiorly into the right frontal sinus, as well as FDG avid right level IB, IIA, and IIB cervical lymph nodes. No distant metastatic disease was identified. The patient underwent endoscopic anterior skull base resection and right selective neck dissection with nasoseptal flap reconstruction. At the time of surgery, tumor was noted to extend into the right nasal vestibule, maxillary sinus, ethmoid sinus, sphenoid sinus, dura, and orbit. Pathologic review of the surgical specimen was consistent with poorly differentiated sinonasal undifferentiated carcinoma (SNUC). Additional findings included a positive right anterior dural margin, presence of lymphovascular invasion, and 13 of 52 dissected nodes (levels 1B–4) positive for metastatic carcinoma without extranodal extension. The overall pathological findings were consistent with stage IVB (T4bN2bM0) INI‐1 (SMARCB1)–deficient sinonasal undifferentiated carcinoma by tumor‐node‐metastasis staging system of the American Joint Committee on Cancer 8th edition.

The patient's case was discussed at the Montefiore Medical Center Multidisciplinary Head and Neck and Molecular Tumor board. After extensive review of literature, the consensus was to treat our patient with adjuvant chemoradiation given multiple high risk features, including positive margins. Based on the experience documented by Gray et al. 1, the patient completed four cycles of cisplatin and etoposide with concurrent proton beam therapy (60 Gy in 30 fractions). He tolerated treatment well with manageable nausea and mucositis, although he required a dose reduction of chemotherapy by 20% for neutropenia. Shortly after completing treatment he developed bilateral serous otitis media and required bilateral myringotomy procedures with tympanostomy tubes placed. CT and MRI documented an excellent response to treatment with only mild posttreatment changes.

Subsequent surveillance imaging with MRI of the brain 6 months after completion of adjuvant chemoradiation demonstrated two small enhancing dural based lesions consistent with metastatic disease. PET‐CT at this time was negative for systemic disease. Comprehensive genomic profiling using next‐generation sequencing was performed on the original surgical specimen (FoundationOne). This testing confirmed loss of SMARCB1 without any other molecular alterations identified. The tumor was microsatellite stable and a low tumor mutation burden of one mutation per megabase was noted. After the case was reviewed again at a multidisciplinary tumor board, the patient completed SBRT to his central nervous system (CNS) disease without complication. He remained on close clinical surveillance and 10 months later had progression of CNS disease. Several options were considered including neurosurgical tumor debulking versus additional radiation, however ultimately he was referred for a compassionate use study with the EZH2 inhibitor, tazemetostat.

Introduction

Sinonasal tumors are a group of uncommon heterogeneous malignancies, accounting for 3%–5% of all head and neck cancers. Presenting symptoms frequently are nonspecific including sinus pressure, nasal obstruction, epistaxis, headache, cranial nerve compression symptoms, visual impairment, or periorbital swelling. As a result, these tumors are often clinically silent until more advanced stages. Thus, patients often present with involvement of important surrounding structures, such as the orbit or dura, as well as with cervical lymph node involvement. While squamous cell carcinomas and adenocarcinomas make up the majority of these tumors, a wide range of malignancies can occur in the sinonasal tract including, but not limited to SNUC, esthesioneuroblastoma (ENB), small cell carcinoma, melanoma, lymphoma, and rhabdomyosarcoma.

With increasing molecular testing of tumors, unique subsets of sinonasal tumors, as with other malignancies, have been described by their unique molecular alterations 2, 3. This was reflected in the most recent World Health Organization histological classification of the tumors of the nasal cavity and paranasal sinuses which now includes the following key subtypes: squamous cell carcinoma, intestinal‐type adenocarcinoma, nonintestinal sinonasal adenocarcinoma, NUT midline carcinoma, biphenotypic sinonasal sarcoma, human papillomavirus (HPV)‐related carcinoma with adenoid cystic features, SMARCB1 (INI‐1)–deficient sinonasal carcinoma, renal cell‐like adenocarcinoma, sinonasal lymphoepithelial carcinoma, and SNUC.

The underlying etiologies of these diverse sinonasal cancers are largely unknown; however, documented risk factors include cigarette smoking, a previous history of radiation, and oncogenic viruses, such as HPV. In addition, a link between various occupational carcinogens including hardwood dust, and leather dust has been identified, particularly with intestinal‐type adenocarcinomas of the sinonasal tract.

There is evidence that sinonasal squamous cell carcinoma associated with inverted sinonasal (Schneiderian) papilloma (ISP) represents another biologically distinct sinonasal tumor. Udager et al. demonstrated activating EGFR exon 19 and 20 mutations in 88% of ISP and 77% of ISP‐associated sinonasal squamous cell carcinoma. Evidence of an etiologic link was provided by concordant EGFR genotypes between matched pairs of ISP and associated sinonasal squamous cell carcinoma 4. Additional HPV DNA testing in this cohort of patients revealed that either an EGFR mutation or HPV infection was present in all cases of ISP and ISP‐associated sinonasal squamous cell carcinoma, and these findings were essentially mutually exclusive of each other. Further evidence that these findings represent unique mechanisms of oncogenesis is the predominantly low risk subtypes of HPV found in these cases as opposed to the high risk subtypes seen more commonly in non‐ISP–associated sinonasal squamous cell tumors 5.

Despite improvements in overall survival rates for sinonasal carcinomas, morbidity and mortality remain high, with many patients presenting with locally advanced disease. Multimodality treatment remains the mainstay of treatment, including surgery, radiation, and chemotherapy; however, recurrence rates are generally high, and additional treatment options are needed. Thus, identification of molecular pathways as drivers of these malignancies remains crucial for accurate classification and more importantly for the development of targeted therapies and clinical trials for these biologically defined subsets of patients.

Histopathology and Immunohistochemistry: The Diagnostic Dilemma

Histological evaluation of INI‐1/SMARCB1–deficient sinonasal carcinomas demonstrates highly infiltrative tumors in the submucosal tissues of the nasal cavity and sinuses often with bone invasion. Lesions are characterized by nests or sheets and cord like architecture that may lack glandular or squamous features. Additional histological features include rhabdoid and basaloid cells or focal clear cell features. A variety of sinonasal tumors can present with overlapping poorly differentiated or undifferentiated morphology, and initial considerations for the surgical pathologist facing a “small round cell tumor” of the sinonasal tract include melanoma, lymphoma, and rhabdomyosarcoma (Table 1). After entities such as these have been ruled out, further testing should account for malignancies with neuroendocrine features such as ENB and high‐grade neuroendocrine carcinomas like small cell or large cell carcinomas. When left with a nonspecific poorly differentiated carcinoma of the sinonasal tract, the differential includes SNUC, and further delineation should routinely include immunohistochemistry testing for INI‐1/SMARCB1, SMARCA4, and NUT. Additional molecular testing is also available for INI‐1 mutations as well as fluorescence in situ hybridization testing for NUT translocation t(15;19).

Table 1.

Helpful morphological features and useful stains in poorly differentiated or undifferentiated sinonasal tumor types

Tumor type	Basic morphology	IHC
Mucosal melanoma	Spindle and epithelioid cells that may show melanin pigment, possible in situ element present	Positive S100, HMB‐45, Melan‐A
Extranodal NK/T cell lymphoma, nasal type	Discohesive polymorphous small to large cells with extensive angiodestructive growth and geographic necrosis	Positive CD45, EBER (ISH), CD56
HPV‐mediated squamous cell carcinoma	Cohesive growth of cells with high nuclear to cytoplasmic ratio with basaloid morphology with focal keratinization	Positive p40, p16, cytokeratin stains
WHO type III nasopharyngeal carcinoma (lymphoepithelial‐like carcinoma)	Syncytial growth of tumor cells with prominent associated lymphoplasmacytic reactive inflammatory infiltrate	Positive EBER (ISH), cytokeratins, p40
Rhabdomyosarcoma (alveolar type)	Tumor cells separated into nests “alveoli” by fibrous septa; large eosinophilic cells “strap cells” with cross striations	Positive desmin, myogenin, MyoD1
Olfactory neuroblastoma	Salt and pepper chromatin, rosettes, neurofibrillary matrix	Positive chromogranin, CD56, synaptophysin Sustentacular cells positive for S100, negative cytokeratin
High grade neuroendocrine carcinoma (small cell or large cell carcinoma)	Small cell: nuclear molding, necrosis, crush artifact, high mitotic rate Large cell: prominent nucleoli, high mitotic rate	Positive chromogranin, synaptophysin, CD56, TTF‐1, cytokeratin
Sinonasal undifferentiated carcinoma (SNUC)	Undifferentiated sheets and nests of pleomorphic, high grade tumor cells, necrosis, lacking glandular or squamous morphology	Positive cytokeratin
Inverted sinonasal (schneiderian) papilloma–associated sinonasal squamous cell carcinoma	Inverted “ribbonlike” pattern and nests of immature squamous epithelial cell associated with neutrophilic intraepithelial inflammation	Positive p63, p40, and cytokeratins

Abbreviations: HPV, human papillomavirus; IHC, immunohistochemistry; ISH, in situ hybridization; WHO, World Health Organization.

INI‐1 (SMARCB1)–Deficient Malignancies

SMARCB1 is known to be deleted in various cancer types 6, 7. Deficiency of SMARCB1 was first recognized as a distinguishing feature of atypical teratoid and rhabdoid tumor of the central nervous system and malignant rhabdoid tumors of the kidney and soft tissue 7, 8, 9, 10. Since then, the list of SMARCB1‐deficient tumors has grown to include epithelioid sarcoma, renal medullary carcinoma, myoepithelial carcinoma of soft tissue, epithelioid malignant peripheral nerve sheath tumor, extraskeletal myxoid chondrosarcoma, and sinonasal undifferentiated carcinoma 6, 11, 12, 13, 14. Malignant rhabdoid tumors, typically seen in infancy, were shown to have biallelic inactivation of the SMARCB1 gene in the vast majority of these tumors. Most of these cases are felt to be sporadic, but germline mutations have also been documented. Although this was the first evidence to suggest alterations in SWItch/Sucrose Nonfermentable (SWI/SNF) complexes driving carcinogenesis, subsequent genome sequencing has revealed a variety of mutations in SMARCB1 as well as other SWI/SNF genes across several malignancies 15.

Functional and Clinical Significance of SMARCB1/INI‐1 Gene

SWI/SNF complexes are a family of ATP‐dependent multi‐subunit chromatin remodeling complexes found in both prokaryotes and eukaryotes. The exact mechanism by which these complexes mediate chromatin remodeling is not fully understood, but there is evidence that they are involved in nucleosome remodeling by disrupting histone‐DNA contacts 16. SMARCB1/INI‐1 (also known as BAF47) is a core subunit of the SWI/SNF complex, encoded at chromosome 22q11.2, and acts as a tumor suppressor by regulating cell proliferation and gene transcription. 17, 18, 19. The INI‐1 protein is ubiquitously expressed in normal eukaryotic cell nuclei and is involved in multiple molecular pathways that are altered in cancer development, including epigenetic pathways and chromatin remodeling through activation of polycomb proteins (PRC2), cell cycle inhibition via cyclin D1 suppression, activation of retinoblastoma tumor suppressor gene, induction of tumor suppressor protein P16, and inhibition of WNT/β‐catenin oncogenic signaling pathway (Fig. 3) 17, 20, 21, 22, 23, 24.

Figure 3.

Functional and clinical significance of INI‐1/SMARCB1. SMARCB1 with SWI/SNF complex inhibits cell cycle progression through inhibition of cyclin D1, histone methylation repression through PRC2 complex inhibition and tumor promoter gene downregulation through WNT pathway inhibition.

Abbreviations: PRC2, polycomb protein; RB, retinoblastoma; SWI/SNF, SWItch/Sucrose Nonfermentable.

Potential Strategies to Target the INI‐1/SMARCB1 Pathway

Currently, aggressive multimodality treatment of INI‐1–deficient sinonasal carcinomas is based on experience with other sinonasal malignancies including case series of SNUC. When possible, patients are often treated with surgical excision followed by adjuvant radiation or concurrent chemoradiation. Also under investigation is the use of induction chemotherapy followed by surgery and adjuvant radiation in the treatment of sinonasal cancer (NCT03493425). Unfortunately, many patients with INI‐1–mutated tumors either relapse early or become refractory to standard chemoradiation, making these cases challenging to face as a clinician. Thus, new targeted therapies, potentially exploiting the loss of INI‐1, are needed.

Animal and human studies have shown that SWI/SNF tumor suppressor proteins act as antagonists of the polycomb gene enhancer of zeste homolog 2 (EZH2). EZH2 is a catalytic subunit of the PRC2 polycomb complex mediating histone methylation resulting in tumor suppressor gene silencing, oncogenic transformation, metastasis development, and drug resistance 25, 26, 27, 28. Several studies have shown that the SWI/SNF complex directly binds to the EZH2 promoter and suppresses expression of the EZH2 gene. Loss of INI‐1 disrupts the SWI/SNF complex function and thereby leads to increased activity in EZH2. Activation of EZH2 upregulates oncogenic pathways including myc, sonic hedgehog, and WNT/b‐catenin and suppresses transcription of tumor suppressor genes 22, 25, 28. EZH2 is therefore a promising therapeutic target in INI‐1–deficient malignancies, and several inhibitors of EZH2 have been developed and are currently being tested in human clinical trials 27. There is evidence that this pathway can for example be effectively targeted by tazemetostat (EPZ‐6438), a potent small molecule that selectively inhibits EZH2 15, 16, 17, 18. The competing mechanism of tazemetostat makes this a potential targeted therapy for INI‐1–deficient malignancies (Fig. 4).

Figure 4.

Mechanism of Tazemetostat in SMARCB1/INI‐1–deficiency. (A): SMARCB1 within the SWI/SNF complex inhibits PRC2/EZH2 function. This leads to histone H3K27 methylation inhibition and expression of cell cycle suppressor genes including p16 and decreased activity of cell cycle promoter genes (e.g., cyclin D1). (B): SMARCB1 inactivation leads to histone methylation and tumor suppressor gene downregulation, Tazemetostat (EPZ‐6438) is a selective oral inhibitor of EZH2. EZH2 inhibits the downstream pathway similar to SMARCB1.

Abbreviations: PRC2, polycomb protein; SWI/SNF, SWItch/Sucrose Nonfermentable.

Indeed, tazemetostat has been successfully tested in several phase I and phase II, open‐label, multicenter clinical trials in various cancer types including diffuse large B‐cell lymphoma, follicular lymphoma, SMARCA4 negative and INI‐1–negative tumors, synovial sarcoma, mesothelioma, and adult malignant rhabdoid tumor of the ovary (NCT02601950, NCT02601950, NCT02601937, NCT02601937, NCT03213665). The first in‐human phase I study investigating the safety, clinical activity, and pharmacokinetics of tazemetostat enrolled 64 patients with INI‐1–deficient advanced solid tumors or B‐cell non‐Hodgkin lymphoma 29. Tazemetostat showed a favorable safety profile and early antitumor activity leading to the phase II study that is currently underway. Other ongoing trials include a phase II study of tazemetostat in INI‐negative tumors or relapsed and refractory synovial sarcoma (NCT02601950) and a phase II pediatric MATCH trial in patients with solid tumors, non‐Hodgkin lymphoma, or histiocytic disorders with an EZH2, SMARCB1, or SMARCA4 gene mutation (NCT03213665).

The accurate diagnosis of poorly or undifferentiated sinonasal carcinomas remains a significant challenge given the heterogeneous group of malignancies that can arise and the overlapping histopathologic features. Furthermore, there is a paucity of data to guide management of these often aggressive subsets of tumors. Nonetheless, recent discoveries now allow more detailed molecular characterization which must be included in the workup of appropriate carcinomas of the sinonasal tract, such as SMARCB1, SMARCA4, NUT, HPV, and EBV testing. This will ensure proper recognition of these unique emerging entities but even more importantly guide personalized management including referral for clinical trials designed for molecularly defined subtypes.

Disclosures

The authors indicated no financial relationships.