Hereditary SWI/SNF complex deficiency syndromes

The SWItch Sucrose non-fermentable (SWI/SNF) complex is a highly conserved multi-subunit complex of proteins encoded by numerous genes mapped to different chromosomal regions. The complex regulates the process of chromatin remodelling and hence plays a central role in the epigenetic regulation of gene expression, cell proliferation and differentiation. During the last three decades, the SWI/SNF complex has been increasingly recognized as a central molecular event driving the initiation and/or progression of several benign and malignant neoplasms of different anatomic origin and having diverse histomorphological appearance. Atypical teratoid/rhabdoid tumors (AT/RT) and renal/extrarenal malignant rhabdoid tumors of childhood, epithelioid sarcoma and small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) represent the most commonly recognized SWI/SNF-driven neoplasms. Approximately one-third of pediatric malignant rhabdoid tumors are linked to germline SWI/SNF alterations (SMARCB1/INI1, rarely SMARCA4) resulting in occasional familial clustering of these highly aggressive malignancies (so-called rhabdoid tumor predisposition syndrome, RTPS, types 1 and 2, respectively). However, more recently, inherited SWI/SNF-deficiency has been linked to several benign syndromic tumors including a subset of familial schwannomatosis (linked to SMARCB1) and multiple meningiomas (linked to SMARCE1) as well as others. Beyond neoplasms, several congenital developmental functional disorders such as Coffin-Siris syndrome and intellectual disability are now known to be SWI/SNF-related. The latter are essentially not associated with SWI/SNF-driven neoplasms, although at least anecdotal cases have documented concurrence of both neoplastic and developmental disorders. This review summarizes the most important SWI/SNF-driven diseases with a main focus on neoplasms.     

Consistent SMARCB1 homozygous deletions in epithelioid sarcoma and in a subset of myoepithelial carcinomas can be reliably detected by FISH in archival material

Epithelioid sarcomas (ES) are mesenchymal neoplasms subclassified into distal and proximal subtypes based on their distinct clinical presentations and histologic features. Consistent loss of SMARCB1 nuclear expression has been considered as the hallmark abnormality for both subtypes, a feature shared with atypical teratoid/rhabdoid tumor of infancy (ATRT). While virtually all ATRTs harbor underlying SMARCB1 somatic or germline alterations, mechanisms of SMARCB1 inactivation in ES are less well defined. To further define mechanisms of SMARCB1 inactivation a detailed molecular analysis was performed on 40 ES (25 proximal and 15 distal ES, with classic morphology and negative SMARCB1 expression) for their genomic status of SMARCB1 and related genes encoding the SWI/SNF subunits (PBRM1, BRG1, BRM, SMARCC1/2 and ARID1A) by FISH using custom BAC probes. An additional control group was included spanning a variety of 41 soft tissue neoplasms with either rhabdoid/epithelioid features or selected histotypes previously shown to lack SMARCB1 by IHC. Furthermore, 12 ES were studied by array CGH (aCGH) and an independent TMA containing 50 additional ES cases was screened for Aurora Kinase A (AURKA) and cyclin D1 immunoexpression. Homozygous SMARCB1 deletions were found by FISH in 36/40 ES (21/25 proximal‐type). One of the distal‐type ES displayed homozygous SMARCB1 deletion in the tumor cells, along with a heterozygous deletion within normal tissue, finding confirmed by array CGH. None of the proximal ES lacking homozygous SMARCB1 deletions displayed alterations in other SWI/SNF subunits gene members. Among controls, only the SMARCB1‐immunonegative myoepithelial carcinomas displayed SMARCB1 homozygous deletions in 3/5 cases, while no gene specific abnormalities were seen among all other histologic subtypes of sarcomas tested regardless of the SMARCB1 protein status. There was no consistent pattern of AURKA and Cyclin D1 expression. The array CGH was successful in 9/12 ES, confirming the SMARCB1 and other SWI/SNF genes copy numbers detected by FISH. Our study confirms the shared pathogenesis of proximal and distal ES, showing consistent SMARCB1 homozygous deletions. Additionally we report the first ES case associated with a SMARCB1 constitutional deletion, establishing a previously undocumented link with ATRT. Alternative mechanisms of SMARCB1 inactivation in SMARCB1‐disomic ES remain to be identified, but appear unrelated to large genomic abnormalities in other SWI/SNF subunits. © 2014 Wiley Periodicals, Inc.     

Rhabdoid Tumors: An Initial Clue to the Role of Chromatin Remodeling in Cancer

The discovery of biallelic, inactivating SMARCB1 mutations in rhabdoid tumors (RTs) over a decade ago represented the first recognized link between chromatin remodeling and tumor suppression. SMARCB1 is a core subunit of the SWI/SNF chromatin remodeling complex, and the recent emergence of frequent mutations in genes that encode subunits of this complex across a wide variety of cancers suggests that perturbation of this chromatin remodeling complex constitutes a key driver of cancer formation. Despite the highly aggressive nature of RTs, they are genetically simple cancers that appear to lack chromosomal instability and contain very few mutations. Indeed, the mutation rate in RTs is among the lowest of all cancers sequenced, with loss of SMARCB1 as essentially the sole recurrent event. Given the genetic simplicity of this disease, understanding the chromatin dysregulation caused by SMARCB1 loss may provide more general insight into how epigenetic alterations can contribute to oncogenic transformation and may reveal opportunities for targeted therapy not only of RT but also the variety of other SWI/SNF mutant cancers.     

SWI/SNF-deficient head and neck neoplasms: An overview

With wide-spread use of next generation sequencing tools in surgical pathology, a variety of neoplasms have been increasingly recognized to be associated with specific recurrent defining genetic abnormalities. This has led to recognition of new genetically defined entities and refinements of preexisting heterogeneous neoplastic categories. Among these, neoplasms associated with inactivating mutations involving different subunits of the SWI/SNF chromatin remodeling complex have received special attention. In the head and neck area, SMARCB1 (INI1) and SMARCA4 (BRG1) are the main two SWI/SNF components responsible for several recently described highly aggressive undifferentiated malignancies with predilection for the soft tissue of the neck (SMARCB1-deficient malignant rhabdoid tumors in children and rare epithelioid sarcoma cases in adults) and the sinonasal tract (SMARCB1-deficient sinonasal carcinoma including a small subset of adenocarcinomas, SMARCA4-deficient sinonasal undifferentiated carcinoma and SMARCA4-deficient sinonasal teratocarcinosarcoma). Molecular studies confirmed paucity of additional genetic abnormalities in these diseases underlining the central role of SWI/SNF deficiency as the primary and frequently sole genetic driver of these lethal diseases. Initiation of clinical trials using drugs that target the SWI/SNF collapse encourages recognition and correct classification of these morphologically frequently overlapping malignancies and underpins the role of SWI/SNF immunohistochemistry as emerging powerful adjunct tool in surgical pathology of the head and neck.     

Infrequent SMARCB1/INI1 gene alteration in epithelioid sarcoma: a useful tool in distinguishing epithelioid sarcoma from malignant rhabdoid tumor

Loss of SMARCB1/INI1 protein expression is considered useful for confirming a histologic diagnosis of malignant rhabdoid tumor. However, loss of SMARCB1/INI1 protein expression has recently been reported in other tumors as well, including a few cases of epithelioid sarcoma. In addition, the histopathologic differences between proximal-type epithelioid sarcoma and malignant rhabdoid tumor have not been conclusively defined. We analyzed SMARCB1/INI1 protein expression in 54 epithelioid sarcoma (proximal-type, 25; distal-type, 29) and examined alterations of the SMARCB1/INI1 gene in the cases lacking protein expression. We found that 19 (76.0%) proximal-type epithelioid sarcoma and 27 (93.1%) distal-type epithelioid sarcoma showed loss of SMARCB1/INI1 protein expression. Analysis of 39 cases with loss of protein expression revealed 4 cases (10.3%) with SMARCB1/INI1 gene alterations at the DNA level (homozygous deletion, 2; 1- or 2-bp deletion, 2) that could have induced the loss of gene products, and all 4 of these were proximal-type epithelioid sarcoma. Epithelioid sarcoma was thus associated with a high frequency of loss of SMARCB1/INI1 protein expression similar to that in malignant rhabdoid tumor. However, the frequency of SMARCB1/INI1 gene alteration at the DNA level in proximal-type epithelioid sarcoma was significantly lower than that in malignant rhabdoid tumor. In addition, the prognosis of patients with malignant rhabdoid tumor is significantly worse than that of patients with proximal-type epithelioid sarcoma (P = .001). Therefore, proximal-type epithelioid sarcoma and malignant rhabdoid tumor are suggested to be distinctive tumors with respect to the mechanism of the loss of SMARCB1/INI1 protein expression. Analysis of alterations in the SMARCB1/INI1 gene may thus be a useful diagnostic tool to distinguish proximal-type epithelioid sarcoma from malignant rhabdoid tumor.     

Novel germ-line deletion of SNF5/INI1/SMARCB1 gene in neonate presenting with congenital malignant rhabdoid tumor of kidney and brain primitive neuroectodermal tumor

We describe a neonate who had a rare tumor combination of a malignant rhabdoid tumor of the kidney (MRTK) and a brain primitive neuroectodermal tumor (PNET). Genetic alterations of the SNF5/INI1/SMARCB1 gene were investigated by PCR-single-strand conformation polymorphism (SSCP), loss of heterozygosity (LOH), sequence, and karyotyping analyses, and the gene expression level was determined by real-time quantitative RT-PCR analysis. PCR band signals of each exon of the hSNF5/INI1 were weak or nearly undetectable in both MRTK and PNET, whereas those of the corresponding normal kidney were clearly detected. Aberrantly migrating SSCP bands led to identification of a nucleotide change in intron 8. Although this was regarded as a polymorphism, only the changed nucleotide was observed in the normal kidney of the patient. Allelic states in the parents were heterozygous for the polymorphism in the father and homozygous for the normal sequence in the mother. Thus, it was evident that a substantial genetic part of the maternal normal allele including SNF5/INI1 was deleted as a de novo germ-line mutation. In both tumors, LOH at microsatellite loci on the long arm of chromosome 22 was evident, and expression of SNF5/INI1 mRNA was drastically decreased compared to that in control tissues (0.7-3.9 vs. 123.6-153.5). Deletion of a substantial genetic part demonstrated in our patient is the novel appearance of a germ-line deletion of the SNF5/INI1 gene. Additional large somatic deletions resulted in total inactivation of the gene in both tumors. Our patient provides evidence for an important role of SNF5/INI1germ-line mutation in predisposing patients to multiple rhabdoid tumors.     

SMARCB1/INI1 missense mutation in mucinous carcinoma with rhabdoid features

Malignant rhabdoid tumor (MRT) is a rare and aggressive tumor associated with deletion or mutation of a tumor suppressor gene SMARCB1/INI1, a member of the SWI/SNF chromatin-remodeling complex. Reported herein is a case of pancreatic mucinous carcinoma accompanying rhabdoid features with immunohistochemical and ultrastructural studies as well as analysis of the SMARCB1/INI1 gene. A 65-year-old woman presented with a 2 month history of abdominal and chest pain. A well-defined grayish tan fish-flesh mass (11 x 9 x 7 cm) with focal mucinous area was present in the pancreatic tail. Microscopically, the tumor had a biphasic growth pattern: a mucinous carcinoma component and a poorly differentiated carcinoma component with rhabdoid features showing loosely cohesive cells with abundant eosinophilic cytoplasm, displaced nuclei, and prominent nucleoli. The rhabdoid component coexpressed vimentin and cytokeratin. Sequencing analysis of the DNA extracted from the mucinous and rhabdoid components showed a missense mutation CCC to ACC in codon 116 of the SMARCB1/INI1 gene. Being aware of rhabdoid features would help diagnose this rare and aggressive malignant tumor and may provide an opportunity for further evaluation of SMARCB1/INI1 gene alteration and determination of its prognostic significance.     

SWI/SNF-deficient neoplasms of the genitourinary tract

Since the discovery of association of SMARCB1 mutations with malignant rhabdoid tumors and renal medullary carcinoma, mutations in genes of the SWI/SNF chromatin remodeling complex have been increasingly identified across a diverse spectrum of neoplasms. As a group, SWI/SNF complex subunit mutations are now recognized to be the second most frequent type of mutations across tumors. SMARCB1 mutations were originally reported in malignant rhabdoid tumors of the kidney and thought to be pathognomonic for this tumor. However, more broadly, recognition of typical rhabdoid cytomorphology and SMARCB1 mutations beyond rhabdoid tumors has changed our understanding of the pathobiology of these tumors. While mutations of SWI/SNF complex are diagnostic of rhabdoid tumors and renal medullary carcinoma, their clinical relevance extends to potential prognostic and predictive utility in other tumors as well. Beyond SMARCB1, the PBRM1 and ARID1A genes are the most frequently altered members of the SWI/SNF complex in genitourinary neoplasms, especially in clear cell renal cell carcinoma and urothelial carcinoma. In this review, we provide an overview of alterations in the SWI/SNF complex encountered in genitourinary neoplasms and discuss their increasing clinical importance.     

A case of renal cell carcinoma unclassified with medullary phenotype without detectable gene deletion

Renal cell carcinoma unclassified with medullary phenotype (RCCU‐MP) is a rare variant of renal medullary carcinoma (RMC) characterized by loss of SMARCB1 (INI1 / SNF5 / BAF47) protein expression in patients without sickle cell trait. Here, we report a case of RCCU‐MP in a Japanese patient who had experienced colon cancer 13 years ago, gastric cancer 11 years ago and lung cancer 9 years ago and had received hemodialysis for 15 years. This is the first report of RCCU‐MP in Japan. The patient was not of African descent, and did not have SCT or any other hereditary blood abnormality typical of RMC. The tumor was located in the left kidney, and was composed histologically of rhabdoid cells with marked lymphocyte infiltration; it was immunohistochemically negative for SMARCB1. We were, however, unable to detect mutation in the SMARCB1 gene, reduced messengerRNA expression, or deletion or translocation of chromosome 22, where the SMARCB1 gene is located. These results suggest that RCCU‐MP may not involve the hemizygous loss of this gene noted in typical RMC cases.     

Molecularly confirmed primary malignant rhabdoid tumor of the urinary bladder: implications of accurate diagnosis

Malignant rhabdoid tumors (MRTs) are well recognized in the kidney and extrarenal sites such as soft tissues, retroperitoneum, and bladder but are classified as atypical teratoid/rhabdoid tumors in the central nervous system. The unifying features of both extracranial MRT and atypical teratoid/rhabdoid tumors are the exon deletions/mutations of the SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1) gene in 22q11.23 and resulting loss of SMARCB1/INI1 (integrase interactor 1) protein expression by immunohistochemistry. We herein report a case of extrarenal rhabdoid tumor confined to the bladder in a 3-year-old child, diagnosed by histopathology and confirmed by immunohistochemical and molecular studies. This is only the fourth molecularly proven primary MRT of the bladder to be reported. The patient's peripheral blood was negative for the deletions observed in the tumor, thereby confirming a sporadic origin for the tumor. Given the possible dismal outcome, urgency for definitive diagnosis to institute intensive multimodality therapy, histopathologic differential diagnosis with rhabdomyosarcoma and urothelial carcinoma with rhabdoid features, and lack of consensus management guidelines, oncologists, urologists, and pathologists must be aware of this entity. Evaluation for a germ line SMARCB1 alteration may greatly aid risk stratification and family planning.     

Cribriform neuroepithelial tumor: molecular characterization of a SMARCB1‐deficient non‐rhabdoid tumor with favorable long‐term outcome

Rhabdoid phenotype and loss of SMARCB1 expression in a brain tumor are characteristic features of atypical teratoid/rhabdoid tumors (ATRT). Rare non‐rhabdoid brain tumors showing cribriform growth pattern and SMARCB1 loss have been designated cribriform neuroepithelial tumor (CRINET). Small case series suggest that CRINETs may have a relatively favorable prognosis. However, the long‐term outcome is unclear and it remains uncertain whether CRINET represents a distinct entity or a variant of ATRT. Therefore, 10 CRINETs were clinically and molecularly characterized and compared with 10 ATRTs of each of three recently described molecular subgroups (i.e. ATRT‐TYR, ATRT‐SHH and ATRT‐MYC) using Illumina Infinium HumanMethylation450 arrays, FISH, MLPA, and sequencing. Furthermore, outcome was compared to a larger cohort of 27 children with ATRT‐TYR. Median age of the 6 boys and 4 girls harboring a CRINET was 20 months. On histopathological examination, all CRINETs demonstrated a cribriform growth pattern and distinct tyrosinase staining. On unsupervised cluster analysis of methylation data, all CRINETs examined exclusively clustered within the ATRT‐TYR molecular subgroup. As ATRT‐TYR, CRINETs mainly showed large heterozygous 22q deletions (9/10) and SMARCB1 mutations of the other allele. In two patients, SMARCB1 mutations were also present in the germline. Estimated mean overall survival in patients with CRINETs was 125 months (95% confidence interval 100–151 months) as compared to only 53 (33–74) months in patients with ATRTs of the ATRT‐TYR subgroup (Log‐Rank P < 0.05). In conclusion, CRINET represents a SMARCB1‐deficient non‐rhabdoid tumor, which shares molecular similarities with the ATRT‐TYR subgroup but has distinct histopathological features and favorable long‐term outcome.     

High‐resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors

Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high‐resolution genome‐wide analysis was performed using a molecular inversion probe single‐nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin‐fixed paraffin‐embedded express) on DNA isolated from 18 formalin‐fixed paraffin‐embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation‐dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT. © 2012 Wiley Periodicals, Inc.     

SWI/SNF-deficient malignancies of the female genital tract

Mutations and other molecular events involving subunits of the SWI/SNF chromatin remodelling complex are common in a wide variety of malignancies, including those arising at various sites in the female genital tract. Endometrioid and clear cell carcinomas in the uterine corpus and ovary not uncommonly contain mutations in ARID1A and these also occur in other endometriosis-associated ovarian neoplasms such as seromucinous tumours. In these organs, mutations in SMARCA4, SMARCB1, ARID1A and ARID1B (with subsequent loss of corresponding protein expression as a reliable surrogate) are relatively common in undifferentiated carcinomas, including the undifferentiated component of dedifferentiated carcinoma. SMARCA4 mutations are extremely common (almost ubiquitous) in small cell carcinoma of the ovary of hypercalcaemic type (SCCOHT), occurring in about 98% of these neoplasms, often in association with epigenetic SMARCA2 loss. SMARCB1-deficient vulval neoplasms include epithelioid sarcoma and myoepithelial carcinoma, as well as related malignancies which defy easy classification. Recently the spectrum of SWI/SNF deficient female genital malignancies has been expanded to include SMARCA4-deficient undifferentiated uterine sarcoma and mural nodules of anaplastic carcinoma in ovarian mucinous neoplasms.     

Chromosome 22q deletions in atypical teratoid/rhabdoid tumors in adults

Atypical teratoid/rhabdoid tumors (AT/RTs) are rare, malignant brain tumors that usually occur in the posterior fossa. Both AT/RT and the analogous tumor outside the brain, malignant rhabdoid tumor, share a polyphenotypic immunoprofile and frequent 22q deletions with inactivation of the IN11/hSNF5 gene. Reports, so far, indicate that AT/RTs occur almost exclusively in children, most of whom are 5-years-old or less. The rarity of the tumor and the polyphenotypic immunoprofile, characterized by antigen expression that is often patchy, make diagnosis in adults difficult and controversial. We describe three AT/RTs in adults in which the diagnoses were supported by detection of 22q11.2 deletions, INI1 mutation and/or loss of INI1 protein expression. Two patients were female, ages 20 and 31 and one was male, age 45.Two tumors occurred in the sella or sellar region and one in the cerebellum. In all cases, fluorescence in situ hybridization with probes to the BCR (22q11.2) and NF2 (22q12) regions of chromosome 22 revealed single copy deletions of BCR with normal dosages of NF2 and, in all cases, immunohistochemistry demonstrated loss of INI1 protein expression. In one case, a single base pair deletion was detected in the INI1/hSNF5 gene. These molecular findings confirm the occurrence of AT/RTs in adults. Although rare, AT/RT should be considered in the differential diagnosis of poorly differentiated intracranial tumors in adults.     

SMARCB1 (INI1)-deficient thyroid carcinoma: A novel entity expanding the spectrum of tumors with INI1 loss

BackgroundBiallelic loss of SMARCB1/INI1 is associated with highly aggressive malignancies, namely renal and extra-renal malignant rhabdoid tumors, and atypical teratoid/ rhabdoid tumor. Increasing availability of molecular testing and immunohistochemical stains acting as surrogate tools to genetic analysis has led to an increasing recognition of SMARCB1 loss in a variety of neoplasms. Interestingly, many of these lack the typical rhabdoid features ascribed to this group of tumors, making their identification difficult.Case presentationWe describe the cytological, histological, immunohistochemical and molecular features of the first case of primary SMARCB1 (INI1)-deficient carcinoma of the thyroid gland in literature. The tumor was unique in various aspects; apart from never having been documented at this location, it showed extensive glandular differentiation, mimicking metastatic adenocarcinoma.ConclusionAwareness of this novel entity is essential to avoid misdiagnosis, and for appropriate management, especially in an era of increased feasibility of targeted therapy.     

Small cell undifferentiated (SCUD) hepatoblastomas: All malignant rhabdoid tumors?

Small cell undifferentiated (SCUD) hepatoblastoma is a rare variant of hepatoblastoma with poor outcome and loss of INI1 expression, sharing this with malignant rhabdoid tumors (MRT). We studied all tumors from the files of the Kiel Pediatric Tumor Registry (KTR) with the initial diagnosis of SCUD and MRT. After re‐review, we performed immunistochemistry, fluorescence in situ hybridization, and multiplex ligation dependent probe amplification for loss of expression and deletion of INI1/SMARCB1 in 23 tumors. Morphologically, 12 of the tumors had a small cell morphology, 9 showed the typical picture of MRT, and 2 were composed of both small cells and rhabdoid cells. All but 1 of the 23 tumors showed loss of INI1 protein expression by immunohistochemistry. Nineteen of the INI1 negative tumors were analyzed by FISH technique and all showed a deletion of the INI1/SMARCB1 gene (17 homozygous deletions, 2 heterozygous deletions). We investigated 14 of these cases by multiplex ligation dependent probe amplification and verified the deletions in all cases. In conclusion, we postulate that SCUD hepatoblastoma is not a hepatoblastoma but represents a malignant rhabdoid tumor of the liver. © 2016 Wiley Periodicals, Inc.