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SMARCB1/INI1-deficient undifferentiated tumour of the thorax: a case report and review of the literature
Abstract
The 5th WHO classification of thoracic tumours includes thoracic SMARCA4-deficient undifferentiated tumour (SMARCA4-UT) among the “other epithelial tumours of the lung” chapter. Herein, we present a case of undifferentiated thoracic neoplasm with retention of SMARCA4 expression, lack of NUT fusion protein and loss of SMARCB1/INI1 expression. After presenting the clinical and pathological features of the tumour, we carried out a review of the literature on the same topic. Albeit very rare, we believe this entity should be included in the heterogeneous group of undifferentiated neoplasms of the thorax.
Introduction
SMARCB1, also known as INI1, is a tumour suppressor gene located on chromosome 22 and is one of the subunits of the SWI/SNF chromatin remodelling complex, which plays a critical role in regulating gene expression and chromatin organization 1. Genomic alterations in SMARCB1 subunit, as in other SWI/SNF complex subunits such as SMARCA4, SMARCA2 and ARID1A, and their oncogenic implications have been long discussed.
The 5th WHO classification of thoracic tumours includes thoracic SMARCA4-deficient undifferentiated tumour (SMARCA4-UT) among the “other epithelial tumours of the lung” chapter 2. These neoplasms are defined as high-grade malignant tumours showing undifferentiated and, less frequently, rhabdoid morphology and defective immunohistochemical expression of SMARCA4 (or BRG1). They typically involve the mediastinum, lung and/or pleura with variable infiltration of the chest wall. SMARCA4-UT typically shows complete loss of SMARCA4 expression, even though nearly 25% of cases only exhibit only a reduced expression, which is frequently associated with SMARCA2 (or BRM) loss and SMARCB1 retention. Histologically, these neoplasms consist of solid proliferations of large and discohesive elements with variable pleomorphism and prominent nucleoli. Mitosis and necrosis are common and rhabdoid elements can also be identified. Immunohistochemically, they often show a focal and weak expression of cytokeratins, but some cases may be completely unreactive. Diffuse positivity for synaptophysin has been reported, whereas TTF1, p40, WT1 and claudin-4 staining are much more variable, even with just focal positivity 3,4.
On the other hand, most of the initially described SMARCB1-deficient neoplasms were considered epithelioid sarcomas or tumours characterised by a “rhabdoid phenotype” (for example malignant rhabdoid tumours (MRTs) of the kidney, or central nervous system atypical teratoid/rhabdoid tumours (AT/RTs) 5,6. As of today, deletion in this gene has been identified in numerous other neoplasms, broadly referred to as SMARCB1-deficient cancers, which are characterised by a highly stable genome with SMARCB1 often being the only mutated gene 7. SMARCB1-deficient renal medullary carcinoma and SMARCB1-deficient sinonasal carcinoma are both recently reported entities associated with this unique gene alteration, together with paediatric poorly differentiated chordoma, myoepithelial carcinomas and other highly aggressive and rare tumours of the GI tract, pancreas, urologic and gynaecologic tract 8-17. Recent estimates show a prevalence for SMARCB1 alterations in all cancers between 1.4% and 5% 18,19. Moreover, germline heterozygous mutations of SMARCB1 characterise hereditary syndromes such as Rhabdoid Tumour Predisposition Syndrome 1 (RTPS1) and familial schwannomatosis 20-22.
Given the wide distribution of tumour entities related to SMARCB1 deficiency in many body sites, such an inactivation is conversely exceedingly rare in thoracic neoplasms, and little is known about its clinical and prognostic role. Hereafter, we present a case of SMARCB1(INI1)-deficient intrathoracic undifferentiated tumour diagnosed in our Institution and revise the literature regarding few other similar occurrences.
Case presentation
A 38-year-old man never smoker with an otherwise unremarkable medical history was referred to the otorhinolaryngology department of our Institution for recurring episodes of haemoptysis. Fibro-laryngoscopy showed no significant alterations. A thoraco-abdominal CT scan was performed for persisting symptoms: the scan showed a 58x48 mm solid mass, grossly rounded, with clear edges and arterial vascularisation, peripherally located in the lateral segment of the right middle lobe (RML) (Fig. 1). Lung parenchyma surrounding the lesion showed ground glass opacity with crazy-paving pattern, secondary to alveolar haemorrhage. No other focal lesion was detected in lung parenchyma, as well as pleural and pericardial effusion, hilar, mediastinal, and axillary lymphadenopathy or alterations in abdominal organs.
The patient underwent a pulmonary needle biopsy of the lesion: at histopathological examination, solid sheets of undifferentiated, non-keratinizing, medium size, round cells were seen, with occasionally vacuolated cytoplasm, perivascular palisading, and focal necrosis. Rhabdoid elements were lacking. Neoplastic cells were positive for CK AE1/AE3, CK 5/6, CK7, and claudin-4, negative for CK20 (although rare elements were observed with a faint positivity), CD99, FLI-1, TLE, S-100, SALL4, TTF-1, synaptophysin, CD56, NSE, GATA3 and NUT. Staining for p40 was positive in as many as 60% of the neoplastic elements. Proliferating fraction, measured through Ki-67 immunostaining, was estimated in around 25% of neoplastic cells. While SMARCA4/BRG1 and SMARCA2/BRM were retained, SMARB1/INI-1 (25/BAF47, Gennova Scientific, 1:50) was completely lost in all tumour cells, with a background of internal positive controls, testifying the specificity of immunostaining (Fig. 2). PD-L1 immunohistochemistry did not show any expression.
Genomic profiling in order to identify potential druggable targets was performed by targeted DNA- and RNA-based Next Generation Sequencing (NGS) on the Ion S5™ System using Oncomine™ Focus Assay (OFA) (ThermoFisher Scientific), which enables the detection of hotspot variants in 35 genes, copy number variations (CNVs) in 19 genes and the presence of driver fusions in 23 genes. No pathogenic variant, fusion and/or amplification was detected in the genes being included in the panel.
The final pathological report concluded for a non-keeratinising squamous cell carcinoma, with the indication to a comprehensive clinical-instrumental evaluation (with particular regard to the head and neck district), to exclude any metastasis. Once the scenario of a metastasis was ruled out, the diagnosis was revised as SMARCB1-deficient undifferentiated tumour (SMARCB1-UT), also in light of the patient’s never-smoker status and the peculiar histologic, immunohistochemical and molecular traits.
As total-body PET and a head CT scan excluded metastasis, the patient was scheduled to undergo right lobectomy with hilar and mediastinal lymphadenectomy, but he refused any further treatment.
Nine months after the diagnosis, the patient was evaluated several times, for a period of four months, in an external emergency department for worsening exertional dyspnoea with concomitant pleural effusion. A new thorax CT scan showed a bulky lesion (around 150 mm) at the right inferior lobe, associated with a left mediastinal shift and multiple mediastinal and subcarinal enlarged lymph nodes, the largest measuring 85 x 68 mm. The patient was admitted with a diagnosis of “undifferentiated right lung cancer”, cT4N2M0, with supervening S. Pneumoniae sepsis and severe anaemia which required transfusion support. Antibiotic therapy with piperacillin/tazobactam and a first-line carboplatinum and paclitaxel-based chemotherapy were thus administered.
One month after completing the first chemotherapy cycle, the patient was further admitted with severe dyspnoea and haemoptysis, requiring palliative treatment: he died of the disease shortly after, 11 months after the initial diagnosis on biopsy.
Review of the literature
To review the most recent literature regarding SMARCB1/INI1 deficient thoracic tumours, we performed a PubMed search from 2002 to 2022 using the terms “SMARCB1/INI1 deficient thoracic tumours”, “SMARCB1/INI1 deficient lung carcinoma” and “SMARCB1/INI1 deficient lung cancer”, which showed 14 results. Of these, 5 were reports of SMARCB1/INI1 intrathoracic carcinomas 23-27, for a total of 14 individual cases (the present included), whose clinical and demographical characteristics are summarised in Table I.
The vast majority of the reviewed cases were from male patients (12/14, 85.7%), with a mean age of 55.4 years (median age 62.5 years), ranging from 20 to 77 years. Six subjects were active or past smokers and six were never-smokers (data were not available for two patients).
The reported neoplasms had a mean diameter of 7.1 cm (median diameter 5.8 cm), with diameter being specified in 11/14 cases, where 2 two of them involved the entire parietal pleural surface and another was multifocal. The latter exhibited extensive involvement or infiltration of pleural layers, mediastinal space, and surrounding anatomical structures and presented as locally advanced lesion at the time of the initial diagnosis. More than half of tumours were considered as being of lung origin (8/14, 57.1%), four (28.6%) grew along pleural surface or mainly invaded thoracic wall and two (14.3%) formed mediastinal masses, either anterior or posterior (the latter, with oesophagus encasement). Overall, six of the patients (42.8%) showed lymph node or visceral metastasis at diagnosis: four of them had nodal involvement alone and four had distant localisations (two of which with negative regional lymph nodes).
Thoracic SMARCB1-deficient undifferentiated tumours behaved aggressively and determined a rapid death. Eleven patients died of disease (mean survival 12.7 months, median survival 10 months, range 1-53 months), one was lost during follow up and only two of them were successfully treated with a combination of immunotherapy and neoadjuvant chemotherapy regimen (combination of Iipilimumab/nivolumab and gemcitabine/carboplatin in one patient and of pembrolizumab and nab-paclitaxel/carboplatin in the other), with radiologic response (more precise data regarding survival and follow-up are missing).
Histologically (Tab. II), neoplastic cells showed variable immunoreactivity for cytokeratins (8 out of 12 tested cases were positive for CK AE1/AE3) and for claudin-4, an epithelial marker (reaction was positive in 5 out of 11 cases). Similarly, there was no uniform immunohistochemical profile for markers of squamous, glandular, or neuroendocrine differentiation: p40 positive staining was observed in 2/7 cases, TTF-1 in a single sample (out of 12 tested samples) and synaptophysin in 2/12 cases. SMARCA4/BRG1 expression was consistently retained in 11/11 samples. NUT was negative in 2/2 tested cases.
Data regarding the molecular profile of the neoplasms were available for every reported case. Mutations, deletions and/or copy number variations in SMARCB1/INI1 were variably described. Except for two cases respectively characterised by copy number alterations in EGFR and loss of STK11, no other pathogenically relevant gene alteration was found (notably KRAS, RET, ROS1, EGFR, ALK, etc.). Furthermore, tumours generally showed a low/intermediate tumour mutational burden (TMB) and microsatellite stability (MSS). PD-L1 expression was assessed in three cases only, the present included: expression was negative in one case, lower than 1% in another and around 20% in still another.
A detailed summary of the histological and molecular findings is reported in Table III (Supplementary Data).
Discussion
Thoracic SMARCB1/INI1-deficient undifferentiated tumours are a rarely described entity characterised, in the reviewed cohort, by a variable but aggressive clinical presentation and a poor prognosis.
According to the literature, patients tend to be younger than usually observed in lung cancer (mean age 55.4 years) and, remarkably, almost one third of the patients (4/14, 28.6%) were younger than 40 years. Data suggest the lack of a definite correlation with smoking habit: half of the patients for whom anamnestic information was available was not smokers (neither active or former) and one patient with a smoking history was diagnosed at 25-year-old.
These neoplasms tend to widely occupy the thorax, with huge size and common involvement of pleural surface, thoracic wall, and mediastinal structures including lymph nodes. Survival data suggest an aggressive behaviour and a relentless clinical course, also due to the lack of effective therapy and molecular targets.
Histologically, SMARCB1-UT feature solid pattern of growth, invariable association with necrosis. intermediate (present case) to large-size cells, and an epithelioid or rhabdoid appearance. Immunophenotype seems to be of little help in framing these neoplasms, also considering master gene regulators, such as TTF-1, the most employed marker for lung adenocarcinoma, which is however rarely expressed, or especially p40 (a marker of squamous differentiation) can be even significantly expressed in the tumour, rising issues of differential diagnosis with non-keeratinising squamous cell carcinoma of the lung (NK-SCC). In this regard, the lack of smoking history and the young age of the patients should alert to the possibility of facing with a tumour entity other than conventional SCC. Occasionally, an at least focal positivity for synaptophysin has been observed, raising the possibility of mistakenly considering diagnosis of neuroendocrine carcinoma. Claudin-4 can also be variably expressed: several reported cases showed loss of expression, potentially misclassifying these tumours as high-grade or undifferentiated sarcoma. In brief, SMARCB1-UT tend to closely resemble upon histology and immunoprofile other molecularly defined undifferentiated thoracic neoplasms, such as SMARCA4/BRG1-deficient undifferentiated tumours or NUT carcinomas.
From a molecular standpoint, no potential therapeutic targets have been thus far identified. As already demonstrated by Haberecker et al., SMARCB1/INI1-UT have a low mutational burden and do not present the most common mutations typically associated with lung ADK and SCC, leaving the “traditional” chemotherapy approach as the only viable strategy for these patients 24.
Though extremely uncommon and challenging from a diagnostic perspective, thoracic SMARCB1/INI1-deficient undifferentiated tumours are gaining increasing attention, due to the recent inclusion of SMARCA4-UT in the latest WHO classification. The identification of this subset of neoplasms is crucial to open the possibility to future therapies. Suspect should rise whenever facing a high grade undifferentiated thoracic tumour with epithelioid, rhabdoid or round cell features, regardless of its location and the age of the patient. Differential diagnosis should also include SMARCA4-UT and NUT carcinoma 2, as well as poorly differentiated non-small cell carcinoma (in particular adenocarcinoma for TTF-1 reactivity or squamous cell carcinoma for p40 immunolabelling) and neuroendocrine carcinoma for sharing neuroendocrine markers.
Although a very small number of undifferentiated tumours with loss of SMARCB1 are reported, the next WHO classification should hopefully include SMARCB1-UT as a new entry among thoracic neoplasms.
CONFLICTS OF INTEREST STATEMENT
C.L. reports honoraria from Roche. All other authors declare no conflict of interest.
FUNDING
This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
AUTHORS’ CONTRIBUTIONS
All the authors contributed equally.
ETHICAL CONSIDERATION
The research was conducted ethically, with all study procedures being performed in accordance with the requirements of the World Medical Association’s Declaration of Helsinki.
Written informed consent was obtained from each patient for study participation and data publication.
History
Received: December 13, 2023
Accepted: January 19, 2024
Figures and tables
Figure 1.CT image of the reported case. Thoracic computed tomography at initial diagnosis. The image shows a grossly rounded, solid formation located peripherically in the right middle lobe of the lung.
Figure 2.Histopathological and immunohistochemical features of the tumour. Haematoxylin and eosin staining of the lesion showed a solid proliferation of small, round, undifferentiated cells with focal necrosis, occasional cytoplasmic vacuolisation and perivascular palisading (a). Neoplastic cells stained positive for p40 (50% of the neoplastic cells) and negative for TTF-1 and synaptophysin (b, c, d). Immunohistochemical study of the expression of SMARCA4/BRG1 (e) and SMARCB1/INI1 (f) demonstrated the retention of the former and the complete loss of staining, with positive internal control, of the latter.
| Authors | Ref | Patient | Gender | Age (years) | Smoking history (Y/N) | Tumour site | Tumour size (cm) | Lymphnode metastasis (Y/N) | Site of distant metastasis | cTNM staging1 | Treatment | Follow up/Months | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Yoshida K, Fujiwara Y, et al. | 23 | 1 | F | 33 | N | Left pleura | Multiple tumours | N | None | cTxN0M0 | Adjuvant CT | DOD/10 | |
| Haberecker M, Buhler MM, et al. | 24 | 2 | F | 20 | N | Anterior mediastinum | ~4 | N | Bone, lung3, soft tissue and nerve plexus | cTxN0M1c | Adjuvant CT | DOD/16 | |
| 3 | M | 25 | Y | Pleura/thoracic wall, axilla | 15,8 | Y | Pleura | cT4N2M1a | Adjuvant CT | DOD/17 | |||
| 4 | M | 51 | Y | Lung, central/hilar | 4-5 | Y | Pleura | cT2bN2M1a | Adjuvant CT | DOD/6 | |||
| 5 | M | 56 | Y | Pleura | -2 | N | None | cTxN0M0 | Adjuvant CT | DOD/1 | |||
| 6 | M | 76 | NA | Lung, subpleural | 3,5 | N | NA | cT2aN0M0 | NA | NA/2 | |||
| 7 | M | 73 | Y | Lung, central/hilar | 5 | Y | Liver, adrenal gland | cT2bN2M1c | Neoadjuvant and adjuvant CT | DOD/7 | |||
| 8 | M | 64 | Y | Pleura | -2 | N | None | cT3N0M0 | Adjuvant CT | DOD/10 | |||
| 9 | M | 72 | Y | Lung, central/hilar | 9 | N | Lung3 | cT4N0M1a | Adjuvant CT | DOD/53 | |||
| 10 | M | 77 | N | Posterior mediastinum/esophagus | 10 | N | None | cT4N0M0 | Neoadjuvant CT | DOD/4 | |||
| Zhou YH, Qin S, et al. | 25 | 11 | M | 74 | NA | Lung, RUL | 3,5 | N | None | cT2NcMx | Neoadjuvant RT | DOD/5+4 | |
| Rickard JA, Burr M, et al. | 26 | 12 | M | 60s5 | N | Lung, LLL | 8,6 | Y | Liver | cT4N2M1c | Neoadjuvant CT | AWD | |
| Chen J, Wang J | 27 | 13 | M | 61 | N | Lung, LUL | 8,8 | Y | None | cT4N2M0 | Neoadjuvant and adjuvant CT | NED/4+6 | |
| Present case | - | 14 | M | 38 | N | Lung, RML | 5,8 | N | None | cT3N0M0 | Neoadjuvant CT | DOD/11 | |
| 1 according to the available data, 2 entire lateral parietal pleura, 3 data regarding precise location not available, 4 patient was alive with disease after 5 months of radiotherapic treatment and died of disease after therapeutic failure (interval is not reported in the original article), 5 in the original article, the authors report that the patient is in his sixties with no further clarification, 6 in the original article, no further clarification is given on the follow-up time | |||||||||||||
| AWD alive with disease, CT chemotherapy treatment, DOD died of disease, IHC immunohistochemistry, LLL left lower lobe, LUL left upper lobe, NA not available, NED no evidence of disease, RML right middle lobe, RUL right upper lobe | |||||||||||||
| Morphological features, IHC and molecular findings | n (%)* | |
|---|---|---|
| Morphological data | Solid growth | 5/14 (35.7%) |
| Epithelioid morphology | 4/14 (28.6%) | |
| Rhabdoid morphology | 2/14 (14.3%) | |
| Undifferentiated/dedifferentiated morphology | 2/14 (14.3%) | |
| Mixed epithelioid and rhabdoid morphology | 2/14 (14.3%) | |
| Necrosis | 12/14 (85.7%) | |
| Immunohistochemical positivity | PanCK | 8/12 (66.7%) |
| TTF-1 | 1/13 (7.7%) | |
| p40 | 4/8 (50.0%) | |
| Synaptophysin | 3/13 (23.1%) | |
| Claudin-4 | 5/11 (40.4%) | |
| SMARCA4/BRG1 | 11/11 (100%) | |
| Molecular data | SMARCB1 mutation, deletion or CNV | 13/13 (100%) |
| EGFR mutation | 1/13 (7.7%) | |
| ALK mutation | 0/11 (0.0%) | |
| KRAS mutation | 0/10 (0.0%) | |
| RET mutation | 0/2 (0.0%) | |
| ROS1 mutation | 0/2 (0.0%) | |
| STK11 mutation | 1/10 (10.0%) | |
| *For immunohistochemical and molecular data, cumulative percentage is calculated on the number of tested cases | ||
| CNV copy number variation, IHC immunohistochemistry, PanCK pan-cytokeratin | ||
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