SMARCB1 Loss in Poorly Differentiated Chordomas Drives Tumor Progression

SMARCB1 orchestrates cellular plasticity and oncogenic pathways in typical and chondroid chordomas

Chordomas are rare, aggressive tumors of the axial skeleton with limited treatment options. Genetic alterations in SMARCB1, a tumor suppressor gene, have been implicated in poorly differentiated chordomas, but their role in typical and chondroid subtypes remains unclear. This study examined 42 chordoma samples (26 typical, 16 chondroid) for SMARCB1 genetic alterations, expression patterns, and associated pathways. SMARCB1 knockdown experiments were conducted in chordoma cell lines, followed by comprehensive transcriptome analysis. No exonic SMARCB1 mutations were identified, but heterozygous loss was observed in 3/26 typical chordomas. SMARCB1 expression positively correlated with patient survival and epithelial-mesenchymal markers. Functional studies revealed that SMARCB1 knockdown significantly enhanced cell proliferation, migration, and invasion. Transcriptome analysis demonstrated enrichment of MYC targets, E2F targets, and cell cycle pathways in SMARCB1-low samples, while cellular adhesion pathways were downregulated. Notably, SLPI, LBH, and LOXL2 were significantly downregulated in SMARCB1-low samples. SMARCB1 plays an important role in chordoma progression, influencing prognosis and cellular behavior, despite infrequent genetic alterations. Its effects on key oncogenic pathways and cellular plasticity suggest potential for targeted therapies. These findings provide new insights into chordoma biology and lay the groundwork for developing SMARCB1-based prognostic tools and personalized treatment strategies.

Exploring perspectives on skull base chordoma management: a modified Delphi approach to consensus

OBJECTIVE

Current treatment for skull base chordomas utilizes both surgical resection and adjuvant radiation, but recent studies have demonstrated evidence that has brought the use of adjuvant radiotherapy into question. Chordomas differ greatly in molecular makeup and proliferation. These factors have led to significant variation in management across providers. We used a modified Delphi approach to work towards consensus on standardized operative definitions and evidence-based management of chordomas.

METHODS

Our multidisciplinary panel included participants representing the AANS/CNS Tumor Section and North American Skull Base Society (NASBS) with a track record of publishing on chordoma management. Our approach involved a four-step process: one statement-generation round, two voting rounds to establish consensus and refine statements, and a final external validation round by NASBS members. Anonymous voting was completed via Qualtrics surveys.

RESULTS

The statement-generation process produced 65 statements. Through the Delphi process, 36 statements reached consensus during the first round and an additional 17 were refined for further consensus in the second round. Moderate (67-80%) or strong (> 80%) consensus was achieved for 43 final statements. Forty-one items were externally validated. There was consensus that an endoscopic endonasal approach should be utilized whenever possible. They defined the tumor characteristics (molecular and cytogenic) to consider before offering adjuvant radiotherapy.

CONCLUSIONS

This modified Delphi study generated consensus on 41 statements regarding skull base chordoma management. These statements aim to shed light on the consensus among providers regarding the use of surgery, neoadjuvant radiation, adjuvant radiation, adjuvant systemic therapies, and treatment of recurrence for chordoma.

Pediatric Chordoma: A Tale of Two Genomes

Little is known about the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known genetic susceptibility loci. A comprehensive genomic analysis of the nuclear and mitochondrial genomes in pediatric chordoma has not yet been reported. In this study, we performed WES and mtDNA genome sequencing on 29 chordomas from 23 pediatric patients. Findings were compared with that from whole-genome sequencing datasets of 80 adult patients with skull base chordoma. In the pediatric chordoma cohort, 81% of the somatic mtDNA mutations were observed in NADH complex genes, which is significantly enriched compared with the rest of the mtDNA genes (P = 0.001). In adult chordomas, mtDNA mutations were also enriched in the NADH complex genes (P < 0.0001). Furthermore, a progressive increase in heteroplasmy of nonsynonymous mtDNA mutations was noted in patients with multiple tumors (P = 0.0007). In the nuclear genome, rare likely germline in-frame indels in ARID1B, a member of the SWI/SNF complex located at 6q25.3, were observed in five pediatric patients (22%) and four patients in the adult cohort (5%). The frequency of rare ARID1B indels in the pediatric cohort is significantly higher than that in the adult cohort (P = 0.0236, Fisher's exact test), but they were both significantly higher than that in the ethnicity-matched populations (P < 5.9e-07 and P < 0.0001174, respectively). Implications: germline ARID1B indels and mtDNA aberrations seem important for chordoma genesis, especially in pediatric chordoma.

Targeting SWI/SNF Complexes in Cancer: Pharmacological Approaches and Implications

SWI/SNF enzymes are heterogeneous multi-subunit complexes that utilize the energy from ATP hydrolysis to remodel chromatin structure, facilitating transcription, DNA replication, and repair. In mammalian cells, distinct sub-complexes, including cBAF, ncBAF, and PBAF exhibit varying subunit compositions and have different genomic functions. Alterations in the SWI/SNF complex and sub-complex functions are a prominent feature in cancer, making them attractive targets for therapeutic intervention. Current strategies in cancer therapeutics involve the use of pharmacological agents designed to bind and disrupt the activity of SWI/SNF complexes or specific sub-complexes. Inhibitors targeting the catalytic subunits, SMARCA4/2, and small molecules binding SWI/SNF bromodomains are the primary approaches for suppressing SWI/SNF function. Proteolysis-targeting chimeras (PROTACs) were generated by the covalent linkage of the bromodomain or ATPase-binding ligand to an E3 ligase-binding moiety. This engineered connection promotes the degradation of specific SWI/SNF subunits, enhancing and extending the impact of this pharmacological intervention in some cases. Extensive preclinical studies have underscored the therapeutic potential of these drugs across diverse cancer types. Encouragingly, some of these agents have progressed from preclinical research to clinical trials, indicating a promising stride toward the development of effective cancer therapeutics targeting SWI/SNF complex and sub-complex functions.

SMARCB1/INI1 loss in skull base conventional chordomas: a clinicopathological and molecular analysis

Introduction

The loss of SMARCB1/INI1 protein has been recently described in poorly differentiated chordoma, an aggressive and rare disease variant typically arising from the skull base.

Methods

Retrospective study aimed at 1) examining the differential immunohistochemical expression of SMARCB1/INI1 in conventional skull base chordomas, including the chondroid subtype; 2) evaluating SMARCB1 gene deletions/copy number gain; and 3) analyzing the association of SMARCB1/INI1 expression with clinicopathological parameters and patient survival.

Results

65 patients (35 men and 30 women) affected by conventional skull base chordoma, 15 with chondroid subtype, followed for >48 months after surgery were collected. Median age at surgery was 50 years old (range 9-79). Mean tumor size was 3.6 cm (range 2-9.5). At immunohistochemical evaluation, a partial loss of SMARCB1/INI1 (>10% of neoplastic examined cells) was observed in 21 (32.3%) cases; the remaining 43 showed a strong nuclear expression. Fluorescence in situ hybridization (FISH) analysis was performed in 15/21 (71.4%) cases of the chordomas with partial SMARCB1/INI1 loss of expression. Heterozygous deletion of SMARCB1 was identified in 9/15 (60%) cases and was associated to copy number gain in one case; no deletion was found in the other 6 (40%) cases, 3 of which presenting with a copy number gain. No correlations were found between partial loss of SMARCB1/INI1 and the clinicopathological parameters evaluated (i.e., age, tumor size, gender, tumor size and histotype). Overall 5-year survival and 5-year disease-free rates were 82% and 59%, respectively. According to log-rank test analysis the various clinico-pathological parameters and SMARCB1/INI1 expression did not impact on overall and disease free-survival.

Discussion

Partial loss of SMARCB1/INI1, secondary to heterozygous deletion and/or copy number gain of SMARCB1, is not peculiar of aggressive forms, but can be identified by immunohistochemistry in a significant portion of conventional skull base chordomas, including the chondroid subtype. The variable protein expression does not appear to correlate with clinicopathological parameters, nor survival outcomes, but still, it could have therapeutic implications.

The SWI/SNF Complex: A Frequently Mutated Chromatin Remodeling Complex in Cancer

The switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is a global regulator of gene expression known to maintain nucleosome-depleted regions at active enhancers and promoters. The mammalian SWI/SNF protein subunits are encoded by 29 genes and 11-15 subunits including an ATPase domain of either SMARCA4 (BRG1) or SMARCA2 (BRM) are assembled into a complex. Based on the distinct subunits, SWI/SNF are grouped into 3 major types (subfamilies): the canonical BRG1/BRM-associated factor (BAF/cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (GBAF/ncBAF). Pan-cancer genome sequencing studies have shown that nearly 25% of all cancers bear mutations in subunits of the SWI/SNF complex, many of which are loss of function (LOF) mutations, suggesting a tumor suppressor role. Inactivation of SWI/SNF complex subunits causes widespread epigenetic dysfunction, including increased dependence on antagonistic components such as polycomb repressor complexes (PRC1/2) and altered enhancer regulation, likely promoting an oncogenic state leading to cancer. Despite the prevalence of mutations, most SWI/SNF-mutant cancers lack targeted therapeutic strategies. Defining the dependencies created by LOF mutations in SWI/SNF subunits will identify better targets for these cancers.