1
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. Am J Hum Genet 2024; 111:1282-1300. [PMID: 38834072 PMCID: PMC11267525 DOI: 10.1016/j.ajhg.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
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Affiliation(s)
- Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Pagé C Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christopher A Jin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Matthew T Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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2
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Magrath JW, Sampath SS, Flinchum DA, Hartono AB, Goldberg IN, Boehling JR, Savkovic SD, Lee SB. Comprehensive Transcriptomic Analysis of EWSR1::WT1 Targets Identifies CDK4/6 Inhibitors as an Effective Therapy for Desmoplastic Small Round Cell Tumors. Cancer Res 2024; 84:1426-1442. [PMID: 38588409 PMCID: PMC11063761 DOI: 10.1158/0008-5472.can-23-3334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/28/2023] [Accepted: 02/07/2024] [Indexed: 04/10/2024]
Abstract
Desmoplastic small round cell tumors (DSRCT) are a type of aggressive, pediatric sarcoma characterized by the EWSR1::WT1 fusion oncogene. Targeted therapies for DSRCT have not been developed, and standard multimodal therapy is insufficient, leading to a 5-year survival rate of only 15% to 25%. Here, we depleted EWSR1::WT1 in DSRCT and established its essentiality in vivo. Transcriptomic analysis revealed that EWSR1::WT1 induces unique transcriptional alterations compared with WT1 and other fusion oncoproteins and that EWSR1::WT1 binding directly mediates gene upregulation. The E-KTS isoform of EWSR1::WT1 played a dominant role in transcription, and it bound to the CCND1 promoter and stimulated DSRCT growth through the cyclin D-CDK4/6-RB axis. Treatment with the CDK4/6 inhibitor palbociclib successfully reduced growth in two DSRCT xenograft models. As palbociclib has been approved by the FDA for the treatment of breast cancer, these findings demonstrate the sensitivity of DSRCT to palbociclib and support immediate clinical investigation of palbociclib for treating this aggressive pediatric cancer. SIGNIFICANCE EWSR1::WT1 is essential for desmoplastic small round cell tumors and upregulates the cyclin D-CDK4/6-RB axis that can be targeted with palbociclib, providing a targeted therapeutic strategy for treating this deadly tumor type.
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Affiliation(s)
- Justin W. Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Dane A. Flinchum
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Alifiani B. Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Ilon N. Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Julia R. Boehling
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Suzana D. Savkovic
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Sean B. Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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3
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Magrath JW, Goldberg IN, Truong DD, Hartono AB, Sampath SS, Jackson CE, Ghosh A, Cardin DL, Zhang H, Ludwig JA, Lee SB. Enzalutamide induces cytotoxicity in desmoplastic small round cell tumor independent of the androgen receptor. Commun Biol 2024; 7:411. [PMID: 38575753 PMCID: PMC10995187 DOI: 10.1038/s42003-024-06003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, pediatric cancer caused by the EWSR1::WT1 fusion protein. DSRCT predominantly occurs in males, which comprise 80-90% of the patient population. While the reason for this male predominance remains unknown, one hypothesis is that the androgen receptor (AR) plays a critical role in DSRCT and elevated testosterone levels in males help drive tumor growth. Here, we demonstrate that AR is highly expressed in DSRCT relative to other fusion-driven sarcomas and that the AR antagonists enzalutamide and flutamide reduce DSRCT growth. However, despite these findings, which suggest an important role for AR in DSRCT, we show that DSRCT cell lines form xenografts in female mice at the same rate as male mice and AR depletion does not significantly alter DSRCT growth in vitro. Further, we find that AR antagonists reduce DSRCT growth in cells depleted of AR, establishing an AR-independent mechanism of action. These findings suggest that AR dependence is not the reason for male predominance in DSRCT and that AR-targeted therapies may provide therapeutic benefit primarily through an AR-independent mechanism that requires further elucidation.
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Affiliation(s)
- Justin W Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Ilon N Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Danh D Truong
- Sarcoma Medical Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alifiani B Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Chandler E Jackson
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Anushka Ghosh
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Derrick L Cardin
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Haitao Zhang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Joseph A Ludwig
- Sarcoma Medical Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sean B Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA.
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4
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Magrath JW, Flinchum DA, Hartono AB, Sampath SS, O'Grady TM, Baddoo M, Haoyang L, Xu X, Flemington EK, Lee SB. Transcriptomic analysis identifies B-lymphocyte kinase as a therapeutic target for desmoplastic small round cell tumor cancer stem cell-like cells. Oncogenesis 2024; 13:2. [PMID: 38177125 PMCID: PMC10767073 DOI: 10.1038/s41389-023-00504-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Desmoplastic small round cell tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15-25%, necessitating the development of novel therapeutics, especially those able to target chemoresistant subpopulations. Novel in vitro cancer stem cell-like (CSC-like) culture conditions increase the expression of stemness markers (SOX2, NANOG) and reduce DSRCT cell line susceptibility to chemotherapy while maintaining the ability of DSRCT cells to form xenografts. To gain insights into this chemoresistant model, RNA-seq was performed to elucidate transcriptional alterations between DSRCT cells grown in CSC-like spheres and normal 2-dimensional adherent state. Commonly upregulated and downregulated genes were identified and utilized in pathway analysis revealing upregulation of pathways related to chromatin assembly and disassembly and downregulation of pathways including cell junction assembly and extracellular matrix organization. Alterations in chromatin assembly suggest a role for epigenetics in the DSRCT CSC-like state, which was further investigated with ATAC-seq, identifying over 10,000 differentially accessible peaks, including 4444 sphere accessible peaks and 6,120 adherent accessible peaks. Accessible regions were associated with higher gene expression, including increased accessibility of the CSC marker SOX2 in CSC-like culture conditions. These analyses were further utilized to identify potential CSC therapeutic targets, leading to the identification of B-lymphocyte kinase (BLK) as a CSC-enriched, EWSR1-WT1-regulated, druggable target. BLK inhibition and knockdown reduced CSC-like properties, including abrogation of tumorsphere formation and stemness marker expression. Importantly, BLK knockdown reduced DSRCT CSC-like cell chemoresistance, making its inhibition a promising target for future combination therapy.
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Affiliation(s)
- Justin W Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Dane A Flinchum
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Alifiani B Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
- Department of Molecular & Medical Pharmacology, University of California Los Angeles, 630 Charles E Young Dr. S., Los Angeles, CA, 90095, USA
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Tina M O'Grady
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Melody Baddoo
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Liang Haoyang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Xiaojiang Xu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Erik K Flemington
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA
| | - Sean B Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, USA.
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5
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Magrath JW, Goldberg IN, Truong DD, Hartono AB, Sampath SS, Jackson CE, Ghosh A, Cardin DL, Zhang H, Ludwig JA, Lee SB. Enzalutamide Induces Cytotoxicity in Desmoplastic Small Round Cell Tumor Independent of the Androgen Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.06.565842. [PMID: 37986851 PMCID: PMC10659336 DOI: 10.1101/2023.11.06.565842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, pediatric cancer caused by the EWSR1::WT1 fusion protein. DSRCT predominantly occurs in males, which comprise 80-90% of the patient population. While the reason for this male predominance remains unknown, one hypothesis is that the androgen receptor (AR) plays a critical role in DSRCT and elevated testosterone levels in males help drive tumor growth. Here, we demonstrate that AR is highly expressed in DSRCT relative to other fusion-driven sarcomas and that the AR antagonists enzalutamide and flutamide reduce DSRCT growth. However, despite these findings, which suggest an important role for AR in DSRCT, we show that DSRCT cell lines form xenografts in female mice at the same rate as male mice and AR depletion does not significantly alter DSRCT growth in vitro. Further, we find that AR antagonists reduce DSRCT growth in cells depleted of AR, establishing an AR-independent mechanism of action. These findings suggest that AR dependence is not the reason for male predominance in DSRCT and that AR-targeted therapies may provide therapeutic benefit primarily through an AR-independent mechanism that requires further elucidation.
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Affiliation(s)
- Justin W Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Ilon N Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Danh D Truong
- Sarcoma Medical Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alifiani B Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Shruthi Sanjitha Sampath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Chandler E Jackson
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Anushka Ghosh
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Derrick L Cardin
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Haitao Zhang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Joseph A Ludwig
- Sarcoma Medical Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sean B Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
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6
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Feng S, Wei F, Shi H, Chen S, Wang B, Huang D, Luo L. Roles of salt‑inducible kinases in cancer (Review). Int J Oncol 2023; 63:118. [PMID: 37654200 PMCID: PMC10546379 DOI: 10.3892/ijo.2023.5566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023] Open
Abstract
Salt inducible kinases (SIKs) with three subtypes SIK1, SIK2 and SIK3, belong to the AMP‑activated protein kinase family. They are expressed ubiquitously in humans. Under normal circumstances, SIK1 regulates adrenocortical function in response to high salt or adrenocorticotropic hormone stimulation, SIK2 is involved in cell metabolism, controlling insulin signaling and gluconeogenesis and SIK3 coordinates with the mTOR complex, promoting cancer. The dysregulation of SIKs has been widely detected in various types of cancers. Based on most of the existing studies, SIK1 is mostly considered a tumor inhibitor, SIK2 and SIK3 are usually associated with tumor promotion. However, the functions of SIKs have shown contradictory in certain tumors, suggesting that SIKs cannot be simply classified as oncogenes or tumor suppressor genes. The present review provided a comprehensive summary of the roles of SIKs in the initiation and progression of different cancers, aiming to elucidate their clinical value and discuss potential strategies for targeting SIKs in cancer therapy.
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Affiliation(s)
- Shenghui Feng
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Fangyi Wei
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Haoran Shi
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shen Chen
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Bangqi Wang
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Deqiang Huang
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Lingyu Luo
- Department of Gastroenterology, Research Institute of Digestive Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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7
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Magrath JW, Flinchum DA, Hartono AB, Goldberg IN, Espinosa-Cotton M, Moroz K, Cheung NKV, Lee SB. Genomic Breakpoint Characterization and Transcriptome Analysis of Metastatic, Recurrent Desmoplastic Small Round Cell Tumor. Sarcoma 2023; 2023:6686702. [PMID: 37457440 PMCID: PMC10344636 DOI: 10.1155/2023/6686702] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare pediatric cancer caused by the EWSR1-WT1 fusion oncogene. Despite initial response to chemotherapy, DSRCT has a recurrence rate of over 80% leading to poor patient prognosis with a 5-year survival rate of only 15-25%. Owing to the rarity of DSRCT, sample scarcity is a barrier in understanding DSRCT biology and developing effective therapies. Utilizing a novel pair of primary and recurrent DSRCTs, we present the first map of DSRCT genomic breakpoints and the first comparison of gene expression alterations between primary and recurrent DSRCT. Our genomic breakpoint map includes the lone previously published DSRCT genomic breakpoint, the breakpoint from our novel primary/recurrent DSRCT pair, as well as the breakpoints of five available DSRCT cell lines and five additional DSRCTs. All mapped breakpoints were unique and most breakpoints included a 1-3 base pair microhomology suggesting microhomology-mediated end-joining as the mechanism of translocation fusion and providing novel insights into the etiology of DSRCT. Through RNA-sequencing analysis, we identified altered genes and pathways between primary and recurrent DSRCTs. Upregulated pathways in the recurrent tumor included several DNA repair and mRNA splicing-related pathways, while downregulated pathways included immune system function and focal adhesion. We further found higher expression of the EWSR1-WT1 upregulated gene set in the recurrent tumor as compared to the primary tumor and lower expression of the EWSR1-WT1 downregulated gene set, suggesting the EWSR1-WT1 fusion continues to play a prominent role in recurrent tumors. The identified pathways including upregulation of DNA repair and downregulation of immune system function may help explain DSRCT's high rate of recurrence and can be utilized to improve the understanding of DSRCT biology and identify novel therapies to both help prevent recurrence and treat recurrent tumors.
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Affiliation(s)
- Justin W. Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Dane A. Flinchum
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Alifiani B. Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Ilon N. Goldberg
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | | | - Krzysztof Moroz
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
| | - Nai-Kong V. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean B. Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, 1430 Tulane Ave. New Orleans, LA, USA
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Hovsepyan S, Giani C, Pasquali S, Di Giannatale A, Chiaravalli S, Colombo C, Orbach D, Bergamaschi L, Vennarini S, Gatz SA, Gasparini P, Berlanga P, Casanova M, Ferrari A. Desmoplastic small round cell tumor: from state of the art to future clinical prospects. Expert Rev Anticancer Ther 2023; 23:471-484. [PMID: 37017324 DOI: 10.1080/14737140.2023.2200171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/06/2023]
Abstract
INTRODUCTION Desmoplastic small round cell tumor (DSRCT) is an extremely rare and highly aggressive soft tissue sarcoma, presenting mainly in male adolescents and young adults with multiple nodules disseminated within the abdominopelvic cavity. Despite a multimodal approach including aggressive cytoreductive surgery, intensive multi-agent chemotherapy, and postoperative whole abdominopelvic radiotherapy, the prognosis for DSRCT remains dismal. Median progression-free survival ranges between 4 and 21 months, and overall survival between 17 and 60 months, with the 5-year overall survival rate in the range of 10-20%. AREA COVERED This review discusses the treatment strategies used for DSRCT over the years, the state of the art of current treatments, and future clinical prospects. EXPERT OPINION The unsatisfactory outcomes for patients with DSRCT warrant investigations into innovative treatment combinations. An international multidisciplinary and multi-stakeholder collaboration, involving both pediatric and adult sarcoma communities, is needed to propel preclinical model generation and drug development, and innovative clinical trial designs to enable the timely testing of treatments involving novel agents guided by biology to boost the chances of survival for patients with this devastating disease.
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Affiliation(s)
- Shushan Hovsepyan
- Department of Pediatric Oncology, Pediatric Cancer and Blood Disorders Center of Armenia, Yerevan, Armenia
| | - Claudia Giani
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sandro Pasquali
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Sarcoma Service, Department of Surgery, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Di Giannatale
- Department of Hematology/Oncology, Hematology/Oncology, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Stefano Chiaravalli
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Colombo
- Sarcoma Service, Department of Surgery, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniel Orbach
- SIREDO Oncology Center, Institut Curie, PSL University, Paris, France
| | - Luca Bergamaschi
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sabina Vennarini
- Pediatric Radiotherapy Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Susanne Andrea Gatz
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Patrizia Gasparini
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave-Roussy, Villejuif, France
| | - Michela Casanova
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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9
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Nguyen K, Hebert K, McConnell E, Cullen N, Cheng T, Awoyode S, Martin E, Chen W, Wu T, Alahari SK, Izadpanah R, Collins-Burow BM, Lee SB, Drewry DH, Burow ME. LKB1 Signaling and Patient Survival Outcomes in Hepatocellular Carcinoma. Pharmacol Res 2023; 192:106757. [PMID: 37023992 DOI: 10.1016/j.phrs.2023.106757] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
The liver is a major organ that is involved in essential biological functions such as digestion, nutrient storage, and detoxification. Furthermore, it is one of the most metabolically active organs with active roles in regulating carbohydrate, protein, and lipid metabolism. Hepatocellular carcinoma is a cancer of the liver that is associated in settings of chronic inflammation such as viral hepatitis, repeated toxin exposure, and fatty liver disease. Furthermore, liver cancer is the most common cause of death associated with cirrhosis and is the 3rd leading cause of global cancer deaths. LKB1 signaling has been demonstrated to play a role in regulating cellular metabolism under normal and nutrient deficient conditions. Furthermore, LKB1 signaling has been found to be involved in many cancers with most reports identifying LKB1 to have a tumor suppressive role. In this review, we use the KMPlotter database to correlate RNA levels of LKB1 signaling genes and hepatocellular carcinoma patient survival outcomes with the hopes of identifying potential biomarkers clinical usage. Based on our results STRADß, CAB39L, AMPKα, MARK2, SIK1, SIK2, BRSK1, BRSK2, and SNRK expression has a statistically significant impact on patient survival.
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Affiliation(s)
- Khoa Nguyen
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Katherine Hebert
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Emily McConnell
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Nicole Cullen
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Thomas Cheng
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Susanna Awoyode
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Elizabeth Martin
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Weina Chen
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA, USA
| | - Reza Izadpanah
- Applied Stem Cell Laboratory, Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Sean B Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - David H Drewry
- UNC Eshelman School of Pharmacy and UNC Lineberger Comprehensive Cancer Center, Chemical Biology and Medicinal Chemistry Division, SGC-UNC, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew E Burow
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
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Magrath JW, Kang HJ, Hartono A, Espinosa-Cotton M, Somwar R, Ladanyi M, Cheung NKV, Lee SB. Desmoplastic small round cell tumor cancer stem cell-like cells resist chemotherapy but remain dependent on the EWSR1-WT1 oncoprotein. Front Cell Dev Biol 2022; 10:1048709. [PMID: 36506091 PMCID: PMC9732033 DOI: 10.3389/fcell.2022.1048709] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
Desmoplastic Small Round Cell Tumor (DSRCT) is a rare and aggressive pediatric cancer driven by the EWSR1-WT1 fusion oncogene. Combinations of chemotherapy, radiation and surgery are not curative, and the 5-years survival rate is less than 25%. One potential explanation for refractoriness is the existence of a cancer stem cell (CSC) subpopulation able escape current treatment modalities. However, no study to-date has examined the role of CSCs in DSRCT or established in vitro culture conditions to model this subpopulation. In this study, we investigated the role of stemness markers in DSRCT survival and metastasis, finding that elevated levels of SOX2 and NANOG are associated with worse survival in sarcoma patients and are elevated in metastatic DSRCT tumors. We further develop the first in vitro DSRCT CSC model which forms tumorspheres, expresses increased levels of stemness markers (SOX2, NANOG, KLF4, and OCT4), and resists doxorubicin chemotherapy treatment. This model is an important addition to the DSRCT tool kit and will enable investigation of this critical DSRCT subpopulation. Despite lower sensitivity to chemotherapy, the DSRCT CSC model remained sensitive to knockdown of the EWSR1-WT1 fusion protein, suggesting that future therapies directed against this oncogenic driver have the potential to treat both DSRCT bulk tumor and CSCs.
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Affiliation(s)
- Justin W. Magrath
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hong-Jun Kang
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Alifiani Hartono
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Madelyn Espinosa-Cotton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Romel Somwar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Nai-Kong V. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sean B. Lee
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
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