1001
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Wawrzyniak E, Kotkowska A, Blonski JZ, Siemieniuk-Rys M, Ziolkowska E, Giannopoulos K, Robak T, Korycka-Wolowiec A. Clonal evolution in CLL patients as detected by FISH versus chromosome banding analysis, and its clinical significance. Eur J Haematol 2013; 92:91-101. [DOI: 10.1111/ejh.12215] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Ewa Wawrzyniak
- Department of Hematology; Medical University; Lodz Poland
| | | | | | | | | | | | - Tadeusz Robak
- Department of Hematology; Medical University; Lodz Poland
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1002
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Chung KF, Adcock IM. How variability in clinical phenotypes should guide research into disease mechanisms in asthma. Ann Am Thorac Soc 2013; 10 Suppl:S109-17. [PMID: 24313760 PMCID: PMC3960989 DOI: 10.1513/annalsats.201304-087aw] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 06/14/2013] [Indexed: 12/15/2022] Open
Abstract
Asthma is increasingly being considered as a collection of different phenotypes that present with intermittent wheezing. Unbiased approaches to classifying asthma have led to the identification of distinct phenotypes based on age of onset of disease, atopic state, disease severity or activity, degree of chronic airflow obstruction, and sputum eosinophilia. Linking phenotypes to known disease mechanism is likely to be more fruitful in determining the potential targets necessary for successful therapies of specific endotypes. A "Th2-high expression" signature from the epithelium of patients with asthma identifies a subset of patients with high eosinophilia and good therapeutic responsiveness to corticosteroids. Other characteristic traits of asthma include noneosinophilic asthma, corticosteroid insensitivity, obesity-associated, and exacerbation-prone. Further progress into asthma mechanisms will be driven by unbiased data integration of multiscale data sets from omics technologies with those phenotypic characteristics and by using mathematical modeling. This will lead to the discovery of new pathways and their integration into endotypes and also set up further hypothesis-driven research. Continued iteration through experimentation or modeling will be needed to refine the phenotypes that relate to outcomes and also delineate specific treatments for specific phenotypes.
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Affiliation(s)
- Kian Fan Chung
- Airways Disease, National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Ian M. Adcock
- Biomedical Research Unit, Royal Brompton Hospital, London, United Kingdom
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1003
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Abstract
AbstractThe management of chronic lymphocytic leukemia (CLL) is undergoing profound changes. Several new drugs have been approved for CLL treatment (fludarabine, bendamustine, and the monoclonal antibodies alemtuzumab, rituximab, and ofatumumab) and many more drugs are in advanced clinical development to be approved for this disease. In addition, the extreme heterogeneity of the clinical course and our improved ability to foresee the prognosis of this leukemia by the use of clinical, biological, and genetic parameters now allow us to characterize patients with a very mild onset and course, an intermediate prognosis, or a very aggressive course with high-risk leukemia. Therefore, it becomes increasingly challenging to select the right treatment strategy for each condition. This article summarizes the currently available diagnostic and therapeutic tools and gives an integrated recommendation of how to manage CLL in 2013. Moreover, I propose a strategy how we might integrate the novel agents for CLL therapy into sequential treatment approaches in the near future.
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1004
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Knudsen PB, Hanna B, Ohl S, Sellner L, Zenz T, Döhner H, Stilgenbauer S, Larsen TO, Lichter P, Seiffert M. Chaetoglobosin A preferentially induces apoptosis in chronic lymphocytic leukemia cells by targeting the cytoskeleton. Leukemia 2013; 28:1289-98. [PMID: 24280868 DOI: 10.1038/leu.2013.360] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/08/2013] [Accepted: 11/20/2013] [Indexed: 12/19/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B cells. One of the major challenges in treatment of CLL is the achievement of a complete remission to prevent relapse of disease originating from cells within lymphoid tissues and subsequent chemoresistance. In search for novel drugs that target CLL cells in protective microenvironments, we performed a fungal extract screen using cocultures of primary CLL cells with bone marrow-derived stromal cells. A secondary metabolite produced by Penicillium aquamarinium was identified as Chaetoglobosin A (ChA), a member of the cytochalasan family that showed preferential induction of apoptosis in CLL cells, even under culture conditions that mimic lymphoid tissues. In vitro testing of 89 CLL cases revealed effective targeting of CLL cells by ChA, independent of bad prognosis characteristics, like 17p deletion or TP53 mutation. To provide insight into its mechanism of action, we showed that ChA targets filamentous actin in CLL cells and thereby induces cell-cycle arrest and inhibits membrane ruffling and cell migration. Our data further revealed that ChA prevents CLL cell activation and sensitizes them for treatment with PI3K and BTK inhibitors, suggesting this compound as a novel potential drug for CLL.
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Affiliation(s)
- P B Knudsen
- 1] Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany [2] Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - B Hanna
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Ohl
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - L Sellner
- 1] Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany [2] Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - T Zenz
- 1] Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany [2] Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - H Döhner
- Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - T O Larsen
- Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - P Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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1005
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1006
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Abstract
Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome.
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1007
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Acquisition of MYD88 L265P mutation during treatment of diffuse large B cell lymphoma of the parotid gland. Virchows Arch 2013; 464:121-4. [DOI: 10.1007/s00428-013-1514-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/29/2013] [Accepted: 11/07/2013] [Indexed: 10/26/2022]
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1008
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Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, Rosenberg M, Goetz EM, Sullivan RJ, Farlow DN, Friedrich DC, Anderka K, Perrin D, Johannessen CM, McKenna A, Cibulskis K, Kryukov G, Hodis E, Lawrence DP, Fisher S, Getz G, Gabriel SB, Carter SL, Flaherty KT, Wargo JA, Garraway LA. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov 2013; 4:61-8. [PMID: 24265154 DOI: 10.1158/2159-8290.cd-13-0631] [Citation(s) in RCA: 372] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP-ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabrafenib monotherapy. Mechanisms of clinical resistance to combined RAF/MEK inhibition are unknown. We performed whole-exome sequencing (WES) and whole-transcriptome sequencing (RNA-seq) on pretreatment and drug-resistant tumors from five patients with acquired resistance to dabrafenib/trametinib. In three of these patients, we identified additional mitogen-activated protein kinase (MAPK) pathway alterations in the resistant tumor that were not detected in the pretreatment tumor, including a novel activating mutation in MEK2 (MEK2(Q60P)). MEK2(Q60P) conferred resistance to combined RAF/MEK inhibition in vitro, but remained sensitive to inhibition of the downstream kinase extracellular signal-regulated kinase (ERK). The continued MAPK signaling-based resistance identified in these patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.
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Affiliation(s)
- Nikhil Wagle
- 1Department of Medical Oncology, Dana-Farber Cancer Institute; 2Department of Medicine, Brigham and Women's Hospital; 3Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston; 4Broad Institute of Harvard and MIT; and 5Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
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1009
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Abstract
DNA sequencing has taught us much about the structure of cancer genomes and enabled the discovery of novel genes that drive and maintain tumorigenesis. With the advent and application of next-generation massively parallel sequencing technologies, one can rapidly generate and analyze data from the cellular "-omes": genomes, exomes, and transcriptomes. This review highlights recent genomic discoveries in signal transduction, metabolism, epigenetic modifications, cell cycle and genome maintenance, RNA processing, and transcription. Additionally, genomic sequencing has revealed the complexity of the cancer genome and has enabled the discovery of functional rearrangements with therapeutic and diagnostic potentials.
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Affiliation(s)
- Juliann Chmielecki
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, Massachusetts 02115;
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1010
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Tumour heterogeneity and cancer cell plasticity. Nature 2013; 501:328-37. [PMID: 24048065 PMCID: PMC4521623 DOI: 10.1038/nature12624] [Citation(s) in RCA: 1665] [Impact Index Per Article: 151.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/10/2013] [Indexed: 02/06/2023]
Abstract
Phenotypic and functional heterogeneity arise among cancer cells within the same tumour as a consequence of genetic change, environmental differences and reversible changes in cell properties. Some cancers also contain a hierarchy in which tumorigenic cancer stem cells differentiate into non-tumorigenic progeny. However, it remains unclear what fraction of cancers follow the stem-cell model and what clinical behaviours the model explains. Studies using lineage tracing and deep sequencing could have implications for the cancer stem-cell model and may help to determine the extent to which it accounts for therapy resistance and disease progression.
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1011
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The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013; 501:338-45. [PMID: 24048066 DOI: 10.1038/nature12625] [Citation(s) in RCA: 1546] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/13/2013] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed extensive genetic diversity both between and within tumours. This heterogeneity affects key cancer pathways, driving phenotypic variation, and poses a significant challenge to personalized cancer medicine. A major cause of genetic heterogeneity in cancer is genomic instability. This instability leads to an increased mutation rate and can shape the evolution of the cancer genome through a plethora of mechanisms. By understanding these mechanisms we can gain insight into the common pathways of tumour evolution that could support the development of future therapeutic strategies.
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1012
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Markman JL, Rekechenetskiy A, Holler E, Ljubimova JY. Nanomedicine therapeutic approaches to overcome cancer drug resistance. Adv Drug Deliv Rev 2013; 65:1866-79. [PMID: 24120656 PMCID: PMC5812459 DOI: 10.1016/j.addr.2013.09.019] [Citation(s) in RCA: 477] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 09/29/2013] [Accepted: 09/30/2013] [Indexed: 12/27/2022]
Abstract
Nanomedicine is an emerging form of therapy that focuses on alternative drug delivery and improvement of the treatment efficacy while reducing detrimental side effects to normal tissues. Cancer drug resistance is a complicated process that involves multiple mechanisms. Here we discuss the major forms of drug resistance and the new possibilities that nanomedicines offer to overcome these treatment obstacles. Novel nanomedicines that have a high ability for flexible, fast drug design and production based on tumor genetic profiles can be created making drug selection for personal patient treatment much more intensive and effective. This review aims to demonstrate the advantage of the young medical science field, nanomedicine, for overcoming cancer drug resistance. With the advanced design and alternative mechanisms of drug delivery known for different nanodrugs including liposomes, polymer conjugates, micelles, dendrimers, carbon-based, and metallic nanoparticles, overcoming various forms of multi-drug resistance looks promising and opens new horizons for cancer treatment.
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Affiliation(s)
- Janet L Markman
- Nanomedicine Research Center, Department of Neurosurgery at Cedars-Sinai Medical Center, Los Angeles, CA, United States
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1013
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Mansouri L, Sutton LA, Ljungström V, Sörqvist EF, Gunnarsson R, Smedby KE, Juliusson G, Stamatopoulos K, Nilsson M, Rosenquist R. Feasibility of targeted next-generation sequencing of the TP53 and ATM genes in chronic lymphocytic leukemia. Leukemia 2013; 28:694-6. [PMID: 24172824 DOI: 10.1038/leu.2013.322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- L Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - L-A Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - V Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - E F Sörqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - R Gunnarsson
- Department of Laboratory Medicine, Clinical Genetics, Lund University, Lund, Sweden
| | - K E Smedby
- Department of Medicine, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - G Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Lund, Sweden
| | - K Stamatopoulos
- 1] Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden [2] Institute of Applied Biosciences, CERTH, Thessaloniki, Greece [3] Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - M Nilsson
- 1] Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden [2] Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - R Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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1014
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Arruga F, Gizdic B, Serra S, Vaisitti T, Ciardullo C, Coscia M, Laurenti L, D'Arena G, Jaksic O, Inghirami G, Rossi D, Gaidano G, Deaglio S. Functional impact of NOTCH1 mutations in chronic lymphocytic leukemia. Leukemia 2013; 28:1060-70. [PMID: 24170027 DOI: 10.1038/leu.2013.319] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 02/06/2023]
Abstract
The purpose of this study was to compare the expression and function of NOTCH1 in chronic lymphocytic leukemia (CLL) patients harboring a wild-type (WT) or mutated NOTCH1 gene. NOTCH1 mRNA and surface protein expression levels were independent of the NOTCH1 gene mutational status, consistent with the requirement for NOTCH1 signaling in this leukemia. However, compared with NOTCH1-WT CLL, mutated cases displayed biochemical and transcriptional evidence of an intense activation of the NOTCH1 pathway. In vivo, expression and activation of NOTCH1 was highest in CLL cells from the lymph nodes as confirmed by immunohistochemistry. In vitro, the NOTCH1 pathway was rapidly downregulated, suggesting that signaling relies upon micro-environmental interactions even in NOTCH1-mutated cases. Accordingly, co-culture of Jagged1(+) (the NOTCH1 ligand) nurse-like cells with autologous CLL cells sustained NOTCH1 activity over time and mediated CLL survival and resistance against pro-apoptotic stimuli, both abrogated when NOTCH1 signaling was pharmacologically switched off. Together, these results show that NOTCH1 mutations have stabilizing effects on the NOTCH1 pathway in CLL. Furthermore, micro-environmental interactions appear critical in activating the NOTCH1 pathway both in WT and mutated patients. Finally, NOTCH1 signals may create conditions that favor drug resistance, thus making NOTCH1 a potential molecular target in CLL.
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Affiliation(s)
- F Arruga
- Department of Medical Sciences, University of Turin, School of Medicine, Turin, Italy
| | - B Gizdic
- 1] Department of Medical Sciences, University of Turin, School of Medicine, Turin, Italy [2] Department of Hematology, Dubrava University Hospital, Zagreb, Croatia
| | - S Serra
- 1] Department of Medical Sciences, University of Turin, School of Medicine, Turin, Italy [2] Human Genetics Foundation (HuGeF), Turin, Italy
| | - T Vaisitti
- Department of Medical Sciences, University of Turin, School of Medicine, Turin, Italy
| | - C Ciardullo
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - M Coscia
- Division of Hematology, Laboratory of Hematology Oncology, Center of Experimental Research and Medical Studies, Cittá della Salute e della Scienza University Hospital, Turin, Italy
| | - L Laurenti
- Institute of Hematology, Catholic University of the Sacred Heart, Rome, Italy
| | - G D'Arena
- Department of Onco-Hematology, IRCCS Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture, Italy
| | - O Jaksic
- Department of Hematology, Dubrava University Hospital, Zagreb, Croatia
| | - G Inghirami
- Department of Molecular Biotechnology and Health Sciences, Center of Experimental Research and Medical Studies, University of Turin, Turin, Italy
| | - D Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - G Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - S Deaglio
- 1] Department of Medical Sciences, University of Turin, School of Medicine, Turin, Italy [2] Human Genetics Foundation (HuGeF), Turin, Italy
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1015
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Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc Natl Acad Sci U S A 2013; 110:18250-5. [PMID: 24145436 DOI: 10.1073/pnas.1314608110] [Citation(s) in RCA: 381] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive tumor, but a subset of patients may follow an indolent clinical course. To understand the mechanisms underlying this biological heterogeneity, we performed whole-genome and/or whole-exome sequencing on 29 MCL cases and their respective matched normal DNA, as well as 6 MCL cell lines. Recurrently mutated genes were investigated by targeted sequencing in an independent cohort of 172 MCL patients. We identified 25 significantly mutated genes, including known drivers such as ataxia-telangectasia mutated (ATM), cyclin D1 (CCND1), and the tumor suppressor TP53; mutated genes encoding the anti-apoptotic protein BIRC3 and Toll-like receptor 2 (TLR2); and the chromatin modifiers WHSC1, MLL2, and MEF2B. We also found NOTCH2 mutations as an alternative phenomenon to NOTCH1 mutations in aggressive tumors with a dismal prognosis. Analysis of two simultaneous or subsequent MCL samples by whole-genome/whole-exome (n = 8) or targeted (n = 19) sequencing revealed subclonal heterogeneity at diagnosis in samples from different topographic sites and modulation of the initial mutational profile at the progression of the disease. Some mutations were predominantly clonal or subclonal, indicating an early or late event in tumor evolution, respectively. Our study identifies molecular mechanisms contributing to MCL pathogenesis and offers potential targets for therapeutic intervention.
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1016
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Abstract
Myelodysplasia is a diagnostic feature of myelodysplastic syndromes (MDSs) but is also found in other myeloid neoplasms. Its molecular basis has been recently elucidated by means of massive parallel sequencing studies. About 90% of MDS patients carry ≥1 oncogenic mutations, and two thirds of them are found in individuals with a normal karyotype. Driver mutant genes include those of RNA splicing (SF3B1, SRSF2, U2AF1, and ZRSR2), DNA methylation (TET2, DNMT3A, and IDH1/2), chromatin modification (ASXL1 and EZH2), transcription regulation (RUNX1), DNA repair (TP53), signal transduction (CBL, NRAS, and KRAS), and cohesin complex (STAG2). Only 4 to 6 genes are consistently mutated in ≥10% MDS patients, whereas a long tail of ∼50 genes are mutated less frequently. At presentation, most patients typically have 2 or 3 driver oncogenic mutations and hundreds of background mutations. MDS driver genes are also frequently mutated in other myeloid neoplasms. Reliable genotype/phenotype relationships include the association of the SF3B1 mutation with refractory anemia with ring sideroblasts, TET2/SRSF2 comutation with chronic myelomonocytic leukemia, and activating CSF3R mutation with chronic neutrophilic leukemia. Although both founding and subclonal driver mutations have been shown to have prognostic significance, prospective clinical trials that include the molecular characterization of the patient's genome are now needed.
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1017
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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: 216] [Impact Index Per Article: 19.6] [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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1018
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Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W, Zhao Z. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med 2013; 5:91. [PMID: 24112718 PMCID: PMC3971343 DOI: 10.1186/gm495] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 10/02/2013] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Driven by high throughput next generation sequencing technologies and the pressing need to decipher cancer genomes, computational approaches for detecting somatic single nucleotide variants (sSNVs) have undergone dramatic improvements during the past 2 years. The recently developed tools typically compare a tumor sample directly with a matched normal sample at each variant locus in order to increase the accuracy of sSNV calling. These programs also address the detection of sSNVs at low allele frequencies, allowing for the study of tumor heterogeneity, cancer subclones, and mutation evolution in cancer development. METHODS We used whole genome sequencing (Illumina Genome Analyzer IIx platform) of a melanoma sample and matched blood, whole exome sequencing (Illumina HiSeq 2000 platform) of 18 lung tumor-normal pairs and seven lung cancer cell lines to evaluate six tools for sSNV detection: EBCall, JointSNVMix, MuTect, SomaticSniper, Strelka, and VarScan 2, with a focus on MuTect and VarScan 2, two widely used publicly available software tools. Default/suggested parameters were used to run these tools. The missense sSNVs detected in these samples were validated through PCR and direct sequencing of genomic DNA from the samples. We also simulated 10 tumor-normal pairs to explore the ability of these programs to detect low allelic-frequency sSNVs. RESULTS Out of the 237 sSNVs successfully validated in our cancer samples, VarScan 2 and MuTect detected the most of any tools (that is, 204 and 192, respectively). MuTect identified 11 more low-coverage validated sSNVs than VarScan 2, but missed 11 more sSNVs with alternate alleles in normal samples than VarScan 2. When examining the false calls of each tool using 169 invalidated sSNVs, we observed >63% false calls detected in the lung cancer cell lines had alternate alleles in normal samples. Additionally, from our simulation data, VarScan 2 identified more sSNVs than other tools, while MuTect characterized most low allelic-fraction sSNVs. CONCLUSIONS Our study explored the typical false-positive and false-negative detections that arise from the use of sSNV-calling tools. Our results suggest that despite recent progress, these tools have significant room for improvement, especially in the discrimination of low coverage/allelic-frequency sSNVs and sSNVs with alternate alleles in normal samples.
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Affiliation(s)
- Qingguo Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fei Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ; Department of Oncology, Shanghai Medical College, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Donald Hucks
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly Brown Dahlman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William Pao
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA ; Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
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1019
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Hertlein E, Beckwith KA, Lozanski G, Chen TL, Towns WH, Johnson AJ, Lehman A, Ruppert AS, Bolon B, Andritsos L, Lozanski A, Rassenti L, Zhao W, Jarvinen TM, Senter L, Croce CM, Symer DE, de la Chapelle A, Heerema NA, Byrd JC. Characterization of a new chronic lymphocytic leukemia cell line for mechanistic in vitro and in vivo studies relevant to disease. PLoS One 2013; 8:e76607. [PMID: 24130782 PMCID: PMC3793922 DOI: 10.1371/journal.pone.0076607] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 08/26/2013] [Indexed: 12/30/2022] Open
Abstract
Studies of chronic lymphocytic leukemia (CLL) have yielded substantial progress, however a lack of immortalized cell lines representative of the primary disease has hampered a full understanding of disease pathogenesis and development of new treatments. Here we describe a novel CLL cell line (OSU-CLL) generated by EBV transformation, which displays a similar cytogenetic and immunophenotype observed in the patient’s CLL (CD5 positive with trisomy 12 and 19). A companion cell line was also generated from the same patient (OSU-NB). This cell line lacked typical CLL characteristics, and is likely derived from the patient’s normal B cells. In vitro migration assays demonstrated that OSU-CLL exhibits migratory properties similar to primary CLL cells whereas OSU-NB has significantly reduced ability to migrate spontaneously or towards chemokine. Microarray analysis demonstrated distinct gene expression patterns in the two cell lines, including genes on chromosomes 12 and 19, which is consistent with the cytogenetic profile in this cell line. Finally, OSU-CLL was readily transplantable into NOG mice, producing uniform engraftment by three weeks with leukemic cells detectable in the peripheral blood spleen and bone marrow. These studies describe a new CLL cell line that extends currently available models to study gene function in this disease.
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Affiliation(s)
- Erin Hertlein
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Kyle A. Beckwith
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Gerard Lozanski
- Department of Pathology, the Ohio State University, Columbus, Ohio, United States of America
| | - Timothy L. Chen
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - William H. Towns
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Amy J. Johnson
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Amy Lehman
- Center for Biostatistics, the Ohio State University, Columbus, Ohio, United States of America
| | - Amy S. Ruppert
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Brad Bolon
- Department of Veterinary Biosciences and the Comparative Pathology and Mouse Phenotyping Shared Resource, the Ohio State University, Columbus, Ohio, United States of America
| | - Leslie Andritsos
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Arletta Lozanski
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
| | - Laura Rassenti
- Moores University of California-San Diego Cancer Center, University of California San Diego, California, United States of America
| | - Weiqiang Zhao
- Department of Pathology, the Ohio State University, Columbus, Ohio, United States of America
| | - Tiina M. Jarvinen
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center at the Ohio State University, Columbus, Ohio, United States of America
| | - Leigha Senter
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center at the Ohio State University, Columbus, Ohio, United States of America
| | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center at the Ohio State University, Columbus, Ohio, United States of America
| | - David E. Symer
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center at the Ohio State University, Columbus, Ohio, United States of America
| | - Albert de la Chapelle
- Department of Molecular Virology, Immunology and Medical Genetics, Division of Human Cancer Genetics, Comprehensive Cancer Center at the Ohio State University, Columbus, Ohio, United States of America
| | - Nyla A. Heerema
- Department of Pathology, the Ohio State University, Columbus, Ohio, United States of America
| | - John C. Byrd
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, Ohio, United States of America
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1020
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A revised NOTCH1 mutation frequency still impacts survival while the allele burden predicts early progression in chronic lymphocytic leukemia. Leukemia 2013; 28:436-9. [PMID: 24177259 DOI: 10.1038/leu.2013.289] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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1021
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Chong IY, Cunningham D, Barber LJ, Campbell J, Chen L, Kozarewa I, Fenwick K, Assiotis I, Guettler S, Garcia-Murillas I, Awan S, Lambros M, Starling N, Wotherspoon A, Stamp G, Gonzalez-de-Castro D, Benson M, Chau I, Hulkki S, Nohadani M, Eltahir Z, Lemnrau A, Orr N, Rao S, Lord CJ, Ashworth A. The genomic landscape of oesophagogastric junctional adenocarcinoma. J Pathol 2013; 231:301-10. [DOI: 10.1002/path.4247] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Irene Y Chong
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - David Cunningham
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Louise J Barber
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - James Campbell
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Lina Chen
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Iwanka Kozarewa
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Kerry Fenwick
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Ioannis Assiotis
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Sebastian Guettler
- Structural Biology of Cell Signalling Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Isaac Garcia-Murillas
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Saima Awan
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Maryou Lambros
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Tumour Profiling Unit; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Naureen Starling
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Andrew Wotherspoon
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Gordon Stamp
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | | | - Martin Benson
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Ian Chau
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Sanna Hulkki
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Mahrokh Nohadani
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Zakaria Eltahir
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Alina Lemnrau
- Complex Trait Genetics Laboratory; The Institute of Cancer Research; London SW3 6JB UK
| | - Nicholas Orr
- Complex Trait Genetics Laboratory; The Institute of Cancer Research; London SW3 6JB UK
| | - Sheela Rao
- Royal Marsden Hospital NHS Foundation Trust; Downs Road Sutton SM2 5PT UK
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
- Cancer Research UK Gene Function Laboratory; The Institute of Cancer Research; 237 Fulham Road, London SW3 6JB UK
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1022
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Norell H, Moretta A, Silva-Santos B, Moretta L. At the Bench: Preclinical rationale for exploiting NK cells and γδ T lymphocytes for the treatment of high-risk leukemias. J Leukoc Biol 2013; 94:1123-39. [PMID: 24108703 DOI: 10.1189/jlb.0613312] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NK cells and γδ T lymphocytes display potent cytolytic activity against leukemias and CMV-infected cells and are thus, promising immune effector cells in the context of allo-HSCT. NK cells express HLA class I-specific inhibitory receptors and preferentially kill HLA class I(low) tumors or virus-infected cells. Killing occurs upon engagement of activating NKRs with ligands that are up-regulated on tumors and infected cells. A similar activating receptor/ligand interaction strategy is used by γδ T cells, which in addition, use their TCRs for recognition of phosphorylated antigens and still largely undefined ligands on tumor cells. In the haploidentical allo-HSCT setting, alloreactive NK cells, derived from donor HSCs, can exert potent antileukemia activity and kill residual patient DCs and T cells, thus preventing GvHD and graft rejection. However, generation of KIR(+) alloreactive NK cells from HSCs requires many weeks, during which leukemia relapses, and life-threatening infections may occur. Importantly, mature NK cells and γδ T cells can control certain infectious agents efficiently, in particular, limit CMV reactivation, and infusion of such donor cells at the time of HSCT has been implemented. Development of novel, cell-based immunotherapies, allowing improved trafficking and better targeting, will endow NK cells and γδ T lymphocytes with enhanced anti-tumor activity, also making them key reagents for therapies against solid tumors. The clinical aspects of using NK cells and γδ T lymphocytes against hematological malignancies, including the allo-HSCT context, are reviewed in the related side-by-side paper by Locatelli and colleagues [1].
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1023
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Jain P, Le X, Young KH, Patel KP, Wang S, Pei L, Barron LL, Abruzzo L, O'Brien S. Sequential lymphomas or clonally unrelated richter syndrome of chronic lymphocytic leukemia into mantle cell lymphoma. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2013; 13:606-9. [PMID: 23763914 DOI: 10.1016/j.clml.2013.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 02/03/2023]
MESH Headings
- Bone Marrow/pathology
- Cell Transformation, Neoplastic
- Disease Progression
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymph Nodes/pathology
- Lymphoma, Mantle-Cell/diagnosis
- Lymphoma, Mantle-Cell/pathology
- Male
- Middle Aged
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Affiliation(s)
- Preetesh Jain
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, TX
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1024
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Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45:1134-40. [PMID: 24071852 PMCID: PMC3966983 DOI: 10.1038/ng.2760] [Citation(s) in RCA: 1301] [Impact Index Per Article: 118.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed in 37% of cancers, was associated with higher rates of every other type of SCNA, TP53 mutations, CCNE1 amplifications and alterations of the PPP2R complex. SCNAs that were internal to chromosomes tended to be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their generation. Significantly recurrent focal SCNAs were observed in 140 regions, including 102 without known oncogene or tumor suppressor gene targets and 50 with significantly mutated genes. Amplified regions without known oncogenes were enriched for genes involved in epigenetic regulation. When levels of genomic disruption were accounted for, 7% of region pairs were anticorrelated, and these regions tended to encompass genes whose proteins physically interact, suggesting related functions. These results provide insights into mechanisms of generation and functional consequences of cancer-related SCNAs.
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Affiliation(s)
- Travis I Zack
- Broad Institute, Cambridge, Massachusetts, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Biophysics Program, Harvard University, Boston, Massachusetts, USA
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1025
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Scott LM, Rebel VI. Acquired mutations that affect pre-mRNA splicing in hematologic malignancies and solid tumors. J Natl Cancer Inst 2013; 105:1540-9. [PMID: 24052622 DOI: 10.1093/jnci/djt257] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The application of next-generation sequencing technologies to interrogate the genome of human hematologic malignancies is providing promising insights into their molecular etiology and into the pathogenesis of seemingly unrelated malignancies. Among the somatic mutations identified by this approach are ones that target components of the spliceosome, a ribonucleoprotein complex responsible for the posttranscriptional processing of primary transcripts to form mature messenger RNA species. These mutations were initially detected in patients with chronic lymphocytic leukemia or a myelodysplastic syndrome, but can also occur at relatively high frequency in some solid tumors, including uveal malignant melanoma, adenocarcinoma of the lung, and estrogen receptor-positive breast cancers. Their presence in a variety of malignancies suggests that the spliceosomal mutations may play a fundamental role in defining the malignant phenotype. The development and testing of drugs that eliminate cells bearing a spliceosomal mutation, or normalize their altered transcript splicing patterns, are therefore a priority. Here, we summarize the effects of spliceosome-associated mutations on transcript processing in vitro and in vivo, and their impact on disease initiation and/or progression and patient outcome. Moreover, we discuss the therapeutic potential of compounds already known to target splicing factor 3B subunit 1 (SF3B1), an essential component of the spliceosome that is frequently mutated.
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Affiliation(s)
- Linda M Scott
- Affiliations of authors: Diamantina Institute, and Faculty of Health Sciences, School of Medicine, University of Queensland, Brisbane, Queensland, Australia (LMS); Translational Research Institute, Brisbane, Queensland, Australia (LMS); Greehey Children's Cancer Research Institute, Cancer Therapy and Research Center, and the Department of Cellular and Structural Biology, University of Texas Health Sciences Center at San Antonio (VIR)
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1026
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Abstract
Our understanding of the pathogenesis of lymphoid malignancies has been transformed by next-generation sequencing. The studies in this review have used whole-genome, exome, and transcriptome sequencing to identify recurring structural genetic alterations and sequence mutations that target key cellular pathways in acute lymphoblastic leukemia (ALL) and the lymphomas. Although each tumor type is characterized by a unique genomic landscape, several cellular pathways are mutated in multiple tumor types-transcriptional regulation of differentiation, antigen receptor signaling, tyrosine kinase and Ras signaling, and epigenetic modifications-and individual genes are mutated in multiple tumors, notably TCF3, NOTCH1, MYD88, and BRAF. In addition to providing fundamental insights into tumorigenesis, these studies have also identified potential new markers for diagnosis, risk stratification, and therapeutic intervention. Several genetic alterations are intuitively "druggable" with existing agents, for example, kinase-activating lesions in high-risk B-cell ALL, NOTCH1 in both leukemia and lymphoma, and BRAF in hairy cell leukemia. Future sequencing efforts are required to comprehensively define the genetic basis of all lymphoid malignancies, examine the relative roles of germline and somatic variation, dissect the genetic basis of clonal heterogeneity, and chart a course for clinical sequencing and translation to improved therapeutic outcomes.
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1027
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Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 2013; 230:356-64. [PMID: 23716380 DOI: 10.1002/path.4214] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 01/17/2023]
Abstract
Intratumour heterogeneity (ITH) may foster tumour adaptation and compromise the efficacy of personalized medicine approaches. The scale of heterogeneity within a tumour (intratumour heterogeneity) relative to genetic differences between tumours (intertumour heterogeneity) is unknown. To address this, we obtained 48 biopsies from eight stage III and IV clear cell renal cell carcinomas (ccRCCs) and used DNA copy-number analyses to compare biopsies from the same tumour with 440 single tumour biopsies from the Cancer Genome Atlas (TCGA). Unsupervised hierarchical clustering of TCGA and multi-region ccRCC samples revealed segregation of samples from the same tumour into unrelated clusters; 25% of multi-region samples appeared more similar to unrelated samples than to any other sample originating from the same tumour. We found that the majority of recurrent DNA copy number driver aberrations in single biopsies were not present ubiquitously in late-stage ccRCCs and were likely to represent subclonal events acquired during tumour progression. Such heterogeneous subclonal genetic alterations within individual tumours may impair the identification of robust ccRCC molecular subtypes classified by distinct copy number alterations and clinical outcomes. The co-existence of distinct subclonal copy number events in different regions of individual tumours reflects the diversification of individual ccRCCs through multiple evolutionary routes and may contribute to tumour sampling bias and impact upon tumour progression and clinical outcome.
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1028
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Rehwinkel J, Maelfait J, Bridgeman A, Rigby R, Hayward B, Liberatore RA, Bieniasz PD, Towers GJ, Moita LF, Crow YJ, Bonthron DT, Reis e Sousa C. SAMHD1-dependent retroviral control and escape in mice. EMBO J 2013; 32:2454-62. [PMID: 23872947 PMCID: PMC3770946 DOI: 10.1038/emboj.2013.163] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/01/2013] [Indexed: 12/12/2022] Open
Abstract
SAMHD1 is a host restriction factor for human immunodeficiency virus 1 (HIV-1) in cultured human cells. SAMHD1 mutations cause autoimmune Aicardi-Goutières syndrome and are found in cancers including chronic lymphocytic leukaemia. SAMHD1 is a triphosphohydrolase that depletes the cellular pool of deoxynucleoside triphosphates, thereby preventing reverse transcription of retroviral genomes. However, in vivo evidence for SAMHD1's antiviral activity has been lacking. We generated Samhd1 null mice that do not develop autoimmune disease despite displaying a type I interferon signature in spleen, macrophages and fibroblasts. Samhd1(-/-) cells have elevated deoxynucleoside triphosphate (dNTP) levels but, surprisingly, SAMHD1 deficiency did not lead to increased infection with VSV-G-pseudotyped HIV-1 vectors. The lack of restriction is likely attributable to the fact that dNTP concentrations in SAMHD1-sufficient mouse cells are higher than the KM of HIV-1 reverse transcriptase (RT). Consistent with this notion, an HIV-1 vector mutant bearing an RT with lower affinity for dNTPs was sensitive to SAMHD1-dependent restriction in cultured cells and in mice. This shows that SAMHD1 can restrict lentiviruses in vivo and that nucleotide starvation is an evolutionarily conserved antiviral mechanism.
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Affiliation(s)
- Jan Rehwinkel
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Maelfait
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Rigby
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bruce Hayward
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Rachel A Liberatore
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - Luis F Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - David T Bonthron
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
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1029
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Using network biology to bridge pharmacokinetics and pharmacodynamics in oncology. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2013; 2:e71. [PMID: 24005988 PMCID: PMC4026631 DOI: 10.1038/psp.2013.38] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/03/2013] [Indexed: 01/12/2023]
Abstract
If mathematical modeling is to be used effectively in cancer drug development, future models must take into account both the mechanistic details of cellular signal transduction networks and the pharmacokinetics (PK) of drugs used to inhibit their oncogenic activity. In this perspective, we present an approach to building multiscale models that capture systems-level architectural features of oncogenic signaling networks, and describe how these models can be used to design combination therapies and identify predictive biomarkers in silico.
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1030
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Cuthill K, Devereux S. How I treat patients with relapsed chronic lymphocytic leukaemia. Br J Haematol 2013; 163:423-35. [DOI: 10.1111/bjh.12549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 01/29/2023]
Affiliation(s)
- Kirsty Cuthill
- Department of Haematological Medicine; Kings College; London UK
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1031
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Jethwa A, Hüllein J, Stolz T, Blume C, Sellner L, Jauch A, Sill M, Kater AP, te Raa GD, Geisler C, van Oers M, Dietrich S, Dreger P, Ho AD, Paruzynski A, Schmidt M, von Kalle C, Glimm H, Zenz T. Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia. Br J Haematol 2013; 163:496-500. [PMID: 24032483 DOI: 10.1111/bjh.12539] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/19/2013] [Indexed: 01/21/2023]
Abstract
Recurrent gene mutations contribute to the pathogenesis of chronic lymphocytic leukaemia (CLL). We developed a next-generation sequencing (NGS) platform to determine the genetic profile, intratumoural heterogeneity, and clonal structure of two independent CLL cohorts. TP53, SF3B1, and NOTCH1 were most frequently mutated (16.3%, 16.9%, 10.7%). We found evidence for subclonal mutations in 67.5% of CLL cases with mutations of cancer consensus genes. We observed selection of subclones and found initial evidence for convergent mutations in CLL. Our data suggest that assessment of (sub)clonal structure may need to be integrated into analysis of the mutational profile in CLL.
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Affiliation(s)
- Alexander Jethwa
- Department of Translational Oncology, National Centre for Tumour Diseases (NCT) and German Cancer Research Centre (DKFZ), Heidelberg, Germany
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1032
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Landau DA, Carter SL, Getz G, Wu CJ. Clonal evolution in hematological malignancies and therapeutic implications. Leukemia 2013; 28:34-43. [PMID: 23979521 DOI: 10.1038/leu.2013.248] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/22/2013] [Accepted: 08/14/2013] [Indexed: 12/19/2022]
Abstract
The ability of cancer to evolve and adapt is a principal challenge to therapy in general and to the paradigm of targeted therapy in particular. This ability is fueled by the co-existence of multiple, genetically heterogeneous subpopulations within the cancer cell population. Increasing evidence has supported the idea that these subpopulations are selected in a Darwinian fashion, by which the genetic landscape of the tumor is continuously reshaped. Massively parallel sequencing has enabled a recent surge in our ability to study this process, adding to previous efforts using cytogenetic methods and targeted sequencing. Altogether, these studies reveal the complex evolutionary trajectories occurring across individual hematological malignancies. They also suggest that while clonal evolution may contribute to resistance to therapy, treatment may also hasten the evolutionary process. New insights into this process challenge us to understand the impact of treatment on clonal evolution and inspire the development of novel prognostic and therapeutic strategies.
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Affiliation(s)
- D A Landau
- 1] Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA [2] Broad Institute, Cambridge, MA, USA [3] Department of Hematology, Yale Cancer Center, New Haven, CT, USA [4] Université Paris Diderot, Paris, France
| | | | - G Getz
- 1] Broad Institute, Cambridge, MA, USA [2] Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA
| | - C J Wu
- 1] Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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1033
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Zhang S, Kipps TJ. The pathogenesis of chronic lymphocytic leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2013; 9:103-18. [PMID: 23987584 DOI: 10.1146/annurev-pathol-020712-163955] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by the clonal expansion of CD5(+)CD23(+) B cells in blood, marrow, and second lymphoid tissues. Gene-expression profiling and phenotypic studies suggest that CLL is probably derived from CD5(+) B cells similar to those found in the blood of healthy adults. Next-generation sequencing has revealed recurrent genetic lesions that are implicated in CLL pathogenesis and/or disease progression. The biology of CLL is entwined with its microenvironment, in which accessory cells can promote leukemia cell growth and/or survival. Recently, much attention has been focused on the CLL B cell receptor (BCR) and on chemokine receptors that enable CLL cells to home to lymphoid tissues and to establish the leukemia microenvironment. Agents that can interfere with BCR signaling or chemokine-receptor signaling, or that target surface antigens selectively expressed on CLL cells, promise to have significant therapeutic benefit in patients with this disease.
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Affiliation(s)
- Suping Zhang
- Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, California 92093;
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1034
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Abstract
Hematology Oncology has a rich history including few crucial therapeutic innovations. These were possible because of the evolution of the cell and molecular biology allowing a better understanding of basic mechanisms of cancerogenesis. We propose here to summarize the most important therapeutic innovations since the beginning of Hematology/Oncology history. We also describe evolution of therapeutic strategies themselves. New insights and therapeutic perspectives for next future are also discussed.
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1035
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Jimenez-Zepeda VH, Chng WJ, Schop RF, Braggio E, Leis JF, Kay N, Fonseca R. Recurrent Chromosome Abnormalities Define Nonoverlapping Unique Subgroups of Tumors in Patients With Chronic Lymphocytic Leukemia and Known Karyotypic Abnormalities. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2013; 13:467-76. [DOI: 10.1016/j.clml.2013.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/02/2013] [Accepted: 05/02/2013] [Indexed: 11/16/2022]
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1036
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Oesper L, Mahmoody A, Raphael BJ. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol 2013; 14:R80. [PMID: 23895164 PMCID: PMC4054893 DOI: 10.1186/gb-2013-14-7-r80] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/29/2013] [Indexed: 12/11/2022] Open
Abstract
Tumor samples are typically heterogeneous, containing admixture by normal, non-cancerous cells and one or more subpopulations of cancerous cells. Whole-genome sequencing of a tumor sample yields reads from this mixture, but does not directly reveal the cell of origin for each read. We introduce THetA (Tumor Heterogeneity Analysis), an algorithm that infers the most likely collection of genomes and their proportions in a sample, for the case where copy number aberrations distinguish subpopulations. THetA successfully estimates normal admixture and recovers clonal and subclonal copy number aberrations in real and simulated sequencing data. THetA is available at http://compbio.cs.brown.edu/software/.
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1037
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Knoechel B, Lohr JG. Genomics of lymphoid malignancies reveal major activation pathways in lymphocytes. J Autoimmun 2013; 45:15-23. [PMID: 23880067 DOI: 10.1016/j.jaut.2013.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 01/21/2023]
Abstract
Breakdown of tolerance leads to autoimmunity due to emergence of autoreactive T or B cell clones. Autoimmune diseases predispose to lymphoid malignancies and lymphoid malignancies, conversely, can manifest as autoimmune diseases. While it has been clear for a long time that a competitive advantage and uncontrolled growth of lymphocytes contribute to the pathogenesis of both lymphoid malignancies as well as autoimmune diseases, the overlap of the underlying mechanisms has been less well described. Next generation sequencing has led to massive expansion of the available genomic data in many diseases over the last five years. These data allow for comparison of the molecular pathogenesis between autoimmune diseases and lymphoid malignancies. Here, we review the similarities between autoimmune diseases and lymphoid malignancies: 1) Both, autoimmune diseases and lymphoid malignancies are characterized by activation of the same T and B cell signaling pathways, and dysregulation of these pathways can occur through genetic or epigenetic events. 2) In both scenarios, clonal and subclonal evolution of lymphocytes contribute to disease. 3) Development of both diseases not only depends on T or B cell intrinsic factors, such as germline or somatic mutations, but also on environmental factors. These include infections, the presence of other immune cells in the microenvironment, and the cytokine milieu. A better mechanistic understanding of the parallels between lymphomagenesis and autoimmunity may help the development of precision treatment strategies with rationally designed therapeutic agents.
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Affiliation(s)
- Birgit Knoechel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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1038
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Braggio E, Egan JB, Fonseca R, Stewart AK. Lessons from next-generation sequencing analysis in hematological malignancies. Blood Cancer J 2013; 3:e127. [PMID: 23872706 PMCID: PMC3730204 DOI: 10.1038/bcj.2013.26] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/14/2013] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing has led to a revolution in the study of hematological malignancies with a substantial number of publications and discoveries in the last few years. Significant discoveries associated with disease diagnosis, risk stratification, clonal evolution and therapeutic intervention have been generated by this powerful technology. As part of the post-genomic era, sequencing analysis will likely become part of routine clinical testing and the challenge will ultimately be successfully transitioning from gene discovery to preventive and therapeutic intervention as part of individualized medicine strategies. In this report, we review recent advances in the understanding of hematological malignancies derived through genome-wide sequence analysis.
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Affiliation(s)
- E Braggio
- Mayo Clinic in Arizona, 13400 East Shea Boulevard, Scottsdale, AZ, USA
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1039
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Falisi E, Novella E, Visco C, Guercini N, Maura F, Giaretta I, Pomponi F, Nichele I, Finotto S, Montaldi A, Neri A, Rodeghiero F. B-cell receptor configuration and mutational analysis of patients with chronic lymphocytic leukaemia and trisomy 12 reveal recurrent molecular abnormalities. Hematol Oncol 2013; 32:22-30. [PMID: 23861036 DOI: 10.1002/hon.2086] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/15/2013] [Accepted: 06/04/2013] [Indexed: 01/02/2023]
Abstract
Trisomy 12 (+12) is the third most frequent cytogenetic aberration in chronic lymphocytic leukaemia (CLL) retrievable both as the sole chromosomal abnormality or in association with additional alterations. NOTCH1 mutations are known to be more prevalent among +12 patients, whereas mutations of FBXW7, a gene involved in NOTCH1 degradation, that lead to the constitutional activation of NOTCH1 have not been investigated in this setting. We analyzed a unicentric cohort of 44 +12 patients with CLL for mutations of TP53, NOTCH1 and FBXW7 genes, and we correlated them with B-cell receptor (BCR) configurations. FBXW7, TP53 and NOTCH1 mutations were identified in 4.5%, 6.8% and 18.2% of patients, respectively. FBXW7 and NOTCH1 mutations appeared in a mutually exclusive fashion, suggesting that both aberrations might affect the same biological pathway. We found that 44.1% of +12 CLL patients had stereotyped B-cell receptors, which is significantly higher than that observed in patients with CLL and no +12 (27%, p = 0.01). Subsets #1, #8, #10, #28 and #59 were the most represented stereotyped patterns, and IGHV4-39*01 was the gene configuration most commonly used. There was a significantly higher risk for Richter's syndrome (RS) transformation in patients with NOTCH1 or FBXW7 mutations, with four of the seven (57%) patients developing RS and characterized at least by one of the two abnormalities. These observations suggest that, similarly to the aberrations of NOTCH1, FBXW7 gene mutations may also result in cell proliferation and evasion from apoptosis in patients with +12 CLL. Together with the extremely high frequency of stereotyped BCRs and RS transformation, these abnormalities appear to cluster in these CLL patients with additional chromosome 12, suggesting a connection with the prognosis of the disease.
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Affiliation(s)
- Erika Falisi
- Department of Hematology and Cell Therapy, S. Bortolo Hospital, Vicenza, Italy
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1040
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De Sousa E Melo F, Vermeulen L, Fessler E, Medema JP. Cancer heterogeneity--a multifaceted view. EMBO Rep 2013; 14:686-95. [PMID: 23846313 DOI: 10.1038/embor.2013.92] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/17/2013] [Indexed: 12/11/2022] Open
Abstract
Cancers of various organs have been categorized into distinct subtypes after increasingly sophisticated taxonomies. Additionally, within a seemingly homogeneous subclass, individual cancers contain diverse tumour cell populations that vary in important cancer-specific traits such as clonogenicity and invasive potential. Differences that exist between and within a given tumour type have hampered significantly both the proper selection of patients that might benefit from therapy, as well as the development of new targeted agents. In this review, we discuss the differences associated with organ-specific cancer subtypes and the factors that contribute to intra-tumour heterogeneity. It is of utmost importance to understand the biological causes that distinguish tumours as well as distinct tumour cell populations within malignancies, as these will ultimately point the way to more rational anti-cancer treatments.
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Affiliation(s)
- Felipe De Sousa E Melo
- Laboratory for Experimental Oncology & Radiobiology, Centre for Experimental Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
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1041
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Cowell CF, Weigelt B, Sakr RA, Ng CKY, Hicks J, King TA, Reis-Filho JS. Progression from ductal carcinoma in situ to invasive breast cancer: revisited. Mol Oncol 2013; 7:859-69. [PMID: 23890733 DOI: 10.1016/j.molonc.2013.07.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/04/2013] [Indexed: 12/21/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is an intraductal neoplastic proliferation of epithelial cells that is separated from the breast stroma by an intact layer of basement membrane and myoepithelial cells. DCIS is a non-obligate precursor of invasive breast cancer, and up to 40% of these lesions progress to invasive disease if untreated. Currently, it is not possible to predict accurately which DCIS would be more likely to progress to invasive breast cancer as neither the significant drivers of the invasive transition have been identified, nor has the clinical utility of tests predicting the likelihood of progression been demonstrated. Although molecular studies have shown that qualitatively, synchronous DCIS and invasive breast cancers are remarkably similar, there is burgeoning evidence to demonstrate that intra-tumor genetic heterogeneity is observed in a subset of DCIS, and that the process of progression to invasive disease may constitute an 'evolutionary bottleneck', resulting in the selection of subsets of tumor cells with specific genetic and/or epigenetic aberrations. Here we review the clinical challenge posed by DCIS, the contribution of the microenvironment and genetic aberrations to the progression from in situ to invasive breast cancer, the emerging evidence of the impact of intra-tumor genetic heterogeneity on this process, and strategies to combat this heterogeneity.
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Affiliation(s)
- Catherine F Cowell
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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1042
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Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013. [PMID: 23770567 DOI: 10.1038/nature12213.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
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Affiliation(s)
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paz Polak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Gregory V Kryukov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | | | | | - Scott L Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Craig H Mermel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steven A Roberts
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Adam Kiezun
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Peter S Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Genome Sciences, University of Washington, Seattle, WA 98195
| | - Yotam Drier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.,Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lihua Zou
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Alex H Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Elena Helman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lauren Ambrogio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | | | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Maria L Cortés
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Douglas Voet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel DiCara
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Pei Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lee Lichtenstein
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - David I Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Timothy Fennell
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Marcin Imielinski
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Bryan Hernandez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Eran Hodis
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan Baca
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Austin M Dulak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jens Lohr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dan-Avi Landau
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Yale Cancer Center, Department of Hematology, New Haven, CT
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | | | | | - Amnon Koren
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Steven A McCarroll
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Jaume Mora
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Brian Crompton
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Robert Onofrio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Wendy Winckler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Charles W M Roberts
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | | | - Kimberly Stegmaier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Adam J Bass
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Dmitry A Gordenin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Shamil Sunyaev
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
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1043
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Spinelli R, Pirola A, Redaelli S, Sharma N, Raman H, Valletta S, Magistroni V, Piazza R, Gambacorti-Passerini C. Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases. Mol Genet Genomic Med 2013; 1:246-59. [PMID: 24498620 PMCID: PMC3865592 DOI: 10.1002/mgg3.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/13/2022] Open
Abstract
Point mutations in intronic regions near mRNA splice junctions can affect the splicing process. To identify novel splicing variants from exome sequencing data, we developed a bioinformatics splice-site prediction procedure to analyze next-generation sequencing (NGS) data (SpliceFinder). SpliceFinder integrates two functional annotation tools for NGS, ANNOVAR and MutationTaster and two canonical splice site prediction programs for single mutation analysis, SSPNN and NetGene2. By SpliceFinder, we identified somatic mutations affecting RNA splicing in a colon cancer sample, in eight atypical chronic myeloid leukemia (aCML), and eight CML patients. A novel homozygous splicing mutation was found in APC (NM_000038.4:c.1312+5G>A) and six heterozygous in GNAQ (NM_002072.2:c.735+1C>T), ABCC3 (NM_003786.3:c.1783-1G>A), KLHDC1 (NM_172193.1:c.568-2A>G), HOOK1 (NM_015888.4:c.1662-1G>A), SMAD9 (NM_001127217.2:c.1004-1C>T), and DNAH9 (NM_001372.3:c.10242+5G>A). Integrating whole-exome and RNA sequencing in aCML and CML, we assessed the phenotypic effect of mutations on mRNA splicing for GNAQ, ABCC3, HOOK1. In ABCC3 and HOOK1, RNA-Seq showed the presence of aberrant transcripts with activation of a cryptic splice site or intron retention, validated by the reverse transcription-polymerase chain reaction (RT-PCR) in the case of HOOK1. In GNAQ, RNA-Seq showed 22% of wild-type transcript and 78% of mRNA skipping exon 5, resulting in a 4–6 frameshift fusion confirmed by RT-PCR. The pipeline can be useful to identify intronic variants affecting RNA sequence by complementing conventional exome analysis.
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Affiliation(s)
- Roberta Spinelli
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Alessandra Pirola
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Sara Redaelli
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Nitesh Sharma
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Hima Raman
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Simona Valletta
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Vera Magistroni
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Health Sciences, University of Milano-Bicocca Monza, Italy ; Hematology and Clinical Research Unit, San Gerardo Hospital Monza, Italy
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1044
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Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Punctuated evolution of prostate cancer genomes. Cell 2013; 153:666-77. [PMID: 23622249 DOI: 10.1016/j.cell.2013.03.021] [Citation(s) in RCA: 915] [Impact Index Per Article: 83.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/17/2013] [Accepted: 03/19/2013] [Indexed: 10/26/2022]
Abstract
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.
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1045
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1046
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Soldini D, Campo E. Genetic sequencing studies in Burkitt's lymphoma: what can we learn about tumorigenesis? Expert Rev Hematol 2013; 6:219-21. [PMID: 23782073 DOI: 10.1586/ehm.13.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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1047
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Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks. Semin Cancer Biol 2013; 23:279-85. [PMID: 23791722 DOI: 10.1016/j.semcancer.2013.06.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/04/2013] [Accepted: 06/09/2013] [Indexed: 02/05/2023]
Abstract
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones.
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1048
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Wang E, Zou J, Zaman N, Beitel LK, Trifiro M, Paliouras M. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance. Semin Cancer Biol 2013; 23:286-92. [PMID: 23792107 DOI: 10.1016/j.semcancer.2013.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 06/09/2013] [Indexed: 02/08/2023]
Abstract
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients.
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Affiliation(s)
- Edwin Wang
- National Research Council Canada, Montreal, Canada.
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1049
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Abstract
Alterations in the single-stranded telomere-binding protein POT1 have recently been identified in chronic lymphocytic leukemia. This discovery provides novel insights into how genomic instability induced by dysfunctional telomeres contributes to tumorigenesis.
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Affiliation(s)
- Sandy Chang
- Department of Laboratory Medicine and Pathology at Yale University School of Medicine, New Haven, Connecticut, USA.
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1050
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Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013; 499:214-218. [PMID: 23770567 PMCID: PMC3919509 DOI: 10.1038/nature12213] [Citation(s) in RCA: 3880] [Impact Index Per Article: 352.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 04/22/2013] [Indexed: 11/09/2022]
Abstract
Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here, we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false positive findings that overshadow true driver events. Here, we show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumor-normal pairs and discover extraordinary variation in (i) mutation frequency and spectrum within cancer types, which shed light on mutational processes and disease etiology, and (ii) mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and allow true cancer genes to rise to attention.
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