1
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Schönherz AA, Bødker JS, Schmitz A, Brøndum RF, Jakobsen LH, Roug AS, Severinsen MT, El-Galaly TC, Jensen P, Johnsen HE, Bøgsted M, Dybkær K. Normal myeloid progenitor cell subset-associated gene signatures for acute myeloid leukaemia subtyping with prognostic impact. PLoS One 2020; 15:e0229593. [PMID: 32324791 PMCID: PMC7179860 DOI: 10.1371/journal.pone.0229593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/10/2020] [Indexed: 12/30/2022] Open
Abstract
Acute myeloid leukaemia (AML) is characterised by phenotypic heterogeneity, which we hypothesise is a consequence of deregulated differentiation with transcriptional reminiscence of the normal compartment or cell-of-origin. Here, we propose a classification system based on normal myeloid progenitor cell subset-associated gene signatures (MAGS) for individual assignments of AML subtypes. We generated a MAGS classifier including the progenitor compartments CD34+/CD38- for haematopoietic stem cells (HSCs), CD34+/CD38+/CD45RA- for megakaryocyte-erythroid progenitors (MEPs), and CD34+/CD38+/CD45RA+ for granulocytic-monocytic progenitors (GMPs) using regularised multinomial regression with three discrete outcomes and an elastic net penalty. The regularisation parameters were chosen by cross-validation, and MAGS assignment accuracy was validated in an independent data set (N = 38; accuracy = 0.79) of sorted normal myeloid subpopulations. The prognostic value of MAGS assignment was studied in two clinical cohorts (TCGA: N = 171; GSE6891: N = 520) and had a significant prognostic impact. Furthermore, multivariate Cox regression analysis using the MAGS subtype, FAB subtype, cytogenetics, molecular genetics, and age as explanatory variables showed independent prognostic value. Molecular characterisation of subtypes by differential gene expression analysis, gene set enrichment analysis, and mutation patterns indicated reduced proliferation and overrepresentation of RUNX1 and IDH2 mutations in the HSC subtype; increased proliferation and overrepresentation of CEBPA mutations in the MEP subtype; and innate immune activation and overrepresentation of WT1 mutations in the GMP subtype. We present a differentiation-dependent classification system for AML subtypes with distinct pathogenetic and prognostic importance that can help identify candidates poorly responding to combination chemotherapy and potentially guide alternative treatments.
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Affiliation(s)
- Anna A. Schönherz
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Rasmus Froberg Brøndum
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Lasse Hjort Jakobsen
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Anne Stidsholt Roug
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Marianne T. Severinsen
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tarec C. El-Galaly
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Paw Jensen
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Hans Erik Johnsen
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- * E-mail:
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2
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A multiple myeloma classification system that associates normal B-cell subset phenotypes with prognosis. Blood Adv 2019; 2:2400-2411. [PMID: 30254104 DOI: 10.1182/bloodadvances.2018018564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Despite the recent progress in treatment of multiple myeloma (MM), it is still an incurable malignant disease, and we are therefore in need of new risk stratification tools that can help us to understand the disease and optimize therapy. Here we propose a new subtyping of myeloma plasma cells (PCs) from diagnostic samples, assigned by normal B-cell subset associated gene signatures (BAGS). For this purpose, we combined fluorescence-activated cell sorting and gene expression profiles from normal bone marrow (BM) Pre-BI, Pre-BII, immature, naïve, memory, and PC subsets to generate BAGS for assignment of normal BM subtypes in diagnostic samples. The impact of the subtypes was analyzed in 8 available data sets from 1772 patients' myeloma PC samples. The resulting tumor assignments in available clinical data sets exhibited similar BAGS subtype frequencies in 4 cohorts from de novo MM patients across 1296 individual cases. The BAGS subtypes were significantly associated with progression-free and overall survival in a meta-analysis of 916 patients from 3 prospective clinical trials. The major impact was observed within the Pre-BII and memory subtypes, which had a significantly inferior prognosis compared with other subtypes. A multiple Cox proportional hazard analysis documented that BAGS subtypes added significant, independent prognostic information to the translocations and cyclin D classification. BAGS subtype analysis of patient cases identified transcriptional differences, including a number of differentially spliced genes. We identified subtype differences in myeloma at diagnosis, with prognostic impact and predictive potential, supporting an acquired B-cell trait and phenotypic plasticity as a pathogenetic hallmark of MM.
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3
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Nørgaard CH, Jakobsen LH, Gentles AJ, Dybkær K, El-Galaly TC, Bødker JS, Schmitz A, Johansen P, Herold T, Spiekermann K, Brown JR, Klitgaard JL, Johnsen HE, Bøgsted M. Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow - A proof of concept study. PLoS One 2018; 13:e0193249. [PMID: 29513759 PMCID: PMC5841735 DOI: 10.1371/journal.pone.0193249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 11/26/2022] Open
Abstract
Diagnostic and prognostic evaluation of chronic lymphocytic leukemia (CLL) involves blood cell counts, immunophenotyping, IgVH mutation status, and cytogenetic analyses. We generated B-cell associated gene-signatures (BAGS) based on six naturally occurring B-cell subsets within normal bone marrow. Our hypothesis is that by segregating CLL according to BAGS, we can identify subtypes with prognostic implications in support of pathogenetic value of BAGS. Microarray-based gene-expression samples from eight independent CLL cohorts (1,024 untreated patients) were BAGS-stratified into pre-BI, pre-BII, immature, naïve, memory, or plasma cell subtypes; the majority falling within the memory (24.5-45.8%) or naïve (14.5-32.3%) categories. For a subset of CLL patients (n = 296), time to treatment (TTT) was shorter amongst early differentiation subtypes (pre-BI/pre-BII/immature) compared to late subtypes (memory/plasma cell, HR: 0.53 [0.35-0.78]). Particularly, pre-BII subtype patients had the shortest TTT among all subtypes. Correlates derived for BAGS subtype and IgVH mutation (n = 405) revealed an elevated mutation frequency in late vs. early subtypes (71% vs. 45%, P < .001). Predictions for BAGS subtype resistance towards rituximab and cyclophosphamide varied for rituximab, whereas all subtypes were sensitive to cyclophosphamide. This study supports our hypothesis that BAGS-subtyping may be of tangible prognostic and pathogenetic value for CLL patients.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Agents, Immunological/therapeutic use
- B-Lymphocyte Subsets/metabolism
- Bone Marrow/metabolism
- Cyclophosphamide/therapeutic use
- Drug Resistance, Neoplasm/physiology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Microarray Analysis
- Middle Aged
- Prognosis
- Proof of Concept Study
- Retrospective Studies
- Rituximab/therapeutic use
- Survival Analysis
- Time-to-Treatment
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Affiliation(s)
| | - Lasse Hjort Jakobsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Andrew J. Gentles
- Departments of Medicine and Biomedical Data Science, Stanford, California, United States of America
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Preben Johansen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Tobias Herold
- Department of Internal Medicine 3, University of Munich, Munich, Germany
| | | | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Josephine L. Klitgaard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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4
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Nielsen KR, Rodrigo-Domingo M, Steffensen R, Baech J, Bergkvist KS, Oosterhof L, Schmitz A, Bødker JS, Johansen P, Vogel U, Vangsted A, Dybkær K, Bøgsted M, Johnsen HE. Interactions between SNPs affecting inflammatory response genes are associated with multiple myeloma disease risk and survival. Leuk Lymphoma 2017; 58:2695-2704. [DOI: 10.1080/10428194.2017.1306643] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - John Baech
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Kim S Bergkvist
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Liesbeth Oosterhof
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Preben Johansen
- Department of Hematopathology, Aalborg University Hospital, Aalborg, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Anette Vangsted
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- The Department of Clinical Medicine, Aalborg University, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- The Department of Clinical Medicine, Aalborg University, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- The Department of Clinical Medicine, Aalborg University, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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5
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Johnsen HE, Bøgsted M, Schmitz A, Bødker JS, El-Galaly TC, Johansen P, Valent P, Zojer N, Van Valckenborgh E, Vanderkerken K, van Duin M, Sonneveld P, Perez-Andres M, Orfao A, Dybkær K. The myeloma stem cell concept, revisited: from phenomenology to operational terms. Haematologica 2016; 101:1451-1459. [PMID: 27903712 DOI: 10.3324/haematol.2015.138826] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 08/30/2016] [Indexed: 11/09/2022] Open
Abstract
The concept of the myeloma stem cell may have important therapeutic implications, yet its demonstration has been hampered by a lack of consistency in terms and definitions. Here, we summarize the current documentation and propose single-cell in vitro studies for future translational studies. By the classical approach, a CD19-/CD45low/-/CD38high/CD138+ malignant plasma cell, but not the CD19+/CD38low/- memory B cell compartment, is enriched for tumorigenic cells that initiate myeloma in xenografted immunodeficient mice, supporting that myeloma stem cells are present in the malignant PC compartment. Using a new approach, analysis of c-DNA libraries from CD19+/CD27+/CD38- single cells has identified clonotypic memory B cell, suggested to be the cell of origin. This is consistent with multiple myeloma being a multistep hierarchical process before or during clinical presentation. We anticipate that further characterization will require single cell geno- and phenotyping combined with clonogenic assays. To implement such technologies, we propose a revision of the concept of a myeloma stem cell by including operational in vitro assays to describe the cellular components of origin, initiation, maintenance, and evolution of multiple myeloma. These terms are in accordance with recent (2012) consensus statements on the definitions, assays, and nomenclature of cancer stem cells, which is technically precise without completely abolishing established terminology. We expect that this operational model will be useful for future reporting of parameters used to identify and characterize the multiple myeloma stem cells. We strongly recommend that these parameters include validated standard technologies, reproducible assays, and, most importantly, supervised prospective sampling of selected biomaterial which reflects clinical stages, disease spectrum, and therapeutic outcome. This framework is key to the characterization of the cellular architecture of multiple myeloma and its use in precision medicine.
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Affiliation(s)
- Hans Erik Johnsen
- Department of Haematology Aalborg University Hospital, Denmark .,Clinical Cancer Research Center, Aalborg University Hospital, Denmark.,The Department of Clinical Medicine, Aalborg University, Denmark
| | - Martin Bøgsted
- Department of Haematology Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark.,The Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Tarec Christoffer El-Galaly
- Department of Haematology Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark.,The Department of Clinical Medicine, Aalborg University, Denmark
| | - Preben Johansen
- Department of Hematopathology, Aalborg University Hospital, Denmark
| | - Peter Valent
- The Department of Internal Medicine I, Division of Hematology Medical University of Vienna, Austria
| | - Niklas Zojer
- Wilhelminen Cancer Research Institute and Ludwig Boltzmann Cluster Oncology, First Department of Medicine, Center for Oncology and Hematology, Vienna, Austria
| | - Els Van Valckenborgh
- Department of Hematology and Immunology-Myeloma Center, Vrije University Brussels, Belgium
| | - Karin Vanderkerken
- Department of Hematology and Immunology-Myeloma Center, Vrije University Brussels, Belgium
| | - Mark van Duin
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Pieter Sonneveld
- Department of Hematology, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Martin Perez-Andres
- Department of Medicine and Cytometry Service (NUCLEUS), Cancer Research Center (IBMCC, USAL-CSIC), Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Spain
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (NUCLEUS), Cancer Research Center (IBMCC, USAL-CSIC), Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Spain
| | - Karen Dybkær
- Department of Haematology Aalborg University Hospital, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Denmark.,The Department of Clinical Medicine, Aalborg University, Denmark
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6
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Bergkvist KS, Nørgaard MA, Bøgsted M, Schmitz A, Nyegaard M, Gaihede M, Bæch J, Grønholdt ML, Jensen FS, Johansen P, Urup T, El-Galaly TC, Madsen J, Bødker JS, Dybkær K, Johnsen HE. Characterization of memory B cells from thymus and its impact for DLBCL classification. Exp Hematol 2016; 44:982-990.e11. [PMID: 27297329 DOI: 10.1016/j.exphem.2016.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 05/09/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
The rare memory B cells in thymus (Thy) are considered the cells of origin for primary mediastinal large B-cell lymphoma. The objectives of the present study were to characterize the normal memory B-cell compartment in Thy and to support its association with primary mediastinal B-cell lymphoma. Seven paired human tissue samples from Thy and sternum bone marrow (BM) were harvested during cardiac surgery. B-cell subsets were phenotyped by Euroflow standard and fluorescence-activated cell sorting for microarray analysis on the Human Exon 1.0 ST Arrays platform. Differentially expressed genes between Thy and BM memory B cells were identified and correlated with the molecular subclasses of diffuse large B-cell lymphoma. Within Thy, 4% (median; range 2%-14%) of the CD45(+) hematopoietic cells were CD19(+) B cells, with a major fraction being CD27(+)/CD38(-) memory B cells (median 80%, range 76%-93%). The BM contained 14% (median; range 3%-27%), of which only a minor fraction (median 5%, range 2%-10%) were memory B cells. Global gene expression analysis of the memory B-cell subsets from the two compartments identified 133 genes upregulated in Thy, including AICDA, REL, STAT1, TNF family, SLAMF1, CD80, and CD86. In addition, exons 4 and 5 in the 3' end of AICDA were more highly expressed in Thy than in BM. The Thy memory B-cell gene profile was overexpressed in primary mediastinal B-cell lymphoma compared with other diffuse large B-cell lymphoma subclasses. The present study describes a Thy memory B-cell subset and its gene profile correlated with primary mediastinal B-cell lymphomas, suggesting origin from Thy memory B cells.
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Affiliation(s)
| | - Martin Agge Nørgaard
- Department of Cardiothoracic Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Mette Nyegaard
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - John Bæch
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - Preben Johansen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Thomas Urup
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Tarec C El-Galaly
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Jakob Madsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
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7
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Nielsen KR, Steffensen R, Bendtsen MD, Rodrigo-Domingo M, Baech J, Haunstrup TM, Bergkvist KS, Schmitz A, Boedker JS, Johansen P, Dybkaeær K, Boeøgsted M, Johnsen HE. Inherited Inflammatory Response Genes Are Associated with B-Cell Non-Hodgkin's Lymphoma Risk and Survival. PLoS One 2015; 10:e0139329. [PMID: 26448050 PMCID: PMC4598167 DOI: 10.1371/journal.pone.0139329] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Malignant B-cell clones are affected by both acquired genetic alterations and by inherited genetic variations changing the inflammatory tumour microenvironment. METHODS We investigated 50 inflammatory response gene polymorphisms in 355 B-cell non-Hodgkin's lymphoma (B-NHL) samples encompassing 216 diffuse large B cell lymphoma (DLBCL) and 139 follicular lymphoma (FL) and 307 controls. The effect of single genes and haplotypes were investigated and gene-expression analysis was applied for selected genes. Since interaction between risk genes can have a large impact on phenotype, two-way gene-gene interaction analysis was included. RESULTS We found inherited SNPs in genes critical for inflammatory pathways; TLR9, IL4, TAP2, IL2RA, FCGR2A, TNFA, IL10RB, GALNT12, IL12A and IL1B were significantly associated with disease risk and SELE, IL1RN, TNFA, TAP2, MBL2, IL5, CX3CR1, CHI3L1 and IL12A were, associated with overall survival (OS) in specific diagnostic entities of B-NHL. We discovered noteworthy interactions between DLBCL risk alleles on IL10 and IL4RA and FL risk alleles on IL4RA and IL4. In relation to OS, a highly significant interaction was observed in DLBCL for IL4RA (rs1805010) * IL10 (rs1800890) (HR = 0.11 (0.02-0.50)). Finally, we explored the expression of risk genes from the gene-gene interaction analysis in normal B-cell subtypes showing a different expression of IL4RA, IL10, IL10RB genes supporting a pathogenetic effect of these interactions in the germinal center. CONCLUSIONS The present findings support the importance of inflammatory genes in B-cell lymphomas. We found association between polymorphic sites in inflammatory response genes and risk as well as outcome in B-NHL and suggest an effect of gene-gene interactions during the stepwise oncogenesis.
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MESH Headings
- Aged
- Alleles
- Female
- Genotype
- Haplotypes
- Humans
- Interleukin-10/genetics
- Interleukin-10/metabolism
- Interleukin-10 Receptor beta Subunit/genetics
- Interleukin-10 Receptor beta Subunit/metabolism
- Interleukin-4/genetics
- Interleukin-4/metabolism
- Interleukin-4 Receptor alpha Subunit/genetics
- Interleukin-4 Receptor alpha Subunit/metabolism
- Linkage Disequilibrium
- Lymphoma, Follicular/etiology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/mortality
- Lymphoma, Large B-Cell, Diffuse/etiology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Male
- Middle Aged
- Odds Ratio
- Polymorphism, Single Nucleotide
- Proportional Hazards Models
- Risk
- Survival Analysis
- Transcriptome
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Affiliation(s)
- Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - John Baech
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Thure Mors Haunstrup
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Preben Johansen
- Department of Haematopathology, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkaeær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Martin Boeøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- * E-mail:
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8
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Petri A, Dybkær K, Bøgsted M, Thrue CA, Hagedorn PH, Schmitz A, Bødker JS, Johnsen HE, Kauppinen S. Long Noncoding RNA Expression during Human B-Cell Development. PLoS One 2015; 10:e0138236. [PMID: 26394393 PMCID: PMC4578992 DOI: 10.1371/journal.pone.0138236] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/26/2015] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n = 7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n = 6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as “guilt by association”. By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations.
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Affiliation(s)
- Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Charlotte Albæk Thrue
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Peter H. Hagedorn
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- * E-mail:
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Rasmussen SM, Bilgrau AE, Schmitz A, Falgreen S, Bergkvist KS, Tramm AM, Baech J, Jacobsen CL, Gaihede M, Kjeldsen MK, Bødker JS, Dybkaer K, Bøgsted M, Johnsen HE. Stable phenotype of B-cell subsets following cryopreservation and thawing of normal human lymphocytes stored in a tissue biobank. CYTOMETRY PART B-CLINICAL CYTOMETRY 2014; 88:40-9. [PMID: 25327569 DOI: 10.1002/cyto.b.21192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/23/2014] [Accepted: 09/18/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. METHODS We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are no phenotypic differences between cryopreserved and fresh B-cell subsets." Subsequently, we performed an uncontrolled comparison of tonsil tissue samples. RESULTS By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. CONCLUSIONS We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue-specific comparative analysis.
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