1
|
Yenamandra A, Akgun Y, Zarnegar S, Zhao K, Gardner A, Henderson S, Ricardo R, Wang Y, Christensen M. 136. Rare but recurrent translocations, Clustered Genomic Aberrations in Early T-cell Precursor Acute Lymphoblastic Leukemia. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
2
|
Guess T, Potts CR, Bhat P, Cartailler JA, Brooks A, Holt C, Yenamandra A, Wheeler FC, Savona MR, Cartailler JP, Ferrell PB. Distinct Patterns of Clonal Evolution Drive Myelodysplastic Syndrome Progression to Secondary Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:316-329. [PMID: 35522837 PMCID: PMC9610896 DOI: 10.1158/2643-3230.bcd-21-0128] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 02/22/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Clonal evolution in myelodysplastic syndrome (MDS) can result in clinical progression and secondary acute myeloid leukemia (sAML). To dissect changes in clonal architecture associated with this progression, we performed single-cell genotyping of paired MDS and sAML samples from 18 patients. Analysis of single-cell genotypes revealed patient-specific clonal evolution and enabled the assessment of single-cell mutational cooccurrence. We discovered that changes in clonal architecture proceed via distinct patterns, classified as static or dynamic, with dynamic clonal architectures having a more proliferative phenotype by blast count fold change. Proteogenomic analysis of a subset of patients confirmed that pathogenic mutations were primarily confined to primitive and mature myeloid cells, though we also identify rare but present mutations in lymphocyte subsets. Single-cell transcriptomic analysis of paired sample sets further identified gene sets and signaling pathways involved in two cases of progression. Together, these data define serial changes in the MDS clonal landscape with clinical and therapeutic implications. SIGNIFICANCE Precise clonal trajectories in MDS progression are made possible by single-cell genomic sequencing. Here we use this technology to uncover the patterns of clonal architecture and clonal evolution that drive the transformation to secondary AML. We further define the phenotypic and transcriptional changes of disease progression at the single-cell level. See related article by Menssen et al., p. 330 (31). See related commentary by Romine and van Galen, p. 270. This article is highlighted in the In This Issue feature, p. 265.
Collapse
Affiliation(s)
- Tiffany Guess
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Chad R. Potts
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Pawan Bhat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Justin A. Cartailler
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Austin Brooks
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Clinton Holt
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Ferrin C. Wheeler
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Michael R. Savona
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Jean-Philippe Cartailler
- Creative Data Solutions Shared Resource, Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee
| | - P. Brent Ferrell
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.,Corresponding Author: P. Brent Ferrell Jr, Vanderbilt University Medical Center, 777 Preston Research Building, 2220 Pierce Avenue, Nashville, TN 37232. Phone: 615-875-8619; E-mail:
| |
Collapse
|
3
|
Yenamandra A, Guess T, Gardner A, Smith R, Wang Y, Strickland S. 59. Constellation of rare genetic abnormalities associated with MECOM rearrangement in AML. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2021.05.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
4
|
Smith RB, Solem EP, Metz EC, Wheeler FC, Phillips JA, Yenamandra A. Clinical diagnosis of neurofibromatosis type I in multiple family members due to cosegregation of a unique balanced translocation with disruption of the NF1 locus: Testing considerations for accurate diagnosis. Am J Med Genet A 2021; 185:1222-1227. [PMID: 33415784 DOI: 10.1002/ajmg.a.62071] [Citation(s) in RCA: 2] [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: 06/23/2020] [Revised: 12/13/2020] [Accepted: 12/19/2020] [Indexed: 11/12/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder that causes a predisposition to develop tumors along the peripheral nervous system. The NF1 gene, located at 17q11.2, has the highest mutation rate among known human genes and about half of NF1 patients have de novo pathogenic variants. We present a case of clinical NF1 diagnoses in multiple family members with phenotypes ranging from mild to severe. Chromosome analysis of the 3-year-old female proband with NF1 resulted in an abnormal karyotype that was inherited from her mother: 46,XX,t(4;17)(q21.3;q11.2) mat. However, no NF1 genetic variants were identified by either NGS analysis of NF1 DNA coding regions, deletion-duplication studies, or by cytogenomic microarray copy number analysis. Follow-up chromosome studies of the proband's two male siblings demonstrated cosegregation of the same balanced translocation and a clinical diagnosis of NF1. Based on the cosegregation of the translocation with the NF1 clinical presentation in this family, we hypothesized that the NF1 gene may have been disrupted by this unique rearrangement. Subsequent fluorescence in situ hybridization (FISH) analysis of the metaphase cells of an affected sibling revealed a disruption of the NF1 gene confirming the underlying basis of the clinical NF1 presentation in this family. The utilization of traditional cytogenetic as well as evolving molecular methods was not only pivotal in the diagnosis of NF1 and management for this family, but is also pertinent to other patients with a family history of NF1.
Collapse
Affiliation(s)
- Rebecca B Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Genetics Associates Inc., Nashville, Tennessee, USA
| | - Emily P Solem
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Emma C Metz
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Ferrin C Wheeler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - John A Phillips
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| |
Collapse
|
5
|
Shah KP, Carroll CM, Mosse C, Yenamandra A, Borinstein SC. Sustained remission in a patient with PDGFR-beta-rearranged T-lymphoblastic lymphoma and complete remission with dasatinib. Pediatr Blood Cancer 2020; 67:e28026. [PMID: 31571404 DOI: 10.1002/pbc.28026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kaustav P Shah
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Clinton M Carroll
- Division of Hematology-Oncology, Department of Pediatrics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Claudio Mosse
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Pathology and Laboratory Medicine Service, VA Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Scott C Borinstein
- Division of Hematology-Oncology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
6
|
Sethi TK, Kovach AE, Grover NS, Huang LC, Lee LA, Rubinstein SM, Wang Y, Morgan DS, Greer JP, Park SI, Ann Thompson-Arildsen M, Yenamandra A, Vnencak-Jones CL, Reddy NM. Clinicopathologic correlates of MYD88 L265P mutation and programmed cell death (PD-1) pathway in primary central nervous system lymphoma. Leuk Lymphoma 2019; 60:2880-2889. [PMID: 31184237 DOI: 10.1080/10428194.2019.1620942] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/11/2022]
Abstract
Primary central nervous system lymphoma (PCNSL) patients have a poorer prognosis than systemic lymphoma. Gain-of-function MYD88 c.794T > C (p. L265P) mutation and programed cell death-1 (PD-1) pathway alterations are potential targetable pathways. Our study objective was to determine the clinicopathologic correlates of MYD88 mutation and PD-1 alterations in PCNSL and the impact of Epstein-Barr virus (EBV) infection. We studied 53 cases including 13 EBV-associated (EBVpos) PCNSL, 49% harbored MYD88 mutation, none seen in EBVpos PCNSL. MYD88 protein expression did not correlate with MYD88 mutation. T-cell and macrophage infiltration was common. All PD-L1-positive tumors were EBVpos. Two PD-L1 positive tumors showed 9p24.1/PD-L1 locus alterations by Fluorescence In Situ Hybridization. T cells and macrophages expressed PD-1 and/or PD-L1 in 98% and 83% cases, respectively. MYD88 mutation or protein expression and PD-1 or PD-L1 expression did not predict outcome. We hypothesize that EBVpos PCNSL has a distinct activation mechanism, independent of genetic alterations.
Collapse
Affiliation(s)
- Tarsheen K Sethi
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexandra E Kovach
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Natalie S Grover
- Division of Hematology-Oncology, Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Li-Ching Huang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Laura A Lee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Samuel M Rubinstein
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yang Wang
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David S Morgan
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John P Greer
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Mary Ann Thompson-Arildsen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cindy L Vnencak-Jones
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nishitha M Reddy
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
7
|
Smith RB, Hollis AE, Hodge A, Straub M, Hughes C, Yenamandra A. 49. A single institution experience of CRLF2 rearranged pediatric acute lymphoblastic leukemia/lymphoma. Cancer Genet 2019. [DOI: 10.1016/j.cancergen.2019.04.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
Collapse
Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
| |
Collapse
|
9
|
Akkari Y, Baugn L, Bruyere H, Hagelstrom T, Pitel B, Raca G, Smolarek T, Yenamandra A, Meredith M. 19. Evidence-based review of genomic aberrations in T-ALL: Strategy and progress of CGC T-ALL Working Group. Cancer Genet 2018. [DOI: 10.1016/j.cancergen.2018.04.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Wheeler FC, Kim AS, Mosse CA, Shaver AC, Yenamandra A, Seegmiller AC. Limited Utility of Fluorescence In Situ Hybridization for Recurrent Abnormalities in Acute Myeloid Leukemia at Diagnosis and Follow-up. Am J Clin Pathol 2018. [PMID: 29538617 DOI: 10.1093/ajcp/aqy002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is classified in part by recurrent cytogenetic abnormalities, often detected by both fluorescent in situ hybridization (FISH) and karyotype. The goal of this study was to assess the utility of FISH and karyotyping at diagnosis and follow-up. METHODS Adult AML samples at diagnosis or follow-up with karyotype and FISH were identified. Concordance was determined, and clinical characteristics and outcomes for discordant results were evaluated. RESULTS Karyotype and FISH results were concordant in 193 (95.0%) of 203 diagnostic samples. In 10 cases, FISH detected an abnormality, but karyotype was normal. Of these, one had a FISH result with clinical significance. In follow-up cases, 17 (8.1%) of 211 showed FISH-positive discordant results; most were consistent with low-level residual disease. CONCLUSIONS Clinically significant discordance between karyotype and AML FISH is uncommon. Consequently, FISH testing can safely be omitted from most of these samples. Focused FISH testing is more useful at follow-up, for minimal residual disease detection.
Collapse
Affiliation(s)
- Ferrin C Wheeler
- Department of Pathology and Laboratory Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Claudio A Mosse
- Department of Pathology and Laboratory Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Aaron C Shaver
- Department of Pathology and Laboratory Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Ashwini Yenamandra
- Department of Pathology and Laboratory Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Adam C Seegmiller
- Department of Pathology and Laboratory Medicine, Vanderbilt University Medical Center, Nashville, TN
| |
Collapse
|
11
|
Dent LL, Mandape SN, Pratap S, Dong J, Davis J, Gaddy JA, Amoah K, Damo S, Marshall DR, Jones J, Brandt T, Diaz G, Wang Q, Gary T, Yenamandra A, Ghattas MZ, Elrakaiby M, Aziz RK, Zedan HH, Elmassry M, ElRakaiby M, Aziz RK, Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK, Dini P, Loux SC, Scoggin KE, Esteller-Vico A, Squires EL, Troedsson MHT, Daels P, Ball BA, De Silva K, Bailey E, Stephens JC, Kalbfleisch TS, Dolin CE, Poole LG, Wilkey DW, Rouchka EC, Arteel GE, Barati MT, Merchant ML, Higashi RM, Fan TWM, Moseley H, Lane AN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proc 2017. [PMCID: PMC5667591 DOI: 10.1186/s12919-017-0078-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
12
|
Hodge JC, Kanagal-Shamanna R, Xu X, Bryke C, Dash D, Dixon-Mciver A, Greipp P, Huxley E, Jeffries S, Lennon PA, Quintero-Rivera F, Shetty S, Sukhanova M, Tucker T, Yenamandra A, Slovak ML, Iqbal A, Fang M, Raca G. Genomic Copy Number Aberrations and Copy Neutral Loss of Heterozygosity Evaluation in Myeloid Neoplasms: Evidence-Based Recommendations for Clinical Genetic Testing From the Myeloid Malignancies Working Group of the Cancer Genomics Consortium. Cancer Genet 2017. [DOI: 10.1016/j.cancergen.2017.04.017] [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]
|
13
|
Smith MC, Cohen DN, Greig B, Yenamandra A, Vnencak-Jones C, Thompson MA, Kim AS. The ambiguous boundary between EBV-related hemophagocytic lymphohistiocytosis and systemic EBV-driven T cell lymphoproliferative disorder. Int J Clin Exp Pathol 2014; 7:5738-5749. [PMID: 25337215 PMCID: PMC4203186] [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] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 08/21/2014] [Indexed: 06/04/2023]
Abstract
Epstein Barr virus (EBV)-related hemophagocytic lymphohistiocytosis (EBV-HLH) is a form of acquired, infection-related HLH which typically represents a fulminant presentation of an acute EBV infection of CD8+ T cells with 30-50% mortality rate. Systemic EBV-positive lymphoproliferative disease of childhood (SE-LPD) is a rare T cell lymphoproliferative disorder predominantly arising in the setting of acute EBV infection, often presenting with HLH. Since both entities have been associated with clonal T cell populations, the discrimination between these diseases is often ambiguous. We report a unique case of a 21 years old female who presented with clinical and laboratory findings of florid HLH in the setting of markedly elevated EBV titers (>1 million) and an aberrant T cell population shown to be clonal by flow cytometry, karyotype, and molecular studies. This case raises the differential of EBV-HLH versus SE-LPD. Review of the literature identified 74 cases of reported EBV-HLH and 21 cases of SE-LPD with associated HLH in 25 studies. Of those cases with available outcome data, 62 of 92 cases (67%) were fatal. Of 60 cases in which molecular clonality was demonstrated, 37 (62%) were fatal, while all 14 cases (100%) demonstrating karyotypic abnormalities were fatal. Given the karyotypic findings in this sentinel case, a diagnosis of SE-LPD was rendered. The overlapping clinical and pathologic findings suggest that EBV-HLH and SE-LPD are a biologic continuum, rather than discrete entities. The most clinically useful marker of mortality was an abnormal karyotype rather than other standards of clonality assessment.
Collapse
MESH Headings
- Biopsy
- Diagnosis, Differential
- Epstein-Barr Virus Infections/diagnosis
- Epstein-Barr Virus Infections/genetics
- Epstein-Barr Virus Infections/immunology
- Epstein-Barr Virus Infections/pathology
- Epstein-Barr Virus Infections/virology
- Female
- Flow Cytometry
- Herpesvirus 4, Human/isolation & purification
- Humans
- Immunohistochemistry
- Karyotyping
- Lymphohistiocytosis, Hemophagocytic/diagnosis
- Lymphohistiocytosis, Hemophagocytic/genetics
- Lymphohistiocytosis, Hemophagocytic/immunology
- Lymphohistiocytosis, Hemophagocytic/pathology
- Lymphohistiocytosis, Hemophagocytic/virology
- Lymphoma, T-Cell/diagnosis
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell/surgery
- Lymphoma, T-Cell/virology
- Peripheral Blood Stem Cell Transplantation
- Predictive Value of Tests
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
- Treatment Outcome
- Young Adult
Collapse
Affiliation(s)
- Megan C Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Daniel N Cohen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Bruce Greig
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Cindy Vnencak-Jones
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Mary Ann Thompson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| | - Annette S Kim
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center Nashville TN, USA
| |
Collapse
|
14
|
Ondrejka SL, Jegalian AG, Kim AS, Chabot-Richards DS, Giltnane J, Czuchlewski DR, Shetty S, Sekeres MA, Yenamandra A, Head D, Jagasia M, Hsi ED. PDGFRB-rearranged T-lymphoblastic leukemia/lymphoma occurring with myeloid neoplasms: the missing link supporting a stem cell origin. Haematologica 2014; 99:e148-51. [PMID: 24951465 DOI: 10.3324/haematol.2014.105452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Sarah L Ondrejka
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Armin G Jegalian
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Annette S Kim
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | | | - Jennifer Giltnane
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - David R Czuchlewski
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Shashirekha Shetty
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Mikkael A Sekeres
- Department of Hematologic Oncology and Blood Disorders, Cleveland Clinic, OH
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - David Head
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Madan Jagasia
- Section of Hematology-Stem Cell Transplant, Vanderbilt and University Medical Center, Nashville, TN, USA
| | - Eric D Hsi
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| |
Collapse
|
15
|
Yenamandra A, Wheeler F, Hollis A, Barba L, Wang Y, Geng L. Detection of Genomic Imbalances Involved in Common Chromosomal Rearrangements of Acute Leukemia by Cytogenomic SNP Microarray Analysis. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
16
|
Chmielecki J, Peifer M, Viale A, Hutchinson K, Giltnane J, Socci ND, Hollis CJ, Dean RS, Yenamandra A, Jagasia M, Kim AS, Davé UP, Thomas RK, Pao W. Systematic screen for tyrosine kinase rearrangements identifies a novel C6orf204-PDGFRB fusion in a patient with recurrent T-ALL and an associated myeloproliferative neoplasm. Genes Chromosomes Cancer 2011; 51:54-65. [DOI: 10.1002/gcc.20930] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/12/2011] [Indexed: 01/31/2023] Open
|
17
|
Chmielecki J, Peifer M, Viale A, Hutchinson K, Giltnane J, Socci ND, Yenamandra A, Jagasia M, Kim AS, Dave U, Thomas RK, Pao W. Abstract 4977: Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables discovery of a novel C6orf204-PDGFRβ fusion in a patient with T-ALL and eosinophilia. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tyrosine kinase (TK) fusion proteins result from genomic rearrangements that juxtapose TK signaling domains with various upstream partners. Since tumor cells can become dependent upon the resultant constitutive kinase activity for tumorigenesis and survival, TK fusions serve as attractive therapeutic targets. However, identification of TK fusions in cancers has been hindered by experimental techniques that lack sufficient sensitivity and throughput. To overcome these challenges, we developed a screen to systematically identify TK fusions in tumor DNA. This method involves selective capture of regions upstream of GXGXXG kinase motifs where TK fusion breakpoints are likely to occur followed by next generation sequencing and custom computational analysis. This approach was previously validated using cell line DNA (Chmielecki et al, ‘10). Here, we used an improved version of our platform to identify a novel TK fusion using DNA isolated from whole blood of a patient with recurrent precursor T lymphoblastic lymphoma (T-ALL) who presented with new leukocytosis and bone marrow findings compatible with a myeloproliferative neoplasm (MPN) with eosinophilia. Cytogenetic analysis of a bone marrow aspirate prior to treatment for the patient's MPN revealed a karyotype with a t(5;6)(q33-34;q23). At recurrence, a 5q33/PDGFRβ rearrangement with a breakpoint proximal to the MYB locus on chromosome 6 was identified with fluorescence in situ hybridization (FISH). Prior to allogeneic hematopoietic cell transplantation, a brief trial of imatinib confirmed responsiveness of eosinophilia. To identify the exact fusion breakpoint, 3 µg of whole blood genomic DNA was subjected to genomic capture followed by paired-end SOLiD sequencing. Fusion candidates were validated by direct sequencing of PCR products generated with breakpoint spanning primers. Analysis of the recovered sequences identified a fusion involving c6orf204 upstream of the PDGFRβ TK domain. 5’-RACE confirmed expression of c6orf204-PDGFRβ mRNA in the patient's blood cells. Motif analysis of the 5’ c6orf204 sequence present within the fusion revealed a coiled-coil domain, which likely facilitates dimerization of the kinase, as observed in other TK fusions (e.g. BCR-ABL). Interestingly, retrospective FISH studies of the patient's diagnostic lymph node involved by T-ALL also revealed the presence of a PDGFRβ rearrangement. These data suggest that the rearrangement occurred in a multi-potent progenitor cell that gave rise to both the T-ALL and MPN. This finding is analogous to 8p MPNs involving FGFR1, but has not yet been reported with PDGFRβ. Further biochemical analysis of this TK fusion is currently underway, and additional tumor samples are undergoing screening for other novel TK fusions. This work was supported by an SU2C-AACR Innovative Research Grant to WP.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4977. doi:10.1158/1538-7445.AM2011-4977
Collapse
Affiliation(s)
| | - Martin Peifer
- 2Max Planck Institute University of Cologne, Cologne, Germany
| | - Agnes Viale
- 3Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Utpal Dave
- 4Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Roman K. Thomas
- 2Max Planck Institute University of Cologne, Cologne, Germany
| | - William Pao
- 4Vanderbilt-Ingram Cancer Center, Nashville, TN
| |
Collapse
|
18
|
Bhaskara S, Knutson SK, Jiang G, Chandrasekharan MB, Wilson AJ, Zheng S, Yenamandra A, Locke K, Yuan JL, Bonine-Summers AR, Wells CE, Kaiser JF, Washington MK, Zhao Z, Wagner FF, Sun ZW, Xia F, Holson EB, Khabele D, Hiebert SW. Hdac3 is essential for the maintenance of chromatin structure and genome stability. Cancer Cell 2010; 18:436-47. [PMID: 21075309 PMCID: PMC3004468 DOI: 10.1016/j.ccr.2010.10.022] [Citation(s) in RCA: 275] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 06/16/2010] [Accepted: 08/23/2010] [Indexed: 01/10/2023]
Abstract
Hdac3 is essential for efficient DNA replication and DNA damage control. Deletion of Hdac3 impaired DNA repair and greatly reduced chromatin compaction and heterochromatin content. These defects corresponded to increases in histone H3K9,K14ac; H4K5ac; and H4K12ac in late S phase of the cell cycle, and histone deposition marks were retained in quiescent Hdac3-null cells. Liver-specific deletion of Hdac3 culminated in hepatocellular carcinoma. Whereas HDAC3 expression was downregulated in only a small number of human liver cancers, the mRNA levels of the HDAC3 cofactor NCOR1 were reduced in one-third of these cases. siRNA targeting of NCOR1 and SMRT (NCOR2) increased H4K5ac and caused DNA damage, indicating that the HDAC3/NCOR/SMRT axis is critical for maintaining chromatin structure and genomic stability.
Collapse
Affiliation(s)
- Srividya Bhaskara
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Sarah K. Knutson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Guochun Jiang
- Department of Radiation Oncology Vanderbilt University Medical Center, Nashville, TN 37212
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37212
| | | | - Andrew J. Wilson
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Vanderbilt University Medical Center, Nashville, TN 37212
| | - Siyuan Zheng
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232
- Bioinformatics Resource Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | | | | | - Jia-ling Yuan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | | | | | | | - M. Kay Washington
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Zhongming Zhao
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37212
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232
- Bioinformatics Resource Center, Vanderbilt University School of Medicine, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Florence F. Wagner
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142
| | - Zu-Wen Sun
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Fen Xia
- Department of Radiation Oncology Vanderbilt University Medical Center, Nashville, TN 37212
| | - Edward B. Holson
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142
| | - Dineo Khabele
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37212
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Vanderbilt University Medical Center, Nashville, TN 37212
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232
- To whom correspondence should be sent: Department of Biochemistry, 512 Preston Research Building, Vanderbilt University School of Medicine, 23rd and Pierce Ave., Nashville Tennessee, 37232, Phone: (615) 936-3582; Fax: (615) 936-1790;
| |
Collapse
|
19
|
Abstract
DDB1, a component of a Cul4A ubiquitin ligase complex, promotes nucleotide excision repair (NER) and regulates DNA replication. We have investigated the role of human DDB1 in maintaining genome stability. DDB1-depleted cells accumulate DNA double-strand breaks in widely dispersed regions throughout the genome and have activated ATM and ATR cell cycle checkpoints. Depletion of Cul4A yields similar phenotypes, indicating that an E3 ligase function of DDB1 is important for genome maintenance. In contrast, depletion of DDB2, XPA, or XPC does not cause activation of DNA damage checkpoints, indicating that defects in NER are not involved. One substrate of DDB1-Cul4A that is crucial for preventing genome instability is Cdt1. DDB1-depleted cells exhibit increased levels of Cdt1 protein and rereplication, despite containing other Cdt1 regulatory mechanisms. The rereplication, accumulation of DNA damage, and activation of checkpoint responses in DDB1-depleted cells require entry into S phase and are partially, but not completely, suppressed by codepletion of Cdt1. Therefore, DDB1 prevents DNA lesions from accumulating in replicating human cells, in part by regulating Cdt1 degradation.
Collapse
Affiliation(s)
- Courtney A Lovejoy
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | |
Collapse
|
20
|
|
21
|
Yenamandra A, Zhou X, Trinchitella L, Susin M, Sastry S, Mehta L. Renal cell carcinoma with X;1 translocation in a child with Klinefelter syndrome. Am J Med Genet 1998; 77:281-4. [PMID: 9600736] [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] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Klinefelter syndrome (KS) is a sex chromosome abnormality occurring in 1 in 1,000 males. An association with leukemia, germ cell tumor, and male breast cancer has been suggested in KS. Such information is important for professionals caring for KS patients as the condition is frequently not clinically recognizable until after puberty. We report on a renal cell carcinoma (RCC) in a 10-year-old boy with KS. He developed intermittent hematuria at age 10 years and was diagnosed with a right kidney mass, which on pathology was identified as RCC. In addition, he was known to have learning disabilities and language delays. Analysis of peripheral blood chromosomes showed a 47,XXY karyotype while analysis of tumor cells demonstrated clonal abnormalities including a translocation between chromosomes X and 1, designated 47,XXYc,t(X;1)(p11.2;q21)[6]/47,XXYc,t(X;1),r(Xp)[2]/46,X XYc,-X,t(X;1)[7]. Renal cell carcinoma is rare in childhood and is not previously reported in KS. The oncogenetic significance of the chromosomal regions involved in this translocation is discussed in relation to the congenital abnormality of the patient.
Collapse
Affiliation(s)
- A Yenamandra
- Cell Genetics Laboratory, North Shore University Hospital, Manhasset, New York 11030, USA
| | | | | | | | | | | |
Collapse
|
22
|
Abstract
A 45,X chromosome complement was found in the lymphocytes and skin fibroblast cultures of a male infant with minor facial anomalies and gastrointestinal abnormalities. Fluorescence in situ hybridization (FISH) studies with DNA probes specific for the entire Y chromosome (painting) and SRY identified insertion of a short piece of Y chromosome DNA, including the SRY region, into a der(4) chromosome at 4p15. FISH studies with DNA probes specific for Wolf-Hirschhorn syndrome (WHS) and telomere of 4p indicated that these 2 regions were intact and that the insertion of Y DNA had occurred proximal to the WHS region. High-resolution chromosome analysis performed after FISH studies showed an altered banding pattern of 4p at the region of insertion. The typical Giemsa dark band of 4p15 was consistently replaced by a gray band; this probably indicates deletion of the distal part of 4p15. The consequences of the double-chromosome anomaly in this patient were discussed in relation to his phenotype.
Collapse
Affiliation(s)
- A Yenamandra
- Center for Human and Molecular Genetics, UMDNJ-NJ Medical School, Newark, USA
| | | | | | | | | |
Collapse
|
23
|
Aviv H, Lieber C, Yenamandra A, Desposito F. Familial transmission of a deletion of chromosome 21 derived from a translocation between chromosome 21 and an inverted chromosome 22. Am J Med Genet 1997; 70:399-403. [PMID: 9182781] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chromosome analysis of a newborn boy with Down syndrome resulted in the identification of a family with an unusual derivative chromosome 22. The child has 46 chromosomes, including two chromosomes 21, one normal chromosome 22, and a derivative chromosome 22. Giemsa banding and fluorescent in situ hybridization (FISH) studies show that the derivative chromosome is chromosome 22 with evidence of both paracentric and pericentric inversions, joined to the long arm of chromosome 21 from 21q21.2 to qter. The rearrangement results in partial trisomy 21 extending from 21q21.2 to 21q terminus in the patient. The child's mother, brother, maternal aunt, and maternal grandmother are all carriers of the derivative chromosome. All have 45 chromosomes, with one normal chromosome 21, one normal chromosome 22, and the derivative chromosome 22. The rearrangement results in the absence of the short arm, the centromere, and the proximal long arm of chromosome 21 (del 21pter-21q21.2) in carriers. Carriers of the derivative chromosome in this family have normal physical appearance, mild learning disabilities and poor social adjustment.
Collapse
Affiliation(s)
- H Aviv
- Center for Human and Molecular Genetics, UMDNJ-NJ Medical School, Newark, New Jersey 07103, USA
| | | | | | | |
Collapse
|