SMARCB1 Loss in Poorly-differentiated Chordomas Drives Tumor Progression
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ABSTRACT:
PROVIDER: PRJNA901898 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22298251_1.fastq.gz | Fastqsanger.gz | |||
| SRR22298251_2.fastq.gz | Fastqsanger.gz | |||
| SRR22298252_1.fastq.gz | Fastqsanger.gz | |||
| SRR22298252_2.fastq.gz | Fastqsanger.gz | |||
| SRR22298253_1.fastq.gz | Fastqsanger.gz |
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Project description:Poorly-differentiated (PD) chordoma, a tumor found mainly in children, adolescents and young adults is a rare, aggressive tumor originating from notochordal tissue, with limited therapeutic options. SMARCB1, a core component of the BAF and PBAF chromatin remodeling complexes, is the most frequently mutated gene in PD chordomas, the most aggressive form of this cancer. In this study, we employed cellular models of SMARCB1-negative PD chordomas to characterize expression of SWI/SNF complex members and determine the impact of SMARCB1 re-expression on cell growth as well as the transcriptional landscape by RNA-seq. We generated 2 SMARCB1-negative PD chordoma cell lines, CH22 and UM-Chor5, with an inducible SMARCB1 expression system. After 72 hours of induction of SMARCB1 re-expression, we observed continued growth of both SMARCB1-negative PD chordoma cell lines. This is in striking contrast to SMARCB1-deficient rhabdoid cell lines, where we found SMARCB1 re-expression inhibits growth completely. We also found the lack of growth inhibition may arise from the loss of CDKN2A/p16INK4A expression in all poorly differentiated chordoma cell lines which correlated well with the gene expression data. SMARCB1 re-expression in both CH22 and UM-Chor5 cells showed downregulation for rRNA and RNA processing as well as metabolic processing. Upregulated differentially expressed genes included those involved in cell adhesion, cell migration, and development. Taken together, our data establish SMARCB1 re-expression in PD chordomas alters the repertoire of SWI/SNF complexes, perhaps restoring those associated with cellular differentiation. Our findings support a model where SMARCB1 inactivation blocks the conversion of growth-promoting SWI/SNF complexes to differentiation-inducing ones.
2022-12-21 | GSE217999 | GEO
Project description:Poorly differentiated (PD) chordoma, a rare, aggressive tumor originating from notochordal tissue, shows loss of SMARCB1 expression, a core component of the Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes. To determine the impact of SMARCB1 re-expression on cell growth and gene expression, two SMARCB1-negative PD chordoma cell lines with an inducible SMARCB1 expression system were generated. After 72 hours of induction of SMARCB1, both SMARCB1-negative PD chordoma cell lines continued to proliferate. This result contrasted with those observed with SMARCB1-negative rhabdoid cell lines in which SMARCB1 re-expression caused the rapid inhibition of growth. We found that the lack of growth inhibition may arise from the loss of CDKN2A (p16INK4A) expression in PD chordoma cell lines. RNA-sequencing of cell lines after SMARCB1 re-expression showed a down-regulation for rRNA and RNA processing as well as metabolic processing and increased expression of genes involved in cell adhesion, cell migration, and development. Taken together, these data establish that SMARCB1 re-expression in PD chordomas alters the repertoire of SWI/SNF complexes, perhaps restoring those associated with cellular differentiation. These novel findings support a model in which SMARCB1 inactivation blocks the conversion of growth-promoting SWI/SNF complexes to differentiation-inducing ones, and they implicate SMARCB1 loss as a late event in tumorigenic progression. Importantly, the absence of growth inhibition after SMARCB1 restoration creates a unique opportunity to identify therapeutic vulnerabilities.
| S-EPMC10123523 | biostudies-literature
Project description:In the present study, a 36-year-old male presented with left scrotal enlargement without an obvious cause, accompanied by a feeling of heaviness. Imaging examinations revealed a left testicular malignancy, the patient underwent left testicular mass removal,and the postoperative pathology results revealed a highly malignant germ cell tumor, with a tendency toward poorly differentiated embryonal carcinoma or seminoma. After surgery, the condition of the patient deteriorated rapidly, and distant tumor metastasis occurred. Lymph node puncture pathology results revealed poorly differentiated carcinoma consistent with SMARCB1/INI-1 deletion. Despite the use of chemotherapy, radiotherapy, immunotherapy and targeted therapy, the patient died 11 months after surgery. To the best of our knowledge, this is the first case report of a SMARCB1/INI1-deficient Poorly differentiated testicular carcinoma, which is very similar to testicular spermatocytic carcinoma in clinical diagnosis and deserves differentiation for future clinical diagnoses.This report provides important insights into the diagnosis and treatment of SMARCB1/INI1-deficient testicular malignancy. SMARCB1 is a crucial tumor suppressor gene, and its deficiency is closely associated with the development of various malignant tumors. The identification of this case suggests that future research should further explore the molecular mechanisms of SMARCB1-deficient tumors, particularly their role in testicular malignancies. Additionally, the diagnostic process of this case highlights that SMARCB1/INI1-deficient tumors can be clinically very similar to spermatocytic carcinoma of the testis, which can easily lead to misdiagnosis. Therefore, future clinical practice should emphasize the detection of SMARCB1/INI1 expression status, especially in the context of highly aggressive and rapidly progressing testicular malignancies, where immunohistochemical testing for SMARCB1/INI1 should be considered to confirm the diagnosis. In terms of treatment, this case demonstrates the highly aggressive nature and resistance to conventional therapies of SMARCB1/INI1-deficient tumors. Despite the patient receiving multiple treatments, disease progression could not be halted. This underscores the need for the development of novel therapeutic strategies targeting SMARCB1/INI1-deficient tumors, such as combinations of immune checkpoint inhibitors and targeted therapies, or other emerging immunotherapeutic approaches. Moreover, the treatment course of this patient also reflects the importance of individualized treatment plans. Future research should further explore precision medicine strategies based on tumor genetic profiles to improve patient survival rates and quality of life.
| S-EPMC11922841 | biostudies-literature
Project description:Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
2023-10-20 | GSE218111 | GEO
Project description:Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
2023-10-20 | GSE218114 | GEO
Project description:Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
2023-10-20 | GSE218113 | GEO
Project description:Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
2023-10-20 | GSE218112 | GEO
Project description:Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer. Yet, their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
2023-10-20 | GSE218110 | GEO
Project description:Pten and Dicer1 loss in the mouse uterus causes poorly-differentiated endometrial adenocarcinoma
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Project description:SMARCB1 (Snf5/Ini1/Baf47) is a potent tumor suppressor, the loss of which serves as the diagnostic feature in Malignant Rhabdoid Tumors (MRT) and Atypical Teratoid/Rhabdoid Tumors (AT/RT), two highly aggressive forms of pediatric neoplasms. Here, we restore Smarcb1 expression in cells derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice. Profiling Smarcb1 dependent gene expression we find genes which are dependent on Smarcb1 expression to be enriched for ECM and cell adhesion functions. We identify Igfbp7, which is related to the insulin-like growth factor binding proteins family, as a downstream target of Smarcb1 transcriptional activity, and show that re-introduction of Igfbp7 alone can hinder tumor development. Two cancer cell lines, 167 and 365, derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice were re-infected with a retro-viral vector for Smarcb1 re-expression or an empty retro-viral vector as control. Total-RNA was collected 3 days post infection so as to enrich for direct targets of Smarcb1 transcriptionaly regulated genes
2013-12-31 | E-GEOD-46017 | biostudies-arrayexpress