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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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Chen Y, Karaca E, Robin NH, Goodloe D, Al-Beshri A, Dean SJ, Hurst ACE, Carroll AJ, Mikhail FM. DLG2 intragenic exonic deletions reinforce the link to neurodevelopmental disorders and suggest a potential association with congenital anomalies and dysmorphism. Genet Med 2024; 26:101010. [PMID: 37860969 DOI: 10.1016/j.gim.2023.101010] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
PURPOSE Multiple studies suggest an association between DLG2 and neurodevelopmental disorders and indicate the haploinsufficiency of this gene; however, few cases have been thoroughly described. We performed additional studies to confirm this clinical association and DLG2 haploinsufficiency. METHODS Chromosomal microarray analysis was performed on 11,107 patients at the Cytogenetics Laboratory at the University of Alabama at Birmingham. The Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database were selected for the association analysis. Fifty-nine patients from the literature and DECIPHER, all having DLG2 intragenic deletions, were included for comprehensive analysis of the distribution of these deletions. RESULTS A total of 13 patients with DLG2 intragenic deletions, from 10 families in our cohort, were identified. Nine of 10 probands presented with clinical features of neurodevelopmental disorders. Congenital anomalies and dysmorphism were common in our cohort of patients. Association analysis showed that the frequency of DLG2 deletions in our cohort is significantly higher than those in the Database of Genomic Variants-Gold Standard Variants and the Genome Aggregation Database. Most of DLG2 intragenic deletions identified in 69 unrelated patients from our cohort, the literature, and DECIPHER map to the 5' region of the gene, with a hotspot centered around HPin7, exon 8, and HPin8. CONCLUSION Our findings reinforce the link between DLG2 intragenic deletions and neurodevelopmental disorders, strongly support the haploinsufficiency of this gene, and indicate that these deletions might also have an association with congenital anomalies and dysmorphism.
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Affiliation(s)
- Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Dallas, TX
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Ali Al-Beshri
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - S Joy Dean
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.
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Blackburn PR, McGee RB, Mostafavi R, Carroll AJ, Mikhail FM, Armstrong GT, Furtado LV, Chiang J, Wheeler DA, Carey SS, Nichols KE, Upadhyaya SA. Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome. Genes Chromosomes Cancer 2024; 63:e23195. [PMID: 37548271 DOI: 10.1002/gcc.23195] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/19/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
Rhabdoid Tumor Predisposition Syndrome 1 (RTPS1) confers an increased risk of developing rhabdoid tumors and is caused by germline mutations in SMARCB1. RTPS1 should be evaluated in all individuals with rhabdoid tumor and is more likely in those with a young age at presentation (occasionally congenital presentation), multiple primary tumors, or a family history of rhabdoid tumor or RTPS1. Proband genetic testing is the standard method for diagnosing RTPS1. Most known RTPS1-related SMARCB1 gene mutations are copy number variants (CNVs) or single nucleotide variants/indels, but structural variant analysis (SVA) is not usually included in the molecular evaluation. Here, we report two children with RTPS1 presenting with atypical teratoid/rhabdoid tumor (ATRT) who had constitutional testing showing balanced chromosome translocations involving SMARCB1. Patient 1 is a 23-year-old female diagnosed with pineal region ATRT at 7 months who was found to have a de novo, constitutional t(16;22)(p13.3;q11.2). Patient 2 is a 24-month-old male diagnosed with a posterior fossa ATRT at 14 months, with subsequent testing showing a constitutional t(5;22)(q14.1;q11.23). These structural rearrangements have not been previously reported in RTPS1. While rare, these cases suggest that structural variants should be considered in the evaluation of children with rhabdoid tumors to provide more accurate genetic counseling on the risks of developing tumors, the need for surveillance, and the risks of passing the disorder on to future children. Further research is needed to understand the prevalence, clinical features, and tumor risks associated with RTPS1-related constitutional balanced translocations.
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Affiliation(s)
- Patrick R Blackburn
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rose B McGee
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Roya Mostafavi
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Larissa V Furtado
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jason Chiang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Steven S Carey
- Department of Hospitalist Medicine, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim E Nichols
- Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Santhosh A Upadhyaya
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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Belnap N, Price-Smith A, Ramsey K, Leka K, Abraham A, Lieberman E, Hassett K, Potu S, Rudy N, Smith K, Mikhail FM, Monaghan KG, Hendershot A, Mourmans J, Descartes M, Huentelman MJ, Sills J, Rangasamy S, Narayanan V. Inherited CSNK2A1 variants in families with Okur-Chung neurodevelopmental syndrome. Clin Genet 2023; 104:607-609. [PMID: 37491870 DOI: 10.1111/cge.14408] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023]
Abstract
Pedigree showing the autosomal dominant inheritance pattern of CSNK21 variants in families presenting with OCNDS. (A) Maternal inheritance to two daughters in Family 1, (B) Paternal inheritance to a daughter in Family 2, and (C) Maternal inheritance to two sons in Family 3.
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Affiliation(s)
- Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Aiai Price-Smith
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Keri Ramsey
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Kamawela Leka
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Anna Abraham
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Emma Lieberman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Katie Hassett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Sai Potu
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Natasha Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kirstin Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | | | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | | | - Sampath Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
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Dunn-Valadez S, Bathini S, Purdy KE, Bachiashvili K, Bhatia R, Jamy O, Rangaraju S, Mehta A, Godby K, Goyal G, Worth S, Oliver JD, Mikhail FM, Choi JK, Morlote D, Reddy VB, Vachhani P. Utility of end of induction bone marrow biopsy and survival outcomes in acute promyelocytic leukemia treated with fixed-dose induction regimen. Leuk Lymphoma 2023; 64:1673-1680. [PMID: 37493540 DOI: 10.1080/10428194.2023.2234529] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
Significant variations exist related to the end of induction practices in the management of Acute Promyelocytic Leukemia (APL). These variations include all-trans retinoic acid (ATRA)-arsenic trioxide (ATO) in fixed doses versus continuation until hematologic complete remission (CR) and performance versus omission of post-induction bone marrow biopsy to confirm morphological CR. A retrospective chart review was conducted of 61 patients (42 low/intermediate-risk and 19 high-risk) aged ≥ 18 years with newly diagnosed APL treated with fixed duration ATRA-ATO +/- cytoreduction at a tertiary medical center from December 2012 through March 2020. Of the 54 patients with post-induction bone marrow biopsy results, 52 (96%) demonstrated no morphologic evidence of APL while the remaining were equivocal. After 2.6 years median follow-up, no relapses occurred. The estimated 2-year overall survival rate of 95% suggests excellent outcomes with a fixed ATO induction regimen and safe omission of post-induction bone marrow biopsy irrespective of hematologic parameters.
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Affiliation(s)
- Sydney Dunn-Valadez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Srilakshmi Bathini
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kathleen E Purdy
- Department of Medical Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kimo Bachiashvili
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ravi Bhatia
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Omer Jamy
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sravanti Rangaraju
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amitkumar Mehta
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kelly Godby
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gaurav Goyal
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarah Worth
- Department of Pharmacy, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Josh D Oliver
- Department of Pharmacy, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John K Choi
- Division of Anatomic Pathology and Neuropathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Diana Morlote
- Division of Anatomic Pathology and Neuropathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishnu B Reddy
- Division of Anatomic Pathology and Neuropathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pankit Vachhani
- Div of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Stackhouse CT, Anderson JC, Yue Z, Nguyen T, Eustace NJ, Langford CP, Wang J, Rowland JR, Xing C, Mikhail FM, Cui X, Alrefai H, Bash RE, Lee KJ, Yang ES, Hjelmeland AB, Miller CR, Chen JY, Gillespie GY, Willey CD. An in vivo model of glioblastoma radiation resistance identifies long non-coding RNAs and targetable kinases. JCI Insight 2022; 7:148717. [PMID: 35852875 PMCID: PMC9462495 DOI: 10.1172/jci.insight.148717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/07/2022] [Indexed: 12/03/2022] Open
Abstract
Key molecular regulators of acquired radiation resistance in recurrent glioblastoma (GBM) are largely unknown, with a dearth of accurate preclinical models. To address this, we generated 8 GBM patient-derived xenograft (PDX) models of acquired radiation therapy–selected (RTS) resistance compared with same-patient, treatment-naive (radiation-sensitive, unselected; RTU) PDXs. These likely unique models mimic the longitudinal evolution of patient recurrent tumors following serial radiation therapy. Indeed, while whole-exome sequencing showed retention of major genomic alterations in the RTS lines, we did detect a chromosome 12q14 amplification that was associated with clinical GBM recurrence in 2 RTS models. A potentially novel bioinformatics pipeline was applied to analyze phenotypic, transcriptomic, and kinomic alterations, which identified long noncoding RNAs (lncRNAs) and targetable, PDX-specific kinases. We observed differential transcriptional enrichment of DNA damage repair pathways in our RTS models, which correlated with several lncRNAs. Global kinomic profiling separated RTU and RTS models, but pairwise analyses indicated that there are multiple molecular routes to acquired radiation resistance. RTS model–specific kinases were identified and targeted with clinically relevant small molecule inhibitors. This cohort of in vivo RTS patient-derived models will enable future preclinical therapeutic testing to help overcome the treatment resistance seen in patients with GBM.
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Affiliation(s)
| | | | - Zongliang Yue
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | - Thanh Nguyen
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | | | | | - Jelai Wang
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | - James R. Rowland
- Department of Physics, The Ohio State University, Columbus, Ohio, USA
| | | | - Fady M. Mikhail
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Xiangqin Cui
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | | | - Ryan E. Bash
- Division of Neuropathology, Department of Pathology, and
| | | | | | - Anita B. Hjelmeland
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - C. Ryan Miller
- Division of Neuropathology, Department of Pathology, and
| | - Jake Y. Chen
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
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Li G, Holly T, Kelly DR, Reddy V, Mikhail FM, Carroll AJ, Kutny MA. Therapy-related Myeloid Neoplasms in Children: A Single-institute Study. J Pediatr Hematol Oncol 2022; 44:e109-e113. [PMID: 33625084 DOI: 10.1097/mph.0000000000002097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/10/2021] [Indexed: 11/26/2022]
Abstract
Therapy-related myeloid neoplasm (t-MN) in the pediatric population is not well characterized. We studied 12 pediatric patients diagnosed with t-MN in our institution since 2006. The median age at the t-MN diagnoses was 14.8 years (range, 9 to 20 y). The primary malignancies included 9 solid tumors and 3 hematopoietic malignancies. Rhabdomyosarcoma (n=4) was the most common primary malignancy. Five of the 9 patients with solid tumors and all 3 patients with hematopoietic malignancies had primary neoplasms involving bone marrow. The median latency period was 5.2 years (range, 1.8 to 13.8 y). Thrombocytopenia was present in all patients at the t-MN diagnoses. Complete or partial monosomy of chromosome 5 or 7 were the 2 most common cytogenetic abnormalities. A quarter of patients demonstrated a genetic predisposition to t-MN: 1 with Li-Fraumeni syndrome with a germline TP53 R248Q mutation, 1 with Noonan syndrome with a somatic mutation (PTPN11 S502T), and 1 with a constitutive chromosomal translocation [t(X;9)(p22;q34)] and a germline TP53 L130V mutation. Outcomes remain poor. Two patients survived 3 and 5.1 years after hematopoietic stem cell transplantation.
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Affiliation(s)
- Geling Li
- Department of Pathology and Laboratory Medicine, Children's of Alabama
- Departments of Pathology
| | - Taylor Holly
- Department of Pediatrics, Division of Hematology and Oncology
| | - David R Kelly
- Department of Pathology and Laboratory Medicine, Children's of Alabama
- Departments of Pathology
| | | | - Fady M Mikhail
- Genetics, University of Alabama at Birmingham, Birmingham, AL
| | | | - Matthew A Kutny
- Department of Pediatrics, Division of Hematology and Oncology
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Abstract
Studies on mice have shown that the Smad Ubiquitin Regulatory Factor-1 (SMURF1) gene negatively regulates osteoblast function and the response to bone morphogenetic protein in a dose-dependent fashion (Chan et al. in Mol Cell Biol 27(16):5776-5789, https://doi.org/10.1128/MCB.00218-07, 2007; Yamashita et al. in Cell 121(1):101-113, https://doi.org/10.1016/j.cell.2005.01.035, 2005). In addition, a tumorigenic role for SMURF1 has been implicated due to the interference with apoptosis signals (Nie et al. in J Biol Chem 285(30):22818-22830, https://doi.org/10.1074/jbc.M110.126920, 2010; Wang et al. in Nat Commun 5:4901, https://doi.org/10.1038/ncomms5901, 2014). A 10-year-old girl with a history of severe developmental delay, infantile seizures, and B-cell lymphoma, in remission for approximately 3.5 years, was referred to the metabolic bone clinic for fractures and low bone mineral density. Array comparative genomic hybridization revealed a pathogenic microduplication in chromosome 7 at bands 7q21.3q22.1 that encompasses the SMURF1 gene. The clinical features of this child are congruous with the phenotype as ascribed excess Smurf1 mutations in mice. This is the first case description of osteoporosis in a child secondary to a microduplication involving SMURF1 gene.
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Affiliation(s)
- Rawan Al-Rawi
- Department of Pediatrics, University of Alabama at Birmingham, 1601 4th Avenue South, 1600 7th AVE S, Birmingham, AL, 35233-1711, USA.
| | - Ali Al-Beshri
- Department of Internal Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth McCormick
- Department of Pediatrics, University of Alabama at Birmingham, 1601 4th Avenue South, 1600 7th AVE S, Birmingham, AL, 35233-1711, USA
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Shah G, Mikhail FM, Bachiasvili K, Vachhani P, Erba HP, Papadantonakis N. Outcomes of high-risk acute promyelocytic leukemia patients treated with arsenic trioxide (ATO)/all trans retinoic acid (ATRA) based induction and consolidation without maintenance phase: A case Series. Hematol Oncol Stem Cell Ther 2019; 13:143-146. [PMID: 31629725 DOI: 10.1016/j.hemonc.2019.08.006] [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: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 10/25/2022] Open
Abstract
Patients with high-risk acute promyelocytic leukemia (APL) have inferior outcomes compared with patients with low-risk APL, predominantly due to higher risk of early mortality related to hemorrhage. The majority of regimens contain prolonged maintenance, but the impact of this phase is not clear in the era of all trans retinoic acid (ATRA) and arsenic trioxide (ATO). We present a retrospective analysis of 10 patients that were treated for high risk APL based on the consolidation treatment phase of APL 0406 study without subsequent maintenance. With a median follow up of 38 months, all patients remain in remission.
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Affiliation(s)
- Gaurav Shah
- Department of Internal Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham,AL, USA
| | - Kimo Bachiasvili
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pankit Vachhani
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harry P Erba
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Nikolaos Papadantonakis
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Bernstock JD, Totten AH, Elkahloun AG, Johnson KR, Hurst AC, Goldman F, Groves AK, Mikhail FM, Atkinson TP. Recurrent microdeletions at chromosome 2p11.2 are associated with thymic hypoplasia and features resembling DiGeorge syndrome. J Allergy Clin Immunol 2019; 145:358-367.e2. [PMID: 31600545 DOI: 10.1016/j.jaci.2019.09.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 08/22/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Thymic hypoplasia/aplasia occurs as a part of DiGeorge syndrome, which has several known genetic causes, and with loss-of-function mutations in forkhead box N1 (FOXN1). OBJECTIVE We sought to determine the cause of selective T-cell lymphopenia with inverted kappa/lambda ratio in several kindreds. METHODS Patients were identified through newborn screening for severe combined immunodeficiency using the T-cell receptor excision circle assay. Those found to have selective T-cell lymphopenia underwent testing with chromosomal microarray analysis. Three-week-old mice heterozygous for a loss-of-function mutation in forkhead box I3 (FOXI3), a candidate gene within the common deleted region found in patients, were compared with wild-type littermates. Assessments included body and organ weights, flow cytometric analysis of thymocytes and splenocytes, and histologic/transcriptomic analyses of thymic tissue. RESULTS Five kindreds with similar immunophenotypes that included selective T-cell lymphopenia had overlapping microdeletions at chromosome 2p11.2 that spanned FOXI3 and, in most cases, the immunoglobulin kappa light chain locus. Studies in a mouse knockout strain for FOXI3 revealed smaller body weights and relatively lower thymus weights in heterozygous compared with wild-type animals. Histology and flow cytometry on spleens and thymi from 3-week-old pups for T- and B-cell subsets and epithelial cells did not show any significant qualitative or quantitative differences. Transcriptomic analysis of thymic RNA revealed divergence in global transcriptomic signatures, and Ingenuity Pathway Analysis revealed predicted dysfunction in epithelial adherens junctions. CONCLUSIONS Microdeletions at chromosome 2p11.2 are associated with T-cell lymphopenia and probable thymic hypoplasia in human subjects, and haploinsufficiency for FOXI3, a candidate gene within the deleted region, is the likely underlying cause.
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Affiliation(s)
- Joshua D Bernstock
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Arthur H Totten
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Abdel G Elkahloun
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Md
| | - Kory R Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Md
| | - Anna C Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Ala
| | - Frederick Goldman
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala
| | - Andrew K Groves
- Department of Neuroscience and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Ala
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Ala.
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11
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Carroll AJ, Shago M, Mikhail FM, Raimondi SC, Hirsch BA, Loh ML, Raetz EA, Borowitz MJ, Wood BL, Maloney KW, Mattano LA, Larsen EC, Gastier-Foster J, Stonerock E, Ell D, Kahwash S, Devidas M, Harvey RC, Chen IML, Willman CL, Hunger SP, Winick NJ, Carroll WL, Rao KW, Heerema NA. Masked hypodiploidy: Hypodiploid acute lymphoblastic leukemia (ALL) mimicking hyperdiploid ALL in children: A report from the Children's Oncology Group. Cancer Genet 2019; 238:62-68. [PMID: 31425927 DOI: 10.1016/j.cancergen.2019.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 03/26/2019] [Revised: 06/28/2019] [Accepted: 07/27/2019] [Indexed: 10/26/2022]
Abstract
Hyperdiploidy with greater than 50 chromosomes is usually associated with favorable prognosis in pediatric acute lymphoblastic leukemia (ALL), whereas hypodiploidy with ≤43 chromosomes is associated with extremely poor prognosis. Sometimes, hypodiploidy is "masked" and patients do not have a karyotypically visible clone with ≤43 chromosomes. Instead, their abnormal karyotypes contain 50-78 or more chromosomes from doubling of previously hypodiploid cells. When the hypodiploid and doubled hyperdiploid clones are both present, patients can be identified by traditional test methods [karyotype, DNA Index (DI), fluorescence in situ hybridization (FISH)], but the incidence of masked hypodiploid cases in which only the doubled clone is visible is unknown. We analyzed 7013 patients with B-ALL enrolled in COG AALL03B1 (2003-2011) for whom chromosome studies were available. Of 115 patients with hypodiploidy (25-39 chromosomes), karyotypes of 40 showed only the hypodiploid clone, 47 showed mosaicism with both hypodiploid and hyperdiploid (doubled) karyotypes, and 28 with masked hypodiploidy showed only a hyperdiploid (doubled) clone. Unique karyotypic signatures were identified, and widespread loss of heterozygosity (LOH) was seen in the microsatellite panel for all patients with masked hypodiploidy. An increased awareness of the unusual karyotypic profile associated with a doubled hypodiploid clone and coordinated use of DI, FISH, and LOH studies when indicated can identify patients with masked hypodiploidy and allow appropriate treatment selection.
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Affiliation(s)
- Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Mary Shago
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Susana C Raimondi
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Betsy A Hirsch
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mignon L Loh
- Department of Pediatrics, UCSF Medical Center-Mission Bay, San Francisco, CA, USA
| | - Elizabeth A Raetz
- Department of Pediatrics, New York University Medical Center, New York, NY, USA
| | - Michael J Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Brent L Wood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Eric C Larsen
- Maine Children's Cancer Program, Scarborough, ME, USA
| | - Julie Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Eileen Stonerock
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Denise Ell
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Samir Kahwash
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Meenakshi Devidas
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | | | - I-Ming L Chen
- University of New Mexico Cancer Center, Albuquerque, NM, USA
| | | | - Stephen P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naomi J Winick
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William L Carroll
- Department of Pediatrics, New York University Medical Center, New York, NY, USA
| | - Kathleen W Rao
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, OH, USA
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12
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Woodfin T, Stoops C, Philips JB, Lose E, Mikhail FM, Hurst A. Menkes disease complicated by concurrent Koolen-de Vries syndrome (17q21.31 deletion). Mol Genet Genomic Med 2019; 7:e829. [PMID: 31250568 PMCID: PMC6687649 DOI: 10.1002/mgg3.829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/06/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 02/02/2023] Open
Abstract
Background Koolen‐de Vries (KdV) syndrome is caused by a 17q21.31 deletion leading to clinical symptoms of hypotonia and developmental delay and can present with abnormal hair texture. Menkes disease is an X‐linked recessive inherited disease caused by pathogenic variants in ATP7A, which leads to profound copper deficiency. Method We identified an infant male who presented with prematurity, hypotonia, and dysmorphic features for whom a family history of clinical Menkes disease was revealed after discussion with the clinical genetics team. Results Although initial first‐tier genetic testing identified Kdv syndrome (17q21.31 syndrome), the family history led the team to consider a second diagnostic possibility, and testing of ATP7A revealed a pathogenic variant (c.601C>T, p.R201X). Conclusion Menkes disease and KdV syndrome may both present with hypotonia and abnormal hair, in addition to seizures and failure to thrive. While these genetic conditions have overlapping clinical features, they have different natural histories and different therapeutic options. Here, we report on a patient affected with both disorders and review the diagnostic and therapeutic difficulties this presented.
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Affiliation(s)
- Taylor Woodfin
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Christine Stoops
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Joseph B Philips
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Edward Lose
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anna Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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13
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Upadia J, Gonzales PR, Atkinson TP, Schroeder HW, Robin NH, Rudy NL, Mikhail FM. A previously unrecognized 22q13.2 microdeletion syndrome that encompasses TCF20 and TNFRSF13C. Am J Med Genet A 2018; 176:2791-2797. [PMID: 30216695 DOI: 10.1002/ajmg.a.40492] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/01/2018] [Accepted: 07/03/2018] [Indexed: 12/23/2022]
Abstract
Phelan-McDermid syndrome (PMS, OMIM 606232) is a heterozygous contiguous gene microdeletion syndrome occurring at the distal region of chromosome 22q13. This deletion encompasses the SHANK3 gene at 22q13.33, which is thought to be the critical gene for the neurodevelopmental features seen in this syndrome. PMS is typically characterized by intellectual disability, autism spectrum disorder, absent to severely delayed speech, neonatal hypotonia, and dysmorphic features. Two patients presenting with classic clinical features of PMS have been reported to have interstitial microdeletions in the 22q13.2 region that map proximal to the SHANK3 gene (0.54 and 0.72 Mb, respectively). Here, we describe a 13-month-old girl with a de novo 1.16 Mb interstitial deletion in the 22q13.2 region who presented with global developmental delay, subtle dysmorphic features, and immunodeficiency. This deletion overlaps with the two previously published cases and five cases from the DECIPHER database. All eight patients share features common to patients with PMS including developmental delay and language delay, which suggests that this represents a previously unrecognized microdeletion syndrome in the 22q13.2 region. Our patient's deletion encompasses the TCF20 and TNFRSF13C genes, which are thought to play causative roles in the patient's neurodevelopmental and immunological features, respectively.
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Affiliation(s)
- Jariya Upadia
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Patrick R Gonzales
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Harry W Schroeder
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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14
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Upadia J, Philips JB, Robin NH, Lose EJ, Mikhail FM. A case report of chromosome 17q22-qter trisomy with distinct clinical presentation and review of the literature. Clin Case Rep 2018; 6:612-616. [PMID: 29636925 PMCID: PMC5889218 DOI: 10.1002/ccr3.1298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 07/18/2017] [Revised: 10/04/2017] [Accepted: 10/18/2017] [Indexed: 11/14/2022] Open
Abstract
Terminal 17q trisomy is very rare but a recognizable genetic syndrome. The majority of cases reported are inherited from a balanced translocation carrier. This syndrome involves many organs and the severity ranges from mild to severe depending on the size of the 17q gain.
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Affiliation(s)
- Jariya Upadia
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama USA
| | - Joseph B Philips
- Department of Pediatrics University of Alabama at Birmingham Birmingham Alabama USA
| | - Nathaniel H Robin
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama USA
| | - Edward J Lose
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama USA
| | - Fady M Mikhail
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama USA
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15
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Ullman D, Baumgartner E, Wnukowski N, Koenig G, Mikhail FM, Pavlidakey P, Peker D. Therapy-associated myelodysplastic syndrome with monosomy 7 arising in a Muir-Torre Syndrome patient carrying SETBP1 mutation. Mol Clin Oncol 2018; 8:306-309. [PMID: 29435294 DOI: 10.3892/mco.2017.1532] [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: 09/13/2017] [Accepted: 11/30/2017] [Indexed: 11/06/2022] Open
Abstract
Muir-Torre Syndrome (MTS) is a rare hereditary autosomal dominant cancer syndrome and is linked to hereditary non-polyposis colorectal carcinoma (Lynch Syndrome). Individuals develop various skin neoplasms in addition to colorectal, endometrial and upper gastrointestinal malignancies. Therapy-associated myelodysplastic syndrome (T-MDS) is an aggressive hematologic malignancy and is considered a pre-leukemic phase. T-MDS is associated with prior exposure to chemo- and radiotherapy that potentially results in DNA damage. The current case report presents a 74-year-old male MTS patient with prior history of solid tumors and radiation therapy with new onset cytopenia. A subsequent bone marrow biopsy revealed multilineage dysplasia with a high blast count and a diagnosis of high grade T-MDS was rendered. FISH and G-banded karyotype analyses revealed 5q deletion and monosomy 7. This is a unique case of T-MDS arising in the setting of MTS. Secondary malignancies including MDS and acute leukemia may occur in cancer survivors and are often associated with an unfavorable prognosis. This case demonstrates the need to be aware of the risk of secondary hematologic malignancies in cancer patients and a thorough clinical and lab work-up are warranted in patients with persistent or transfusion requiring cytopenia(s).
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Affiliation(s)
- David Ullman
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Erin Baumgartner
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Nicholas Wnukowski
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Gabe Koenig
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Peter Pavlidakey
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Deniz Peker
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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16
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Stevens TM, Qarmali M, Morlote D, Mikhail FM, Swensen J, Gatalica Z, Siegal GP, Conry RM. Malignant Ewing-Like Neoplasm With an EWSR1-KLF15 Fusion: At the Crossroads of a Myoepithelial Carcinoma and a Ewing-Like Sarcoma. A Case Report With Treatment Options. Int J Surg Pathol 2018; 26:440-447. [PMID: 29390927 DOI: 10.1177/1066896918755009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present a case of a malignant Ewing-like neoplasm of the parotid gland in a 20-year-old woman with an EWSR1-KLF15 gene fusion that presented with pulmonary metastasis. Despite the fact that the tumor was essentially immunohistochemically negative for keratins, p63, and p40, we interpret this neoplasm as an unusual form of a high-grade myoepithelial carcinoma based on its focal plasmacytoid cytology, chondromyxoid matrix, SOX10, S100 protein, and calponin expression, and the knowledge that the EWSR1-KLF15 gene fusion has, to date, only been identified in 2 tumors, both myoepithelial carcinomas of the kidney. We also present a cytogenetic analysis of this unusual tumor. This "Ewing-like myoepithelial carcinoma" initially did not respond to 2 cycles of ifosfamide and etoposide alternated with a cycle of cytoxan, adriamycin, and vincristine, a standard regimen for Ewing sarcoma. Subsequent oral pazopanib therapy did result in a reduction of the patient's pulmonary and nodal disease.
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17
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Rojnueangnit K, Mikhail FM, Cui X, Yu S, Robin NH. Predictor(s) of Abnormal Array Comparative Genomic Hybridization Results in Patients with Cleft Lip and/or Palate. Cleft Palate Craniofac J 2018; 52:724-31. [DOI: 10.1597/14-088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] Open
Abstract
Objectives Cleft lip and/or cleft palate (CL/P) occurs either as an isolated anomaly or as one manifestation of genetic syndromes. Chromosomal abnormalities from karyotype analysis are commonly seen in cases of nonisolated CL/P. This study was designed to evaluate the usefulness of clinical array comparative genomic hybridization (aCGH) testing in patients with CL/P. Our objectives were to identify the clinical phenotypes that are predicative of an abnormal aCGH result, correlate aCGH results with language outcome, and analyze the data in the abnormal aCGH results group. Methods Nonisolated CL/P patients who had clinical aCGH testing performed between 2009 and 2012 in the University of Alabama at Birmingham cytogenetics lab were enrolled. The demographic data, clinical phenotypes, and speech outcome were collected. Results Two hundred forty-five nonisolated CL/P patients were studied, with 62 having an abnormal aCGH result compared to 183 patients with a normal aCGH result. The presence of developmental delay/intellectual disability (DD/ID), dysmorphic features, congenital anomalies, and/or family history of DD/ID were significantly higher in the abnormal aCGH group ( P < .05). Neither the aCGH results nor the type of CL/P correlated with speech outcome. Finally, analysis of the abnormal aCGH result group revealed that DD/ID had a strong positive association with the copy number variation pathogenicity and the number of genes involved. Conclusions This study demonstrated the diagnostic value of clinical aCGH testing in CL/P patients who present with DD/ID, dysmorphic features, other congenital anomalies, and/or family history of DD/ID.
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Affiliation(s)
- Kitiwan Rojnueangnit
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Fady M. Mikhail
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiangqin Cui
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shaohua Yu
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H. Robin
- Department of Genetics; Department of Biostatistics; Department of Biostatistics; Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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18
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Akkari Y, Baughn L, Hagelstrom RT, Hiemenz M, Mikhail FM, Shao L, Hirsch B. Practice Guidelines for Genetic/Genomic Testing in Pediatric B-Lineage Acute Lymphoblastic Leukemia (B-ALL): A Cancer Genomics Consortium (CGC) Workgroup. Cancer Genet 2017. [DOI: 10.1016/j.cancergen.2017.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Shea LK, Mikhail FM, Forero-Torres A, Davis RS. Concomitant imatinib and ibrutinib in a patient with chronic myelogenous leukemia and chronic lymphocytic leukemia. Clin Case Rep 2017; 5:899-901. [PMID: 28588835 PMCID: PMC5458012 DOI: 10.1002/ccr3.974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 09/29/2016] [Revised: 03/10/2017] [Accepted: 03/23/2017] [Indexed: 11/07/2022] Open
Abstract
The availability of kinase and other small‐molecule inhibitors to treat hematologic malignancies is increasing. Accordingly, novel regimens that employ these therapeutics are rapidly evolving. Herein we report the safe and effective administration of two targeted kinase inhibitors in a patient with concomitant chronic myelogenous leukemia and chronic lymphocytic leukemia.
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Affiliation(s)
- Lauren K Shea
- Department of Medicine University of Alabama at Birmingham Birmingham Alabama
| | - Fady M Mikhail
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama
| | - Andres Forero-Torres
- Department of Medicine University of Alabama at Birmingham Birmingham Alabama.,Comprehensive Cancer Center University of Alabama at Birmingham Birmingham Alabama
| | - Randall S Davis
- Department of Medicine University of Alabama at Birmingham Birmingham Alabama.,Comprehensive Cancer Center University of Alabama at Birmingham Birmingham Alabama.,Department of Microbiology University of Alabama at Birmingham Birmingham Alabama.,Department of Biochemistry and Molecular Genetics University of Alabama at Birmingham Birmingham Alabama
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20
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Affiliation(s)
- Bruce R. Korf
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama
| | - Fady M. Mikhail
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama
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21
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Rosenblum F, Koenig RG, Mikhail FM, Porterfield JR, Nix JW, Eltoum IEA. An adolescent with large cell calcifying sertoli cell tumor of the testis and undiagnosed Carney Complex: A case report. Diagn Cytopathol 2017; 45:634-639. [PMID: 28276158 DOI: 10.1002/dc.23700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 07/05/2016] [Revised: 12/09/2016] [Accepted: 02/16/2017] [Indexed: 11/09/2022]
Abstract
Carney Complex (CNC) is a rare autosomal dominant condition with characteristic clinical presentation, tumor development, and unique genetic mutation. We present a unique case and literature review of CNC in which two neoplasms characteristic of this complex were initially diagnosed through cytological fine needle aspirate specimens, leading to the identification of CNC, with subsequent surgical and cytogenetic confirmation. Diagn. Cytopathol. 2017;45:634-639. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Frida Rosenblum
- Department of Pathology, University of Alabama, Birmingham, Alabama, 35294
| | | | - Fady M Mikhail
- Department of Pathology, University of Alabama, Birmingham, Alabama, 35294
| | - John R Porterfield
- Department of Pathology, University of Alabama, Birmingham, Alabama, 35294
| | - Jeffrey W Nix
- Department of Pathology, University of Alabama, Birmingham, Alabama, 35294
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22
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Hollenbeck D, Williams CL, Drazba K, Descartes M, Korf BR, Rutledge SL, Lose EJ, Robin NH, Carroll AJ, Mikhail FM. Clinical relevance of small copy-number variants in chromosomal microarray clinical testing. Genet Med 2016; 19:377-385. [PMID: 27632688 DOI: 10.1038/gim.2016.132] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/21/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (<500 kb) has not been well established in a clinical setting. METHODS We investigated the clinical significance of all nonpolymorphic small, nonrecurrent CNVs (<500 kb) in patients referred for CMA clinical testing over a period of 6 years, from 2009 to 2014 (a total of 4,417 patients). We excluded from our study patients with benign or likely benign CNVs and patients with only recurrent microdeletions/microduplications <500 kb. RESULTS In total, 383 patients (8.67%) were found to carry at least one small, nonrecurrent CNV, of whom 176 patients (3.98%) had one small CNV classified as a variant of uncertain significance (VUS), 45 (1.02%) had two or more small VUS CNVs, 20 (0.45%) had one small VUS CNV and a recurrent CNV, 113 (2.56%) had one small pathogenic or likely pathogenic CNV, 17 (0.38%) had two or more small pathogenic or likely pathogenic CNVs, and 12 (0.27%) had one small pathogenic or likely pathogenic CNV and a recurrent CNV. Within the pathogenic group, 80 of 142 patients (56% of all small pathogenic CNV cases) were found to have a single whole-gene or exonic deletion. The themes that emerged from our study are presented in the Discussion section. CONCLUSIONS Our study demonstrates the diagnostic clinical relevance of small, nonrecurrent CNVs <500 kb during CMA clinical testing and underscores the need for careful clinical interpretation of these CNVs.Genet Med 19 4, 377-385.
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Affiliation(s)
- Dana Hollenbeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Crescenda L Williams
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Current address: Children's Health Hospital, Dallas, Texas, USA
| | - Kathryn Drazba
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Edward J Lose
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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23
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Mikhail FM, Heerema NA, Rao KW, Burnside RD, Cherry AM, Cooley LD. Section E6.1-6.4 of the ACMG technical standards and guidelines: chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. Genet Med 2016; 18:635-42. [PMID: 27124785 DOI: 10.1038/gim.2016.50] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 12/30/2022] Open
Abstract
DISCLAIMER These American College of Medical Genetics and Genomics standards and guidelines are developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these standards and guidelines. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Cytogenetic analyses of hematological neoplasms are performed to detect and characterize clonal chromosomal abnormalities that have important diagnostic, prognostic, and therapeutic implications. At the time of diagnosis, cytogenetic abnormalities assist in the diagnosis of such disorders and can provide important prognostic information. At the time of relapse, cytogenetic analysis can be used to confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the standards and guidelines applicable to chromosome studies of neoplastic blood and bone marrow-acquired chromosomal abnormalities. This updated Section E6.1-6.4 has been incorporated into and supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the 2009 Edition (Revised 01/2010), American College of Medical Genetics and Genomics Standards and Guidelines for Clinical Genetics Laboratories.Genet Med 18 6, 635-642.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen W Rao
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Pathology, University of North Carolina, Chapel Hill, North Carolina, USA.,Deceased
| | - Rachel D Burnside
- Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, North Carolina, USA
| | - Athena M Cherry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri Kansas City Medical School, Kansas City, Missouri, USA
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VanValkenburg ME, Pruitt GI, Brill IK, Costa L, Ehtsham M, Justement IT, Innis-Shelton RD, Salzman D, Reddy ESP, Godby KN, Mikhail FM, Carroll AJ, Reddy VB, Sanderson RD, Justement LB, Sanders PW, Brown EE. Family history of hematologic malignancies and risk of multiple myeloma: differences by race and clinical features. Cancer Causes Control 2015; 27:81-91. [PMID: 26596855 PMCID: PMC4703620 DOI: 10.1007/s10552-015-0685-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/16/2015] [Indexed: 11/30/2022]
Abstract
Purpose Multiple myeloma (MM) is the most common hematologic malignancy affecting Blacks in the USA, with standardized incidence rates that are twofold to threefold higher than Whites. The rationale for the disparity is unclear. Methods Using participants enrolled in the Molecular And Genetic Epidemiology study of myeloma (259 MM cases; 461 controls), we examined the risk of MM associated with family history of cancer, differences by race and among cases, defining clinical features. Risk estimates were calculated using odds ratios and corresponding 95% confidence intervals from logistic regression adjusted for confounders. Results Overall, MM risk in cases with relatives affected with any hematologic malignancy was significantly elevated compared to controls (OR 1.89, 95% CI 1.25–2.86). Myeloma risk associated with a family history of MM was higher than the risk associated with any hematologic malignancy (OR 3.75, 95% CI 1.75–8.05), and the effect was greater for Blacks (OR 20.9, 95% CI 2.59–168) than Whites (OR 2.04, 95% 0.83–5.04), among cases with early onset (≤60 years; OR 4.58, 95% CI 1.21–17.3) and with increasing numbers of affected relatives (p trend = 0.001). Overall, frequencies of end organ damage differed in cases with relatives affected with any hematologic malignancy and significantly more cases exhibited κ light chain restriction (OR 3.23, 95% CI 1.13–9.26). Conclusions The excess risk of MM observed in Blacks and the variation in clinical features observed in MM patients according to family history of hematologic malignancy may be attributed to a shared germline and environmental susceptibility. Electronic supplementary material The online version of this article (doi:10.1007/s10552-015-0685-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- MaryAnn E VanValkenburg
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294-3300, USA
| | - Gwendolyn I Pruitt
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ilene K Brill
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Luciano Costa
- Division of Hematology and Medical Oncology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Maryam Ehtsham
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA.,School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ian T Justement
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA.,School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Racquel D Innis-Shelton
- Division of Hematology and Medical Oncology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donna Salzman
- Division of Hematology and Medical Oncology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E Shyam P Reddy
- Cancer Biology Program, Department of Obstetrics and Gynecology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Kelly N Godby
- Division of Hematology and Medical Oncology, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fady M Mikhail
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew J Carroll
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishnu B Reddy
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294-3300, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ralph D Sanderson
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294-3300, USA.,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Louis B Justement
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul W Sanders
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Division of Nephrology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Veterans Affairs Medical Center, Birmingham, AL, USA
| | - Elizabeth E Brown
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294-3300, USA. .,UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA. .,, 1824 6th Avenue South, WTI 602C, Birmingham, AL, 35294-3300, USA.
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Williams CL, Nelson KR, Grant JH, Mikhail FM, Robin NH. Cleft palate in a patient with the nested 22q11.2 LCR C to D deletion. Am J Med Genet A 2015; 170A:260-2. [PMID: 26419407 DOI: 10.1002/ajmg.a.37408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Crescenda L Williams
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katherine R Nelson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - John H Grant
- Division of Plastic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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26
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Hamm JA, Carroll AJ, Mikhail FM, Korf BR, Finley WH. Partial trisomy 21: A fifty-year follow-up visit. Am J Med Genet A 2015; 167:1610-3. [DOI: 10.1002/ajmg.a.37031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/08/2015] [Indexed: 11/06/2022]
Affiliation(s)
- J. Austin Hamm
- Department of Genetics at the University of Alabama at Birmingham; Birmingham Alabama
| | - Andrew J. Carroll
- Department of Genetics at the University of Alabama at Birmingham; Birmingham Alabama
| | - Fady M. Mikhail
- Department of Genetics at the University of Alabama at Birmingham; Birmingham Alabama
| | - Bruce R. Korf
- Department of Genetics at the University of Alabama at Birmingham; Birmingham Alabama
| | - Wayne H. Finley
- Department of Genetics at the University of Alabama at Birmingham; Birmingham Alabama
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27
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Rodriguez-Buritica D, Rojnueangnit K, Messiaen LM, Mikhail FM, Robin NH. Sex-discordant monochorionic twins with blood and tissue chimerism. Am J Med Genet A 2015; 167A:872-7. [DOI: 10.1002/ajmg.a.37022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/02/2015] [Indexed: 11/10/2022]
Affiliation(s)
- David Rodriguez-Buritica
- Division of Genetics, Department of Pediatrics; School of Medicine University of Texas at Houston; Houston Texas
- Department of Genetics; University of Alabama at Birmingham; Birmingham Alabama
| | - Kitiwan Rojnueangnit
- Department of Pediatrics, Faculty of Medicine; Thammasat University; Bangkok Thailand
- Department of Genetics; University of Alabama at Birmingham; Birmingham Alabama
| | - Ludwine M. Messiaen
- Department of Genetics; University of Alabama at Birmingham; Birmingham Alabama
| | - Fady M. Mikhail
- Department of Genetics; University of Alabama at Birmingham; Birmingham Alabama
| | - Nathaniel H. Robin
- Department of Genetics; University of Alabama at Birmingham; Birmingham Alabama
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28
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Hamm JA, Mikhail FM, Hollenbeck D, Farmer M, Robin NH. Incidental detection of cancer predisposition gene copy number variations by array comparative genomic hybridization. J Pediatr 2014; 165:1057-9.e1-4. [PMID: 25201531 DOI: 10.1016/j.jpeds.2014.07.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 04/08/2014] [Revised: 06/20/2014] [Accepted: 07/23/2014] [Indexed: 02/06/2023]
Abstract
We describe 2 pediatric patients who presented to medical genetics clinic for evaluation and were incidentally found via array comparative genomic hybridization to have pathogenic copy number variations of cancer predisposition genes. We subsequently reviewed 3554 previous array comparative genomic hybridization results to estimate the frequency of similar incidental findings.
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Affiliation(s)
- J Austin Hamm
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Dana Hollenbeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Meagan Farmer
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL; Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL; Department of Otolarnygology, University of Alabama at Birmingham, Birmingham, AL.
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29
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Abstract
The goal of any clinical laboratory should be to provide patients with the most accurate test results possible. This is accomplished through various overlapping programs that continuously monitor and optimize all aspects of a test, including decisions by the laboratory to offer a test, the decision of providers to request the test, the testing itself, and the reporting of results to the referral source and patient. The levels at which test performance and accuracy can be optimized are encompassed under quality control (QC) and quality assurance (QA). The monitoring of QC and QA problems allows for the integration of these parameters into a total quality management program. This unit reviews QC and QA guidelines, in addition to discussing how to establish a quality assurance program.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michael S Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
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30
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Hsiao MC, Piotrowski A, Alexander J, Callens T, Fu C, Mikhail FM, Claes KBM, Messiaen L. Palindrome-mediated and replication-dependent pathogenic structural rearrangements within the NF1 gene. Hum Mutat 2014; 35:891-8. [PMID: 24760680 DOI: 10.1002/humu.22569] [Citation(s) in RCA: 10] [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: 01/24/2014] [Accepted: 04/17/2014] [Indexed: 11/09/2022]
Abstract
Palindromic sequences can form hairpin structures or cruciform extrusions, which render them susceptible to genomic rearrangements. A 197-bp long palindromic AT-rich repeat (PATRR17) is located within intron 40 of the neurofibromatosis type 1 (NF1) gene (17q11.2). Through comprehensive NF1 analysis, we identified six unrelated patients with a rearrangement involving intron 40 (five deletions and one reciprocal translocation t(14;17)(q32;q11.2)). We hypothesized that PATRR17 may be involved in these rearrangements thereby causing NF1. Breakpoint cloning revealed that PATRR17 was indeed involved in all of the rearrangements. As microhomology was present at all breakpoint junctions of the deletions identified, and PATRR17 partner breakpoints were located within 7.1 kb upstream of PATRR17, fork stalling and template switching/microhomology-mediated break-induced replication was the most likely rearrangement mechanism. For the reciprocal translocation case, a 51 bp insertion at the translocation breakpoints mapped to a short sequence within PATRR17, proximal to the breakpoint, suggesting a multiple stalling and rereplication process, in contrast to previous studies indicating a purely replication-independent mechanism for PATRR-mediated translocations. In conclusion, we show evidence that PATRR17 is a hotspot for pathogenic intragenic deletions within the NF1 gene and suggest a novel replication-dependent mechanism for PATRR-mediated translocation.
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Affiliation(s)
- Meng-Chang Hsiao
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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31
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Mikhail FM, Burnside RD, Rush B, Ibrahim J, Godshalk R, Rutledge SL, Robin NH, Descartes MD, Carroll AJ. The recurrent distal 22q11.2 microdeletions are often de novo and do not represent a single clinical entity: a proposed categorization system. Genet Med 2013; 16:92-100. [PMID: 23765049 DOI: 10.1038/gim.2013.79] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/25/2013] [Indexed: 01/06/2023] Open
Abstract
PURPOSE The five segmental duplications (LCR22-D to -H) at the distal region of chromosome 22 band q11.2 in the region immediately distal to the DiGeorge/velocardiofacial syndrome deleted region have been implicated in the recurrent distal 22q11.2 microdeletions. To date, the distal 22q11.2 microdeletions have been grouped together as a single clinical entity despite the fact that these deletions are variable in size and position depending on the mediating LCR22s. METHODS Here, we report 13 new unrelated patients with variable size deletions in the distal 22q11.2 region as shown by cytogenomic array analyses. We compare our patients' clinical features with those of previously reported cases to better dissect the phenotypic correlations based on the deletion size and position. RESULTS Six patients had the 1.1-Mb deletion flanked by LCR22-D and -E, and presented clinically with a phenotype consistent with previously reported cases with distal 22q11.2 microdeletions. Three patients had the 1.8-Mb deletion flanked by LCR22-D and -F, and presented with a similar phenotype. Four patients had the 700-kb deletion flanked by LCR22-E and -F, and presented with a milder phenotype that lacked growth restriction and cardiovascular defects. CONCLUSION We suggest that the recurrent distal 22q11.2 microdeletions do not represent a single clinical entity, and propose categorizing these deletions into three types according to their genomic position. All three deletion types are thought to be pathogenic and are most often de novo. They all share some presenting features but also have their unique features and risks.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rachel D Burnside
- Laboratory Corporation of America, Research Triangle Park, North Carolina, USA
| | - Brooke Rush
- Laboratory Corporation of America, Research Triangle Park, North Carolina, USA
| | - Jennifer Ibrahim
- Department of Pediatrics, Division of Genetics, St. Joseph's Children's Hospital, Paterson, New Jersey, USA
| | - Robin Godshalk
- Department of Pediatrics, Division of Genetics, St. Joseph's Children's Hospital, Paterson, New Jersey, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Maria D Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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32
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Kazmi SJ, Byer SJ, Eckert JM, Turk AN, Huijbregts RP, Brossier NM, Grizzle WE, Mikhail FM, Roth KA, Carroll SL. Transgenic mice overexpressing neuregulin-1 model neurofibroma-malignant peripheral nerve sheath tumor progression and implicate specific chromosomal copy number variations in tumorigenesis. Am J Pathol 2013; 182:646-67. [PMID: 23321323 PMCID: PMC3586689 DOI: 10.1016/j.ajpath.2012.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/19/2012] [Accepted: 11/13/2012] [Indexed: 12/12/2022]
Abstract
Patients with neurofibromatosis type 1 (NF1) develop benign plexiform neurofibromas that frequently progress to become malignant peripheral nerve sheath tumors (MPNSTs). A genetically engineered mouse model that accurately models plexiform neurofibroma-MPNST progression in humans would facilitate identification of somatic mutations driving this process. We previously reported that transgenic mice overexpressing the growth factor neuregulin-1 in Schwann cells (P(0)-GGFβ3 mice) develop MPNSTs. To determine whether P(0)-GGFβ3 mice accurately model human neurofibroma-MPNST progression, cohorts of these animals were monitored through death and were necropsied; 94% developed multiple neurofibromas, with 70% carrying smaller numbers of MPNSTs. Nascent MPNSTs were identified within neurofibromas, suggesting that these sarcomas arise from neurofibromas. Although neurofibromin expression was maintained, P(0)-GGFβ3 MPNSTs exhibited Ras hyperactivation, as in human NF1-associated MPNSTs. P(0)-GGFβ3 MPNSTs also exhibited abnormalities in the p16(INK4A)-cyclin D/CDK4-Rb and p19(ARF)-Mdm-p53 pathways, analogous to their human counterparts. Array comparative genomic hybridization (CGH) demonstrated reproducible chromosomal alterations in P(0)-GGFβ3 MPNST cells (including universal chromosome 11 gains) and focal gains and losses affecting 39 neoplasia-associated genes (including Pten, Tpd52, Myc, Gli1, Xiap, and Bbc3/PUMA). Array comparative genomic hybridization also identified recurrent focal copy number variations affecting genes not previously linked to neurofibroma or MPNST pathogenesis. We conclude that P(0)-GGFβ3 mice represent a robust model of neurofibroma-MPNST progression useful for identifying novel genes driving neurofibroma and MPNST pathogenesis.
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Affiliation(s)
- Syed J. Kazmi
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Stephanie J. Byer
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Jenell M. Eckert
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Amy N. Turk
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Nicole M. Brossier
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell Biology, The University of Alabama at Birmingham, Birmingham, Alabama
- Medical Scientist Training Program, The University of Alabama at Birmingham, Birmingham, Alabama
| | - William E. Grizzle
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M. Mikhail
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Kevin A. Roth
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Steven L. Carroll
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell Biology, The University of Alabama at Birmingham, Birmingham, Alabama
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33
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Nunez AL, Jhala NC, Carroll AJ, Mikhail FM, Reddy VVB, Xian RR, Jhala DN. Endoscopic ultrasound and endobronchial ultrasound-guided fine-needle aspiration of deep-seated lymphadenopathy: Analysis of 1338 cases. Cytojournal 2012; 9:14. [PMID: 22615712 PMCID: PMC3352588 DOI: 10.4103/1742-6413.95845] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [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: 12/27/2011] [Accepted: 03/12/2012] [Indexed: 02/07/2023] Open
Abstract
Background: We retrospectively studied 1338 samples of lymph nodes obtained by endoscopic and endobronchial ultrasound-guided fine needle aspiration biopsy (EUS and EBUS-FNAB) with an objective of characterizing the utility of this diagnostic modality in the assessment of deep-seated lymphadenopathy. The secondary aims were to establish the utility in the diagnosis of lymphoma and to determine the number of passes required to obtain adequate cellularity for flow cytometric analysis. Materials and Methods: On-site assessment was performed by a cytopathologist using Diff-Quik (American Scientific Products, McGraw Park, IL) stain. In addition, Papanicolaou and immunohistochemical stains were performed and additional samples were sent for flow cytometric analyses (n = 145). The final cytologic diagnosis was correlated with surgical pathology diagnosis and/or clinical follow-up. In select cases, fluorescence in situ hybridization analysis with specific probes was performed on Diff-Quik smears. Results: Both morphology as well as ancillary studies (flow cytometry or immunohistochemical stain and/or fluorescence in situ hybridization) show that EUS and EBUS-FNA are effective techniques to detect and stage intrathoracic and intra-abdominal tumors. Operating characteristics show that these are highly sensitive (89%) and specific (100%) techniques for the diagnosis of lymphoma. At least two passes provided an average of 5.66 million cells (range, 0.12-62.32 million) for lymphoma cases. Conclusions: EUS and EBUS-FNA are powerful modalities to stage malignancies and at least two passes can provide adequate cells for flow cytometric analysis. We also demonstrate that fluorescence in situ hybridization analysis can be performed on Diff-Quik-stained and mounted smears.
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Affiliation(s)
- Amberly L Nunez
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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34
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Mikhail FM, Lose EJ, Robin NH, Descartes MD, Rutledge KD, Rutledge SL, Korf BR, Carroll AJ. Clinically relevant single gene or intragenic deletions encompassing critical neurodevelopmental genes in patients with developmental delay, mental retardation, and/or autism spectrum disorders. Am J Med Genet A 2012; 155A:2386-96. [PMID: 22031302 DOI: 10.1002/ajmg.a.34177] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent studies suggest that copy number variations (CNVs) encompassing several genes involved in neurodevelopmental pathways are associated with a variety of neuropsychiatric phenotypes, including developmental delay (DD), mental retardation (MR), and autism spectrum disorders (ASDs). Here we present eight patients in a cohort of approximately 1,200 patients referred for clinical array CGH testing for various neurodevelopmental phenotypes,whowere identified to carry small (<1.0Mb with the majority <500 kb) either total gene or intragenic deletions encompassing critical synaptic and other neurodevelopmental genes. The presentations of these patients included variable degrees of DD, speech problems, learning disabilities, MR, autistic-like features, and mild non-specific dysmorphic features. These genes belong to four functional categories, including neuronal transcription factor genes (NFIA at 1p31.3, MEF2C at 5q14.3, andCAMAT1at 1p36.23p36.31), neuron-specific splicing factor genes (RBFOX1 at 16p13.2p13.3), genes involved in synapse formation and maintenance (CNTNAP2 at 7q35 and LRFN5 at 14q21.2), and genes involved in neurotransmission (CHRNA7 at 15q13.3 and IL1RAPL1 at Xp21.2p21.3). Our report expands the list of neurodevelopmental genes deleted in various neurobehavioral phenotypes, expands the phenotypes caused by haploinsufficiency of previously reported critical neurodevelopmental genes, and elucidates the clinical relevance and need for careful clinical interpretation of some small CNVs<500 kb. This report also suggests that small clinically relevant deletions encompassing critical synaptic and other neurodevelopmental genes can present clinically with various neurobehavioral phenotypes, which implies the existence of overlapping neuronal pathways in the pathogenesis of these phenotypes.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, 35294, USA.
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35
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Descartes M, Mikhail FM, Franklin JC, McGrath TM, Bebin M. Monosomy1p36.3 and trisomy 19p13.3 in a child with periventricular nodular heterotopia. Pediatr Neurol 2011; 45:274-8. [PMID: 21907895 DOI: 10.1016/j.pediatrneurol.2011.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/01/2011] [Indexed: 11/20/2022]
Abstract
Monosomy 1p36 is a clinically recognizable syndrome that is considered to be the most common terminal deletion syndrome. It has characteristic clinical features that include craniofacial dysmorphism, congenital anomalies, hearing deficits, developmental delay, mental retardation, hypotonia, seizures, and brain anomalies. Brain anomalies in patients with 1p36 deletion are frequent but inconsistent. To date, 2 cases with monosomy 1p36 associated with periventricular nodular heterotopia (PNH) have been reported. We report a 2-month-old boy with multiple congenital anomalies; brain magnetic resonance imaging revealed PNH. The first 2 described cases were pure terminal deletions, whereas our patient carried unbalanced translocation due to an adjacent 1 segregation of a balanced maternal translocation, resulting in monosomy 1p36.3 and trisomy 19p13.3 identified by whole-genome array comparative genomic hybridization analysis. Our patient, with a smaller deletion that the 2 previously reported cases, can help narrow the critical region for PNH in association with the 1p36 deletion. Several potential candidate genes are discussed.
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Affiliation(s)
- Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA.
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36
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Vaklavas C, Steciuk MR, Ren Y, Baird MF, Mikhail FM, Foran JM. A case of acute promyelocytic leukemia without RARα rearrangement and apparently normal cytogenetics. Clin Lymphoma Myeloma Leuk 2011; 11:521-4. [PMID: 21729689 DOI: 10.1016/j.clml.2011.03.036] [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] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 02/26/2011] [Accepted: 03/01/2011] [Indexed: 11/27/2022]
Affiliation(s)
- Christos Vaklavas
- Division of Hematology and Oncology, University of Alabama at Birmingham, USA.
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37
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Zvereff V, Yao S, Ramsey J, Mikhail FM, Vijzelaar R, Messiaen L. Identification of PKHD1 multiexon deletions using multiplex ligation-dependent probe amplification and quantitative polymerase chain reaction. Genet Test Mol Biomarkers 2010; 14:505-10. [PMID: 20575693 DOI: 10.1089/gtmb.2009.0188] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Mutations in the PKHD1 gene are responsible for autosomal recessive polycystic kidney disease (ARPKD). Using exon scanning by denaturing high-performance liquid chromatography (dHPLC) or bidirectional sequencing of all exons constituting the longest open reading frame, the mutation detection rate reaches approximately 82% and minor lesion mutations include truncating, splice, and missense mutations. AIM The main aim of this study was to screen ARPKD patients in whom only one pathogenic PKHD1 mutation was identified after bidirectional sequencing of the longest open reading frame, for gene copy number alterations by employing multiplex ligation-dependent probe amplification complemented with quantitative real-time polymerase chain reaction. RESULTS Sixteen ARPKD probands were studied in whom only one clearly pathogenic mutation was previously identified. One patient with a suspected homozygous deletion of the exons 1-37 was also included in this cohort. Three distinct PKHD1 germ-line deletions were identified. Two of these deletions encompassed multiple exons of PKHD1 extending far beyond the 5' and 3' untranslated regions of the gene, and spanning at least 170 and 470 kb, respectively. The third 3.7 kb intragenic deletion affected only exons 20-21 of the PKHD1 gene. Thus, this is the first report presenting analysis of the entire PKHD1 longest open reading frame for gene deletions/duplications in a select cohort of ARPKD patients, in whom previously only one mutation was identified after bidirectional sequencing of the entire longest open reading frame. CONCLUSIONS The data indicate that multiplex ligation-dependent probe amplification is a sensitive and rapid method to identify PKHD1 deletions. Our study demonstrates that dosage analysis will increase the PKHD1 mutation detection rate and should be performed as a complementary assay in patients suspected to have ARPKD in the absence of two clear pathogenic mutations.
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Affiliation(s)
- Val Zvereff
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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Burnside RD, Lose EJ, Domínguez MG, Sánchez-Corona J, Rivera H, Carroll AJ, Mikhail FM. Molecular cytogenetic characterization of two cases with constitutional distal 11q duplication/triplication. Am J Med Genet A 2009; 149A:1516-22. [DOI: 10.1002/ajmg.a.32906] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Descartes M, Franklin J, de Ståhl TD, Piotrowski A, Bruder CE, Dumanski JP, Carroll AJ, Mikhail FM. Distal 22q11.2 microduplication encompassing theBCRgene. Am J Med Genet A 2008; 146A:3075-81. [DOI: 10.1002/ajmg.a.32572] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Descartes M, Hain JZ, Conklin M, Franklin J, Mikhail FM, Lachman RS, Nolet S, Messiaen LM. Molecular characterization of a patient with an interstitial 1q deletion [del(1)(q24.1q25.3)] and distinctive skeletal abnormalities. Am J Med Genet A 2008; 146A:2937-43. [DOI: 10.1002/ajmg.a.32550] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mikhail FM, Sathienkijkanchai A, Robin NH, Prucka S, Biggerstaff JS, Komorowski J, Andersson R, Bruder CEG, Piotrowski A, Diaz de Ståhl T, Dumanski JP, Carroll AJ. Overlapping phenotype of Wolf-Hirschhorn and Beckwith-Wiedemann syndromes in a girl with der(4)t(4;11)(pter;pter). Am J Med Genet A 2008; 143A:1760-6. [PMID: 17603794 DOI: 10.1002/ajmg.a.31821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 11/07/2022]
Abstract
We report on an 8-month-old girl with a novel unbalanced chromosomal rearrangement, consisting of a terminal deletion of 4p and a paternal duplication of terminal 11p. Each of these is associated with the well-known clinical phenotypes of Wolf-Hirschhorn syndrome (WHS) and Beckwith-Wiedemann syndrome (BWS), respectively. She presented for clinical evaluation of dysmorphic facial features, developmental delay, atrial septal defect (ASD), and left hydronephrosis. High-resolution cytogenetic analysis revealed a normal female karyotype, but subtelomeric fluorescence in situ hybridization (FISH) analysis revealed a der(4)t(4;11)(pter;pter). Both FISH and microarray CGH studies clearly demonstrated that the WHS critical regions 1 and 2 were deleted, and that the BWS imprinted domains (ID) 1 and 2 were duplicated on the der(4). Parental chromosome analysis revealed that the father carried a cryptic balanced t(4;11)(pter;pter). As expected, our patient manifests findings of both WHS (a growth retardation syndrome) and BWS (an overgrowth syndrome). We compare her unique phenotypic features with those that have been reported for both syndromes.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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Burnside RD, Mikhail FM, Cosper PC. A prenatally ascertained X;Y translocation characterized using conventional and molecular cytogenetics. Am J Med Genet A 2008; 146A:1221-4. [DOI: 10.1002/ajmg.a.32265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mikhail FM, Descartes M, Piotrowski A, Andersson R, Diaz de Ståhl T, Komorowski J, Bruder CEG, Dumanski JP, Carroll AJ. A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene. Am J Med Genet A 2007; 143A:2178-84. [PMID: 17676630 DOI: 10.1002/ajmg.a.31882] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [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: 11/08/2022]
Abstract
Susceptibility of the chromosome 22q11.2 region to rearrangements has been recognized on the basis of common clinical disorders such as the DiGeorge/velocardiofacial syndrome (DG/VCFs). Recent evidence has implicated low-copy repeats (LCRs); also known as segmental duplications; on 22q as mediators of nonallelic homologous recombination (NAHR) that result in rearrangements of 22q11.2. It has been shown that both deletion and duplication events can occur as a result of NAHR caused by unequal crossover of LCRs. Here we report on the clinical, cytogenetic and array CGH studies of a 15-year-old Hispanic boy with history of learning and behavior problems. We suggest that he represents a previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 just telomeric to the DG/VCFs typically deleted region and encompassing the BCR gene. Using a 32K BAC array CGH chip we were able to refine and precisely narrow the breakpoints of this microdeletion, which was estimated to be 1.55-1.92 Mb in size and to span approximately 20 genes. This microdeletion region is flanked by LCR clusters containing several modules with a very high degree of sequence homology (>95%), and therefore could play a causal role in its origin.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Korf B, M Mikhail F. Overview of genetic diagnosis in cancer. Curr Protoc Hum Genet 2007; Chapter 10:Unit 10.1. [PMID: 18428403 DOI: 10.1002/0471142905.hg1001s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Both cytogenetic and molecular genetic studies can contribute to the management of patients with cancer. In some cases genetic markers are specific to particular tumor types and are useful in diagnosis. This can be helpful in distinguishing histologically similar tumors that may respond differently to treatment and can sometimes be of prognostic value. Genetic markers can also be tools for following the response of a tumor to therapy, providing a sensitive means of detection of relapse. This introductory unit considers some of the types of genetic changes that occur in association with malignancies and major approaches used in their detection.
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Affiliation(s)
- Bruce Korf
- University of Alabama at Birmingham, Birmingham, Alabama, USA
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Mikhail FM, McIlvried D, Holt RL, Messiaen L, Descartes MD, Carroll AJ. Complete trisomy 17p syndrome in a girl with der(14)t(14;17)(p11.2;p11.2). Am J Med Genet A 2007; 140:1647-54. [PMID: 16835929 DOI: 10.1002/ajmg.a.31330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 11/06/2022]
Abstract
We report on an 8-year-old girl with near-complete trisomy 17p syndrome due to a de novo unbalanced t(14;17)(p11.2;p11.2). She has features consistent with the previously described cases with complete trisomy 17p, including pre- and post-natal growth retardation, motor and mental retardation, skeletal anomalies, clinodactyly of the 5th finger, hypertrichosis, as well as facial characteristics including microcephaly, receding forehead, ptosis, low-set malformed ears, smooth philtrum, high-arched palate, and a short broad neck. Fluorescence in situ hybridization showed that the breakpoints were p11.2 for both chromosome 14 and 17. Microsatellite analysis showed that the duplicated 17p was of paternal origin, and indicated that the breakpoint involving 17p11.2 is most likely located within the approximately 1-Mb segment from the centromere, and not involving the proximal Smith-Magenis syndrome (SMS) low copy repeat. We compare the clinical features of our patient with those previously reported to further delineate the phenotype of complete trisomy 17p syndrome.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Abstract
Converging studies from many investigators indicate that RUNX1 has a critical role in the correct maintenance of essential cellular functions during embryonic development and after birth. The discovery that this gene is also frequently mutated in human leukemia has increased the interest in the role that RUNX1 plays in both normal and transforming pathways. Here, we provide an overview of the many roles of RUNX1 in hematopoietic self-renewal and differentiation and summarize the information that is currently available on the many mechanisms of RUNX1 deregulation in human leukemia.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Senyuk V, Li D, Zakharov A, Mikhail FM, Nucifora G. The Distal Zinc Finger Domain of AML1/MDS1/EVI1 Is an Oligomerization Domain Involved in Induction of Hematopoietic Differentiation Defects in Primary Cells In vitro. Cancer Res 2005; 65:7603-11. [PMID: 16140925 DOI: 10.1158/0008-5472.can-05-0412] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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] [Indexed: 11/16/2022]
Abstract
AML1/MDS1/EVI1 (AME) is a chimeric transcription factor produced by the (3;21)(q26;q22) translocation. This chromosomal translocation is associated with de novo and therapy-related acute myeloid leukemia and with the blast crisis of chronic myelogenous leukemia. AME is obtained by in-frame fusion of the AML1 and MDS1/EVI1 (ME) genes. The mechanisms by which AME induces a neoplastic transformation in bone marrow cells are unknown. AME interacts with the corepressors CtBP and HDAC1, and it was shown that AME is a repressor in contrast to the parent transcription factors AML1 and ME, which are transcription activators. Studies with murine bone marrow progenitors indicated that the introduction of a point mutation that destroys the CtBP-binding consensus impairs but does not abolish the disruption of cell differentiation and replication associated with AME expression, suggesting that additional events are required. Several chimeric proteins, such as AML1/ETO, BCR/ABL, and PML/RARa, are characterized by the presence of a self-interaction domain critical for transformation. We report that AME is also able to oligomerize and displays a complex pattern of self-interaction that involves at least three oligomerization regions, one of which is the distal zinc finger domain. Although the deletion of this short domain does not preclude the self-interaction of AME, it significantly reduces the differentiation defects caused in vitro by AME in primary murine bone marrow progenitors. The addition of a point mutation that inhibits CtBP binding completely abrogates the effects of AME on differentiation, suggesting that AME induces hematopoietic differentiation defects through at least two separate but cooperating pathways.
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Affiliation(s)
- Vitalyi Senyuk
- Department of Pathology and The Cancer Center, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
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Buonamici S, Li D, Mikhail FM, Sassano A, Platanias LC, Colamonici O, Anastasi J, Nucifora G. EVI1 Abrogates Interferon-α Response by Selectively Blocking PML Induction. J Biol Chem 2005; 280:428-36. [PMID: 15519999 DOI: 10.1074/jbc.m410836200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 11/06/2022] Open
Abstract
EVI1 is an oncogene frequently associated with chronic and acute myeloid leukemia. In hematopoietic cells, EVI1 impairs several pathways including proliferation, differentiation, and apoptosis. Interferon-alpha (IFN-alpha) is a powerful cytokine that controls the immune response and limits the expansion of several tissues including bone marrow. These properties contribute to the effectiveness of IFN-alpha in the treatment of many neoplastic disorders especially chronic myeloid leukemia. We report here that in murine hematopoietic progenitors the expression of EVI1 completely abrogates the antiproliferative and apoptotic effects of IFN-alpha. EVI1 does not repress the JAK/STAT signaling pathway or the activation of many IFN-responsive genes. On the contrary, EVI1 prolongs the phosphorylation of STAT1 and the activation of an IFN-dependent reporter gene. However, EVI1 specifically represses the IFN-dependent induction of the tumor suppressor PML and blocks the apoptotic pathways activated by PML. We show that the position of the ISRE, which is located within the first exon of PML, is critical to block PML induction by IFN-alpha. The relocation of the ISRE to a position upstream of the transcription start site is sufficient to re-establish the response to IFN in the presence of EVI1. Our data suggest that stabilized STAT1 phosphorylation and prolonged binding of the STAT1 complex to the first exon could impair PML transcription and inhibit the activation of PML-dependent apoptotic pathways resulting in loss of IFN response. These results point to a novel mechanism utilized by an oncogene to escape normal cell response to growth-controlling cytokines.
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Affiliation(s)
- Silvia Buonamici
- Department of Pathology and Cancer Center, University of Illinois, Chicago, Illinois 60607, USA
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Mikhail FM, Coignet L, Hatem N, Mourad ZI, Farawela HM, El Kaffash DM, Farahat N, Nucifora G. A novel gene, FGA7, is fused to RUNX1/AML1 in a t(4;21)(q28;q22) in a patient with T-cell acute lymphoblastic leukemia. Genes Chromosomes Cancer 2004; 39:110-8. [PMID: 14695990 DOI: 10.1002/gcc.10302] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [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] [Indexed: 11/11/2022] Open
Abstract
AML1 is among the most frequent targets of chromosomal rearrangements in human leukemias. We report here the molecular analysis of a t(4;21)(q28;q22) that has disrupted AML1 in a patient with de novo T-cell acute lymphoblastic leukemia. By using 3'-RACE analysis, we show that this rearrangement results in the fusion of a novel gene immediately downstream of exon 5 or exon 6 of AML1, indicating that the AML1 breakpoint lies in intron 6 and that alternative fusion splice variants are generated. The sequence of the novel gene, located at 4q28, does not have any significant homology with any of the known genes in the human GenBank DNA database. However, the first 118 bases are identical to a part of a human ovarian EST. Also, its high homology with mouse and rat sequences suggests that this sequence most probably represents a part of a novel gene, which we named FGA7 (Fused Gene 7 to AML1). Following the AML1 open reading frame, the FGA7 sequence encodes an unknown protein of 27 amino acids. We isolated three bacterial artificial chromosome (BAC) clones that contain the FGA7 sequence and confirmed the breakpoint of the gene on the patient's metaphase spreads by fluorescence in situ hybridization using these BACs as probes. RT-PCR and Northern blot analyses revealed that FGA7 is expressed in ovarian and skeletal muscle tissues. The predicted AML1-FGA7 chimeric proteins contained a limited number of residues fused to AML1 in a situation similar to that reported for the AML1-EAP fusion that is a product of t(3;21). It is possible that the expression of a constitutively shortened AML1 could compete with full-length AML1 and act as a dominant negative inhibitor of the promoters that the core binding factor activates.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 4/genetics
- Cloning, Molecular
- Core Binding Factor Alpha 2 Subunit
- DNA, Neoplasm/genetics
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Neoplastic/genetics
- Gene Library
- Genes/genetics
- Humans
- In Situ Hybridization, Fluorescence/methods
- Leukemia-Lymphoma, Adult T-Cell/genetics
- Mice
- Molecular Sequence Data
- Oncogene Proteins, Fusion/genetics
- Organ Specificity/genetics
- Proto-Oncogene Proteins
- Rats
- Transcription Factors/genetics
- Translocation, Genetic/genetics
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Affiliation(s)
- Fady M Mikhail
- Department of Clinical Pathology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
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Senyuk V, Chakraborty S, Mikhail FM, Zhao R, Chi Y, Nucifora G. The leukemia-associated transcription repressor AML1/MDS1/EVI1 requires CtBP to induce abnormal growth and differentiation of murine hematopoietic cells. Oncogene 2002; 21:3232-40. [PMID: 12082639 DOI: 10.1038/sj.onc.1205436] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [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: 11/21/2001] [Revised: 02/15/2002] [Accepted: 02/21/2002] [Indexed: 11/08/2022]
Abstract
The leukemia-associated fusion gene AML1/MDS1/EVI1 (AME) encodes a chimeric transcription factor that results from the (3;21)(q26;q22) translocation. This translocation is observed in patients with therapy-related myelodysplastic syndrome (MDS), with chronic myelogenous leukemia during the blast crisis (CML-BC), and with de novo or therapy-related acute myeloid leukemia (AML). AME is obtained by in-frame fusion of the AML1 and MDS1/EVI1 genes. We have previously shown that AME is a transcriptional repressor that induces leukemia in mice. In order to elucidate the role of AME in leukemic transformation, we investigated the interaction of AME with the transcription co-regulator CtBP1 and with members of the histone deacetylase (HDAC) family. In this report, we show that AME physically interacts in vivo with CtBP1 and HDAC1 and that these co-repressors require distinct regions of AME for interaction. By using reporter gene assays, we demonstrate that AME represses gene transcription by CtBP1-dependent and CtBP1-independent mechanisms. Finally, we show that the interaction between AME and CtBP1 is biologically important and is necessary for growth upregulation and abnormal differentiation of the murine hematopoietic precursor cell line 32Dc13 and of murine bone marrow progenitors.
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Affiliation(s)
- Vitalyi Senyuk
- Department of Pathology, The Cancer Center, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA
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