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Küçükosmanoglu A, Scoarta S, Houweling M, Spinu N, Wijnands T, Geerdink N, Meskers C, Kanev GK, Kiewiet B, Kouwenhoven M, Noske D, Wurdinger T, Pouwer M, Wolff M, Westerman BA. A Real-world Toxicity Atlas Shows that Adverse Events of Combination Therapies Commonly Result in Additive Interactions. Clin Cancer Res 2024; 30:1685-1695. [PMID: 38597991 PMCID: PMC11016889 DOI: 10.1158/1078-0432.ccr-23-0914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 01/10/2024] [Indexed: 04/11/2024]
Abstract
PURPOSE Combination therapies are a promising approach for improving cancer treatment, but it is challenging to predict their resulting adverse events in a real-world setting. EXPERIMENTAL DESIGN We provide here a proof-of-concept study using 15 million patient records from the FDA Adverse Event Reporting System (FAERS). Complex adverse event frequencies of drugs or their combinations were visualized as heat maps onto a two-dimensional grid. Adverse event frequencies were shown as colors to assess the ratio between individual and combined drug effects. To capture these patterns, we trained a convolutional neural network (CNN) autoencoder using 7,300 single-drug heat maps. In addition, statistical synergy analyses were performed on the basis of BLISS independence or χ2 testing. RESULTS The trained CNN model was able to decode patterns, showing that adverse events occur in global rather than isolated and unique patterns. Patterns were not likely to be attributed to disease symptoms given their relatively limited contribution to drug-associated adverse events. Pattern recognition was validated using trial data from ClinicalTrials.gov and drug combination data. We examined the adverse event interactions of 140 drug combinations known to be avoided in the clinic and found that near all of them showed additive rather than synergistic interactions, also when assessed statistically. CONCLUSIONS Our study provides a framework for analyzing adverse events and suggests that adverse drug interactions commonly result in additive effects with a high level of overlap of adverse event patterns. These real-world insights may advance the implementation of new combination therapies in clinical practice.
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Affiliation(s)
- Asli Küçükosmanoglu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Silvia Scoarta
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Megan Houweling
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Nicoleta Spinu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Thomas Wijnands
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Niek Geerdink
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Carolien Meskers
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Georgi K. Kanev
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bert Kiewiet
- SAS, Cary, North Carolina
- ITsPeople, Zaltbommel, the Netherlands
| | - Mathilde Kouwenhoven
- Department of Neurology, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - David Noske
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Tom Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Bart A. Westerman
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
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2
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Kiebach J, de Vries-Ten Have J, van Duijnhoven FJB, Kok DE, van Lanen AS, Kouwenhoven EA, de Wilt JHW, Schrauwen RWM, Kampman E, Winkels RM, Wesselink E. Hematocrit Is Associated with Cancer-Related Fatigue in Colorectal Cancer Survivors: A Longitudinal Analysis. Cancer Epidemiol Biomarkers Prev 2024; 33:411-418. [PMID: 38180352 DOI: 10.1158/1055-9965.epi-23-1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Cancer-related fatigue (CRF) is a frequent symptom in colorectal cancer survivors. It is unknown to what extent anemia may contribute to CRF in colorectal cancer survivors. This study aimed to investigate the association between hematocrit, as marker for anemia, and CRF among colorectal cancer survivors from diagnosis until two years thereafter. METHODS The study population included 1,506 newly diagnosed colorectal cancer survivors at any stage of disease from a prospective cohort study. Hematocrit and CRF (EORTC QLQ-C30) were assessed at diagnosis, six months, and two years after diagnosis. Multivariable logistic regression or multivariable linear mixed models were used to assess the associations of hematocrit with CRF prevalence, or CRF severity over time, respectively. RESULTS A low hematocrit (levels <40% men/<36% women) was present in a third of the survivors at diagnosis and six months thereafter, and among 16% two years after diagnosis. The prevalence of CRF was 15% at diagnosis, peaked at 27% at six months, and was 14% two years after diagnosis. Hematocrit was associated with the prevalence of CRF at diagnosis [OR, 0.92; confidence interval (CI), 0.88-0.95], 6 months (OR, 0.89; 95% CI, 0.86-0.92), and 2 years (OR, 0.91; CI, 0.87-0.96) after diagnosis. Lower hematocrit was associated with higher severity of CRF over time (beta-coefficient = 1.3; CI, 1.5-1.1). CONCLUSIONS Lower hematocrit levels were longitudinally associated with a higher prevalence and severity of CRF in colorectal cancer. IMPACT Our findings emphasize the importance of long-term anemia monitoring and a potential role of anemia in CRF among colorectal cancer survivors.
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Affiliation(s)
- Joann Kiebach
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Judith de Vries-Ten Have
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Consumption and Healthy Lifestyles Chair group, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Anne-Sophie van Lanen
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Johannes H W de Wilt
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ruud W M Schrauwen
- Department of Gastroenterology and Hepatology, Bernhoven, Uden, the Netherlands
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Renate M Winkels
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
| | - Evertine Wesselink
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
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Andronikou C, Burdova K, Dibitetto D, Lieftink C, Malzer E, Kuiken HJ, Gogola E, Ray Chaudhuri A, Beijersbergen RL, Hanzlikova H, Jonkers J, Rottenberg S. PARG-deficient tumor cells have an increased dependence on EXO1/FEN1-mediated DNA repair. EMBO J 2024; 43:1015-1042. [PMID: 38360994 PMCID: PMC10943112 DOI: 10.1038/s44318-024-00043-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Targeting poly(ADP-ribose) glycohydrolase (PARG) is currently explored as a therapeutic approach to treat various cancer types, but we have a poor understanding of the specific genetic vulnerabilities that would make cancer cells susceptible to such a tailored therapy. Moreover, the identification of such vulnerabilities is of interest for targeting BRCA2;p53-deficient tumors that have acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) through loss of PARG expression. Here, by performing whole-genome CRISPR/Cas9 drop-out screens, we identify various genes involved in DNA repair to be essential for the survival of PARG;BRCA2;p53-deficient cells. In particular, our findings reveal EXO1 and FEN1 as major synthetic lethal interactors of PARG loss. We provide evidence for compromised replication fork progression, DNA single-strand break repair, and Okazaki fragment processing in PARG;BRCA2;p53-deficient cells, alterations that exacerbate the effects of EXO1/FEN1 inhibition and become lethal in this context. Since this sensitivity is dependent on BRCA2 defects, we propose to target EXO1/FEN1 in PARPi-resistant tumors that have lost PARG activity. Moreover, EXO1/FEN1 targeting may be a useful strategy for enhancing the effect of PARG inhibitors in homologous recombination-deficient tumors.
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Affiliation(s)
- Christina Andronikou
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Kamila Burdova
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Diego Dibitetto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Elke Malzer
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Hana Hanzlikova
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20, Prague 4, Czech Republic
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088, Bern, Switzerland.
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4
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Hummelink K, Tissier R, Bosch LJ, Krijgsman O, van den Heuvel MM, Theelen WS, Damotte D, Goldwasser F, Leroy K, Smit EF, Meijer GA, Thommen DS, Monkhorst K. A Dysfunctional T-cell Gene Signature for Predicting Nonresponse to PD-1 Blockade in Non-small Cell Lung Cancer That Is Suitable for Routine Clinical Diagnostics. Clin Cancer Res 2024; 30:814-823. [PMID: 38088895 PMCID: PMC10870113 DOI: 10.1158/1078-0432.ccr-23-1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/17/2024]
Abstract
PURPOSE Because PD-1 blockade is only effective in a minority of patients with advanced-stage non-small cell lung cancer (NSCLC), biomarkers are needed to guide treatment decisions. Tumor infiltration by PD-1T tumor-infiltrating lymphocytes (TIL), a dysfunctional TIL pool with tumor-reactive capacity, can be detected by digital quantitative IHC and has been established as a novel predictive biomarker in NSCLC. To facilitate translation of this biomarker to the clinic, we aimed to develop a robust RNA signature reflecting a tumor's PD-1T TIL status. EXPERIMENTAL DESIGN mRNA expression analysis using the NanoString nCounter platform was performed in baseline tumor samples from 41 patients with advanced-stage NSCLC treated with nivolumab that were selected on the basis of PD-1T TIL infiltration by IHC. Samples were included as a training cohort (n = 41) to develop a predictive gene signature. This signature was independently validated in a second cohort (n = 42). Primary outcome was disease control at 12 months (DC 12 m), and secondary outcome was progression-free and overall survival. RESULTS Regularized regression analysis yielded a signature using 12 out of 56 differentially expressed genes between PD-1T IHC-high tumors from patients with DC 12 m and PD-1T IHC-low tumors from patients with progressive disease (PD). In the validation cohort, 6/6 (100%) patients with DC 12 m and 23/36 (64%) with PD were correctly classified with a negative predictive value (NPV) of 100% and a positive predictive value of 32%. CONCLUSIONS The PD-1T mRNA signature showed a similar high sensitivity and high NPV as the digital IHC quantification of PD-1T TIL. This finding provides a straightforward approach allowing for easy implementation in a routine diagnostic clinical setting.
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Affiliation(s)
- Karlijn Hummelink
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Renaud Tissier
- Biostatistics Unit, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Linda J.W. Bosch
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michel M. van den Heuvel
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Willemijn S.M.E. Theelen
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Diane Damotte
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - François Goldwasser
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - Karen Leroy
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
- Department of Biochemistry, Hôpital Cochin, Européen Georges Pompidou, APHP Centre, Paris, France
| | - Egbert F. Smit
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniela S. Thommen
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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5
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Castro Eiro MD, Hioki K, Li L, Wilmsen MEP, Kiernan CH, Brouwers-Haspels I, van Meurs M, Zhao M, de Wit H, Grashof DGB, van de Werken HJG, Mueller YM, Schliehe C, Temizoz B, Kobiyama K, Ishii KJ, Katsikis PD. TLR9 plus STING Agonist Adjuvant Combination Induces Potent Neopeptide T Cell Immunity and Improves Immune Checkpoint Blockade Efficacy in a Tumor Model. J Immunol 2024; 212:455-465. [PMID: 38063488 PMCID: PMC10784725 DOI: 10.4049/jimmunol.2300038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 11/10/2023] [Indexed: 01/14/2024]
Abstract
Immune checkpoint blockade (ICB) immunotherapies have emerged as promising strategies for the treatment of cancer; however, there remains a need to improve their efficacy. Determinants of ICB efficacy are the frequency of tumor mutations, the associated neoantigens, and the T cell response against them. Therefore, it is expected that neoantigen vaccinations that boost the antitumor T cell response would improve ICB therapy efficacy. The aim of this study was to develop a highly immunogenic vaccine using pattern recognition receptor agonists in combination with synthetic long peptides to induce potent neoantigen-specific T cell responses. We determined that the combination of the TLR9 agonist K-type CpG oligodeoxynucleotides (K3 CpG) with the STING agonist c-di-AMP (K3/c-di-AMP combination) significantly increased dendritic cell activation. We found that immunizing mice with 20-mer of either an OVA peptide, low-affinity OVA peptides, or neopeptides identified from mouse melanoma or lung mesothelioma, together with K3/c-di-AMP, induced potent Ag-specific T cell responses. The combined K3/c-di-AMP adjuvant formulation induced 10 times higher T cell responses against neopeptides than the TLR3 agonist polyinosinic:polycytidylic acid, a derivative of which is the leading adjuvant in clinical trials of neoantigen peptide vaccines. Moreover, we demonstrated that our K3/c-di-AMP vaccine formulation with 20-mer OVA peptide was capable of controlling tumor growth and improving survival in B16-F10-OVA tumor-bearing C57BL/6 mice and synergized with anti-PD-1 treatment. Together, our findings demonstrate that the K3/c-di-AMP vaccine formulation induces potent T cell immunity against synthetic long peptides and is a promising candidate to improve neoantigen vaccine platform.
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Affiliation(s)
- Melisa D. Castro Eiro
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Kou Hioki
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ling Li
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Merel E. P. Wilmsen
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Caoimhe H. Kiernan
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Inge Brouwers-Haspels
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjan van Meurs
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Manzhi Zhao
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Harm de Wit
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Dwin G. B. Grashof
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Yvonne M. Mueller
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christopher Schliehe
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Burcu Temizoz
- Division of Vaccine Science, Department of Microbiology and Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ken J. Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Peter D. Katsikis
- Department of Immunology; Erasmus University Medical Center, Rotterdam, the Netherlands
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Badhai J, Landman N, Pandey GK, Song JY, Hulsman D, Krijgsman O, Chandrasekaran G, Berns A, van Lohuizen M. Combined Inhibition of EZH2 and FGFR is Synergistic in BAP1-deficient Malignant Mesothelioma. Cancer Res Commun 2024; 4:18-27. [PMID: 38054839 PMCID: PMC10763530 DOI: 10.1158/2767-9764.crc-23-0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/02/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
Malignant mesothelioma is a highly aggressive tumor with a survival of only 4-18 months after diagnosis. Treatment options for this disease are limited. Immune checkpoint blockade using ipilimumab and nivolumab has recently been approved as a frontline therapy, but this led to only a small improvement in overall patient survival. As more than half of patients with mesothelioma have alterations in the gene encoding for BAP1 this could be a potential marker for targeted therapies. In this study, we investigated the synergistic potential of combining EZH2 inhibition together with FGFR inhibition for treatment of BAP1-deficient malignancies. The efficacy of the combination was evaluated using human and murine preclinical models of mesothelioma and uveal melanoma in vitro. The efficacy of the combination was further validated in vivo by using BAP1-deficient mesothelioma xenografts and autochthonous mouse models. In vitro data showed sensitivity to the combined inhibition in BAP1-deficient mesothelioma and uveal melanoma tumor cell lines but not for BAP1-proficient subtypes. In vivo data showed susceptibility to the combination of BAP1-deficient xenografts and demonstrated an increase of survival in autochthonous models of mesothelioma. These results highlight the potential of this novel drug combination for the treatment of mesothelioma using BAP1 as a biomarker. Given these encouraging preclinical results, it will be important to clinically explore dual EZH2/FGFR inhibition in patients with BAP1-deficient malignant mesothelioma and justify further exploration in other BAP1 loss-associated tumors. SIGNIFICANCE Despite the recent approval of immunotherapy, malignant mesothelioma has limited treatment options and poor prognosis. Here, we observe that EZH2 inhibitors dramatically enhance the efficacy of FGFR inhibition, sensitising BAP1-mutant mesothelioma and uveal melanoma cells. The striking synergy of EZH2 and FGFR inhibition supports clinical investigations for BAP1-mutant tumors.
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Affiliation(s)
- Jitendra Badhai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Nick Landman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Gaurav Kumar Pandey
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
- Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Gayathri Chandrasekaran
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
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7
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Zhang Y, Kubiak AM, Bailey TS, Claessen L, Hittmeyer P, Dubois L, Theys J, Lambin P. Development of a CRISPR-Cas12a system for efficient genome engineering in clostridia. Microbiol Spectr 2023; 11:e0245923. [PMID: 37947521 PMCID: PMC10715149 DOI: 10.1128/spectrum.02459-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Continued efforts in developing the CRISPR-Cas systems will further enhance our understanding and utilization of Clostridium species. This study demonstrates the development and application of a genome-engineering tool in two Clostridium strains, Clostridium butyricum and Clostridium sporogenes, which have promising potential as probiotics and oncolytic agents. Particular attention was given to the folding of precursor crRNA and the role of this process in off-target DNA cleavage by Cas12a. The results provide the guidelines necessary for efficient genome engineering using this system in clostridia. Our findings not only expand our fundamental understanding of genome-engineering tools in clostridia but also improve this technology to allow use of its full potential in a plethora of biotechnological applications.
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Affiliation(s)
- Yanchao Zhang
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aleksandra M. Kubiak
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Exomnis Biotech BV, Maastricht, The Netherlands
| | - Tom S. Bailey
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Luuk Claessen
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Philip Hittmeyer
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Ludwig Dubois
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Jan Theys
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Philippe Lambin
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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8
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van der Pol Y, Tantyo NA, Evander N, Hentschel AE, Wever BM, Ramaker J, Bootsma S, Fransen MF, Lenos KJ, Vermeulen L, Schneiders FL, Bahce I, Nieuwenhuijzen JA, Steenbergen RD, Pegtel DM, Moldovan N, Mouliere F. Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing. EMBO Mol Med 2023; 15:e17282. [PMID: 37942753 DOI: 10.15252/emmm.202217282] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability and speed and can be biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) sequencing we can achieve delivery of genomic and fragmentomic data from liquid biopsies. Copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 h from sample collection. The tumor-derived cfDNA fraction calculated from plasma of lung cancer patients and urine of bladder cancer patients was highly correlated (R = 0.98) with the tumor fraction calculated from short-read sequencing of the same samples. cfDNA size profile, fragmentation patterns, fragment-end composition, and nucleosome profiling near transcription start sites in plasma and urine exhibited the typical cfDNA features. Additionally, a high proportion of long tumor-derived cfDNA fragments (> 300 bp) are recovered in plasma and urine using ONT sequencing. ONT sequencing is a cost-effective, fast, and deployable approach for obtaining genomic and fragmentomic results from liquid biopsies, allowing the analysis of previously understudied cfDNA populations.
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Affiliation(s)
- Ymke van der Pol
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Normastuti Adhini Tantyo
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Nils Evander
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Anouk E Hentschel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Birgit Mm Wever
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jip Ramaker
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Marieke F Fransen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Famke L Schneiders
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Idris Bahce
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jakko A Nieuwenhuijzen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Renske Dm Steenbergen
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Norbert Moldovan
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Florent Mouliere
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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9
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Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
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Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Center for Molecular MedicineUMC UtrechtUtrechtThe Netherlands
| | | | - Merel Roest
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel Roden
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja Tesselaar
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maliha Wajahat
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Isabel Mayayo‐Peralta
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Gabriela Gomez
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
| | - Maarten Altelaar
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening CentreNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Balázs Győrffy
- TTK Cancer Biomarker Research GroupInstitute of EnzymologyBudapestHungary
- Department of Bioinformatics and 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Leonie Young
- Endocrine Oncology Research Group, Department of SurgeryThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Sabine Linn
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Freemasons Centre for Male Health and WellbeingUniversity of AdelaideAdelaideSAAustralia
| | - Theresa Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Damir Vareslija
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Alexander Swarbrick
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
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10
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Jamieson A, Vermij L, Kramer CJ, Jobsen JJ, Jürgemlienk-Schulz I, Lutgens L, Mens JW, Haverkort MA, Slot A, Nout RA, Oosting J, Carlson J, Howitt BE, Ip PP, Lax SF, McCluggage WG, Singh N, McAlpine JN, Creutzberg CL, Horeweg N, Gilks CB, Bosse T. Clinical Behavior and Molecular Landscape of Stage I p53-Abnormal Low-Grade Endometrioid Endometrial Carcinomas. Clin Cancer Res 2023; 29:4949-4957. [PMID: 37773079 PMCID: PMC10690141 DOI: 10.1158/1078-0432.ccr-23-1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/09/2023] [Accepted: 09/25/2023] [Indexed: 09/30/2023]
Abstract
PURPOSE The clinical significance of the p53-abnormal (p53abn) molecular subtype in stage I low-grade endometrioid endometrial carcinoma (EEC) is debated. We aimed to review pathologic and molecular characteristics, and outcomes of stage I low-grade p53abn EEC in a large international cohort. EXPERIMENTAL DESIGN Previously diagnosed stage I p53abn EC (POLE-wild-type, mismatch repair-proficient) low-grade EEC from Canadian retrospective cohorts and PORTEC-1&2 trials were included. Pathology review was performed by six expert gynecologic pathologists blinded to p53 status. IHC profiling, next-generation sequencing, and shallow whole-genome sequencing was performed. Kaplan-Meier method was used for survival analysis. RESULTS We identified 55 stage I p53abn low-grade EEC among 3,387 cases (2.5%). On pathology review, 17 cases (31%) were not diagnosed as low-grade EEC by any pathologists, whereas 26 cases (47%) were diagnosed as low-grade EEC by at least three pathologists. The IHC and molecular profile of the latter cases were consistent with low-grade EEC morphology (ER/PR positivity, patchy p16 expression, PIK3CA and PTEN mutations) but they also showed features of p53abn EC (TP53 mutations, many copy-number alterations). These cases had a clinically relevant risk of disease recurrence (5-year recurrence-free survival 77%), with pelvic and/or distant recurrences observed in 12% of the patients. CONCLUSIONS A subset of p53abn EC is morphologically low-grade EEC and exhibit genomic instability. Even for stage I disease, p53abn low-grade EEC are at substantial risk of disease recurrence. These findings highlight the clinical relevance of universal p53-testing, even in low-grade EEC, to identify women at increased risk of recurrence.
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Affiliation(s)
- Amy Jamieson
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, Canada
| | - Lisa Vermij
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Claire J.H. Kramer
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan J. Jobsen
- Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Ina Jürgemlienk-Schulz
- Department of Radiation Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Jan Willem Mens
- Department of Radiation Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Annerie Slot
- Radiotherapeutic Institute Friesland, Leeuwarden, the Netherlands
| | - Remi A. Nout
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joseph Carlson
- Department of Pathology, University of Southern California, Los Angeles
| | - Brooke E. Howitt
- Department of Pathology, Stanford University School of Medicine, Palo Alto
| | - Philip P.C. Ip
- Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sigurd F. Lax
- Department of Pathology, Hospital Graz II, Medical University of Graz, Graz, and Johannes Kepler University, Linz, Austria
| | - W. Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, United Kingdom
| | - Naveena Singh
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jessica N. McAlpine
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, Canada
| | - Carien L. Creutzberg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nanda Horeweg
- Department of Radiation Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - C. Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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11
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Spaan CN, de Boer RJ, Smit WL, van der Meer JH, van Roest M, Vermeulen JL, Koelink PJ, Becker MA, Go S, Silva J, Faller WJ, van den Brink GR, Muncan V, Heijmans J. Grp78 is required for intestinal Kras-dependent glycolysis proliferation and adenomagenesis. Life Sci Alliance 2023; 6:e202301912. [PMID: 37643866 PMCID: PMC10465924 DOI: 10.26508/lsa.202301912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
In development of colorectal cancer, mutations in APC are often followed by mutations in oncogene KRAS The latter changes cellular metabolism and is associated with the Warburg phenomenon. Glucose-regulated protein 78 (Grp78) is an important regulator of the protein-folding machinery, involved in processing and localization of transmembrane proteins. We hypothesize that targeting Grp78 in Apc and Kras (AK)-mutant intestines interferes with the metabolic phenotype imposed by Kras mutations. In mice with intestinal epithelial mutations in Apc, Kras G12D and heterozygosity for Grp78 (AK-Grp78 HET ) adenoma number and size is decreased compared with AK-Grp78 WT mice. Organoids from AK-Grp78 WT mice exhibited a glycolysis metabolism which was completely rescued by Grp78 heterozygosity. Expression and correct localization of glucose transporter GLUT1 was diminished in AK-Grp78 HET cells. GLUT1 inhibition restrained the increased growth observed in AK-mutant organoids, whereas AK-Grp78 HET organoids were unaffected. We identify Grp78 as a critical factor in Kras-mutated adenomagenesis. This can be attributed to a critical role for Grp78 in GLUT1 expression and localization, targeting glycolysis and the Warburg effect.
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Affiliation(s)
- Claudia N Spaan
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Ruben J de Boer
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Wouter L Smit
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jonathan Hm van der Meer
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Manon van Roest
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jacqueline Lm Vermeulen
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Pim J Koelink
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Marte Aj Becker
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Simei Go
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Joana Silva
- Department of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - William J Faller
- Department of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Gijs R van den Brink
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Vanesa Muncan
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Jarom Heijmans
- https://ror.org/05grdyy37 Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, Netherlands
- https://ror.org/05grdyy37 Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, Netherlands
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12
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van den Bulk J, Verdegaal EM, van der Ploeg M, Visser M, Nunes JB, de Ru AH, Tjokrodirijo RT, Ijsselsteijn ME, Janssen NI, van der Breggen R, de Bruin L, de Kok P, Janssen GM, Ruano D, Kapiteijn EH, van Veelen PA, de Miranda NF, van der Burg SH. Neoantigen Targetability in Progressive Advanced Melanoma. Clin Cancer Res 2023; 29:4278-4288. [PMID: 37540567 PMCID: PMC10570682 DOI: 10.1158/1078-0432.ccr-23-1106] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/23/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
PURPOSE The availability of (neo)antigens and the infiltration of tumors by (neo)antigen-specific T cells are crucial factors in cancer immunotherapy. In this study, we aimed to investigate the targetability of (neo)antigens in advanced progessive melanoma and explore the potential for continued T-cell-based immunotherapy. EXPERIMENTAL DESIGN We examined a cohort of eight patients with melanoma who had sequential metastases resected at early and later time points. Antigen-presenting capacity was assessed using IHC and flow cytometry. T-cell infiltration was quantified through multiplex immunofluorescence. Whole-exome and RNA sequencing were conducted to identify neoantigens and assess the expression of neoantigens and tumor-associated antigens. Mass spectrometry was used to evaluate antigen presentation. Tumor recognition by autologous T cells was assessed by coculture assays with cell lines derived from the metastatic lesions. RESULTS We observed similar T-cell infiltration in paired early and later metastatic (LM) lesions. Although elements of the antigen-presenting machinery were affected in some LM lesions, both the early and later metastasis-derived cell lines were recognized by autologous T cells. At the genomic level, the (neo)antigen landscape was dynamic, but the (neo)antigen load was stable between paired lesions. CONCLUSIONS Our findings indicate that subsequently isolated tumors from patients with late-stage melanoma retain sufficient antigen-presenting capacity, T-cell infiltration, and a stable (neo)antigen load, allowing recognition of tumor cells by T cells. This indicates a continuous availability of T-cell targets in metastases occurring at different time points and supports further exploration of (neo)antigen-specific T-cell-based therapeutic approaches for advanced melanoma.
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Affiliation(s)
- Jitske van den Bulk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els M.E. Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marten Visser
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Joana B. Nunes
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud H. de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Rayman T.N. Tjokrodirijo
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Natasja I. Janssen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ruud van der Breggen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Linda de Bruin
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Pita de Kok
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - George M.C. Janssen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen H.W. Kapiteijn
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A. van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Sjoerd H. van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
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13
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Lefrère H, Moore K, Floris G, Sanders J, Seignette IM, Bismeijer T, Peters D, Broeks A, Hooijberg E, Van Calsteren K, Neven P, Warner E, Peccatori FA, Loibl S, Maggen C, Han SN, Jerzak KJ, Annibali D, Lambrechts D, de Visser KE, Wessels L, Lenaerts L, Amant F. Poor Outcome in Postpartum Breast Cancer Patients Is Associated with Distinct Molecular and Immunologic Features. Clin Cancer Res 2023; 29:3729-3743. [PMID: 37449970 PMCID: PMC10502474 DOI: 10.1158/1078-0432.ccr-22-3645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/23/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Patients with postpartum breast cancer diagnosed after cessation of breastfeeding (postweaning, PP-BCPW) have a particularly poor prognosis compared with patients diagnosed during lactation (PP-BCDL), or to pregnant (Pr-BC) and nulliparous (NP-BC) patients, regardless of standard prognostic characteristics. Animal studies point to a role of the involution process in stimulation of tumor growth in the mammary gland. However, in women, the molecular mechanisms that underlie this poor prognosis of patients with PP-BCPW remain vastly underexplored, due to of lack of adequate patient numbers and outcome data. EXPERIMENTAL DESIGN We explored whether distinct prognostic features, common to all breast cancer molecular subtypes, exist in postpartum tumor tissue. Using detailed breastfeeding data, we delineated the postweaning period in PP-BC as a surrogate for mammary gland involution and performed whole transcriptome sequencing, immunohistochemical, and (multiplex) immunofluorescent analyses on tumor tissue of patients with PP-BCPW, PP-BCDL, Pr-BC, and NP-BC. RESULTS We found that patients with PP-BCPW having a low expression level of an immunoglobulin gene signature, but high infiltration of plasma B cells, have an increased risk for metastasis and death. Although PP-BCPW tumor tissue was also characterized by an increase in CD8+ cytotoxic T cells and reduced distance among these cell types, these parameters were not associated with differential clinical outcomes among groups. CONCLUSIONS These data point to the importance of plasma B cells in the postweaning mammary tumor microenvironment regarding the poor prognosis of PP-BCPW patients. Future prospective and in-depth research needs to further explore the role of B-cell immunobiology in this specific group of young patients with breast cancer.
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Affiliation(s)
- Hanne Lefrère
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
- Department of Gynaecology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kat Moore
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giuseppe Floris
- Department of Imaging and Pathology, Unit of Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, Unit of Translational Cell & Tissue Research, University Hospitals Leuven, Leuven, Belgium
- Multidisciplinary Breast Centre, UZ-KU Leuven Cancer Institute (LKI), University Hospitals Leuven, Leuven, Belgium
| | - Joyce Sanders
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Iris M. Seignette
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dennis Peters
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Erik Hooijberg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kristel Van Calsteren
- Departement of Reproduction and regeneration, Division Women and Child, Feto-Maternal Medicine, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
- Multidisciplinary Breast Centre, UZ-KU Leuven Cancer Institute (LKI), University Hospitals Leuven, Leuven, Belgium
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Ellen Warner
- Division of Medical Oncology, Department of Medicine, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Fedro Alessandro Peccatori
- Division of Gynaecological Oncology, Department of Gynaecology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Sibylle Loibl
- German Breast Group, Neu-Isenburg, Hessen, Germany
- Centre for Haematology and Oncology Bethanien, Frankfurt, Germany
| | - Charlotte Maggen
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
- Department of Obstetrics and Prenatal Medicine, University Hospital Brussels, Brussels, Belgium
| | - Sileny N. Han
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Katarzyna J. Jerzak
- Division of Medical Oncology, Department of Medicine, Sunnybrook Odette Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Daniela Annibali
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Karin E. de Visser
- Oncode Institute, Utrecht, The Netherlands
- Division of Tumour Biology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Liesbeth Lenaerts
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
| | - Frédéric Amant
- Department of Oncology, Laboratory of Gynaecological Oncology, KU Leuven, Leuven, Belgium
- Department of Gynaecology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Gynaecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
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14
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Chen L, Pronk E, van Dijk C, Bian Y, Feyen J, van Tienhoven T, Yildirim M, Pisterzi P, de Jong MM, Bastidas A, Hoogenboezem RM, Wevers C, Bindels EM, Löwenberg B, Cupedo T, Sanders MA, Raaijmakers MH. A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML. Blood Cancer Discov 2023; 4:394-417. [PMID: 37470778 PMCID: PMC10472197 DOI: 10.1158/2643-3230.bcd-23-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/09/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Cancer initiation is orchestrated by an interplay between tumor-initiating cells and their stromal/immune environment. Here, by adapted single-cell RNA sequencing, we decipher the predicted signaling between tissue-resident hematopoietic stem/progenitor cells (HSPC) and their neoplastic counterparts with their native niches in the human bone marrow. LEPR+ stromal cells are identified as central regulators of hematopoiesis through predicted interactions with all cells in the marrow. Inflammatory niche remodeling and the resulting deprivation of critical HSPC regulatory factors are predicted to repress high-output hematopoietic stem cell subsets in NPM1-mutated acute myeloid leukemia (AML), with relative resistance of clonal cells. Stromal gene signatures reflective of niche remodeling are associated with reduced relapse rates and favorable outcomes after chemotherapy across all genetic risk categories. Elucidation of the intercellular signaling defining human AML, thus, predicts that inflammatory remodeling of stem cell niches drives tissue repression and clonal selection but may pose a vulnerability for relapse-initiating cells in the context of chemotherapeutic treatment. SIGNIFICANCE Tumor-promoting inflammation is considered an enabling characteristic of tumorigenesis, but mechanisms remain incompletely understood. By deciphering the predicted signaling between tissue-resident stem cells and their neoplastic counterparts with their environment, we identify inflammatory remodeling of stromal niches as a determinant of normal tissue repression and clinical outcomes in human AML. See related commentary by Lisi-Vega and Méndez-Ferrer, p. 349. This article is featured in Selected Articles from This Issue, p. 337.
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Affiliation(s)
- Lanpeng Chen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eline Pronk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Claire van Dijk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Yujie Bian
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Jacqueline Feyen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tim van Tienhoven
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Meltem Yildirim
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Paola Pisterzi
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Madelon M.E. de Jong
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Alejandro Bastidas
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Chiel Wevers
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eric M. Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tom Cupedo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mathijs A. Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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15
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de Vries I, Ammerlaan D, Heidebrecht T, Celie PH, Geerke DP, Joosten RP, Perrakis A. Distant sequence regions of JBP1 contribute to J-DNA binding. Life Sci Alliance 2023; 6:e202302150. [PMID: 37328191 PMCID: PMC10276184 DOI: 10.26508/lsa.202302150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
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Affiliation(s)
- Ida de Vries
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Danique Ammerlaan
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick Hn Celie
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
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16
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Boyd LNC, Ali M, Puik JR, Meijer LL, Le Large TYS, van Laarhoven HWM, Giovannetti E, Kazemier G. hENT1 as a Predictive Biomarker in PDAC-Letter. Clin Cancer Res 2023; 29:2944. [PMID: 37525961 DOI: 10.1158/1078-0432.ccr-22-3827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 08/02/2023]
Affiliation(s)
- Lenka N C Boyd
- Amsterdam UMC, location Vrije Universiteit, Department of Surgery, Amsterdam, the Netherlands
- Amsterdam UMC, location Vrije Universiteit, Department of Medical Oncology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Mahsoem Ali
- Amsterdam UMC, location Vrije Universiteit, Department of Surgery, Amsterdam, the Netherlands
- Amsterdam UMC, location Vrije Universiteit, Department of Medical Oncology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Jisce R Puik
- Amsterdam UMC, location Vrije Universiteit, Department of Surgery, Amsterdam, the Netherlands
- Amsterdam UMC, location Vrije Universiteit, Department of Medical Oncology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Laura L Meijer
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Tessa Y S Le Large
- Amsterdam UMC, location Vrije Universiteit, Department of Surgery, Amsterdam, the Netherlands
- Amsterdam UMC, location Vrije Universiteit, Department of Medical Oncology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Hanneke W M van Laarhoven
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Oncology, the Netherlands
| | - Elisa Giovannetti
- Amsterdam UMC, location Vrije Universiteit, Department of Medical Oncology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Geert Kazemier
- Amsterdam UMC, location Vrije Universiteit, Department of Surgery, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
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17
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Truong MA, Cané-Gasull P, de Vries SG, Nijenhuis W, Wardenaar R, Kapitein LC, Foijer F, Lens SM. A kinesin-based approach for inducing chromosome-specific mis-segregation in human cells. EMBO J 2023; 42:e111559. [PMID: 37038978 PMCID: PMC10183822 DOI: 10.15252/embj.2022111559] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 04/12/2023] Open
Abstract
Various cancer types exhibit characteristic and recurrent aneuploidy patterns. The origins of these cancer type-specific karyotypes are still unknown, partly because introducing or eliminating specific chromosomes in human cells still poses a challenge. Here, we describe a novel strategy to induce mis-segregation of specific chromosomes in different human cell types. We employed Tet repressor or nuclease-dead Cas9 to link a microtubule minus-end-directed kinesin (Kinesin14VIb) from Physcomitrella patens to integrated Tet operon repeats and chromosome-specific endogenous repeats, respectively. By live- and fixed-cell imaging, we observed poleward movement of the targeted loci during (pro)metaphase. Kinesin14VIb-mediated pulling forces on the targeted chromosome were counteracted by forces from kinetochore-attached microtubules. This tug-of-war resulted in chromosome-specific segregation errors during anaphase and revealed that spindle forces can heavily stretch chromosomal arms. By single-cell whole-genome sequencing, we established that kinesin-induced targeted mis-segregations predominantly result in chromosomal arm aneuploidies after a single cell division. Our kinesin-based strategy opens the possibility to investigate the immediate cellular responses to specific aneuploidies in different cell types; an important step toward understanding how tissue-specific aneuploidy patterns evolve.
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Affiliation(s)
- My Anh Truong
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sippe G de Vries
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wilco Nijenhuis
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Susanne Ma Lens
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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18
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Buoninfante OA, Pilzecker B, Spanjaard A, de Groot D, Prekovic S, Song JY, Lieftink C, Ayidah M, Pritchard CEJ, Vivié J, Mcgrath KE, Huijbers IJ, Philipsen S, von Lindern M, Zwart W, Beijersbergen R, Palis J, van den Berk PCM, Jacobs H. Mammalian life depends on two distinct pathways of DNA damage tolerance. Proc Natl Acad Sci U S A 2023; 120:e2216055120. [PMID: 36669105 PMCID: PMC9942833 DOI: 10.1073/pnas.2216055120] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA damage threatens genomic integrity and instigates stem cell failure. To bypass genotoxic lesions during replication, cells employ DNA damage tolerance (DDT), which is regulated via PCNA ubiquitination and REV1. DDT is conserved in all domains of life, yet its relevance in mammals remains unclear. Here, we show that inactivation of both PCNA-ubiquitination and REV1 results in embryonic and adult lethality, and the accumulation of DNA damage in hematopoietic stem and progenitor cells (HSPCs) that ultimately resulted in their depletion. Our results reveal the crucial relevance of DDT in the maintenance of stem cell compartments and mammalian life in unperturbed conditions.
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Affiliation(s)
| | - Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Daniël de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, 3584 CXUtrecht, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Matilda Ayidah
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Colin E. J. Pritchard
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, 1066 CXAmsterdam, The Netherlands
| | - Judith Vivié
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, 3584 CTUtrecht, The Netherlands
| | - Kathleen E. Mcgrath
- Department of Pediatrics, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY14642
| | - Ivo J. Huijbers
- Mouse Clinic for Cancer and Aging Research, Transgenic Facility, The Netherlands Cancer Institute, 1066 CXAmsterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus Medical Center, 3015CNRotterdam, The Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratories, 1066CXAmsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, NY14642
| | - Paul C. M. van den Berk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066CXAmsterdam, The Netherlands
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19
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Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep 2021; 22:e51913. [PMID: 33890711 PMCID: PMC8183412 DOI: 10.15252/embr.202051913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/- ) CRC models and an indirect co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that the absence of Ndrg4 does not trigger any functional or morphological GI abnormalities. However, combining in vivo, in vitro, and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance migration capacities of CRC cells, and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
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Affiliation(s)
- Nathalie Vaes
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Simone L Schonkeren
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Glenn Rademakers
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Amy M Holland
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Marion J Gijbels
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Molecular GeneticsCardiovascular Research Institute Maastricht (CARIM)MaastrichtThe Netherlands
- Department of Medical BiochemistryAcademic Medical CenterAmsterdamThe Netherlands
| | - Tom G Keulers
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Meike de Wit
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Laura Moonen
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jaleesa R M Van der Meer
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Edith van den Boezem
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Tim G A M Wolfs
- Department of PediatricsGROW‐School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - David W Threadgill
- Department of Molecular and Cellular MedicineTexas A&M University Health Science CenterCollege StationTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Jeroen Demmers
- Proteomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS) and Translational Research Center for Gastrointestinal Disorders (TARGID)Department of Chronic Diseases, Metabolism and AgeingKU LeuvenLeuvenBelgium
| | - Kim M Smits
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Kasper M A Rouschop
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Werend Boesmans
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Biomedical Research Institute (BIOMED)Hasselt UniversityHasseltBelgium
| | - Robert M W Hofstra
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
| | - Veerle Melotte
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
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