1
|
Tiso F, Hebeda KM, Langemeijer SMC, de Graaf AO, Martens JHA, Koorenhof-Scheele TN, Knops R, Kroeze LI, van der Reijden BA, Jansen JH. Erythroid predominance in bone marrow biopsies of AML patients after decitabine treatment correlates with mutation profile and complete remission. Pathobiology 2024:000538953. [PMID: 38643752 DOI: 10.1159/000538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024] Open
Abstract
INTRODUCTION Acute myeloid leukemia (AML) patients may receive hypomethylating agents (HMAs) such as decitabine (DAC) as part of their treatment. Not all patients respond to this therapy, and if they do the clinical response may occur only after 3 to 6 courses of treatment. Hence, early biomarkers predicting response would be very useful. METHODS We retrospectively analyzed a cohort of 22 AML patients who were treated with DAC. Histology of the bone marrow biopsy, pathogenic mutations and methylation status were related to the treatment response. RESULTS In 8/22 (36%) patients, an erythroid dominant response (EDR) pattern, defined as a ratio of myeloid cells/erythroid cells < 1, was observed. In the remaining 14 cases a myeloid predominance was preserved during treatment. No difference in the hypomethylating effect of DAC treatment was observed in patients with and without EDR, as global 5-methylcytosine levels dropped similarly in both groups. Mutational analysis by NGS using a panel of commonly mutated genes in AML, showed that patients with an early EDR harbored on average less mutations, with U2AF1 mutations occurring more frequently, whereas RUNX1 mutations were underrepresented compared to non-EDR cases. Interestingly, the development of an EDR correlated with complete remission (7/8 cases with an EDR versus only 2/14 cases without an EDR). CONCLUSION We conclude that early histological bone marrow examination for the development of an EDR may be helpful to predict response in AML patients during treatment with DAC.
Collapse
|
2
|
Berendsen MR, van Bladel DA, Hesius E, Berganza Irusquieta C, Rijntjes J, van Spriel AB, van der Spek E, Pruijt JF, Kroeze LI, Hebeda KM, Croockewit S, Stevens WB, van Krieken JHJ, Groenen PJ, van den Brand M, Scheijen B. Clonal Relationship and Mutation Analysis in Lymphoplasmacytic Lymphoma/Waldenström Macroglobulinemia Associated With Diffuse Large B-cell Lymphoma. Hemasphere 2023; 7:e976. [PMID: 37928625 PMCID: PMC10621888 DOI: 10.1097/hs9.0000000000000976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/21/2023] [Indexed: 11/07/2023] Open
Abstract
Patients with lymphoplasmacytic lymphoma/Waldenström macroglobulinemia (LPL/WM) occasionally develop diffuse large B-cell lymphoma (DLBCL). This mostly results from LPL/WM transformation, although clonally unrelated DLBCL can also arise. LPL/WM is characterized by activating MYD88L265P (>95%) and CXCR4 mutations (~30%), but the genetic drivers of transformation remain to be identified. Here, in thirteen LPL/WM patients who developed DLBCL, the clonal relationship of LPL and DLBCL together with mutations contributing to transformation were investigated. In 2 LPL/WM patients (15%), high-throughput sequencing of immunoglobulin gene rearrangements showed evidence of >1 clonal B-cell population in LPL tissue biopsies. In the majority of LPL/WM patients, DLBCL presentations were clonally related to the dominant clone in LPL, providing evidence of transformation. However, in 3 patients (23%), DLBCL was clonally unrelated to the major malignant B-cell clone in LPL, of which 2 patients developed de novo DLBCL. In this study cohort, LPL displayed MYD88L265P mutation in 8 out of eleven patients analyzed (73%), while CXCR4 mutations were observed in 6 cases (55%). MYD88WT LPL biopsies present in 3 patients (27%) were characterized by CD79B and TNFAIP3 mutations. Upon transformation, DLBCL acquired novel mutations targeting BTG1, BTG2, CD79B, CARD11, TP53, and PIM1. Together, we demonstrate variable clonal B-cell dynamics in LPL/WM patients developing DLBCL, and the occurrence of clonally unrelated DLBCL in about one-quarter of LPL/WM patients. Moreover, we identified commonly mutated genes upon DLBCL transformation, which together with preserved mutations already present in LPL characterize the mutational landscape of DLBCL occurrences in LPL/WM patients.
Collapse
Affiliation(s)
| | - Diede A.G. van Bladel
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva Hesius
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemiek B. van Spriel
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Johannes F.M. Pruijt
- Department of Hematology, Jeroen Bosch Hospital, ‘s-Hertogenbosch, The Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Konnie M. Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sandra Croockewit
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wendy B.C. Stevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
3
|
van Bladel DAG, Stevens WBC, Kroeze LI, de Groen RAL, de Groot FA, van der Last-Kempkes JLM, Berendsen MR, Rijntjes J, Luijks JACW, Bonzheim I, van der Spek E, Plattel WJ, Pruijt JFM, de Jonge-Peeters SDPWM, Velders GA, Lensen C, van Bladel ER, Federmann B, Hoevenaars BM, Pastorczak A, van der Werff ten Bosch J, Vermaat JSP, Nooijen PTGA, Hebeda KM, Fend F, Diepstra A, van Krieken JHJM, Groenen PJTA, van den Brand M, Scheijen B. A significant proportion of classic Hodgkin lymphoma recurrences represents clonally unrelated second primary lymphoma. Blood Adv 2023; 7:5911-5924. [PMID: 37552109 PMCID: PMC10558751 DOI: 10.1182/bloodadvances.2023010412] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/26/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023] Open
Abstract
Despite high cure rates in classic Hodgkin lymphoma (cHL), relapses are observed. Whether relapsed cHL represents second primary lymphoma or an underlying T-cell lymphoma (TCL) mimicking cHL is underinvestigated. To analyze the nature of cHL recurrences, in-depth clonality testing of immunoglobulin (Ig) and T-cell receptor (TCR) rearrangements was performed in paired cHL diagnoses and recurrences among 60 patients, supported by targeted mutation analysis of lymphoma-associated genes. Clonal Ig rearrangements were detected by next-generation sequencing (NGS) in 69 of 120 (58%) diagnoses and recurrence samples. The clonal relationship could be established in 34 cases, identifying clonally related relapsed cHL in 24 of 34 patients (71%). Clonally unrelated cHL was observed in 10 of 34 patients (29%) as determined by IG-NGS clonality assessment and confirmed by the identification of predominantly mutually exclusive gene mutations in the paired cHL samples. In recurrences of >2 years, ∼60% of patients with cHL for whom the clonal relationship could be established showed a second primary cHL. Clonal TCR gene rearrangements were identified in 14 of 125 samples (11%), and TCL-associated gene mutations were detected in 7 of 14 samples. Retrospective pathology review with integration of the molecular findings were consistent with an underlying TCL in 5 patients aged >50 years. This study shows that cHL recurrences, especially after 2 years, sometimes represent a new primary cHL or TCL mimicking cHL, as uncovered by NGS-based Ig/TCR clonality testing and gene mutation analysis. Given the significant therapeutic consequences, molecular testing of a presumed relapse in cHL is crucial for subsequent appropriate treatment strategies adapted to the specific lymphoma presentation.
Collapse
Affiliation(s)
| | - Wendy B. C. Stevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ruben A. L. de Groen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fleur A. de Groot
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Irina Bonzheim
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | | | - Wouter J. Plattel
- Department of Hematology, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | - Gerjo A. Velders
- Department of Internal Medicine, Gelderse Vallei Hospital, Ede, The Netherlands
| | - Chantal Lensen
- Department of Hematology, Bernhoven Hospital, Uden, The Netherlands
| | - Esther R. van Bladel
- Department of Internal Medicine, Slingeland Hospital, Doetinchem, The Netherlands
| | - Birgit Federmann
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
- Department of Translational Immunology, German Cancer Research Center, Medical Hospital Tübingen, Tübingen, Germany
| | | | - Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Jutte van der Werff ten Bosch
- Department of Pediatric Hematology and Oncology, University Hospital Brussels, Brussels, Belgium
- Department of Pediatrics, Paola Children’s Hospital, Antwerp, Belgium
| | - Joost S. P. Vermaat
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Konnie M. Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Falko Fend
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
4
|
van den Brand M, Möbs M, Otto F, Kroeze LI, Gonzalez de Castro D, Stamatopoulos K, Davi F, Bravetti C, Kolijn PM, Vlachonikola E, Stewart JP, Pott C, Hummel M, Darzentas N, Langerak AW, Fend F, Groenen PJTA. EuroClonality-NGS Recommendations for Evaluation of B-Cell Clonality Analysis by Next-Generation Sequencing: A Structured Approach with the DEPART Algorithm. J Mol Diagn 2023; 25:729-739. [PMID: 37467928 DOI: 10.1016/j.jmoldx.2023.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality-NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon-based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.
Collapse
Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Franziska Otto
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Gonzalez de Castro
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Frederic Davi
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Clotilde Bravetti
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - P Martijn Kolijn
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - J Peter Stewart
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W Langerak
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
5
|
Slootbeek PHJ, Kloots ISH, van Oort IM, Kroeze LI, Schalken JA, Bloemendal HJ, Mehra N. Cross-Resistance between Platinum-Based Chemotherapy and PARP Inhibitors in Castration-Resistant Prostate Cancer. Cancers (Basel) 2023; 15:2814. [PMID: 37345149 DOI: 10.3390/cancers15102814] [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] [Received: 04/07/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Patients with metastatic castration-resistant prostate cancer (mCRPC) harbouring homologous recombination repair-related gene aberrations (HRRm) can derive meaningful benefits from both platinum-based chemotherapy (PlCh) and PARP inhibitors (PARPi). Cross-resistance between these agents is well-recognised in other tumour types but data on prostate cancer is lacking. In this retrospective pre-planned study, we assessed 28 HRRm mCRPC patients who received PlCh and PARPi. Progression-free survival (PFS) on initial therapy was longer than on subsequent therapy (median 5.3 vs. 3.4 months, p = 0.016). The median PFS of PlCh was influenced by the order of agents, with 3.6 months shorter PFS after PARPi than when administered first. The median PFS of PARPi was less influenced, with 0.9 months shorter PFS after PlCh than before. In the PARPi-first subgroup, six out of 16 evaluable patients (37.5%) had a >50% PSA decline to PlCh, and two of eight (25.0%) had a radiographic response to PlCh. In the PlCh-first subgroup, 6/10 (60.0%) had a >50% PSA decline, and 5/9 (55.6%) had a radiographic response to PARPi. These data show >40% of the cohort is sensitive to a subsequent HRR-targeting agent. PlCh appears to induce less cross-resistance than PARPi. Additional data on resistance mechanisms will be crucial in defining an optimal treatment sequence in HRRm mCRPC patients.
Collapse
Affiliation(s)
- Peter H J Slootbeek
- Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Iris S H Kloots
- Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Inge M van Oort
- Department of Urology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jack A Schalken
- Department of Urology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Haiko J Bloemendal
- Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| |
Collapse
|
6
|
Mehra N, Kloots I, Vlaming M, Aluwini S, Dewulf E, Oprea-Lager DE, van der Poel H, Stoevelaar H, Yakar D, Bangma CH, Bekers E, van den Bergh R, Bergman AM, van den Berkmortel F, Boudewijns S, Dinjens WN, Fütterer J, van der Hulle T, Jenster G, Kroeze LI, van Kruchten M, van Leenders G, van Leeuwen PJ, de Leng WW, van Moorselaar RJA, Noordzij W, Oldenburg RA, van Oort IM, Oving I, Schalken JA, Schoots IG, Schuuring E, Smeenk RJ, Vanneste BG, Vegt E, Vis AN, de Vries K, Willemse PPM, Wondergem M, Ausems M. Genetic Aspects and Molecular Testing in Prostate Cancer: A Report from a Dutch Multidisciplinary Consensus Meeting. EUR UROL SUPPL 2023; 49:23-31. [PMID: 36874601 PMCID: PMC9975012 DOI: 10.1016/j.euros.2022.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Background Germline and tumour genetic testing in prostate cancer (PCa) is becoming more broadly accepted, but testing indications and clinical consequences for carriers in each disease stage are not yet well defined. Objective To determine the consensus of a Dutch multidisciplinary expert panel on the indication and application of germline and tumour genetic testing in PCa. Design setting and participants The panel consisted of 39 specialists involved in PCa management. We used a modified Delphi method consisting of two voting rounds and a virtual consensus meeting. Outcome measurements and statistical analysis Consensus was reached if ≥75% of the panellists chose the same option. Appropriateness was assessed by the RAND/UCLA appropriateness method. Results and limitations Of the multiple-choice questions, 44% reached consensus. For men without PCa having a relevant family history (familial PCa/BRCA-related hereditary cancer), follow-up by prostate-specific antigen was considered appropriate. For patients with low-risk localised PCa and a family history of PCa, active surveillance was considered appropriate, except in case of the patient being a BRCA2 germline pathogenic variant carrier. Germline and tumour genetic testing should not be done for nonmetastatic hormone-sensitive PCa in the absence of a relevant family history of cancer. Tumour genetic testing was deemed most appropriate for the identification of actionable variants, with uncertainty for germline testing. For tumour genetic testing in metastatic castration-resistant PCa, consensus was not reached for the timing and panel composition. The principal limitations are as follows: (1) a number of topics discussed lack scientific evidence, and therefore the recommendations are partly opinion based, and (2) there was a small number of experts per discipline. Conclusions The outcomes of this Dutch consensus meeting may provide further guidance on genetic counselling and molecular testing related to PCa. Patient summary A group of Dutch specialists discussed the use of germline and tumour genetic testing in prostate cancer (PCa) patients, indication of these tests (which patients and when), and impact of these tests on the management and treatment of PCa.
Collapse
Affiliation(s)
- Niven Mehra
- Department of Medical Oncology, Radboud UMC, Nijmegen, The Netherlands
- Corresponding author. Department of Medical Oncology, Radboud University Medical Centre, Postbus 9101, 6500 HB Nijmegen, The Netherlands. Tel. +31 243610354; Fax: +31 243615025.
| | - Iris Kloots
- Department of Medical Oncology, Radboud UMC, Nijmegen, The Netherlands
| | - Michiel Vlaming
- Division Laboratories, Pharmacy and biomedical Genetics, Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Shafak Aluwini
- Department of Radiation Oncology, UMCG, Groningen, The Netherlands
| | - Els Dewulf
- Centre for Decision Analysis & Support, Ismar Healthcare NV, Lier, Belgium
| | - Daniela E. Oprea-Lager
- Department of Radiology & Nuclear Medicine, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Henk van der Poel
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
- Department of Urology, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Herman Stoevelaar
- Centre for Decision Analysis & Support, Ismar Healthcare NV, Lier, Belgium
| | - Derya Yakar
- Department of Radiology, UMCG, Groningen, The Netherlands
- Department of Radiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Chris H. Bangma
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | - Elise Bekers
- Department of Pathology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | - Andries M. Bergman
- Department of Medical Oncology and Oncogenomics, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | - Steve Boudewijns
- Department of Medical Oncology, Bravis Hospital, Roosendaal, The Netherlands
| | | | - Jurgen Fütterer
- Department of Medical Imaging, Radboud UMC, Nijmegen, The Netherlands
| | - Tom van der Hulle
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Michel van Kruchten
- Department of Medical Oncology, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Pim J. van Leeuwen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | | | | | - Walter Noordzij
- Department of Nuclear Medicine & Molecular Imaging, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | - Irma Oving
- Department of Internal Medicine, Ziekenhuis Groep Twente, Almelo, The Netherlands
| | | | - Ivo G. Schoots
- Department of Radiology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert J. Smeenk
- Department of Radiation Oncology, Radboud UMC, Nijmegen, The Netherlands
| | - Ben G.L. Vanneste
- Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
- Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Erik Vegt
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - André N. Vis
- Department of Urology, Amsterdam University Medical Centers, VU University, Amsterdam, The Netherlands
| | - Kim de Vries
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Maurits Wondergem
- Department of Nuclear Medicine, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Margreet Ausems
- Division Laboratories, Pharmacy and biomedical Genetics, Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| |
Collapse
|
7
|
Groenen PJTA, van den Brand M, Kroeze LI, Amir AL, Hebeda KM. Read the clonotype: Next-generation sequencing-based lymphocyte clonality analysis and perspectives for application in pathology. Front Oncol 2023; 13:1107171. [PMID: 36845702 PMCID: PMC9945094 DOI: 10.3389/fonc.2023.1107171] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Clonality assessment using the unique rearrangements of immunoglobulin (IG) and T-cell receptor (TR) genes in lymphocytes is a widely applied supplementary test for the diagnosis of B-cell and T-cell lymphoma. To enable a more sensitive detection and a more precise comparison of clones compared with conventional clonality analysis based on fragment analysis, the EuroClonality NGS Working Group developed and validated a next-generation sequencing (NGS)-based clonality assay for detection of the IG heavy and kappa light chain and TR gene rearrangements for formalin-fixed and paraffin-embedded tissues. We outline the features and advantages of NGS-based clonality detection and discuss potential applications for NGS-based clonality testing in pathology, including site specific lymphoproliferations, immunodeficiency and autoimmune disease and primary and relapsed lymphomas. Also, we briefly discuss the role of T-cell repertoire of reactive lymphocytic infiltrations in solid tumors and B-lymphoma.
Collapse
Affiliation(s)
- Patricia J. T. A. Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Patricia J. T. A. Groenen,
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Pathology-DNA, Location Rijnstate Hospital, Arnhem, Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Avital L. Amir
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Konnie M. Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
8
|
Berendsen MR, Bladel DAGV, Hesius E, de Groot FA, Kroeze LI, Rijntjes J, Luijks JACW, Hoevenaars B, Halilovic A, Nooijen P, Bladel EV, Jonge-Peeters SD, Lensen C, Pruijt H, van der Spek E, Vermaat JSP, Hess C, Hebeda KM, Stevens WBC, van Krieken JHJM, van den Brand M, Groenen PJTA, Scheijen B. Detection of Second Primary Lymphoma in Late Diffuse Large B-cell Lymphoma Recurrences. Mod Pathol 2023; 36:100119. [PMID: 36805792 DOI: 10.1016/j.modpat.2023.100119] [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] [Received: 10/21/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 02/04/2023]
Abstract
Approximately one-third of patients with diffuse large B-cell lymphoma (DLBCL) relapse and often require salvage chemotherapy followed by autologous stem cell transplantation. In most cases, the clonal relationship between the first diagnosis and subsequent relapse is not assessed, thereby potentially missing the identification of second primary lymphoma. In this study, the clonal relationship of 59 paired DLBCL diagnoses and recurrences was established by next-generation sequencing-based detection of immunoglobulin gene rearrangements. Among 50 patients with interpretable results, 43 patients (86%) developed clonally related relapsed disease. This was observed in 100% of early recurrences (<2 years), 80% of the recurrences with an interval between 2 and 5 years, and 73% of late recurrences (≥5 years). On the other hand, 7 (14%) out of 50 patients displayed different dominant clonotypes in primary DLBCL and clinical recurrences, confirming the occurrence of second primary DLBCL; 37% of DLBCL recurrences that occurred ≥4 years after diagnosis were shown to be second primary lymphomas. The clonally unrelated cases were Epstein-Barr virus positive in 43% of the cases, whereas this was only 5% in the relapsed DLBCL cases. In conclusion, next-generation sequencing-based clonality testing in late recurrences should be considered in routine diagnostics to distinguish relapse from second primary lymphoma, as this latter group of patients with DLBCL may benefit from less-intensive treatment strategies.
Collapse
Affiliation(s)
- Madeleine R Berendsen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Diede A G van Bladel
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Eva Hesius
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fleur A de Groot
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen A C W Luijks
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigiet Hoevenaars
- Department of Pathology, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Altuna Halilovic
- Department of Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Peet Nooijen
- Department of Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | - Esther van Bladel
- Department of Hematology, Slingeland Hospital, Doetinchem, The Netherlands
| | | | - Chantal Lensen
- Department of Hematology, Bernhoven Hospital, Uden, The Netherlands
| | - Hans Pruijt
- Department of Hematology Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | | | - Joost S P Vermaat
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Corine Hess
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Konnie M Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wendy B C Stevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J Han J M van Krieken
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| |
Collapse
|
9
|
de Bitter TJJ, de Reuver PR, de Savornin Lohman EAJ, Kroeze LI, Vink-Börger ME, van Vliet S, Simmer F, von Rhein D, Jansen EAM, Verheij J, van Herpen CML, Nagtegaal ID, Ligtenberg MJL, van der Post RS. Comprehensive clinicopathological and genomic profiling of gallbladder cancer reveals actionable targets in half of patients. NPJ Precis Oncol 2022; 6:83. [DOI: 10.1038/s41698-022-00327-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
AbstractGallbladder cancer (GBC) is a rare, highly aggressive malignancy with a 5-year survival rate of 5–10% in advanced cases, highlighting the need for more effective therapies. The aim of this study was to identify potentially actionable therapeutic targets for GBC. Specimens and clinicopathological data of 642 GBC patients, diagnosed between 2000 and 2019 were collected using the Dutch Pathology Registry (PALGA) and the Netherlands Cancer Registry. All cases were histologically reviewed and a subset was subjected to a comprehensive next generation sequencing panel. We assessed mutations and gene amplifications in a panel of 54 actionable genes, tumor-mutational burden (TMB), and microsatellite instability (MSI). Additionally, the entire cohort was screened for HER2, PD-L1, pan-TRK, and p53 expression with immunohistochemistry. Histopathological subtypes comprised biliary-type adenocarcinoma (AC, 69.6%), intestinal-type AC (20.1%) and other subtypes (10.3%). The median total TMB was 5.5 mutations/Mb (range: 0–161.1) and 17.7% of evaluable cases had a TMB of >10 mutations/Mb. MSI was observed in two cases. Apart from mutations in TP53 (64%), tumors were molecularly highly heterogeneous. Half of the tumors (50%) carried at least one molecular alteration that is targetable in other tumor types, including alterations in CDKN2A (6.0% biallelically inactivated), ERBB2 (9.3%) and PIK3CA (10%). Immunohistochemistry results correlated well with NGS results for HER2 and p53: Pearson r = 0.82 and 0.83, respectively. As half of GBC patients carry at least one potentially actionable molecular alteration, molecular testing may open the way to explore targeted therapy options for GBC patients.
Collapse
|
10
|
Kroeze LI, Scheijen B, Hebeda KM, Rijntjes J, Luijks JACW, Evers D, Hobo W, Groenen PJTA, van den Brand M. PAX5 P80R-mutated B-cell acute lymphoblastic leukemia with transformation to histiocytic sarcoma: clonal evolution assessment using NGS-based immunoglobulin clonality and mutation analysis. Virchows Arch 2022:10.1007/s00428-022-03428-y. [PMID: 36241730 DOI: 10.1007/s00428-022-03428-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
Clonality assessment by the detection of immunoglobulin (IG) gene rearrangements is an important method to determine whether two concurrent or subsequent lymphoid malignancies in one patient are clonally related. Here, we report the detailed clonality analysis in a patient with a diagnosis of B-cell acute lymphoblastic leukemia (B-ALL) followed by a histiocytic sarcoma (HS), in which we were able to study clonal evolution by applying next generation sequencing (NGS) to identify IG rearrangements and gene mutations. Using the sequence information of the NGS-based IG clonality analysis, multiple related subclones could be distinguished in the PAX5 P80R-mutated B-ALL. Notably, only one of these subclones evolved into HS after acquiring a RAF1 mutation. This case demonstrates that NGS-based IG clonality assessment and mutation analysis provide clear added value for clonal comparison and thereby improves clinicobiological understanding.
Collapse
Affiliation(s)
- Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.
| | - B Scheijen
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - K M Hebeda
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands
| | - J Rijntjes
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands
| | - J A C W Luijks
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands
| | - D Evers
- Department of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - W Hobo
- Department of Laboratory Medicine - Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - P J T A Groenen
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands
| | - M van den Brand
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, the Netherlands
| |
Collapse
|
11
|
van Wilpe S, Simnica D, Slootbeek P, van Ee T, Pamidimarri Naga S, Gorris MAJ, van der Woude LL, Sultan S, Koornstra RHT, van Oort IM, Gerritsen WR, Kroeze LI, Simons M, van Leenders GJLH, Binder M, de Vries IJM, Mehra N. Homologous recombination repair deficient prostate cancer represents an immunologically distinct subtype. Oncoimmunology 2022; 11:2094133. [PMID: 35800157 PMCID: PMC9255222 DOI: 10.1080/2162402x.2022.2094133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/24/2022] Open
Abstract
Homologous recombination repair deficiency (HRD) is observed in 10% of patients with castrate-resistant prostate cancer (PCa). Preliminary data suggest that HRD-PCa might be more responsive to immune checkpoint inhibitors (ICIs). In this study, we compare the tumor immune landscape and peripheral T cell receptor (TCR) repertoire of patients with and without HRD-PCa to gain further insight into the immunogenicity of HRD-PCa. Immunohistochemistry was performed on tumor tissue of 81 patients, including 15 patients with HRD-PCa. Peripheral TCR sequencing was performed in a partially overlapping cohort of 48 patients, including 16 patients with HRD-PCa. HRD patients more frequently had intratumoral CD3+, CD3+CD8−FoxP3− or Foxp3+ TILs above median compared to patients without DNA damage repair alterations (DDRwt; CD3+ and Foxp3+: 77% vs 35%, p = .013; CD3+CD8−FoxP3−: 80% vs 44%, p = .031). No significant difference in CD8+ TILs or PD-L1 expression was observed. In peripheral blood, HRD patients displayed a more diverse TCR repertoire compared to DDRwt patients (p = .014). Additionally, HRD patients shared TCR clusters with low generation probability, suggesting patient-overlapping T cell responses. A pooled analysis of clinical data from 227 patients with molecularly characterized PCa suggested increased efficacy of ICIs in HRD-PCa. In conclusion, patients with HRD-PCa display increased TIL density and an altered peripheral TCR repertoire. Further research into the efficacy of ICIs and the presence of shared neoantigens in HRD-PCa is warranted.
Collapse
Affiliation(s)
- Sandra van Wilpe
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Donjetë Simnica
- Department of Internal Medicine IV, Oncology/Haematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Peter Slootbeek
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas van Ee
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Mark A. J. Gorris
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Lieke L. van der Woude
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Shabaz Sultan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Inge M. van Oort
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Winald R. Gerritsen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Michiel Simons
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Haematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - I. Jolanda M. de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
12
|
van Bladel DAG, Stevens WBC, van den Brand M, Kroeze LI, Groenen PJTA, van Krieken JHJM, Hebeda KM, Scheijen B. Novel Approaches in Molecular Characterization of Classical Hodgkin Lymphoma. Cancers (Basel) 2022; 14:cancers14133222. [PMID: 35805000 PMCID: PMC9264882 DOI: 10.3390/cancers14133222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/29/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The unique tumor composition of classical Hodgkin lymphoma (cHL), with only a small fraction of malignant Hodgkin and Reed–Sternberg cells within the tumor tissue, has created many challenges to characterize the genetic alterations that drive this lymphoid malignancy. Major advances in sequencing technologies and detailed analysis of circulating tumor DNA in blood samples of patients have provided important contributions to enhance our understanding of the pathogenesis of cHL. In this review, we provide an overview of the recent advances in genotyping the clonal and mutational landscape of cHL. In addition, we discuss different next-generation sequencing applications to characterize tumor tissue and cell-free DNA, which are now available to improve the diagnosis of cHL, and to monitor therapeutic response or disease progression during treatment and follow up of cHL patients. Abstract Classical Hodgkin lymphoma (cHL) represents a B-cell lymphoproliferative disease characterized by clonal immunoglobulin gene rearrangements and recurrent genomic aberrations in the Hodgkin Reed–Sternberg cells in a reactive inflammatory background. Several methods are available for the molecular analysis of cHL on both tissue and cell-free DNA isolated from blood, which can provide detailed information regarding the clonal composition and genetic alterations that drive lymphoma pathogenesis. Clonality testing involving the detection of immunoglobulin and T cell receptor gene rearrangements, together with mutation analysis, represent valuable tools for cHL diagnostics, especially for patients with an atypical histological or clinical presentation reminiscent of a reactive lesion or another lymphoma subtype. In addition, clonality assessment may establish the clonal relationship of composite or subsequent lymphoma presentations within one patient. During the last few decades, more insight has been obtained on the molecular mechanisms that drive cHL development, including recurrently affected signaling pathways (e.g., NF-κB and JAK/STAT) and immune evasion. We provide an overview of the different approaches to characterize the molecular composition of cHL, and the implementation of these next-generation sequencing-based techniques in research and diagnostic settings.
Collapse
Affiliation(s)
- Diede A. G. van Bladel
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
- Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Wendy B. C. Stevens
- Radboud University Medical Center, Department of Hematology, 6525 GA Nijmegen, The Netherlands;
| | - Michiel van den Brand
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
- Pathology-DNA, Rijnstate Hospital, 6815 AD Arnhem, The Netherlands
| | - Leonie I. Kroeze
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
| | - Patricia J. T. A. Groenen
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
| | - J. Han J. M. van Krieken
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
| | - Konnie M. Hebeda
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
| | - Blanca Scheijen
- Radboud University Medical Center, Department of Pathology, 6525 GA Nijmegen, The Netherlands; (D.A.G.v.B.); (M.v.d.B.); (L.I.K.); (P.J.T.A.G.); (J.H.J.M.v.K.); (K.M.H.)
- Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Correspondence:
| |
Collapse
|
13
|
van Ravensteijn SG, Versleijen-Jonkers YM, Hillebrandt-Roeffen MH, Nederkoorn M, Gorris MA, Verrijp K, Kroeze LI, de Bitter TJ, de Voer RM, Flucke UE, Desar IM. Abstract LB140: The genomic landscape of primary and secondary angiosarcomas, a rare heterogenous group of soft tissue sarcomas. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Angiosarcomas (AS) are a rare heterogenous group of soft tissue sarcomas (STS) that form in the lining of blood vessels or lymphatic vessels. They comprise of primary (de novo) AS and secondary AS. The etiology of primary AS is unknown. Secondary AS arise due to DNA damaging factors like prior radiotherapy (RT), ultraviolet (UV) light exposure or chronic lymphedema (Stewart Treves syndrome). Treatment options are limited and their prognosis is poor. Development of new treatment strategies is difficult due to the rarity of these subgroups of STS. Genomic profiling of primary and secondary AS may provide a rationale for targeted treatment strategies.
Method: Tumor samples were retrospectively collected from patients diagnosed with AS in the Netherlands. Patients were categorized as primary/secondary AS. Genomic profiles were analyzed using “TruSight Oncology 500”, a Next Generation Sequencing panel that analyzes variants in 523 cancer relevant genes.
Results: Tumor DNA from 51 treatment naive AS patients was analyzed. The cohort comprised of 26 patients with a primary AS, divided in 5 subgroups: Heart (n=5, 10%), primary breast (n=5, 10%), skin not UV associated (n=4, 8%), soft tissue (n=5, 10%) and visceral (n=7, 14%) AS. The other 25 patients had a secondary AS, subdivided in RT-associated (n=13, 25%), Stewart Treves (n=5, 10%) and UV-associated (n=7, 14%) AS. Mean Tumor Mutational Burden (TMB) was 7.1 mutations per Mb for all patients (4.2 mut/Mb in primary AS vs 10.1 in secondary AS, p = 0.91). High TMB (≥10 mut/Mb) was found in 6 patients (12%) divided over 3 subgroups: UV associated AS (n=3/7 (43%)), visceral AS (n=2/7 (28%)) and skin not UV associated AS (n=1/4 (25%)). No patients were microsatellite instable. A pathogenic mutation, amplification or deletion was identified in 82% of all patients (n=42, 70% of primary AS vs 100% of secondary AS (p=<0.01)). In 36 patients (71%) at least one (likely) pathogenic mutation was detected (54% primary vs 88% secondary AS, (p=0,013)). In 20 patients (39%) a mutation in the DNA damage response (DDR) pathway was detected (12% primary vs 68% secondary AS (p=<0.01)). The most frequently found mutations were TP53 (10%), BRAF (6%), ERCC4 (6%), PTPRD (6%), WETD2 (6%), SETD2 (6%) and PIK3CA (4%). Amplifications were found in 49% (n=25) of all patients (15% primary vs 84% secondary AS, (p=<0,01)). MYC amplifications were detected in 41% of all patients (15% of primary vs 68% of secondary AS), including 100% of Stewart Treves AS, 92% of RT associated AS and 75% of skin not UV associated AS. FLT4 (20%) and CRKL (12%) amplifications occurred only in secondary AS. FLT4 was seen in 31% of RT-associated AS.
Conclusion: We showed a clear distinction in genomic profiles of AS subgroups with specific pathogenic alterations. Especially secondary AS may benefit from treatment with ICI based on frequent MYC amplifications, DDR mutations, and high TMB. These data show clear evidence for the development of future treatment strategies with targeted therapy and ICI for this rare heterogeneous group of STS.
Citation Format: Stefan G. van Ravensteijn, Yvonne M. Versleijen-Jonkers, Melissa H. Hillebrandt-Roeffen, Maikel Nederkoorn, Mark A. Gorris, Kiek Verrijp, Leonie I. Kroeze, Tessa J. de Bitter, Richarda M. de Voer, Uta E. Flucke, Ingrid M. Desar. The genomic landscape of primary and secondary angiosarcomas, a rare heterogenous group of soft tissue sarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB140.
Collapse
|
14
|
van Ravensteijn SG, Versleijen-Jonkers YMH, Hillebrandt-Roeffen MHS, Weidema ME, Nederkoorn MJL, Gorris MAJ, Verrijp K, Kroeze LI, de Bitter T, de Voer RM, Flucke UE, Desar I. Which angiosarcoma subtypes may benefit from immunotherapy? J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.11572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11572 Background: Angiosarcomas (AS) are aggressive mesenchymal tumors arising from cells with endothelial properties. They include de novo primary AS (pAS), and secondary AS (sAS) due to prior radiotherapy, UV exposure or chronic lymphedema. Treatment options are limited and their prognosis is poor. Development of new treatment strategies is difficult due to the heterogeneity and rarity of AS. We hypothesize that immunological and genomic profiles are significantly different between pAS and sAS and may result in different immune checkpoint inhibition (ICI) based treatment strategies. Methods: Tumor samples from AS patients were retrospectively collected. Patients were categorized as pAS or sAS. Lymphocytes were analyzed using multiplex immunohistochemistry on tissue microarrays. Genomic profiling was performed in a selected subgroup with “TruSight Oncology 500”, a Next Generation Sequencing panel containing 523 cancer related genes. Results: Immunological data were analyzed from 257 AS patients. The cohort comprised 80 pAS patients and 177 sAS patients. The median density of CD3+ T cells was 250 cells/mm2 in pAS vs 452 cells/mm2 in sAS (p< 0.001). Median CD4+ T helper cell density was 128 cells/mm2 in pAS vs 246 cells/mm2 in secondary AS (p< 0.001). The median density of CD8+ cytotoxic T cells was 85 cells/mm2 in pAS vs 111 cells/mm2 in sAS ( p= 0.057). Density of FoxP3+ T regulatory cells was higher in sAS (median 42 cells/mm2) compared to pAS (median 23 cells/mm2) (p< 0.001). The median count of CD20+ B cells in pAS was 24 cells/mm2 compared to 32 cells/mm2 in sAS ( p= 0.533). Genomic analysis was performed on tumor DNA from 51 patients (25 pAS and 26 sAS). Median tumor mutational burden (TMB) was 3.2 (range 0.8-11.9) mutations per megabase (mut/Mb) in pAS vs 3.9 (range 0.0-99.6) in sAS ( p= 0.485). No microsatellite instability was detected. A pathogenic mutation, gene amplification or gene loss was identified in 82% of all patients (n = 42, 70% of pAS vs 100% of sAS ( p< 0.01)). In 36 patients (71%) at least one (likely) pathogenic mutation was detected (54% pAS vs 88% sAS, ( p= 0.013)). In 20 patients (39%) mutations in the DNA damage response (DDR) pathway were detected (12% pAS vs 68% sAS ( p< 0.01)). The most frequently found mutated genes were TP53 (10%), BRAF (6%), ERCC4 (6%), PTPRD (6%), WETD2 (6%) and SETD2 (6%). Amplifications were found in 49% (n = 25) of all patients (15% pAS vs 84% sAS, ( p< 0,01)). MYC amplifications were most common and were detected in 15% of pAS and 68% of sAS. Immune profiles of the 51 genomically characterized patients are currently under further investigation. Conclusions: We showed a clear distinction in immunological and genomic profiles between pAS and sAS. The potential benefit of ICI seems to be most promising in sAS with a T cell inflamed tumor microenvironment, frequent MYC amplifications, DDR mutations, and high mutational load, while in pAS boosting strategies to enhance susceptibility to ICI might be interesting for further investigation.
Collapse
Affiliation(s)
| | | | | | | | | | - Mark AJ Gorris
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Kiek Verrijp
- Department of Tumour Immunology, Radboudumc, Nijmegen, Netherlands
| | | | | | | | - Uta E Flucke
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ingrid Desar
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
15
|
Gorris MAJ, van der Woude LL, Kroeze LI, Bol K, Verrijp K, Amir AL, Meek J, Textor J, Figdor CG, de Vries IJM. Paired primary and metastatic lesions of patients with ipilimumab-treated melanoma: high variation in lymphocyte infiltration and HLA-ABC expression whereas tumor mutational load is similar and correlates with clinical outcome. J Immunother Cancer 2022; 10:e004329. [PMID: 35550553 PMCID: PMC9109111 DOI: 10.1136/jitc-2021-004329] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) can lead to long-term responses in patients with metastatic melanoma. Still many patients with melanoma are intrinsically resistant or acquire secondary resistance. Previous studies have used primary or metastatic tumor tissue for biomarker assessment. Especially in melanoma, metastatic lesions are often present at different anatomical sites such as skin, lymph nodes, and visceral organs. The anatomical site may directly affect the tumor microenvironment (TME). To evaluate the impact of tumor evolution on the TME and on ICI treatment outcome, we directly compared paired primary and metastatic melanoma lesions for tumor mutational burden (TMB), HLA-ABC status, and tumor infiltrating lymphocytes (TILs) of patients that received ipilimumab. METHODS TMB was analyzed by sequencing primary and metastatic melanoma lesions using the TruSight Oncology 500 assay. Tumor tissues were subjected to multiplex immunohistochemistry to assess HLA-ABC status and for the detection of TIL subsets (B cells, cytotoxic T cells, helper T cells, and regulatory T cells), by using a machine-learning algorithm. RESULTS While we observed a very good agreement between TMB of matched primary and metastatic melanoma lesions (intraclass coefficient=0.921), such association was absent for HLA-ABC status, TIL density, and subsets thereof. Interestingly, analyses of different metastatic melanoma lesions within a single patient revealed that TIL density and composition agreed remarkably well, rejecting the hypothesis that the TME of different anatomical sites affects TIL infiltration. Similarly, the HLA-ABC status between different metastatic lesions within patients was also comparable. Furthermore, high TMB, of either primary or metastatic melanoma tissue, directly correlated with response to ipilimumab, whereas lymphocyte density or composition did not. Loss of HLA-ABC in the metastatic lesion correlated to a shorter progression-free survival on ipilimumab. CONCLUSIONS We confirm the link between TMB and HLA-ABC status and the response to ipilimumab-based immunotherapy in melanoma, but no correlation was found for TIL density, neither in primary nor metastatic lesions. Our finding that TMB between paired primary and metastatic melanoma lesions is highly stable, demonstrates its independency of the time point and location of acquisition. TIL and HLA-ABC status in metastatic lesions of different anatomical sites are highly similar within an individual patient.
Collapse
Affiliation(s)
- Mark A J Gorris
- Tumor Immunology, Radboudumc, Nijmegen, The Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | - Lieke L van der Woude
- Tumor Immunology, Radboudumc, Nijmegen, The Netherlands
- Oncode Institute, Nijmegen, The Netherlands
- Pathology, Radboudumc, Nijmegen, The Netherlands
| | | | - Kalijn Bol
- Medical Oncology, Radboudumc, Nijmegen, The Netherlands
| | - Kiek Verrijp
- Oncode Institute, Nijmegen, The Netherlands
- Pathology, Radboudumc, Nijmegen, The Netherlands
| | | | - Jelena Meek
- Tumor Immunology, Radboudumc, Nijmegen, The Netherlands
| | - Johannes Textor
- Department of Tumor Immunology, Radboudumc, Nijmegen, The Netherlands
- Data Science Group, Institute for Computing and Information Sciences, Radboud Universiteit, Nijmegen, The Netherlands
| | - Carl G Figdor
- Tumor Immunology, Radboudumc, Nijmegen, The Netherlands
- Oncode Institute, Nijmegen, The Netherlands
| | | |
Collapse
|
16
|
Slootbeek PHJ, Kloots ISH, Smits M, van Oort IM, Gerritsen WR, Schalken JA, Ligtenberg MJL, Grünberg K, Kroeze LI, Bloemendal HJ, Mehra N. Impact of molecular tumour board discussion on targeted therapy allocation in advanced prostate cancer. Br J Cancer 2022; 126:907-916. [PMID: 34912074 PMCID: PMC8927341 DOI: 10.1038/s41416-021-01663-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/16/2021] [Accepted: 12/01/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Molecular tumour boards (MTB) optimally match oncological therapies to patients with genetic aberrations. Prostate cancer (PCa) is underrepresented in these MTB discussions. This study describes the impact of routine genetic profiling and MTB referral on the outcome of PCa patients in a tertiary referral centre. METHODS All PCa patients that received next-generation sequencing results and/or were discussed at an MTB between Jan 1, 2017 and Jan 1, 2020 were included. Genetically matched therapies (GMT) in clinical trials or compassionate use were linked to actionable alterations. Response to these agents was retrospectively evaluated. RESULTS Out of the 277 genetically profiled PCa patients, 215 (78%) were discussed in at least one MTB meeting. A GMT was recommended to 102 patients (47%), of which 63 patients (62%) initiated the GMT. The most recommended therapies were PARP inhibitors (n = 74), programmed death-(ligand) 1 inhibitors (n = 21) and tyrosine kinase inhibitors (n = 19). Once started, 41.3% had a PFS of ≥6 months, 43.5% a PSA decline ≥50% and 38.5% an objective radiographic response. CONCLUSION Recommendation for a GMT is achieved in almost half of the patients with advanced prostate cancer, with GMT initiation leading to durable responses in over 40% of patients. These data justify routine referral of selected PCa patients to MTB's.
Collapse
Affiliation(s)
- Peter H J Slootbeek
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
- Radboud University Medical Centre, Radboud institute for Molecular Life sciences, Department of Experimental Urology, Nijmegen, The Netherlands
| | - Iris S H Kloots
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Minke Smits
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Inge M van Oort
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Urology, Nijmegen, The Netherlands
| | - Winald R Gerritsen
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Jack A Schalken
- Radboud University Medical Centre, Radboud institute for Molecular Life sciences, Department of Experimental Urology, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Katrien Grünberg
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands
| | - Haiko J Bloemendal
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Niven Mehra
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands.
| |
Collapse
|
17
|
Slootbeek PHJ, Kloots ISH, Smits M, van Oort IM, Gerritsen WR, Schalken JA, Ligtenberg MJL, Grünberg K, Kroeze LI, Bloemendal HJ, Mehra N. Correction to: Impact of molecular tumour board discussion on targeted therapy allocation in advanced prostate cancer. Br J Cancer 2022; 126:1108. [PMID: 35210590 PMCID: PMC8980086 DOI: 10.1038/s41416-022-01765-y] [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)
- Peter H J Slootbeek
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands.,Radboud University Medical Centre, Radboud institute for Molecular Life sciences, Department of Experimental Urology, Nijmegen, The Netherlands
| | - Iris S H Kloots
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Minke Smits
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Inge M van Oort
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Urology, Nijmegen, The Netherlands
| | - Winald R Gerritsen
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Jack A Schalken
- Radboud University Medical Centre, Radboud institute for Molecular Life sciences, Department of Experimental Urology, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands.,Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Katrien Grünberg
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Radboud University Medical Centre, Radboud Institute for Molecular Life sciences, Department of Pathology, Nijmegen, The Netherlands
| | - Haiko J Bloemendal
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Niven Mehra
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Department of Medical Oncology, Nijmegen, The Netherlands.
| |
Collapse
|
18
|
Kloots ISH, Slootbeek PH, Smits M, van Helvert S, Kroeze LI, Kets M, Grünberg K, van Ipenburg J, Ligtenberg M, Schalken JA, van Oort IM, Bloemendal H, Gerritsen WR, Mehra N. First results of the PROMPT trial: Precision oncology allocation in patients with early castration-resistant prostate cancer following routine molecular profiling. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
40 Background: Castration-resistant prostate cancer (CRPC) comprises distinct molecular actionable subtypes. Radboudumc, a tertiary referral center for PCa, hosts a Molecular Tumor Board (MTB), and frequently sees CRPC patients (pts) for referral for genetic testing. In the period 2017-2020, almost 50% of heavily pre-treated CRPC pts received a recommendation for a genetically matched therapy (GMT). In 2020 we initiated the PROMPT trial (NCT04746300) to prospectively study the impact of routine early molecular characterization in CRPC. Increased GMT utilization of targeted- and immunotherapy may improve outcome and quality of life of pts with metastatic CRPC, and lead to lower medical resource utilization (MRU). Here we report on first results from our observational trial. Methods: Within the PROMPT trial, prior to receiving first- or second line standard of care CRPC therapy, up to 300 pts were offered molecular tumor characterization with the TruSightOncology 500 panel (TSO500). Formalin-fixed paraffin-embedded prostate or metastatic tissue biopsies were used, preferably newly obtained. To assess both mutations and copy number alterations, the TSO500 required a minimal tumor cell percentage (TC%) of 30%. Results were discussed within the Radboudumc MTB for GMT recommendation. Actionable targets were defined per Precision Medicine Working group criteria and, when druggable, within the Drug Rediscovery Protocol trial (NCT02925234). All pts with tumor mutations carrying with a risk for cancer predisposition were referred for genetic counselling. Follow-up with patient-reported outcomes (EORTC QLQ-C30, EQ5D, BPI & EPIC-26 questionnaires) and MRU was conducted every 3 months until withdrawal or death. Results: From February 2020 until October 2021 we included 284 consecutive CRPC pts with a median age of 70 years (range 46-86) with a median follow-up of 6.8 months. Newly obtained biopsies and archival material was used in 131 and 126 pts, respectively. Median TC% was 60% (range: 20-90%). TSO500 results could be reported in 254 (89%) cases, with at least one putative clinically relevant aberration in 188 evaluable pts (74%). In 100 pts (39,4%) ≥ 1 druggable target was found. Most common actionable alterations were in PTEN (19%), BRCA2 (9%) or in mismatch-repair genes or resulting in high tumor mutational burden (5%). Out of the 100 druggable pts, 31 pts (31%) initiated a form of GMT, 4 pts (4%; 2 BRCA2, 2 PTEN) died prior to receiving GMT, in 65 pts (65%) GMT is pending as they receive standard of care. Conclusions: Routine molecular profiling early in the CRPC setting is feasible in a tertiary referral center with a MTB and high volume of CRPC pts. Almost 40% CRPC pts harbored an actionable target with 31% of these pts already allocated to a GMT. Failure rates of NGS were low at 11%.
Collapse
Affiliation(s)
- Iris S. H. Kloots
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter H.J. Slootbeek
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Minke Smits
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sjoerd van Helvert
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marleen Kets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Katrien Grünberg
- Department of Pathology and Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jolique van Ipenburg
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marjolijn Ligtenberg
- Department of Pathology and Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jack A. Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Inge M. van Oort
- Department of Urology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Haiko Bloemendal
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Winald R. Gerritsen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
19
|
van den Heuvel GRM, Kroeze LI, Ligtenberg MJL, Grünberg K, Jansen EAM, von Rhein D, de Voer RM, van den Heuvel MM. Mutational signature analysis in non-small cell lung cancer patients with a high tumor mutational burden. Respir Res 2021; 22:302. [PMID: 34819052 PMCID: PMC8611965 DOI: 10.1186/s12931-021-01871-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer death worldwide. With the growing number of targeted therapies and the introduction of immuno-oncology (IO), personalized medicine has become standard of care in patients with metastatic disease. The development of predictive and prognostic biomarkers is of great importance. Mutational signatures harbor potential clinical value as predictors of therapy response in cancer. Here we set out to investigate particular mutational processes by assessing mutational signatures and associations with clinical features, tumor mutational burden (TMB) and targetable mutations. METHODS In this retrospective study, we studied tumor DNA from patients with non-small cell lung cancer (NSCLC) irrespective of stage. The samples were sequenced using a 2 megabase (Mb) gene panel. On each sample TMB was determined and defined as the total number of single nucleotide mutations per Mb (mut/Mb) including non-synonymous mutations. Mutational signature profiling was performed on tumor samples in which at least 30 somatic single base substitutions (SBS) were detected. RESULTS In total 195 samples were sequenced. Median total TMB was 10.3 mut/Mb (range 0-109.3). Mutational signatures were evaluated in 76 tumor samples (39%; median TMB 15.2 mut/Mb). SBS signature 4 (SBS4), associated with tobacco smoking, was prominently present in 25 of 76 samples (33%). SBS2 and/or SBS13, both associated with activity of the AID/APOBEC family of cytidine deaminases, were observed in 11 of 76 samples (14%). SBS4 was significantly more present in early stages (I and II) versus advanced stages (III and IV; P = .005). CONCLUSION In a large proportion of NSCLC patients tissue panel sequencing with a 2 Mb panel can be used to determine the mutational signatures. In general, mutational signature SBS4 was more often found in early versus advanced stages of NSCLC. Further studies are needed to determine the clinical utility of mutational signature analyses.
Collapse
Affiliation(s)
- Guus R M van den Heuvel
- Department of Pulmonology, Radboud University Medical Center, Postbox 9101, 6500 HB, Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Michel M van den Heuvel
- Department of Pulmonology, Radboud University Medical Center, Postbox 9101, 6500 HB, Nijmegen, The Netherlands.
| |
Collapse
|
20
|
Koopman B, Groen HJ, Ligtenberg MJ, Grünberg K, Monkhorst K, de Langen AJ, Boelens MC, Paats MS, von der Thüsen JH, Dinjens WN, Solleveld N, van Wezel T, Gelderblom H, Hendriks LE, Speel EM, Theunissen TE, Kroeze LI, Mehra N, Piet B, van der Wekken AJ, ter Elst A, Timens W, Willems SM, Meijers RW, de Leng WW, van Lindert AS, Radonic T, Hashemi SM, Heideman DA, Schuuring E, van Kempen LC. Multicenter Comparison of Molecular Tumor Boards in The Netherlands: Definition, Composition, Methods, and Targeted Therapy Recommendations. Oncologist 2021; 26:e1347-e1358. [PMID: 33111480 PMCID: PMC8342588 DOI: 10.1002/onco.13580] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Molecular tumor boards (MTBs) provide rational, genomics-driven, patient-tailored treatment recommendations. Worldwide, MTBs differ in terms of scope, composition, methods, and recommendations. This study aimed to assess differences in methods and agreement in treatment recommendations among MTBs from tertiary cancer referral centers in The Netherlands. MATERIALS AND METHODS MTBs from all tertiary cancer referral centers in The Netherlands were invited to participate. A survey assessing scope, value, logistics, composition, decision-making method, reporting, and registration of the MTBs was completed through on-site interviews with members from each MTB. Targeted therapy recommendations were compared using 10 anonymized cases. Participating MTBs were asked to provide a treatment recommendation in accordance with their own methods. Agreement was based on which molecular alteration(s) was considered actionable with the next line of targeted therapy. RESULTS Interviews with 24 members of eight MTBs revealed that all participating MTBs focused on rare or complex mutational cancer profiles, operated independently of cancer type-specific multidisciplinary teams, and consisted of at least (thoracic and/or medical) oncologists, pathologists, and clinical scientists in molecular pathology. Differences were the types of cancer discussed and the methods used to achieve a recommendation. Nevertheless, agreement among MTB recommendations, based on identified actionable molecular alteration(s), was high for the 10 evaluated cases (86%). CONCLUSION MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational cancer profiles. We propose a "Dutch MTB model" for an optimal, collaborative, and nationally aligned MTB workflow. IMPLICATIONS FOR PRACTICE Interpretation of genomic analyses for optimal choice of target therapy for patients with cancer is becoming increasingly complex. A molecular tumor board (MTB) supports oncologists in rationalizing therapy options. However, there is no consensus on the most optimal setup for an MTB, which can affect the quality of recommendations. This study reveals that the eight MTBs associated with tertiary cancer referral centers in The Netherlands are similar in setup and reach a high agreement in recommendations for rare or complex mutational profiles. The Dutch MTB model is based on a collaborative and nationally aligned workflow with interinstitutional collaboration and data sharing.
Collapse
Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Harry J.M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marjolijn J.L. Ligtenberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
- Department of Human Genetics, Radboud University Medical CenterNijmegenThe Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Adrianus J. de Langen
- Department of Thoracic Oncology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mirjam C. Boelens
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Marthe S. Paats
- Department of Pulmonary Medicine, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Jan H. von der Thüsen
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Winand N.M. Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center RotterdamRotterdamThe Netherlands
| | - Nienke Solleveld
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Tom van Wezel
- Department of Pathology, Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of Pathology, Leiden University Medical CenterLeidenThe Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical CenterLeidenThe Netherlands
| | - Lizza E. Hendriks
- Department of Pulmonary Diseases, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Ernst‐Jan M. Speel
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Tom E. Theunissen
- Department of Pathology, GROW‐School for Oncology and Developmental Biology, Maastricht University Medical CenterMaastrichtThe Netherlands
| | - Leonie I. Kroeze
- Department of Pathology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical CenterNijmegenThe Netherlands
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical CenterNijmegenThe Netherlands
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Ruud W.J. Meijers
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | - Wendy W.J. de Leng
- Department of Pathology, University Medical Center UtrechtUtrechtThe Netherlands
| | | | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sayed M.S. Hashemi
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Daniëlle A.M. Heideman
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center GroningenGroningenThe Netherlands
| |
Collapse
|
21
|
van den Brand M, Rijntjes J, Möbs M, Steinhilber J, van der Klift MY, Heezen KC, Kroeze LI, Reigl T, Porc J, Darzentas N, Luijks JACW, Scheijen B, Davi F, ElDaly H, Liu H, Anagnostopoulos I, Hummel M, Fend F, Langerak AW, Groenen PJTA. Next-Generation Sequencing-Based Clonality Assessment of Ig Gene Rearrangements: A Multicenter Validation Study by EuroClonality-NGS. J Mol Diagn 2021; 23:1105-1115. [PMID: 34186174 DOI: 10.1016/j.jmoldx.2021.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Ig gene (IG) clonality analysis has an important role in the distinction of benign and malignant B-cell lymphoid proliferations and is mostly performed with the conventional EuroClonality/BIOMED-2 multiplex PCR protocol and GeneScan fragment size analysis. Recently, the EuroClonality-NGS Working Group developed a method for next-generation sequencing (NGS)-based IG clonality analysis. Herein, we report the results of an international multicenter biological validation of this novel method compared with the gold standard EuroClonality/BIOMED-2 protocol, based on 209 specimens of reactive and neoplastic lymphoproliferations. NGS-based IG clonality analysis showed a high interlaboratory concordance (99%) and high concordance with conventional clonality analysis (98%) for the molecular conclusion. Detailed analysis of the individual IG heavy chain and kappa light chain targets showed that NGS-based clonality analysis was more often able to detect a clonal rearrangement or yield an interpretable result. NGS-based and conventional clonality analysis detected a clone in 96% and 95% of B-cell neoplasms, respectively, and all but one of the reactive cases were scored polyclonal. We conclude that NGS-based IG clonality analysis performs comparable to conventional clonality analysis. We provide critical parameters for interpretation and discuss a first step toward a quantitative scoring approach for NGS clonality results. Considering the advantages of NGS-based clonality analysis, including its high sensitivity and possibilities for accurate clonal comparison, this supports implementation in diagnostic practice.
Collapse
Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Steinhilber
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Michèle Y van der Klift
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kim C Heezen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomas Reigl
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Jakub Porc
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Brno, Czech Republic; Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeroen A C W Luijks
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frédéric Davi
- Hematology Department, Hospital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Hesham ElDaly
- Histopathology Department, Coventry University Hospitals National Health Service Trust, Coventry, United Kingdom; Clinical Pathology Department, Cairo University, Cairo, Egypt
| | - Hongxiang Liu
- Haematopathology and Oncology Diagnostics Service, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | |
Collapse
|
22
|
Leenders AM, Kroeze LI, Rijntjes J, Luijks J, Hebeda KM, Darzentas N, Langerak AW, van den Brand M, Groenen PJTA. Multiple Immunoglobulin κ Gene Rearrangements within a Single Clone Unraveled by Next-Generation Sequencing-Based Clonality Assessment. J Mol Diagn 2021; 23:1097-1104. [PMID: 34020040 DOI: 10.1016/j.jmoldx.2021.05.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/14/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Clonality assessment of the Ig heavy- and light-chain genes (IGH and IGK) using GeneScan analysis is an important supplemental assay in diagnostic testing for lymphoma. Occasionally cases with an IGK rearrangement pattern that cannot readily be assigned to a monoclonal lymphoma are encountered, whereas the occurrence of biclonal lymphomas is rare, and the result of the IGH locus of these cases is in line with monoclonality. Three such ambiguous cases were assessed for clonality using next-generation sequencing. Information on the sequences of the rearrangements, combined with knowledge of the complex organization of the IGK locus, pointed to two explanations that can attribute seemingly biclonal IGK rearrangements to a single clone. In two cases, this explanation involved inversion rearrangements on the IGK locus, whereas in the third case, the cross-reactivity of primers generated an additional clonal product. In conclusion, next-generation sequencing-based clonality assessment allows for the detection of both inversion rearrangements and the cross-reactivity of primers, and can therefore facilitate the interpretation of cases of lymphoma with complex IGK rearrangement patterns.
Collapse
Affiliation(s)
- A Meilinde Leenders
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jeroen Luijks
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Konnie M Hebeda
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory for Medical Immunology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | |
Collapse
|
23
|
de Bitter TJJ, Kroeze LI, de Reuver PR, van Vliet S, Vink-Börger E, von Rhein D, Jansen EAM, Nagtegaal ID, Ligtenberg MJL, van der Post RS. Unraveling Neuroendocrine Gallbladder Cancer: Comprehensive Clinicopathologic and Molecular Characterization. JCO Precis Oncol 2021; 5:PO.20.00487. [PMID: 34036234 PMCID: PMC8140808 DOI: 10.1200/po.20.00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/25/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Neuroendocrine carcinomas and mixed neuroendocrine non-neuroendocrine neoplasms of the gallbladder (NE GBC) are rare and highly aggressive entities. The cell of origin of NE GBC has been a matter of controversy. Here, we performed a comparative histopathologic and molecular analysis of NE GBC cases and, if present, associated precancerous lesions. PATIENTS AND METHODS We selected cases diagnosed between 2000 and 2019 in the Netherlands. Precursors and carcinomas were immunohistochemically compared and analyzed for mutations, gene amplifications, microsatellite instability, and tumor mutational burden using an next-generation sequencing panel containing 523 cancer-related genes. In addition, presence of fusion genes was analyzed using a panel of 55 genes. RESULTS Sixty percent of neuroendocrine cases (6/10) presented with a precursor lesion, either intracholecystic papillary neoplasm (n = 3) or biliary intraepithelial neoplasia (n = 3). Immunohistochemically, neuroendocrine components were different from the epithelial precursor lesions. Molecular profiling, however, revealed TP53 mutations shared between different components in five of six cases, indicating a clonal relation. Furthermore, 40% of cases (4/10) harbored at least one potentially actionable alteration. This included (likely) pathogenic mutations in RAD54L, ATM, and BRCA2; amplifications of ERBB2 and MDM2; and a gene fusion involving FGFR3-TACC3. All cases were microsatellite-stable and had a tumor mutational burden of < 10 mutations/Mb. CONCLUSION Our data provide insight into the development of NE GBC and suggest a common origin of precancerous epithelial lesions and invasive neuroendocrine components, favoring the hypothesis of lineage transformation. Moreover, nearly half of the NE GBCs carried at least one potentially actionable molecular alteration, highlighting the importance of molecular testing in this highly lethal cancer.
Collapse
Affiliation(s)
- Tessa J J de Bitter
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philip R de Reuver
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elisa Vink-Börger
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
24
|
van der Doelen MJ, Mehra N, van Oort IM, Looijen-Salamon MG, Janssen MJR, Custers JAE, Slootbeek PHJ, Kroeze LI, Bruchertseifer F, Morgenstern A, Haberkorn U, Kratochwil C, Nagarajah J, Gerritsen WR. Clinical outcomes and molecular profiling of advanced metastatic castration-resistant prostate cancer patients treated with 225Ac-PSMA-617 targeted alpha-radiation therapy. Urol Oncol 2020; 39:729.e7-729.e16. [PMID: 33353867 DOI: 10.1016/j.urolonc.2020.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Targeted alpha-radiation therapy (TAT) with 225Ac-labeled prostate-specific membrane antigen (PSMA) ligands is a promising novel treatment option for metastatic castration-resistant prostate cancer (mCRPC) patients. However, limited data are available on efficacy, quality of life (QoL), and pretherapeutic biomarkers. The aim of this study was to evaluate the efficacy of 225Ac-PSMA TAT and impact on QoL in advanced mCRPC, and to explore predictive biomarkers on pretherapeutic metastatic tissue biopsies. METHODS Observational cohort study including consecutive patients treated with 225Ac-PSMA TAT between February 2016 and July 2018. Primary endpoint was overall survival (OS). Furthermore, prostate-specific antigen (PSA) changes, radiological response, safety, QoL, and xerostomia were evaluated. Biopsies were analyzed with immunohistochemistry and next-generation sequencing. RESULTS Thirteen patients were included. Median OS was 8.5 months for the total cohort and 12.6 months for PSMA radioligand therapy-naïve patients. PSA declines of ≥90% and ≥50% were observed in 46% and 69% of patients, respectively. Six patients were radiologically evaluable; 50% showed partial response. All patients showed >90% total tumor volume reduction on PET imaging. Patients experienced clinically relevant decrease of pain and QoL improvement in physical and role functioning domains. Xerostomia persisted during follow-up. Patients with high baseline immunohistochemical PSMA expression or DNA damage repair alterations tended to have longer OS. CONCLUSIONS TAT with 225Ac-PSMA resulted in remarkable survival and biochemical responses in advanced mCRPC patients. Patients experienced clinically relevant QoL improvement, although xerostomia was found to be nontransient. Baseline immunohistochemical PSMA expression and DNA damage repair status are potential predictive biomarkers of response to 225Ac-PSMA TAT.
Collapse
Affiliation(s)
- Maarten J van der Doelen
- Radboud University Medical Center, Department of Medical Oncology, Nijmegen, The Netherlands; Radboud University Medical Center, Department of Urology, Nijmegen, The Netherlands.
| | - Niven Mehra
- Radboud University Medical Center, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Inge M van Oort
- Radboud University Medical Center, Department of Urology, Nijmegen, The Netherlands
| | | | - Marcel J R Janssen
- Radboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The Netherlands
| | - José A E Custers
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department of Medical Psychology, Nijmegen, The Netherlands
| | - Peter H J Slootbeek
- Radboud University Medical Center, Department of Medical Oncology, Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Radboud University Medical Center, Department of Pathology, Nijmegen, The Netherlands
| | - Frank Bruchertseifer
- European Commission, Joint Research Centre, Nuclear Safety and Security, Karlsruhe, Germany
| | - Alfred Morgenstern
- European Commission, Joint Research Centre, Nuclear Safety and Security, Karlsruhe, Germany
| | - Uwe Haberkorn
- University Hospital Heidelberg, Department of Nuclear Medicine, Germany
| | | | - James Nagarajah
- Radboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The Netherlands; Technical University Munich, Klinikum rechts der Isar, Department of Nuclear Medicine, Munich, Germany
| | - Winald R Gerritsen
- Radboud University Medical Center, Department of Medical Oncology, Nijmegen, The Netherlands
| |
Collapse
|
25
|
Slootbeek PHJ, Duizer ML, van der Doelen MJ, Kloots ISH, Kuppen MCP, Westgeest HM, Uyl-de Groot CA, Pamidimarri Naga S, Ligtenberg MJL, van Oort IM, Gerritsen WR, Schalken JA, Kroeze LI, Bloemendal HJ, Mehra N. Impact of DNA damage repair defects and aggressive variant features on response to carboplatin-based chemotherapy in metastatic castration-resistant prostate cancer. Int J Cancer 2020; 148:385-395. [PMID: 32965028 PMCID: PMC7756382 DOI: 10.1002/ijc.33306] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 06/22/2020] [Revised: 08/08/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Platinum‐based chemotherapy is not standard of care for unselected or genetically selected metastatic castration‐resistant prostate cancer (mCRPC) patients. A retrospective assessment of 71 patients was performed on platinum use in the Netherlands. Genetically unselected patients yielded low response rates. For a predefined subanalysis of all patients with comprehensive next‐generation sequencing, 30 patients were grouped based on the presence of pathogenic aberrations in genes associated with DNA damage repair (DDR) or aggressive variant prostate cancer (AVPC). Fourteen patients (47%) were DDR deficient (DDRd), of which seven with inactivated BRCA2 (BRCA2mut). Six patients classified as AVPC. DDRd patients showed beneficial biochemical response to carboplatin, largely driven by all BRCA2mut patients having >50% prostate‐specific antigen (PSA) decline and objective radiographic response. In the wild‐type BRCA2 subgroup, 35% had a >50% PSA decline (P = .006) and 16% radiographic response (P < .001). Median overall survival was 21 months for BRCA2mut patients vs 7 months (P = .041) for those with functional BRCA2. AVPC patients demonstrated comparable responses to non‐AVPC, including a similar overall survival, despite the poor prognosis for this subgroup. In the scope of the registration of poly‐(ADP)‐ribose polymerase inhibitors (PARPi) for mCRPC, we provide initial insights on cross‐resistance between PARPi and platinum compounds. By combining the literature and our study, we identified 18 patients who received both agents. In this cohort, only BRCA2mut patients treated with platinum first (n = 4), responded to both agents. We confirm that BRCA2 inactivation is associated with meaningful responses to carboplatin, suggesting a role for both PARPi and platinum‐based chemotherapy in preselected mCRPC patients. What's new? Platinum‐based chemotherapy is not standard of care for unselected or genetically‐selected patients with metastatic castration‐resistant prostate cancer (mCRPC). However, several studies have shown that platinum‐based chemotherapy may still have a role in postponing progression in selected patient groups. This new study investigating DNA damage repair gene alterations and response to platinum‐based chemotherapy provides evidence that deep and durable responses are primarily associated with patients harbouring BRCA2 inactivation. Based on these data and the limited available literature, platinum‐based chemotherapy followed by PARP inhibition is potentially emerging as the optimal treatment sequence in pre‐selected mCRPC patients.
Collapse
Affiliation(s)
- Peter H J Slootbeek
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marleen L Duizer
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maarten J van der Doelen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris S H Kloots
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Malou C P Kuppen
- Institute for Medical Technology Assessment (iMTA), Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Hans M Westgeest
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands
| | - Carin A Uyl-de Groot
- Institute for Medical Technology Assessment (iMTA), Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Samhita Pamidimarri Naga
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Inge M van Oort
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Winald R Gerritsen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jack A Schalken
- Department of Experimental Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Haiko J Bloemendal
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
26
|
McConnell L, Houghton O, Stewart P, Gazdova J, Srivastava S, Kim C, Catherwood M, Strobl A, Flanagan AM, Oniscu A, Kroeze LI, Groenen P, Taniere P, Salto-Tellez M, Gonzalez D. A novel next generation sequencing approach to improve sarcoma diagnosis. Mod Pathol 2020; 33:1350-1359. [PMID: 32047232 DOI: 10.1038/s41379-020-0488-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 10/16/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 02/08/2023]
Abstract
Sarcoma is a rare disease affecting both bone and connective tissue and with over 100 pathologic entities, differential diagnosis can be difficult. Complementing immune-histological diagnosis with current ancillary diagnostic techniques, including FISH and RT-PCR, can lead to inconclusive results in a significant number of cases. We describe here the design and validation of a novel sequencing tool to improve sarcoma diagnosis. A NGS DNA capture panel containing probes for 87 fusion genes and 7 genes with frequent copy number changes was designed and optimized. A cohort of 113 DNA samples extracted from soft-tissue and bone sarcoma FFPE material with clinical FISH and/or RT-PCR results positive for either a translocation or gene amplification was used for validation of the NGS method. Sarcoma-specific translocations or gene amplifications were confirmed in 110 out of 113 cases using FISH and/or RT-PCR as gold-standard. MDM2/CDK4 amplification and a total of 25 distinct fusion genes were identified in this cohort of patients using the NGS approach. Overall, the sensitivity of the NGS panel is 97% with a specificity of 100 and 0% failure rate. Targeted NGS appears to be a feasible and cost-effective approach to improve sarcoma subtype diagnosis with the ability to screen for a wide range of genetic aberrations in one test.
Collapse
Affiliation(s)
| | - Oisín Houghton
- Belfast Health & Social Care Trust, Belfast, BT9 7AB, UK
| | - Peter Stewart
- CCRCB, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Jana Gazdova
- CCRCB, Queen's University Belfast, Belfast, BT9 7AE, UK
| | | | - Chang Kim
- CCRCB, Queen's University Belfast, Belfast, BT9 7AE, UK
| | | | - Anna Strobl
- Royal National Orthopedic Hospital Stanmore, Middlesex, HA7 4LP, UK
- UCL Cancer Institute, London, WC1E 6BT, UK
| | - Adrienne M Flanagan
- Royal National Orthopedic Hospital Stanmore, Middlesex, HA7 4LP, UK
- UCL Cancer Institute, London, WC1E 6BT, UK
| | - Anca Oniscu
- Pathology Department at the Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Patricia Groenen
- Department of Pathology, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Philippe Taniere
- Pathology Department at Queen's Elizabeth Hospital Birmingham, Birmingham, B15 2TH, UK
| | - Manuel Salto-Tellez
- CCRCB, Queen's University Belfast, Belfast, BT9 7AE, UK
- Belfast Health & Social Care Trust, Belfast, BT9 7AB, UK
| | - David Gonzalez
- CCRCB, Queen's University Belfast, Belfast, BT9 7AE, UK.
- Belfast Health & Social Care Trust, Belfast, BT9 7AB, UK.
| |
Collapse
|
27
|
Steeghs EMP, Kroeze LI, Tops BBJ, van Kempen LC, Ter Elst A, Kastner-van Raaij AWM, Hendriks-Cornelissen SJB, Hermsen MJW, Jansen EAM, Nederlof PM, Schuuring E, Ligtenberg MJL, Eijkelenboom A. Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material. BMC Cancer 2020; 20:291. [PMID: 32264863 PMCID: PMC7137451 DOI: 10.1186/s12885-020-06785-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 10/21/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023] Open
Abstract
Background Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultaneous detection of predictive markers, including mutations, gene amplifications and MSI, will save valuable material, time and costs. Methods Using a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach, we developed an NGS panel allowing detection of predictive mutations in 33 genes, gene amplifications of 13 genes and microsatellite instability (MSI) by the evaluation of 55 microsatellite markers. The panel was designed to target all clinically relevant single and multiple nucleotide mutations in routinely available lung cancer, colorectal cancer, melanoma, and gastro-intestinal stromal tumor samples, but is useful for a broader set of tumor types. Results The smMIP-based NGS panel was successfully validated and cut-off values were established for reliable gene amplification analysis (i.e. relative coverage ≥3) and MSI detection (≥30% unstable loci). After validation, 728 routine diagnostic tumor samples including a broad range of tumor types were sequenced with sufficient sensitivity (2.4% drop-out), including samples with low DNA input (< 10 ng; 88% successful), low tumor purity (5–10%; 77% successful), and cytological material (90% successful). 75% of these tumor samples showed ≥1 (likely) pathogenic mutation, including targetable mutations (e.g. EGFR, BRAF, MET, ERBB2, KIT, PDGFRA). Amplifications were observed in 5.5% of the samples, comprising clinically relevant amplifications (e.g. MET, ERBB2, FGFR1). 1.5% of the tumor samples were classified as MSI-high, including both MSI-prone and non-MSI-prone tumors. Conclusions We developed a comprehensive workflow for predictive analysis of diagnostic tumor samples. The smMIP-based NGS analysis was shown suitable for limited amounts of histological and cytological material. As smMIP technology allows easy adaptation of panels, this approach can comply with the rapidly expanding molecular markers.
Collapse
Affiliation(s)
- Elisabeth M P Steeghs
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Leon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Mandy J W Hermsen
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
| |
Collapse
|
28
|
van der Doelen MJ, Isaacsson Velho P, Slootbeek PH, Pamidimarri Naga S, Bormann M, van Helvert S, Kroeze LI, van Oort IM, Gerritsen WR, Antonarakis ES, Mehra N. Overall survival using radium-223 (Ra223) in metastatic castrate-resistant prostate cancer (mCRPC) patients with and without DNA damage repair (DDR) defects. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
121 Background: Ra223 is a therapeutic option for mCRPC patients (pts) with symptomatic bone metastases. DDR-defective prostate cancers, specifically those with homologous recombination deficiency (HRD), accumulate irreparable DNA damage following genotoxic treatment. This study assessed presence or absence of DDR alterations in mCRPC pts treated with Ra223, investigating the effect on efficacy and overall survival (OS). Methods: All pts included were treated with Ra223 and had genomic results from a comprehensive next-generation sequencing panel of DDR genes that directly or indirectly led to HRD, from primary or metastatic tissue. Exclusion criteria were prior platinum-based chemotherapy or treatment with poly-ADP ribose polymerase inhibitors (PARPi). Pts were grouped by presence (DDR+) or absence (DDR-) of pathogenic somatic and/or germline aberrations in DDR genes. Primary endpoint was OS, and secondary endpoints were time to alkaline phosphatase (ALP) progression, time to next systemic therapy and biochemical responses; comparing DDR+ and DDR– groups. Results: 93 pts were included in this two-centre retrospective study. Median age was 68 years. 56% received prior chemotherapy. Baseline characteristics where comparable between DDR status subgroups. 28 (30%) pts had mutations in DDR genes, most frequently occurring in ATM (8.6%), BRCA2 (6.5%), and CDK12 (4.3%) genes. DDR+ pts showed prolonged OS (median 36.3 vs. 17.0 months; HR 2.29; 95% CI 1.21-4.32; P= 0.01). Median time to alkaline phosphatase progression was 6.9 months for DDR+ pts and 5.8 months for DDR- pts (HR 1.48; 95% CI 0.87-2.50; P =0.15), and median time to next systemic therapy was 8.9 months for DDR+ pts and 7.3 months for DDR- pts (HR 1.58; 95% CI 0.94-2.64; P =0.08). A higher proportion of DDR+ pts completed Ra223 therapy (79% vs 47%; P= 0.05). No differences in biochemical (prostate-specific antigen, ALP) responses were seen. Conclusions: Pts harboring deleterious DDR aberrations more commonly completed Ra223, and derived a greater OS benefit. These findings need prospective confirmation, but support combination of Ra223 with PARPi or ATR inhibitors in DDR-defective mCRPC pts.
Collapse
Affiliation(s)
| | | | | | | | - Maren Bormann
- Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | | | | | | | - Niven Mehra
- Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
29
|
van Boxtel W, Verhaegh GW, van Engen-van Grunsven IA, van Strijp D, Kroeze LI, Ligtenberg MJ, van Zon HB, Hendriksen Y, Keizer D, van de Stolpe A, Schalken JA, van Herpen CM. Prediction of clinical benefit from androgen deprivation therapy in salivary duct carcinoma patients. Int J Cancer 2019; 146:3196-3206. [PMID: 31745978 PMCID: PMC7187215 DOI: 10.1002/ijc.32795] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 06/20/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Androgen deprivation therapy (ADT) is first‐line palliative treatment in androgen receptor‐positive (AR+) salivary duct carcinoma (SDC), and response rates are 17.6–50.0%. We investigated potential primary ADT resistance mechanisms for their predictive value of clinical benefit from ADT in a cohort of recurrent/metastatic SDC patients receiving palliative ADT (n = 30). We examined mRNA expression of androgen receptor (AR), AR splice variant‐7, intratumoral androgen synthesis enzyme‐encoding genes AKR1C3, CYP17A1, SRD5A1 and SRD5A2, AR protein expression, ERBB2 (HER2) gene amplification and DNA mutations in driver genes. Furthermore, functional AR pathway activity was determined using a previously reported Bayesian model which infers pathway activity from AR target gene expression levels. SRD5A1 expression levels and AR pathway activity scores were significantly higher in patients with clinical benefit from ADT compared to those without benefit. Survival analysis showed a trend toward a longer median progression‐free survival for patients with high SRD5A1 expression levels and high AR pathway activity scores. The AR pathway activity analysis, and not SRD5A1 expression, also showed a trend toward better disease‐free survival in an independent cohort of locally advanced SDC patients receiving adjuvant ADT (n = 14) after surgical tumor resection, and in most cases a neck dissection (13/14 patients) and postoperative radiotherapy (13/14 patients). In conclusion, we are the first to describe that AR pathway activity may predict clinical benefit from ADT in SDC patients, but validation in a prospective study is needed. What's new? Androgen deprivation therapy (ADT) is a leading treatment strategy in the palliative care of patients with androgen receptor (AR)‐positive salivary duct carcinoma (SDC). However, while as many as half of patients may respond to ADT, resistance frequently emerges, undermining its use. In this investigation of primary ADT resistance mechanisms, expression of the androgen synthesis enzyme‐encoding gene SRD5A1 and functional activity of the AR pathway were found to predict clinical benefit from ADT in SDC patients. High AR pathway activity scores were further linked to improved disease‐free survival in SDC patients with locally advanced disease who received adjuvant ADT.
Collapse
Affiliation(s)
- Wim van Boxtel
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolein J Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Yara Hendriksen
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Diederick Keizer
- Molecular Pathway Diagnostics, Philips Healthworks, Eindhoven, The Netherlands
| | | | - Jack A Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carla M van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
30
|
Berger G, Gerritsen M, Yi G, Koorenhof-Scheele TN, Kroeze LI, Stevens-Kroef M, Yoshida K, Shiraishi Y, van den Berg E, Schepers H, Huls G, Mulder AB, Ogawa S, Martens JHA, Jansen JH, Vellenga E. Ring sideroblasts in AML are associated with adverse risk characteristics and have a distinct gene expression pattern. Blood Adv 2019; 3:3111-3122. [PMID: 31648334 PMCID: PMC6849935 DOI: 10.1182/bloodadvances.2019000518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/14/2019] [Indexed: 12/24/2022] Open
Abstract
Ring sideroblasts (RS) emerge as result of aberrant erythroid differentiation leading to excessive mitochondrial iron accumulation, a characteristic feature for myelodysplastic syndromes (MDS) with mutations in the spliceosome gene SF3B1. However, RS can also be observed in patients diagnosed with acute myeloid leukemia (AML). The objective of this study was to characterize RS in patients with AML. Clinically, RS-AML is enriched for ELN adverse risk (55%). In line with this finding, 35% of all cases had complex cytogenetic aberrancies, and TP53 was most recurrently mutated in this cohort (37%), followed by DNMT3A (26%), RUNX1 (25%), TET2 (20%), and ASXL1 (19%). In contrast to RS-MDS, the incidence of SF3B1 mutations was low (8%). Whole-exome sequencing and SNP array analysis on a subset of patients did not uncover a single genetic defect underlying the RS phenotype. Shared genetic defects between erythroblasts and total mononuclear cell fraction indicate common ancestry for the erythroid lineage and the myeloid blast cells in patients with RS-AML. RNA sequencing analysis on CD34+ AML cells revealed differential gene expression between RS-AML and non RS-AML cases, including genes involved in megakaryocyte and erythroid differentiation. Furthermore, several heme metabolism-related genes were found to be upregulated in RS- CD34+ AML cells, as was observed in SF3B1mut MDS. These results demonstrate that although the genetic background of RS-AML differs from that of RS-MDS, they have certain downstream effector pathways in common.
Collapse
Affiliation(s)
- Gerbrig Berger
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mylene Gerritsen
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Guoqiang Yi
- Department of Molecular Biology, Radboud University, Nijmegen, The Netherlands
| | | | | | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kenichi Yoshida
- Department of Pathology & Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Hein Schepers
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Geert Huls
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - André B Mulder
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Seishi Ogawa
- Department of Pathology & Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan; and
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinksa Institute, Stockholm, Sweden
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Nijmegen, The Netherlands
| | | | - Edo Vellenga
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
31
|
Eijkelenboom A, Tops BBJ, van den Berg A, van den Brule AJC, Dinjens WNM, Dubbink HJ, Ter Elst A, Geurts-Giele WRR, Groenen PJTA, Groenendijk FH, Heideman DAM, Huibers MMH, Huijsmans CJJ, Jeuken JWM, van Kempen LC, Korpershoek E, Kroeze LI, de Leng WWJ, van Noesel CJM, Speel EJM, Vogel MJ, van Wezel T, Nederlof PM, Schuuring E, Ligtenberg MJL. Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics. Virchows Arch 2019; 474:673-680. [PMID: 30888490 PMCID: PMC6581937 DOI: 10.1007/s00428-019-02555-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/04/2018] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 01/09/2023]
Abstract
Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.
Collapse
Affiliation(s)
- Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anke van den Berg
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Léon C van Kempen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ernst-Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.
| |
Collapse
|
32
|
da Silva-Coelho P, Kroeze LI, Yoshida K, Koorenhof-Scheele TN, Knops R, van de Locht LT, de Graaf AO, Massop M, Sandmann S, Dugas M, Stevens-Kroef MJ, Cermak J, Shiraishi Y, Chiba K, Tanaka H, Miyano S, de Witte T, Blijlevens NMA, Muus P, Huls G, van der Reijden BA, Ogawa S, Jansen JH. Clonal evolution in myelodysplastic syndromes. Nat Commun 2017; 8:15099. [PMID: 28429724 PMCID: PMC5530598 DOI: 10.1038/ncomms15099] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [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: 07/11/2016] [Accepted: 02/24/2017] [Indexed: 02/08/2023] Open
Abstract
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5–11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment. The application of disease-modifying therapy may create an evolutionary bottleneck after which more complex MDS, but also unrelated clones of haematopoietic cells, may emerge. In addition, subclones that acquired an additional mutation associated with treatment resistance (TP53) or disease progression (NRAS, KRAS) may be detected months before clinical changes become apparent. Monitoring the genetic landscape during the disease may help to guide treatment decisions. Myelodysplastic syndromes are a broad group of haematopoietic malignancies that often progress to acute myeloid leukaemia. Here, the authors show that linear and branched evolution occurs within myelodysplastic syndrome and these patterns can be impacted by treatment.
Collapse
Affiliation(s)
- Pedro da Silva-Coelho
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands.,Department of Haematology, Centro Hospitalar de São João and Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto 4200-319, Portugal
| | - Leonie I Kroeze
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan
| | - Theresia N Koorenhof-Scheele
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Ruth Knops
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Louis T van de Locht
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Aniek O de Graaf
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Marion Massop
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Marian J Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic
| | - Yuichi Shiraishi
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Kenichi Chiba
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Hiroko Tanaka
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639 Japan
| | - Theo de Witte
- Department of Tumor Immunology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Nicole M A Blijlevens
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Petra Muus
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Gerwin Huls
- Department of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands.,Department of Hematology, University Medical Centre Groningen, PO Box 30001, 9700 RB Groningen, The Netherlands
| | - Bert A van der Reijden
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8501, Japan
| | - Joop H Jansen
- Laboratory of Hematology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
| |
Collapse
|
33
|
von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol Cell 2016; 62:983. [PMID: 27315559 PMCID: PMC4914604 DOI: 10.1016/j.molcel.2016.06.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
34
|
von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol Cell 2016; 62:848-861. [PMID: 27237052 PMCID: PMC4914828 DOI: 10.1016/j.molcel.2016.04.025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [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: 02/05/2016] [Revised: 04/04/2016] [Accepted: 04/21/2016] [Indexed: 12/20/2022]
Abstract
Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos. Impaired DNA methylation maintenance is the cause of global demethylation in naive ESCs Loss of H3K9me2 and UHRF1 lead to impaired maintenance targeting to replication foci TET enzymes are not required for global demethylation Mathematical model accurately predicts global 5mC and 5hmC during epigenetic resetting
Collapse
Affiliation(s)
| | - Mario Iurlaro
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ning Qing Liu
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ali Salehzadeh-Yazdi
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Edoardo Petrini
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Inês Milagre
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhenqing Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Tatyana B Nesterova
- Developmental Epigenetics Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hehuang Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands.
| |
Collapse
|
35
|
Kroeze LI, van der Reijden BA, Jansen JH. 5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:144-54. [PMID: 25579174 DOI: 10.1016/j.bbcan.2015.01.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/02/2015] [Accepted: 01/04/2015] [Indexed: 12/26/2022]
Abstract
The epigenetic mark 5-hydroxymethylcytosine (5hmC) has gained interest since 2009, when it was discovered that Ten-Eleven-Translocation (TET) proteins catalyze the conversion of 5-methylcytosine (5mC) into 5hmC. This conversion appears to be an intermediate step in the active DNA demethylation pathway. Factors that regulate DNA hydroxymethylation are frequently affected in cancer, leading to deregulated 5hmC levels. In this review, we will discuss the regulation of DNA hydroxymethylation, defects in this pathway in cancer, and novel therapies that may correct deregulated (hydroxy)methylation of DNA.
Collapse
Affiliation(s)
- Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| |
Collapse
|
36
|
Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HHD, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC, Benedetti R, Altucci L, Jansen JH, Walter J, Gut IG, Marks H, Stunnenberg HG. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 2013; 13:360-9. [PMID: 23850244 DOI: 10.1016/j.stem.2013.06.002] [Citation(s) in RCA: 336] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/03/2013] [Accepted: 06/07/2013] [Indexed: 12/22/2022]
Abstract
The use of two kinase inhibitors (2i) enables derivation of mouse embryonic stem cells (ESCs) in the pluripotent ground state. Using whole-genome bisulfite sequencing (WGBS), we show that male 2i ESCs are globally hypomethylated compared to conventional ESCs maintained in serum. In serum, female ESCs are hypomethyated similarly to male ESCs in 2i, and DNA methylation is further reduced in 2i. Regions with elevated DNA methylation in 2i strongly correlate with the presence of H3K9me3 on endogenous retroviruses (ERVs) and imprinted loci. The methylome of male ESCs in serum parallels postimplantation blastocyst cells, while 2i stalls ESCs in a hypomethylated, ICM-like state. WGBS analysis during adaptation of 2i ESCs to serum suggests that deposition of DNA methylation is largely random, while loss of DNA methylation during reversion to 2i occurs passively, initiating at TET1 binding sites. Together, our analysis provides insight into DNA methylation dynamics in cultured ESCs paralleling early developmental processes.
Collapse
Affiliation(s)
- Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences NCMLS, Radboud University, 6525GA, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|