101
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Presence of multiple recurrent mutations confers poor trial outcome of relapsed/refractory CLL. Blood 2015; 126:2110-7. [PMID: 26316624 DOI: 10.1182/blood-2015-05-647578] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/15/2015] [Indexed: 12/22/2022] Open
Abstract
Although TP53, NOTCH1, and SF3B1 mutations may impair prognosis of patients with chronic lymphocytic leukemia (CLL) receiving frontline therapy, the impact of these mutations or any other, alone or in combination, remains unclear at relapse. The genome of 114 relapsed/refractory patients included in prospective trials was screened using targeted next-generation sequencing of the TP53, SF3B1, ATM, NOTCH1, XPO1, SAMHD1, MED12, BIRC3, and MYD88 genes. We performed clustering according to both number and combinations of recurrent gene mutations. The number of genes affected by mutation was ≥ 2, 1, and 0 in 43 (38%), 49 (43%), and 22 (19%) respectively. Recurrent combinations of ≥ 2 mutations of TP53, SF3B1, and ATM were found in 22 (19%) patients. This multiple-hit profile was associated with a median progression-free survival of 12 months compared with 22.5 months in the remaining patients (P = .003). Concurrent gene mutations are frequent in patients with relapsed/refractory CLL and are associated with worse outcome.
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102
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Ryan RJH, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov 2015; 5:1058-71. [PMID: 26229090 DOI: 10.1158/2159-8290.cd-15-0370] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED B-cell lymphomas frequently contain genomic rearrangements that lead to oncogene activation by heterologous distal regulatory elements. We used a novel approach called "pinpointing enhancer-associated rearrangements by chromatin immunoprecipitation," or PEAR-ChIP, to simultaneously map enhancer activity and proximal rearrangements in lymphoma cell lines and patient biopsies. This method detects rearrangements involving known cancer genes, including CCND1, BCL2, MYC, PDCD1LG2, NOTCH1, CIITA, and SGK1, as well as novel enhancer duplication events of likely oncogenic significance. We identify lymphoma subtype-specific enhancers in the MYC locus that are silenced in lymphomas with MYC-activating rearrangements and are associated with germline polymorphisms that alter lymphoma risk. We show that BCL6-locus enhancers are acetylated by the BCL6-activating transcription factor MEF2B, and can undergo genomic duplication, or target the MYC promoter for activation in the context of a "pseudo-double-hit" t(3;8)(q27;q24) rearrangement linking the BCL6 and MYC loci. Our work provides novel insights regarding enhancer-driven oncogene activation in lymphoma. SIGNIFICANCE We demonstrate a novel approach for simultaneous detection of genomic rearrangements and enhancer activity in tumor biopsies. We identify novel mechanisms of enhancer-driven regulation of the oncogenes MYC and BCL6, and show that the BCL6 locus can serve as an enhancer donor in an "enhancer hijacking" translocation.
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Affiliation(s)
- Russell J H Ryan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Yotam Drier
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Holly Whitton
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - M Joel Cotton
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Jasleen Kaur
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Robbyn Issner
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Shawn Gillespie
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Charles B Epstein
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Aliyah R Sohani
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ephraim P Hochberg
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts.
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103
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Mansur MB, van Delft FW, Colman SM, Furness CL, Gibson J, Emerenciano M, Kempski H, Clappier E, Cave H, Soulier J, Pombo-de-Oliveira MS, Greaves M, Ford AM. Distinctive genotypes in infants with T-cell acute lymphoblastic leukaemia. Br J Haematol 2015. [PMID: 26205622 PMCID: PMC4737125 DOI: 10.1111/bjh.13613] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Infant T‐cell acute lymphoblastic leukaemia (iT‐ALL) is a very rare and poorly defined entity with a poor prognosis. We assembled a unique series of 13 infants with T‐ALL, which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by single nucleotide polymorphism‐array to identify genomic losses and gains. In three cases, we identified a recurrent somatic deletion on chromosome 3. These losses result in the complete deletion of MLF1 and have not previously been described in T‐ALL. We observed two cases with an 11p13 deletion (LMO2‐related), one of which also harboured a deletion of RB1. Another case presented a large 11q14·1‐11q23·2 deletion that included ATM and only five patients (38%) showed deletions of CDKN2A/B. Four cases showed NOTCH1 mutations; in one case FBXW7 was the sole mutation and three cases showed alterations in PTEN. KMT2A rearrangements (KMT2A‐r) were detected in three out of 13 cases. For three patients, mutations and copy number alterations (including deletion of PTEN) could be backtracked to birth using neonatal blood spot DNA, demonstrating an in utero origin. Overall, our data indicates that iT‐ALL has a diverse but distinctive profile of genotypic abnormalities when compared to T‐ALL in older children and adults.
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Affiliation(s)
- Marcela B Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.,Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Susan M Colman
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jane Gibson
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Mariana Emerenciano
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Helena Kempski
- Paediatric Malignancy Cytogenetics Unit, Institute of Child Health & Great Ormond Street Hospital, London, UK
| | | | - Hélène Cave
- Department of Genetics, Robert Debré Hospital, APHP, Paris, France
| | - Jean Soulier
- Haematology Laboratory, Saint-Louis Louis Hospital, APHP, Paris, France
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Program, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Anthony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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104
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Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, Clot G, Colado E, Colomer D, Costa D, Delgado J, Enjuanes A, Estivill X, Ferrando AA, Gelpí JL, González B, González S, González M, Gut M, Hernández-Rivas JM, López-Guerra M, Martín-García D, Navarro A, Nicolás P, Orozco M, Payer ÁR, Pinyol M, Pisano DG, Puente DA, Queirós AC, Quesada V, Romeo-Casabona CM, Royo C, Royo R, Rozman M, Russiñol N, Salaverría I, Stamatopoulos K, Stunnenberg HG, Tamborero D, Terol MJ, Valencia A, López-Bigas N, Torrents D, Gut I, López-Guillermo A, López-Otín C, Campo E. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature 2015. [DOI: 10.1038/nature14666] [Citation(s) in RCA: 625] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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105
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Krem MM, Press OW, Horwitz MS, Tidwell T. Mechanisms and clinical applications of chromosomal instability in lymphoid malignancy. Br J Haematol 2015; 171:13-28. [PMID: 26018193 DOI: 10.1111/bjh.13507] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lymphocytes are unique among cells in that they undergo programmed DNA breaks and translocations, but that special property predisposes them to chromosomal instability (CIN), a cardinal feature of neoplastic lymphoid cells that manifests as whole chromosome- or translocation-based aneuploidy. In several lymphoid malignancies translocations may be the defining or diagnostic markers of the diseases. CIN is a cornerstone of the mutational architecture supporting lymphoid neoplasia, though it is perhaps one of the least understood components of malignant transformation in terms of its molecular mechanisms. CIN is associated with prognosis and response to treatment, making it a key area for impacting treatment outcomes and predicting prognoses. Here we will review the types and mechanisms of CIN found in Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma and the lymphoid leukaemias, with emphasis placed on pathogenic mutations affecting DNA recombination, replication and repair; telomere function; and mitotic regulation of spindle attachment, centrosome function, and chromosomal segregation. We will discuss the means by which chromosome-level genetic aberrations may give rise to multiple pathogenic mutations required for carcinogenesis and conclude with a discussion of the clinical applications of CIN and aneuploidy to diagnosis, prognosis and therapy.
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Affiliation(s)
- Maxwell M Krem
- Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Oliver W Press
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marshall S Horwitz
- Department of Pathology and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Timothy Tidwell
- Department of Pathology and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
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106
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Diolaiti D, McFerrin L, Carroll PA, Eisenman RN. Functional interactions among members of the MAX and MLX transcriptional network during oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1849:484-500. [PMID: 24857747 PMCID: PMC4241192 DOI: 10.1016/j.bbagrm.2014.05.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/23/2014] [Accepted: 05/14/2014] [Indexed: 01/27/2023]
Abstract
The transcription factor MYC and its related family members MYCN and MYCL have been implicated in the etiology of a wide spectrum of human cancers. Compared to other oncoproteins, such as RAS or SRC, MYC is unique because its protein coding region is rarely mutated. Instead, MYC's oncogenic properties are unleashed by regulatory mutations leading to unconstrained high levels of expression. Under both normal and pathological conditions MYC regulates multiple aspects of cellular physiology including proliferation, differentiation, apoptosis, growth and metabolism by controlling the expression of thousands of genes. How a single transcription factor exerts such broad effects remains a fascinating puzzle. Notably, MYC is part of a network of bHLHLZ proteins centered on the MYC heterodimeric partner MAX and its counterpart, the MAX-like protein MLX. This network includes MXD1-4, MNT, MGA, MONDOA and MONDOB proteins. With some exceptions, MXD proteins have been functionally linked to cell cycle arrest and differentiation, while MONDO proteins control cellular metabolism. Although the temporal expression patterns of many of these proteins can differ markedly they are frequently expressed simultaneously in the same cellular context, and potentially bind to the same, or similar DNA consensus sequence. Here we review the activities and interactions among these proteins and propose that the broad spectrum of phenotypes elicited by MYC deregulation is intimately connected to the functions and regulation of the other network members. Furthermore, we provide a meta-analysis of TCGA data suggesting that the coordinate regulation of the network is important in MYC driven tumorigenesis. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Daniel Diolaiti
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Lisa McFerrin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Patrick A Carroll
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA.
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107
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Remo A, Simeone I, Pancione M, Parcesepe P, Finetti P, Cerulo L, Bensmail H, Birnbaum D, Van Laere SJ, Colantuoni V, Bonetti F, Bertucci F, Manfrin E, Ceccarelli M. Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer. J Transl Med 2015; 13:138. [PMID: 25928084 PMCID: PMC4438533 DOI: 10.1186/s12967-015-0492-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/14/2015] [Indexed: 01/30/2023] Open
Abstract
Background Inflammatory breast cancer (IBC) is the most rare and aggressive variant of breast cancer (BC); however, only a limited number of specific gene signatures with low generalization abilities are available and few reliable biomarkers are helpful to improve IBC classification into a molecularly distinct phenotype. We applied a network-based strategy to gain insight into master regulators (MRs) linked to IBC pathogenesis. Methods In-silico modeling and Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) on IBC/non-IBC (nIBC) gene expression data (n = 197) was employed to identify novel master regulators connected to the IBC phenotype. Pathway enrichment analysis was used to characterize predicted targets of candidate genes. The expression pattern of the most significant MRs was then evaluated by immunohistochemistry (IHC) in two independent cohorts of IBCs (n = 39) and nIBCs (n = 82) and normal breast tissues (n = 15) spotted on tissue microarrays. The staining pattern of non-neoplastic mammary epithelial cells was used as a normal control. Results Using in-silico modeling of network-based strategy, we identified three top enriched MRs (NFAT5, CTNNB1 or β-catenin, and MGA) strongly linked to the IBC phenotype. By IHC assays, we found that IBC patients displayed a higher number of NFAT5-positive cases than nIBC (69.2% vs. 19.5%; p-value = 2.79 10-7). Accordingly, the majority of NFAT5-positive IBC samples revealed an aberrant nuclear expression in comparison with nIBC samples (70% vs. 12.5%; p-value = 0.000797). NFAT5 nuclear accumulation occurs regardless of WNT/β-catenin activated signaling in a substantial portion of IBCs, suggesting that NFAT5 pathway activation may have a relevant role in IBC pathogenesis. Accordingly, cytoplasmic NFAT5 and membranous β-catenin expression were preferentially linked to nIBC, accounting for the better prognosis of this phenotype. Conclusions We provide evidence that NFAT-signaling pathway activation could help to identify aggressive forms of BC and potentially be a guide to assignment of phenotype-specific therapeutic agents. The NFAT5 transcription factor might be developed into routine clinical practice as a putative biomarker of IBC phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0492-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Remo
- Department of Pathology, Mater Salutis Hospital, Legnago, Italy.
| | - Ines Simeone
- Department of Science and Technology, University of Sannio, Benevento, Italy. .,Qatar Computing Research Institute (QCRI), Qatar Foundation, Doha, Qatar.
| | - Massimo Pancione
- Department of Science and Technology, University of Sannio, Benevento, Italy.
| | - Pietro Parcesepe
- Department of Pathology and Diagnosis, University of Verona, Verona, Italy.
| | - Pascal Finetti
- Department of Molecular Oncology, Institut Paoli-Calmettes, U1068 Inserm, Marseille, France.
| | - Luigi Cerulo
- Department of Science and Technology, University of Sannio, Benevento, Italy. .,Bioinformatics Laboratory, BIOGEM, Ariano Irpino, Avellino, Italy.
| | - Halima Bensmail
- Qatar Computing Research Institute (QCRI), Qatar Foundation, Doha, Qatar.
| | - Daniel Birnbaum
- Department of Molecular Oncology, Institut Paoli-Calmettes, U1068 Inserm, Marseille, France.
| | | | - Vittorio Colantuoni
- Department of Science and Technology, University of Sannio, Benevento, Italy.
| | - Franco Bonetti
- Department of Pathology and Diagnosis, University of Verona, Verona, Italy.
| | - François Bertucci
- Department of Molecular Oncology, Institut Paoli-Calmettes, U1068 Inserm, Marseille, France.
| | - Erminia Manfrin
- Department of Pathology and Diagnosis, University of Verona, Verona, Italy.
| | - Michele Ceccarelli
- Department of Science and Technology, University of Sannio, Benevento, Italy. .,Qatar Computing Research Institute (QCRI), Qatar Foundation, Doha, Qatar.
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108
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TCL1 targeting miR-3676 is codeleted with tumor protein p53 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2015; 112:2169-74. [PMID: 25646413 DOI: 10.1073/pnas.1500010112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL) is the most common human leukemia and dysregulation of the T-cell leukemia/lymphoma 1 (TCL1) oncogene is a contributing event in the pathogenesis of the aggressive form of this disease based on transgenic mouse studies. To determine a role of microRNAs on the pathogenesis of the aggressive form of CLL we studied regulation of TCL1 expression in CLL by microRNAs. We identified miR-3676 as a regulator of TCL1 expression. We demonstrated that miR-3676 targets three consecutive 28-bp repeats within 3'UTR of TCL1 and showed that miR-3676 is a powerful inhibitor of TCL1. We further showed that miR-3676 expression is significantly down-regulated in four groups of CLL carrying the 11q deletions, 13q deletions, 17p deletions, or a normal karyotype compared with normal CD19(+) cord blood and peripheral blood B cells. In addition, the sequencing of 539 CLL samples revealed five germ-line mutations in six samples (1%) in miR-3676. Two of these mutations were loss-of-function mutations. Because miR-3676 is located at 17p13, only 500-kb centromeric of tumor protein p53 (Tp53), and is codeleted with Tp53, we propose that loss of miR-3676 causes high levels of TCL1 expression contributing to CLL progression.
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109
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Abstract
Tiny changes in our genomes can enhance oncogene expression and contribute to tumorigenesis
[Also see Report by
Mansour
et al.
]
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Affiliation(s)
- Anna Vähärautio
- Genome-Scale Biology Program, University of Helsinki, Finland
| | - Jussi Taipale
- Genome-Scale Biology Program, University of Helsinki, Finland
- Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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110
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Strefford JC. The genomic landscape of chronic lymphocytic leukaemia: biological and clinical implications. Br J Haematol 2014; 169:14-31. [PMID: 25496136 DOI: 10.1111/bjh.13254] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) remains at the forefront of the genetic analysis of human tumours, principally due its prevalence, protracted natural history and accessibility to suitable material for analysis. With the application of high-throughput genetic technologies, we have an unbridled view of the architecture of the CLL genome, including a comprehensive description of the copy number and mutational landscape of the disease, a detailed picture of clonal evolution during pathogenesis, and the molecular mechanisms that drive genomic instability and therapeutic resistance. This work has nuanced the prognostic importance of established copy number alterations, and identified novel prognostically relevant gene mutations that function within biological pathways that are attractive treatment targets. Herein, an overview of recent genomic discoveries will be reviewed, with associated biological and clinical implications, and a view into how clinical implementation may be facilitated.
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Affiliation(s)
- Jonathan C Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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111
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Zent CS, Burack WR. Mutations in chronic lymphocytic leukemia and how they affect therapy choice: focus on NOTCH1, SF3B1, and TP53. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2014; 2014:119-124. [PMID: 25696844 DOI: 10.1182/asheducation-2014.1.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a relatively small number of recurrent genetic defects. These can be evaluated by clinically available methods such as fluorescent in situ hybridization and targeted sequencing approaches to provide data that can be very helpful in prognostication and planning of treatment. Acquired defects in the p53 pathway, activating mutations of NOTCH1, and dysfunctional mutations of SF3B1 and BIRC3 identify patients with higher risk of progressive disease, poorer responses to conventional chemoimmunotherapy, and shorter survival. Risk stratification using these data can identify patients with aggressive CLL who require careful monitoring and are unlikely to have durable responses to chemoimmunotherapy at disease progression. Patients with defective DNA damage repair mechanisms because of p53 dysfunction should be considered for non-chemotherapy-based regimens including tyrosine kinase inhibitors, BCL2 inhibitors, monoclonal antibodies, and immunological therapies including allogeneic transplantation and chimeric antigen receptor-targeted T cells. Conversely, patients with no high-risk mutations can usually be monitored for a prolonged time and are likely to have durable responses to chemoimmunotherapy at disease progression. New technologies for genetic analysis such as targeted next-generation sequencing have the potential to make these analyses cheaper, faster, and more widely available. Comprehensive genetic analysis of patients both at diagnosis and before treatment for progressive disease could become an integral component of care for CLL.
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MESH Headings
- Clonal Evolution
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/physiopathology
- Mutation/genetics
- Receptor, Notch1/genetics
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Clive S Zent
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY
| | - W Richard Burack
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY
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112
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Huemer M, Rebhandl S, Zaborsky N, Gassner FJ, Hainzl S, Weiss L, Hebenstreit D, Greil R, Geisberger R. AID induces intraclonal diversity and genomic damage in CD86(+) chronic lymphocytic leukemia cells. Eur J Immunol 2014; 44:3747-57. [PMID: 25179679 PMCID: PMC4276288 DOI: 10.1002/eji.201344421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 08/01/2014] [Accepted: 08/29/2014] [Indexed: 02/04/2023]
Abstract
The activation-induced cytidine deaminase (AID) mediates somatic hypermutation and class switch recombination of the Ig genes by directly deaminating cytosines to uracils. As AID causes a substantial amount of off-target mutations, its activity has been associated with lymphomagenesis and clonal evolution of B-cell malignancies. Although it has been shown that AID is expressed in B-cell chronic lymphocytic leukemia (CLL), a clear analysis of in vivo AID activity in this B-cell malignancy remained elusive. In this study performed on primary human CLL samples, we report that, despite the presence of a dominant VDJ heavy chain region, a substantial intraclonal diversity was observed at VDJ as well as at IgM switch regions (Sμ), showing ongoing AID activity in vivo during disease progression. This AID-mediated heterogeneity was higher in CLL subclones expressing CD86, which we identified as the proliferative CLL fraction. Finally, CD86 expression correlated with shortened time to first treatment and increased γ-H2AX focus formation. Our data demonstrate that AID is active in CLL in vivo and thus, AID likely contributes to clonal evolution of CLL.
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Affiliation(s)
- Michael Huemer
- Laboratory for Immunological and Molecular Cancer Research, Department of Internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
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113
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Hartmann L, Stephenson CF, Verkamp SR, Johnson KR, Burnworth B, Hammock K, Brodersen LE, de Baca ME, Wells DA, Loken MR, Zehentner BK. Detection of clonal evolution in hematopoietic malignancies by combining comparative genomic hybridization and single nucleotide polymorphism arrays. Clin Chem 2014; 60:1558-68. [PMID: 25320376 DOI: 10.1373/clinchem.2014.227785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Array comparative genomic hybridization (aCGH) has become a powerful tool for analyzing hematopoietic neoplasms and identifying genome-wide copy number changes in a single assay. aCGH also has superior resolution compared with fluorescence in situ hybridization (FISH) or conventional cytogenetics. Integration of single nucleotide polymorphism (SNP) probes with microarray analysis allows additional identification of acquired uniparental disomy, a copy neutral aberration with known potential to contribute to tumor pathogenesis. However, a limitation of microarray analysis has been the inability to detect clonal heterogeneity in a sample. METHODS This study comprised 16 samples (acute myeloid leukemia, myelodysplastic syndrome, chronic lymphocytic leukemia, plasma cell neoplasm) with complex cytogenetic features and evidence of clonal evolution. We used an integrated manual peak reassignment approach combining analysis of aCGH and SNP microarray data for characterization of subclonal abnormalities. We compared array findings with results obtained from conventional cytogenetic and FISH studies. RESULTS Clonal heterogeneity was detected in 13 of 16 samples by microarray on the basis of log2 values. Use of the manual peak reassignment analysis approach improved resolution of the sample's clonal composition and genetic heterogeneity in 10 of 13 (77%) patients. Moreover, in 3 patients, clonal disease progression was revealed by array analysis that was not evident by cytogenetic or FISH studies. CONCLUSIONS Genetic abnormalities originating from separate clonal subpopulations can be identified and further characterized by combining aCGH and SNP hybridization results from 1 integrated microarray chip by use of the manual peak reassignment technique. Its clinical utility in comparison to conventional cytogenetic or FISH studies is demonstrated.
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114
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Rozovski U, Hazan-Halevy I, Keating MJ, Estrov Z. Personalized medicine in CLL: current status and future perspectives. Cancer Lett 2014; 352:4-14. [PMID: 23879961 PMCID: PMC3871981 DOI: 10.1016/j.canlet.2013.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 01/12/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is the most common hematologic malignancy in the Western Hemisphere. Despite advances in research and the development of effective treatment regimens, CLL is still largely an incurable disease. Although several prognostic factors have been identified in recent years, most of the new prognostic factors are not utilized, and treatment decisions are still based on clinical staging and limited use of cytogenetic analysis. Patients with advanced disease are treated at diagnosis, whereas others, regardless of their prognostic indicators, are offered treatment only at disease progression. Furthermore, treatment guidelines for elderly or "unfit" patients are unavailable because most CLL trials have included mostly younger, healthier patients. Given theheterogeneity of the clinical manifestations and prognosis of CLL, patients are likely to benefit from a personalized therapeutic approach. Recent advances in CLL pathobiology research, the use of high-throughput technologies, and most importantly, the introduction of novel targeted therapies with high efficacy and low toxicity are currently transforming the treatment of CLL. A personalized approach that includes early intervention in selected patients with CLL is likely to bring physicians closer to the goal of attaining cures in most patients with CLL.
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Affiliation(s)
- Uri Rozovski
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Inbal Hazan-Halevy
- Laboratory of Nanomedicine, Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michael J Keating
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zeev Estrov
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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115
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Atypical spindle cell lipoma: a clinicopathologic, immunohistochemical, and molecular study emphasizing its relationship to classical spindle cell lipoma. Virchows Arch 2014; 465:97-108. [PMID: 24659226 DOI: 10.1007/s00428-014-1568-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/22/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
We studied a series of spindle cell lipomas arising in atypical sites and showing unusual morphologic features (which we called atypical spindle cell lipoma) to assess if these lesions have the same chromosomal alterations as classical spindle cell lipoma but different from those found in atypical lipomatous tumor/well-differentiated liposarcoma. We investigated alterations of different genes in the 13q14 region and the amplification status of the MDM2 and CDK4 genes at 12q14-15 by multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) analysis. In the atypical spindle cell lipomas, MLPA revealed deletions in the two nearest flanking genes of RB1 (ITM2B and RCBTB2) and in multiple important exons of RB1. In contrast, in classical spindle cell lipomas, a less complex loss of RB1 exons was found but no deletion of ITM2B and RCBTB2. Moreover, MLPA identified a deletion of the DLEU1 gene, a finding which has not been reported earlier. We propose an immunohistochemical panel for lipomatous tumors which comprises of MDM2, CDK4, p16, Rb, which we have found useful in discriminating between atypical or classical spindle cell lipomas and other adipocytic neoplasms, especially atypical lipomatous tumor/well-differentiated liposarcoma. Our findings strengthen the link between atypical spindle cell lipoma and classical spindle cell lipoma, and differentiate them from atypical lipomatous tumor/well-differentiated liposarcoma.
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116
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Role of miR-15/16 in CLL. Cell Death Differ 2014; 22:6-11. [PMID: 24971479 DOI: 10.1038/cdd.2014.87] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 02/07/2023] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL) is the most common adult leukemia. The most common chromosomal abnormalities detectable by cytogenetics include deletion at 13q (55%), 11q (18%), trisomy 12 (12-16%) and 17p (8%). In 2002, we discovered that a microRNA cluster miR-15a/miR-16-1 (miR-15/16) is the target of 13q deletions in CLL. MicroRNAs encoded by the miR-15/16 locus (miR-15 and miR-16) function as tumor suppressors. Expression of these miRNAs downregulated in CLL, melanoma, colorectal cancer, bladder cancer and other solid tumors. miR-15/16 cluster targets multiple oncogenes, including BCL2, Cyclin D1, MCL1 and others. The most important target of miR-15/16 in CLL is arguably BCL2, as BCL2 is overexpressed in almost all CLLs. In this review, we discuss the discovery, functions, clinical relevance and treatment opportunities related to miR-15/16.
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117
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Strati P, Keating MJ, O'Brien SM, Ferrajoli A, Burger J, Faderl S, Tambaro FP, Jain N, Wierda WG. Outcomes of first-line treatment for chronic lymphocytic leukemia with 17p deletion. Haematologica 2014; 99:1350-5. [PMID: 24859876 DOI: 10.3324/haematol.2014.104661] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Although uncommon in treatment-naive patients with chronic lymphocytic leukemia, deletion 17p is a high-risk disease characteristic. We analyzed and reported outcomes for 63 patients with deletion 17p chronic lymphocytic leukemia who received first-line therapy at our institution; at time of first treatment, 81% had unmutated immunoglobulin heavy chain variable gene and 58% had complex karyotype. Forty-nine patients (76%) received first-line fludarabine, cyclophosphamide, rituximab-based therapy, 6 (11%) received rituximab-based and 8 (13%) received lenalidomide-based treatment. Overall, the complete plus nodular partial remission rate was 33%; on multivariable model, higher complete plus nodular partial remission rate was observed in patients with less than 50% cells positive for deletion 17p, and a higher probability of achieving at least a partial remission was observed with fludarabine, cyclophosphamide, rituximab-based treatment. After a median follow up of 33 months (range 1-89 months), the estimated median progression-free survival was 14 months (95% confidence interval 10-18) and estimated median overall survival was 63 months (95% confidence interval 43-83). In multivariable analysis, factors independently associated with longer progression-free survival were response to treatment and absence of complex karyotype. Achievement of complete plus nodular partial remission rate and mutated immunoglobulin heavy chain variable gene were independently associated with longer overall survival in multivariable model. Complex karyotype was associated with increased risk for Richter's transformation. New first-line strategies and agents must aim at both improving response and maintaining remission in patients with deletion 17p, particularly in the presence of complex karyotype.
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Affiliation(s)
- Paolo Strati
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Michael J Keating
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Susan M O'Brien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Alessandra Ferrajoli
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Jan Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Stefan Faderl
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | | | - Nitin Jain
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - William G Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center Houston, TX, USA
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118
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Genetic abnormalities in chronic lymphocytic leukemia: where we are and where we go. BIOMED RESEARCH INTERNATIONAL 2014; 2014:435983. [PMID: 24967369 PMCID: PMC4054680 DOI: 10.1155/2014/435983] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/22/2014] [Indexed: 12/17/2022]
Abstract
Chromosomal abnormalities in chronic lymphocytic leukemia (CLL) are detected in up to 80% of patients. Among them, deletions of 11q, 13q, 17p, and trisomy 12 have a known prognostic value and play an important role in CLL pathogenesis and evolution, determining patients outcome and therapeutic strategies. Standard methods used to identify these genomic aberrations include both conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH). Although FISH analyses have been implemented as the gold standard, CGC allows the identification of chromosomal translocations and complex karyotypes, the latest associated with poor outcome. Genomic arrays have a higher resolution that allows the detection of cryptic abnormalities, although these have not been fully implemented in routine laboratories. In the last years, next generation sequencing (NGS) methods have identified a wide range of gene mutations (e.g., TP53, NOTCH1, SF3B1, and BIRC3) which have improved our knowledge about CLL development, allowing us to refine both the prognostic subgroups and better therapeutic strategies. Clonal evolution has also recently arisen as a key point in CLL, integrating cytogenetic alterations and mutations in a dynamic model that improve our understanding about its clinical course and relapse.
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Veronese A, Pepe F, Chiacchia J, Pagotto S, Lanuti P, Veschi S, Di Marco M, D'Argenio A, Innocenti I, Vannata B, Autore F, Marchisio M, Wernicke D, Verginelli F, Leone G, Rassenti LZ, Kipps TJ, Mariani-Costantini R, Laurenti L, Croce CM, Visone R. Allele-specific loss and transcription of the miR-15a/16-1 cluster in chronic lymphocytic leukemia. Leukemia 2014; 29:86-95. [PMID: 24732594 PMCID: PMC4198514 DOI: 10.1038/leu.2014.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 02/07/2023]
Abstract
Deregulation of the miR-15a/16-1 cluster has a key role in the pathogenesis of chronic lymphocytic leukemia (CLL), a clinically heterogeneous disease with indolent and aggressive forms. The miR-15a/16-1 locus is located at 13q14, the most frequently deleted region in CLL. Starting from functional investigations of a rare SNP upstream the miR cluster, we identified a novel allele-specific mechanism that exploits a cryptic activator region to recruit the RNA polymerase III for miR-15a/16-1 transcription. This regulation of the miR-15a/16- locus is independent of the DLEU2 host gene, which is often transcribed monoallellically by RPII. We found that normally one allele of miR-15a/16-1 is transcribed by RNAPII, the other one by RNAPIII. In our subset of CLL patients harboring 13q14 deletions, exclusive RNA polymerase III (RPIII)-driven transcription of the miR-15a/16-1 was the consequence of loss of the RPII-regulated allele and correlated with high expression of the poor prognostic marker ZAP70 (P=0.019). Thus, our findings point to a novel biological process, characterized by double allele-specific transcriptional regulation of the miR-15a/16-1 locus by alternative mechanisms. Differential usage of these mechanisms may distinguish at onset aggressive from indolent forms of CLL. This provides a basis for the clinical heterogeneity of the CLL patients carrying 13q14 deletions.
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Affiliation(s)
- A Veronese
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - F Pepe
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - J Chiacchia
- Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy
| | - S Pagotto
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - P Lanuti
- Department of Medicine and Aging Science, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - S Veschi
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - M Di Marco
- Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - A D'Argenio
- Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy
| | - I Innocenti
- Department of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - B Vannata
- Department of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - F Autore
- Department of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - M Marchisio
- Department of Medicine and Aging Science, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - D Wernicke
- Department of Molecular Virology, Immunology, and Medical Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - F Verginelli
- Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy
| | - G Leone
- Department of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - L Z Rassenti
- 1] Department of Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Chronic Lymphocytic Leukemia Research Consortium, San Diego, CA, USA
| | - T J Kipps
- 1] Department of Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Chronic Lymphocytic Leukemia Research Consortium, San Diego, CA, USA
| | - R Mariani-Costantini
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - L Laurenti
- Department of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - C M Croce
- 1] Department of Molecular Virology, Immunology, and Medical Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA [2] Chronic Lymphocytic Leukemia Research Consortium, San Diego, CA, USA
| | - R Visone
- 1] Unit of General Pathology, Aging Research Center (Ce.S.I.), G. d'Annunzio University Foundation, Chieti, Italy [2] Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
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120
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Link JM, Hurlin PJ. The activities of MYC, MNT and the MAX-interactome in lymphocyte proliferation and oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:554-62. [PMID: 24731854 DOI: 10.1016/j.bbagrm.2014.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/29/2022]
Abstract
The MYC family of proteins plays essential roles in embryonic development and in oncogenesis. Efforts over the past 30 years to define the transcriptional activities of MYC and how MYC functions to promote proliferation have produced evolving models of MYC function. One picture that has emerged of MYC and its partner protein MAX is of a transcription factor complex with a seemingly unique ability to stimulate the transcription of genes that are epigenetically poised for transcription and to amplify the transcription of actively transcribed genes. During lymphocyte activation, MYC is upregulated and stimulates a pro-proliferative program in part through the upregulation of a wide variety of metabolic effector genes that facilitate cell growth and cell cycle progression. MYC upregulation simultaneously sensitizes cells to apoptosis and activated lymphocytes and lymphoma cells have pro-survival attributes that allow MYC-driven proliferation to prevail. For example, the MAX-interacting protein MNT is upregulated in activated lymphocytes and was found to protect lymphocytes from MYC-dependent apoptosis. Here we review the activities of MYC, MNT and other MAX interacting proteins in the setting of T and B cell activation and oncogenesis. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Jason M Link
- Shriners Hospitals for Children Portland, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Peter J Hurlin
- Shriners Hospitals for Children Portland, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Cell and Developmental Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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121
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Cooke SL, Shlien A, Marshall J, Pipinikas CP, Martincorena I, Tubio JM, Li Y, Menzies A, Mudie L, Ramakrishna M, Yates L, Davies H, Bolli N, Bignell GR, Tarpey PS, Behjati S, Nik-Zainal S, Papaemmanuil E, Teixeira VH, Raine K, O’Meara S, Dodoran MS, Teague JW, Butler AP, Iacobuzio-Donahue C, Santarius T, Grundy RG, Malkin D, Greaves M, Munshi N, Flanagan AM, Bowtell D, Martin S, Larsimont D, Reis-Filho JS, Boussioutas A, Taylor JA, Hayes ND, Janes SM, Futreal PA, Stratton MR, McDermott U, Campbell PJ. Processed pseudogenes acquired somatically during cancer development. Nat Commun 2014; 5:3644. [PMID: 24714652 PMCID: PMC3996531 DOI: 10.1038/ncomms4644] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/13/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5' truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context.
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Affiliation(s)
- Susanna L. Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Adam Shlien
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - John Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Inigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jose M.C. Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lucy Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Helen Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Niccolo Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- University of Cambridge, Cambridge CB2 0XY, UK
| | - Graham R. Bignell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Patrick S. Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- University of Cambridge, Cambridge CB2 0XY, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, Rayne Institute, University College London, London WC1E 6JF, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sarah O’Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maryam S. Dodoran
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jon W. Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | | | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - David Malkin
- Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | - Mel Greaves
- Institute for Cancer Research, Sutton, London SM2 5NG, UK
| | - Nikhil Munshi
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Adrienne M. Flanagan
- Lungs for Living Research Centre, Rayne Institute, University College London, London WC1E 6JF, UK
- Royal National Orthopaedic Hospital, Middlesex HA7 4LP, UK
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Denis Larsimont
- Department of Pathology, Jules Bordet Institute, 1000 Brussels, Belgium
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial-Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Alex Boussioutas
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Jack A. Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27713, USA
| | - Neil D. Hayes
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Sam M. Janes
- Lungs for Living Research Centre, Rayne Institute, University College London, London WC1E 6JF, UK
| | - P. Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Addenbrooke’s NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- University of Cambridge, Cambridge CB2 0XY, UK
- Addenbrooke’s NHS Foundation Trust, Cambridge CB2 0QQ, UK
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Baliakas P, Iskas M, Gardiner A, Davis Z, Plevova K, Nguyen-Khac F, Malcikova J, Anagnostopoulos A, Glide S, Mould S, Stepanovska K, Brejcha M, Belessi C, Davi F, Pospisilova S, Athanasiadou A, Stamatopoulos K, Oscier D. Chromosomal translocations and karyotype complexity in chronic lymphocytic leukemia: a systematic reappraisal of classic cytogenetic data. Am J Hematol 2014; 89:249-55. [PMID: 24166834 DOI: 10.1002/ajh.23618] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/14/2013] [Accepted: 10/21/2013] [Indexed: 02/02/2023]
Abstract
The significance of chromosomal translocations (CTRAs) and karyotype complexity (KC) in chronic lymphocytic leukemia (CLL) remains uncertain. To gain insight into these issues, we evaluated a series of 1001 CLL cases with reliable classic cytogenetic data obtained within 6 months from diagnosis before any treatment. Overall, 320 cases were found to carry ≥ 1 CTRAs. The most frequent chromosome breakpoints were 13q, followed by 14q, 18q, 17q, and 17p; notably, CTRAs involving chromosome 13q showed a wide spectrum of translocation partners. KC (≥ 3 aberrations) was detected in 157 cases and significantly (P < 0.005) associated with unmutated IGHV genes and aberrations of chromosome 17p. Furthermore, it was identified as an independent prognostic factor for shorter time-to-first-treatment. CTRAs were assigned to two categories (i) CTRAs present in the context of KC, often with involvement of chromosome 17p aberrations, occurring mostly in CLL with unmutated IGHV genes; in such cases, we found that KC rather than the presence of CTRAs per se negatively impacts on survival; (ii) CTRAs in cases without KC, having limited if any impact on survival. On this evidence, we propose that all CTRAs in CLL are not equivalent but rather develop by different processes and are associated with distinct clonal behavior.
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Affiliation(s)
- Panagiotis Baliakas
- Hematology Department and HCT Unit; G. Papanicolaou Hospital; Thessaloniki Greece
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala Sweden
| | - Michalis Iskas
- Hematology Department and HCT Unit; G. Papanicolaou Hospital; Thessaloniki Greece
| | - Anne Gardiner
- Department of Haematology; Royal Bournemouth Hospital; Bournemouth United Kingdom
| | - Zadie Davis
- Department of Haematology; Royal Bournemouth Hospital; Bournemouth United Kingdom
| | - Karla Plevova
- Department of Internal Medicine, Hematology and Oncology; University Hospital Brno and Central European Institute of Technology, Masaryk University; Brno Czech Republic
| | - Florence Nguyen-Khac
- Hematology Department and University Pierre et Marie Curie; Hôpital Pitié-Salpètrière; Paris France
| | - Jitka Malcikova
- Department of Internal Medicine, Hematology and Oncology; University Hospital Brno and Central European Institute of Technology, Masaryk University; Brno Czech Republic
| | | | - Sharron Glide
- Department of Haematology; Royal Bournemouth Hospital; Bournemouth United Kingdom
| | - Sarah Mould
- Department of Haematology; Royal Bournemouth Hospital; Bournemouth United Kingdom
| | - Kristina Stepanovska
- Department of Internal Medicine, Hematology and Oncology; University Hospital Brno and Central European Institute of Technology, Masaryk University; Brno Czech Republic
| | - Martin Brejcha
- Department of Hematology; J.G. Mendel Cancer Center Novy Jicin; Czech Republic
| | | | - Frederic Davi
- Hematology Department and University Pierre et Marie Curie; Hôpital Pitié-Salpètrière; Paris France
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology; University Hospital Brno and Central European Institute of Technology, Masaryk University; Brno Czech Republic
| | | | - Kostas Stamatopoulos
- Hematology Department and HCT Unit; G. Papanicolaou Hospital; Thessaloniki Greece
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala Sweden
- Institute of Applied Biosciences; CERTH Thessaloniki Greece
| | - David Oscier
- Department of Haematology; Royal Bournemouth Hospital; Bournemouth United Kingdom
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123
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Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C. Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia. Cancer Discov 2014; 4:348-61. [PMID: 24356097 PMCID: PMC4134522 DOI: 10.1158/2159-8290.cd-13-0349] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL.
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MESH Headings
- Aged
- Chromosomes, Human
- CpG Islands
- DNA Methylation
- Disease Progression
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Leukemic
- Genetic Heterogeneity
- Genome, Human
- Genomic Instability
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
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Affiliation(s)
- Christopher C. Oakes
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Rainer Claus
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine, University of Freiburg Medical Center, Freiburg
| | - Lei Gu
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Jennifer Hüllein
- Department of Translational Oncology, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Manuela Zucknick
- Division of Biostatistics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - David Brocks
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Olga Bogatyrova
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Christopher R. Schmidt
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Laura Rassenti
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Thomas J. Kipps
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Daniel Mertens
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Internal Medicine III, University of Ulm, Ulm
| | - Peter Lichter
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm
| | | | - John C. Byrd
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | - Thorsten Zenz
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine V, University of Heidelberg, Heidelberg
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
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124
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Rose-Zerilli MJJ, Forster J, Parker H, Parker A, Rodríguez AE, Chaplin T, Gardiner A, Steele AJ, Collins A, Young BD, Skowronska A, Catovsky D, Stankovic T, Oscier DG, Strefford JC. ATM mutation rather than BIRC3 deletion and/or mutation predicts reduced survival in 11q-deleted chronic lymphocytic leukemia: data from the UK LRF CLL4 trial. Haematologica 2014; 99:736-42. [PMID: 24584352 DOI: 10.3324/haematol.2013.098574] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ATM mutation and BIRC3 deletion and/or mutation have independently been shown to have prognostic significance in chronic lymphocytic leukemia. However, the relative clinical importance of these abnormalities in patients with a deletion of 11q encompassing the ATM gene has not been established. We screened a cohort of 166 patients enriched for 11q-deletions for ATM mutations and BIRC3 deletion and mutation and determined the overall and progression-free survival among the 133 of these cases treated within the UK LRF CLL4 trial. SNP6.0 profiling demonstrated that BIRC3 deletion occurred in 83% of 11q-deleted cases and always co-existed with ATM deletion. For the first time we have demonstrated that 40% of BIRC3-deleted cases have concomitant deletion and mutation of ATM. While BIRC3 mutations were rare, they exclusively occurred with BIRC3 deletion and a wild-type residual ATM allele. In 11q-deleted cases, we confirmed that ATM mutation was associated with a reduced overall and progression-free survival comparable to that seen with TP53 abnormalities, whereas BIRC3 deletion and/or mutation had no impact on overall and progression-free survival. In conclusion, in 11q-deleted patients treated with first-line chemotherapy, ATM mutation rather than BIRC3 deletion and/or mutation identifies a subgroup with a poorer outcome.
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125
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Abstract
Fludarabine refractoriness (FR) represents an unsolved clinical problem of chronic lymphocytic leukemia (CLL) management. Although next-generation sequencing studies have led to the identification of a number of genes frequently mutated in FR-CLL, a comprehensive evaluation of the FR-CLL genome has not been reported. Toward this end, we studied 10 FR-CLLs by combining whole-exome sequencing and copy number aberration (CNA) analysis, which showed an average of 16.3 somatic mutations and 4 CNAs per sample. Screening of recurrently mutated genes in 48 additional FR-CLLs revealed that ~70% of FR-CLLs carry ≥1 mutation in genes previously associated with CLL clinical course, including TP53 (27.5%), NOTCH1 (24.1%), SF3B1 (18.9%), and BIRC3 (15.5%). In addition, this analysis showed that 10.3% of FR-CLL cases display mutations of the FAT1 gene, which encodes for a cadherin-like protein that negatively regulates Wnt signaling, consistent with a tumor suppressor role. The frequency of FAT1-mutated cases was significantly higher in FR-CLL than in unselected CLLs at diagnosis (10.3% vs 1.1%, P = .004), suggesting a role in the development of a high-risk phenotype. These findings have general implications for the mechanisms leading to FR and point to Wnt signaling as a potential therapeutic target in FR-CLL.
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126
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Pei J, Robu V, Feder M, Cheung M, Neumann-Domer E, Talarchek J, Dulaimi E, Millenson MM, Testa JR. Copy neutral loss of heterozygosity in 20q in chronic lymphocytic leukemia/small lymphocytic lymphoma. Cancer Genet 2014; 207:98-102. [PMID: 24704113 DOI: 10.1016/j.cancergen.2014.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 01/26/2023]
Abstract
Single nucleotide polymorphism (SNP)-based chromosome microarray analysis was used to uncover copy neutral loss of heterozygosity (LOH) in the long arm of chromosome 20 in blood or bone marrow specimens from three patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). All three patients presented with lymph node enlargement. Whereas one of the patients has had a complicated clinical course, the other two have a more indolent disease. Sequence analysis of the tumor suppressor gene ASXL1, which is located in 20q and is commonly mutated in malignant myeloid diseases and occasionally in CLL/SLL specimens, revealed no mutations in our three patients with copy neutral LOH in 20q. The possible contribution of other imprinted microRNAs and antisense genes residing in 20q to the pathogenesis of a subset of CLL/SLL patients is discussed. These findings illustrate the value of SNP arrays for the detection of novel recurrent genomic alterations that may contribute to CLL/SLL onset or progression.
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Affiliation(s)
- Jianming Pei
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Valentin Robu
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Madelyn Feder
- Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Mitchell Cheung
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Erin Neumann-Domer
- Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Essel Dulaimi
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael M Millenson
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Joseph R Testa
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA.
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127
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Monti S, Deambrogi C, Rinaldi A, Bertoni F, Gaidano G, Rossi D. MYC network mutations in high-risk chronic lymphocytic leukaemia. Hematol Oncol 2014; 32:155-7. [PMID: 24449520 DOI: 10.1002/hon.2117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/16/2013] [Accepted: 10/18/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Sara Monti
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
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128
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Acquired chromosomal anomalies in chronic lymphocytic leukemia patients compared with more than 50,000 quasi-normal participants. Cancer Genet 2014; 207:19-30. [PMID: 24613276 DOI: 10.1016/j.cancergen.2014.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 01/03/2014] [Accepted: 01/11/2014] [Indexed: 11/23/2022]
Abstract
Pretherapy patients with chronic lymphocytic leukemia (CLL) from US Intergroup trial E2997 were analyzed with single nucleotide polymorphism microarrays to detect acquired chromosomal anomalies. The four CLL-typical anomalies (11q-, +12, 13q-, and 17p-) were found at expected frequencies. Acquired anomalies in other regions account for 70% of the total detected anomalies, and their number per participant has a significant effect on progression-free survival after adjusting for the effects of 17p- (and other covariates). These results were compared with those from a previous study of more than 50,000 participants from the GENEVA consortium of genome-wide association studies, which analyzed individuals with a variety of medical conditions and healthy controls. The percentage of individuals with acquired anomalies is vastly different between the two studies (GENEVA 0.8%; E2997 80%). The composition of the anomalies also differs, with GENEVA having a higher percentage of acquired uniparental disomies and a lower percentage of deletions. The four common CLL anomalies are among the most frequent in GENEVA participants, some of whom may have CLL-precursor conditions or early stages of CLL. However, the patients from E2997 (and other studies of symptomatic CLL) have recurrent acquired anomalies that were not found in GENEVA participants, thus identifying genomic changes that may be unique to symptomatic stages of CLL.
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129
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Rapini N, Lidano R, Pietrosanti S, Vitiello G, Grimaldi C, Postorivo D, Nardone AM, Del Bufalo F, Brancati F, Manca Bitti ML. De novo 13q13.3-21.31 deletion involving RB1 gene in a patient with hemangioendothelioma of the liver. Ital J Pediatr 2014; 40:5. [PMID: 24433316 PMCID: PMC3896849 DOI: 10.1186/1824-7288-40-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/12/2013] [Indexed: 01/29/2023] Open
Abstract
Interstitial deletions of the long arm of chromosome 13 (13q) are related with variable phenotypes, according to the size and the location of the deleted region. The main clinical features are moderate/severe mental and growth retardation, cranio-facial dysmorphism, variable congenital defects and increased susceptibility to tumors. Here we report a 3-year-old girl carrying a de novo 13q13.3-21.32 interstitial deletion. She showed developmental delay, growth retardation and mild dysmorphism including curly hair, high forehead, short nose, thin upper lip and long philtrum. An abnormal mass was surgically removed from her liver resulting in a hemangioendothelioma. Array analysis allowed us to define a deleted region of about 27.87 Mb, which includes the RB1 gene. This is the first report of a 13q deletion associated with infantile hemangioendothelioma of the liver.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Francesco Brancati
- Medical Genetics Unit, Policlinico Tor Vergata University Hospital, Viale Oxford, 81-00133 Rome, Italy.
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130
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Stevens-Kroef MJ, van den Berg E, Olde Weghuis D, Geurts van Kessel A, Pfundt R, Linssen-Wiersma M, Benjamins M, Dijkhuizen T, Groenen PJ, Simons A. Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling. Mol Cytogenet 2014; 7:3. [PMID: 24401281 PMCID: PMC3905918 DOI: 10.1186/1755-8166-7-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characteristic genomic abnormalities in patients with B cell chronic lymphocytic leukemia (CLL) have been shown to provide important prognostic information. Fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA), currently used in clinical diagnostics of CLL, are targeted tests aimed at specific genomic loci. Microarray-based genomic profiling is a new high-resolution tool that enables genome-wide analyses. The aim of this study was to compare two recently launched genomic microarray platforms, i.e., the CytoScan HD Array (Affymetrix) and the HumanOmniExpress Array (Illumina), with FISH and MLPA to ascertain whether these latter tests can be replaced by either one of the microarray platforms in a clinical diagnostic setting. RESULT Microarray-based genomic profiling and FISH were performed in all 28 CLL patients. For an unbiased comparison of the performance of both microarray platforms 9 patients were evaluated on both platforms, resulting in the identification of exactly identical genomic aberrations. To evaluate the detection limit of the microarray platforms we included 7 patients in which the genomic abnormalities were present in a relatively low percentage of the cells (range 5-28%) as previously determined by FISH. We found that both microarray platforms allowed the detection of copy number abnormalities present in as few as 16% of the cells. In addition, we found that microarray-based genomic profiling allowed the identification of genomic abnormalities that could not be detected by FISH and/or MLPA, including a focal TP53 loss and copy neutral losses of heterozygosity of chromosome 17p. CONCLUSION From our results we conclude that although the microarray platforms exhibit a somewhat lower limit of detection compared to FISH, they still allow the detection of copy number abnormalities present in as few as 16% of the cells. By applying similar interpretation criteria, the results obtained from both platforms were comparable. In addition, we conclude that both microarray platforms allow the identification of additional potential prognostic relevant abnormalities such as focal TP53 deletions and copy neutral losses of heterozygosity of chromosome 17p, which would have remained undetected by FISH or MLPA. The prognostic relevance of these novel genomic alterations requires further evaluation in prospective clinical trials.
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Affiliation(s)
- Marian Jpl Stevens-Kroef
- Department of Human Genetics, Radboud university medical center, P,O, Box 9101, Nijmegen 6500 HB, The Netherlands.
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131
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Conacci-Sorrell M, McFerrin L, Eisenman RN. An overview of MYC and its interactome. Cold Spring Harb Perspect Med 2014; 4:a014357. [PMID: 24384812 DOI: 10.1101/cshperspect.a014357] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review is intended to provide a broad outline of the biological and molecular functions of MYC as well as of the larger protein network within which MYC operates. We present a view of MYC as a sensor that integrates multiple cellular signals to mediate a broad transcriptional response controlling many aspects of cell behavior. We also describe the larger transcriptional network linked to MYC with emphasis on the MXD family of MYC antagonists. Last, we discuss evidence that the network has evolved for millions of years, dating back to the emergence of animals.
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132
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SAMHD1 is mutated recurrently in chronic lymphocytic leukemia and is involved in response to DNA damage. Blood 2013; 123:1021-31. [PMID: 24335234 DOI: 10.1182/blood-2013-04-490847] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase and a nuclease that restricts HIV-1 in noncycling cells. Germ-line mutations in SAMHD1 have been described in patients with Aicardi-Goutières syndrome (AGS), a congenital autoimmune disease. In a previous longitudinal whole genome sequencing study of chronic lymphocytic leukemia (CLL), we revealed a SAMHD1 mutation as a potential founding event. Here, we describe an AGS patient carrying a pathogenic germ-line SAMHD1 mutation who developed CLL at 24 years of age. Using clinical trial samples, we show that acquired SAMHD1 mutations are associated with high variant allele frequency and reduced SAMHD1 expression and occur in 11% of relapsed/refractory CLL patients. We provide evidence that SAMHD1 regulates cell proliferation and survival and engages in specific protein interactions in response to DNA damage. We propose that SAMHD1 may have a function in DNA repair and that the presence of SAMHD1 mutations in CLL promotes leukemia development.
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133
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Sankunny M, Parikh RA, Lewis DW, Gooding WE, Saunders WS, Gollin SM. Targeted inhibition of ATR or CHEK1 reverses radioresistance in oral squamous cell carcinoma cells with distal chromosome arm 11q loss. Genes Chromosomes Cancer 2013; 53:129-43. [PMID: 24327542 DOI: 10.1002/gcc.22125] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 01/08/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC), a subset of head and neck squamous cell carcinoma (HNSCC), is the eighth most common cancer in the U.S.. Amplification of chromosomal band 11q13 and its association with poor prognosis has been well established in OSCC. The first step in the breakage-fusion-bridge (BFB) cycle leading to 11q13 amplification involves breakage and loss of distal 11q. Distal 11q loss marked by copy number loss of the ATM gene is observed in 25% of all Cancer Genome Atlas (TCGA) tumors, including 48% of HNSCC. We showed previously that copy number loss of distal 11q is associated with decreased sensitivity (increased resistance) to ionizing radiation (IR) in OSCC cell lines. We hypothesized that this radioresistance phenotype associated with ATM copy number loss results from upregulation of the compensatory ATR-CHEK1 pathway, and that knocking down the ATR-CHEK1 pathway increases the sensitivity to IR of OSCC cells with distal 11q loss. Clonogenic survival assays confirmed the association between reduced sensitivity to IR in OSCC cell lines and distal 11q loss. Gene and protein expression studies revealed upregulation of the ATR-CHEK1 pathway and flow cytometry showed G2 M checkpoint arrest after IR treatment of cell lines with distal 11q loss. Targeted knockdown of the ATR-CHEK1 pathway using CHEK1 or ATR siRNA or a CHEK1 small molecule inhibitor (SMI, PF-00477736) resulted in increased sensitivity of the tumor cells to IR. Our results suggest that distal 11q loss is a useful biomarker in OSCC for radioresistance that can be reversed by ATR-CHEK1 pathway inhibition.
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Affiliation(s)
- Madhav Sankunny
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA; University of Pittsburgh Cancer Institute, Pittsburgh, PA
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134
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Fabbri G, Khiabanian H, Holmes AB, Wang J, Messina M, Mullighan CG, Pasqualucci L, Rabadan R, Dalla-Favera R. Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome. ACTA ACUST UNITED AC 2013; 210:2273-88. [PMID: 24127483 PMCID: PMC3804949 DOI: 10.1084/jem.20131448] [Citation(s) in RCA: 225] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Characterization of the pattern of clonal evolution from CLL to RS, the genetic determinants of CLL transformation to RS, and the pathogenetic relationship between RS and classical non–CLL-associated de novo DLBCL. Richter syndrome (RS) derives from the rare transformation of chronic lymphocytic leukemia (CLL) into an aggressive lymphoma, most commonly of the diffuse large B cell lymphoma (DLBCL) type. The molecular pathogenesis of RS is only partially understood. By combining whole-exome sequencing and copy-number analysis of 9 CLL-RS pairs and of an extended panel of 43 RS cases, we show that this aggressive disease typically arises from the predominant CLL clone by acquiring an average of ∼20 genetic lesions/case. RS lesions are heterogeneous in terms of load and spectrum among patients, and include those involved in CLL progression and chemorefractoriness (TP53 disruption and NOTCH1 activation) as well as some not previously implicated in CLL or RS pathogenesis. In particular, disruption of the CDKN2A/B cell cycle regulator is associated with ∼30% of RS cases. Finally, we report that the genomic landscape of RS is significantly different from that of de novo DLBCL, suggesting that they represent distinct disease entities. These results provide insights into RS pathogenesis, and identify dysregulated pathways of potential diagnostic and therapeutic relevance.
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Affiliation(s)
- Giulia Fabbri
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, 2 Department of Pathology and Cell Biology, 3 Departments of Genetics and Development and of Microbiology and Immunology and 4 Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032
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135
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Two main genetic pathways lead to the transformation of chronic lymphocytic leukemia to Richter syndrome. Blood 2013; 122:2673-82. [DOI: 10.1182/blood-2013-03-489518] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key Points
Richter syndrome has genomic complexity intermediate between chronic lymphocytic leukemia and diffuse large B-cell lymphoma. Inactivation of TP53 and of CDKN2A is a main mechanism in the transformation to Richter syndrome.
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136
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Improgo MR, Brown JR. Genomic approaches to chronic lymphocytic leukemia. Hematol Oncol Clin North Am 2013; 27:157-71. [PMID: 23561468 DOI: 10.1016/j.hoc.2013.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This article discusses recent advances in genomic approaches used to understand chronic lymphocytic leukemia. Tools for analyzing DNA-level lesions are described, data obtained from these various platforms summarized, and the clinical relevance of these findings discussed.
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Affiliation(s)
- Ma Reina Improgo
- Department of Medical Oncology, Dana-Farber Cancer Institute, CLL Center, Harvard Medical School, Boston, MA 02215, USA
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137
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Defective DROSHA processing contributes to downregulation of MiR-15/-16 in chronic lymphocytic leukemia. Leukemia 2013; 28:98-107. [PMID: 23974981 DOI: 10.1038/leu.2013.246] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 08/07/2013] [Accepted: 08/08/2013] [Indexed: 12/21/2022]
Abstract
The MIR-15A/-16-1 tumor suppressor microRNAs (miRNAs) are deleted in leukemic cells from more than 50% of patients with chronic lymphocytic leukemia (CLL). As these miRNAs are also less abundant in patients without genomic deletion, their downregulation in CLL is likely to be caused by additional mechanisms. We found the primary transcripts (pri-miRNAs) of MIR-15a/-16/-15b to be elevated and processing intermediates (precursor miRNAs) to be reduced in cells from CLL patients (22/38) compared with non-malignant B-cells (n=14), indicating a block of miRNA maturation at the DROSHA processing step. Using a luciferase reporter assay for pri-miR processing we validated the defect in primary CLL cells. The block of miRNA maturation is restricted to specific miRNAs and can be found in the cell line MEC-2, but not in MEC-1, even though both are derived from the same CLL patient. In these cells, the RNA-specific deaminase ADARB1 leads to reduced pri-miRNA processing, but full processing efficiency is recovered upon deletion of the RNA-binding domains or nuclear localization of ADARB1. Thus, we show that, apart from genomic deletion or transcriptional downregulation, aberrant processing of miRNA leads to specific reduction of miRNAs in leukemic cells. This represents a novel oncogenic mechanism in the pathogenesis of CLL.
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138
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Alsolami R, Knight SJL, Schuh A. Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia? Per Med 2013; 10:361-376. [PMID: 24611071 PMCID: PMC3943176 DOI: 10.2217/pme.13.33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is low-grade lymphoma of mature B cells and it is considered to be the most common type of hematological malignancy in the western world. CLL is characterized by a chronically relapsing course and clinical and biological heterogeneity. Many patients do not require any treatment for years. Although important progress has been made in the treatment of CLL, none of the conventional treatment options are curative. Recurrent chromosomal abnormalities have been identified and are associated with prognosis and pathogenesis of the disease. More recently, unbiased genome-wide technologies have identified multiple additional recurrent aberrations. The precise predictive value of these has not been established, but it is likely that the genetic heterogeneity observed at least partly reflects the clinical variability. The present article reviews our current knowledge of predictive markers in CLL using whole-genome technologies.
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Affiliation(s)
- Reem Alsolami
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- King Abdulaziz University, Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Samantha JL Knight
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anna Schuh
- Oxford National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
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139
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Landau DA, Wu CJ. Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics. Genome Med 2013; 5:47. [PMID: 23731665 PMCID: PMC3706960 DOI: 10.1186/gm451] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genetic research owing to its prevalence and the accessibility of sample material. Recently, genome-wide technologies have been intensively applied to CLL genetics, with remarkable progress. Single nucleotide polymorphism arrays have identified recurring chromosomal aberrations, thereby focusing functional studies on discrete genomic lesions and leading to the first implication of somatic microRNA disruption in cancer. Next-generation sequencing (NGS) has further transformed our understanding of CLL by identifying novel recurrently mutated putative drivers, including the unexpected discovery of somatic mutations affecting spliceosome function. NGS has further enabled in-depth examination of the transcriptional and epigenetic changes in CLL that accompany genetic lesions, and has shed light on how different driver events appear at different stages of disease progression and clonally evolve with relapsed disease. In addition to providing important insights into disease biology, these discoveries have significant translational potential. They enhance prognosis by highlighting specific lesions associated with poor clinical outcomes (for example, driver events such as mutations in the splicing factor subunit gene SF3B1) or with increased clonal heterogeneity (for example, the presence of subclonal driver mutations). Here, we review new genomic discoveries in CLL and discuss their possible implications in the era of precision medicine.
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Affiliation(s)
- Dan A Landau
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Broad Institute, Cambridge, MA 02142, USA ; Department of Hematology, Yale Cancer Center, New Haven, CT 06510, USA ; Université Paris Diderot, Paris 75013, France
| | - Catherine J Wu
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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140
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Rosenquist R, Cortese D, Bhoi S, Mansouri L, Gunnarsson R. Prognostic markers and their clinical applicability in chronic lymphocytic leukemia: where do we stand? Leuk Lymphoma 2013; 54:2351-64. [PMID: 23480493 DOI: 10.3109/10428194.2013.783913] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease where the majority of patients have an indolent disease course, while others may experience a far more aggressive disease, treatment failure and poor overall survival. During the last two decades, there has been an intense search to find novel biomarkers that can predict prognosis as well as guide treatment decisions. Two of the most reliable molecular prognostic markers, both of which are offered in routine diagnostics, are the immunoglobulin heavy chain variable (IGHV) gene mutational status and fluorescence in situ hybridization (FISH) detection of prognostically relevant genomic aberrations (e.g. 11q-, 13q-, +12 and 17p-). In addition to these markers, a myriad of additional biomarkers have been postulated as potential prognosticators in CLL, on the protein (e.g. CD38, ZAP70, TCL1), the RNA (e.g. LPL, CLLU1, micro-RNAs) and the genomic (e.g. TP53, NOTCH1, SF3B1 and BIRC3 mutations) level. Efforts are now being made to test these novel markers in larger patient cohorts as well as in prospective trials, with the ultimate goal to combine the "best" markers in a "CLL prognostic index" applicable for the individual patient. Although it is clear that these studies have significantly improved our knowledge regarding both prognostication and the biology of the disease, there is still an immediate need for recognizing biomarkers that can predict therapy response, and efforts should now focus on addressing this pertinent issue. In the present article, we review the extensive literature in the field of prognostic markers in CLL, focus on the most clinically relevant markers and discuss future directions regarding biomarkers in CLL.
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Affiliation(s)
- Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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141
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Bassaganyas L, Beà S, Escaramís G, Tornador C, Salaverria I, Zapata L, Drechsel O, Ferreira PG, Rodriguez-Santiago B, Tubio JMC, Navarro A, Martín-García D, López C, Martínez-Trillos A, López-Guillermo A, Gut M, Ossowski S, López-Otín C, Campo E, Estivill X. Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis. Leukemia 2013; 27:2376-9. [PMID: 23612016 PMCID: PMC3865532 DOI: 10.1038/leu.2013.127] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- L Bassaganyas
- 1] Center for Genomic Regulation (CRG), Barcelona, Spain [2] Pompeu Fabra University (UPF) Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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142
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Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 2013; 152:714-26. [PMID: 23415222 DOI: 10.1016/j.cell.2013.01.019] [Citation(s) in RCA: 1069] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/15/2012] [Accepted: 01/06/2013] [Indexed: 02/06/2023]
Abstract
Clonal evolution is a key feature of cancer progression and relapse. We studied intratumoral heterogeneity in 149 chronic lymphocytic leukemia (CLL) cases by integrating whole-exome sequence and copy number to measure the fraction of cancer cells harboring each somatic mutation. We identified driver mutations as predominantly clonal (e.g., MYD88, trisomy 12, and del(13q)) or subclonal (e.g., SF3B1 and TP53), corresponding to earlier and later events in CLL evolution. We sampled leukemia cells from 18 patients at two time points. Ten of twelve CLL cases treated with chemotherapy (but only one of six without treatment) underwent clonal evolution, predominantly involving subclones with driver mutations (e.g., SF3B1 and TP53) that expanded over time. Furthermore, presence of a subclonal driver mutation was an independent risk factor for rapid disease progression. Our study thus uncovers patterns of clonal evolution in CLL, providing insights into its stepwise transformation, and links the presence of subclones with adverse clinical outcomes.
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143
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Kempin S. Update on Chronic Lymphocytic Leukemia: Overview of New Agents and Comparative Analysis. Curr Treat Options Oncol 2013; 14:144-55. [DOI: 10.1007/s11864-013-0229-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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144
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145
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Mian M, Rinaldi A, Mensah AA, Rossi D, Ladetto M, Forconi F, Marasca R, Uhr M, Stussi G, Kwee I, Cavalli F, Gaidano G, Zucca E, Bertoni F. Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH. Ann Oncol 2013; 24:1378-84. [PMID: 23372049 DOI: 10.1093/annonc/mds646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Genomic complexity can predict the clinical course of patients affected by chronic lymphocytic leukemia (CLL) with a normal FISH. However, large studies are still lacking. Here, we analyzed a large series of CLL patients and also carried out the so far largest comparison of FISH versus single-nucleotide polymorphism (SNP) array in this disease. PATIENTS AND METHODS SNP-array data were derived from a previously reported dataset. RESULTS Seventy-seven of 329 CLL patients (23%) presented with a normal FISH. At least one large (>5 Mb) genomic aberration was detected by SNP array in 17 of 77 patients (22%); this finding significantly affected TTT. There was no correlation with the presence of TP53 mutations. In multivariate analysis, including age, Binet stage, IGHV genes mutational status and large genomic lesion, the latter three factors emerged as independent prognosticators. The concordance between FISH and SNP array varied between 84 and 97%, depending on the specific genomic locus investigated. CONCLUSIONS SNP array detected additional large genomic aberrations not covered by the standard FISH panel predicting the outcome of CLL patients.
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Affiliation(s)
- M Mian
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
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146
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Acquired Genomic Copy Number Aberrations in CLL. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 792:47-86. [DOI: 10.1007/978-1-4614-8051-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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