SMARCB1-deficient Tumors of Childhood: A Practical Guide

Pediatric Renal Tumors: Updates in the Molecular Era

Molecular characterization has led to advances in the understanding of pediatric renal tumors, including the association of pediatric cystic nephromas with DICER1 tumor syndrome, the metanephric family of tumors with somatic BRAF mutations, the characterization of ETV6-NTRK3-negative congenital mesoblastic nephromas, the expanded spectrum of gene fusions in translocation renal cell carcinoma, the relationship of clear cell sarcoma of the kidney with other BCOR-altered tumors, and the pathways affected by SMARCB1 alterations in rhabdoid tumors of the kidney. These advances have implications for diagnosis, classification, and treatment of pediatric renal tumors.

The epigenomics of sarcoma

Epigenetic regulation is critical to physiological control of development, cell fate, cell proliferation, genomic integrity and, fundamentally, transcriptional regulation. This epigenetic control occurs at multiple levels including through DNA methylation, histone modification, nucleosome remodelling and modulation of the 3D chromatin structure. Alterations in genes that encode chromatin regulators are common among mesenchymal neoplasms, a collection of more than 160 tumour types including over 60 malignant variants (sarcomas) that have unique and varied genetic, biological and clinical characteristics. Herein, we review those sarcomas in which chromatin pathway alterations drive disease biology. Specifically, we emphasize examples of dysregulation of each level of epigenetic control though mechanisms that include alterations in metabolic enzymes that regulate DNA methylation and histone post-translational modifications, mutations in histone genes, subunit loss or fusions in chromatin remodelling and modifying complexes, and disruption of higher-order chromatin structure. Epigenetic mechanisms of tumorigenesis have been implicated in mesenchymal tumours ranging from chondroblastoma and giant cell tumour of bone to chondrosarcoma, malignant peripheral nerve sheath tumour, synovial sarcoma, epithelioid sarcoma and Ewing sarcoma - all diseases that present in a younger patient population than most cancers. Finally, we review current and potential future approaches for the development of sarcoma therapies based on this emerging understanding of chromatin dysregulation.

Renal malignant tumor with the loss of INI1 expression and WT1 positive in a 3-year-old boy: a case report

Wilms’ tumor is the most common primary renal malignancy in children (80%) and the less common tumors include renal cell carcinoma, rhabdoid tumor, clear cell sarcoma, cellular congenital mesoblastic nephroma and medullary carcinoma, all of which originate from renal parenchyma. The tumors originating from renal pelvis are rare. The immunohistochemistry (IHC) showed INI1 deletion with the WT1 positive which has not been reported as we know. A 3-year-old boy was admitted to hospital for vomiting. An ultrasonography examination revealed a mass in the right kidney, medium echo, as well as hydronephrosis with collecting system separation of 3.5 cm. The computed tomography and the magnetic resonance (MR) radical showed that the tumor occupied the right renal pelvis and extended into the ureter. A radical nephroureterectomy was accomplished through a transabdominal approach. The pathologic diagnosis was malignant renal tumor with INI1 deficiency which was atypical in morphology and immunophenotype, but according to immunophenotype renal rhabdomyoid tumor could not be excluded. The patient was treated with carboplatin, etoposide and cyclophosphamide chemotherapy for 6 months. Follow-up studies of the patient showed no indication of recurrence or metastasis 22 months after nephrectomy. The novel findings may expand the spectrum of pediatric renal tumors to include the special malignancy.

Esthesioneuroblastoma in children, adolescents and young adults

The esthesioneuroblastoma (ENB) is characterized as a rare malignant sinonasal tumor of neuroectodermal origin. Its starting point is the olfactory epithelium located in the upper part of the nasal cavities. Different nomenclatures have been proposed, but the most common are "esthesioneuroblastoma" and "olfactory neuroblastoma". ENBs have a bimodal distribution and mainly occur in teenagers, young adults and people aged 50-60. It is a very rare tumor in pediatrics since only around 100 cases have been reported so far. Within ENBs, we can distinguish tumors with different biological behavior ranging from localized forms with slow evolution to aggressive and metastatic forms at onset. In addition, precisely diagnosing undifferentiated tumors and distinguishing them from other etiologies of sinonasal tumors are sometime difficult. Added to its very low incidence, these characteristics make the study of ENB complicated. The standard treatment currently includes broad surgery followed by radiation therapy in localized resectable tumors. Neoadjuvant chemotherapy is indicated in large unresectable tumors and in metastatic forms. However, in certain indications, such as high-grade operable tumors, the role of perioperative chemotherapy remains to be defined. The objective of this analysis is to detail current knowledge regarding ENBs' epidemiological, biological, clinical and radiological characteristics as well as how to manage ENB in young patients.

The novel reversible LSD1 inhibitor SP-2577 promotes anti-tumor immunity in SWItch/Sucrose-NonFermentable (SWI/SNF) complex mutated ovarian cancer

Mutations of the SWI/SNF chromatin remodeling complex occur in 20% of all human cancers, including ovarian cancer. Approximately half of ovarian clear cell carcinomas (OCCC) carry mutations in the SWI/SNF subunit ARID1A, while small cell carcinoma of the ovary hypercalcemic type (SCCOHT) presents with inactivating mutations of the SWI/SNF ATPase SMARCA4 alongside epigenetic silencing of the ATPase SMARCA2. Loss of these ATPases disrupts SWI/SNF chromatin remodeling activity and may also interfere with the function of other histone-modifying enzymes that associate with or are dependent on SWI/SNF activity. One such enzyme is lysine-specific histone demethylase 1 (LSD1/KDM1A), which regulates the chromatin landscape and gene expression by demethylating proteins such as histone H3. Cross-cancer analysis of the TCGA database shows that LSD1 is highly expressed in SWI/SNF-mutated tumors. SCCOHT and OCCC cell lines have shown sensitivity to the reversible LSD1 inhibitor SP-2577 (Seclidemstat), suggesting that SWI/SNF-deficient ovarian cancers are dependent on LSD1 activity. Moreover, it has been shown that inhibition of LSD1 stimulates interferon (IFN)-dependent anti-tumor immunity through induction of endogenous retroviral elements and may thereby overcome resistance to checkpoint blockade. In this study, we investigated the ability of SP-2577 to promote anti-tumor immunity and T-cell infiltration in SCCOHT and OCCC cell lines. We found that SP-2577 stimulated IFN-dependent anti-tumor immunity in SCCOHT and promoted the expression of PD-L1 in both SCCOHT and OCCC. Together, these findings suggest that the combination therapy of SP-2577 with checkpoint inhibitors may induce or augment immunogenic responses of SWI/SNF-mutated ovarian cancers and warrants further investigation.

Cutaneous manifestations of congenital malignant rhabdoid tumor: Unusual papillomatous plaques and other skin presentations

BACKGROUND/OBJECTIVES

Malignant rhabdoid tumors (MRT) are highly aggressive tumors with a predilection for the kidney, central nervous system, and soft tissues that usually affect young children under three years of age. Primary presentation in the skin is rarely reported, and features of the cutaneous manifestations are not well described. We report six cases of metastatic MRT that first manifested with congenital nodules and masses in the skin.

METHODS

Retrospective case series.

RESULTS

The cutaneous presentation of MRT may be heterogeneous and can present with solitary or multifocal skin lesions. Congenital polypoidal and papillomatous plaques, including those with histologic features of neurovascular hamartoma, appear to be a unique presentation of MRT in the infant.

CONCLUSIONS

Malignant rhabdoid tumor should be considered in the differential diagnosis of unusual skin tumors in neonates and infants.

Molecular hallmarks of renal medullary carcinoma: more to c-MYC than meets the eye

Renal medullary carcinoma (RMC) is a lethal disease that predominantly afflicts young individuals with sickle cell trait. Our recently reported molecular profiling of primary untreated RMC tissues elucidated distinct genomic and immune hallmarks of RMC, and identified MYC-induced replication stress as a targetable vulnerability for this disease.

A metastatic distal-type epithelioid sarcoma: Case report and review

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Epithelioid Sarcoma is a rare soft tissue tumor with an aggressive nature.

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Certain biomarker positivity or negativity can help distinguish from other tumors.

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SMARCB1 loss is predominant in most Epithelioid Sarcomas.

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Wide surgical excision is main treatment, but biomarker-targeted therapy is growing.

Introduction

Epithelioid sarcoma is known as one of the rarest types of sarcomas and was identified as its own diagnosis by Dr. Franz Enzinger in 1970 after his realization of its massive overlap with many other diseases. This tumor has an aggressive clinical course with high recurrence and metastasis rates.

Presentation of case

This report will detail the case of a 39-year-old male who was diagnosed with Epithelioid Sarcoma and later succumbed to this disease.

Discussion

This report will emphasize epithelioid sarcoma morphology and immunohistochemistry with discussions on predisposition, prognostic factors, and current options for treatment modalities.

Conclusion

Future studies are needed to determine clear predisposition and screening practices; however modern pharmaceuticals have shown hopes of optimizing the course of this cancer.

Comprehensive Molecular Characterization Identifies Distinct Genomic and Immune Hallmarks of Renal Medullary Carcinoma

Renal medullary carcinoma (RMC) is a highly lethal malignancy that mainly afflicts young individuals of African descent and is resistant to all targeted agents used to treat other renal cell carcinomas. Comprehensive genomic and transcriptomic profiling of untreated primary RMC tissues was performed to elucidate the molecular landscape of these tumors. We found that RMC was characterized by high replication stress and an abundance of focal copy-number alterations associated with activation of the stimulator of the cyclic GMP-AMP synthase interferon genes (cGAS-STING) innate immune pathway. Replication stress conferred a therapeutic vulnerability to drugs targeting DNA-damage repair pathways. Elucidation of these previously unknown RMC hallmarks paves the way to new clinical trials for this rare but highly lethal malignancy.

The roles of mutated SWI/SNF complexes in the initiation and development of hepatocellular carcinoma and its regulatory effect on the immune system: A review

Hepatocellular carcinoma (HCC) is a primary liver malignancy with a high global prevalence and a dismal prognosis. Studies are urgently needed to examine the molecular pathogenesis and biological characteristics of HCC. Chromatin remodelling, an integral component of the DNA damage response, protects against DNA damage‐induced genome instability and tumorigenesis by triggering the signalling events that activate the interconnected DNA repair pathways. The SWI/SNF complexes are one of the most extensively investigated adenosine triphosphate‐dependent chromatin remodelling complexes, and mutations in genes encoding SWI/SNF subunits are frequently observed in various human cancers, including HCC. The mutated SWI/SNF complex subunits exert dual functions by accelerating or inhibiting HCC initiation and progression. Furthermore, the abnormal SWI/SNF complexes influence the transcription of interferon‐stimulated genes, as well as the differentiation, activation and recruitment of several immune cell types. In addition, they exhibit synergistic effects with immune checkpoint inhibitors in the treatment of diverse tumour types. Therefore, understanding the mutations and deficiencies of the SMI/SNF complexes, together with the associated functional mechanisms, may provide a novel strategy to treat HCC through targeting the related genes or modulating the tumour microenvironment.

Loss of BRG1 (SMARCA4) Immunoexpression in a Pediatric Non-Central Nervous System Tumor Cohort

Malignant rhabdoid tumors and atypical teratoid/rhabdoid tumors of the central nervous system are primitive malignancies associated with a poor prognosis. These tumors have previously been characterized by inactivation of the switch/sucrose nonfermenting (SWI/SNF) chromatin remodeling complex protein integrase interactor 1 (INI1), encoded by the SMARCB1 gene. In the last decade, sporadic publications have shown that a different SWI/SNF protein, brahma-related gene 1 (BRG1), encoded by the SMARCA4 gene, is associated with a similar rhabdoid phenotype and possible germline mutation termed rhabdoid tumor predisposition syndrome type 2. We sought to determine the presence of BRG1 expression in pediatric embryonal tumors. Using a local tissue microarray consisting of 28 tumors diagnosed as having an undifferentiated, polyphenotypic, or rhabdoid morphology, expression of BRG1 by immunohistochemistry was performed. Four cases showed loss of INI1, while 3 of the remaining 24 cases demonstrated loss of BRG1. Two cases were diagnosed as soft tissue sarcomas, and 1 case was diagnosed as a small cell carcinoma of the ovary, hypercalcemic type. Survival ranged from less than 6 months after diagnosis to more than 5 years at the time of last follow-up. In conclusion, we demonstrate that BRG1 immunohistochemistry is a useful second-line immunostain for the workup of undifferentiated, polyphenotypic or rhabdoid pediatric tumors that demonstrate retained expression of INI1.

A case of malignant rhabdoid tumor mimicking yolk sac tumor

Malignant rhabdoid tumors (MRTs) are rare, highly aggressive embryonal neoplasms caused by biallelic alterations of the SMARCB1 gene. MRTs may occur in any soft tissue, but extracranial extrarenal MRTs are extremely rare. Diagnosis of MRTs in unusual locations and with an uncharacteristic cytomorphology that mimics other tumors is difficult. This was an atypical case of MRT in a 15-year-old female with tumors that closely resembled yolk sac tumors. It was extremely challenging to diagnose the tumors without confirming the SMARCB1 status.

Inhibition of MYC by the SMARCB1 tumor suppressor

SMARCB1 encodes the SNF5 subunit of the SWI/SNF chromatin remodeler. SNF5 also interacts with the oncoprotein transcription factor MYC and is proposed to stimulate MYC activity. The concept that SNF5 is a coactivator for MYC, however, is at odds with its role as a tumor-suppressor, and with observations that loss of SNF5 leads to activation of MYC target genes. Here, we reexamine the relationship between MYC and SNF5 using biochemical and genome-wide approaches. We show that SNF5 inhibits the DNA-binding ability of MYC and impedes target gene recognition by MYC in cells. We further show that MYC regulation by SNF5 is separable from its role in chromatin remodeling, and that reintroduction of SNF5 into SMARCB1-null cells mimics the primary transcriptional effects of MYC inhibition. These observations reveal that SNF5 antagonizes MYC and provide a mechanism to explain how loss of SNF5 can drive malignancy.

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination

The SWI/SNF complex is a critical regulator of pluripotency in human embryonic stem cells (hESCs), and individual subunits have varied and specific roles during development and in diseases. The core subunit SMARCB1 is required for early embryonic survival, and mutations can give rise to atypical teratoid/rhabdoid tumors (AT/RTs) in the pediatric central nervous system. We report that in contrast to other studied systems, SMARCB1 represses bivalent genes in hESCs and antagonizes chromatin accessibility at super-enhancers. Moreover, and consistent with its established role as a CNS tumor suppressor, we find that SMARCB1 is essential for neural induction but dispensable for mesodermal or endodermal differentiation. Mechanistically, we demonstrate that SMARCB1 is essential for hESC super-enhancer silencing in neural differentiation conditions. This genomic assessment of hESC chromatin regulation by SMARCB1 reveals a novel positive regulatory function at super-enhancers and a unique lineage-specific role in regulating hESC differentiation.

Our bodies contain trillions of cells that play a wide variety of roles. Despite looking and behaving very differently to one another, all of these ‘mature’ cells somehow descend from a single fertilized egg that contains just one set of genes. This process is partially controlled by how ‘accessible’ genetic material is to the cell machinery that switches genes on or off. For example, in immature brain cells, genes required for memory are accessible, but genes needed to produce bone are not.

The developing embryo needs to control gene accessibility carefully to ensure that the right genes become available at the right time, and that crucial genes are not incorrectly ‘hidden’. In humans, the protein SMARCB1 plays an important role in this process: if damaged or deleted, development will be severely disrupted, sometimes causing brain cancer early in life. However, it remains unclear how exactly SMARCB1 regulates the accessibility of its ‘target’ genes. Now, Langer et al. set out to answer this question, and also to determine which parts of the body need SMARCB1 to develop properly.

Human stem cells can develop into multiple mature cell types if given the right signals. Langer et al. found reducing levels of SMARCB1 prevented stem cells from maturing into brain cells, but not other kinds of cells. This suggests that SMARCB1 has a specific role in brain development, which is consistent with its devastating effect on brain health when damaged.

A detailed analysis of genetic activity and DNA accessibility showed that SMARCB1 was doing this by switching off specific regions of DNA, called stem cell super-enhancers. These regions normally enhance the activity of genes that maintain stem cells in their immature state: when certain super-enhancers are turned off by SMARCB1, this allows stem cells to progress towards a brain cell fate.

These results help us understand why damage to SMARCB1 during development causes brain cancer more often than other kinds of cancer. In the future, they could also help explain how certain types of cancer form, which would be the first step towards knowing how to treat them.

A BAFfling liver aspirate: Metastatic high grade SMARCA4 deficient undifferentiated gastroesophageal junction carcinoma masquerading as a hematolymphoid malignancy

Undifferentiated malignant SMARCA4-deficient neoplasms are rare, recently characterized, high grade, potentially lethal malignancies. Such tumors are characterized by the loss of BRG1 encoded by SMARCA4, a key component of the Switch/Sucrose Non-Fermenting (SWI/SNF) chromatin remodeling complex. As this complex, also referred as BAF (BRG1/BRM associated factors) complex, is involved in the epigenetic control of hundreds of genes, including those involved in lineage-specific differentiation, BAF-deficient tumors, show minimal or no differentiation and are difficult to classify. Their fine needle aspiration (FNA) cytologic features are still poorly defined. Here, we describe a 70-year-old man who presented with thickening of the wall of the distal esophagus and stomach and multiple liver and lung lesions. Liver FNA showed relatively uniform dispersed malignant cells with high nucleus: cytoplasm ratio, scant microvacuolated cytoplasm, eccentric nuclei and prominent nucleoli. Mitoses, necrotic debris, nuclear streak artifact, "ghost cells" and focal rhabdoid cytoplasmic inclusions were also present. The liver core biopsy and GI biopsies demonstrated sinusoidal and respectively submucosal involvement by a high grade undifferentiated malignant neoplasm. The tumor cells were negative for all applied markers on immunohistochemistry and flow cytometry, and only showed CD138 and weak PAX5 staining. After an initial diagnosis of hematolymphoid neoplasm, additional stains showed intact INI1 protein and loss of BRG1 protein immunoexpression, establishing the accurate diagnosis. This case highlights the difficulties and potential pitfalls encountered in the FNA diagnosis of BAF-deficient tumors, the accurate diagnosis of which is important due to their lack of response to conventional therapy and potential response to targeted therapy.

Renal Medullary Carcinoma: a Report of the Current Literature

PURPOSE OF THE REVIEW

We present an updated report of renal medullary carcinoma (RMC), a rare and aggressive condition.

RECENT FINDINGS

There is a majority of male patients, of African descent, in the second or third decade of life. In differential diagnosis, other tumors, such as malignant rhabdoid tumor (MRT), vinculin-anaplastic lymphoma kinase (VCL-ALK) translocation renal cell carcinoma, and collecting duct carcinoma, may present difficulties. Abnormalities of tumor suppressor gene SMARCB1 have been found in RMC. Reported symptoms were hematuria, pain, weight loss, respiratory distress, palpable mass, cough, and fever. Most patients present with metastases at diagnosis. There is no definite recommended treatment, and protocols are extrapolated from other malignancies, with nephrectomy and systemic therapies being most frequently used. Response to treatment and prognosis remain very poor. RMC is a rare and aggressive tumor. Definitive diagnosis requires histological assessment and the presence of sickle-cell hemoglobinopathies.