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Zhang X, Schuhmachers P, Mourão A, Giansanti P, Murer A, Thumann S, Kuklik‐Roos C, Beer S, Hauck SM, Hammerschmidt W, Küppers R, Kuster B, Raab M, Strebhardt K, Sattler M, Münz C, Kempkes B. PLK1-dependent phosphorylation restrains EBNA2 activity and lymphomagenesis in EBV-infected mice. EMBO Rep 2021; 22:e53007. [PMID: 34605140 PMCID: PMC8647151 DOI: 10.15252/embr.202153007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
While Epstein-Barr virus (EBV) establishes a life-long latent infection in apparently healthy human immunocompetent hosts, immunodeficient individuals are at particular risk to develop lymphoproliferative B-cell malignancies caused by EBV. A key EBV protein is the transcription factor EBV nuclear antigen 2 (EBNA2), which initiates B-cell proliferation. Here, we combine biochemical, cellular, and in vivo experiments demonstrating that the mitotic polo-like kinase 1 (PLK1) binds to EBNA2, phosphorylates its transactivation domain, and thereby inhibits its biological activity. EBNA2 mutants that impair PLK1 binding or prevent EBNA2 phosphorylation are gain-of-function mutants. They exhibit enhanced transactivation capacities, accelerate the proliferation of infected B cells, and promote the development of monoclonal B-cell lymphomas in infected mice. Thus, PLK1 coordinates the activity of EBNA2 to attenuate the risk of tumor incidences in favor of the establishment of latency in the infected but healthy host.
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Affiliation(s)
- Xiang Zhang
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Patrick Schuhmachers
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - André Mourão
- Institute of Structural BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of ChemistryBavarian NMR CenterTechnical University of MunichGarchingGermany
| | - Piero Giansanti
- Chair of Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Anita Murer
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - Sybille Thumann
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Cornelia Kuklik‐Roos
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Sophie Beer
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core FacilityHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Wolfgang Hammerschmidt
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research)University Hospital EssenEssenGermany
| | - Bernhard Kuster
- Chair of Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
- Bavarian Center for Biomolecular Mass SpectrometryTechnical University of MunichFreisingGermany
| | - Monika Raab
- Department of Gynecology and ObstetricsJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Klaus Strebhardt
- Department of Gynecology and ObstetricsJohann Wolfgang Goethe UniversityFrankfurt am MainGermany
| | - Michael Sattler
- Institute of Structural BiologyHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthNeuherbergGermany
- Department of ChemistryBavarian NMR CenterTechnical University of MunichGarchingGermany
| | - Christian Münz
- Viral ImmunbiologyInstitute of Experimental ImmunologyUniversity of ZürichZürichSwitzerland
| | - Bettina Kempkes
- Research Unit Gene Vectors, Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMünchenGermany
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Piezoelectric Ultrasonic Biological Microdissection Device Based on a Novel Flexure Mechanism for Suppressing Vibration. MICROMACHINES 2021; 12:mi12020196. [PMID: 33668595 PMCID: PMC7918422 DOI: 10.3390/mi12020196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 01/22/2023]
Abstract
Biological microdissection has a wide range of applications in the field of molecular pathology. The current laser-assisted dissection technology is expensive. As an economical microdissection method, piezoelectric ultrasonic microdissection has broad application prospects. However, the performance of the current piezoelectric ultrasonic microdissection technology is unsatisfactory. This paper aims to solve the problems of the low dissecting precision and excessive wear of the dissecting needle caused by the harmful lateral vibration of the present piezoelectric ultrasonic microdissection device. A piezoelectric ultrasonic microdissection device based on a novel flexure mechanism is proposed. By analyzing the flexure hinge flexibility, the type of flexure beam and the optimal design parameters are determined. Through harmonic response simulation analysis, the newly designed microdissection device with a vibration-suppressing mechanism achieves the best vibration effect when the driving frequency is 28 kHz. Under this driving frequency, the lateral vibration suppression effect is improved by 68% compared to the traditional effect without vibration suppression. Then, based on 3D printing technology, a prototype of a novel microdissection device is produced, and its performance is tested. Experiments on dissecting needle vibration tests show that the flexure mechanism does indeed suppress the lateral vibration of the needle tip. We conducted various tissue dissection experiments on paraffin tissue sections. First, we determine the optimal dissecting parameters (driving voltage, frequency, feed speed, cutting angle) of the new equipment through various parameter dissecting experiments. Then, we adopt these optimal dissecting parameters to perform three kinds of dissecting experiments on mouse tissue paraffin section (liver, lung, bone), dissecting experiments on tissue sections of different thicknesses (3 μm, 4 μm, 5 μm), sampling and extraction experiments on complete tissue. The new device has a better dissecting performance for paraffin tissue sections below a 5 μm thickness and can complete various dissecting tasks. Finally, we compare the wear of the dissecting needles of the new and old devices after the same dissecting tasks. The results prove that the suppression of harmful lateral vibration not only significantly improves the dissecting effect but also increases the service life and durability of the dissecting needle, which is beneficial for reducing the equipment costs.
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Bewarder M, Kiefer M, Moelle C, Goerens L, Stilgenbauer S, Christofyllakis K, Kaddu-Mulindwa D, Fadle N, Regitz E, Neumann F, Hoth M, Preuss KD, Pfreundschuh M, Thurner L. Integration of the B-Cell Receptor Antigen Neurabin-I/SAMD14 Into an Antibody Format as New Therapeutic Approach for the Treatment of Primary CNS Lymphoma. Front Oncol 2020; 10:580364. [PMID: 33282736 PMCID: PMC7689012 DOI: 10.3389/fonc.2020.580364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Recently, neurabin-I and SAMD14 have been described as the autoantigenic target of approximately 66% of B-cell receptors (BCRs) of primary central nervous system lymphomas (PCNSL). Neurabin-I and SAMD14 share a highly homologous SAM domain that becomes immunogenic after atypical hyper-N-glycosylation (SAMD14 at ASN339 and neurabin-I at ASN1277). This post-translational modification of neurabin-I and SAMD14 seems to lead to a chronic immune reaction with B-cell receptor activation contributing to lymphoma genesis of PCNSLs. The selective tropism of PCNSL to the CNS corresponds well to the neurabin-I and SAMD14 protein expression pattern. When conjugated to Pseudomonas Exotoxin A (ETA´), the PCNSL reactive epitope exerts cytotoxic effects on lymphoma cells expressing a SAMD14/neurabin-I reactive BCR. Thus, the reactive epitopes of SAMD14/neurabin-I might be useful to establish additional therapeutic strategies against PCNSL. To test this possibility, we integrated the PCNSL-reactive epitope of SAMD14/neurabin-I into a heavy-chain-only Fab antibody format in substitution of the variable region. Specific binding of the prokaryotically produced SAMD14/neurabin-I Fab-antibody to lymphoma cells and their internalization were determined by flow cytometry. Since no established EBV-negative PCNSL cell line exists, we used the ABC-DLBCL cell lines OCI-Ly3 and U2932, which were transfected to express a SAMD14/neurabin-I reactive BCR. The SAMD14/neurabin-I Fab antibody bound specifically to DLBCL cells expressing a BCR with reactivity to SAMD14/neurabin-I and not to unmanipulated DLBCL cell lines. Eukaryotically produced full-length IgG antibodies are well established as immunotherapy format. Therefore, the PCNSL-reactive epitope of SAMD14/neurabin-I was cloned into a full-length IgG1 format replacing the variable domains of the light and heavy chains. The IgG1-format SAMD14/neurabin-I construct was found to specifically bind to target lymphoma cells expressing a SAMD14/neurabin-I reactive B cell receptor. In addition, it induced dose-dependent relative cytotoxicity against these lymphoma cells when incubated with PBMCs. Control DLBCL cells are not affected at any tested concentration. When integrated into the Fab-format and IgG1-format, the PCNSL-reactive epitope of SAMD14/neurabin-I functions as B-cell receptor Antigen for Reverse targeting (BAR). In particular, the IgG1-format BAR-body approach represents a very attractive therapeutic format for the treatment of PCNSLs, considering its specificity against SAMD14/neurabin-I reactive BCRs and the well-known pharmacodynamic properties of IgG antibodies.
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Affiliation(s)
- Moritz Bewarder
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | - Maximilian Kiefer
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Clara Moelle
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Lisa Goerens
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Stephan Stilgenbauer
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | | | | | - Natalie Fadle
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Evi Regitz
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Frank Neumann
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Markus Hoth
- Biophysics, CIPMM, Saarland University, Homburg, Germany
| | - Klaus-Dieter Preuss
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany
| | - Michael Pfreundschuh
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
| | - Lorenz Thurner
- José Carreras Center for Immuno- and Gene Therapy, Saarland University Medical Center, Homburg, Germany.,Internal Medicine I, Saarland University Medical Center, Homburg, Germany
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Lymphocyte predominant cells detect Moraxella catarrhalis-derived antigens in nodular lymphocyte-predominant Hodgkin lymphoma. Nat Commun 2020; 11:2465. [PMID: 32424289 PMCID: PMC7235000 DOI: 10.1038/s41467-020-16375-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) is a rare lymphoma of B-cell origin with frequent expression of functional B-cell receptors (BCRs). Here we report that expression cloning followed by antigen screening identifies DNA-directed RNA polymerase beta’ (RpoC) from Moraxella catarrhalis as frequent antigen of BCRs of IgD+ LP cells. Patients show predominance of HLA-DRB1*04/07 and the IgVH genes encode extraordinarily long CDR3s. High-titer, light-chain-restricted anti-RpoC IgG1/κ-type serum-antibodies are additionally found in these patients. RpoC and MID/hag, a superantigen co-expressed by Moraxella catarrhalis that is known to activate IgD+ B cells by binding to the Fc domain of IgD, have additive activation effects on the BCR, the NF-κB pathway and the proliferation of IgD+ DEV cells expressing RpoC-specific BCRs. This suggests an additive antigenic and superantigenic stimulation of B cells with RpoC-specific IgD+ BCRs under conditions of a permissive MHC-II haplotype as a model of NLPHL lymphomagenesis, implying future treatment strategies. Nodular lymphocyte-predominant Hodgkin lymphoma with IgD+ lymphocyte-predominant (LP) cells is a rare clinical distinct lymphoma subset of B-cell origin. Here the authors show that antigens expressed by Moraxella catarrhalis are recognized by B cell receptors of IgD+ LP cells, suggesting the contribution of chronic antigen stimulation to lymphomagenesis.
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Kiil K, Bein J, Schuhmacher B, Thurner L, Schneider M, Hansmann ML, Hartmann S. A high number of IgG4-positive plasma cells rules out nodular lymphocyte predominant Hodgkin lymphoma. Virchows Arch 2018; 473:759-764. [PMID: 30259184 DOI: 10.1007/s00428-018-2460-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 12/17/2022]
Abstract
Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is a subtype of Hodgkin lymphoma that frequently shows a nodal growth pattern with abundant reactive B cells in the microenvironment. Early NLPHL cases can be particularly difficult to differentiate from progressively transformed germinal centers (PTGC). Since PTGC have been described to be IgG4 associated in a relatively high proportion of cases, the aim of the present study was to determine if IgG4 immunostaining can be helpful in the differential diagnosis between NLPHL and PTGC. We furthermore aimed to learn if LP cells can express IgG4. For this purpose, 58 cases of PTGC and 56 cases of NLPHL were assessed using IgG4 immunostaining. We could confirm that a significant number of PTGC cases showed high numbers of IgG4-positive plasma cells (22/58, 38%), whereas hot spot areas of IgG4-positive plasma cells were not found in any of the NLPHL cases. In lymph node areas with the differential diagnosis of NLPHL and PTGC, IgG4 immunostaining can therefore provide a helpful diagnostic tool to rule out NLPHL when a high number of IgG4-positive plasma cells are encountered. We also assessed 13 cases with a combination of NLPHL and PTGC in the same lymph node. Five of these cases presented hot spot areas of IgG4-positive plasma cells in the PTGC regions, while no significant numbers of IgG4-positive plasma cells were observed in the NLPHL part of the lymph node. LP cells were never IgG4 positive. Furthermore, immunoglobulin heavy chain rearrangements of single IgG4-positive plasma cells were analyzed, revealing a polyclonal plasma cell population. In summary, our data suggest that IgG4 immunostaining can provide additional information in the diagnostic workup of cases with the differential diagnosis of NLPHL and PTGC. IgG4's inefficiency in clearing antigens may explain why lymph nodes with PTGC are usually strongly enlarged and develop a high number of hyperplastic germinal centers. Polyclonal immunoglobulin heavy chain rearrangements in IgG4-positive plasma cells further support the hypothesis that PTGC represent a misled immune reaction.
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Affiliation(s)
- Kati Kiil
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany
| | - Julia Bein
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany
| | - Bianca Schuhmacher
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany
| | - Lorenz Thurner
- José Carreras Center for Immuno- and Gene Therapy and Internal Medicine I, Saarland University Medical School, Homburg, Saar, Germany
| | - Markus Schneider
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany
| | - Martin-Leo Hansmann
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany.,Reference and Consultant Center for Lymph Node and Lymphoma Pathology, Goethe University, Frankfurt am Main, Germany.,Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Senckenberg Institute of Pathology, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany. .,Reference and Consultant Center for Lymph Node and Lymphoma Pathology, Goethe University, Frankfurt am Main, Germany.
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Hyper- N-glycosylated SAMD14 and neurabin-I as driver autoantigens of primary central nervous system lymphoma. Blood 2018; 132:2744-2753. [PMID: 30249786 DOI: 10.1182/blood-2018-03-836932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/12/2018] [Indexed: 01/01/2023] Open
Abstract
To address the role of chronic antigenic stimulation in primary central nervous system lymphoma (PCNSL), we searched for autoantigens and identified sterile α-motif domain containing protein 14 (SAMD14) and neural tissue-specific F-actin binding protein I (neurabin-I) as autoantigenic targets of the B-cell receptors (BCRs) from 8/12 PCNSLs. In the respective cases, SAMD14 and neurabin-I were atypically hyper-N-glycosylated (SAMD14 at ASN339 and neurabin-I at ASN1277), explaining their autoimmunogenicity. SAMD14 and neurabin-I induced BCR pathway activation and proliferation of aggressive lymphoma cell lines transfected with SAMD14- and neurabin-I-reactive BCRs. Moreover, the BCR binding epitope of neurabin-I conjugated to truncated Pseudomonas exotoxin-killed lymphoma cells expressing the respective BCRs. These results support the role of chronic antigenic stimulation by posttranslationally modified central nervous system (CNS) driver autoantigens in the pathogenesis of PCNSL, serve as an explanation for their CNS tropism, and provide the basis for a novel specific treatment approach.
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LRPAP1 is a frequent proliferation-inducing antigen of BCRs of mantle cell lymphomas and can be used for specific therapeutic targeting. Leukemia 2018; 33:148-158. [PMID: 29955130 DOI: 10.1038/s41375-018-0182-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/28/2023]
Abstract
The predominant usage of VH4-34 and V3-21 and reports of stereotyped CDR3s suggest a shared antigenic target of B-cell receptors (BCR) from mantle cell lymphomas (MCL). To identify the target antigens of MCL-BCRs, BCRs from 21 patients and seven MCL cell lines were recombinantly expressed and used for antigen screening. The BCRs from 8/21 patients and 2/7 MCL cell lines reacted specifically with the autoantigen low-density lipoprotein receptor-related protein-associated protein 1 (LRPAP1). High-titered and light chain-restricted anti-LRPAP1 serum antibodies were found in MCL patients, but not in controls. LRPAP1 induced proliferation by BCR pathway activation, while an LRPAP1-ETA' toxin-conjugate specifically killed MCL cells with LRPAP1-specific BCRs. Our results suggest a role of LRPAP1 in lymphomagenesis and maintenance of a considerable proportion of MCL cases by chronic autoantigenic stimulation, likely evolving from a chronic autoreactive B-cell response. Importantly, LRPAP1 can be used for a novel therapeutic approach that targets MCL with LRPAP1-reactive BCRs with high specificity.
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Weniger MA, Tiacci E, Schneider S, Arnolds J, Rüschenbaum S, Duppach J, Seifert M, Döring C, Hansmann ML, Küppers R. Human CD30+ B cells represent a unique subset related to Hodgkin lymphoma cells. J Clin Invest 2018; 128:2996-3007. [PMID: 29889102 DOI: 10.1172/jci95993] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
Very few B cells in germinal centers (GCs) and extrafollicular (EF) regions of lymph nodes express CD30. Their specific features and relationship to CD30-expressing Hodgkin and Reed/Sternberg (HRS) cells of Hodgkin lymphoma are unclear but highly relevant, because numerous patients with lymphoma are currently treated with an anti-CD30 immunotoxin. We performed a comprehensive analysis of human CD30+ B cells. Phenotypic and IgV gene analyses indicated that CD30+ GC B lymphocytes represent typical GC B cells, and that CD30+ EF B cells are mostly post-GC B cells. The transcriptomes of CD30+ GC and EF B cells largely overlapped, sharing a strong MYC signature, but were strikingly different from conventional GC B cells and memory B and plasma cells, respectively. CD30+ GC B cells represent MYC+ centrocytes redifferentiating into centroblasts; CD30+ EF B cells represent active, proliferating memory B cells. HRS cells shared typical transcriptome patterns with CD30+ B cells, suggesting that they originate from these lymphocytes or acquire their characteristic features during lymphomagenesis. By comparing HRS to normal CD30+ B cells we redefined aberrant and disease-specific features of HRS cells. A remarkable downregulation of genes regulating genomic stability and cytokinesis in HRS cells may explain their genomic instability and multinuclearity.
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Affiliation(s)
| | | | | | - Judith Arnolds
- Department of Otorhinolaryngology, University of Duisburg-Essen, Essen, Germany
| | | | | | - Marc Seifert
- Institute of Cell Biology (Cancer Research), and
| | - Claudia Döring
- Dr. Senckenberg Institute of Pathology, University of Frankfurt/Main, Medical School, Frankfurt, Germany
| | - Martin-Leo Hansmann
- Dr. Senckenberg Institute of Pathology, University of Frankfurt/Main, Medical School, Frankfurt, Germany.,Frankfurt Institute for Advanced Studies, Frankfurt, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), and
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Flow cytometric sorting coupled with exon capture sequencing identifies somatic mutations in archival lymphoma tissues. J Transl Med 2017; 97:1364-1374. [PMID: 28783138 PMCID: PMC8843235 DOI: 10.1038/labinvest.2017.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/13/2017] [Accepted: 05/25/2017] [Indexed: 02/05/2023] Open
Abstract
The enormous number of archived formalin-fixed paraffin-embedded (FFPE) tissues available are a valuable resource of material for research. However, the use of such tissues poses many challenges, among which is the difficulty of isolating different cell populations within the tissue. In this study, we used tissue from two types of non-Hodgkin lymphoma as a model to demonstrate a method we have established and optimized to separate FFPE samples into distinct tumor and nonmalignant populations. Using FFPE reactive tonsil sections, various approaches for antigen retrieval and labeling, and the effectiveness of flow cytometric sorting were tested. We found that, among the 11 cell surface or intracellular antigen markers investigated, CD3ɛ, CD79A, LAT, PD-1, and PAX5 could be successfully labeled after antigen retrieval in Tris-EDTA buffer (pH 8.0) at 65 °C for 60 min, and 1.8-2.7 μg DNA per million cells could be extracted after sorting with DNA quality similar to that of tissue without staining or sorting. To test whether we could perform next-generation sequencing using a custom capture platform on sorted cells, we used three lymphoma cases with FFPE tissues which had been stored for 1 to 4 years. We demonstrated that the DNA from sorted cells was adequate for exon capture sequencing. By comparing the sequencing results between neoplastic and normal populations, somatic mutations could be clearly identified in the tumor population with variant frequencies as low as 11.7%.The corresponding normal fraction clearly helps in the analysis of somatic mutations and the exclusion of artifacts. This study provides an approach using flow cytometric sorting to separate different cellular populations in paraffin-embedded tissues and to unambiguously distinguish somatic mutations from germline variants or artifacts. This approach is also useful in enriching the tumor component in samples with heterogeneous components and low tumor content.
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Single-cell genome and transcriptome processing prior to high-throughput sequencing. Methods Mol Biol 2015; 1293:83-114. [PMID: 26040683 DOI: 10.1007/978-1-4939-2519-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Single-cell genome and transcriptome characterizations will probe to be decisive within the stem cells research, especially to describe appropriately the genetic impact of the diverse stem cells populations that are present in each organism. In the present chapter, we describe in detail how to prepare sequencing libraries out of single cells, for whole genome DNA and mRNA sequencing.
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Tucci FA, Broering R, Lutterbeck M, Schlaak JF, Küppers R. Intrahepatic B-cell follicles of chronically hepatitis C virus-infected individuals lack signs of an ectopic germinal center reaction. Eur J Immunol 2014; 44:1842-50. [DOI: 10.1002/eji.201344378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/05/2014] [Accepted: 03/04/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Felicia A. Tucci
- Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
| | - Ruth Broering
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Melanie Lutterbeck
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Joerg F. Schlaak
- Department of Gastroenterology and Hepatology; University of Duisburg-Essen; University Hospital; Essen Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Essen Germany
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