1
|
Galimberti S, Genuardi E, Mazziotta F, Iovino L, Morabito F, Grassi S, Ciabatti E, Guerrini F, Petrini M. The Minimal Residual Disease in Non-Hodgkin's Lymphomas: From the Laboratory to the Clinical Practice. Front Oncol 2019; 9:528. [PMID: 31293969 PMCID: PMC6606710 DOI: 10.3389/fonc.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023] Open
Abstract
Minimal residual disease (MRD) in non-Hodgkin's lymphomas (NHLs) still represents matter of interest and debate: indeed, the new available treatments offer higher rates of complete responses and MRD negativity than in the past, with a positive impact on the long-term survival. Furthermore, the introduction of more sensitive and accurate molecular techniques, such as digital PCR (ddPCR) and the next generation sequencing techniques (NGS), increased the possibility of identifying molecular targets to be followed after therapy (such as rearrangement of immunoglobulins, fusion genes, or mutations). This review focused on how molecular biology can help to detect MRD in different types of NHLs and how MRD can change the clinical practice in 2019. In follicular lymphoma (FL), contamination of the grafts and molecular disease persistence after transplantation represent a negative prognostic factors. The combination of Rituximab or Obinutuzumab with Bendamustine seems to be the most effective way to clear MRD in FL patients receiving chemo-immunotherapy (further studies are in progress), and also 90Yttrium-Ibritumomab-Tiuxetan offers a deep clearance of molecular disease. Finally, molecular MRD can further stratify PET-negative cases, with subjects both PET- and MRD-negative presenting the best outcome. In aggressive lymphomas, MRD has a relevant prognostic power and can represent the platform for immunotherapy (such as CAR-T). In diffuse large B-cell lymphoma (DLBCL), the assessment of MRD in the plasma (where cell-free DNA and exosomes circulate) seems to be more predictive than the bone marrow analysis or peripheral blood mononuclear cells. Finally, NGS technologies could be more useful than the classical "patient allele-specific PCR" because they can identify any possible clone emerging during the treatment or follow-up, even if different from that identified at diagnosis, thus predicting relapse. After all, the present available molecular approaches can move MRD from the bench side to the clinical practice.
Collapse
Affiliation(s)
- Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Turin, Italy
| | - Francesco Mazziotta
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Clinical and Translational Sciences School of Doctorate, University of Pisa, Pisa, Italy
| | - Fortunato Morabito
- Hematology Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel.,Biotechnology Research Unit, Cosenza, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Elena Ciabatti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| |
Collapse
|
2
|
Hüllein J, Słabicki M, Rosolowski M, Jethwa A, Habringer S, Tomska K, Kurilov R, Lu J, Scheinost S, Wagener R, Huang Z, Lukas M, Yavorska O, Helfrich H, Scholtysik R, Bonneau K, Tedesco D, Küppers R, Klapper W, Pott C, Stilgenbauer S, Burkhardt B, Löffler M, Trümper LH, Hummel M, Brors B, Zapatka M, Siebert R, Kreuz M, Keller U, Huber W, Zenz T. MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma. Cancer Res 2019; 79:3125-3138. [DOI: 10.1158/0008-5472.can-18-3438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022]
|
3
|
Seitz V, Schaper S, Dröge A, Lenze D, Hummel M, Hennig S. A new method to prevent carry-over contaminations in two-step PCR NGS library preparations. Nucleic Acids Res 2015; 43:e135. [PMID: 26152304 PMCID: PMC4787772 DOI: 10.1093/nar/gkv694] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/25/2015] [Indexed: 11/12/2022] Open
Abstract
Two-step PCR procedures are an efficient and well established way to generate amplicon libraries for NGS sequencing. However, there is a high risk of cross-contamination by carry-over of amplicons from first to second amplification rounds, potentially leading to severe misinterpretation of results. Here we describe a new method able to prevent and/or to identify carry-over contaminations by introducing the K-box, a series of three synergistically acting short sequence elements. Our K-boxes are composed of (i) K1 sequences for suppression of contaminations, (ii) K2 sequences for detection of possible residual contaminations and (iii) S sequences acting as separators to avoid amplification bias. In order to demonstrate the effectiveness of our method we analyzed two-step PCR NGS libraries derived from a multiplex PCR system for detection of T-cell receptor beta gene rearrangements. We used this system since it is of high clinical relevance and may be affected by very low amounts of contaminations. Spike-in contaminations are effectively blocked by the K-box even at high rates as demonstrated by ultra-deep sequencing of the amplicons. Thus, we recommend implementation of the K-box in two-step PCR-based NGS systems for research and diagnostic applications demanding high sensitivity and accuracy.
Collapse
Affiliation(s)
- Volkhard Seitz
- Institute of Pathology, Charité-University Medicine Berlin, Campus Benjamin Franklin, Berlin, Germany HS Diagnomics GmbH, Berlin, Germany
| | | | | | - Dido Lenze
- Institute of Pathology, Charité-University Medicine Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-University Medicine Berlin, Campus Benjamin Franklin, Berlin, Germany
| | | |
Collapse
|
4
|
Blume CJ, Hotz-Wagenblatt A, Hüllein J, Sellner L, Jethwa A, Stolz T, Slabicki M, Lee K, Sharathchandra A, Benner A, Dietrich S, Oakes CC, Dreger P, te Raa D, Kater AP, Jauch A, Merkel O, Oren M, Hielscher T, Zenz T. p53-dependent non-coding RNA networks in chronic lymphocytic leukemia. Leukemia 2015; 29:2015-23. [DOI: 10.1038/leu.2015.119] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/02/2015] [Accepted: 04/30/2015] [Indexed: 12/23/2022]
|
5
|
Daum S, Chekhun VF, Todor IN, Lukianova NY, Shvets YV, Sellner L, Putzker K, Lewis J, Zenz T, de Graaf IAM, Groothuis GMM, Casini A, Zozulia O, Hampel F, Mokhir A. Improved Synthesis of N-Benzylaminoferrocene-Based Prodrugs and Evaluation of Their Toxicity and Antileukemic Activity. J Med Chem 2015; 58:2015-24. [DOI: 10.1021/jm5019548] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Steffen Daum
- Department
of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Vasiliy F. Chekhun
- R. E. Kavetsky
Institute of Experimental Pathology, Oncology, and Radiobiology of
the National Academy of Sciences of Ukraine, Vasilkivska 45, 03022 Kyiv, Ukraine
| | - Igor N. Todor
- R. E. Kavetsky
Institute of Experimental Pathology, Oncology, and Radiobiology of
the National Academy of Sciences of Ukraine, Vasilkivska 45, 03022 Kyiv, Ukraine
| | - Natalia Yu. Lukianova
- R. E. Kavetsky
Institute of Experimental Pathology, Oncology, and Radiobiology of
the National Academy of Sciences of Ukraine, Vasilkivska 45, 03022 Kyiv, Ukraine
| | - Yulia V. Shvets
- R. E. Kavetsky
Institute of Experimental Pathology, Oncology, and Radiobiology of
the National Academy of Sciences of Ukraine, Vasilkivska 45, 03022 Kyiv, Ukraine
| | - Leopold Sellner
- Department
of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer
Feld 460, 69120 Heidelberg, Germany
- Department
of Medicine V, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Kerstin Putzker
- Chemical Biology Core
Facility, European Molecular Biology Laboratory Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Joe Lewis
- Chemical Biology Core
Facility, European Molecular Biology Laboratory Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thorsten Zenz
- Department
of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer
Feld 460, 69120 Heidelberg, Germany
- Department
of Medicine V, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Inge A. M. de Graaf
- Department
of Pharmacokinetics, Toxicology and Targeting, Groningen Research
Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Geny M. M. Groothuis
- Department
of Pharmacokinetics, Toxicology and Targeting, Groningen Research
Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Angela Casini
- Department
of Pharmacokinetics, Toxicology and Targeting, Groningen Research
Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Oleksii Zozulia
- Department
of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Frank Hampel
- Department
of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| | - Andriy Mokhir
- Department
of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg, Henkestraße 42, 91054 Erlangen, Germany
| |
Collapse
|
6
|
Bohers E, Mareschal S, Bertrand P, Viailly PJ, Dubois S, Maingonnat C, Ruminy P, Tilly H, Jardin F. Activating somatic mutations in diffuse large B-cell lymphomas: lessons from next generation sequencing and key elements in the precision medicine era. Leuk Lymphoma 2014; 56:1213-22. [DOI: 10.3109/10428194.2014.941836] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
7
|
Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C. Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia. Cancer Discov 2014; 4:348-61. [PMID: 24356097 PMCID: PMC4134522 DOI: 10.1158/2159-8290.cd-13-0349] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL.
Collapse
MESH Headings
- Aged
- Chromosomes, Human
- CpG Islands
- DNA Methylation
- Disease Progression
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Leukemic
- Genetic Heterogeneity
- Genome, Human
- Genomic Instability
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
Collapse
Affiliation(s)
- Christopher C. Oakes
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Rainer Claus
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine, University of Freiburg Medical Center, Freiburg
| | - Lei Gu
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Jennifer Hüllein
- Department of Translational Oncology, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Manuela Zucknick
- Division of Biostatistics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - David Brocks
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Olga Bogatyrova
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Christopher R. Schmidt
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
| | - Laura Rassenti
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Thomas J. Kipps
- Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California
| | - Daniel Mertens
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Internal Medicine III, University of Ulm, Ulm
| | - Peter Lichter
- Division of Molecular Genetics, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm
| | | | - John C. Byrd
- Division of Hematology, The Ohio State University, Columbus, Ohio
| | - Thorsten Zenz
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- Department of Medicine V, University of Heidelberg, Heidelberg
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ)
- The German Cancer Consortium, Germany
| |
Collapse
|
8
|
Andrulis M, Lehners N, Capper D, Penzel R, Heining C, Huellein J, Zenz T, von Deimling A, Schirmacher P, Ho AD, Goldschmidt H, Neben K, Raab MS. Targeting the BRAF V600E Mutation in Multiple Myeloma. Cancer Discov 2013; 3:862-9. [DOI: 10.1158/2159-8290.cd-13-0014] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|