1
|
Chu C, Ljungström V, Tran A, Jin H, Park PJ. Contribution of de novo retroelements to birth defects and childhood cancers. medRxiv 2024:2024.04.15.24305733. [PMID: 38699361 PMCID: PMC11065029 DOI: 10.1101/2024.04.15.24305733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Insertion of active retroelements-L1s, Alu s, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of de novo retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program. Using an improved version of our tool xTea (x-Transposable element analyzer) that incorporates a deep-learning module, we identified 162 DNRTs, as well as 2 pseudogene insertions. Several variants are likely to be causal, such as a de novo Alu insertion that led to the ablation of a whole exon in the NF1 gene in a proband with brain tumor. We observe a high de novo SVA insertion burden in both high-intolerance loss-of-function genes and exons as well as more frequent de novo Alu insertions of paternal origin. We also identify potential mosaic DNRTs from embryonic stages. Our study reveals the important roles of DNRTs in causing birth defects and predisposition to childhood cancers.
Collapse
|
2
|
Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
Collapse
Affiliation(s)
- Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedikt Geiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ben-Isvy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Geng
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Gao T, Kastriti ME, Ljungström V, Heinzel A, Tischler AS, Oberbauer R, Loh PR, Adameyko I, Park PJ, Kharchenko PV. A pan-tissue survey of mosaic chromosomal alterations in 948 individuals. Nat Genet 2023; 55:1901-1911. [PMID: 37904053 PMCID: PMC10838621 DOI: 10.1038/s41588-023-01537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/18/2023] [Indexed: 11/01/2023]
Abstract
Genetic mutations accumulate in an organism's body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue survey of mosaic chromosomal alterations (mCAs) in 948 healthy individuals from the Genotype-Tissue Expression project, augmenting RNA-based allelic imbalance estimation with haplotype phasing. We found that approximately a quarter of the individuals carry a clonally-expanded mCA in at least one tissue, with incidence strongly correlated with age. The prevalence and genome-wide patterns of mCAs vary considerably across tissue types, suggesting tissue-specific mutagenic exposure and selection pressures. The mCA landscapes in normal adrenal and pituitary glands resemble those in tumors arising from these tissues, whereas the same is not true for the esophagus and skin. Together, our findings show a widespread age-dependent emergence of mCAs across normal human tissues with intricate connections to tumorigenesis.
Collapse
Affiliation(s)
- Teng Gao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maria Eleni Kastriti
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Heinzel
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Rainer Oberbauer
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
| |
Collapse
|
4
|
Bonfiglio S, Sutton LA, Ljungström V, Capasso A, Pandzic T, Weström S, Foroughi-Asl H, Skaftason A, Gellerbring A, Lyander A, Gandini F, Gaidano G, Trentin L, Bonello L, Reda G, Bödör C, Stavroyianni N, Tam CS, Marasca R, Forconi F, Panayiotidis P, Ringshausen I, Jaksic O, Frustaci AM, Iyengar S, Coscia M, Mulligan SP, Ysebaert L, Strugov V, Pavlovsky C, Walewska R, Österborg A, Cortese D, Ranghetti P, Baliakas P, Stamatopoulos K, Scarfò L, Rosenquist R, Ghia P. BTK and PLCG2 remain unmutated in one-third of patients with CLL relapsing on ibrutinib. Blood Adv 2023; 7:2794-2806. [PMID: 36696464 PMCID: PMC10279547 DOI: 10.1182/bloodadvances.2022008821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/07/2022] [Accepted: 01/01/2023] [Indexed: 01/26/2023] Open
Abstract
Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after ≥1 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.
Collapse
MESH Headings
- Humans
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Drug Resistance, Neoplasm/genetics
- Piperidines
- Recurrence
Collapse
Affiliation(s)
- Silvia Bonfiglio
- Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy
- Division of Experimental Oncology, B cell Neoplasia Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Antonella Capasso
- Strategic Research Program on CLL, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Simone Weström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Hassan Foroughi-Asl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anna Gellerbring
- Clinical Genomics Stockholm, Science for Life Laboratory, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lyander
- Clinical Genomics Stockholm, Science for Life Laboratory, Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Francesca Gandini
- Division of Experimental Oncology, B cell Neoplasia Unit, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology, University of Padua, Italy
| | - Lisa Bonello
- Molecular Pathology Unit, A.O.U Città della Salute e della Scienza, Torino, Italy
- Department of Molecular Biotechnologies and Health Sciences, Università di Torino, Italy
| | - Gianluigi Reda
- Department of Hematology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Csaba Bödör
- HCEMM-SU Molecular Oncohematology Research Group, Budapest, Hungary
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Niki Stavroyianni
- Department of Hematology and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Constantine S. Tam
- Department of Hematology, Alfred Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Roberto Marasca
- Department of Medical and Surgical Sciences, Hematology Unit, University of Modena and Reggio Emilia, Modena, Italy
| | - Francesco Forconi
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Department of Hematology, University Hospital National Health Service Trust, Southampton, United Kingdom
| | - Panayiotis Panayiotidis
- Department of Propaedeutic Internal Medicine, Laiko Hospital, University of Athens, Athens, Greece
| | - Ingo Ringshausen
- Department of Hematology, University of Cambridge, Cambridge, United Kingdom
| | | | - Anna Maria Frustaci
- Department of Hematology, Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | - Sunil Iyengar
- Department of Haemato-Oncology, Royal Marsden Hospital, London, United Kingdom
| | - Marta Coscia
- Department of Molecular Biotechnologies and Health Sciences, Università di Torino, Italy
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy
| | - Stephen P. Mulligan
- Department of Haematology, Royal North Shore Hospital, University of Sydney, Sydney, Australia
| | - Loïc Ysebaert
- Département d'Hématologie, Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
| | | | | | - Renata Walewska
- Department of Molecular Pathology, University Hospitals Dorset, Bournemouth, United Kingdom
| | - Anders Österborg
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Ranghetti
- Division of Experimental Oncology, B cell Neoplasia Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Lydia Scarfò
- Division of Experimental Oncology, B cell Neoplasia Unit, IRCCS Ospedale San Raffaele, Milan, Italy
- Strategic Research Program on CLL, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Paolo Ghia
- Division of Experimental Oncology, B cell Neoplasia Unit, IRCCS Ospedale San Raffaele, Milan, Italy
- Strategic Research Program on CLL, IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| |
Collapse
|
5
|
Lee JJK, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ. ERα-associated translocations underlie oncogene amplifications in breast cancer. Nature 2023; 618:1024-1032. [PMID: 37198482 PMCID: PMC10307628 DOI: 10.1038/s41586-023-06057-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
Abstract
Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.
Collapse
Affiliation(s)
- Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Youngsook Lucy Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Emma V Watson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Stephen J Elledge
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - David Pellman
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Engvall M, Karlsson Y, Kuchinskaya E, Jörnegren Å, Mathot L, Pandzic T, Palle J, Ljungström V, Cavelier L, Hellström Lindberg E, Cammenga J, Baliakas P. Familial platelet disorder due to germline exonic deletions in RUNX1: a diagnostic challenge with distinct alterations of the transcript isoform equilibrium. Leuk Lymphoma 2022; 63:2311-2320. [PMID: 35533071 DOI: 10.1080/10428194.2022.2067997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Germline pathogenic variants in RUNX1 are associated with familial platelet disorder with predisposition to myeloid malignancies (FPD/MM) with intragenic deletions in RUNX1 accounting for almost 7% of all reported variants. We present two new pedigrees with FPD/MM carrying two different germline RUNX1 intragenic deletions. The aforementioned deletions encompass exons 1-2 and 9-10 respectively, with the exon 9-10 deletion being previously unreported. RNA sequencing of patients carrying the exon 9-10 deletion revealed a fusion with LINC00160 resulting in a change in the 3' sequence of RUNX1. Expression analysis of the transcript isoform demonstrated altered RUNX1a/b/c ratios in carriers from both families compared to controls. Our data provide evidence on the impact of intragenic RUNX1 deletions on transcript isoform expression and highlight the importance of routinely performing copy number variant analysis in patients with suspected MM with germline predisposition.
Collapse
Affiliation(s)
- Marie Engvall
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ylva Karlsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ekaterina Kuchinskaya
- Department of Clinical Pathology and Clinical Genetics, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Åsa Jörnegren
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Josefine Palle
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva Hellström Lindberg
- Department of Medicine, Division of Hematology, Huddinge, Karolinska University Hospital, Stockholm, Sweden.,Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jörg Cammenga
- Department of Hematology, Linköping University Hospital, Linköping, Sweden.,Department of Molecular Medicine and Virology (MMV), Division of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
7
|
Voso M, Pandzic T, Falconi G, Denčić‐Fekete M, De Bellis E, Scarfo L, Ljungström V, Iskas M, Del Poeta G, Ranghetti P, Laidou S, Cristiano A, Plevova K, Imbergamo S, Engvall M, Zucchetto A, Salvetti C, Mauro FR, Stavroyianni N, Cavelier L, Ghia P, Stamatopoulos K, Fabiani E, Baliakas P. Clonal haematopoiesis as a risk factor for therapy‐related myeloid neoplasms in patients with chronic lymphocytic leukaemia treated with chemo‐(immuno)therapy. Br J Haematol 2022; 198:103-113. [DOI: 10.1111/bjh.18129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/23/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Maria‐Teresa Voso
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
- Department of Clinical Genetics Uppsala University Hospital Uppsala Sweden
| | - Giulia Falconi
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
| | | | - Eleonora De Bellis
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
| | - Lydia Scarfo
- Strategic Research Programme in CLL, Division of Experimental Oncology IRCCS Ospedale San Raffaele and Università Vita‐Salute San Raffaele Milan Italy
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
- Department of Clinical Genetics Uppsala University Hospital Uppsala Sweden
| | - Michail Iskas
- Hematology Department and HCT Unit, G. Papanicolaou Hospital Thessaloniki Greece
| | - Giovanni Del Poeta
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
| | - Pamela Ranghetti
- Strategic Research Programme in CLL, Division of Experimental Oncology IRCCS Ospedale San Raffaele and Università Vita‐Salute San Raffaele Milan Italy
| | - Stamatia Laidou
- Institute of Applied Biosciences Center for Research and Technology Hellas Thessaloniki Greece
| | - Antonio Cristiano
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
| | - Karla Plevova
- Institute of Medical Genetics and Genomics Faculty of Medicine Masaryk University Brno Czech Republic
- Department of Internal Medicine – Haematology and Oncology University Hospital Brno Brno Czech Republic
| | - Silvia Imbergamo
- Hematology and Clinical Immunology, Department of Hematology Hospital of Padua Padua Italy
| | - Marie Engvall
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
- Department of Clinical Genetics Uppsala University Hospital Uppsala Sweden
| | - Antonella Zucchetto
- Clinical and Experimental Onco‐Hematology Unit Centro di Riferimento Oncologico di Aviano (CRO), IRCCS Aviano Italy
| | | | - Francesca R. Mauro
- Department of Translational and Precision Medicine, Hematology 'Sapienza' University Rome Italy
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital Thessaloniki Greece
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
- Department of Clinical Genetics Uppsala University Hospital Uppsala Sweden
| | - Paolo Ghia
- Strategic Research Programme in CLL, Division of Experimental Oncology IRCCS Ospedale San Raffaele and Università Vita‐Salute San Raffaele Milan Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences Center for Research and Technology Hellas Thessaloniki Greece
- Department of Molecular Medicine and Surgery Karolinska Institutet Stockholm Sweden
| | - Emiliano Fabiani
- Department of Biomedicine and Prevention University of Tor Vergata Rome Italy
- UniCamillus‐Saint Camillus International University of Health Sciences Rome Italy
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
- Department of Clinical Genetics Uppsala University Hospital Uppsala Sweden
| |
Collapse
|
8
|
Kolijn PM, Muggen AF, Ljungström V, Agathangelidis A, Wolvers-Tettero ILM, Beverloo HB, Pál K, Hengeveld PJ, Darzentas N, Hendriks RW, van Dongen JJM, Rosenquist R, Langerak AW. Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:740083. [PMID: 34513715 PMCID: PMC8427434 DOI: 10.3389/fonc.2021.740083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Key processes in the onset and evolution of chronic lymphocytic leukemia (CLL) are thought to include chronic (antigenic) activation of mature B cells through the B cell receptor (BcR), signals from the microenvironment, and acquisition of genetic alterations. Here we describe three families in which two or more siblings were affected by CLL. We investigated whether there are immunogenetic similarities in the leukemia-specific immunoglobulin heavy (IGH) and light (IGL/IGK) chain gene rearrangements of the siblings in each family. Furthermore, we performed array analysis to study if similarities in CLL-associated chromosomal aberrations are present within each family and screened for somatic mutations using paired tumor/normal whole-genome sequencing (WGS). In two families a consistent IGHV gene mutational status (one IGHV-unmutated, one IGHV-mutated) was observed. Intriguingly, the third family with four affected siblings was characterized by usage of the lambda IGLV3-21 gene, with the hallmark R110 mutation of the recently described clinically aggressive IGLV3-21R110 subset. In this family, the CLL-specific rearrangements in two siblings could be assigned to either stereotyped subset #2 or the immunogenetically related subset #169, both of which belong to the broader IGLV3-21R110 subgroup. Consistent patterns of cytogenetic aberrations were encountered in all three families. Furthermore, the CLL clones carried somatic mutations previously associated with IGHV mutational status, cytogenetic aberrations and stereotyped subsets, respectively. From these findings, we conclude that similarities in immunogenetic characteristics in familial CLL, in combination with genetic aberrations acquired, point towards shared underlying mechanisms behind CLL development within each family.
Collapse
Affiliation(s)
- P Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Alice F Muggen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Ingrid L M Wolvers-Tettero
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Karol Pál
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Paul J Hengeveld
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | | | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| |
Collapse
|
9
|
Maffei R, Fiorcari S, Atene CG, Martinelli S, Scarfò L, Bonfiglio S, Maccaferri M, Ljungström V, Zucchini P, Forghieri F, Potenza L, Ghia P, Marasca R, Trenti T, Tagliafico E, Luppi M. A single-tube multiplex method for monitoring mutations in cysteine 481 of Bruton Tyrosine Kinase (BTK) gene in chronic lymphocytic leukemia patients treated with ibrutinib. Leuk Lymphoma 2021; 62:2018-2021. [PMID: 33663302 DOI: 10.1080/10428194.2021.1894643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Rossana Maffei
- Hematology Division, Department of Oncology and Hematology, A.O.U of Modena-Policlinico, Modena, Italy
| | - Stefania Fiorcari
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Claudio Giacinto Atene
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Martinelli
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Lydia Scarfò
- Division of Experimental Hematology, Laboratory of B cell Neoplasia, Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Silvia Bonfiglio
- Division of Experimental Hematology, Laboratory of B cell Neoplasia, Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Monica Maccaferri
- Hematology Division, Department of Oncology and Hematology, A.O.U of Modena-Policlinico, Modena, Italy
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Patrizia Zucchini
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Forghieri
- Hematology Division, Department of Oncology and Hematology, A.O.U of Modena-Policlinico, Modena, Italy
| | - Leonardo Potenza
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Ghia
- Division of Experimental Hematology, Laboratory of B cell Neoplasia, Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milano, Italy
| | - Roberto Marasca
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Tommaso Trenti
- Department of Laboratory Medicine and Pathology, Unità Sanitaria Locale, Modena, Italy
| | - Enrico Tagliafico
- Center for Genome Research, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Mario Luppi
- Hematology Division, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| |
Collapse
|
10
|
Mathioudaki A, Ljungström V, Melin M, Arendt ML, Nordin J, Karlsson Å, Murén E, Saksena P, Meadows JRS, Marinescu VD, Sjöblom T, Lindblad-Toh K. Author Correction: Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort. Sci Rep 2021; 11:5310. [PMID: 33649492 PMCID: PMC7921395 DOI: 10.1038/s41598-021-84929-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Argyri Mathioudaki
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Viktor Ljungström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
| | - Malin Melin
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
| | - Maja Louise Arendt
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessika Nordin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Murén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Pushpa Saksena
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Voichita D Marinescu
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
11
|
Sutton LA, Ljungström V, Enjuanes A, Cortese D, Skaftason A, Tausch E, Stano Kozubik K, Nadeu F, Armand M, Malcikova J, Pandzic T, Forster J, Davis Z, Oscier D, Rossi D, Ghia P, Strefford JC, Pospisilova S, Stilgenbauer S, Davi F, Campo E, Stamatopoulos K, Rosenquist R, On Behalf Of The European Research Initiative On Cll Eric. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 2021; 106:682-691. [PMID: 32273480 PMCID: PMC7927885 DOI: 10.3324/haematol.2019.234716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF <5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF >5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
Collapse
Affiliation(s)
- Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University,Ulm, Germany
| | - Katerina Stano Kozubik
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Marine Armand
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Jikta Malcikova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jade Forster
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Davide Rossi
- Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greec
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | | |
Collapse
|
12
|
Amini RM, Ljungström V, Abdulla M, Cavelier L, Pandzic T, Hollander P, Enblad G, Baliakas P. Clonal hematopoiesis in patients with high-grade B-cell lymphoma is associated with inferior outcome. Am J Hematol 2020; 95:E287-E289. [PMID: 32628289 DOI: 10.1002/ajh.25927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/18/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Rose-Marie Amini
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Maysaa Abdulla
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Peter Hollander
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gunilla Enblad
- Experimental and Clinical Oncology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| |
Collapse
|
13
|
Nunes L, Aasebø K, Mathot L, Ljungström V, Edqvist PH, Sundström M, Dragomir A, Pfeiffer P, Ameur A, Ponten F, Mezheyeuski A, Sorbye H, Sjöblom T, Glimelius B. Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis. Acta Oncol 2020; 59:417-426. [PMID: 31924107 DOI: 10.1080/0284186x.2019.1711169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background: We have reported that BRAF V600E mutations and microsatellite instability-high (MSI-H) are more prevalent in a population-based cohort of metastatic colorectal cancer (mCRC) patients than has been reported from clinical trials or hospital-based patient groups. The aim was to explore if other mutations in mCRC differ in prevalence between these cohorts in relation to mismatch repair status and primary tumor location and if presence of bone or brain metastases is associated with any mutations.Material and methods: A population-based cohort of 798 mCRC patients from three regions in Scandinavia was used. Forty-four cancer related genes were investigated in a custom designed Ampliseq hotspot panel. Differences in survival were analyzed using the Kaplan-Meier estimator and the Cox regression analysis.Results: Determination of mutations was possible in 449/501 patients for 40/44 genes. Besides BRAF V600E, seen in 19% of the tumors, none of the other mutations appeared more prevalent than in trial cohorts. BRAF V600E and MSI-H, seen in 8%, were associated with poor prognosis as was right-sided primary tumor location (39%) when compared to left-sided and rectum together; however, in a multivariable regression, only the BRAF mutation retained its statistical significance. No other mutations were associated with poor prognosis. ERBB2 alterations were more common if bone metastases were present at diagnosis (17% vs. 4%, p = .011). No association was found for brain metastases. Fifty-two percent had an alteration that is treatable with an FDA-approved targeted therapy, chiefly by EGFR-inhibitor for RAS wild-type and a check-point inhibitor for MSI-H tumors.Conclusions: Right-sided tumor location, BRAF V600E mutations, but no other investigated mutation, and MSI-H are more commonly seen in an unselected cohort than is reported from clinical patient cohorts, likely because they indicate poor prognosis. Half of the patients have a tumor that is treatable with an already FDA-approved targeted drug for mCRC.
Collapse
Affiliation(s)
- Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kristine Aasebø
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Magnus Sundström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anca Dragomir
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Per Pfeiffer
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Halfdan Sorbye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
14
|
Tsagiopoulou M, Papakonstantinou N, Moysiadis T, Mansouri L, Ljungström V, Duran-Ferrer M, Malousi A, Queirós AC, Plevova K, Bhoi S, Kollia P, Oscier D, Anagnostopoulos A, Trentin L, Ritgen M, Pospisilova S, Stavroyianni N, Ghia P, Martin-Subero JI, Pott C, Rosenquist R, Stamatopoulos K. DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy. Clin Epigenetics 2019; 11:177. [PMID: 31791414 PMCID: PMC6889736 DOI: 10.1186/s13148-019-0783-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023] Open
Abstract
Background In order to gain insight into the contribution of DNA methylation to disease progression of chronic lymphocytic leukemia (CLL), using 450K Illumina arrays, we determined the DNA methylation profiles in paired pre-treatment/relapse samples from 34 CLL patients treated with chemoimmunotherapy, mostly (n = 31) with the fludarabine-cyclophosphamide-rituximab (FCR) regimen. Results The extent of identified changes in CLL cells versus memory B cells from healthy donors was termed “epigenetic burden” (EB) whereas the number of changes between the pre-treatment versus the relapse sample was termed “relapse changes” (RC). Significant (p < 0.05) associations were identified between (i) high EB and short time-to-first-treatment (TTFT); and, (ii) few RCs and short time-to-relapse. Both the EB and the RC clustered in specific genomic regions and chromatin states, including regulatory regions containing binding sites of transcription factors implicated in B cell and CLL biology. Conclusions Overall, we show that DNA methylation in CLL follows different dynamics in response to chemoimmunotherapy. These epigenetic alterations were linked with specific clinical and biological features.
Collapse
Affiliation(s)
- Maria Tsagiopoulou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Andigoni Malousi
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ana C Queirós
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Karla Plevova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sujata Bhoi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagoula Kollia
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padua, Italy
| | - Matthias Ritgen
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
15
|
Agathangelidis A, Ljungström V, Scarfò L, Fazi C, Gounari M, Pandzic T, Sutton LA, Stamatopoulos K, Tonon G, Rosenquist R, Ghia P. Highly similar genomic landscapes in monoclonal B-cell lymphocytosis and ultra-stable chronic lymphocytic leukemia with low frequency of driver mutations. Haematologica 2018; 103:865-873. [PMID: 29449433 PMCID: PMC5927998 DOI: 10.3324/haematol.2017.177212] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/07/2018] [Indexed: 01/07/2023] Open
Abstract
Despite the recent discovery of recurrent driver mutations in chronic lymphocytic leukemia, the genetic factors involved in disease onset remain largely unknown. To address this issue, we performed whole-genome sequencing in 11 individuals with monoclonal B- cell lymphocytosis, both of the low-count and high-count subtypes, and 5 patients with ultra-stable chronic lymphocytic leukemia (>10 years without progression from initial diagnosis). All three entities were indistinguishable at the genomic level exhibiting low genomic complexity and similar types of somatic mutations. Exonic mutations were not frequently identified in putative chronic lymphocytic leukemia driver genes in all settings, including low-count monoclonal B-cell lymphocytosis. To corroborate these findings, we also performed deep sequencing in 11 known frequently mutated genes in an extended cohort of 28 monoclonal B-cell lymphocytosis/chronic lymphocytic leukemia cases. Interestingly, shared mutations were detected between clonal B cells and paired polymorphonuclear cells, strengthening the notion that at least a fraction of somatic mutations may occur before disease onset, likely at the hematopoietic stem cell level. Finally, we identified previously unreported non-coding variants targeting pathways relevant to B-cell and chronic lymphocytic leukemia development, likely associated with the acquisition of the characteristic neoplastic phenotype typical of both monoclonal B-cell lymphocytosis and chronic lymphocytic leukemia.
Collapse
Affiliation(s)
- Andreas Agathangelidis
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lydia Scarfò
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Claudia Fazi
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Maria Gounari
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy.,Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| |
Collapse
|
16
|
Mathot L, Kundu S, Ljungström V, Svedlund J, Moens L, Adlerteg T, Falk-Sörqvist E, Rendo V, Bellomo C, Mayrhofer M, Cortina C, Sundström M, Micke P, Botling J, Isaksson A, Moustakas A, Batlle E, Birgisson H, Glimelius B, Nilsson M, Sjöblom T. Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer. Cancer Res 2017; 77:1730-1740. [PMID: 28108514 DOI: 10.1158/0008-5472.can-16-1921] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/12/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022]
Abstract
The contribution of somatic mutations to metastasis of colorectal cancers is currently unknown. To find mutations involved in the colorectal cancer metastatic process, we performed deep mutational analysis of 676 genes in 107 stages II to IV primary colorectal cancer, of which half had metastasized. The mutation prevalence in the ephrin (EPH) family of tyrosine kinase receptors was 10-fold higher in primary tumors of metastatic colorectal than in nonmetastatic cases and preferentially occurred in stage III and IV tumors. Mutational analyses in situ confirmed expression of mutant EPH receptors. To enable functional studies of EPHB1 mutations, we demonstrated that DLD-1 colorectal cancer cells expressing EPHB1 form aggregates upon coculture with ephrin B1 expressing cells. When mutations in the fibronectin type III and kinase domains of EPHB1 were compared with wild-type EPHB1 in DLD-1 colorectal cancer cells, they decreased ephrin B1-induced compartmentalization. These observations provide a mechanistic link between EPHB receptor mutations and metastasis in colorectal cancer. Cancer Res; 77(7); 1730-40. ©2017 AACR.
Collapse
Affiliation(s)
- Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Snehangshu Kundu
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Viktor Ljungström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Jessica Svedlund
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Lotte Moens
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Tom Adlerteg
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Elin Falk-Sörqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Verónica Rendo
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Claudia Bellomo
- Department of Medical Biochemistry and Microbiology, Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Sweden
| | - Markus Mayrhofer
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Carme Cortina
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Magnus Sundström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Patrick Micke
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Johan Botling
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Sweden
| | - Eduard Batlle
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helgi Birgisson
- Department of Surgical Sciences, Colorectal Surgery, Uppsala University, Sweden
| | - Bengt Glimelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden.
| |
Collapse
|
17
|
Mansouri L, Noerenberg D, Young E, Mylonas E, Abdulla M, Frick M, Asmar F, Ljungström V, Schneider M, Yoshida K, Skaftason A, Pandzic T, Gonzalez B, Tasidou A, Waldhueter N, Rivas-Delgado A, Angelopoulou M, Ziepert M, Arends CM, Couronné L, Lenze D, Baldus CD, Bastard C, Okosun J, Fitzgibbon J, Dörken B, Drexler HG, Roos-Weil D, Schmitt CA, Munch-Petersen HD, Zenz T, Hansmann ML, Strefford JC, Enblad G, Bernard OA, Ralfkiaer E, Erlanson M, Korkolopoulou P, Hultdin M, Papadaki T, Grønbæk K, Lopez-Guillermo A, Ogawa S, Küppers R, Stamatopoulos K, Stavroyianni N, Kanellis G, Rosenwald A, Campo E, Amini RM, Ott G, Vassilakopoulos TP, Hummel M, Rosenquist R, Damm F. Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma. Blood 2016; 128:2666-2670. [PMID: 27670424 DOI: 10.1182/blood-2016-03-704528] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/16/2016] [Indexed: 12/19/2022] Open
Abstract
We recently reported a truncating deletion in the NFKBIE gene, which encodes IκBε, a negative feedback regulator of NF-κB, in clinically aggressive chronic lymphocytic leukemia (CLL). Because preliminary data indicate enrichment of NFKBIE aberrations in other lymphoid malignancies, we screened a large patient cohort (n = 1460) diagnosed with different lymphoid neoplasms. While NFKBIE deletions were infrequent in follicular lymphoma, splenic marginal zone lymphoma, and T-cell acute lymphoblastic leukemia (<2%), slightly higher frequencies were seen in diffuse large B-cell lymphoma, mantle cell lymphoma, and primary central nervous system lymphoma (3% to 4%). In contrast, a remarkably high frequency of NFKBIE aberrations (46/203 cases [22.7%]) was observed in primary mediastinal B-cell lymphoma (PMBL) and Hodgkin lymphoma (3/11 cases [27.3%]). NFKBIE-deleted PMBL patients were more often therapy refractory (P = .022) and displayed inferior outcome compared with wild-type patients (5-year survival, 59% vs 78%; P = .034); however, they appeared to benefit from radiotherapy (P =022) and rituximab-containing regimens (P = .074). NFKBIE aberrations remained an independent factor in multivariate analysis (P = .003) and when restricting the analysis to immunochemotherapy-treated patients (P = .008). Whole-exome sequencing and gene expression profiling verified the importance of NF-κB deregulation in PMBL. In summary, we identify NFKBIE aberrations as a common genetic event across B-cell malignancies and highlight NFKBIE deletions as a novel poor-prognostic marker in PMBL.
Collapse
Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Noerenberg
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Emma Young
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elena Mylonas
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Maysaa Abdulla
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mareike Frick
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Fazila Asmar
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Viktor Ljungström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Markus Schneider
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aron Skaftason
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Blanca Gonzalez
- Department of Pathology, Hospital Clinic and Institut d'Investigacions Biomediques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Anna Tasidou
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | - Nils Waldhueter
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | | | - Maria Angelopoulou
- Department of Haematology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Marita Ziepert
- Institute for Medical Informatics, Statistics, and Epidemiology, University at Leipzig, Leipzig, Germany
| | | | - Lucile Couronné
- Service d'Hématologie Adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Dido Lenze
- Institute of Pathology, Charité, University Medical Center, Berlin, Germany
| | - Claudia D Baldus
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Christian Bastard
- INSERM U918, Université de Rouen, Centre Henri Becquerel, Rouen, France
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Bernd Dörken
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Damien Roos-Weil
- Université Paris-Sud, Orsay, France
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Clemens A Schmitt
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - Helga D Munch-Petersen
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Thorsten Zenz
- Departments of Molecular Therapy in Haematology and Oncology and Translational Oncology, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
- Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Martin-Leo Hansmann
- Dr. Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - Jonathan C Strefford
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gunilla Enblad
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olivier A Bernard
- Université Paris-Sud, Orsay, France
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Elisabeth Ralfkiaer
- Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Martin Erlanson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Penelope Korkolopoulou
- Department of Pathology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | | | - Kirsten Grønbæk
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Niki Stavroyianni
- Hematology Department and Hematopoietic Cell Transplantation Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - George Kanellis
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Elias Campo
- Department of Pathology, Hospital Clinic and Institut d'Investigacions Biomediques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Rose-Marie Amini
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; and
| | - Theodoros P Vassilakopoulos
- Department of Haematology, National and Kapodistrian University of Athens, Laikon General Hospital, Athens, Greece
| | - Michael Hummel
- Institute of Pathology, Charité, University Medical Center, Berlin, Germany
| | - Richard Rosenquist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Frederik Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
18
|
Young E, Noerenberg D, Mansouri L, Ljungström V, Frick M, Sutton LA, Blakemore SJ, Galan-Sousa J, Plevova K, Baliakas P, Rossi D, Clifford R, Roos-Weil D, Navrkalova V, Dörken B, Schmitt CA, Smedby KE, Juliusson G, Giacopelli B, Blachly JS, Belessi C, Panagiotidis P, Chiorazzi N, Davi F, Langerak AW, Oscier D, Schuh A, Gaidano G, Ghia P, Xu W, Fan L, Bernard OA, Nguyen-Khac F, Rassenti L, Li J, Kipps TJ, Stamatopoulos K, Pospisilova S, Zenz T, Oakes CC, Strefford JC, Rosenquist R, Damm F. EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia. Leukemia 2016; 31:1547-1554. [PMID: 27890934 DOI: 10.1038/leu.2016.359] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/04/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022]
Abstract
Recurrent mutations within EGR2 were recently reported in advanced-stage chronic lymphocytic leukemia (CLL) patients and associated with a worse outcome. To study their prognostic impact, 2403 CLL patients were examined for mutations in the EGR2 hotspot region including a screening (n=1283) and two validation cohorts (UK CLL4 trial patients, n=366; CLL Research Consortium (CRC) patients, n=490). Targeted deep-sequencing of 27 known/postulated CLL driver genes was also performed in 38 EGR2-mutated patients to assess concurrent mutations. EGR2 mutations were detected in 91/2403 (3.8%) investigated cases, and associated with younger age at diagnosis, advanced clinical stage, high CD38 expression and unmutated IGHV genes. EGR2-mutated patients frequently carried ATM lesions (42%), TP53 aberrations (18%) and NOTCH1/FBXW7 mutations (16%). EGR2 mutations independently predicted shorter time-to-first-treatment (TTFT) and overall survival (OS) in the screening cohort; they were confirmed associated with reduced TTFT and OS in the CRC cohort and independently predicted short OS from randomization in the UK CLL4 cohort. A particularly dismal outcome was observed among EGR2-mutated patients who also carried TP53 aberrations. In summary, EGR2 mutations were independently associated with an unfavorable prognosis, comparable to CLL patients carrying TP53 aberrations, suggesting that EGR2-mutated patients represent a new patient subgroup with very poor outcome.
Collapse
Affiliation(s)
- E Young
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - D Noerenberg
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - L Mansouri
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - V Ljungström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - M Frick
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - L-A Sutton
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - S J Blakemore
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - J Galan-Sousa
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - K Plevova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - P Baliakas
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - D Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy.,Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - R Clifford
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - D Roos-Weil
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
| | - V Navrkalova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - B Dörken
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - C A Schmitt
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany
| | - K E Smedby
- Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, and Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - G Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Lund University, Lund, Sweden
| | - B Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - J S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - C Belessi
- Hematology Department, General Hospital of Nikea, Piraeus, Greece
| | - P Panagiotidis
- First Department of Propaedeutic Medicine, School of Medicine, University of Athens, Athens, Greece
| | - N Chiorazzi
- Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - F Davi
- Laboratory of Hematology and Universite Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France
| | - A W Langerak
- Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - D Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - A Schuh
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - G Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - P Ghia
- Università Vita-Salute San Raffaele, Milan, Italy.,Division of Experimental Oncology and Department of Onco-Hematology, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Scientific Institute, Milan, Italy
| | - W Xu
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing, China
| | - L Fan
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing, China
| | - O A Bernard
- INSERM, U1170, Institut Gustave Roussy, Villejuif, France
| | - F Nguyen-Khac
- Laboratory of Hematology and Universite Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France
| | - L Rassenti
- Division of Hematology/Oncology, Department of Medicine, University of California at San Diego/Moores Cancer Center, La Jolla, CA, USA
| | - J Li
- Department of Hematology, the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing, China
| | - T J Kipps
- Division of Hematology/Oncology, Department of Medicine, University of California at San Diego/Moores Cancer Center, La Jolla, CA, USA
| | - K Stamatopoulos
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden.,Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - S Pospisilova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - T Zenz
- Department of Molecular Therapy in Haematology and Oncology (G250) and Department of Translational Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine V, University Hospital Heidelberg, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - C C Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - J C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - R Rosenquist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - F Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité, University Medical Center, Berlin, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| |
Collapse
|
19
|
Navrkalova V, Young E, Baliakas P, Radova L, Sutton LA, Plevova K, Mansouri L, Ljungström V, Ntoufa S, Davis Z, Juliusson G, Smedby KE, Belessi C, Panagiotidis P, Touloumenidou T, Davi F, Langerak AW, Ghia P, Strefford JC, Oscier D, Mayer J, Stamatopoulos K, Pospisilova S, Rosenquist R, Trbusek M. ATM mutations in major stereotyped subsets of chronic lymphocytic leukemia: enrichment in subset #2 is associated with markedly short telomeres. Haematologica 2016; 101:e369-73. [PMID: 27479817 DOI: 10.3324/haematol.2016.142968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic Department of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Emma Young
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lenka Radova
- Department of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic Department of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Zadie Davis
- Department of Molecular Pathology, Royal Bournemouth Hospital, UK
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Tasoula Touloumenidou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Frederic Davi
- Laboratory of Hematology, Hospital Pitie-Salpetriere and University Pierre and Marie Curie, Paris, France
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - David Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, UK
| | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic Department of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| |
Collapse
|
20
|
Bhoi S, Ljungström V, Baliakas P, Mattsson M, Smedby KE, Juliusson G, Rosenquist R, Mansouri L. Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2. Epigenetics 2016; 11:449-55. [PMID: 27128508 DOI: 10.1080/15592294.2016.1178432] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Based on the methylation status of 5 single CpG sites, a novel epigenetic classification of chronic lymphocytic leukemia (CLL) was recently proposed, classifying CLL patients into 3 clinico-biological subgroups with different outcome, termed memory like CLL (m-CLL), naïve like CLL (n-CLL), and a third intermediate CLL subgroup (i-CLL). While m-CLL and n-CLL patients at large corresponded to patients carrying mutated and unmutated IGHV genes, respectively, limited information exists regarding the less defined i-CLL group. Using pyrosequencing, we investigated the prognostic impact of the proposed 5 CpG signature in a well-characterized CLL cohort (135 cases), including IGHV-mutated and unmutated patients as well as clinically aggressive stereotyped subset #2 patients. Overall, we confirmed the signature's association with established prognostic markers. Moreover, in the presence of the IGHV mutational status, the epigenetic signature remained independently associated with both time-to-first-treatment and overall survival in multivariate analyses. As a prime finding, we observed that subset #2 patients were predominantly classified as i-CLL, probably reflecting their borderline IGHV mutational status (97-99% germline identity), though having a similarly poor prognosis as n-CLL patients. In summary, we validated the epigenetic classifier as an independent factor in CLL prognostication and provide further evidence that subset #2 is a member of the i-CLL group, hence supporting the existence of a third, intermediate epigenetic subgroup.
Collapse
Affiliation(s)
- Sujata Bhoi
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Viktor Ljungström
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Panagiotis Baliakas
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Mattias Mattsson
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden.,b Department of Medical Sciences , Uppsala University , Uppsala , Sweden
| | - Karin E Smedby
- c Department of Medicine Solna , Clinical Epidemiology Unit, Karolinska Institutet , Stockholm , Sweden
| | - Gunnar Juliusson
- d Department of Laboratory Medicine , Stem Cell Center, Hematology and Transplantation, Lund University , Lund , Sweden
| | - Richard Rosenquist
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Larry Mansouri
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| |
Collapse
|
21
|
Pandzic T, Larsson J, He L, Kundu S, Ban K, Akhtar-Ali M, Hellström AR, Schuh A, Clifford R, Blakemore SJ, Strefford JC, Baumann T, Lopez-Guillermo A, Campo E, Ljungström V, Mansouri L, Rosenquist R, Sjöblom T, Hellström M. Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia. Clin Cancer Res 2016; 22:6217-6227. [PMID: 26957556 DOI: 10.1158/1078-0432.ccr-15-2903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE To identify resistance mechanisms for the chemotherapeutic drug fludarabine in chronic lymphocytic leukemia (CLL), as innate and acquired resistance to fludarabine-based chemotherapy represents a major challenge for long-term disease control. EXPERIMENTAL DESIGN We used piggyBac transposon-mediated mutagenesis, combined with next-generation sequencing, to identify genes that confer resistance to fludarabine in a human CLL cell line. RESULTS In total, this screen identified 782 genes with transposon integrations in fludarabine-resistant pools of cells. One of the identified genes is a known resistance mediator DCK (deoxycytidine kinase), which encodes an enzyme that is essential for the phosphorylation of the prodrug to the active metabolite. BMP2K, a gene not previously linked to CLL, was also identified as a modulator of response to fludarabine. In addition, 10 of 782 transposon-targeted genes had previously been implicated in treatment resistance based on somatic mutations seen in patients refractory to fludarabine-based therapy. Functional characterization of these genes supported a significant role for ARID5B and BRAF in fludarabine sensitivity. Finally, pathway analysis of transposon-targeted genes and RNA-seq profiling of fludarabine-resistant cells suggested deregulated MAPK signaling as involved in mediating drug resistance in CLL. CONCLUSIONS To our knowledge, this is the first forward genetic screen for chemotherapy resistance in CLL. The screen pinpointed novel genes and pathways involved in fludarabine resistance along with previously known resistance mechanisms. Transposon screens can therefore aid interpretation of cancer genome sequencing data in the identification of genes modifying sensitivity to chemotherapy. Clin Cancer Res; 22(24); 6217-27. ©2016 AACR.
Collapse
Affiliation(s)
- Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Kenneth Ban
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden.,Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Institute of Molecular and Cell Biology, A*STAR, Singapore
| | - Muhammad Akhtar-Ali
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Anders R Hellström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Schuh
- Radcliffe Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Ruth Clifford
- Radcliffe Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Stuart J Blakemore
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tycho Baumann
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Elias Campo
- Unitat de Hematología, Hospital Clíınic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden
| | - Mats Hellström
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
22
|
Moens LNJ, Falk-Sörqvist E, Ljungström V, Mattsson J, Sundström M, La Fleur L, Mathot L, Micke P, Nilsson M, Botling J. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples. J Mol Diagn 2015; 17:729-39. [PMID: 26354930 DOI: 10.1016/j.jmoldx.2015.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/29/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.
Collapse
Affiliation(s)
- Lotte N J Moens
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Magnus Sundström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Linnéa La Fleur
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
| | - Johan Botling
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden.
| |
Collapse
|
23
|
Crona J, Ljungström V, Welin S, Walz MK, Hellman P, Björklund P. Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma. PLoS One 2015; 10:e0133210. [PMID: 26230854 PMCID: PMC4521794 DOI: 10.1371/journal.pone.0133210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/24/2015] [Indexed: 11/28/2022] Open
Abstract
Background Recent studies have demonstrated equal quality of targeted next generation sequencing (NGS) compared to Sanger Sequencing. Whereas these novel sequencing processes have a validated robust performance, choice of enrichment method and different available bioinformatic software as reliable analysis tool needs to be further investigated in a diagnostic setting. Methods DNA from 21 patients with genetic variants in SDHB, VHL, EPAS1, RET, (n=17) or clinical criteria of NF1 syndrome (n=4) were included. Targeted NGS was performed using Truseq custom amplicon enrichment sequenced on an Illumina MiSEQ instrument. Results were analysed in parallel using three different bioinformatics pipelines; (1) Commercially available MiSEQ Reporter, fully automatized and integrated software, (2) CLC Genomics Workbench, graphical interface based software, also commercially available, and ICP (3) an in-house scripted custom bioinformatic tool. Results A tenfold read coverage was achieved in between 95-98% of targeted bases. All workflows had alignment of reads to SDHA and NF1 pseudogenes. Compared to Sanger sequencing, variant calling revealed a sensitivity ranging from 83 to 100% and a specificity of 99.9-100%. Only MiSEQ reporter identified all pathogenic variants in both sequencing runs. Conclusions We conclude that targeted next generation sequencing have equal quality compared to Sanger sequencing. Enrichment specificity and the bioinformatic performance need to be carefully assessed in a diagnostic setting. As acceptable accuracy was noted for a fully automated bioinformatic workflow, we suggest that processing of NGS data could be performed without expert bioinformatics skills utilizing already existing commercially available bioinformatics tools.
Collapse
Affiliation(s)
- Joakim Crona
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
- * E-mail:
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185, Uppsala, Sweden
| | - Staffan Welin
- Departments of Medical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Martin K. Walz
- Department for Surgery and Centre of Minimal Invasive Surgery, Kliniken Essen-Mitte, Academic Teaching Hospital of the University of Duisburg-Essen, DE-45136 Essen, Germany
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| | - Peyman Björklund
- Department of Surgical Sciences, Uppsala University, SE-75185, Uppsala, Sweden
| |
Collapse
|
24
|
Mansouri L, Sutton LA, Ljungström V, Bondza S, Arngården L, Bhoi S, Larsson J, Cortese D, Kalushkova A, Plevova K, Young E, Gunnarsson R, Falk-Sörqvist E, Lönn P, Muggen AF, Yan XJ, Sander B, Enblad G, Smedby KE, Juliusson G, Belessi C, Rung J, Chiorazzi N, Strefford JC, Langerak AW, Pospisilova S, Davi F, Hellström M, Jernberg-Wiklund H, Ghia P, Söderberg O, Stamatopoulos K, Nilsson M, Rosenquist R. Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2015; 212:833-43. [PMID: 25987724 PMCID: PMC4451125 DOI: 10.1084/jem.20142009] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/23/2015] [Indexed: 12/24/2022]
Abstract
Mansouri et al. applied targeted deep sequencing to identify mutations within NF-κB core complex genes in CLL. NFKBIE, the gene encoding the inhibitory IκBε molecule, was most frequently mutated, especially in poor-prognostic subgroups of CLL. The authors show that NFKBIE mutations were associated with significantly reduced IkBε expression and p65 inhibition, ultimately leading to NF-κB activation and a more aggressive disease. NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis.
Collapse
Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Sina Bondza
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Linda Arngården
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Sujata Bhoi
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Jimmy Larsson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Diego Cortese
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Antonia Kalushkova
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, 601 77 Brno, Czech Republic
| | - Emma Young
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Rebeqa Gunnarsson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Peter Lönn
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Alice F Muggen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, 3000 CE Rotterdam, Netherlands
| | - Xiao-Jie Yan
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, 141 86 Huddinge, Stockholm, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Karin E Smedby
- Clinical Epidemiology Unit, Department of Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Chrysoula Belessi
- Hematology Department, General Hospital of Nikea, 18454 Piraeus, Greece
| | - Johan Rung
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Nicholas Chiorazzi
- The Karches Center for Chronic Lymphocytic Leukemia Research, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Jonathan C Strefford
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, England, UK
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, 3000 CE Rotterdam, Netherlands
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, 601 77 Brno, Czech Republic
| | - Frederic Davi
- Department of Hematology, Pitié-Salpêtrière Hospital, F-75013 Paris, France Cordeliers Research Center, UMR_S 1138, UPMC University of Paris 6, F-75005 Paris, France
| | - Mats Hellström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Helena Jernberg-Wiklund
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Paolo Ghia
- Divisione di Oncologia Sperimentale, Dipartimento di Onco-Ematologia, IRCCS Istituto Scientifico San Raffaele and Fondazione Centro San Raffaele, 20132 Milano, Italy Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Ola Söderberg
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden Institute of Applied Biosciences, Center for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Mats Nilsson
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, 751 05 Uppsala, Sweden
| |
Collapse
|
25
|
Kiflemariam S, Ljungström V, Pontén F, Sjöblom T. Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers. Am J Pathol 2015; 185:1600-9. [PMID: 25864925 DOI: 10.1016/j.ajpath.2015.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/08/2015] [Accepted: 02/18/2015] [Indexed: 01/16/2023]
Abstract
The tyrosine kinome and phosphatome harbor oncogenes and tumor suppressor genes and important regulators of angiogenesis and tumor stroma formation. To provide a better understanding of their potential roles in cancer, we analyzed the expression of 85 tyrosine kinases and 42 tyrosine phosphatases by in situ hybridization 48 human normal and 24 tumor tissue specimens. Nine-tenths of the assessed transcripts had tumor cell expression concordant with expression array databases. Further, pan-cancer expression of AATK, PTPRK, and PTPRU and expression of PTPRS in a subset of tumors were observed. To demonstrate tumor subcompartment resolution, we validated the predicted tumor stroma-specific markers HTRA1, HTRA3, MXRA5, MXRA8, and SERPING1 in situ. In addition to known vascular and stromal markers such as PDGFRB, we observed stromal expression of PTK6 and TNS1 and vascular expression of INSR, PTPRF, PTPRG, PTPRU, and TNS1, of which INSR emerged as a tumor-specific vessel marker. This study demonstrates the feasibility of large-scale analyses to chart the transcriptome in situ in human cancers and their ability to identify novel cancer biomarkers.
Collapse
Affiliation(s)
- Sara Kiflemariam
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
26
|
Parry M, Rose-Zerilli MJ, Ljungström V, Gibson J, Wang J, Walewska R, Parker H, Parker A, Davis Z, Gardiner A, McIver-Brown N, Kalpadakis C, Xochelli A, Anagnostopoulos A, Fazi C, de Castro DG, Dearden C, Pratt G, Rosenquist R, Ashton-Key M, Forconi F, Collins A, Ghia P, Matutes E, Pangalis G, Stamatopoulos K, Oscier D, Strefford JC. Genetics and Prognostication in Splenic Marginal Zone Lymphoma: Revelations from Deep Sequencing. Clin Cancer Res 2015; 21:4174-4183. [PMID: 25779943 DOI: 10.1158/1078-0432.ccr-14-2759] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/03/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Mounting evidence supports the clinical significance of gene mutations and immunogenetic features in common mature B-cell malignancies. EXPERIMENTAL DESIGN We undertook a detailed characterization of the genetic background of splenic marginal zone lymphoma (SMZL), using targeted resequencing and explored potential clinical implications in a multinational cohort of 175 patients with SMZL. RESULTS We identified recurrent mutations in TP53 (16%), KLF2 (12%), NOTCH2 (10%), TNFAIP3 (7%), MLL2 (11%), MYD88 (7%), and ARID1A (6%), all genes known to be targeted by somatic mutation in SMZL. KLF2 mutations were early, clonal events, enriched in patients with del(7q) and IGHV1-2*04 B-cell receptor immunoglobulins, and were associated with a short median time to first treatment (0.12 vs. 1.11 years; P = 0.01). In multivariate analysis, mutations in NOTCH2 [HR, 2.12; 95% confidence interval (CI), 1.02-4.4; P = 0.044] and 100% germline IGHV gene identity (HR, 2.19; 95% CI, 1.05-4.55; P = 0.036) were independent markers of short time to first treatment, whereas TP53 mutations were an independent marker of short overall survival (HR, 2.36; 95 % CI, 1.08-5.2; P = 0.03). CONCLUSIONS We identify key associations between gene mutations and clinical outcome, demonstrating for the first time that NOTCH2 and TP53 gene mutations are independent markers of reduced treatment-free and overall survival, respectively.
Collapse
Affiliation(s)
- Marina Parry
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Jane Gibson
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Renata Walewska
- Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Helen Parker
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anton Parker
- Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Zadie Davis
- Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Anne Gardiner
- Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Neil McIver-Brown
- Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Christina Kalpadakis
- Department of Hematology, School of Medicine, University of Crete, Heraklion, Greece
| | - Aliki Xochelli
- Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greece
| | | | - Claudia Fazi
- Division of Molecular Oncology, Department of Onco-Haematology, IRCCS Istituto Scientifico San Raffaele, Fondazione Centro San Raffaele, Università Vita-Salute San Raffaele, Milan, Italy
| | - David Gonzalez de Castro
- Heamato-oncology Unit, Division of Molecular Pathology, Institute for Cancer Research, Sutton, UK
| | - Claire Dearden
- Heamato-oncology Unit, Division of Molecular Pathology, Institute for Cancer Research, Sutton, UK
| | - Guy Pratt
- School of Cancer Studies, University of Birmingham, Birmingham, UK; Department of Haematology, Heart of England NHS Foundation Trust, Birmingham, UK
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Margaret Ashton-Key
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Francesco Forconi
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, UK
| | - Paolo Ghia
- Division of Molecular Oncology, Department of Onco-Haematology, IRCCS Istituto Scientifico San Raffaele, Fondazione Centro San Raffaele, Università Vita-Salute San Raffaele, Milan, Italy
| | - Estella Matutes
- Haematopathology Unit, Hospital Clinic, Barcelona University, Villarroel, Barcelona, Spain
| | | | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greece.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - David Oscier
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Department of Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| |
Collapse
|
27
|
Sutton LA, Ljungström V, Mansouri L, Young E, Cortese D, Navrkalova V, Malcikova J, Muggen AF, Trbusek M, Panagiotidis P, Davi F, Belessi C, Langerak AW, Ghia P, Pospisilova S, Stamatopoulos K, Rosenquist R. Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting. Haematologica 2014; 100:370-6. [PMID: 25480502 DOI: 10.3324/haematol.2014.109777] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Next-generation sequencing has revealed novel recurrent mutations in chronic lymphocytic leukemia, particularly in patients with aggressive disease. Here, we explored targeted re-sequencing as a novel strategy to assess the mutation status of genes with prognostic potential. To this end, we utilized HaloPlex targeted enrichment technology and designed a panel including nine genes: ATM, BIRC3, MYD88, NOTCH1, SF3B1 and TP53, which have been linked to the prognosis of chronic lymphocytic leukemia, and KLHL6, POT1 and XPO1, which are less characterized but were found to be recurrently mutated in various sequencing studies. A total of 188 chronic lymphocytic leukemia patients with poor prognostic features (unmutated IGHV, n=137; IGHV3-21 subset #2, n=51) were sequenced on the HiSeq 2000 and data were analyzed using well-established bioinformatics tools. Using a conservative cutoff of 10% for the mutant allele, we found that 114/180 (63%) patients carried at least one mutation, with mutations in ATM, BIRC3, NOTCH1, SF3B1 and TP53 accounting for 149/177 (84%) of all mutations. We selected 155 mutations for Sanger validation (variant allele frequency, 10-99%) and 93% (144/155) of mutations were confirmed; notably, all 11 discordant variants had a variant allele frequency between 11-27%, hence at the detection limit of conventional Sanger sequencing. Technical precision was assessed by repeating the entire HaloPlex procedure for 63 patients; concordance was found for 77/82 (94%) mutations. In summary, this study demonstrates that targeted next-generation sequencing is an accurate and reproducible technique potentially suitable for routine screening, eventually as a stand-alone test without the need for confirmation by Sanger sequencing.
Collapse
Affiliation(s)
- Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Emma Young
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Diego Cortese
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Veronika Navrkalova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alice F Muggen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Martin Trbusek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- Laboratory of Hematology and Universite Pierre et Marie Curie, Hopital Pitie-Salpetriere, Paris, France
| | | | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Paolo Ghia
- Università Vita-Salute San Raffaele, Milan, Italy Division of Molecular Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden Institute of Applied Biosciences, CERTH, Thessaloniki, Greece Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| |
Collapse
|
28
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| |
Collapse
|
29
|
Staaf J, Akerström T, Ljungström V, Larsson S, Karlsson T, Skogseid B, Bergsten P. [Early bridge between preclinical and clinical research]. Lakartidningen 2012; 109:898. [PMID: 22642061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
|