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Harrison DJ, Qumseya A, Xue W, Arnold M, Lautz TB, Hiniker SM, Thomas SM, Venkatramani R, Weiss AR, Mascarenhas L. Adolescents and young adults with rhabdomyosarcoma: A report from the Soft Tissue Sarcoma Committee of the Children's Oncology Group. Pediatr Blood Cancer 2024; 71:e30847. [PMID: 38282125 PMCID: PMC11078272 DOI: 10.1002/pbc.30847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/02/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
INTRODUCTION The impact of established prognostic factors on survival outcomes for childhood rhabdomyosarcoma (RMS) have not been well described in the adolescent and young adult (AYA) RMS patient population. METHODS This is a retrospective analysis of patients with newly diagnosed RMS enrolled between 1997 and 2016 on seven previously reported Children's Oncology Group (COG) clinical trials. Demographics, clinical features, treatment details, and outcome data were collected. Five-year event-free survival (EFS) and overall survival (OS) were estimated for patients diagnosed at age 15-39 years and those diagnosed under age 15 years using the Kaplan-Meier method. Log-rank test was used to compare prognostic factors for EFS and OS. Factors significant in the univariable analysis were included in a Cox proportional hazards regression model. Nonsignificant covariates were removed from the multiple regression model. RESULTS Total 2151 patients including 402 AYAs were analyzed. AYAs were more likely to present with primary tumors ≥5 cm in size, metastatic disease, alveolar histology, and have FOXO1 fusions compared to children. Five-year EFS for the AYA cohort was 44.2% versus 67% for children (p < .001), and 5-year OS was 52% for the AYA cohort versus 78% for children (p < .001). Multivariable analysis revealed tumor site, size and invasiveness, clinical group, and histology were prognostic in AYAs. CONCLUSION AYAs with RMS have a poorer prognosis compared to younger children due to multiple factors. Further research focused on AYAs to better understand RMS biology and improve treatments is critical to improve survival.
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Affiliation(s)
| | - Amira Qumseya
- University of Florida, Gainesville, FL (Qumsiya A, Xue W)
| | - Wei Xue
- University of Florida, Gainesville, FL (Qumsiya A, Xue W)
| | - Michael Arnold
- University of Colorado, Anschutz Medical Campus, Aurora, CO (Arnold MA) Children’s Hospital Colorado, Aurora, CO (Arnold MA)
| | - Timothy B. Lautz
- Ann & Robert H Lurie Children’s Hospital of Chicago, Northwestern University, Chicago IL (Lautz T)
| | | | | | - Rajkumar Venkatramani
- Baylor College of Medicine/Dan L Duncan Comprehensive Cancer Center, Houston, TX (Venkatramani R)
| | | | - Leo Mascarenhas
- Children’s Hospital Los Angeles and University of Southern California Keck School of Medicine, Los Angeles, CA (Mascarenhas L)
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Wachtel M, Surdez D, Grünewald TGP, Schäfer BW. Functional Classification of Fusion Proteins in Sarcoma. Cancers (Basel) 2024; 16:1355. [PMID: 38611033 PMCID: PMC11010897 DOI: 10.3390/cancers16071355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Sarcomas comprise a heterogeneous group of malignant tumors of mesenchymal origin. More than 80 entities are associated with different mesenchymal lineages. Sarcomas with fibroblastic, muscle, bone, vascular, adipocytic, and other characteristics are distinguished. Nearly half of all entities contain specific chromosomal translocations that give rise to fusion proteins. These are mostly pathognomonic, and their detection by various molecular techniques supports histopathologic classification. Moreover, the fusion proteins act as oncogenic drivers, and their blockade represents a promising therapeutic approach. This review summarizes the current knowledge on fusion proteins in sarcoma. We categorize the different fusion proteins into functional classes, including kinases, epigenetic regulators, and transcription factors, and describe their mechanisms of action. Interestingly, while fusion proteins acting as transcription factors are found in all mesenchymal lineages, the others have a more restricted pattern. Most kinase-driven sarcomas belong to the fibroblastic/myofibroblastic lineage. Fusion proteins with an epigenetic function are mainly associated with sarcomas of unclear differentiation, suggesting that epigenetic dysregulation leads to a major change in cell identity. Comparison of mechanisms of action reveals recurrent functional modes, including antagonism of Polycomb activity by fusion proteins with epigenetic activity and recruitment of histone acetyltransferases by fusion transcription factors of the myogenic lineage. Finally, based on their biology, we describe potential approaches to block the activity of fusion proteins for therapeutic intervention. Overall, our work highlights differences as well as similarities in the biology of fusion proteins from different sarcomas and provides the basis for a functional classification.
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Affiliation(s)
- Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), CH-8008 Zurich, Switzerland
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
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Vicha A, Jencova P, Novakova-Kodetova D, Stolova L, Voriskova D, Vyletalova K, Broz P, Drahokoupilova E, Guha A, Kopecká M, Krskova L. Changes on chromosome 11p15.5 as specific marker for embryonal rhabdomyosarcoma? Genes Chromosomes Cancer 2023; 62:732-739. [PMID: 37530573 DOI: 10.1002/gcc.23194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Rhabdomyosarcomas (RMS) constitute a heterogeneous spectrum of tumors with respect to clinical behavior and tumor morphology. The paternal uniparental disomy (pUPD) of 11p15.5 is a molecular change described mainly in embryonal RMS. In addition to LOH, UPD, the MLPA technique (ME030kit) also determines copy number variants and methylation of H19 and KCNQ1OT1 genes, which have not been systematically investigated in RMS. All 127 RMS tumors were divided by histology and PAX status into four groups, pleomorphic histology (n = 2); alveolar RMS PAX fusion-positive (PAX+; n = 39); embryonal RMS (n = 70) and fusion-negative RMS with alveolar pattern (PAX-RMS-AP; n = 16). The following changes were detected; negative (n = 21), pUPD (n = 75), gain of paternal allele (n = 9), loss of maternal allele (n = 9), hypermethylation of H19 (n = 6), hypomethylation of KCNQ1OT1 (n = 6), and deletion of CDKN1C (n = 1). We have shown no difference in the frequency of pUPD 11p15.5 in all groups. Thus, we have proven that changes in the 11p15.5 are not only specific to the embryonal RMS (ERMS), but are often also present in alveolar RMS (ARMS). We have found changes that have not yet been described in RMS. We also demonstrated new potential diagnostic markers for ERMS (paternal duplication and UPD of whole chromosome 11) and for ARMS PAX+ (hypomethylation KCNQ1OT1).
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Affiliation(s)
- Ales Vicha
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Pavla Jencova
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Daniela Novakova-Kodetova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lucie Stolova
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Dagmar Voriskova
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kristyna Vyletalova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Petr Broz
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
- BIOXSYS, Ústí nad Labem, Czech Republic
| | - Eva Drahokoupilova
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Anasuya Guha
- Department of Otorhinolaryngology, 3rd Faculty of Medicine, Charles University in Prague and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Marie Kopecká
- Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
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Dehner CA, Bell RC, Cao Y, He K, Chrisinger JS, Armstrong AE, Yohe M, Shern J, Hirbe AC. Loss of Chromosome 3q Is a Prognostic Marker in Fusion-Negative Rhabdomyosarcoma. JCO Precis Oncol 2023; 7:e2300037. [PMID: 37738543 PMCID: PMC10861018 DOI: 10.1200/po.23.00037] [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: 01/25/2023] [Revised: 06/05/2023] [Accepted: 07/16/2023] [Indexed: 09/24/2023] Open
Abstract
PURPOSE Soft tissue sarcomas (STS) are rare mesenchymal neoplasms that frequently show complex chromosomal aberrations such as amplifications or deletions of DNA sequences or even whole chromosomes. We recently found that gain of chromosome (chr) 8 is associated with worse overall survival (OS) in STS as a group. We therefore aimed to investigate the overall copy number profile of rhabdomyosarcoma (RMS) to evaluate for prognostic signatures. METHODS Fluorescence in situ hybridization (FISH) testing was performed on a cohort of STS to assess for chr8 gain. Copy number variation (CNV) data from the National Cancer Institute were analyzed to assess for prognostically significant CNV aberrations in FOXO1 fusion-negative (FN)- versus fusion-positive (FP)-RMS. FISH testing was performed on a cohort of FN-RMS to assess for chr3q loss and correlate with outcomes. RESULTS Chr8 gain is a highly prevalent CNV in embryonal RMS and shows slightly improved prognosis. Meanwhile, loss of chr3q was associated with worse outcome in FN-RMS compared with FP-RMS. CONCLUSION The pathogenesis of STS including FN-RMS remains poorly understood, emphasizing the need for new therapeutic advances and adequate risk stratification. Our data demonstrate that loss of chr3q is associated with poor OS in FN-RMS, supporting it as an important tool for risk stratification.
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Affiliation(s)
- Carina A. Dehner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
- Department of Pathology/Dermatopathology, Indiana University, Indianapolis, IN
| | - Robert C. Bell
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Yang Cao
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - Kevin He
- Division of Oncology, Washington University School of Medicine, St Louis, MO
| | - John S.A. Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Amy E. Armstrong
- Division of Pediatric Hematology/Oncology, Washington University School of Medicine, St Louis, MO
| | - Marielle Yohe
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jack Shern
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Angela C. Hirbe
- Division of Oncology, Washington University School of Medicine, St Louis, MO
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5
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Wang M, Sreenivas P, Sunkel BD, Wang L, Ignatius M, Stanton B. The 3D chromatin landscape of rhabdomyosarcoma. NAR Cancer 2023; 5:zcad028. [PMID: 37325549 PMCID: PMC10261698 DOI: 10.1093/narcan/zcad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/27/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with a lack of precision therapy options for patients. We hypothesized that with a general paucity of known mutations in RMS, chromatin structural driving mechanisms are essential for tumor proliferation. Thus, we carried out high-depth in situ Hi-C in representative cell lines and patient-derived xenografts (PDXs) to define chromatin architecture in each major RMS subtype. We report a comprehensive 3D chromatin structural analysis and characterization of fusion-positive (FP-RMS) and fusion-negative RMS (FN-RMS). We have generated spike-in in situ Hi-C chromatin interaction maps for the most common FP-RMS and FN-RMS cell lines and compared our data with PDX models. In our studies, we uncover common and distinct structural elements in large Mb-scale chromatin compartments, tumor-essential genes within variable topologically associating domains and unique patterns of structural variation. Our high-depth chromatin interactivity maps and comprehensive analyses provide context for gene regulatory events and reveal functional chromatin domains in RMS.
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Affiliation(s)
- Meng Wang
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
| | - Prethish Sreenivas
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Benjamin D Sunkel
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
| | - Long Wang
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Myron Ignatius
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Benjamin Z Stanton
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43205, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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6
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Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Investigation of Flavonoid Scaffolds as DAX1 Inhibitors against Ewing Sarcoma through Pharmacoinformatic and Dynamic Simulation Studies. Int J Mol Sci 2023; 24:ijms24119332. [PMID: 37298283 DOI: 10.3390/ijms24119332] [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: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Dosage-sensitive sex reversal, adrenal hypoplasia critical region, on chromosome X, gene 1 (DAX1) is an orphan nuclear receptor encoded by the NR0B1 gene. The functional study showed that DAX1 is a physiologically significant target for EWS/FLI1-mediated oncogenesis, particularly Ewing Sarcoma (ES). In this study, a three-dimensional DAX1 structure was modeled by employing a homology modeling approach. Furthermore, the network analysis of genes involved in Ewing Sarcoma was also carried out to evaluate the association of DAX1 and other genes with ES. Moreover, a molecular docking study was carried out to check the binding profile of screened flavonoid compounds against DAX1. Therefore, 132 flavonoids were docked in the predicted active binding pocket of DAX1. Moreover, the pharmacogenomics analysis was performed for the top ten docked compounds to evaluate the ES-related gene clusters. As a result, the five best flavonoid-docked complexes were selected and further evaluated by Molecular Dynamics (MD) simulation studies at 100 ns. The MD simulation trajectories were evaluated by generating RMSD, hydrogen bond plot analysis, and interaction energy graphs. Our results demonstrate that flavonoids showed interactive profiles in the active region of DAX1 and can be used as potential therapeutic agents against DAX1-mediated augmentation of ES after in-vitro and in-vivo evaluations.
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Affiliation(s)
- Muhammad Yasir
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jinyoung Park
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Won Sun Park
- Department of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Yong-Soo Kwon
- College of Pharmacy, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Hee-Jae Lee
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
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Lak NS, van Zogchel LM, Zappeij-Kannegieter L, Javadi A, van Paemel R, Vandeputte C, De Preter K, De Wilde B, Chicard M, Iddir Y, Schleiermacher G, Ruhen O, Shipley J, Fiocco M, Merks JH, van Noesel MM, van der Schoot CE, Tytgat GA, Stutterheim J. Cell-Free DNA as a Diagnostic and Prognostic Biomarker in Pediatric Rhabdomyosarcoma. JCO Precis Oncol 2023; 7:e2200113. [PMID: 36652664 PMCID: PMC9928631 DOI: 10.1200/po.22.00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
PURPOSE Total cell-free DNA (cfDNA) and tumor-derived cfDNA (ctDNA) can be used to study tumor-derived genetic aberrations. We analyzed the diagnostic and prognostic potential of cfDNA and ctDNA, obtained from pediatric patients with rhabdomyosarcoma. METHODS cfDNA was isolated from diagnostic plasma samples from 57 patients enrolled in the EpSSG RMS2005 study. To study the diagnostic potential, shallow whole genome sequencing (shWGS) and cell-free reduced representation bisulphite sequencing (cfRRBS) were performed in a subset of samples and all samples were tested using droplet digital polymerase chain reaction to detect methylated RASSF1A (RASSF1A-M). Correlation with outcome was studied by combining cfDNA RASSF1A-M detection with analysis of our rhabdomyosarcoma-specific RNA panel in paired cellular blood and bone marrow fractions and survival analysis in 56 patients. RESULTS At diagnosis, ctDNA was detected in 16 of 30 and 24 of 26 patients using shallow whole genome sequencing and cfRRBS, respectively. Furthermore, 21 of 25 samples were correctly classified as embryonal by cfRRBS. RASSF1A-M was detected in 21 of 57 patients. The presence of RASSF1A-M was significantly correlated with poor outcome (the 5-year event-free survival [EFS] rate was 46.2% for 21 RASSF1A-M‒positive patients, compared with 84.9% for 36 RASSF1A-M‒negative patients [P < .001]). RASSF1A-M positivity had the highest prognostic effect among patients with metastatic disease. Patients both negative for RASSF1A-M and the rhabdomyosarcoma-specific RNA panel (28 of 56 patients) had excellent outcome (5-year EFS 92.9%), while double-positive patients (11/56) had poor outcome (5-year EFS 13.6%, P < .001). CONCLUSION Analyzing ctDNA at diagnosis using various techniques is feasible in pediatric rhabdomyosarcoma and has potential for clinical use. Measuring RASSF1A-M in plasma at initial diagnosis correlated significantly with outcome, particularly when combined with paired analysis of blood and bone marrow using a rhabdomyosarcoma-specific RNA panel.
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Affiliation(s)
- Nathalie S.M. Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,Sanquin Research Department, Amsterdam, the Netherlands
| | - Lieke M.J. van Zogchel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,Sanquin Research Department, Amsterdam, the Netherlands
| | | | - Ahmad Javadi
- Sanquin Research Department, Amsterdam, the Netherlands
| | - Ruben van Paemel
- Translational Oncogenomics and Bioinformatics Lab, Department of Biomolecular Medicine & Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
| | - Charlotte Vandeputte
- Translational Oncogenomics and Bioinformatics Lab, Department of Biomolecular Medicine & Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
| | - Katleen De Preter
- Translational Oncogenomics and Bioinformatics Lab, Department of Biomolecular Medicine & Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
| | - Bram De Wilde
- Translational Oncogenomics and Bioinformatics Lab, Department of Biomolecular Medicine & Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
| | - Mathieu Chicard
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, and INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France
| | - Yasmine Iddir
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, and INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Olivia Ruhen
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Marta Fiocco
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,Mathematical Institute, Leiden University, Leiden, the Netherlands,Department of Biomedical Data Science, Medical Statistics Section, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Max M. van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,UMC Utrecht, Division Oncology & Cancer, Utrecht, the Netherlands
| | | | - Godelieve A.M. Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,Sanquin Research Department, Amsterdam, the Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands,Sanquin Research Department, Amsterdam, the Netherlands,Janine Stutterheim, Princess Máxima Center, Heidelberglaan 25, 3435 CS, Utrecht, the Netherlands; e-mail:
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8
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Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Hassan M, Kloczkowski A, Chun W. Exploration of Flavonoids as Lead Compounds against Ewing Sarcoma through Molecular Docking, Pharmacogenomics Analysis, and Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010414. [PMID: 36615603 PMCID: PMC9823950 DOI: 10.3390/molecules28010414] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
Ewing sarcoma (ES) is a highly malignant carcinoma prevalent in children and most frequent in the second decade of life. It mostly occurs due to t(11;22) (q24;q12) translocation. This translocation encodes the oncogenic fusion protein EWS/FLI (Friend leukemia integration 1 transcription factor), which acts as an aberrant transcription factor to deregulate target genes essential for cancer. Traditionally, flavonoids from plants have been investigated against viral and cancerous diseases and have shown some promising results to combat these disorders. In the current study, representative flavonoid compounds from various subclasses are selected and used to disrupt the RNA-binding motif of EWS, which is required for EWS/FLI fusion. By blocking the RNA-binding motif of EWS, it might be possible to combat ES. Therefore, molecular docking experiments validated the binding interaction patterns and structural behaviors of screened flavonoid compounds within the active region of the Ewing sarcoma protein (EWS). Furthermore, pharmacogenomics analysis was used to investigate potential drug interactions with Ewing sarcoma-associated genes. Finally, molecular dynamics simulations were used to investigate the stability of the best selected docked complexes. Taken together, daidzein, kaempferol, and genistein exhibited a result comparable to ifosfamide in the proposed in silico study and can be further analyzed as possible candidate compounds in biological in vitro studies against ES.
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Affiliation(s)
- Muhammad Yasir
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jinyoung Park
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Won Sun Park
- Department of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Yong-Soo Kwon
- College of Pharmacy, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Hee-Jae Lee
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Wanjoo Chun
- Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
- Correspondence: ; Tel.: +82-33-250-8853
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9
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van Zogchel LMJ, Lak NSM, Gelineau NU, Sergeeva I, Stelloo E, Swennenhuis J, Feitsma H, van Min M, Splinter E, Bleijs M, Groot Koerkamp M, Breunis W, Meister MT, Kholossy WH, Holstege FCP, Molenaar JJ, de Leng WWJ, Stutterheim J, van der Schoot CE, Tytgat GAM. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors. Front Oncol 2023; 13:1124737. [PMID: 37152023 PMCID: PMC10157037 DOI: 10.3389/fonc.2023.1124737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. Materials and methods Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. Results TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. Conclusion We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.
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Affiliation(s)
- Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nathalie S. M. Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Margit Bleijs
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Willemijn Breunis
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael Torsten Meister
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Frank C. P. Holstege
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center (UMC) Utrecht and Utrecht University, Utrecht, Netherlands
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Wendy W. J. de Leng
- Department of Pathology, University Medical Center (UMC) Utrecht, Utrecht, Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - C. Ellen van der Schoot
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- *Correspondence: Godelieve A. M. Tytgat,
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10
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Zhang S, Wang J, Liu Q, McDonald WH, Bomber ML, Layden HM, Ellis J, Borinstein SC, Hiebert SW, Stengel KR. PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets. Mol Cell 2022; 82:4428-4442.e7. [PMID: 36395771 PMCID: PMC9731406 DOI: 10.1016/j.molcel.2022.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 08/24/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
Transcriptional control is a highly dynamic process that changes rapidly in response to various cellular and extracellular cues, making it difficult to define the mechanism of transcription factor function using slow genetic methods. We used a chemical-genetic approach to rapidly degrade a canonical transcriptional activator, PAX3-FOXO1, to define the mechanism by which it regulates gene expression programs. By coupling rapid protein degradation with the analysis of nascent transcription over short time courses and integrating CUT&RUN, ATAC-seq, and eRNA analysis with deep proteomic analysis, we defined PAX3-FOXO1 function at a small network of direct transcriptional targets. PAX3-FOXO1 degradation impaired RNA polymerase pause release and transcription elongation at most regulated gene targets. Moreover, the activity of PAX3-FOXO1 at enhancers controlling this core network was surprisingly selective, affecting single elements in super-enhancers. This combinatorial analysis indicated that PAX3-FOXO1 was continuously required to maintain chromatin accessibility and enhancer architecture at regulated enhancers.
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Affiliation(s)
- Susu Zhang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jacob Ellis
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott C Borinstein
- Department of Pediatrics, Vanderbilt University School of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA.
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, New York, NY, USA.
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11
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Manceau L, Richard Albert J, Lollini PL, Greenberg MVC, Gilardi-Hebenstreit P, Ribes V. Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs. PLoS Genet 2022; 18:e1009782. [PMID: 35604932 PMCID: PMC9166405 DOI: 10.1371/journal.pgen.1009782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 06/03/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
The hallmarks of the alveolar subclass of rhabdomyosarcoma are chromosomal translocations that generate chimeric PAX3-FOXO1 or PAX7-FOXO1 transcription factors. Overexpression of either PAX-FOXO1s results in related cell transformation in animal models. Yet, in patients the two structural genetic aberrations they derived from are associated with distinct pathological manifestations. To assess the mechanisms underlying these differences, we generated isogenic fibroblast lines expressing either PAX-FOXO1 paralog. Mapping of their genomic recruitment using CUT&Tag revealed that the two chimeric proteins have distinct DNA binding preferences. In addition, PAX7-FOXO1 binding results in greater recruitment of the H3K27ac activation mark than PAX3-FOXO1 binding and is accompanied by greater transcriptional activation of neighbouring genes. These effects are associated with a PAX-FOXO1-specific alteration in the expression of genes regulating cell shape and the cell cycle. Consistently, PAX3-FOXO1 accentuates fibroblast cellular traits associated with contractility and surface adhesion and limits entry into S phase. In contrast, PAX7-FOXO1 drives cells to adopt an amoeboid shape, reduces entry into M phase, and causes increased DNA damage. Altogether, our results argue that the diversity of rhabdomyosarcoma manifestation arises, in part, from the divergence between the genomic occupancy and transcriptional activity of PAX3-FOXO1 and PAX7-FOXO1. Rhabdomyosarcoma is a class of paediatric soft tissue cancers of genetic origin, but for which the causal links between genetic aberrations and tumour development remain to be deciphered. To answer this question, we focused on the products of two chromosomal translocations that generate the chimeric proteins PAX3-FOXO1 and PAX7-FOXO1. They are composed of the DNA-binding domains of the PAX3 or PAX7 proteins and a single portion of the FOXO1 protein. Several clinical parameters distinguish patients expressing PAX3-FOXO1 or PAX7-FOXO1 and we wondered if these differences could emanate from a different mode of action of the two chimeric proteins. Thus, we generated inducible human fibroblast cell lines expressing one or the other protein. We analysed some molecular and cellular characteristics of these cells 48 hours after induction of PAX3-FOXO1 or PAX7-FOXO1. As it was previously known for PAX3-FOXO1, we showed that PAX7-FOXO1 binds genomic DNA on cis-regulatory regions and activates them. Surprisingly, PAX7-FOXO1 only partially shares the DNA binding sites of PAX3-FOXO1 and its activation potential is stronger than that of PAX3-FOXO1. Thus, PAX3-FOXO1 and PAX7-FOXO1 generate partially divergent transcriptomic signatures, which include genes encoding regulators of cell morphology and cell cycle, two key oncogenic processes. In agreement, our data revealed specificities in these two processes that are either PAX3-FOXO1 or PAX7-FOXO1 dependent. Overall our results demonstrate a differential mode of action between the two chimeric proteins that could in turn participate in the heterogeneity of rhabdomyosarcoma manifestation.
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Affiliation(s)
- Line Manceau
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Pier-Luigi Lollini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | | | | | - Vanessa Ribes
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- * E-mail: (PG-H); (VR)
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12
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Sparber-Sauer M. [Genomic classification and survival of patients with rhabdomyosarcoma: a report from an international consortium]. Strahlenther Onkol 2022; 198:404-407. [PMID: 35230459 DOI: 10.1007/s00066-022-01908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Sparber-Sauer
- Pädiatrie 5 (Hämatologie, Onkologie, Immunologie), Cooperative Weichteilsarkom-Studiengruppe, Stuttgart Cancer Center, Zentrum für Kinder‑, Jugend- und Frauenmedizin, Klinikum der Landeshauptstadt Stuttgart gKAöR, Olgahospital, Stuttgart, Deutschland.
- Medizinische Fakultät, Universität Tübingen, Tübingen, Deutschland.
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13
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Garcia N, Del Pozo V, Yohe ME, Goodwin CM, Shackleford TJ, Wang L, Baxi K, Chen Y, Rogojina AT, Zimmerman SM, Peer CJ, Figg WD, Ignatius MS, Wood KC, Houghton PJ, Vaseva AV. Vertical Inhibition of the RAF-MEK-ERK Cascade Induces Myogenic Differentiation, Apoptosis and Tumor Regression in H/NRAS Q61X-mutant Rhabdomyosarcoma. Mol Cancer Ther 2021; 21:170-183. [PMID: 34737198 PMCID: PMC8742779 DOI: 10.1158/1535-7163.mct-21-0194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/18/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
Oncogenic RAS signaling is an attractive target for fusion-negative rhabdomyosarcoma (FN-RMS). Our study validates the role of the ERK MAPK effector pathway in mediating RAS dependency in a panel of H/NRASQ61X-mutant RMS cells and correlates in vivo efficacy of the MEK inhibitor trametinib with pharmacodynamics of ERK activity. A screen is used to identify trametinib-sensitizing targets and combinations are evaluated in cells and tumor xenografts. We find that the ERK MAPK pathway is central to H/NRASQ61X-dependency in RMS cells, however there is poor in vivo response to clinically relevant exposures with trametinib, which correlates with inefficient suppression of ERK activity. CRISPR screening points to vertical inhibition of the RAF-MEK-ERK cascade by co-suppression of MEK and either CRAF or ERK. CRAF is central to rebound pathway activation following MEK or ERK inhibition. Concurrent CRAF suppression and MEK or ERK inhibition, or concurrent pan-RAF and MEK/ERK inhibition (pan-RAFi + MEKi/ERKi), or concurrent MEK and ERK inhibition (MEKi + ERKi) all synergistically block ERK activity and induce myogenic differentiation and apoptosis. In vivo assessment of pan-RAFi + ERKi or MEKi + ERKi potently suppress growth of H/NRASQ61X RMS tumor xenografts, with pan-RAFi + ERKi being more effective and better tolerated. We conclude that CRAF reactivation limits the activity of single agent MEK/ERK inhibitors in FN-RMS. Vertical targeting of the RAF-MEK-ERK cascade, and particularly co-targeting of CRAF and MEK or ERK, or the combination of pan-RAF inhibitors with MEK or ERK inhibitors, have synergistic activity and potently suppress H/NRASQ61X-mutant RMS tumor growth.
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Affiliation(s)
| | | | | | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
| | | | - Long Wang
- Cancer Therapy & Research Center, The University of Texas Health Science Center
| | - Kunal Baxi
- Greehey Children's Cancer Research Institute, UTHSCSA
| | - Yidong Chen
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio
| | | | | | - Cody J Peer
- Clinical Pharmacology Program, National Cancer Institute
| | - William D Figg
- Clinical Pharmacology Program and Genitourinary Malignancies Branch, National Cancer Institute
| | | | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio
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14
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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15
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Genetic Characterization, Current Model Systems and Prognostic Stratification in PAX Fusion-Negative vs. PAX Fusion-Positive Rhabdomyosarcoma. Genes (Basel) 2021; 12:genes12101500. [PMID: 34680895 PMCID: PMC8535289 DOI: 10.3390/genes12101500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents and accounts for approximately 2% of soft tissue sarcomas in adults. It is subcategorized into distinct subtypes based on histological features and fusion status (PAX-FOXO1/VGLL2/NCOA2). Despite advances in our understanding of the pathobiological and molecular landscape of RMS, the prognosis of these tumors has not significantly improved in recent years. Developing a better understanding of genetic abnormalities and risk stratification beyond the fusion status are crucial to developing better therapeutic strategies. Herein, we aim to highlight the genetic pathways/abnormalities involved, specifically in fusion-negative RMS, assess the currently available model systems to study RMS pathogenesis, and discuss available prognostic factors as well as their importance for risk stratification to achieve optimal therapeutic management.
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16
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Shern JF, Selfe J, Izquierdo E, Patidar R, Chou HC, Song YK, Yohe ME, Sindiri S, Wei J, Wen X, Rudzinski ER, Barkauskas DA, Lo T, Hall D, Linardic CM, Hughes D, Jamal S, Jenney M, Chisholm J, Brown R, Jones K, Hicks B, Angelini P, George S, Chesler L, Hubank M, Kelsey A, Gatz SA, Skapek SX, Hawkins DS, Shipley JM, Khan J. Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium. J Clin Oncol 2021; 39:2859-2871. [PMID: 34166060 PMCID: PMC8425837 DOI: 10.1200/jco.20.03060] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood. Despite aggressive therapy, the 5-year survival rate for patients with metastatic or recurrent disease remains poor, and beyond PAX-FOXO1 fusion status, no genomic markers are available for risk stratification. We present an international consortium study designed to determine the incidence of driver mutations and their association with clinical outcome. PATIENTS AND METHODS Tumor samples collected from patients enrolled on Children's Oncology Group trials (1998-2017) and UK patients enrolled on malignant mesenchymal tumor and RMS2005 (1995-2016) trials were subjected to custom-capture sequencing. Mutations, indels, gene deletions, and amplifications were identified, and survival analysis was performed. RESULTS DNA from 641 patients was suitable for analyses. A median of one mutation was found per tumor. In FOXO1 fusion-negative cases, mutation of any RAS pathway member was found in > 50% of cases, and 21% had no putative driver mutation identified. BCOR (15%), NF1 (15%), and TP53 (13%) mutations were found at a higher incidence than previously reported and TP53 mutations were associated with worse outcomes in both fusion-negative and FOXO1 fusion-positive cases. Interestingly, mutations in RAS isoforms predominated in infants < 1 year (64% of cases). Mutation of MYOD1 was associated with histologic patterns beyond those previously described, older age, head and neck primary site, and a dismal survival. Finally, we provide a searchable companion database (ClinOmics), containing all genomic variants, and clinical annotation including survival data. CONCLUSION This is the largest genomic characterization of clinically annotated rhabdomyosarcoma tumors to date and provides prognostic genetic features that refine risk stratification and will be incorporated into prospective trials.
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MESH Headings
- Adolescent
- Adult
- Biomarkers, Tumor/genetics
- Child
- Child, Preschool
- DNA Mutational Analysis
- Databases, Genetic
- Disease Progression
- Female
- Gene Amplification
- Gene Deletion
- Gene Expression Profiling
- Genetic Predisposition to Disease
- Genomics
- Humans
- INDEL Mutation
- Infant
- Infant, Newborn
- Male
- Phenotype
- Predictive Value of Tests
- Progression-Free Survival
- Rhabdomyosarcoma, Alveolar/genetics
- Rhabdomyosarcoma, Alveolar/mortality
- Rhabdomyosarcoma, Alveolar/pathology
- Rhabdomyosarcoma, Alveolar/therapy
- Rhabdomyosarcoma, Embryonal/genetics
- Rhabdomyosarcoma, Embryonal/mortality
- Rhabdomyosarcoma, Embryonal/pathology
- Rhabdomyosarcoma, Embryonal/therapy
- Risk Assessment
- Risk Factors
- Time Factors
- Transcriptome
- United Kingdom
- United States
- Young Adult
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Affiliation(s)
- Jack F. Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Elisa Izquierdo
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Rajesh Patidar
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Hsien-Chao Chou
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Young K. Song
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Sivasish Sindiri
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Jun Wei
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Erin R. Rudzinski
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Donald A. Barkauskas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA
- Children's Oncology Group, Monrovia, CA
| | - Tammy Lo
- Children's Oncology Group, Monrovia, CA
| | | | | | - Debbie Hughes
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Sabri Jamal
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Meriel Jenney
- Cardiff and Vale UHB, Paeds Oncology, Cardiff, United Kingdom
| | - Julia Chisholm
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Rebecca Brown
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sally George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Michael Hubank
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom
| | - Anna Kelsey
- Department of Paediatric Histopathology, Manchester University NHS Foundation Trust Royal Manchester Childrens Hospital, Manchester, United Kingdom
| | - Susanne A. Gatz
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Stephen X. Skapek
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Douglas S. Hawkins
- Department of Pediatrics, Seattle Children's Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA
| | - Janet M. Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
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17
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Expression of oncogenic HRAS in human Rh28 and RMS-YM rhabdomyosarcoma cells leads to oncogene-induced senescence. Sci Rep 2021; 11:16505. [PMID: 34389744 PMCID: PMC8363632 DOI: 10.1038/s41598-021-95355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/06/2021] [Indexed: 11/08/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. The two predominant histologic variants of RMS, embryonal and alveolar rhabdomyosarcoma (eRMS and aRMS, respectively), carry very different prognoses. While eRMS is associated with an intermediate prognosis, the 5-year survival rate of aRMS is less than 30%. The RMS subtypes are also different at the molecular level-eRMS frequently has multiple genetic alterations, including mutations in RAS and TP53, whereas aRMS often has chromosomal translocations resulting in PAX3-FOXO1 or PAX7-FOXO1 fusions, but otherwise has a "quiet" genome. Interestingly, mutations in RAS are rarely found in aRMS. In this study, we explored the role of oncogenic RAS in aRMS. We found that while ectopic oncogenic HRAS expression was tolerated in the human RAS-driven eRMS cell line RD, it was detrimental to cell growth and proliferation in the human aRMS cell line Rh28. Growth inhibition was mediated by oncogene-induced senescence and associated with increased RB pathway activity and expression of the cyclin-dependent kinase inhibitors p16 and p21. Unexpectedly, the human eRMS cell line RMS-YM, a RAS wild-type eRMS cell line, also exhibited growth inhibition in response to oncogenic HRAS in a manner similar to aRMS Rh28 cells. This work suggests that oncogenic RAS is expressed in a context-dependent manner in RMS and may provide insight into the differential origins and therapeutic opportunities for RMS subtypes.
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18
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Sunkel BD, Wang M, LaHaye S, Kelly BJ, Fitch JR, Barr FG, White P, Stanton BZ. Evidence of pioneer factor activity of an oncogenic fusion transcription factor. iScience 2021; 24:102867. [PMID: 34386729 PMCID: PMC8346656 DOI: 10.1016/j.isci.2021.102867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting. The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains PAX3-FOXO1 engages partial DNA motifs at early timepoints PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility
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Affiliation(s)
- Benjamin D Sunkel
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Meng Wang
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Frederic G Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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HER Tyrosine Kinase Family and Rhabdomyosarcoma: Role in Onset and Targeted Therapy. Cells 2021; 10:cells10071808. [PMID: 34359977 PMCID: PMC8305095 DOI: 10.3390/cells10071808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022] Open
Abstract
Rhabdomyosarcomas (RMS) are tumors of the skeletal muscle lineage. Two main features allow for distinction between subtypes: morphology and presence/absence of a translocation between the PAX3 (or PAX7) and FOXO1 genes. The two main subtypes are fusion-positive alveolar RMS (ARMS) and fusion-negative embryonal RMS (ERMS). This review will focus on the role of receptor tyrosine kinases of the human epidermal growth factor receptor (EGFR) family that is comprised EGFR itself, HER2, HER3 and HER4 in RMS onset and the potential therapeutic targeting of receptor tyrosine kinases. EGFR is highly expressed by ERMS tumors and cell lines, in some cases contributing to tumor growth. If not mutated, HER2 is not directly involved in control of RMS cell growth but can be expressed at significant levels. A minority of ERMS carries a HER2 mutation with driving activity on tumor growth. HER3 is frequently overexpressed by RMS and can play a role in the residual myogenic differentiation ability and in resistance to signaling-directed therapy. HER family members could be exploited for therapeutic approaches in two ways: blocking the HER member (playing a driving role for tumor growth with antibodies or inhibitors) and targeting expressed HER members to vehiculate toxins or immune effectors.
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20
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Context-dependent modulation of aggressiveness of pediatric tumors by individual oncogenic RAS isoforms. Oncogene 2021; 40:4955-4966. [PMID: 34172934 PMCID: PMC8342309 DOI: 10.1038/s41388-021-01904-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/25/2021] [Accepted: 06/09/2021] [Indexed: 02/07/2023]
Abstract
A prototypic pediatric cancer that frequently shows activation of RAS signaling is embryonal rhabdomyosarcoma (ERMS). ERMS also show aberrant Hedgehog (HH)/GLI signaling activity and can be driven by germline mutations in this pathway. We show, that in ERMS cell lines derived from sporadic tumors i.e. from tumors not caused by an inherited genetic variant, HH/GLI signaling plays a subordinate role, because oncogenic mutations in HRAS, KRAS, or NRAS (collectively named oncRAS) inhibit the main HH target GLI1 via the MEK/ERK-axis, but simultaneously increase proliferation and tumorigenicity. oncRAS also modulate expression of stem cell markers in an isoform- and context-dependent manner. In Hh-driven murine ERMS that are caused by a Patched mutation, oncHRAS and mainly oncKRAS accelerate tumor development, whereas oncNRAS induces a more differentiated phenotype. These features occur when the oncRAS mutations are induced at the ERMS precursor stage, but not when induced in already established tumors. Moreover, in contrast to what is seen in human cell lines, oncRAS mutations do not alter Hh signaling activity and marginally affect expression of stem cell markers. Together, all three oncRAS mutations seem to be advantageous for ERMS cell lines despite inhibition of HH signaling and isoform-specific modulation of stem cell markers. In contrast, oncRAS mutations do not inhibit Hh-signaling in Hh-driven ERMS. In this model, oncRAS mutations seem to be advantageous for specific ERMS populations that occur within a specific time window during ERMS development. In addition, this window may be different for individual oncRAS isoforms, at least in the mouse.
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21
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FOXF1 is required for the oncogenic properties of PAX3-FOXO1 in rhabdomyosarcoma. Oncogene 2021; 40:2182-2199. [PMID: 33627785 PMCID: PMC8005492 DOI: 10.1038/s41388-021-01694-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 01/31/2023]
Abstract
The PAX3-FOXO1 fusion protein is the key oncogenic driver in fusion positive rhabdomyosarcoma (FP-RMS), an aggressive soft tissue malignancy with a particularly poor prognosis. Identifying key downstream targets of PAX3-FOXO1 will provide new therapeutic opportunities for treatment of FP-RMS. Herein, we demonstrate that Forkhead Box F1 (FOXF1) transcription factor is uniquely expressed in FP-RMS and is required for FP-RMS tumorigenesis. The PAX3-FOXO1 directly binds to FOXF1 enhancers and induces FOXF1 gene expression. CRISPR/Cas9 mediated inactivation of either FOXF1 coding sequence or FOXF1 enhancers suppresses FP-RMS tumorigenesis even in the presence of PAX3-FOXO1 oncogene. Knockdown or genetic knockout of FOXF1 induces myogenic differentiation in PAX3-FOXO1-positive FP-RMS. Over-expression of FOXF1 decreases myogenic differentiation in primary human myoblasts. In FP-RMS tumor cells, FOXF1 protein binds chromatin near enhancers associated with FP-RMS gene signature. FOXF1 cooperates with PAX3-FOXO1 and E-box transcription factors MYOD1 and MYOG to regulate FP-RMS-specific gene expression. Altogether, FOXF1 functions downstream of PAX3-FOXO1 to promote FP-RMS tumorigenesis.
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22
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The structure and function of protein kinase C-related kinases (PRKs). Biochem Soc Trans 2021; 49:217-235. [PMID: 33522581 PMCID: PMC7925014 DOI: 10.1042/bst20200466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/29/2020] [Accepted: 01/07/2021] [Indexed: 11/17/2022]
Abstract
The protein kinase C-related kinase (PRK) family of serine/threonine kinases, PRK1, PRK2 and PRK3, are effectors for the Rho family small G proteins. An array of studies have linked these kinases to multiple signalling pathways and physiological roles, but while PRK1 is relatively well-characterized, the entire PRK family remains understudied. Here, we provide a holistic overview of the structure and function of PRKs and describe the molecular events that govern activation and autoregulation of catalytic activity, including phosphorylation, protein interactions and lipid binding. We begin with a structural description of the regulatory and catalytic domains, which facilitates the understanding of their regulation in molecular detail. We then examine their diverse physiological roles in cytoskeletal reorganization, cell adhesion, chromatin remodelling, androgen receptor signalling, cell cycle regulation, the immune response, glucose metabolism and development, highlighting isoform redundancy but also isoform specificity. Finally, we consider the involvement of PRKs in pathologies, including cancer, heart disease and bacterial infections. The abundance of PRK-driven pathologies suggests that these enzymes will be good therapeutic targets and we briefly report some of the progress to date.
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23
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Gonzalez Curto G, Der Vartanian A, Frarma YEM, Manceau L, Baldi L, Prisco S, Elarouci N, Causeret F, Korenkov D, Rigolet M, Aurade F, De Reynies A, Contremoulins V, Relaix F, Faklaris O, Briscoe J, Gilardi-Hebenstreit P, Ribes V. The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition. PLoS Genet 2020; 16:e1009164. [PMID: 33175861 PMCID: PMC7682867 DOI: 10.1371/journal.pgen.1009164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/23/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The chromosome translocations generating PAX3-FOXO1 and PAX7-FOXO1 chimeric proteins are the primary hallmarks of the paediatric fusion-positive alveolar subtype of Rhabdomyosarcoma (FP-RMS). Despite the ability of these transcription factors to remodel chromatin landscapes and promote the expression of tumour driver genes, they only inefficiently promote malignant transformation in vivo. The reason for this is unclear. To address this, we developed an in ovo model to follow the response of spinal cord progenitors to PAX-FOXO1s. Our data demonstrate that PAX-FOXO1s, but not wild-type PAX3 or PAX7, trigger the trans-differentiation of neural cells into FP-RMS-like cells with myogenic characteristics. In parallel, PAX-FOXO1s remodel the neural pseudo-stratified epithelium into a cohesive mesenchyme capable of tissue invasion. Surprisingly, expression of PAX-FOXO1s, similar to wild-type PAX3/7, reduce the levels of CDK-CYCLIN activity and increase the fraction of cells in G1. Introduction of CYCLIN D1 or MYCN overcomes this PAX-FOXO1-mediated cell cycle inhibition and promotes tumour growth. Together, our findings reveal a mechanism that can explain the apparent limited oncogenicity of PAX-FOXO1 fusion transcription factors. They are also consistent with certain clinical reports indicative of a neural origin of FP-RMS. The fusion-positive subtype of rhabdomyosarcoma (FP-RMS) is a rare malignant paediatric cancer, whose induction and evolution still remain to be deciphered. Out of the gross genetic aberrations found in these cancers, t(2:13) and t(1,13) chromosome translocations are the first to appear and lead to the expression of fusion proteins made of the DNA binding domains of either PAX3 or PAX7 and the transactivation domain of FOXO1. Both PAX3-FOXO1 and PAX7-FOXO1 have a strong impact on gene transcription, yet they only inefficiently promote the transformation of healthy cells into tumorigenic cells. To address this issue, we have used chick embryos to monitor in vivo the early response of cells to PAX-FOXO1 chimeric proteins. We showed that both proteins, but not the normal PAX3 and PAX7, transform neural cells into cells with FP-RMS molecular features. The PAX-FOXO1s also force polarized epithelial neural cells to adopt a mesenchymal phenotype with tissue invasive properties. However, the PAX-FOXO1s inhibit cell division and hence tumour growth. Genetically re-activating core cell cycle regulators rescues PAX-FOXO1 mediated cell cycle inhibition. Together, our findings bring further support to the idea that the PAX-FOXO1s are stricto sensu oncoproteins, whose oncogenicity is limited by negative effects on cell cycle.
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Affiliation(s)
| | | | | | - Line Manceau
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Lorenzo Baldi
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Selene Prisco
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Frédéric Causeret
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, Paris, France
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Paris, France
| | - Daniil Korenkov
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Muriel Rigolet
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Frédéric Aurade
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
- Sorbonne Université, INSERM, UMRS974, Center for Research in Myology, Paris, France
| | - Aurélien De Reynies
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Contremoulins
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - Frédéric Relaix
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Orestis Faklaris
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | | | - Vanessa Ribes
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- * E-mail:
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Secretory Carcinoma of the Skin: Report of 6 Cases, Including a Case With a Novel NFIX-PKN1 Translocation. Am J Surg Pathol 2020; 43:1092-1098. [PMID: 31045890 DOI: 10.1097/pas.0000000000001261] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Secretory carcinoma of the skin is a rare adnexal carcinoma, which is morphologically and immunohistochemically identical to secretory carcinoma of the breast and is associated with the presence of t (12;15) translocation, resulting in the ETV6-NTRK3 gene fusion. Nineteen cases of primary cutaneous secretory carcinoma have been previously published in the literature. In this study, we describe 6 new cases of secretory carcinoma of the skin. The study group consisted of 5 female patients and 1 male patient, ranging in age from 57 to 98 years (mean: 74.2, median: 74). Locations included the axilla (2), neck, eyelid, thigh, and nipple base, each one. Microscopically, all but 1 tumor were well circumscribed and nonencapsulated and exhibited characteristic abundant secretions within the microcystic and tubular spaces comprised by bland oval, round to cuboidal neoplastic cells. In addition, solid areas and focal pseudopapillae were seen, and, in 1 case, a focal mucinous component with small lakes of mucin containing small tumor nests or tubules of the neoplastic cells was present. The remaining neoplasm was mostly solid and papillary, with only few characteristic lumina containing secretions. Immunohistochemically, all cases expressed S-100 protein, mammaglobin, STAT5, GATA3, and NTRK. ETV6-NTRK3 gene fusion was detected in 5 cases, whereas, in the remaining tumor, a novel NFIX-PKN1 gene fusion was found.
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Abstract
PURPOSE OF REVIEW The current review aims to highlight the frequency of RAS mutations in pediatric leukemias and solid tumors and to propose strategies for targeting oncogenic RAS in pediatric cancers. RECENT FINDINGS The three RAS genes (HRAS, NRAS, and KRAS) comprise the most frequently mutated oncogene family in human cancer. RAS mutations are commonly observed in three of the leading causes of cancer death in the United States, namely lung cancer, pancreatic cancer, and colorectal cancer. The association of RAS mutations with these aggressive malignancies inspired the creation of the National Cancer Institute RAS initiative and spurred intense efforts to develop strategies to inhibit oncogenic RAS, with much recent success. RAS mutations are frequently observed in pediatric cancers; however, recent advances in anti-RAS drug development have yet to translate into pediatric clinical trials. SUMMARY We find that RAS is mutated in common and rare pediatric malignancies and that oncogenic RAS confers a functional dependency in these cancers. Many strategies for targeting RAS are being pursued for malignancies that primarily affect adults and there is a clear need for inclusion of pediatric patients in clinical trials of these agents.
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Chen C, Dorado Garcia H, Scheer M, Henssen AG. Current and Future Treatment Strategies for Rhabdomyosarcoma. Front Oncol 2019; 9:1458. [PMID: 31921698 PMCID: PMC6933601 DOI: 10.3389/fonc.2019.01458] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, and can be subcategorized histologically and/or based on PAX-FOXO1 fusion gene status. Over the last four decades, there have been no significant improvements in clinical outcomes for advanced and metastatic RMS patients, underscoring a need for new treatment options for these groups. Despite significant advancements in our understanding of the genomic landscape and underlying biological mechanisms governing RMS that have informed the identification of novel therapeutic targets, development of these therapies in clinical trials has lagged far behind. In this review, we summarize the current frontline multi-modality therapy for RMS according to pediatric protocols, highlight emerging targeted therapies and immunotherapies identified by preclinical studies, and discuss early clinical trial data and the implications they hold for future clinical development.
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Affiliation(s)
- Celine Chen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Scheer
- Pediatrics 5, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
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27
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The current landscape of rhabdomyosarcomas: an update. Virchows Arch 2019; 476:97-108. [PMID: 31696361 DOI: 10.1007/s00428-019-02676-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/12/2019] [Accepted: 09/22/2019] [Indexed: 01/07/2023]
Abstract
Rhabdomyosarcomas are malignancies associated with a rhabdomyoblastic phenotype which can be demonstrated morphologically or by immunohistochemistry for MYOD1 and myogenin. Rhabdomyosarcomas are currently subdivided into 4 types in the 2013 WHO classification of tumors of soft tissue and bone, including embryonal rhabdomyosarcoma, alveolar rhabdomyosarcoma, spindle cell/sclerosing rhabdomyosarcoma, and pleomorphic rhabdomyosarcoma. Recent studies have significantly impacted this classification with the emergence of three distinct new subtypes of rhabdomyosarcomas, namely rhabdomyosarcoma with MYOD1 mutations, rhabdomyosarcoma with TFCP2 fusions, and rhabdomyosarcoma with VGLL2/NCOA2 fusions. Although all these tumors share the terminology "rhabdomyosarcoma," their morphology, clinical behavior, and underlying molecular alterations are dramatically different. Finally, the presence of a rhabdomyoblastic phenotype within a tumor is by no means a diagnostic of a rhabdomyosarcoma, as this may be seen in many other mesenchymal malignancies, such as mesenchymal chondrosarcomas, malignant peripheral nerve sheaths tumors, and biphenotypic sinonasal sarcomas. In this review, we present the main clinical, morphological, and molecular features of these tumors and discuss the evolution of the current classification.
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28
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Yohe ME, Heske CM, Stewart E, Adamson PC, Ahmed N, Antonescu CR, Chen E, Collins N, Ehrlich A, Galindo RL, Gryder BE, Hahn H, Hammond S, Hatley ME, Hawkins DS, Hayes MN, Hayes-Jordan A, Helman LJ, Hettmer S, Ignatius MS, Keller C, Khan J, Kirsch DG, Linardic CM, Lupo PJ, Rota R, Shern JF, Shipley J, Sindiri S, Tapscott SJ, Vakoc CR, Wexler LH, Langenau DM. Insights into pediatric rhabdomyosarcoma research: Challenges and goals. Pediatr Blood Cancer 2019; 66:e27869. [PMID: 31222885 PMCID: PMC6707829 DOI: 10.1002/pbc.27869] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 12/16/2022]
Abstract
Overall survival rates for pediatric patients with high-risk or relapsed rhabdomyosarcoma (RMS) have not improved significantly since the 1980s. Recent studies have identified a number of targetable vulnerabilities in RMS, but these discoveries have infrequently translated into clinical trials. We propose streamlining the process by which agents are selected for clinical evaluation in RMS. We believe that strong consideration should be given to the development of combination therapies that add biologically targeted agents to conventional cytotoxic drugs. One example of this type of combination is the addition of the WEE1 inhibitor AZD1775 to the conventional cytotoxic chemotherapeutics, vincristine and irinotecan.
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Affiliation(s)
| | | | | | | | - Nabil Ahmed
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030
| | | | | | | | | | - Rene L. Galindo
- University of Texas Southwestern Medical Center, Dallas, TX 75390
| | | | - Heidi Hahn
- University Medical Center Gӧttingen, Gӧttingen, Germany
| | | | - Mark E. Hatley
- St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Douglas S. Hawkins
- Seattle Children’s Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA 98105
| | - Madeline N. Hayes
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA 02114
| | | | - Lee J. Helman
- Children’s Hospital of Los Angeles, Los Angeles, CA 90027
| | | | | | - Charles Keller
- Children’s Cancer Therapy Development Institute, Beaverton, OR 97005
| | - Javed Khan
- National Cancer Institute, Bethesda, MD 20892
| | | | | | - Philip J. Lupo
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Rossella Rota
- Children’s Hospital Bambino Gesù, IRCCS, Rome, Italy
| | | | - Janet Shipley
- The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | | | | | | | | | - David M. Langenau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA 02114
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PKN1 kinase-negative knock-in mice develop splenomegaly and leukopenia at advanced age without obvious autoimmune-like phenotypes. Sci Rep 2019; 9:13977. [PMID: 31562379 PMCID: PMC6764976 DOI: 10.1038/s41598-019-50419-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/30/2019] [Indexed: 01/08/2023] Open
Abstract
Protein kinase N1 (PKN1) knockout (KO) mice spontaneously form germinal centers (GCs) and develop an autoimmune-like disease with age. Here, we investigated the function of PKN1 kinase activity in vivo using aged mice deficient in kinase activity resulting from the introduction of a point mutation (T778A) in the activation loop of the enzyme. PKN1[T778A] mice reached adulthood without external abnormalities; however, the average spleen size and weight of aged PKN1[T778A] mice increased significantly compared to aged wild type (WT) mice. Histologic examination and Southern blot analyses of spleens showed extramedullary hematopoiesis and/or lymphomagenesis in some cases, although without significantly different incidences between PKN1[T778A] and WT mice. Additionally, flow cytometry revealed increased numbers in B220+, CD3+, Gr1+ and CD193+ leukocytes in the spleen of aged PKN1[T778A] mice, whereas the number of lymphocytes, neutrophils, eosinophils, and monocytes was reduced in the peripheral blood, suggesting an advanced impairment of leukocyte trafficking with age. Moreover, aged PKN1[T778A] mice showed no obvious GC formation nor autoimmune-like phenotypes, such as glomerulonephritis or increased anti-dsDNA antibody titer, in peripheral blood. Our results showing phenotypic differences between aged Pkn1-KO and PKN1[T778A] mice may provide insight into the importance of PKN1-specific kinase-independent functions in vivo.
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30
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Hofvander J, Viklund B, Isaksson A, Brosjö O, Vult von Steyern F, Rissler P, Mandahl N, Mertens F. Different patterns of clonal evolution among different sarcoma subtypes followed for up to 25 years. Nat Commun 2018; 9:3662. [PMID: 30201954 PMCID: PMC6131146 DOI: 10.1038/s41467-018-06098-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
To compare clonal evolution in tumors arising through different mechanisms, we selected three types of sarcoma-amplicon-driven well-differentiated liposarcoma (WDLS), gene fusion-driven myxoid liposarcoma (MLS), and sarcomas with complex genomes (CXS)-and assessed the dynamics of chromosome and nucleotide level mutations by cytogenetics, SNP array analysis and whole-exome sequencing. Here we show that the extensive single-cell variation in WDLS has minor impact on clonal key amplicons in chromosome 12. In addition, only a few of the single nucleotide variants in WDLS were present in more than one lesion, suggesting that such mutations are of little significance in tumor development. MLS displays few mutations other than the FUS-DDIT3 fusion, and the primary tumor is genetically sometimes much more complex than its relapses, whereas CXS in general shows a gradual increase of both nucleotide- and chromosome-level mutations, similar to what has been described in carcinomas.
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Affiliation(s)
- Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska Hospital, SE-171 76, Stockholm, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Pehr Rissler
- Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.,Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
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van Erp AEM, Hillebrandt-Roeffen MHS, van Houdt L, Fleuren EDG, van der Graaf WTA, Versleijen-Jonkers YMH. Targeting Anaplastic Lymphoma Kinase (ALK) in Rhabdomyosarcoma (RMS) with the Second-Generation ALK Inhibitor Ceritinib. Target Oncol 2018; 12:815-826. [PMID: 29067644 PMCID: PMC5700232 DOI: 10.1007/s11523-017-0528-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background The receptor tyrosine kinase (RTK) anaplastic lymphoma kinase (ALK) has been implicated in the tumorigenesis of rhabdomyosarcoma (RMS). However, the exact role of ALK in RMS is debatable and remains to be elucidated. Objective To determine the in vitro and in vivo effects and mechanism of action of the second-generation ALK inhibitor ceritinib on RMS cell growth. Methods Effects of ceritinib on cell proliferation, wound healing, cell cycle, and RTK signaling were determined in alveolar and embryonal rhabdomyosarcoma (ARMS, ERMS). In addition, possible synergistic effects of combined treatment with ceritinib and the Abl/Src family kinase inhibitor dasatinib were determined. Results Ceritinib treatment led to decreased cell proliferation, cell cycle arrest, apoptosis, and decreased in vivo tumor growth for the ARMS subtype. ERMS cell lines were less affected and showed no cell cycle arrest or apoptosis. Both subtypes lacked intrinsic ALK phosphorylation, and ceritinib was shown to affect the IGF1R signaling pathway. High levels of phosphorylated Src (Tyr416) were present following ceritinib treatment, making combined treatment with a Src inhibitor a potential treatment option. Combined treatment of ceritinib and dasatinib showed synergistic effects in both ERMS and ARMS cell lines. Conclusion This study shows that monotherapy with an ALK inhibitor, such as ceritinib, in RMS, has no effect on ALK signaling. However, the synergistic effects of ceritinib and dasatinib are promising, most probably due to targeting of IGF1R and Src.![]() Electronic supplementary material The online version of this article (10.1007/s11523-017-0528-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anke E M van Erp
- Department of Medical Oncology, Radboud University Medical Center, P.O. Box 9101, 6500HB, Nijmegen, The Netherlands.
| | | | - Laurens van Houdt
- Department of Medical Oncology, Radboud University Medical Center, P.O. Box 9101, 6500HB, Nijmegen, The Netherlands
| | - Emmy D G Fleuren
- Clinical Studies, Clinical and Translational Sarcoma/Gene Function, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Winette T A van der Graaf
- Department of Medical Oncology, Radboud University Medical Center, P.O. Box 9101, 6500HB, Nijmegen, The Netherlands.,The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London, SW7 3RP, UK
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Yohe ME, Gryder BE, Shern JF, Song YK, Chou HC, Sindiri S, Mendoza A, Patidar R, Zhang X, Guha R, Butcher D, Isanogle KA, Robinson CM, Luo X, Chen JQ, Walton A, Awasthi P, Edmondson EF, Difilippantonio S, Wei JS, Zhao K, Ferrer M, Thomas CJ, Khan J. MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma. Sci Transl Med 2018; 10:eaan4470. [PMID: 29973406 PMCID: PMC8054766 DOI: 10.1126/scitranslmed.aan4470] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
The RAS isoforms are frequently mutated in many types of human cancers, including PAX3/PAX7 fusion-negative rhabdomyosarcoma. Pediatric RMS arises from skeletal muscle progenitor cells that have failed to differentiate normally. The role of mutant RAS in this differentiation blockade is incompletely understood. We demonstrate that oncogenic RAS, acting through the RAF-MEK [mitogen-activated protein kinase (MAPK) kinase]-ERK (extracellular signal-regulated kinase) MAPK effector pathway, inhibits myogenic differentiation in rhabdomyosarcoma by repressing the expression of the prodifferentiation myogenic transcription factor, MYOG. This repression is mediated by ERK2-dependent promoter-proximal stalling of RNA polymerase II at the MYOG locus. Small-molecule screening with a library of mechanistically defined inhibitors showed that RAS-driven RMS is vulnerable to MEK inhibition. MEK inhibition with trametinib leads to the loss of ERK2 at the MYOG promoter and releases the transcriptional stalling of MYOG expression. MYOG subsequently opens chromatin and establishes super-enhancers at genes required for late myogenic differentiation. Furthermore, trametinib, in combination with an inhibitor of IGF1R, potently decreases rhabdomyosarcoma cell viability and slows tumor growth in xenograft models. Therefore, this combination represents a potential therapeutic for RAS-mutated rhabdomyosarcoma.
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Affiliation(s)
- Marielle E Yohe
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
- Pediatric Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Berkley E Gryder
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jack F Shern
- Pediatric Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Young K Song
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Hsien-Chao Chou
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sivasish Sindiri
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Arnulfo Mendoza
- Pediatric Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Rajesh Patidar
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Rajarashi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Donna Butcher
- Pathology/Histotechnology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21702, USA
| | - Kristine A Isanogle
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21701, USA
| | - Christina M Robinson
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21701, USA
| | - Xiaoling Luo
- Collaborative Protein Technology Resource, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jin-Qiu Chen
- Collaborative Protein Technology Resource, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ashley Walton
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21701, USA
| | - Elijah F Edmondson
- Pathology/Histotechnology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21702, USA
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21701, USA
| | - Jun S Wei
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Bethesda, MD 20892, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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Wachtel M, Schäfer BW. PAX3-FOXO1: Zooming in on an “undruggable” target. Semin Cancer Biol 2018; 50:115-123. [DOI: 10.1016/j.semcancer.2017.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/31/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022]
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34
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McKinnon T, Venier R, Yohe M, Sindiri S, Gryder BE, Shern JF, Kabaroff L, Dickson B, Schleicher K, Chouinard-Pelletier G, Menezes S, Gupta A, Zhang X, Guha R, Ferrer M, Thomas CJ, Wei Y, Davani D, Guidos CJ, Khan J, Gladdy RA. Functional screening of FGFR4-driven tumorigenesis identifies PI3K/mTOR inhibition as a therapeutic strategy in rhabdomyosarcoma. Oncogene 2018. [PMID: 29487419 DOI: 10.1038/s41388‐017‐0122‐y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma and outcomes have stagnated, highlighting a need for novel therapies. Genomic analysis of RMS has revealed that alterations in the receptor tyrosine kinase (RTK)/RAS/PI3K axis are common and that FGFR4 is frequently mutated or overexpressed. Although FGFR4 is a potentially druggable receptor tyrosine kinase, its functions in RMS are undefined. This study tested FGFR4-activating mutations and overexpression for the ability to generate RMS in mice. Murine tumor models were subsequently used to discover potential therapeutic targets and to test a dual PI3K/mTOR inhibitor in a preclinical setting. Specifically, we provide the first mechanistic evidence of differential potency in the most common human RMS mutations, V550E or N535K, compared to FGFR4wt overexpression as murine myoblasts expressing FGFR4V550E undergo higher rates of cellular transformation, engraftment into mice, and rapidly form sarcomas that highly resemble human RMS. Murine tumor cells overexpressing FGFR4V550E were tested in an in vitro dose-response drug screen along with human RMS cell lines. Compounds were grouped by target class, and potency was determined using average percentage of area under the dose-response curve (AUC). RMS cells were highly sensitive to PI3K/mTOR inhibitors, in particular, GSK2126458 (omipalisib) was a potent inhibitor of FGFR4V550E tumor-derived cell and human RMS cell viability. FGFR4V550E-overexpressing myoblasts and tumor cells had low nanomolar GSK2126458 EC50 values. Mass cytometry using mouse and human RMS cell lines validated GSK2126458 specificity at single-cell resolution, decreasing the abundance of phosphorylated Akt as well as decreasing phosphorylation of the downstream mTOR effectors 4ebp1, Eif4e, and S6. Moreover, PI3K/mTOR inhibition also robustly decreased the growth of RMS tumors in vivo. Thus, by developing a preclinical platform for testing novel therapies, we identified PI3K/mTOR inhibition as a promising new therapy for this devastating pediatric cancer.
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Affiliation(s)
- Timothy McKinnon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rosemarie Venier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Marielle Yohe
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Sivasish Sindiri
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Berkley E Gryder
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Jack F Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Leah Kabaroff
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Brendan Dickson
- Department of Pathology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Krista Schleicher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Serena Menezes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Abha Gupta
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rajarashi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuhong Wei
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Dariush Davani
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cynthia J Guidos
- Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Rebecca A Gladdy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada. .,Department of Surgery, University of Toronto, Toronto, ON, Canada.
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35
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Functional screening of FGFR4-driven tumorigenesis identifies PI3K/mTOR inhibition as a therapeutic strategy in rhabdomyosarcoma. Oncogene 2018; 37:2630-2644. [PMID: 29487419 DOI: 10.1038/s41388-017-0122-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/03/2017] [Accepted: 12/05/2017] [Indexed: 11/08/2022]
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma and outcomes have stagnated, highlighting a need for novel therapies. Genomic analysis of RMS has revealed that alterations in the receptor tyrosine kinase (RTK)/RAS/PI3K axis are common and that FGFR4 is frequently mutated or overexpressed. Although FGFR4 is a potentially druggable receptor tyrosine kinase, its functions in RMS are undefined. This study tested FGFR4-activating mutations and overexpression for the ability to generate RMS in mice. Murine tumor models were subsequently used to discover potential therapeutic targets and to test a dual PI3K/mTOR inhibitor in a preclinical setting. Specifically, we provide the first mechanistic evidence of differential potency in the most common human RMS mutations, V550E or N535K, compared to FGFR4wt overexpression as murine myoblasts expressing FGFR4V550E undergo higher rates of cellular transformation, engraftment into mice, and rapidly form sarcomas that highly resemble human RMS. Murine tumor cells overexpressing FGFR4V550E were tested in an in vitro dose-response drug screen along with human RMS cell lines. Compounds were grouped by target class, and potency was determined using average percentage of area under the dose-response curve (AUC). RMS cells were highly sensitive to PI3K/mTOR inhibitors, in particular, GSK2126458 (omipalisib) was a potent inhibitor of FGFR4V550E tumor-derived cell and human RMS cell viability. FGFR4V550E-overexpressing myoblasts and tumor cells had low nanomolar GSK2126458 EC50 values. Mass cytometry using mouse and human RMS cell lines validated GSK2126458 specificity at single-cell resolution, decreasing the abundance of phosphorylated Akt as well as decreasing phosphorylation of the downstream mTOR effectors 4ebp1, Eif4e, and S6. Moreover, PI3K/mTOR inhibition also robustly decreased the growth of RMS tumors in vivo. Thus, by developing a preclinical platform for testing novel therapies, we identified PI3K/mTOR inhibition as a promising new therapy for this devastating pediatric cancer.
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36
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PAX3-FOXO1 drives miR-486-5p and represses miR-221 contributing to pathogenesis of alveolar rhabdomyosarcoma. Oncogene 2018; 37:1991-2007. [PMID: 29367756 PMCID: PMC5895609 DOI: 10.1038/s41388-017-0081-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/26/2017] [Accepted: 12/01/2017] [Indexed: 01/02/2023]
Abstract
Rhabdomyosarcoma is the most common soft-tissue sarcoma in childhood and histologically resembles developing skeletal muscle. Alveolar rhabdomyosarcoma (ARMS) is an aggressive subtype with a higher rate of metastasis and poorer prognosis. The majority of ARMS tumors (80%) harbor a PAX3-FOXO1 or less commonly a PAX7-FOXO1 fusion gene. The presence of either the PAX3-FOXO1 or PAX7-FOXO1 fusion gene foretells a poorer prognosis resulting in clinical re-classification as either fusion-positive (FP-RMS) or fusion-negative RMS (FN-RMS). The PAX3/7-FOXO1 fusion genes result in the production of a rogue transcription factors that drive FP-RMS pathogenesis and block myogenic differentiation. Despite knowing the molecular driver of FP-RMS, targeted therapies have yet to make an impact for patients, highlighting the need for a greater understanding of the molecular consequences of PAX3-FOXO1 and its target genes including microRNAs. Here we show FP-RMS patient-derived xenografts and cell lines display a distinct microRNA expression pattern. We utilized both loss- and gain-of function approaches in human cell lines with knockdown of PAX3-FOXO1 in FP-RMS cell lines and expression of PAX3-FOXO1 in human myoblasts and identified microRNAs both positively and negatively regulated by the PAX3-FOXO1 fusion protein. We demonstrate PAX3-FOXO1 represses miR-221/222 that functions as a tumor suppressing microRNA through the negative regulation of CCND2, CDK6, and ERBB3. In contrast, miR-486-5p is transcriptionally activated by PAX3-FOXO1 and promotes FP-RMS proliferation, invasion, and clonogenic growth. Inhibition of miR-486-5p in FP-RMS xenografts decreased tumor growth, illustrating a proof of principle for future therapeutic intervention. Therefore, PAX3-FOXO1 regulates key microRNAs that may represent novel therapeutic vulnerabilities in FP-RMS.
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Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. BMC Cancer 2018; 18:85. [PMID: 29347918 PMCID: PMC5774140 DOI: 10.1186/s12885-017-3977-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected in the late-arising subclones. However, emerging evidence from the sequencing of multiple tumors and tumor regions per individual suggests that late-arising subclones with additional driver mutations are underestimated in single-sample analyses. METHODS To test whether driver mutations generally map to early tumor development, we examined multi-regional tumor sequencing data from 101 individuals reported in 11 published studies. Following previous studies, we annotated mutations as early-arising when all tumors/regions had those mutations (ubiquitous). We then inferred the fraction of mutations occurring early and compared it with late-arising mutations that were found in only single tumors/regions. RESULTS While a large fraction of driver mutations in tumors occurred relatively early in cancers, later driver mutations occurred at least as frequently as the early drivers in a substantial number of patients. This result was robust to many different approaches to annotate driver mutations. The relative frequency of early and late driver mutations varied among patients of the same cancer type and in different cancer types. We found that previous reports of the preponderance of early driver mutations were primarily informed by analysis of single tumor variant allele profiles, with which it is challenging to clearly distinguish between early and late drivers. CONCLUSIONS The origin and preponderance of new driver mutations are not limited to early stages of tumor evolution, with different tumors and regions showing distinct driver mutations and, consequently, distinct characteristics. Therefore, tumors with extensive intratumor heterogeneity appear to have many newly acquired drivers.
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Affiliation(s)
- Karen Gomez
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Louise A. Huuki
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
| | - Brianna S. Spell
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06510 USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511 USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511 USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
- Center for Genomic Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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Abstract
PURPOSE OF REVIEW The purpose of this article was to describe the systemic therapy of genito-urinary sarcomas. RECENT FINDINGS High rate of distant metastasis and high mortality rate has brought interest into the development of new therapeutic approaches. Various modules of chemotherapy were sampled in sarcoma treatment, although clinical response is still unsatisfactory. Chemotherapy in sarcomas can be used as neoadjuvant or adjuvant to the surgery. There is no consensus on the current role of adjuvant chemotherapy. Study results are conflicting; therefore, conclusions drawn from the studies are uncertain. In general, the adjuvant chemotherapy is not standard treatment in adult-type sarcomas. In addition, chemotherapy for advanced and metastatic sarcoma disease, as well as second-line chemotherapy, was discussed. SUMMARY The best treatment for sarcomas in case of organ-confined disease and in selected cases of locally advanced disease seems to be surgery followed by chemotherapy. In case of metastasis stage of sarcoma, preoperative chemotherapy with surgery of residual masses should be considered as first-line treatment followed by postoperative chemotherapy. The treatment of patient with highly advanced disease and/or unresectable metastases should be individualized (chemotherapy, radiotherapy and best supportive care).
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40
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Kieran K, Shnorhavorian M. Current standards of care in bladder and prostate rhabdomyosarcoma. Urol Oncol 2016; 34:93-102. [PMID: 26776454 DOI: 10.1016/j.urolonc.2015.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue tumor in children, and 15% to 20% arise from the genitourinary tract. Multicenter collaborative studies have improved survival substantially, and in addition to excellent oncologic control, current treatment focuses on organ preservation and minimization of late treatment effects. The multiple modalities needed to treat RMS dictate that treating physicians must be familiar with the disease as well as the goals and possible sequelae of treatment with chemotherapy, radiotherapy, and surgery. This article discusses the current standards of care for bladder and prostate RMS.
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Abstract
Rhabdomyosarcoma (RMS) is a myogenic tumor classified as the most frequent soft tissue sarcoma affecting children and adolescents. The histopathological classification includes 5 different histotypes, with 2 most predominant referred as to embryonal and alveolar, the latter being characterized by adverse outcome. The current molecular classification identifies 2 major subsets, those harboring the fused Pax3-Foxo1 transcription factor generating from a recurrent specific translocation (fusion-positive RMS), and those lacking this signature but harboring mutations in the RAS/PI3K/AKT signaling axis (fusion-negative RMS). Since little attention has been devoted to RMS metabolism until now, in this review we summarize the "state of art" of metabolism and discuss how some of the molecular signatures found in this cancer, as observed in other more common tumors, can predict important metabolic challenges underlying continuous cell growth, oxidative stress resistance and metastasis, which could be the subject of future targeted therapies.
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Affiliation(s)
- Eugenio Monti
- a Department of Molecular and Translational Medicine , University of Brescia , Brescia , Italy
| | - Alessandro Fanzani
- a Department of Molecular and Translational Medicine , University of Brescia , Brescia , Italy.,b Interuniversity Institute of Myology , Rome , Italy
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Lupo PJ, Brown AL, Hettmer S. Second malignancy risk among pediatric, adolescent, and young adult survivors of fusion-positive and fusion-negative sarcomas: Results from the SEER database, 1992 through 2012. Cancer 2016; 122:3492-3500. [PMID: 27481314 DOI: 10.1002/cncr.30222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/29/2016] [Accepted: 07/05/2016] [Indexed: 11/08/2022]
Abstract
BACKGROUND The current study builds on the hypothesis that cancer-predisposing germline mutations are less common among patients with fusion-positive (F+) sarcomas compared to those with fusion-negative (F-) sarcomas, resulting in a lower risk of developing second malignant neoplasms (SMNs) in those with F + sarcomas. METHODS Standardized incidence ratios (SIRs) for developing SMNs were evaluated in 4822 survivors of F + and 3963 survivors of F- sarcomas that were diagnosed between 1992 and 2012 in pediatric, adolescent, and young adult patients (aged birth-39 years) and reported in the Surveillance, Epidemiology, and End Results (SEER) database. Cox proportional hazards models (adjusted hazard ratio [aHR]) and competing risk methods (subhazard ratio [sHR]) were used to evaluate SMN risk in those with F- versus F + sarcomas while controlling for demographic and clinical variables. RESULTS SMN risk was found to be nearly 2-fold greater among survivors of F + sarcomas (SIR, 1.86; 95% confidence interval [95% CI], 1.48-2.30) and nearly 3-fold greater among survivors of F- sarcomas (SIR, 2.89; 95% CI, 2.30-3.59) compared with the reference population. Although SMN types were noted to be similar between the fusion groups, the rate of any SMN was noted to be greater among survivors of F- sarcomas (aHR, 1.38 [95% CI, 1.01-1.89] and sHR, 1.27 [95% CI, 0.94-1.73]) when compared with survivors of F + sarcomas. The difference was most notable for solid tumor SMNs after index sarcomas were diagnosed between 2002 and 2012, for which rates of SMN were >2-fold greater among survivors of F- sarcomas (aHR, 2.31 [95% CI, 1.20-4.48] and sHR, 2.24 [95% CI, 1.13-4.43]). CONCLUSIONS The findings of the current study highlight the increased SMN risk experienced by survivors of sarcoma and demonstrate higher SMN rates in survivors of F- sarcomas compared to those with a history of F + sarcomas. Cancer 2016;122:3492-3500. © 2016 American Cancer Society.
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Affiliation(s)
- Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Austin L Brown
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Hanna JA, Garcia MR, Go JC, Finkelstein D, Kodali K, Pagala V, Wang X, Peng J, Hatley ME. PAX7 is a required target for microRNA-206-induced differentiation of fusion-negative rhabdomyosarcoma. Cell Death Dis 2016; 7:e2256. [PMID: 27277678 PMCID: PMC5143388 DOI: 10.1038/cddis.2016.159] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/05/2016] [Accepted: 05/09/2016] [Indexed: 01/12/2023]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. RMS can be parsed based on clinical outcome into two subtypes, fusion-positive RMS (FP-RMS) or fusion-negative RMS (FN-RMS) based on the presence or absence of either PAX3-FOXO1 or PAX7-FOXO1 gene fusions. In both RMS subtypes, tumor cells show histology and a gene expression pattern resembling that of developmentally arrested skeletal muscle. Differentiation therapy is an attractive approach to embryonal tumors of childhood including RMS; however, agents to drive RMS differentiation have not entered the clinic and their mechanisms remain unclear. MicroRNA-206 (miR-206) expression increases through normal muscle development and has decreased levels in RMS compared with normal skeletal muscle. Increasing miR-206 expression drives differentiation of RMS, but the target genes responsible for the relief of the development arrest are largely unknown. Using a combinatorial approach with gene and proteomic profiling coupled with genetic rescue, we identified key miR-206 targets responsible for the FN-RMS differentiation blockade, PAX7, PAX3, NOTCH3, and CCND2. Specifically, we determined that PAX7 downregulation is necessary for miR-206-induced cell cycle exit and myogenic differentiation in FN-RMS but not in FP-RMS. Gene knockdown of targets necessary for miR-206-induced differentiation alone or in combination was not sufficient to phenocopy the differentiation phenotype from miR-206, thus illustrating that miR-206 replacement offers the ability to modulate a complex network of genes responsible for the developmental arrest in FN-RMS. Genetic deletion of miR-206 in a mouse model of FN-RMS accelerated and exacerbated tumor development, indicating that both in vitro and in vivo miR-206 acts as a tumor suppressor in FN-RMS at least partially through downregulation of PAX7. Collectively, our results illustrate that miR-206 relieves the differentiation arrest in FN-RMS and suggests that miR-206 replacement could be a potential therapeutic differentiation strategy.
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Affiliation(s)
- J A Hanna
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - M R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - J C Go
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - D Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - K Kodali
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - V Pagala
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - X Wang
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - J Peng
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - M E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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44
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Bova GS, Kallio HML, Annala M, Kivinummi K, Högnäs G, Häyrynen S, Rantapero T, Kivinen V, Isaacs WB, Tolonen T, Nykter M, Visakorpi T. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud 2016; 2:a000752. [PMID: 27148588 PMCID: PMC4853517 DOI: 10.1101/mcs.a000752] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials.
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Affiliation(s)
- G Steven Bova
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Heini M L Kallio
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Kati Kivinummi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Gunilla Högnäs
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Sergei Häyrynen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Tommi Rantapero
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Virpi Kivinen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Teemu Tolonen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
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Abstract
Li-Fraumeni syndrome (LFS) is a cancer predisposition syndrome caused by a germline mutation of the TP53 gene on chromosome 17p13.1. It has an autosomal dominant pattern of inheritance with high penetrance. These patients have a very high lifetime cumulative risk of developing multiple malignancies and have a strong family history of early-onset malignancies. The protein p53, encoded by TP53, has a complex set of genome-preserving functions initiated during episodes of cellular stress and DNA damage. In LFS, TP53 gene mutations cause the loss of function of p53, leading to downstream events permissive for development of various malignancies throughout life. The LFS component tumors include soft tissue sarcomas, osteosarcoma, premenopausal breast cancer, brain tumors, and adrenal cortical carcinomas. Multiple types of sarcomas have been reported in association with LFS; this review article will focus on the most frequently encountered pediatric sarcomas associated with TP53 mutations.
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Affiliation(s)
- Hernán Correa
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
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Hingorani P, Janeway K, Crompton BD, Kadoch C, Mackall CL, Khan J, Shern JF, Schiffman J, Mirabello L, Savage SA, Ladanyi M, Meltzer P, Bult CJ, Adamson PC, Lupo PJ, Mody R, DuBois SG, Parsons DW, Khanna C, Lau C, Hawkins DS, Randall RL, Smith M, Sorensen PH, Plon SE, Skapek SX, Lessnick S, Gorlick R, Reed DR. Current state of pediatric sarcoma biology and opportunities for future discovery: A report from the sarcoma translational research workshop. Cancer Genet 2016; 209:182-94. [PMID: 27132463 DOI: 10.1016/j.cancergen.2016.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 01/09/2023]
Abstract
Sarcomas are a rare subgroup of pediatric cancers comprised of a variety of bone and soft-tissue tumors. While significant advances have been made in improving outcomes of patients with localized pediatric sarcomas since the addition of systemic chemotherapy to local control many decades ago, outcomes for patients with metastatic and relapsed sarcoma remain poor with few novel therapeutics identified to date. With the advent of new technologies to study cancer genomes, transcriptomes and epigenomes, our understanding of sarcoma biology has improved tremendously in a relatively short period of time. However, much remains to be accomplished in this arena especially with regard to translating all of this new knowledge to the bedside. To this end, a meeting was convened in Philadelphia, PA, on April 18, 2015 sponsored by the QuadW foundation, Children's Oncology Group and CureSearch for Children's Cancer that brought together sarcoma clinicians and scientists from North America to review the current state of pediatric sarcoma biology and ongoing/planned genomics based clinical trials in an effort to identify and bridge knowledge gaps that continue to exist at present. At the conclusion of the workshop, three key objectives that would significantly further our understanding of sarcoma were identified and a proposal was put forward to develop an all-encompassing pediatric sarcoma biology protocol that would address these specific needs. This review summarizes the proceedings of the workshop.
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Affiliation(s)
- Pooja Hingorani
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ, USA.
| | - Katherine Janeway
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Brian D Crompton
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Crystal L Mackall
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jack F Shern
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Schiffman
- Huntsman Cancer Institute & Primary Children's Medical Center, University of Utah, Salt Lake City, UT, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Meltzer
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Peter C Adamson
- Division of Clinical Pharmacology & Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Rajen Mody
- Department of Pediatrics, University Of Michigan, Ann Arbor, MI, USA
| | - Steven G DuBois
- Department of Pediatric Hematology-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - D Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chand Khanna
- Molecular Oncology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ching Lau
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - R Lor Randall
- Huntsman Cancer Institute & Primary Children's Medical Center, University of Utah, Salt Lake City, UT, USA
| | | | - Poul H Sorensen
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Sharon E Plon
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Stephen X Skapek
- Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Lessnick
- Division of Hematology/ Oncology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard Gorlick
- Division of Pediatric Hematology/Oncology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Damon R Reed
- Moffitt Cancer Center, Sarcoma Department, Adolescent and Young Adult Program, Tampa, FL, USA
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47
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Gripp KW, Robbins KM, Sheffield BS, Lee AF, Patel MS, Yip S, Doyle D, Stabley D, Sol-Church K. Paternal uniparental disomy 11p15.5 in the pancreatic nodule of an infant with Costello syndrome: Shared mechanism for hyperinsulinemic hypoglycemia in neonates with Costello and Beckwith-Wiedemann syndrome and somatic loss of heterozygosity in Costello syndrome driving clonal expansion. Am J Med Genet A 2015; 170:559-64. [PMID: 26572961 DOI: 10.1002/ajmg.a.37471] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/01/2015] [Indexed: 11/09/2022]
Abstract
Costello syndrome (CS) entails a cancer predisposition and is caused by activating HRAS mutations, typically arising de novo in the paternal germline. Hypoglycemia is common in CS neonates. A previously reported individual with the rare HRAS p.Gln22Lys had hyperinsulinemic hypoglycemia. Autopsy showed a discrete pancreatic nodule. The morphologic and immunohistochemistry findings, including loss of p57(Kip2) protein, were identical to a focal lesion of congenital hyperinsulinism, however, no KCNJ11 or ABCC8 mutation was identified and germline derived DNA showed no alternation of the maternal or paternal 11p15 alleles. Here we report paternal uniparental disomy (pUPD) within the lesion, similar to the pUPD11p15.5 in Beckwith-Wiedemann syndrome (BWS). The similar extent of the pUPD suggests a similar mechanism driving hyperinsulinemia in both conditions. After coincidental somatic LOH and pUPD, the growth promoting effects of the paternally derived HRAS mutation, in combination with the increased function of the adjacent paternally expressed IGF2, may together result in clonal expansion. Although this somatic LOH within pancreatic tissue resulted in hyperinsulinism, similar LOH in mesenchymal cells may drive embryonal rhabdomyosarcoma (ERMS). Interestingly, biallelic IGF2 expression has been linked to rhabdomyosarcoma tumorigenesis and pUPD11 occurred in all 8 ERMS samples from CS individuals. Somatic KRAS and HRAS mutations occur with comparable frequency in isolated malignancies. Yet, the malignancy risk in CS is notably higher than in Noonan syndrome with a KRAS mutation. It is conceivable that HRAS co-localization with IGF2 and the combined effect of pUPD 11p15.5 on both genes contributes to the oncogenic potential.
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Affiliation(s)
- Karen W Gripp
- Division of Medical Genetics, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
| | - Katherine M Robbins
- Biomedical Research, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
| | | | - Anna F Lee
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Millan S Patel
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Doyle
- Division of Endocrinology, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
| | - Deborah Stabley
- Biomedical Research, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
| | - Katia Sol-Church
- Biomedical Research, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware
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48
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Walther C, Mayrhofer M, Nilsson J, Hofvander J, Jonson T, Mandahl N, Øra I, Gisselsson D, Mertens F. Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis. Genes Chromosomes Cancer 2015; 55:3-15. [DOI: 10.1002/gcc.22285] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Affiliation(s)
- Charles Walther
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Markus Mayrhofer
- Array & Analysis Facility, Science for Life Laboratory, Uppsala University; Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Jakob Hofvander
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Tord Jonson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Nils Mandahl
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Ingrid Øra
- Department of Pediatric Oncology; Skåne University Hospital; Lund Sweden
| | - David Gisselsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
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49
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Deel MD, Li JJ, Crose LES, Linardic CM. A Review: Molecular Aberrations within Hippo Signaling in Bone and Soft-Tissue Sarcomas. Front Oncol 2015; 5:190. [PMID: 26389076 PMCID: PMC4557106 DOI: 10.3389/fonc.2015.00190] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/10/2015] [Indexed: 12/14/2022] Open
Abstract
The Hippo signaling pathway is an evolutionarily conserved developmental network vital for the regulation of organ size, tissue homeostasis, repair and regeneration, and cell fate. The Hippo pathway has also been shown to have tumor suppressor properties. Hippo transduction involves a series of kinases and scaffolding proteins that are intricately connected to proteins in developmental cascades and in the tissue microenvironment. This network governs the downstream Hippo transcriptional co-activators, YAP and TAZ, which bind to and activate the output of TEADs, as well as other transcription factors responsible for cellular proliferation, self-renewal, differentiation, and survival. Surprisingly, there are few oncogenic mutations within the core components of the Hippo pathway. Instead, dysregulated Hippo signaling is a versatile accomplice to commonly mutated cancer pathways. For example, YAP and TAZ can be activated by oncogenic signaling from other pathways, or serve as co-activators for classical oncogenes. Emerging evidence suggests that Hippo signaling couples cell density and cytoskeletal structural changes to morphogenic signals and conveys a mesenchymal phenotype. While much of Hippo biology has been described in epithelial cell systems, it is clear that dysregulated Hippo signaling also contributes to malignancies of mesenchymal origin. This review will summarize the known molecular alterations within the Hippo pathway in sarcomas and highlight how several pharmacologic compounds have shown activity in modulating Hippo components, providing proof-of-principle that Hippo signaling may be harnessed for therapeutic application in sarcomas.
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Affiliation(s)
- Michael D Deel
- Division of Hematology-Oncology, Department of Pediatrics, Duke University School of Medicine , Durham, NC , USA
| | - Jenny J Li
- Duke University School of Medicine , Durham, NC , USA
| | - Lisa E S Crose
- Division of Hematology-Oncology, Department of Pediatrics, Duke University School of Medicine , Durham, NC , USA
| | - Corinne M Linardic
- Division of Hematology-Oncology, Department of Pediatrics, Duke University School of Medicine , Durham, NC , USA ; Department of Pharmacology and Cancer Biology, Duke University School of Medicine , Durham, NC , USA
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