Primary Oropharyngeal SMARCA4-Deficient Carcinoma: Expanding the Diagnostic Spectrum in Head and Neck Cancer

Abstract

With the advent of molecular immunohistochemistry and next generation sequencing, Switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex altered tumors have gained recognition recently. SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily B member 1 (SMARCB1) and SMARCA4 are the primary SWI/SNF components altered in several recently described undifferentiated malignancies in head and neck region with predilection for paranasal sinuses in SMARCB1-deficient tumors and nasal cavity in SMARCA4-deficient tumors. However, to the best of our knowledge, SMARCA4-deficient tumors of the oropharynx have not been described. We present an unusual case of SMARCA4-deficient carcinoma of the oropharynx (palatine tonsil) which is the first case in the literature, expanding the topographic distribution of SMARCA4-deficient tumors in the head and neck region and emphasizing the importance of BRG1 as an essential immunohistochemical marker for the diagnosis of this distinct entity.

Introduction

Inactivating mutations involving elements of the Switch/Sucrose non-fermentable (SW1/SNF) chromatin remodeling complex (CRC) have recently been described in the head and neck and are associated with a distinct clinical and pathological profile. SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily B member 1 (SMARCB1)-deficient carcinoma most commonly presents in the paranasal sinus, while SMARCA4/Brahma related gene (BRG1)-deficient carcinomas predominantly present in the nasal cavity. Oropharynx as a primary site for SMARCA4/BRG1-deficient carcinoma has not been described in the literature [1–5].

The diagnostic hallmark of SMARCA4/BRG1-deficient carcinoma is diffuse loss of protein immunoexpression of BRG1 in tumor cells, along with absence of any specific histological pattern or subtype of tumor. Outside of the head and neck region, SMARCA4-deficient carcinomas have been described elsewhere in lung, Müllerian system, gastrointestinal tract (GIT) and genitourinary tract (GUT). These tumors are associated with an aggressive clinical course and poor prognosis despite multimodality treatment [5–7].

We present a case of SMARCA4-deficient carcinoma of oropharynx (tonsil), expanding the profile and distribution of this emerging tumor type.

Case Report

A 67-year-old male with no significant family history or past medical history presented with pain of the right side of throat (pharynx) radiating to right ear and associated with a globus sensation for 2 months. Direct laryngoscopy revealed enlargement of the right tonsil and vallecula.

Magnetic resonance imaging (MRI) of the neck showed a soft tissue lesion in right tonsillar fossa involving the posterior tonsillar pillar, right lateral and posterior oropharyngeal wall measuring 2.0 × 2.5 cm, with enlarged right level II lymph nodes. Positron emission tomography and computed tomography (PET-CT) scan reaffirmed the MRI findings with no other metabolically active disease elsewhere in the body (Fig. 1).

Fig. 1.

Pretreatment Images: Images a, b, c, d showing right tonsillar lesion with right cervical lymph nodes. Post concurrent chemo-radiotherapy images: Images e, f, g, h, i showing response in right tonsil lesion with right cervical lymph nodes. However, new FDG avid right pleural thickening, right pleural effusion, liver lesions and bone lesions. {18F-FDG PET-CT scan: Image a and e (maximum intensity projection, MIP); Image d, f, g, h, i (fused axial). Axial MRIcontrast: Image b (T1W) and image c (T2W)}

The histopathological examination of the right tonsillar mass revealed sheets and nests of undifferentiated large epithelioid to polygonal tumor cells, with vesicular chromatin, conspicuous nucleoli, conspicuous mitoses and focal necrosis (Fig. 2).

Fig. 2.

Tonsillar biopsy on low power magnification revealed diffuse proliferation of tumor cells in sheets (a). High power magnification showed large atypical epithelioid cells having abundant eosinophilic cytoplasm, irregular nuclear contours, vesicular chromatin and conspicuous nucleoli with many apoptotic figures (b), and areas of necrosis (c) with significant mitosis (d). FNAC smears from right cervical lymph node [e: May Grunwald Giemsa (MGG) and f papanicolaou stain (PAP)] shows loosely cohesive clusters of neoplastic cells which are ovoid to spindled in shape, have copious cytoplasm, irregular nuclei and granular chromatin

By immunohistochemistry (IHC), tumor cells were diffusely positive for pancytokeratin (CK) (clone AE1/AE3), while negative for CK7, leukocyte common antigen (LCA), P40 and P16. Additional testing was negative for synaptophysin, chromogranin, nuclear protein in testis (NUT), and chromogenic in situ hybridization for Epstein-Barr encoding mRNA (EBER-ISH), while expression of integrase interactor-1(INI-1/SMARCB1) was retained. To complete the work-up for undifferentiated carcinoma with large epithelioid cells, BRG1 IHC was performed, showing complete loss of BRG1 (SMARCA4) expression in the tumor cells with retained expression in non-tumoral cells (Fig. 3).

Fig. 3.

On immunohistochemistry (IHC) tumor cells are positive for Pan-cytokeratin (CK) (a), with loss of Brahma related gene (BRG1) expression (b) {the stromal cells (internal control) show retained BRG1 expression} The tumor cells are immunonegative for p40 (c), Nuclear protein in testis (NUT) (d), and synaptophysin (e), with retained Integrase interactor-1 (INI1) expression (f)

Histomorphology and IHC findings provided a tangible evidence for the final diagnosis of SMARCA4/BRG1-deficient carcinoma of the right tonsil (oropharynx). The fine needle aspiration cytology performed from the right level II lymph node was positive for malignant cells, suggestive of metastatic poorly differentiated carcinoma.

The case was discussed in multispecialty tumor board, and the patient was planned for concurrent chemotherapy and intensity-modulated radiation therapy (IMRT). Subsequently, the patient received 6 cycles of weekly Cisplatin 70 mg IV along with Intensity-modulated RT (70Gy/35#). The patient tolerated the treatment well with relief from dysphagia and showed an overall significant clinical response.

However, 2 weeks following completion of therapy, the patient presented with complaints of right-sided chest pain accompanied and shortness of breath. Radiological examination (chest X-ray, ultrasound and CT) showed right-sided multiloculated pleural effusion, which on cytology examination was confirmed to be malignant, consistent with progressive disease

PET-CT showed metabolically inactive right tonsillar thickening and lymph nodes (significant response to treatment at local site); however, there was interval development of recurrent, right-sided pleural effusion and pleural thickening with some infiltrates in the left lung. Metabolically active enlarged mediastinal lymph nodes were seen along with few metabolically active hypodense lesions in the liver (SUV max 6.9; segment IV/VII).

The case was again discussed in tumor board, and in view of distant metastasis and disease progression following treatment, the poor prognosis was explained to the family. The patient was referred for palliative care and succumbed to the disease after one month.

Discussion

In recent years, molecular investigation has led to a proliferation of unique diagnostic entities in the head and neck, many of which have recently been incorporated in the WHO classification of head and neck tumors (5th edition) [2]. Among these, tumors associated with inactivating mutations involving different subunits of the SWI/SNF chromatin-remodeling complex and NUT-rearranged carcinoma have been classified as distinct genetic entities [1, 2, 5].

SWI/SNF is a highly conserved complex of more than 20 different genes mapped to different regions on the chromosomes and plays an important role in regulation of cell proliferation and differentiation through their enrichment at the sites of promoters and enhancers of active genes. Although the precise function of this complex is not completely understood, it has been perceived that the different components of the SWI/SNF complex function as tumor suppressors. Hence, inactivating mutations, deletions and even rarely epigenetic silencing mechanism can lead to gene inactivation, resulting in tumor initiation and loss of respective protein expression by IHC. SMARCB1 (INI1) is a core subunit and SMARCA4 (BRG1) is one of the two catalytic subunits of SWI/SNF mapped to chromosomal region 22q11.2 and 19p13.2, respectively [1, 3, 5].

In the head and neck, SMARCB1-deficient carcinoma is rare and predominantly involves the paranasal sinus, especially ethmoid sinus with peak incidence in 6th decade. SMARCA4-deficient carcinoma is even rarer and predominantly involves the nasal cavity, with peak incidence in 5th decade [2]. Both of these tumors predominantly affect males. Besides the sinonasal region, SMARCA4-deficient malignancies have also been described in thorax, lung, GIT, ovary and GUT; however, there had been no previously documented case described in the oropharynx [1, 5–7].

SMARCA4-deficient malignancies are aggressive, characterized by undifferentiated histomorphology showing large or rhabdoid cells and, less frequently, small basaloid cells. These tumors do not show any specific histological differentiation (no glandular configuration or squamous cell features or palisading pattern) and the diagnosis is supported by negative IHC expression for CK5, P63, P40, NUT, P16 and rare focal expression of CK7. Complete loss of SMARCA4/BRG1 in tumor cells as a consequence of inactivating mutations in SMARCA4 gene, along with retained expression of INI1/SMARCB1, is diagnostic in these cases [1, 3–6].

Interestingly, variable expression of neuroendocrine IHC markers like synaptophysin, chromogranin and CD56 is commonly seen without any nuclear and chromatin features of neuroendocrine differentiation, which may prompt an erroneous diagnosis of large cell neuroendocrine carcinoma [1, 5, 6].

Agaimy et al. [5] has described 10 cases of SMARCA4-deficient carcinoma of the sinonasal region, out of which six cases were initially classified as neuroendocrine carcinoma. All these cases exhibited complete loss of SMARCA4, while SMARCB1/INI1 was retained. Co-loss of SMARCA2 was seen in 1 of 8 cases, and at least focal synaptophysin and chromogranin expression was seen in 9 cases and 4 cases, respectively. Small cell morphology with basaloid features was seen in 3 cases, while rest of the cases showed large cell morphology with or without rhabdoid differentiation. Follow-up was available in 6 cases, of which 4 patients succumbed to disease (median survival: 3 months), while the other two patients were alive with disease, under palliative therapy.

Kakkar et al. [6], had described 12 cases of SMARCA4-deficient sinonasal carcinoma, out of which three cases were previously published. Five cases had the initial diagnosis of teratocarcinosarcoma (TCS), while remaining cases were initially reported as poorly differentiated neuroendocrine carcinoma or poorly differentiated malignant tumor. Multimodality treatment was offered wherever feasible. The follow-up was available in 7 cases, of which 4 patients died within 3 to 35 months after the disease onset. Two patients were alive with residual disease after 7 months and 34 months from the symptoms onset; while single patient was alive without disease after 35 months. SMARCA4 (BRG1) loss was diffuse and complete in tumor cells 10 cases, while 2 cases showed focally retained expression [5, 6].

In the presented case, the pertinent histomorphological differentials were NUT carcinoma, large cell neuroendocrine carcinoma, and lymphoepithelial carcinoma. However, all the neuroendocrine IHC markers (including INSM-1), EBER-ISH and NUT IHC were negative, while diffuse loss of SMARCA4/BRG1 assisted in establishing the final diagnosis.

In the head and neck, SMARCA4/BRG1 loss has also been described in sinonasal teratocarcinosarcoma, an aggressive malignancy. It is suggested that this entity and SMARCA4-deficient sinonasal carcinoma may share common lineage [7].

SMARCA4-deficient sinonasal carcinoma seems to be clinically more aggressive than SMARCB1-deficient carcinoma [1, 5, 8]. The patient in the presented case showed evidence of distant metastasis within 2 weeks of completion of concurrent CT and IMRT, and succumbed to disease after 7-months of diagnosis. This case was also a diagnostic challenge, as there has been no documented case of SMARCA4-deficient oropharyngeal carcinoma in the prevailing literature. Hence, it should always be kept as a histological differential when dealing with undifferentiated carcinoma or malignancy at this site.

Regarding, the treatment of these aggressive SW1/SNF deficient malignancies, no specific therapy has been approved. However, therapeutic opportunities targeting the enhancer of zeste homolog 2 (EZH2), cyclin dependent kinase 4/6 (CDK4/6) and other targets are being developed. Multiple immune checkpoint inhibitors are currently being investigated to exploit the aberrations of SWI/SNF components [1, 9].

Conclusion

SMARCA4/BRG1 deficient carcinomas are rare, aggressive malignancies in head and neck region and may even primarily involve oropharynx which can be misdiagnosed as neuroendocrine carcinoma due to its overlapping histomorphology and immunophenotype. Hence, diligent histopathological examination, judicious IHC panel and familiarization with this entity at this anatomical site is imperative to clinch the precise diagnosis; this carries distinct prognostic and therapeutic implications.

Author Contributions

1. Substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data—Dr. SP, Dr. SG, Dr. MK, Dr. HD, Dr. MG, Dr. JSS, Dr. MG, Dr. AM. 2. Drafting the article and revising it critically for important intellectual content—Dr. SP, Dr. MK, Dr. HD, Dr. AM. 3. Final approval of the version to be published—Dr. SP, Dr. MK, Dr. HD.

Funding

The authors neither received support from any organization for the submitted work, nor was there any funding to conduct the study or to assist with manuscript preparation.

Data Availability

Availability of data and material is possible upon reasonable request, de-identified for maintenance of anonymity and compliance with IRB approval.

Code Availability

Not applicable.

Declarations

Conflict of interest

All authors certify that they have no affiliations with or involvement in any organization or entity with any financial interest or non-financial interest in the subjectmatter or materials discussed in this manuscript.

Ethical Approval

All procedures performed in this study involving human participants were inaccordance with the ethical standards of the institutional and/or national research committee andwith the 1964 Helsinki declaration and its later amendments or comparable ethical standards.The study was approved by the Institutional Review Board (Rajiv Gandhi Cancer Institute &Research Centre), vide the ethical approval letter number Res/SCM/59/2023/63)

Informed Consent

Informed consent was obtained from the subject included in the case report.

Consent to Participate and Publication

Written informed consent was obtained from the patient for publication of this case report and accompanying images.