1
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Koo SC, Schieffer KM, Lee K, Gupta A, Pfau RB, Avenarius MR, Stonerock E, LaHaye S, Fitch J, Setty BA, Roberts R, Ranalli M, Conces MR, Bu F, Mardis ER, Cottrell CE. EGFR internal tandem duplications in fusion-negative congenital and neonatal spindle cell tumors. Genes Chromosomes Cancer 2023; 62:17-26. [PMID: 35801295 DOI: 10.1002/gcc.23087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) assays can sensitively detect somatic variation, and increasingly can enable the identification of complex structural rearrangements. A subset of infantile spindle cell sarcomas, particularly congenital mesoblastic nephromas with classic or mixed histology, have structural rearrangement in the form of internal tandem duplications (ITD) involving EGFR. We performed prospective analysis to identify EGFR ITD through clinical or research studies, as well as retrospective analysis to quantify the frequency of EGFR ITD in pediatric sarcomas. Within our institution, three tumors with EGFR ITD were prospectively identified, all occurring in patients less than 1 year of age at diagnosis, including two renal tumors and one mediastinal soft tissue tumor. These three cases exhibited both cellular and mixed cellular and classic histology. All patients had no evidence of disease progression off therapy, despite incomplete resection. To extend our analysis and quantify the frequency of EGFR ITD in pediatric sarcomas, we retrospectively analyzed a cohort of tumors (n = 90) that were previously negative for clinical RT-PCR-based fusion testing. We identified EGFR ITD in three analyzed cases, all in patients less than 1 year of age (n = 18; 3/18, 17%). Here we expand the spectrum of tumors with EGFR ITD to congenital soft tissue tumors and report an unusual example of an EGFR ITD in a tumor with cellular congenital mesoblastic nephroma histology. We also highlight the importance of appropriate test selection and bioinformatic analysis for identification of this genomic alteration that is unexpectedly common in congenital and infantile spindle cell tumors.
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Affiliation(s)
- Selene C Koo
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristy Lee
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Ajay Gupta
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ruthann B Pfau
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bhuvana A Setty
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ryan Roberts
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mark Ranalli
- Department of Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Miriam R Conces
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Fang Bu
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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2
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De Faria FW, Schieffer KM, Pierson CR, Boue DR, LaHaye S, Miller KE, Amayiri N, Koboldt DC, Lichtenberg T, Leraas K, Brennan P, Kelly B, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE, Rusin J, Finlay JL, Osorio DS. Infantile metastatic ependymoma with a novel molecular profile and favorable outcome to intensive chemotherapy without irradiation: Case-based review. Genes Chromosomes Cancer 2023; 62:39-46. [PMID: 35716171 DOI: 10.1002/gcc.23081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/06/2022] Open
Abstract
Ependymal tumors are the third most common brain tumor under 14 years old. Even though metastatic disease is a rare event, it affects mostly young children and carries an adverse prognosis. The factors associated with dissemination and the best treatment approach have not yet been established and there is limited published data on how to manage metastatic disease, especially in patients under 3 years of age. We provide a review of the literature on clinical characteristics and radiation-sparing treatments for metastatic ependymoma in children under 3 years of age treated. The majority (73%) of the identified cases were above 12 months old and had the PF as the primary site at diagnosis. Chemotherapy-based approaches, in different regimens, were used with radiation reserved for progression or relapse. The prognosis varied among the studies, with an average of 50%-58% overall survival. This study also describes the case of a 7-month-old boy with metastatic posterior fossa (PF) ependymoma, for whom we identified a novel SPECC1L-RAF1 gene fusion using a patient-centric comprehensive molecular profiling protocol. The patient was successfully treated with intensive induction chemotherapy followed by high-dose chemotherapy and autologous hematopoietic progenitor cell rescue (AuHSCR). Currently, the patient is in continuous remission 5 years after his diagnosis, without radiation therapy. The understanding of the available therapeutic approaches may assist physicians in their management of such patients. This report also opens the perspective of newly identified molecular alterations in metastatic ependymomas that might drive more chemo-sensitive tumors.
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Affiliation(s)
- Flavia Watusi De Faria
- Department of Pediatric Hematology and Oncology, Hospital da Criança de Brasilia, Brasilia, Distrito Federal, Brazil.,Department of Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Department of Biomedical Education and Anatomy, Division of Anatomy, The Ohio State University, Columbus, Ohio, USA
| | - Daniel R Boue
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nisreen Amayiri
- Division of Pediatric Hematology/Oncology, King Hussein Cancer Center, Amman, Jordan
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Tara Lichtenberg
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Patrick Brennan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ben Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jerome Rusin
- Department of Radiology, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio, USA
| | - Jonathan L Finlay
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio, USA
| | - Diana S Osorio
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio, USA
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3
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Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V. Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome-Based Resolution of Isoform Complexity. J Mol Diagn 2022; 24:1292-1306. [PMID: 36191838 DOI: 10.1016/j.jmoldx.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023] Open
Abstract
Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular profiling using long-read sequencing improves the resolution of such events. For example, the Pacific Biosciences long-read RNA-sequencing (Iso-Seq) transcriptome protocol provides full-length isoform characterization, discernment of allelic phasing, and isoform discovery, and identifies expressed fusion partners. The Pacific Biosciences Fusion and Long Isoform Pipeline (PB_FLIP) incorporates a suite of RNA-sequencing software analysis tools and scripts to identify expressed fusion partners and isoforms. In addition, sequencing of a commercial reference (Spike-In RNA Variants) with known isoform complexity was performed and demonstrated high recall of the Iso-Seq and PB_FLIP workflow to benchmark our protocol and analysis performance. This study describes the utility of Iso-Seq and PB_FLIP analysis in improving deconvolution of complex structural variants and isoform detection within an institutional pediatric and adolescent/young adult translational cancer research cohort. The exemplar case studies demonstrate that Iso-Seq and PB_FLIP discover novel expressed fusion partners, resolve complex intragenic alterations, and discriminate between allele-specific expression profiles.
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Affiliation(s)
- Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Mariam Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
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4
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Larkin KT, Nicolet D, Kelly BJ, Mrózek K, LaHaye S, Miller KE, Wijeratne S, Wheeler G, Kohlschmidt J, Blachly JS, Mims AS, Walker CJ, Oakes CC, Orwick S, Boateng I, Buss J, Heyrosa A, Desai H, Carroll AJ, Blum W, Powell BL, Kolitz JE, Moore JO, Mayer RJ, Larson RA, Stone RM, Paskett ED, Byrd JC, Mardis ER, Eisfeld AK. High early death rates, treatment resistance, and short survival of Black adolescents and young adults with AML. Blood Adv 2022; 6:5570-5581. [PMID: 35788257 PMCID: PMC9577622 DOI: 10.1182/bloodadvances.2022007544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Survival of patients with acute myeloid leukemia (AML) is inversely associated with age, but the impact of race on outcomes of adolescent and young adult (AYA; range, 18-39 years) patients is unknown. We compared survival of 89 non-Hispanic Black and 566 non-Hispanic White AYA patients with AML treated on frontline Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology protocols. Samples of 327 patients (50 Black and 277 White) were analyzed via targeted sequencing. Integrated genomic profiling was performed on select longitudinal samples. Black patients had worse outcomes, especially those aged 18 to 29 years, who had a higher early death rate (16% vs 3%; P=.002), lower complete remission rate (66% vs 83%; P=.01), and decreased overall survival (OS; 5-year rates: 22% vs 51%; P<.001) compared with White patients. Survival disparities persisted across cytogenetic groups: Black patients aged 18 to 29 years with non-core-binding factor (CBF)-AML had worse OS than White patients (5-year rates: 12% vs 44%; P<.001), including patients with cytogenetically normal AML (13% vs 50%; P<.003). Genetic features differed, including lower frequencies of normal karyotypes and NPM1 and biallelic CEBPA mutations, and higher frequencies of CBF rearrangements and ASXL1, BCOR, and KRAS mutations in Black patients. Integrated genomic analysis identified both known and novel somatic variants, and relative clonal stability at relapse. Reduced response rates to induction chemotherapy and leukemic clone persistence suggest a need for different treatment intensities and/or modalities in Black AYA patients with AML. Higher early death rates suggest a delay in diagnosis and treatment, calling for systematic changes to patient care.
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Affiliation(s)
- Karilyn T. Larkin
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Benjamin J. Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Gregory Wheeler
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - James S. Blachly
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Alice S. Mims
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Christopher J. Walker
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Christopher C. Oakes
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Shelley Orwick
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Isaiah Boateng
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Jill Buss
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Adrienne Heyrosa
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Helee Desai
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - William Blum
- Emory University School of Medicine, Atlanta, GA
| | - Bayard L. Powell
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC
| | - Jonathan E. Kolitz
- Monter Cancer Center, Hofstra Northwell School of Medicine, Lake Success, NY
| | - Joseph O. Moore
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Robert J. Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Electra D. Paskett
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH
- The Center for Cancer Health Equity, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University Comprehensive Cancer Center, Columbus, OH
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH
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5
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Miller KE, Wheeler G, LaHaye S, Schieffer KM, Cearlock S, Venkata LPR, Bravo AO, Grischow OE, Kelly BJ, White P, Pierson CR, Boué DR, Koo SC, Klawinski D, Ranalli MA, Shaikhouni A, Salloum R, Shatara M, Leonard JR, Wilson RK, Cottrell CE, Mardis ER, Koboldt DC. Molecular Heterogeneity in Pediatric Malignant Rhabdoid Tumors in Patients With Multi-Organ Involvement. Front Oncol 2022; 12:932337. [PMID: 35912263 PMCID: PMC9326117 DOI: 10.3389/fonc.2022.932337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Rhabdoid tumors (RTs) of the brain (atypical teratoid/rhabdoid tumor; AT/RT) and extracranial sites (most often the kidney; RTK) are malignant tumors predominantly occurring in children, frequently those with SMARCB1 germline alterations. Here we present data from seven RTs from three pediatric patients who all had multi-organ involvement. The tumors were analyzed using a multimodal molecular approach, which included exome sequencing of tumor and germline comparator and RNA sequencing and DNA array-based methylation profiling of tumors. SMARCB1 germline alterations were identified in all patients and in all tumors. We observed a second hit in SMARCB1 via chr22 loss of heterozygosity. By methylation profiling, all tumors were classified as rhabdoid tumors with a corresponding subclassification within the MYC, TYR, or SHH AT/RT subgroups. Using RNA-seq gene expression clustering, we recapitulated the classification of known AT/RT subgroups. Synchronous brain and kidney tumors from the same patient showed different patterns of either copy number variants, single-nucleotide variants, and/or genome-wide DNA methylation, suggestive of non-clonal origin. Furthermore, we demonstrated that a lung and abdominal metastasis from two patients shared overlapping molecular features with the patient’s primary kidney tumor, indicating the likely origin of the metastasis. In addition to the SMARCB1 events, we identified other whole-chromosome events and single-nucleotide variants in tumors, but none were found to be prognostic, diagnostic, or offer therapeutic potential for rhabdoid tumors. While our findings are of biological interest, there may also be clinical value in comprehensive molecular profiling in patients with multiple rhabdoid tumors, particularly given the potential prognostic and therapeutic implications for different rhabdoid tumor subgroups demonstrated in recent clinical trials and other large cohort studies.
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Affiliation(s)
- Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- *Correspondence: Katherine E. Miller, ; Daniel C. Koboldt,
| | - Gregory Wheeler
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Sydney Cearlock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Lakshmi Prakruthi Rao Venkata
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Alejandro Otero Bravo
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Olivia E. Grischow
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Benjamin J. Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Christopher R. Pierson
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Biomedical Education and Anatomy, Division of Anatomy, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Daniel R. Boué
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Selene C. Koo
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Darren Klawinski
- Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children’s Hospital, Columbus, OH, United States
- Pediatric Neuro-Oncology Program, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Mark A. Ranalli
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Ammar Shaikhouni
- Department of Neurosurgery, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Ralph Salloum
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children’s Hospital, Columbus, OH, United States
- Pediatric Neuro-Oncology Program, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Margaret Shatara
- The Division of Hematology and Oncology, St. Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - Jeffrey R. Leonard
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Neurosurgery, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Richard K. Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Daniel C. Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- *Correspondence: Katherine E. Miller, ; Daniel C. Koboldt,
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6
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Bedrosian TA, Miller KE, Grischow OE, Schieffer KM, LaHaye S, Yoon H, Miller AR, Navarro J, Westfall J, Leraas K, Choi S, Williamson R, Fitch J, Kelly BJ, White P, Lee K, McGrath S, Cottrell CE, Magrini V, Leonard J, Pindrik J, Shaikhouni A, Boué DR, Thomas DL, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Koboldt DC. Detection of brain somatic variation in epilepsy-associated developmental lesions. Epilepsia 2022; 63:1981-1997. [PMID: 35687047 DOI: 10.1111/epi.17323] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified. METHODS We enrolled 50 children who were undergoing epilepsy surgery into a translational research study. Resected tissue was divided for clinical neuropathologic evaluation and genomic analysis. We performed exome and RNA sequencing to identify somatic variation and we confirmed our findings using high-depth targeted DNA sequencing. RESULTS We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). In agreement with previous studies, we identified somatic variation affecting solute carrier family 35 member A2 (SLC35A2) and mechanistic target of rapamycin kinase (MTOR) pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) of patients with Type I focal cortical dysplasia (FCD)s. Somatic variation in mitogen-activated protein kinase (MAPK) pathway genes (i.e., fibroblast growth factor receptor 1 [FGFR1], FGFR2, B-raf proto-oncogene, serine/threonine kinase [BRAF], and KRAS proto-oncogene, GTPase [KRAS]) was associated with low-grade epilepsy-associated developmental tumors. RNA sequencing enabled the detection of somatic structural variation that would have otherwise been missed, and which accounted for more than one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes not yet associated with focal cortical dysplasia. SIGNIFICANCE These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.
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Affiliation(s)
- Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Olivia E Grischow
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Hyojung Yoon
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jason Navarro
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jesse Westfall
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Samantha Choi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Rachel Williamson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Sean McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jeffrey Leonard
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Jonathan Pindrik
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Ammar Shaikhouni
- Department of Neurosurgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Daniel R Boué
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Anatomy, Department of Biomedical Education & Anatomy, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Diana L Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Christopher R Pierson
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Anatomy, Department of Biomedical Education & Anatomy, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Adam P Ostendorf
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Pediatric Neurology, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
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7
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Shatara M, Schieffer KM, Klawinski D, Thomas DL, Pierson CR, Sribnick EA, Jones J, Rodriguez DP, Deeg C, Hamelberg E, LaHaye S, Miller KE, Fitch J, Kelly B, Leraas K, Pfau R, White P, Magrini V, Wilson RK, Mardis ER, Abdelbaki MS, Finlay JL, Boué DR, Cottrell CE, Ghasemi DR, Pajtler KW, Osorio DS. Clinically aggressive pediatric spinal ependymoma with novel MYC amplification demonstrates molecular and histopathologic similarity to newly described MYCN-amplified spinal ependymomas. Acta Neuropathol Commun 2021; 9:192. [PMID: 34895332 PMCID: PMC8665631 DOI: 10.1186/s40478-021-01296-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/20/2021] [Indexed: 12/21/2022] Open
Abstract
Primary spinal cord tumors contribute to ≤ 10% of central nervous system tumors in individuals of pediatric or adolescent age. Among intramedullary tumors, spinal ependymomas make up ~ 30% of this rare tumor population. A twelve-year-old male presented with an intradural, extramedullary mass occupying the dorsal spinal canal from C6 through T2. Gross total resection and histopathology revealed a World Health Organization (WHO) grade 2 ependymoma. He recurred eleven months later with extension from C2 through T1-T2. Subtotal resection was achieved followed by focal proton beam irradiation and chemotherapy. Histopathology was consistent with WHO grade 3 ependymoma. Molecular profiling of the primary and recurrent tumors revealed a novel amplification of the MYC (8q24) gene, which was confirmed by fluorescence in situ hybridization studies. Although MYC amplification in spinal ependymoma is exceedingly rare, a newly described classification of spinal ependymoma harboring MYCN (2p24) amplification (SP-MYCN) has been defined by DNA methylation-array based profiling. These individuals typically present with a malignant progression and dismal outcomes, contrary to the universally excellent survival outcomes seen in other spinal ependymomas. DNA methylation array-based classification confidently classified this tumor as SP-MYCN ependymoma. Notably, among the cohort of 52 tumors comprising the SP-MYCN methylation class, none harbor MYC amplification, highlighting the rarity of this genomic amplification in spinal ependymoma. A literature review comparing our individual to reported SP-MYCN tumors (n = 26) revealed similarities in clinical, histopathologic, and molecular features. Thus, we provide evidence from a single case to support the inclusion of MYC amplified spinal ependymoma within the molecular subgroup of SP-MYCN.
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8
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LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P. Discovery of clinically relevant fusions in pediatric cancer. BMC Genomics 2021; 22:872. [PMID: 34863095 PMCID: PMC8642973 DOI: 10.1186/s12864-021-08094-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Background Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions. Results Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a “known fusion list” prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient’s medical record, both known and novel fusions provided medically meaningful information. Conclusions The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08094-z.
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Affiliation(s)
- Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle J Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Adam C Herman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Grant E Lammi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Natalie Bir
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Wetzel
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Elizabeth A Varga
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ajay Gupta
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA
| | - Bhuvana Setty
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeffrey R Leonard
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Section of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jonathan L Finlay
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Mohamed S Abdelbaki
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Diana S Osorio
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Selene C Koo
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, The Ohio State University, Columbus, OH, USA.,Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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9
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Nordquist EM, Dutta P, Kodigepalli KM, Mattern C, McDermott MR, Trask AJ, LaHaye S, Lindner V, Lincoln J. Tgfβ1-Cthrc1 Signaling Plays an Important Role in the Short-Term Reparative Response to Heart Valve Endothelial Injury. Arterioscler Thromb Vasc Biol 2021; 41:2923-2942. [PMID: 34645278 PMCID: PMC8612994 DOI: 10.1161/atvbaha.121.316450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE Aortic valve disease is a common worldwide health burden with limited treatment options. Studies have shown that the valve endothelium is critical for structure-function relationships, and disease is associated with its dysfunction, damage, or injury. Therefore, therapeutic targets to maintain a healthy endothelium or repair damaged endothelial cells could hold promise. In this current study, we utilize a surgical mouse model of heart valve endothelial cell injury to study the short-term response at molecular and cellular levels. The goal is to determine if the native heart valve exhibits a reparative response to injury and identify the mechanisms underlying this process. Approach and Results: Mild aortic valve endothelial injury and abrogated function was evoked by inserting a guidewire down the carotid artery of young (3 months) and aging (16-18 months) wild-type mice. Short-term cellular responses were examined at 6 hours, 48 hours, and 4 weeks following injury, whereas molecular profiles were determined after 48 hours by RNA-sequencing. Within 48 hours following endothelial injury, young wild-type mice restore endothelial barrier function in association with increased cell proliferation, and upregulation of transforming growth factor beta 1 (Tgfβ1) and the glycoprotein, collagen triple helix repeat containing 1 (Cthrc1). Interestingly, this beneficial response to injury was not observed in aging mice with known underlying endothelial dysfunction. CONCLUSIONS Data from this study suggests that the healthy valve has the capacity to respond to mild endothelial injury, which in short term has beneficial effects on restoring endothelial barrier function through acute activation of the Tgfβ1-Cthrc1 signaling axis and cell proliferation.
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Affiliation(s)
- Emily M. Nordquist
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, Section of Pediatric Cardiology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Punashi Dutta
- Department of Pediatrics, Section of Pediatric Cardiology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Karthik M. Kodigepalli
- Department of Pediatrics, Section of Pediatric Cardiology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Carol Mattern
- Department of Pediatrics, Section of Pediatric Cardiology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Michael R. McDermott
- Center for Cardiovascular Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Aaron J. Trask
- Center for Cardiovascular Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Volkhard Lindner
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine, USA
| | - Joy Lincoln
- Department of Pediatrics, Section of Pediatric Cardiology, Medical College of Wisconsin, Milwaukee, WI, USA
- The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
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10
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Wedekind MF, Miller KE, Chen CY, Wang PY, Hutzen BJ, Currier MA, Nartker B, Roberts RD, Boon L, Conner J, LaHaye S, Kelly BJ, Gordon D, White P, Mardis ER, Cripe TP. Endogenous retrovirus envelope as a tumor-associated immunotherapeutic target in murine osteosarcoma. iScience 2021; 24:102759. [PMID: 34278266 PMCID: PMC8267546 DOI: 10.1016/j.isci.2021.102759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/12/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Osteosarcoma remains one of the deadliest cancers in pediatrics and young adults. We administered two types of immunotherapies, oncolytic virotherapy and immune checkpoint inhibition, to two murine osteosarcoma models and observed divergent results. Mice bearing F420 showed no response, whereas those with K7M2 showed prolonged survival in response to combination therapy. K7M2 had higher expression of immune-related genes and higher baseline immune cell infiltrates, but there were no significant differences in tumor mutational burden or predicted MHC class I binding of nonsynonymous mutations. Instead, we found several mouse endogenous retrovirus sequences highly expressed in K7M2 compared with F420. T cell tetramer staining for one of them, gp70, was detected in mice with K7M2 but not F420, suggesting that endogenous retrovirus proteins are targets for the anti-tumor immune reaction. Given prior observations of endogenous retrovirus expression in human osteosarcomas, our findings may be translatable to human disease.
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Affiliation(s)
- Mary Frances Wedekind
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Chun-Yu Chen
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Pin-Yi Wang
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Brian J. Hutzen
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Mark A. Currier
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Brooke Nartker
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Ryan D. Roberts
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Louis Boon
- Polpharma Biologics, Utrecht, the Netherlands
| | | | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J. Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - David Gordon
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Timothy P. Cripe
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Koo SC, LaHaye S, Kovari BP, Schieffer KM, Ranalli MA, Aldrink JH, Michalsky MP, Colace S, Miller KE, Bedrosian TA, Leraas KM, Voytovich K, Wheeler G, Brennan P, Fitch J, Kelly BJ, McGrath SD, Miller AR, White P, Magrini V, Wilson RK, Mardis ER, Lauwers GY, Baker PB, Cottrell CE. Gastroblastoma with a novel EWSR1-CTBP1 fusion presenting in adolescence. Genes Chromosomes Cancer 2021; 60:640-646. [PMID: 34041825 DOI: 10.1002/gcc.22973] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 11/07/2022] Open
Abstract
Gastroblastomas are rare tumors with a biphasic epithelioid/spindle cell morphology that typically present in early adulthood and have recurrent MALAT1-GLI1 fusions. We describe an adolescent patient with Wiskott-Aldrich syndrome who presented with a large submucosal gastric tumor with biphasic morphology. Despite histologic features consistent with gastroblastoma, a MALAT1-GLI1 fusion was not found in this patient's tumor; instead, comprehensive molecular profiling identified a novel EWSR1-CTBP1 fusion and no other significant genetic alterations. The tumor also overexpressed NOTCH and FGFR by RNA profiling. The novel fusion and expression profile suggest a role for epithelial-mesenchymal transition in this tumor, with potential implications for the pathogenesis of biphasic gastric tumors such as gastroblastoma.
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Affiliation(s)
- Selene C Koo
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Bence P Kovari
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA.,Department of Pathology, University of Szeged, Szeged, Hungary
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mark A Ranalli
- Division of Hematology/Oncology/Bone Marrow Transplant, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Jennifer H Aldrink
- Division of Pediatric Surgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Surgery, The Ohio State University, Columbus, Ohio, USA
| | - Marc P Michalsky
- Division of Pediatric Surgery, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Surgery, The Ohio State University, Columbus, Ohio, USA
| | - Susan Colace
- Division of Hematology/Oncology/Bone Marrow Transplant, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kristen M Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kyle Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Gregory Wheeler
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Patrick Brennan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Gregory Y Lauwers
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Peter B Baker
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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13
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Dutta P, Kodigepalli KM, LaHaye S, Thompson JW, Rains S, Nagel C, Thatcher K, Hinton RB, Lincoln J. KPT-330 Prevents Aortic Valve Calcification via a Novel C/EBPβ Signaling Pathway. Circ Res 2021; 128:1300-1316. [PMID: 33601919 PMCID: PMC8085092 DOI: 10.1161/circresaha.120.318503] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Punashi Dutta
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Karthik M. Kodigepalli
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Stephanie LaHaye
- The Institute for Genomic Medicine at Nationwide Children’s Hospital, Columbus, OH, USA
| | - J. Will Thompson
- Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Sarah Rains
- Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Duke Proteomics and Metabolomics Shared Resource, Durham, NC, USA
| | - Casey Nagel
- Ocean Ridge Biosciences, Deerfield Beach, Florida, USA
| | - Kaitlyn Thatcher
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
| | - Robert B. Hinton
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Joy Lincoln
- Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Pediatric Cardiology, The Herma Heart Institute, Children’s Wisconsin, Milwaukee, WI, USA
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14
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Logan SJ, Schieffer KM, Conces MR, Stonerock E, Miller AR, Fitch J, LaHaye S, Voytovich K, McGrath S, Magrini V, White P, Wilson RK, Mardis ER, Cottrell CE, Koo SC. Novel morphologic findings in PLAG1-rearranged soft tissue tumors. Genes Chromosomes Cancer 2021; 60:577-585. [PMID: 33893698 DOI: 10.1002/gcc.22953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 12/13/2022] Open
Abstract
Oncogenesis in PLAG1-rearranged tumors often results from PLAG1 transcription factor overexpression driven by promoter-swapping between constitutively expressed fusion partners. PLAG1-rearranged tumors demonstrate diverse morphologies. This study adds to this morphologic heterogeneity by introducing two tumors with PLAG1 rearrangements that display distinct histologic features. The first arose in the inguinal region of a 3-year-old, appeared well-circumscribed with a multinodular pattern, and harbored two fusions: ZFHX4-PLAG1 and CHCHD7-PLAG1. The second arose in the pelvic cavity of a 15-year-old girl, was extensively infiltrative and vascularized with an adipocytic component, and demonstrated a COL3A1-PLAG1 fusion. Both showed low-grade cytomorphology, scarce mitoses, no necrosis, and expression of CD34 and desmin. The ZFHX4-/CHCHD7-PLAG1-rearranged tumor showed no evidence of recurrence after 5 months. By contrast, the COL3A1-PLAG1-rearranged tumor quickly recurred following primary excision with positive margins; subsequent re-excision with adjuvant chemotherapy resulted in no evidence of recurrence after 2 years. While both tumors show overlap with benign and malignant fibroblastic and fibrovascular neoplasms, they also display divergent features. These cases highlight the importance of appropriate characterization in soft tissue tumors with unusual clinical and histologic characteristics.
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Affiliation(s)
- Suzanna J Logan
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Miriam R Conces
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - James Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kyle Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Sean McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Selene C Koo
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pathology, The Ohio State University, Columbus, Ohio, USA
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15
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Schieffer KM, Feldman AZ, Kautto EA, McGrath S, Miller AR, Hernandez-Gonzalez ME, LaHaye S, Miller KE, Koboldt DC, Brennan P, Kelly B, Wetzel A, Agarwal V, Shatara M, Conley S, Rodriguez DP, Abu-Arja R, Shaikhkhalil A, Snuderl M, Orr BA, Finlay JL, Osorio DS, Drapeau AI, Leonard JR, Pierson CR, White P, Magrini V, Mardis ER, Wilson RK, Cottrell CE, Boué DR. Molecular classification of a complex structural rearrangement of the RB1 locus in an infant with sporadic, isolated, intracranial, sellar region retinoblastoma. Acta Neuropathol Commun 2021; 9:61. [PMID: 33827698 PMCID: PMC8025529 DOI: 10.1186/s40478-021-01164-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
Retinoblastoma is a childhood cancer of the retina involving germline or somatic alterations of the RB Transcriptional Corepressor 1 gene, RB1. Rare cases of sellar-suprasellar region retinoblastoma without evidence of ocular or pineal tumors have been described. A nine-month-old male presented with a sellar-suprasellar region mass. Histopathology showed an embryonal tumor with focal Flexner-Wintersteiner-like rosettes and loss of retinoblastoma protein (RB1) expression by immunohistochemistry. DNA array-based methylation profiling confidently classified the tumor as pineoblastoma group A/intracranial retinoblastoma. The patient was subsequently enrolled on an institutional translational cancer research protocol and underwent comprehensive molecular profiling, including paired tumor/normal exome and genome sequencing and RNA-sequencing of the tumor. Additionally, Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing was performed from comparator normal and disease-involved tissue to resolve complex structural variations. RNA-sequencing revealed multiple fusions clustered within 13q14.1-q21.3, including a novel in-frame fusion of RB1-SIAH3 predicted to prematurely truncate the RB1 protein. SMRT sequencing revealed a complex structural rearrangement spanning 13q14.11-q31.3, including two somatic structural variants within intron 17 of RB1. These events corresponded to the RB1-SIAH3 fusion and a novel RB1 rearrangement expected to correlate with the complete absence of RB1 protein expression. Comprehensive molecular analysis, including DNA array-based methylation profiling and sequencing-based methodologies, were critical for classification and understanding the complex mechanism of RB1 inactivation in this diagnostically challenging tumor.
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16
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Schieffer KM, Agarwal V, LaHaye S, Miller KE, Koboldt DC, Lichtenberg T, Leraas K, Brennan P, Kelly BJ, Crist E, Rusin J, Finlay JL, Osorio DS, Sribnick EA, Leonard JR, Feldman A, Orr BA, Serrano J, Vasudevaraja V, Snuderl M, White P, Magrini V, Wilson RK, Mardis ER, Boué DR, Cottrell CE. YAP1-FAM118B Fusion Defines a Rare Subset of Childhood and Young Adulthood Meningiomas. Am J Surg Pathol 2021; 45:329-340. [PMID: 33074854 DOI: 10.1097/pas.0000000000001597] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Meningiomas are a central nervous system tumor primarily afflicting adults, with <1% of cases diagnosed during childhood or adolescence. Somatic variation in NF2 may be found in ∼50% of meningiomas, with other genetic drivers (eg, SMO, AKT1, TRAF7) contributing to NF2 wild-type tumors. NF2 is an upstream negative regulator of YAP signaling and loss of the NF2 protein product, Merlin, results in YAP overexpression and target gene transcription. This mechanism of dysregulation is described in NF2-driven meningiomas, but further work is necessary to understand the NF2-independent mechanism of tumorigenesis. Amid our institutional patient-centric comprehensive molecular profiling study, we identified an individual with meningioma harboring a YAP1-FAM118B fusion, previously reported only in supratentorial ependymoma. The tumor histopathology was remarkable, characterized by prominent islands of calcifying fibrous nodules within an overall collagen-rich matrix. To gain insight into this finding, we subsequently evaluated the genetic landscape of 11 additional pediatric and adolescent/young adulthood meningioma patients within the Children's Brain Tumor Tissue Consortium. A second individual harboring a YAP1-FAM118B gene fusion was identified within this database. Transcriptomic profiling suggested that YAP1-fusion meningiomas are biologically distinct from NF2-driven meningiomas. Similar to other meningiomas, however, YAP1-fusion meningiomas demonstrated overexpression of EGFR and MET. DNA methylation profiling further distinguished YAP1-fusion meningiomas from those observed in ependymomas. In summary, we expand the genetic spectrum of somatic alteration associated with NF2 wild-type meningioma to include the YAP1-FAM118B fusion and provide support for aberrant signaling pathways potentially targetable by therapeutic intervention.
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Affiliation(s)
| | - Vibhuti Agarwal
- Division of Hematology, Oncology, and Bone Marrow Transplant
| | | | | | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics
| | | | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | - Patrick Brennan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | | | - Erin Crist
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | | | - Jonathan L Finlay
- Division of Hematology, Oncology, and Bone Marrow Transplant.,Departments of Pediatrics.,Division of Hematology and Oncology, The Ohio State University College of Medicine, Columbus, OH
| | - Diana S Osorio
- Division of Hematology, Oncology, and Bone Marrow Transplant.,Departments of Pediatrics.,Division of Hematology and Oncology, The Ohio State University College of Medicine, Columbus, OH
| | | | | | | | - Brent A Orr
- St. Jude Children's Research Hospital, Memphis, TN
| | - Jonathan Serrano
- Department of Pathology, New York University Langone Health, New York City, NY
| | | | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, NY
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics
| | - Daniel R Boué
- Pathology and Laboratory Medicine, Nationwide Children's Hospital.,Pathology
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine.,Departments of Pediatrics.,Pathology
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17
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Shatara M, Boué DR, Pierson CR, Thomas DL, Sribnick EA, Jones J, Rodriguez DP, Schieffer KM, Deeg C, Hamelberg E, LaHaye S, Magrini V, Wilson RK, Mardis ER, Cottrell CE, Varga EA, AbdelBaki MS, Finlay JL, Osorio DS. EPEN-28. NOVEL ONCOGENE AMPLIFICATION IN SPINAL EPENDYMOMA INVOLVING THE MYC LOCUS (8q24). Neuro Oncol 2020. [PMCID: PMC7715824 DOI: 10.1093/neuonc/noaa222.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report a unique case of spinal ependymoma with classic histology and aggressive clinical behavior which harbored a focal MYC (8q24) amplification. CASE REPORT: A-12-year old male presented with a three months history of back pain and acute onset weakness with ataxia. A spine MRI revealed an avidly enhancing intradural, extramedullary mass occupying the dorsal spinal canal from C6 through T2. The tumor demonstrated mild diffusion restriction and was associated with severe cord compression and mild edema. He underwent gross total resection. Pathological diagnosis was classic grade II ependymoma. Eleven months later, he re-presented with acute onset lower extremity paresthesia and left-handed weakness. Spine MRI demonstrated tumor recurrence extending from C2 through T1-T2 with resultant severe cord compression, again demonstrating avid enhancement and restricted diffusion. He underwent subtotal resection of the mass and focal proton beam irradiation. MOLECULAR CHARACTERISTICS: The patient was enrolled on an institutional comprehensive genomic profiling protocol. The tumor’s copy number profile was complex, including homozygous loss of 17p and notably, amplification of the MYC oncogene. Using fluorescence in situ hybridization, we identified >20 copies of MYC in interphase cells, confirming the gene amplification, while two copies of MYCN (2p24) were seen. DNA methylation further classified this tumor as clustering near posterior fossa group A (score=0.6073) tumors. CONCLUSION We report a unique case of an adolescent male with aggressive spinal ependymoma harboring focal MYC amplification. Testing for MYC amplification may be reasonable in newly-diagnosed spinal ependymomas to aid in characterization.
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Affiliation(s)
- Margaret Shatara
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Diana L Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Eric A Sribnick
- The Division of Pediatric Neurosurgery, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jeremy Jones
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Diana P Rodriguez
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Carol Deeg
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Elizabeth Hamelberg
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Elizabeth A Varga
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Mohamed S AbdelBaki
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jonathan L Finlay
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Diana S Osorio
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
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18
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Shatara M, Gupta A, Arja MHA, Conley SE, Patel P, Boué DR, Pierson CR, Thomas DL, Meyer EK, Shah SH, Jones J, Martin L, McAllister A, Schieffer KM, Varga EA, Leraas K, Lichtenberg T, LaHaye S, Miller KE, Magrini V, Wilson RK, Cottrell CE, Mardis ER, Aldrink JH, Auletta JJ, Pindrik J, Leonard JR, Osorio DS, Finlay JL, Ranalli M, AbdelBaki MS. ATRT-21. RHABDOID PREDISPOSITION SYNDROME: REPORT OF MOLECULAR PROFILES AND TREATMENT APPROACH IN THREE CHILDREN WITH SYNCHRONOUS ATYPICAL TERATOID/RHABDOID TUMOR AND MALIGNANT RHABDOID TUMOR. Neuro Oncol 2020. [PMCID: PMC7715330 DOI: 10.1093/neuonc/noaa222.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Rhabdoid predisposition syndrome is characterized by germline alterations in SMARCB1 or SMARCA4, leading to synchronous or metachronous central nervous system (CNS) and extra-CNS rhabdoid tumors. Rare survivors have been reported to date. METHODS We describe the molecular profiling and treatment regimen of three patients with synchronous atypical teratoid/rhabdoid tumor (ATRT) and malignant rhabdoid tumor of the kidney (MRT-K). All patients underwent radical nephrectomy of the kidney, and gross total resection of the primary CNS tumor was achieved for two patients. An intensive chemotherapy regimen was administered; an induction phase based on the modified Third Intergroup Rhabdomyosarcoma Study (IRS-III) for ATRT followed by a consolidation phase with three cycles of high-dose chemotherapy and autologous hematopoietic progenitor cell rescue, without irradiation. All three patients were enrolled on an institutional comprehensive genomic profiling protocol. RESULTS A germline focal 22q deletion, including SMARCB1, was detected in two patients, while the third patient had a maternally-inherited heterozygous frameshift variant in SMARCB1. Somatic loss of heterozygosity of 22q was identified in all patients, resulting in biallelic inactivation of SMARCB1. Divergent tumor subgroups were described using DNA methylation. The three MRT-K samples were classified as MYC subtype. One ATRT was classified as SHH while the other as TYR. One patient is currently three years off-therapy without evidence of disease, while the other two patients have completed the consolidation phase without recurrent disease. CONCLUSION Molecular profiling of CNS and extra-CNS rhabdoid tumors revealed different epigenetic subgroups. An intensive multimodal therapeutic approach without irradiation may achieve prolonged survival.
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Affiliation(s)
- Margaret Shatara
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Ajay Gupta
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Mohamed H Abu Arja
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Suzanne E Conley
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Priyal Patel
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Diana L Thomas
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Erin K Meyer
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Summit H Shah
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Jeremy Jones
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Lisa Martin
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Aaron McAllister
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Elizabeth A Varga
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Tara Lichtenberg
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Jennifer H Aldrink
- Department of Surgery, Division of Pediatric Surgery, The Ohio State University College of Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Jeffery J Auletta
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jonathan Pindrik
- The Division of Pediatric Neurosurgery, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jeffrey R Leonard
- The Division of Pediatric Neurosurgery, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Diana S Osorio
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jonathan L Finlay
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Mark Ranalli
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Mohamed S AbdelBaki
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
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19
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de Faria FW, Schieffer KM, Pierson C, Boué D, Zumberge N, Rusin J, LaHaye S, Miller KE, Koboldt DC, Lichtenberg T, Leraas K, Brennan P, Kelly B, White P, Magrini V, Wilson RK, Mardis ER, Osorio DS, Leonard J, Finlay JL. EPEN-17. FAVORABLE OUTCOME TO INTENSIVE CHEMOTHERAPY WITHOUT IRRADIATION IN INFANTILE METASTATIC EPENDYMOMA WITH A NOVEL MOLECULAR PROFILE: A CASE REPORT. Neuro Oncol 2020. [PMCID: PMC7715388 DOI: 10.1093/neuonc/noaa222.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Metastatic disease at initial presentation of intracranial ependymoma is an uncommon occurrence with only rare reports of survival and is reportedly more prevalent in the youngest of children. Clinical and molecular characteristics associated with metastatic presentation, their prognostic implications, as well as optimal treatment options for such patients, have not been identified. CASE REPORT: A seven months old child presented with posterior fossa anaplastic ependymoma; following sub-total resection of primary tumor, a spine MRI revealed leptomeningeal dissemination along the cervical spinal cord and nerve roots of the cauda equina. The patient was successfully treated with five cycles of intensive induction chemotherapy (as per Head Start with high-dose methotrexate) followed by three sequential cycles of marrow-ablative chemotherapy and autologous hematopoietic progenitor cell rescue (AuHPCR) without irradiation; he is currently without evidence of the disease now 60 months following initial diagnosis. MOLECULAR/GENOMIC RESULTS: The patient was enrolled on a patient-centric comprehensive molecular profiling protocol, which included paired tumor-normal whole-exome sequencing, RNA sequencing of the disease-involved tissue, and DNA methylation classification. The genomic profile of the tumor was relatively unremarkable, revealing only a terminal gain of chromosome 3p and a terminal deletion of chromosome 22q, suggestive of an unbalanced translocation. Using RNA sequencing, we identified a novel SPECC1L-RAF1 gene fusion. The tumor harbors unique transcriptomic and DNA methylation profiles, failing to discretely classify with well-established ependymoma subgroups. CONCLUSION: Use of genomic profiling techniques provides meaningful information for disease characterization allowing for further expansion of the molecular spectrum associated with malignant disease.
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Affiliation(s)
- Flavia W de Faria
- Department of Pediatric Hematology and Oncology, Hospital da Criança de Brasilia, Brasilia, DF, Brazil
| | | | - Christopher Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Daniel Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Nicholas Zumberge
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Jerome Rusin
- The Department of Radiology, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Tara Lichtenberg
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Patrick Brennan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Benjamin Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Columbus, OH, USA
| | - Diana S Osorio
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jeffrey Leonard
- The Division of Pediatric Neurosurgery, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
| | - Jonathan L Finlay
- The Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children’s Hospital and The Ohio State University, Columbus, OH, USA
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20
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Alnahhas I, LaHaye S, Giglio P, Mardis E, Puduvalli V. An evaluation of MGMT promoter methylation within the methylation subclasses of glioblastoma. Neurooncol Adv 2020; 2:vdaa117. [PMID: 33880446 PMCID: PMC8044669 DOI: 10.1093/noajnl/vdaa117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Iyad Alnahhas
- Division of Neuro-Oncology, Department of Neurology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Pierre Giglio
- Division of Neuro-Oncology, Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Elaine Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Vinay Puduvalli
- Division of Neuro-Oncology, Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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21
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Nordquist E, LaHaye S, Nagel C, Lincoln J. Corrigendum: Postnatal and Adult Aortic Heart Valves Have Distinctive Transcriptional Profiles Associated With Valve Tissue Growth and Maintenance Respectively. Front Cardiovasc Med 2019; 6:164. [PMID: 31799279 PMCID: PMC6874012 DOI: 10.3389/fcvm.2019.00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022] Open
Affiliation(s)
- Emily Nordquist
- Molecular Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, United States.,Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Stephanie LaHaye
- The Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, United States
| | - Casey Nagel
- Ocean Ridge Biosciences, Deerfield Beach, FL, United States
| | - Joy Lincoln
- Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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22
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LaHaye S, Voytovich K, Fitch J, McGrath S, Miller A, Wetzel A, Magrini V, Mardis ER, Wilson RK, White P, Cottrell CE. Abstract 1651: Utilization of an ensemble approach for identification of driver fusions in pediatric cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pediatric cancers, which make up ~1% of cancer diagnoses each year, comprise distinct genomic landscapes compared to adult cancers. Pediatric cancers typically exhibit a “quiet” genome with a reduced number of somatic mutations compared to adult tumors, which tend to carry a high mutational burden. In addition, pediatric tumors are often associated with fusion events, including fusions that involve potentially targetable kinases, as well as transcription factors which can often be targeted downstream. Fusion events can occur through chromosomal rearrangements, large deletions, or insertions. These events can lead to dysregulated gene expression, and can often become a driving event in pediatric cancer. Sensitive and specific detection of these fusion events through the utilization of RNA-seq data has proven to be a difficult task, given the complexities in tumor cellularity and clonality, and the numerous false positive identifications that are typically output from single fusion callers. Additionally, there are confounding issues surrounding memory usage and compute time required for certain fusion calling algorithms. The Institute for Genomic Medicine at Nationwide Children’s Hospital has implemented an ensemble approach, utilizing 7 fusion callers: FusionMap, JAFFA, STAR-Fusion, SOAPfuse, FusionCatcher, MapSplice, and TopHat-Fusion. This approach allows us to identify fusions that have been called by at least 2 of the above algorithms, and also allows for a prioritization approach based on the number of callers that have identified a specific fusion. We have employed this approach on 67 pediatric cancer cases that we have analyzed in a collaborative Institutional Review Board approved protocol which encompasses scientists, genetic counselors, oncologists, and pathologists at Nationwide Children’s Hospital. These cases are comprised of 52 central nervous system (CNS) tumors, 13 solid tumors, and 1 hematologic tumor, to date. To analyze these cases for fusion events, total RNA-seq with ribodepletion was performed on RNA, extracted from either flash frozen or Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples, to generate libraries that were sequenced using 150bp paired-end reads. Through the employment of our ensemble fusion calling approach and a manual knowledge based filtering strategy, we have currently identified 18 clinically meaningful fusions, all of which we have confirmed in a CAP/CLIA laboratory. We have identified both known and novel fusion events, of which several have provided diagnostic value and/or provided targeted treatment options for patients. In conclusion, this method has the potential to offer a streamlined approach to uncover driver fusions in cancer, while also providing additional diagnostics and an opportunity to identify targeted treatment options for patients in a clinical setting.
Citation Format: Stephanie LaHaye, Kyle Voytovich, James Fitch, Sean McGrath, Anthony Miller, Amy Wetzel, Vincent Magrini, Elaine R. Mardis, Richard K. Wilson, Peter White, Catherine E. Cottrell. Utilization of an ensemble approach for identification of driver fusions in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1651.
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Affiliation(s)
| | | | - James Fitch
- Nationwide Children's Hospital, Columbus, OH
| | | | | | - Amy Wetzel
- Nationwide Children's Hospital, Columbus, OH
| | | | | | | | - Peter White
- Nationwide Children's Hospital, Columbus, OH
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23
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LaHaye S, Majumdar U, Yasuhara J, Koenig SN, Matos-Nieves A, Kumar R, Garg V. Developmental origins for semilunar valve stenosis identified in mice harboring congenital heart disease-associated GATA4 mutation. Dis Model Mech 2019; 12:dmm.036764. [PMID: 31138536 PMCID: PMC6602309 DOI: 10.1242/dmm.036764] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 05/16/2019] [Indexed: 12/31/2022] Open
Abstract
Congenital heart defects affect ∼2% of live births and often involve malformations of the semilunar (aortic and pulmonic) valves. We previously reported a highly penetrant GATA4 p.Gly296Ser mutation in familial, congenital atrial septal defects and pulmonic valve stenosis and showed that mice harboring the orthologous G295S disease-causing mutation display not only atrial septal defects, but also semilunar valve stenosis. Here, we aimed to characterize the role of Gata4 in semilunar valve development and stenosis using the Gata4G295Ski/wt mouse model. GATA4 is highly expressed in developing valve endothelial and interstitial cells. Echocardiographic examination of Gata4G295Ski/wt mice at 2 months and 1 year of age identified functional semilunar valve stenosis predominantly affecting the aortic valve with distal leaflet thickening and severe extracellular matrix (ECM) disorganization. Examination of the aortic valve at earlier postnatal timepoints demonstrated similar ECM abnormalities consistent with congenital disease. Analysis at embryonic timepoints showed a reduction in aortic valve cushion volume at embryonic day (E)13.5, predominantly affecting the non-coronary cusp (NCC). Although total cusp volume recovered by E15.5, the NCC cusp remained statistically smaller. As endothelial to mesenchymal transition (EMT)-derived cells contribute significantly to the NCC, we performed proximal outflow tract cushion explant assays and found EMT deficits in Gata4G295Ski/wt embryos along with deficits in cell proliferation. RNA-seq analysis of E15.5 outflow tracts of mutant embryos suggested a disease state and identified changes in genes involved in ECM and cell migration as well as dysregulation of Wnt signaling. By utilizing a mouse model harboring a human disease-causing mutation, we demonstrate a novel role for GATA4 in congenital semilunar valve stenosis. This article has an associated First Person interview with the joint first authors of the paper. Summary: Cellular and molecular characterization of a mutant mouse, harboring a human disease-causing GATA4 variant, identifies cellular deficits in endothelial-to-mesenchymal transition and proliferation that cause abnormal valve remodeling and resultant stenosis.
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Affiliation(s)
- Stephanie LaHaye
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA.,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Uddalak Majumdar
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA.,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Jun Yasuhara
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA.,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sara N Koenig
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA.,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Adrianna Matos-Nieves
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA.,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Rahul Kumar
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH 43205, USA .,The Heart Center, Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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24
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Bosse K, Hans CP, Zhao N, Koenig SN, Huang N, Guggilam A, LaHaye S, Tao G, Lucchesi PA, Lincoln J, Lilly B, Garg V. Corrigendum to "Endothelial nitric oxide signaling regulates Notch1 in aortic valve disease" [J. Mol. Cell. Cardiol. 60 (2013) 27-35]. J Mol Cell Cardiol 2018; 121:307. [PMID: 29778253 DOI: 10.1016/j.yjmcc.2018.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- K Bosse
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - C P Hans
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - N Zhao
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - S N Koenig
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - N Huang
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - A Guggilam
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - S LaHaye
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - G Tao
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - P A Lucchesi
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - J Lincoln
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - B Lilly
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - V Garg
- Center for Cardiovascular Research at Nationwide Children's Hospital, Columbus, OH 43205, USA.
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25
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Nordquist E, LaHaye S, Nagel C, Lincoln J. Postnatal and Adult Aortic Heart Valves Have Distinctive Transcriptional Profiles Associated With Valve Tissue Growth and Maintenance Respectively. Front Cardiovasc Med 2018; 5:30. [PMID: 29740591 PMCID: PMC5928323 DOI: 10.3389/fcvm.2018.00030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Heart valves are organized connective tissues of high mechanical demand. They open and close over 100,000 times a day to preserve unidirectional blood flow by maintaining structure-function relationships throughout life. In affected individuals, structural failure compromises function and often leads to regurgitant blood flow and progressive heart failure. This is most common in degenerative valve disease due to age-related wear and tear, or congenital malformations. At present, the only effective treatment of valve disease is surgical repair or replacement and this is often impermanent and requires anti-coagulation therapy throughout life. Therefore, there is a critical need to discover new alternatives. A promising therapeutic area is tissue regeneration and in non-valvular tissues this requires a tightly regulated genetic “growth program” involving cell proliferation. To explore this in heart valves, we performed RNA-seq analysis to compare transcriptional profiles of aortic valve tissue isolated from mice during stages of growth (postnatal day (PND) 2) and adult maintenance (4 months). Data analysis reveals distinct mRNA profiles at each time point and pathway ontology identifies associated changes in biological functions. The PND2 aortic valve is characterized by extensive cell proliferation and expression of mRNAs related to the extracellular matrix (ECM). At 4 months, proliferation is not significant and a differential set of ECM-related genes are expressed. Interestingly there is enrichment of the defense response biological process at this later time point. Together, these data highlight the unique transcriptome of the postnatal valve during stages of growth and maturation, as well as biological functions associated with adult homeostatic valves. These studies create a platform for future work exploring the molecular programs altered in the onset of heart valve disease after birth and provide insights for the development of mechanistic-based therapies.
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Affiliation(s)
- Emily Nordquist
- Molecular Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, United States.,Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Stephanie LaHaye
- The Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, United States
| | - Casey Nagel
- Ocean Ridge Biosciences, Deerfield Beach, FL, United States
| | - Joy Lincoln
- Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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26
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Koenig SN, LaHaye S, Feller JD, Rowland P, Hor KN, Trask AJ, Janssen PM, Radtke F, Lilly B, Garg V. Notch1 haploinsufficiency causes ascending aortic aneurysms in mice. JCI Insight 2017; 2:91353. [PMID: 29093270 DOI: 10.1172/jci.insight.91353] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 09/29/2017] [Indexed: 12/20/2022] Open
Abstract
An ascending aortic aneurysm (AscAA) is a life-threatening disease whose molecular basis is poorly understood. Mutations in NOTCH1 have been linked to bicuspid aortic valve (BAV), which is associated with AscAA. Here, we describe a potentially novel role for Notch1 in AscAA. We found that Notch1 haploinsufficiency exacerbated the aneurysmal aortic root dilation seen in the Marfan syndrome mouse model and that heterozygous deletion of Notch1 in the second heart field (SHF) lineage recapitulated this exacerbated phenotype. Additionally, Notch1+/- mice in a predominantly 129S6 background develop aortic root dilation, indicating that loss of Notch1 is sufficient to cause AscAA. RNA sequencing analysis of the Notch1.129S6+/- aortic root demonstrated gene expression changes consistent with AscAA. These findings are the first to our knowledge to demonstrate an SHF lineage-specific role for Notch1 in AscAA and suggest that genes linked to the development of BAV may also contribute to the associated aortopathy.
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Affiliation(s)
- Sara N Koenig
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Dorothy M. Davis Heart and Lung Research Institute
| | - Stephanie LaHaye
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Molecular Genetics
| | - James D Feller
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Patrick Rowland
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kan N Hor
- The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, and
| | - Aaron J Trask
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, and
| | - Paul Ml Janssen
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA
| | - Freddy Radtke
- Ecole Polytechnique Fédérale de Lausanne, Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland
| | - Brenda Lilly
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Molecular Genetics
| | - Vidu Garg
- Center for Cardiovascular Research and.,The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Dorothy M. Davis Heart and Lung Research Institute.,Department of Molecular Genetics.,Department of Pediatrics, and
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27
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Basu M, Zhu JY, LaHaye S, Majumdar U, Jiao K, Han Z, Garg V. Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease. JCI Insight 2017; 2:95085. [PMID: 29046480 DOI: 10.1172/jci.insight.95085] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/19/2017] [Indexed: 12/22/2022] Open
Abstract
Birth defects are the leading cause of infant mortality, and they are caused by a combination of genetic and environmental factors. Environmental risk factors may contribute to birth defects in genetically susceptible infants by altering critical molecular pathways during embryogenesis, but experimental evidence for gene-environment interactions is limited. Fetal hyperglycemia associated with maternal diabetes results in a 5-fold increased risk of congenital heart disease (CHD), but the molecular basis for this correlation is unknown. Here, we show that the effects of maternal hyperglycemia on cardiac development are sensitized by haploinsufficiency of Notch1, a key transcriptional regulator known to cause CHD. Using ATAC-seq, we found that hyperglycemia decreased chromatin accessibility at the endothelial NO synthase (Nos3) locus, resulting in reduced NO synthesis. Transcription of Jarid2, a regulator of histone methyltransferase complexes, was increased in response to reduced NO, and this upregulation directly resulted in inhibition of Notch1 expression to levels below a threshold necessary for normal heart development. We extended these findings using a Drosophila maternal diabetic model that revealed the evolutionary conservation of this interaction and the Jarid2-mediated mechanism. These findings identify a gene-environment interaction between maternal hyperglycemia and Notch signaling and support a model in which environmental factors cause birth defects in genetically susceptible infants.
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Affiliation(s)
- Madhumita Basu
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jun-Yi Zhu
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA
| | - Stephanie LaHaye
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Uddalak Majumdar
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kai Jiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zhe Han
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA
| | - Vidu Garg
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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28
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LaHaye S, Corsmeier D, Basu M, Bowman JL, Fitzgerald-Butt S, Zender G, Bosse K, McBride KL, White P, Garg V. Utilization of Whole Exome Sequencing to Identify Causative Mutations in Familial Congenital Heart Disease. ACTA ACUST UNITED AC 2016; 9:320-9. [PMID: 27418595 DOI: 10.1161/circgenetics.115.001324] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 06/27/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common type of birth defect with family- and population-based studies supporting a strong genetic cause for CHD. The goal of this study was to determine whether a whole exome sequencing (WES) approach could identify pathogenic-segregating variants in multiplex CHD families. METHODS AND RESULTS WES was performed on 9 kindreds with familial CHD, 4 with atrial septal defects, 2 with patent ductus arteriosus, 2 with tetralogy of Fallot, and 1 with pulmonary valve dysplasia. Rare variants (<1% minor allele frequency) that segregated with disease were identified by WES, and variants in 69 CHD candidate genes were further analyzed. These selected variants were subjected to in silico analysis to predict pathogenicity and resulted in the discovery of likely pathogenic mutations in 3 of 9 (33%) families. A GATA4 mutation in the transactivation domain, p.G115W, was identified in familial atrial septal defects and demonstrated decreased transactivation ability in vitro. A p.I263V mutation in TLL1 was identified in an atrial septal defects kindred and is predicted to affect the enzymatic functionality of TLL1. A disease-segregating splice donor site mutation in MYH11 (c.4599+1delG) was identified in familial patent ductus arteriosus and found to disrupt normal splicing of MYH11 mRNA in the affected individual. CONCLUSIONS Our findings demonstrate the clinical utility of WES to identify causative mutations in familial CHD and demonstrate the successful use of a CHD candidate gene list to allow for a more streamlined approach enabling rapid prioritization and identification of likely pathogenic variants from large WES data sets. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov; Unique Identifier: NCT0112048.
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Affiliation(s)
- Stephanie LaHaye
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Don Corsmeier
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Madhumita Basu
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Jessica L Bowman
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Sara Fitzgerald-Butt
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Gloria Zender
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Kevin Bosse
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Kim L McBride
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Peter White
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus.
| | - Vidu Garg
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus.
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Abstract
Valvular heart disease is associated with significant morbidity and mortality and often the result of congenital malformations. However, the prevalence is increasing in adults not only because of the growing aging population, but also because of improvements in the medical and surgical care of children with congenital heart valve defects. The success of the Human Genome Project and major advances in genetic technologies, in combination with our increased understanding of heart valve development, has led to the discovery of numerous genetic contributors to heart valve disease. These have been uncovered using a variety of approaches including the examination of familial valve disease and genome-wide association studies to investigate sporadic cases. This review will discuss these findings and their implications in the treatment of valvular heart disease.
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Affiliation(s)
- Stephanie LaHaye
- Center for Cardiovascular and Pulmonary Research and The Heart Center, Room WB4221, Nationwide Children's Hospital, Columbus, OH, 43205, USA
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30
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Bosse K, Hans CP, Zhao N, Koenig SN, Huang N, Guggilam A, LaHaye S, Tao G, Lucchesi PA, Lincoln J, Lilly B, Garg V. Endothelial nitric oxide signaling regulates Notch1 in aortic valve disease. J Mol Cell Cardiol 2013; 60:27-35. [PMID: 23583836 DOI: 10.1016/j.yjmcc.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 03/14/2013] [Accepted: 04/03/2013] [Indexed: 01/22/2023]
Abstract
The mature aortic valve is composed of a structured trilaminar extracellular matrix that is interspersed with aortic valve interstitial cells (AVICs) and covered by endothelium. Dysfunction of the valvular endothelium initiates calcification of neighboring AVICs leading to calcific aortic valve disease (CAVD). The molecular mechanism by which endothelial cells communicate with AVICs and cause disease is not well understood. Using a co-culture assay, we show that endothelial cells secrete a signal to inhibit calcification of AVICs. Gain or loss of nitric oxide (NO) prevents or accelerates calcification of AVICs, respectively, suggesting that the endothelial cell-derived signal is NO. Overexpression of Notch1, which is genetically linked to human CAVD, retards the calcification of AVICs that occurs with NO inhibition. In AVICs, NO regulates the expression of Hey1, a downstream target of Notch1, and alters nuclear localization of Notch1 intracellular domain. Finally, Notch1 and NOS3 (endothelial NO synthase) display an in vivo genetic interaction critical for proper valve morphogenesis and the development of aortic valve disease. Our data suggests that endothelial cell-derived NO is a regulator of Notch1 signaling in AVICs in the development of the aortic valve and adult aortic valve disease.
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Affiliation(s)
- Kevin Bosse
- Center for Cardiovascular and Pulmonary Research at Nationwide Children's Hospital, Columbus, OH 43205, USA
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Brosvic GM, Hecht GS, LaHaye S, Rowe MM, Risser JM, Clementson E, Dihoff RE. Quality-specific differences in rat taste detection performance as a function of stimulus volume. Physiol Behav 1991; 50:711-6. [PMID: 1775544 DOI: 10.1016/0031-9384(91)90007-b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Taste detection performance for representatives of the four taste qualities as a function of stimulus volume (5 x 10(-4) to 1 x 1(-1) ml) was examined in rats using high-precision gustometry, computer-controlled operant procedures, nonparametric signal detection measures of sensitivity and responsivity, and blind control procedures. The overall sensitivity index was positively related to stimulus volume (rs = .60), with optimal detection performance attained with a 5 x 10(-3) ml stimulus volume for salty tastants and a 1 x 10(-2) ml stimulus volume for the other taste qualities. The overall responsivity index was inversely related to stimulus volume (rs = -.47), especially for sour and bitter tastants. These results are consistent with prior observations and demonstrate that operant methods using small tastant samples produce sensitive estimates of the rat's taste detection performance and response bias.
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Affiliation(s)
- G M Brosvic
- Department of Psychology, Rider College, Lawrenceville, NJ 08648-3099
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