1
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Geurts BS, Zeverijn LJ, Leek LVM, van Berge Henegouwen JM, Hoes LR, van der Wijngaart H, van der Noort V, van de Haar J, van Ommen-Nijhof A, Kok M, Roepman P, Jansen AML, de Leng WWJ, de Jonge MJA, Hoeben A, van Herpen CML, Westgeest HM, Wessels LFA, Verheul HMW, Gelderblom H, Voest EE. Efficacy of pembrolizumab and biomarker analysis in patients with WGS-based intermediate to high tumor mutational load: results from the Drug Rediscovery Protocol. Clin Cancer Res 2024:743079. [PMID: 38630551 DOI: 10.1158/1078-0432.ccr-24-0011] [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] [Received: 01/05/2024] [Revised: 02/25/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
PURPOSE To evaluate efficacy of pembrolizumab across multiple cancer types harboring different levels of Whole-Genome Sequencing (WGS)-based tumor mutational load (TML; total of non-synonymous mutations across the genome) in patients included in the Drug Rediscovery Protocol (NCT02925234). PATIENTS AND METHODS Patients with solid, treatment-refractory, microsatellite-stable tumors were enrolled in cohort A: breast cancer TML 140-290, cohort B: tumor-agnostic cohort TML 140-290, and cohort C: tumor-agnostic cohort TML >290. Patients received pembrolizumab 200 mg every three weeks. Primary endpoint was clinical benefit (CB: objective response or stable disease (SD) ≥16 weeks). Pre-treatment tumor biopsies were obtained for WGS and RNA-sequencing. RESULTS Seventy-two evaluable patients with 26 different histotypes were enrolled. CB rate was 13% in cohort A (3/24 with partial response (PR)), 21% in cohort B (3/24 with SD, 2/24 with PR), and 42% in cohort C (4/24 with SD, 6/24 with PR). In cohort C, neoantigen burden estimates and expression of inflammation and innate immune biomarkers were significantly associated with CB. Similar associations were not identified in cohort A and B. In cohort A, CB was significantly associated with mutations in the chromatin remodeling gene PBRM1, while in cohort B, CB was significantly associated with expression of MICA/MICB and butyrophilins. CB and clonal TML were not significantly associated. CONCLUSION While in cohort A pembrolizumab lacked activity, cohort B and cohort C met the study's primary endpoint. Further research is warranted to refine selection of patients with tumors harboring lower TMLs and may benefit from a focus on innate immunity.
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Affiliation(s)
| | | | | | | | - Louisa R Hoes
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Joris van de Haar
- The Netherlands Cancer Institute, Amsterdam, Noord-Holland, Netherlands
| | | | - Marleen Kok
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Anne M L Jansen
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | | | | | - Ann Hoeben
- Maastricht University Medical Centre, Maastricht, Netherlands
| | | | | | | | | | | | - Emile E Voest
- Netherlands Cancer Institute, Amsterdam, Netherlands
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2
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Gil-Jimenez A, van Dijk N, Vos JL, Lubeck Y, van Montfoort ML, Peters D, Hooijberg E, Broeks A, Zuur CL, van Rhijn BWG, Vis DJ, van der Heijden MS, Wessels LFA. Spatial relationships in the urothelial and head and neck tumor microenvironment predict response to combination immune checkpoint inhibitors. Nat Commun 2024; 15:2538. [PMID: 38514623 PMCID: PMC10957922 DOI: 10.1038/s41467-024-46450-1] [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: 05/09/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) can achieve remarkable responses in urothelial cancer (UC), which may depend on tumor microenvironment (TME) characteristics. However, the relationship between the TME, usually characterized by immune cell density, and response to ICI is unclear. Here, we quantify the TME immune cell densities and spatial relationships (SRs) of 24 baseline UC samples, obtained before pre-operative combination ICI treatment, using multiplex immunofluorescence. We describe SRs by approximating the first nearest-neighbor distance distribution with a Weibull distribution and evaluate the association between TME metrics and ipilimumab+nivolumab response. Immune cell density does not discriminate between response groups. However, the Weibull SR metrics of CD8+ T cells or macrophages to their closest cancer cell positively associate with response. CD8+ T cells close to B cells are characteristic of non-response. We validate our SR response associations in a combination ICI cohort of head and neck tumors. Our data confirm that SRs, in contrast to density metrics, are strong biomarkers of response to pre-operative combination ICIs.
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Affiliation(s)
- Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Nick van Dijk
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris L Vos
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yoni Lubeck
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Dennis Peters
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Erik Hooijberg
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Charlotte L Zuur
- Department of Head and Neck Surgery and Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas W G van Rhijn
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Urology, Caritas St. Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - Daniel J Vis
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands.
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3
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Gaillard DHK, Lof P, Sistermans EA, Mokveld T, Horlings HM, Mom CH, Reinders MJT, Amant F, van den Broek D, Wessels LFA, Lok CAR. Evaluating the effectiveness of pre-operative diagnosis of ovarian cancer using minimally invasive liquid biopsies by combining serum human epididymis protein 4 and cell-free DNA in patients with an ovarian mass. Int J Gynecol Cancer 2024:ijgc-2023-005073. [PMID: 38388177 DOI: 10.1136/ijgc-2023-005073] [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] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVE To assess the feasibility of scalable, objective, and minimally invasive liquid biopsy-derived biomarkers such as cell-free DNA copy number profiles, human epididymis protein 4 (HE4), and cancer antigen 125 (CA125) for pre-operative risk assessment of early-stage ovarian cancer in a clinically representative and diagnostically challenging population and to compare the performance of these biomarkers with the Risk of Malignancy Index (RMI). METHODS In this case-control study, we included 100 patients with an ovarian mass clinically suspected to be early-stage ovarian cancer. Of these 100 patients, 50 were confirmed to have a malignant mass (cases) and 50 had a benign mass (controls). Using WisecondorX, an algorithm used extensively in non-invasive prenatal testing, we calculated the benign-calibrated copy number profile abnormality score. This score represents how different a sample is from benign controls based on copy number profiles. We combined this score with HE4 serum concentration to separate cases and controls. RESULTS Combining the benign-calibrated copy number profile abnormality score with HE4, we obtained a model with a significantly higher sensitivity (42% vs 0%; p<0.002) at 99% specificity as compared with the RMI that is currently employed in clinical practice. Investigating performance in subgroups, we observed especially large differences in the advanced stage and non-high-grade serous ovarian cancer groups. CONCLUSION This study demonstrates that cell-free DNA can be successfully employed to perform pre-operative risk of malignancy assessment for ovarian masses; however, results warrant validation in a more extensive clinical study.
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Affiliation(s)
- Duco H K Gaillard
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Pien Lof
- Department of Gynecological Oncology, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Reproduction & Development, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Tom Mokveld
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Hugo Mark Horlings
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Constantijne H Mom
- Department of Gynecological Oncology, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Frédéric Amant
- Department of Gynecological Oncology, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
- Division of Gynecologic Oncology, UZ Leuven, Leuven, Belgium
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christianne A R Lok
- Department of Gynecological Oncology, Center for Gynecologic Oncology Amsterdam, Amsterdam, Netherlands
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4
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Hoekstra ME, Slagter M, Urbanus J, Toebes M, Slingerland N, de Rink I, Kluin RJC, Nieuwland M, Kerkhoven R, Wessels LFA, Schumacher TN. Distinct spatiotemporal dynamics of CD8 + T cell-derived cytokines in the tumor microenvironment. Cancer Cell 2024; 42:157-167.e9. [PMID: 38194914 PMCID: PMC10783802 DOI: 10.1016/j.ccell.2023.12.010] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 10/13/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024]
Abstract
Cells in the tumor microenvironment (TME) influence each other through secretion and sensing of soluble mediators, such as cytokines and chemokines. While signaling of interferon γ (IFNγ) and tumor necrosis factor α (TNFα) is integral to anti-tumor immune responses, our understanding of the spatiotemporal behavior of these cytokines is limited. Here, we describe a single cell transcriptome-based approach to infer which signal(s) an individual cell has received. We demonstrate that, contrary to expectations, CD8+ T cell-derived IFNγ is the dominant modifier of the TME relative to TNFα. Furthermore, we demonstrate that cell pools that show abundant IFNγ sensing are characterized by decreased expression of transforming growth factor β (TGFβ)-induced genes, consistent with IFNγ-mediated TME remodeling. Collectively, these data provide evidence that CD8+ T cell-secreted cytokines should be categorized into local and global tissue modifiers, and describe a broadly applicable approach to dissect cytokine and chemokine modulation of the TME.
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Affiliation(s)
- Mirjam E Hoekstra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten Slagter
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mireille Toebes
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nadine Slingerland
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Iris de Rink
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ron Kerkhoven
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of EEMCS, Delft University of Technology, Delft, the Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
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5
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Liefaard MC, Moore KS, Mulder L, van den Broek D, Wesseling J, Sonke GS, Wessels LFA, Rookus M, Lips EH. Correction To: Tumour-educated platelets for breast cancer detection: biological and technical insights. Br J Cancer 2023; 129:734. [PMID: 37488450 PMCID: PMC10421922 DOI: 10.1038/s41416-023-02371-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Affiliation(s)
- Marte C Liefaard
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kat S Moore
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Clinical Chemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Matti Rookus
- Department of Psychosocial and Epidemiology Research, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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6
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Bhin J, Paes Dias M, Gogola E, Rolfs F, Piersma SR, de Bruijn R, de Ruiter JR, van den Broek B, Duarte AA, Sol W, van der Heijden I, Andronikou C, Kaiponen TS, Bakker L, Lieftink C, Morris B, Beijersbergen RL, van de Ven M, Jimenez CR, Wessels LFA, Rottenberg S, Jonkers J. Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors. Cell Rep 2023; 42:112538. [PMID: 37209095 DOI: 10.1016/j.celrep.2023.112538] [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: 09/06/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis), but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combine molecular profiling with functional analysis of HR of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent reactivation of BRCA1/2. We observe restoration of HR in 62% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we find that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by PARG loss. Furthermore, combined multi-omics analysis identifies additional genes and pathways potentially involved in modulating PARPi response.
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Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mariana Paes Dias
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Bram van den Broek
- Division of Cell Biology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alexandra A Duarte
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wendy Sol
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Christina Andronikou
- Division of Molecular Pathology, Oncode Institute, 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; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Taina S Kaiponen
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Lara Bakker
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, 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; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
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7
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Hutten SJ, de Bruijn R, Lutz C, Badoux M, Eijkman T, Chao X, Ciwinska M, Sheinman M, Messal H, Herencia-Ropero A, Kristel P, Mulder L, van der Waal R, Sanders J, Almekinders MM, Llop-Guevara A, Davies HR, van Haren MJ, Martin NI, Behbod F, Nik-Zainal S, Serra V, van Rheenen J, Lips EH, Wessels LFA, Wesseling J, Scheele CLGJ, Jonkers J. A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression. Cancer Cell 2023; 41:986-1002.e9. [PMID: 37116492 PMCID: PMC10171335 DOI: 10.1016/j.ccell.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/21/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer (IBC). Due to a lack of biomarkers able to distinguish high- from low-risk cases, DCIS is treated similar to early IBC even though the minority of untreated cases eventually become invasive. Here, we characterized 115 patient-derived mouse-intraductal (MIND) DCIS models reflecting the full spectrum of DCIS observed in patients. Utilizing the possibility to follow the natural progression of DCIS combined with omics and imaging data, we reveal multiple prognostic factors for high-risk DCIS including high grade, HER2 amplification, expansive 3D growth, and high burden of copy number aberrations. In addition, sequential transplantation of xenografts showed minimal phenotypic and genotypic changes over time, indicating that invasive behavior is an intrinsic phenotype of DCIS and supporting a multiclonal evolution model. Moreover, this study provides a collection of 19 distributable DCIS-MIND models spanning all molecular subtypes.
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Affiliation(s)
- Stefan J Hutten
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Madelon Badoux
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Timo Eijkman
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Xue Chao
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Marta Ciwinska
- Center for Cancer Biology, VIB, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Michael Sheinman
- Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Hendrik Messal
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Andrea Herencia-Ropero
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Barcelona, Spain
| | - Petra Kristel
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rens van der Waal
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joyce Sanders
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mathilde M Almekinders
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Helen R Davies
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, CB2 0QQ Cambridge, UK; Early Cancer Institute, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2302 BH Leiden, the Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, 2302 BH Leiden, the Netherlands
| | - Fariba Behbod
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, CB2 0QQ Cambridge, UK; Early Cancer Institute, University of Cambridge, CB2 0XZ Cambridge, UK
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jacco van Rheenen
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Diagnostic Oncology, Netherlands Cancer Institute - Antonie van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Colinda L G J Scheele
- Center for Cancer Biology, VIB, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands.
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8
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van Nee MM, Wessels LFA, van de Wiel MA. ecpc: an R-package for generic co-data models for high-dimensional prediction. BMC Bioinformatics 2023; 24:172. [PMID: 37101151 PMCID: PMC10134536 DOI: 10.1186/s12859-023-05289-x] [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: 11/13/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND High-dimensional prediction considers data with more variables than samples. Generic research goals are to find the best predictor or to select variables. Results may be improved by exploiting prior information in the form of co-data, providing complementary data not on the samples, but on the variables. We consider adaptive ridge penalised generalised linear and Cox models, in which the variable-specific ridge penalties are adapted to the co-data to give a priori more weight to more important variables. The R-package ecpc originally accommodated various and possibly multiple co-data sources, including categorical co-data, i.e. groups of variables, and continuous co-data. Continuous co-data, however, were handled by adaptive discretisation, potentially inefficiently modelling and losing information. As continuous co-data such as external p values or correlations often arise in practice, more generic co-data models are needed. RESULTS Here, we present an extension to the method and software for generic co-data models, particularly for continuous co-data. At the basis lies a classical linear regression model, regressing prior variance weights on the co-data. Co-data variables are then estimated with empirical Bayes moment estimation. After placing the estimation procedure in the classical regression framework, extension to generalised additive and shape constrained co-data models is straightforward. Besides, we show how ridge penalties may be transformed to elastic net penalties. In simulation studies we first compare various co-data models for continuous co-data from the extension to the original method. Secondly, we compare variable selection performance to other variable selection methods. The extension is faster than the original method and shows improved prediction and variable selection performance for non-linear co-data relations. Moreover, we demonstrate use of the package in several genomics examples throughout the paper. CONCLUSIONS The R-package ecpc accommodates linear, generalised additive and shape constrained additive co-data models for the purpose of improved high-dimensional prediction and variable selection. The extended version of the package as presented here (version number 3.1.1 and higher) is available on ( https://cran.r-project.org/web/packages/ecpc/ ).
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Affiliation(s)
- Mirrelijn M van Nee
- Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Lodewyk F A Wessels
- Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Computational Cancer Biology, Oncode Institute, Amsterdam, The Netherlands
- Intelligent Systems, Delft University Medical Centers, Delft, The Netherlands
| | - Mark A van de Wiel
- Epidemiology & Data Science, Amsterdam Public Health research institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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9
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Gil-Jimenez A, van Dorp J, Contreras-Sanz A, van der Vos K, Vis DJ, Braaf L, Broeks A, Kerkhoven R, van Kessel KEM, Ribal MJ, Alcaraz A, Wessels LFA, Seiler R, Wright JL, Mengual L, Boormans J, van Rhijn BWG, Black PC, van der Heijden MS. Assessment of Predictive Genomic Biomarkers for Response to Cisplatin-based Neoadjuvant Chemotherapy in Bladder Cancer. Eur Urol 2023; 83:313-317. [PMID: 35965206 DOI: 10.1016/j.eururo.2022.07.023] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/03/2022] [Accepted: 07/26/2022] [Indexed: 01/21/2023]
Abstract
Cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy is recommended for patients with muscle-invasive bladder cancer (MIBC). It has been shown that somatic deleterious mutations in ERCC2, gain-of-function mutations in ERBB2, and alterations in ATM, RB1, and FANCC are correlated with pathological response to NAC in MIBC. The objective of this study was to validate these genomic biomarkers in pretreatment transurethral resection material from an independent retrospective cohort of 165 patients with MIBC who subsequently underwent NAC and radical surgery. Patients with ypT0/Tis/Ta/T1N0 disease after surgery were defined as responders. Somatic deleterious mutations in ERCC2 were found in nine of 68 (13%) evaluable responders and two of 95 (2%) evaluable nonresponders (p = 0.009; FDR = 0.03). No correlation was observed between response and alterations in ERBB2 or in ATM, RB1, or FANCC alone or in combination. In an exploratory analysis, no additional genomic alterations discriminated between responders and nonresponders to NAC. No further associations were identified between the aforementioned biomarkers and pathological complete response (ypT0N0) after surgery. In conclusion, we observed a positive association between deleterious mutations in ERCC2 and pathological response to NAC, but not overall survival or recurrence-free survival. Other previously reported genomic biomarkers were not validated. PATIENT SUMMARY: It is currently unknown which patients will respond to chemotherapy before definitive surgery for bladder cancer. Previous studies described several gene mutations in bladder cancer that correlated with chemotherapy response. This study confirmed that patients with bladder cancer with a mutation in the ERCC2 gene often respond to chemotherapy.
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Affiliation(s)
- Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Jeroen van Dorp
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alberto Contreras-Sanz
- The Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Kristan van der Vos
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel J Vis
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Linde Braaf
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ron Kerkhoven
- Core Facility Genomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim E M van Kessel
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - María José Ribal
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands; Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Roland Seiler
- Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Urology, Hospital Center Biel, Biel, Switzerland
| | - Jonathan L Wright
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lourdes Mengual
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Joost Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Bas W G van Rhijn
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Urology, Caritas St. Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - Peter C Black
- The Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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10
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Voorwerk L, Isaeva OI, Horlings HM, Balduzzi S, Chelushkin M, Bakker NAM, Champanhet E, Garner H, Sikorska K, Loo CE, Kemper I, Mandjes IAM, de Maaker M, van Geel JJL, Boers J, de Boer M, Salgado R, van Dongen MGJ, Sonke GS, de Visser KE, Schumacher TN, Blank CU, Wessels LFA, Jager A, Tjan-Heijnen VCG, Schröder CP, Linn SC, Kok M. PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial. Nat Cancer 2023; 4:535-549. [PMID: 37038006 PMCID: PMC10132987 DOI: 10.1038/s43018-023-00542-x] [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] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
Invasive lobular breast cancer (ILC) is the second most common histological breast cancer subtype, but ILC-specific trials are lacking. Translational research revealed an immune-related ILC subset, and in mouse ILC models, synergy between immune checkpoint blockade and platinum was observed. In the phase II GELATO trial ( NCT03147040 ), patients with metastatic ILC were treated with weekly carboplatin (area under the curve 1.5 mg ml-1 min-1) as immune induction for 12 weeks and atezolizumab (PD-L1 blockade; triweekly) from the third week until progression. Four of 23 evaluable patients had a partial response (17%), and 2 had stable disease, resulting in a clinical benefit rate of 26%. From these six patients, four had triple-negative ILC (TN-ILC). We observed higher CD8+ T cell infiltration, immune checkpoint expression and exhausted T cells after treatment. With this GELATO trial, we show that ILC-specific clinical trials are feasible and demonstrate promising antitumor activity of atezolizumab with carboplatin, particularly for TN-ILC, and provide insights for the design of highly needed ILC-specific trials.
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Affiliation(s)
- Leonie Voorwerk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Olga I Isaeva
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hugo M Horlings
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sara Balduzzi
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maksim Chelushkin
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Noor A M Bakker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Elisa Champanhet
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hannah Garner
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Karolina Sikorska
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Claudette E Loo
- Department of Radiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Inge Kemper
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ingrid A M Mandjes
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michiel de Maaker
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jasper J L van Geel
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Jorianne Boers
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Maaike de Boer
- Department of Medical Oncology, GROW, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marloes G J van Dongen
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Karin E de Visser
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ton N Schumacher
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Christian U Blank
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, GROW, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Carolien P Schröder
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Sabine C Linn
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marleen Kok
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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11
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Gil-Jimenez A, van Dorp J, Contreras-Sanz A, van der Vos K, Vis DJ, Braaf L, Broeks A, Kerkhoven R, van Kessel KEM, Ribal MJ, Alcaraz A, Wessels LFA, Seiler R, Wright JL, Mengual L, Boormans J, van Rhijn BWG, Black PC, van der Heijden MS. Corrigendum to "Assessment of Predictive Genomic Biomarkers for Response to Cisplatin-based Neoadjuvant Chemotherapy in Bladder Cancer" [Eur Urol 2023;83:313-17]. Eur Urol 2023; 83:e165. [PMID: 36907692 DOI: 10.1016/j.eururo.2023.03.002] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Affiliation(s)
- Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Jeroen van Dorp
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alberto Contreras-Sanz
- The Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Kristan van der Vos
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel J Vis
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Linde Braaf
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ron Kerkhoven
- Core Facility Genomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim E M van Kessel
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - María José Ribal
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands; Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Roland Seiler
- Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Urology, Hospital Center Biel, Biel, Switzerland
| | - Jonathan L Wright
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lourdes Mengual
- Laboratory and Department of Urology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Joost Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Bas W G van Rhijn
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Urology, Caritas St. Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - Peter C Black
- The Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Michiel S van der Heijden
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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12
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van de Haar J, Ma X, Ooft SN, van der Helm PW, Hoes LR, Mainardi S, Pinato DJ, Sun K, Salvatore L, Tortora G, Zurlo IV, Leo S, Giampieri R, Berardi R, Gelsomino F, Merz V, Mazzuca F, Antonuzzo L, Rosati G, Stavraka C, Ross P, Rodriquenz MG, Pavarana M, Messina C, Iveson T, Zoratto F, Thomas A, Fenocchio E, Ratti M, Depetris I, Cergnul M, Morelli C, Libertini M, Parisi A, De Tursi M, Zanaletti N, Garrone O, Graham J, Longarini R, Gobba SM, Petrillo A, Tamburini E, La Verde N, Petrelli F, Ricci V, Wessels LFA, Ghidini M, Cortellini A, Voest EE, Valeri N. Codon-specific KRAS mutations predict survival benefit of trifluridine/tipiracil in metastatic colorectal cancer. Nat Med 2023; 29:605-614. [PMID: 36864254 PMCID: PMC10033412 DOI: 10.1038/s41591-023-02240-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Genomics has greatly improved how patients with cancer are being treated; however, clinical-grade genomic biomarkers for chemotherapies are currently lacking. Using whole-genome analysis of 37 patients with metastatic colorectal cancer (mCRC) treated with the chemotherapy trifluridine/tipiracil (FTD/TPI), we identified KRAS codon G12 (KRASG12) mutations as a potential biomarker of resistance. Next, we collected real-world data of 960 patients with mCRC receiving FTD/TPI and validated that KRASG12 mutations were significantly associated with poor survival, also in analyses restricted to the RAS/RAF mutant subgroup. We next analyzed the data of the global, double-blind, placebo-controlled, phase 3 RECOURSE trial (n = 800 patients) and found that KRASG12 mutations (n = 279) were predictive biomarkers for reduced overall survival (OS) benefit of FTD/TPI versus placebo (unadjusted interaction P = 0.0031, adjusted interaction P = 0.015). For patients with KRASG12 mutations in the RECOURSE trial, OS was not prolonged with FTD/TPI versus placebo (n = 279; hazard ratio (HR) = 0.97; 95% confidence interval (CI) = 0.73-1.20; P = 0.85). In contrast, patients with KRASG13 mutant tumors showed significantly improved OS with FTD/TPI versus placebo (n = 60; HR = 0.29; 95% CI = 0.15-0.55; P < 0.001). In isogenic cell lines and patient-derived organoids, KRASG12 mutations were associated with increased resistance to FTD-based genotoxicity. In conclusion, these data show that KRASG12 mutations are biomarkers for reduced OS benefit of FTD/TPI treatment, with potential implications for approximately 28% of patients with mCRC under consideration for treatment with FTD/TPI. Furthermore, our data suggest that genomics-based precision medicine may be possible for a subset of chemotherapies.
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Affiliation(s)
- Joris van de Haar
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xuhui Ma
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Salo N Ooft
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Louisa R Hoes
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
- Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Imperial College Healthcare NHS Trust, London, UK
| | - Kristi Sun
- Imperial College Healthcare NHS Trust, London, UK
| | - Lisa Salvatore
- Oncologia Medica, Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Roma, Italy
- Oncologia Medica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Giampaolo Tortora
- Oncologia Medica, Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Roma, Italy
- Oncologia Medica, Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Silvana Leo
- Medical Oncology, 'Vito Fazzi' Hospital, Lecce, Italy
| | - Riccardo Giampieri
- Department of Oncology, Università Politecnica delle Marche, Azienda Ospedialiera Universitaria delle Marche, Ancona, Italy
| | - Rossana Berardi
- Department of Oncology, Università Politecnica delle Marche, Azienda Ospedialiera Universitaria delle Marche, Ancona, Italy
| | | | - Valeria Merz
- Medical Oncology Unit, Santa Chiara Hospital, Trento, Italy
| | - Federica Mazzuca
- Department of Clinical and Molecular Medicine, Sapienza University, Oncology Unit, Azienda Ospedialiera Universitaria Sant'Andrea, Rome, Italy
| | - Lorenzo Antonuzzo
- Clinical Oncology Unit, Careggi University Hospital, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Gerardo Rosati
- Medical Oncology Unit, S. Carlo Hospital, Potenza, Italy
| | - Chara Stavraka
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Paul Ross
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Maria Grazia Rodriquenz
- Istituto di Ricovero e Cura a Carattere Scientifico Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Michele Pavarana
- Oncology Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Carlo Messina
- Oncology Unit, ARNAS Civico Di Cristina Benfratelli Hospital, Palermo, Italy
| | | | - Federica Zoratto
- Unità Operativa Complessa Oncologia, Ospedale Santa Maria Goretti Latina, Latina, Italy
| | - Anne Thomas
- Leicester Cancer Research Centre, University of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Elisabetta Fenocchio
- Candiolo Cancer Institute FPO Istituto di Ricovero e Cura a Carattere Scientifico Candiolo, Candiolo, Italy
| | | | - Ilaria Depetris
- Division of Medical Oncology, ASL TO4, Ospedale Civile di Ivrea, Ivrea, Italy
| | - Massimiliano Cergnul
- Unità Operativa Oncologia Medica, Ospedale Civile di Legnano, Azienda Socio-Sanitaria Territoriale Ovest Milanese, Legnano, Italy
| | - Cristina Morelli
- Medical Oncology Unit, Department of Systems Medicine, Tor Vergata University Hospital, Rome, Italy
| | | | - Alessandro Parisi
- Department of Oncology, Università Politecnica delle Marche, Azienda Ospedialiera Universitaria delle Marche, Ancona, Italy
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Michele De Tursi
- Dipartimento di Tecnologie Innovative in Medicina & Odontoiatria, Università G. D'Annunzio, Chieti-Pescara, Chieti, Italy
| | - Nicoletta Zanaletti
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori, Istituto di Ricovero e Cura a Carattere Scientifico, Fondazione G. Pascale, Naples, Italy
| | - Ornella Garrone
- Oncology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Janet Graham
- Beatson West of Scotland Cancer Centre, Glasgow, UK
| | | | - Stefania Maria Gobba
- Division of Clinical Oncology, Azienda Socio-Sanitaria Territoriale dei Sette Laghi Varese, Varese, Italy
| | | | | | - Nicla La Verde
- Luigi Sacco Hospital-Polo Universitario, Azienda Socio-Sanitaria Territoriale Fatebenefratelli Sacco, Milan, Italy
| | - Fausto Petrelli
- Oncology Unit, Azienda Socio-Sanitaria Territoriale Bergamo Ovest, Treviglio, Italy
| | - Vincenzo Ricci
- Medical Oncology Unit, Azienda Ospedaliera di Rilievo Nazionale 'San Pio', Benevento, Italy
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Michele Ghidini
- Oncology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Emile E Voest
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Nicola Valeri
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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13
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Liefaard MC, Moore KS, Mulder L, van den Broek D, Wesseling J, Sonke GS, Wessels LFA, Rookus M, Lips EH. Tumour-educated platelets for breast cancer detection: biological and technical insights. Br J Cancer 2023; 128:1572-1581. [PMID: 36765174 PMCID: PMC10070267 DOI: 10.1038/s41416-023-02174-5] [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] [Received: 01/28/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Studies have shown that blood platelets contain tumour-specific mRNA profiles tumour-educated platelets (TEPs). Here, we aim to train a TEP-based breast cancer detection classifier. METHODS Platelet mRNA was sequenced from 266 women with stage I-IV breast cancer and 212 female controls from 6 hospitals. A particle swarm optimised support vector machine (PSO-SVM) and an elastic net-based classifier (EN) were trained on 71% of the study population. Classifier performance was evaluated in the remainder (29%) of the population, followed by validation in an independent set (37 cases and 36 controls). Potential confounding was assessed in post hoc analyses. RESULTS Both classifiers reached an area under the curve (AUC) of 0.85 upon internal validation. Reproducibility in the independent validation set was poor with an AUC of 0.55 and 0.54 for the PSO-SVM and EN classifier, respectively. Post hoc analyses indicated that 19% of the variance in gene expression was associated with hospital. Genes related to platelet activity were differentially expressed between hospitals. CONCLUSIONS We could not validate two TEP-based breast cancer classifiers in an independent validation cohort. The TEP protocol is sensitive to within-protocol variation and revision might be necessary before TEPs can be reconsidered for breast cancer detection.
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Affiliation(s)
- Marte C Liefaard
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kat S Moore
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Clinical Chemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Matti Rookus
- Department of Psychosocial and Epidemiology Research, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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14
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Blomberg OS, Spagnuolo L, Garner H, Voorwerk L, Isaeva OI, van Dyk E, Bakker N, Chalabi M, Klaver C, Duijst M, Kersten K, Brüggemann M, Pastoors D, Hau CS, Vrijland K, Raeven EAM, Kaldenbach D, Kos K, Afonina IS, Kaptein P, Hoes L, Theelen WSME, Baas P, Voest EE, Beyaert R, Thommen DS, Wessels LFA, de Visser KE, Kok M. IL-5-producing CD4 + T cells and eosinophils cooperate to enhance response to immune checkpoint blockade in breast cancer. Cancer Cell 2023; 41:106-123.e10. [PMID: 36525971 DOI: 10.1016/j.ccell.2022.11.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Immune checkpoint blockade (ICB) has heralded a new era in cancer therapy. Research into the mechanisms underlying response to ICB has predominantly focused on T cells; however, effective immune responses require tightly regulated crosstalk between innate and adaptive immune cells. Here, we combine unbiased analysis of blood and tumors from metastatic breast cancer patients treated with ICB with mechanistic studies in mouse models of breast cancer. We observe an increase in systemic and intratumoral eosinophils in patients and mice responding to ICB treatment. Mechanistically, ICB increased IL-5 production by CD4+ T cells, stimulating elevated eosinophil production from the bone marrow, leading to systemic eosinophil expansion. Additional induction of IL-33 by ICB-cisplatin combination or recombinant IL-33 promotes intratumoral eosinophil infiltration and eosinophil-dependent CD8+ T cell activation to enhance ICB response. This work demonstrates the critical role of eosinophils in ICB response and provides proof-of-principle for eosinophil engagement to enhance ICB efficacy.
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Affiliation(s)
- Olga S Blomberg
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Lorenzo Spagnuolo
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hannah Garner
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Leonie Voorwerk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Olga I Isaeva
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ewald van Dyk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Noor Bakker
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Myriam Chalabi
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Gastrointestinal Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Chris Klaver
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maxime Duijst
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kelly Kersten
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marieke Brüggemann
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dorien Pastoors
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Cheei-Sing Hau
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Kim Vrijland
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Elisabeth A M Raeven
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Daphne Kaldenbach
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Kevin Kos
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Inna S Afonina
- VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paulien Kaptein
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Louisa Hoes
- Oncode Institute, Utrecht, the Netherlands; Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Willemijn S M E Theelen
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul Baas
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Emile E Voest
- Oncode Institute, Utrecht, the Netherlands; Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, the Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Karin E de Visser
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands.
| | - Marleen Kok
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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15
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van Wagensveld L, van Baal JOAM, Timmermans M, Gaillard D, Borghuis L, Coffelt SB, Rosenberg EH, Lok CAR, Nijman HW, Kooreman LFS, Sanders J, de Bruijn M, Wessels LFA, van der Wiel R, Rausch C, Broeks A, Kruitwagen RFPM, van der Aa MA, Sonke GS, Schouten PC, Van de Vijver KK, Horlings HM. Homologous Recombination Deficiency and Cyclin E1 Amplification Are Correlated with Immune Cell Infiltration and Survival in High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14235965. [PMID: 36497449 PMCID: PMC9738162 DOI: 10.3390/cancers14235965] [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: 11/02/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND How molecular profiles are associated with tumor microenvironment (TME) in high-grade serous ovarian cancer (HGSOC) is incompletely understood. Therefore, we analyzed the TME and molecular profiles of HGSOC and assessed their associations with overall survival (OS). METHODS Patients with advanced-stage HGSOC treated in three Dutch hospitals between 2008-2015 were included. Patient data were collected from medical records. BRCA1/2 mutation, BRCA1 promotor methylation analyses, and copy number variations were used to define molecular profiles. Immune cells were assessed with immunohistochemical staining. RESULTS 348 patients were categorized as BRCA mutation (BRCAm) (BRCAm or promotor methylation) (30%), non-BRCA mutated HRD (19%), Cyclin E1 (CCNE1)-amplification (13%), non-BRCAmut HRD and CCNE1-amplification (double classifier) (20%), and no specific molecular profile (NSMP) (18%). BRCAm showed highest immune cell densities and CCNE1-amplification lowest. BRCAm showed the most favorable OS (52.5 months), compared to non-BRCAmut HRD (41.0 months), CCNE1-amplification (28.0 months), double classifier (27.8 months), and NSMP (35.4 months). Higher immune cell densities showed a favorable OS compared to lower, also within the profiles. CD8+, CD20+, and CD103+ cells remained associated with OS in multivariable analysis. CONCLUSIONS Molecular profiles and TME are associated with OS. TME differs per profile, with higher immune cell densities showing a favorable OS, even within the profiles. HGSOC does not reflect one entity but comprises different entities based on molecular profiles and TME.
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Affiliation(s)
- Lilian van Wagensveld
- Department of Research and Development, Netherlands Comprehensive Cancer Organization (IKNL), 3511 DT Utrecht, The Netherlands
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Correspondence:
| | - Juliette O. A. M. van Baal
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
| | - Maite Timmermans
- Department of Obstetrics and Gynecology, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Duco Gaillard
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Lauri Borghuis
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Seth B. Coffelt
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Institute of Cancer Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Cancer Research UK, Beatson Institute, Glasgow G61 1BD, UK
| | - Efraim H. Rosenberg
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Christianne A. R. Lok
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
| | - Hans W. Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Loes F. S. Kooreman
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marco de Bruijn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Lodewyk F. A. Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Rianne van der Wiel
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
- BioLizard nv, 9000 Ghent, Belgium
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Roy F. P. M. Kruitwagen
- GROW, School for Oncology and Reproduction, 6229 HX Maastricht, The Netherlands
- Department of Obstetrics and Gynecology, Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Maaike A. van der Aa
- Department of Research and Development, Netherlands Comprehensive Cancer Organization (IKNL), 3511 DT Utrecht, The Netherlands
| | - Gabe S. Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Philip C. Schouten
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Koen K. Van de Vijver
- Department of Gynecology, Center for Gynecologic Oncology Amsterdam (CGOA), 1066 CX Amsterdam, The Netherlands
- Department of Pathology & Cancer Research Institute Ghent (CRIG), Ghent University Hospital, 9000 Ghent, Belgium
| | - Hugo M. Horlings
- Department of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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16
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Kneppers J, Severson TM, Siefert JC, Schol P, Joosten SEP, Yu IPL, Huang CCF, Morova T, Altıntaş UB, Giambartolomei C, Seo JH, Baca SC, Carneiro I, Emberly E, Pasaniuc B, Jerónimo C, Henrique R, Freedman ML, Wessels LFA, Lack NA, Bergman AM, Zwart W. Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential. Nat Commun 2022; 13:7367. [PMID: 36450752 PMCID: PMC9712620 DOI: 10.1038/s41467-022-35135-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Androgen receptor (AR) drives prostate cancer (PCa) development and progression. AR chromatin binding profiles are highly plastic and form recurrent programmatic changes that differentiate disease stages, subtypes and patient outcomes. While prior studies focused on concordance between patient subgroups, inter-tumor heterogeneity of AR enhancer selectivity remains unexplored. Here we report high levels of AR chromatin binding heterogeneity in human primary prostate tumors, that overlap with heterogeneity observed in healthy prostate epithelium. Such heterogeneity has functional consequences, as somatic mutations converge on commonly-shared AR sites in primary over metastatic tissues. In contrast, less-frequently shared AR sites associate strongly with AR-driven gene expression, while such heterogeneous AR enhancer usage also distinguishes patients' outcome. These findings indicate that epigenetic heterogeneity in primary disease is directly informative for risk of biochemical relapse. Cumulatively, our results illustrate a high level of AR enhancer heterogeneity in primary PCa driving differential expression and clinical impact.
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Affiliation(s)
- Jeroen Kneppers
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tesa M Severson
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joseph C Siefert
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pieter Schol
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stacey E P Joosten
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivan Pak Lok Yu
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
| | | | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Ji-Heui Seo
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Sylvan C Baca
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
| | - Isa Carneiro
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Eldon Emberly
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Carmen Jerónimo
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Porto Comprehensive Cancer Center, Porto, Portugal
| | - Matthew L Freedman
- The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, USA
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, USA
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Science, University of British Columbia, Vancouver, Canada
- School of Medicine, Koç University, Istanbul, Turkey
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
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17
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Bouwman P, van der Heijden I, van der Gulden H, de Bruijn R, Braspenning ME, Moghadasi S, Wessels LFA, Vreeswijk MPG, Jonkers J. Correction: Functional Categorization of BRCA1 Variants of Uncertain Clinical Significance in Homologous Recombination Repair Complementation Assays. Clin Cancer Res 2022; 28:4588. [PMID: 36239017 DOI: 10.1158/1078-0432.ccr-22-2662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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18
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Zingg D, Bhin J, Yemelyanenko J, Kas SM, Rolfs F, Lutz C, Lee JK, Klarenbeek S, Silverman IM, Annunziato S, Chan CS, Piersma SR, Eijkman T, Badoux M, Gogola E, Siteur B, Sprengers J, de Klein B, de Goeij-de Haas RR, Riedlinger GM, Ke H, Madison R, Drenth AP, van der Burg E, Schut E, Henneman L, van Miltenburg MH, Proost N, Zhen H, Wientjens E, de Bruijn R, de Ruiter JR, Boon U, de Korte-Grimmerink R, van Gerwen B, Féliz L, Abou-Alfa GK, Ross JS, van de Ven M, Rottenberg S, Cuppen E, Chessex AV, Ali SM, Burn TC, Jimenez CR, Ganesan S, Wessels LFA, Jonkers J. Truncated FGFR2 is a clinically actionable oncogene in multiple cancers. Nature 2022; 608:609-617. [PMID: 35948633 PMCID: PMC9436779 DOI: 10.1038/s41586-022-05066-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 01/19/2021] [Accepted: 07/03/2022] [Indexed: 12/13/2022]
Abstract
Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer1. However, clinical responses to FGFR inhibitors have remained variable1–9, emphasizing the need to better understand which FGFR2 alterations are oncogenic and therapeutically targetable. Here we apply transposon-based screening10,11 and tumour modelling in mice12,13, and find that the truncation of exon 18 (E18) of Fgfr2 is a potent driver mutation. Human oncogenomic datasets revealed a diverse set of FGFR2 alterations, including rearrangements, E1–E17 partial amplifications, and E18 nonsense and frameshift mutations, each causing the transcription of E18-truncated FGFR2 (FGFR2ΔE18). Functional in vitro and in vivo examination of a compendium of FGFR2ΔE18 and full-length variants pinpointed FGFR2-E18 truncation as single-driver alteration in cancer. By contrast, the oncogenic competence of FGFR2 full-length amplifications depended on a distinct landscape of cooperating driver genes. This suggests that genomic alterations that generate stable FGFR2ΔE18 variants are actionable therapeutic targets, which we confirmed in preclinical mouse and human tumour models, and in a clinical trial. We propose that cancers containing any FGFR2 variant with a truncated E18 should be considered for FGFR-targeted therapies. Truncation of exon 18 of FGFR2 (FGFR2ΔE18) is a potent driver mutation in mice and humans, and FGFR-targeted therapy should be considered for patients with cancer expressing stable FGFR2ΔE18 variants.
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Affiliation(s)
- Daniel Zingg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julia Yemelyanenko
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Sjors M Kas
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Sjoerd Klarenbeek
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Stefano Annunziato
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Chang S Chan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Timo Eijkman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Madelon Badoux
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Justin Sprengers
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bim de Klein
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Richard R de Goeij-de Haas
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gregory M Riedlinger
- Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.,Department of Pathology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Hua Ke
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA
| | | | - Anne Paulien Drenth
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Eva Schut
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Linda Henneman
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ellen Wientjens
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ute Boon
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | - Bastiaan van Gerwen
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Luis Féliz
- Incyte Biosciences International, Morges, Switzerland
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College at Cornell University, New York, NY, USA
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA, USA.,Upstate University Hospital, Upstate Medical University, Syracuse, NY, USA
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands.,Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shridar Ganesan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Medicine and Pharmacology, Rutgers University, Piscataway, NJ, USA.
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, The Netherlands. .,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Oncode Institute, Utrecht, The Netherlands.
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19
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Linder S, Hoogstraat M, Stelloo S, Eickhoff N, Schuurman K, de Barros H, Alkemade M, Bekers EM, Severson TM, Sanders J, Huang CCF, Morova T, Altintas UB, Hoekman L, Kim Y, Baca SC, Sjostrom M, Zaalberg A, Hintzen DC, de Jong J, Kluin RJC, de Rink I, Giambartolomei C, Seo JH, Pasaniuc B, Altelaar M, Medema RH, Feng FY, Zoubeidi A, Freedman ML, Wessels LFA, Butler LM, Lack NA, van der Poel H, Bergman AM, Zwart W. Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence. Cancer Discov 2022; 12:2074-2097. [PMID: 35754340 PMCID: PMC7613567 DOI: 10.1158/2159-8290.cd-21-0576] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
Abstract
In prostate cancer, androgen receptor (AR)-targeting agents are very effective in various disease stages. However, therapy resistance inevitably occurs and little is known about how tumor cells adapt to bypass AR suppression. Here, we performed integrative multi-omics analyses on tissues isolated before and after 3 months of AR-targeting enzalutamide monotherapy from high-risk prostate cancer patients enrolled in a neoadjuvant clinical trial. Transcriptomic analyses demonstrated that AR inhibition drove tumors towards a neuroendocrine-like disease state. Additionally, epigenomic profiling revealed massive enzalutamide-induced reprogramming of pioneer factor FOXA1 - from inactive chromatin sites towards active cis-regulatory elements that dictate pro-survival signals. Notably, treatment-induced FOXA1 sites were enriched for circadian clock component ARNTL. Post-treatment ARNTL levels associated with poor outcome, and ARNTL knockout strongly decreased prostate cancer cell growth. Our data highlight a remarkable cistromic plasticity of FOXA1 following AR-targeted therapy, and revealed an acquired dependency on circadian regulator ARNTL, a novel candidate therapeutic target.
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Affiliation(s)
- Simon Linder
- The Netherlands Cancer Institute, Amsterdam, North Holland, Netherlands
| | | | - Suzan Stelloo
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Nils Eickhoff
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | - Elise M Bekers
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Joyce Sanders
- The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Tunc Morova
- University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Sylvan C Baca
- Hungarian Academy of Sciences, Boston, United States
| | - Martin Sjostrom
- University of California, San Francisco, San Francisco, United States
| | | | | | | | - Roelof J C Kluin
- The Netherlands Cancer Institute, Amsterdam, Noord-Holland, Netherlands
| | | | | | - Ji-Heui Seo
- Dana-Farber Cancer Institute, BOSTON, Massachusetts, United States
| | - Bogdan Pasaniuc
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | | | - Rene H Medema
- University Medical Center Utrecht, Amsterdam, Netherlands
| | - Felix Y Feng
- University of California, San Francisco, San Francisco, CA, United States
| | - Amina Zoubeidi
- University of British Columbia, Vancouver, British Colombia, Canada
| | | | | | - Lisa M Butler
- University of Adelaide, School of Medicine and Freemasons Foundation Centre for Men's Health, Adelaide, SA, Australia
| | - Nathan A Lack
- University of British Columbia, Vancouver, BC, Canada
| | | | | | - Wilbert Zwart
- Netherlands Cancer Institute, Amsterdam, Netherlands
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20
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Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet 2022; 54:850-860. [PMID: 35681052 PMCID: PMC9197769 DOI: 10.1038/s41588-022-01082-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 09/17/2021] [Accepted: 04/22/2022] [Indexed: 11/29/2022]
Abstract
Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this question, we performed genomic analyses on the initial DCIS lesion and paired invasive recurrent tumors in 95 patients together with single-cell DNA sequencing in a subset of cases. Our data show that in 75% of cases the invasive recurrence was clonally related to the initial DCIS, suggesting that tumor cells were not eliminated during the initial treatment. Surprisingly, however, 18% were clonally unrelated to the DCIS, representing new independent lineages and 7% of cases were ambiguous. This knowledge is essential for accurate risk evaluation of DCIS, treatment de-escalation strategies and the identification of predictive biomarkers.
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Affiliation(s)
- Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tapsi Kumar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anargyros Megalios
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Lindy L Visser
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Sheinman
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Angelo Fortunato
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Marlous Hoogstraat
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Diego Mallo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Maria Roman-Escorza
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Ahmed A Ahmed
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Mingchu Xu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Wim Brugman
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna K Casasent
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen Clements
- Screening Quality Assurance Service, Public Health England, London, UK
| | - Helen R Davies
- Early Cancer Unit, Hutchison/MRC Research Centre and Academic Department of Medical Genetics, Cambridge Biomedical Research Campus, University of Cambridge, Cambridge, UK
| | - Liping Fu
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anita Grigoriadis
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Timothy M Hardman
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marielle Krete
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra Kristel
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michiel de Maaker
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlo C Maley
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Brian A Menegaz
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frank Nieboer
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Salpie Nowinski
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Sarah Pinder
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Jelmar Quist
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Carolina Salinas-Souza
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Michael Schaapveld
- Division of Psychosocial research and Epidemiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Abeer M Shaaban
- Queen Elizabeth Hospital Birmingham and University of Birmingham, Birmingham, UK
| | - Rana Shami
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Mathini Sridharan
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - John Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Serena Nik-Zainal
- Early Cancer Unit, Hutchison/MRC Research Centre and Academic Department of Medical Genetics, Cambridge Biomedical Research Campus, University of Cambridge, Cambridge, UK
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas E Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alastair M Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Divisions of Diagnostic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK.
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21
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van Dijk N, Gil-Jimenez A, Silina K, van Montfoort ML, Einerhand S, Jonkman L, Voskuilen CS, Peters D, Sanders J, Lubeck Y, Broeks A, Hooijberg E, Vis DJ, van den Broek M, Wessels LFA, van Rhijn BWG, van der Heijden MS. The Tumor Immune Landscape and Architecture of Tertiary Lymphoid Structures in Urothelial Cancer. Front Immunol 2022; 12:793964. [PMID: 34987518 PMCID: PMC8721669 DOI: 10.3389/fimmu.2021.793964] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 10/12/2021] [Accepted: 11/30/2021] [Indexed: 01/01/2023] Open
Abstract
Candidate immune biomarkers have been proposed for predicting response to immunotherapy in urothelial cancer (UC). Yet, these biomarkers are imperfect and lack predictive power. A comprehensive overview of the tumor immune contexture, including Tertiary Lymphoid structures (TLS), is needed to better understand the immunotherapy response in UC. We analyzed tumor sections by quantitative multiplex immunofluorescence to characterize immune cell subsets in various tumor compartments in tumors without pretreatment and tumors exposed to preoperative anti-PD1/CTLA-4 checkpoint inhibitors (NABUCCO trial). Pronounced immune cell presence was found in UC invasive margins compared to tumor and stroma regions. CD8+PD1+ T-cells were present in UC, particularly following immunotherapy. The cellular composition of TLS was assessed by multiplex immunofluorescence (CD3, CD8, FoxP3, CD68, CD20, PanCK, DAPI) to explore specific TLS clusters based on varying immune subset densities. Using a k-means clustering algorithm, we found five distinct cellular composition clusters. Tumors unresponsive to anti-PD-1/CTLA-4 immunotherapy showed enrichment of a FoxP3+ T-cell-low TLS cluster after treatment. Additionally, cluster 5 (macrophage low) TLS were significantly higher after pre-operative immunotherapy, compared to untreated tumors. We also compared the immune cell composition and maturation stages between superficial (submucosal) and deeper TLS, revealing that superficial TLS had more pronounced T-helper cells and enrichment of early TLS than TLS located in deeper tissue. Furthermore, superficial TLS displayed a lower fraction of secondary follicle like TLS than deeper TLS. Taken together, our results provide a detailed quantitative overview of the tumor immune landscape in UC, which can provide a basis for further studies.
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Affiliation(s)
- Nick van Dijk
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Alberto Gil-Jimenez
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Karina Silina
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Sarah Einerhand
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lars Jonkman
- Department of Medical Oncology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Charlotte S Voskuilen
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yoni Lubeck
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Erik Hooijberg
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Daniel J Vis
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | | | - Lodewyk F A Wessels
- Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands.,Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, Netherlands
| | - Bas W G van Rhijn
- Department of Urology, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Michiel S van der Heijden
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, Netherlands
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22
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Mourragui SMC, Loog M, Vis DJ, Moore K, Manjon AG, van de Wiel MA, Reinders MJT, Wessels LFA. Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning. Proc Natl Acad Sci U S A 2021; 118:e2106682118. [PMID: 34873056 PMCID: PMC8670522 DOI: 10.1073/pnas.2106682118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Preclinical models have been the workhorse of cancer research, producing massive amounts of drug response data. Unfortunately, translating response biomarkers derived from these datasets to human tumors has proven to be particularly challenging. To address this challenge, we developed TRANSACT, a computational framework that builds a consensus space to capture biological processes common to preclinical models and human tumors and exploits this space to construct drug response predictors that robustly transfer from preclinical models to human tumors. TRANSACT performs favorably compared to four competing approaches, including two deep learning approaches, on a set of 23 drug prediction challenges on The Cancer Genome Atlas and 226 metastatic tumors from the Hartwig Medical Foundation. We demonstrate that response predictions deliver a robust performance for a number of therapies of high clinical importance: platinum-based chemotherapies, gemcitabine, and paclitaxel. In contrast to other approaches, we demonstrate the interpretability of the TRANSACT predictors by correctly identifying known biomarkers of targeted therapies, and we propose potential mechanisms that mediate the resistance to two chemotherapeutic agents.
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Affiliation(s)
- Soufiane M C Mourragui
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628 XE Delft, The Netherlands
| | - Marco Loog
- Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628 XE Delft, The Netherlands
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Daniel J Vis
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Kat Moore
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Anna G Manjon
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Mark A van de Wiel
- Epidemiology and Biostatistics, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands
- Medical Research Council Biostatistics Unit, Cambridge University, Cambridge CB2 0SR, United Kingdom
| | - Marcel J T Reinders
- Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628 XE Delft, The Netherlands;
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628 XE Delft, The Netherlands
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23
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van Nee MM, Wessels LFA, van de Wiel MA. Flexible co-data learning for high-dimensional prediction. Stat Med 2021; 40:5910-5925. [PMID: 34438466 PMCID: PMC9292202 DOI: 10.1002/sim.9162] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/18/2021] [Accepted: 07/29/2021] [Indexed: 02/06/2023]
Abstract
Clinical research often focuses on complex traits in which many variables play a role in mechanisms driving, or curing, diseases. Clinical prediction is hard when data is high-dimensional, but additional information, like domain knowledge and previously published studies, may be helpful to improve predictions. Such complementary data, or co-data, provide information on the covariates, such as genomic location or P-values from external studies. We use multiple and various co-data to define possibly overlapping or hierarchically structured groups of covariates. These are then used to estimate adaptive multi-group ridge penalties for generalized linear and Cox models. Available group adaptive methods primarily target for settings with few groups, and therefore likely overfit for non-informative, correlated or many groups, and do not account for known structure on group level. To handle these issues, our method combines empirical Bayes estimation of the hyperparameters with an extra level of flexible shrinkage. This renders a uniquely flexible framework as any type of shrinkage can be used on the group level. We describe various types of co-data and propose suitable forms of hypershrinkage. The method is very versatile, as it allows for integration and weighting of multiple co-data sets, inclusion of unpenalized covariates and posterior variable selection. For three cancer genomics applications we demonstrate improvements compared to other models in terms of performance, variable selection stability and validation.
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Affiliation(s)
- Mirrelijn M van Nee
- Epidemiology & Data Science
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Computational Cancer Biology, Oncode Institute, Amsterdam, The Netherlands.,Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Mark A van de Wiel
- Epidemiology & Data Science
- Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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24
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Ragusi MAA, Bismeijer T, van der Velden BHM, Loo CE, Canisius S, Wesseling J, Wessels LFA, Elias SG, Gilhuijs KGA. Contralateral parenchymal enhancement on MRI is associated with tumor proteasome pathway gene expression and overall survival of early ER+/HER2-breast cancer patients. Breast 2021; 60:230-237. [PMID: 34763270 PMCID: PMC8591464 DOI: 10.1016/j.breast.2021.11.002] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/26/2021] [Accepted: 11/02/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose To assess whether contralateral parenchymal enhancement (CPE) on MRI is associated with gene expression pathways in ER+/HER2-breast cancer, and if so, whether such pathways are related to survival. Methods Preoperative breast MRIs were analyzed of early ER+/HER2-breast cancer patients eligible for breast-conserving surgery included in a prospective observational cohort study (MARGINS). The contralateral parenchyma was segmented and CPE was calculated as the average of the top-10% delayed enhancement. Total tumor RNA sequencing was performed and gene set enrichment analysis was used to reveal gene expression pathways associated with CPE (N = 226) and related to overall survival (OS) and invasive disease-free survival (IDFS) in multivariable survival analysis. The latter was also done for the METABRIC cohort (N = 1355). Results CPE was most strongly correlated with proteasome pathways (normalized enrichment statistic = 2.04, false discovery rate = .11). Patients with high CPE showed lower tumor proteasome gene expression. Proteasome gene expression had a hazard ratio (HR) of 1.40 (95% CI = 0.89, 2.16; P = .143) for OS in the MARGINS cohort and 1.53 (95% CI = 1.08, 2.14; P = .017) for IDFS, in METABRIC proteasome gene expression had an HR of 1.09 (95% CI = 1.01, 1.18; P = .020) for OS and 1.10 (95% CI = 1.02, 1.18; P = .012) for IDFS. Conclusion CPE was negatively correlated with tumor proteasome gene expression in early ER+/HER2-breast cancer patients. Low tumor proteasome gene expression was associated with improved survival in the METABRIC data. Contralateral parenchymal enhancement on MRI was associated with tumor proteasome gene expression in ER+/HER2-breast cancer. A high contralateral parenchymal enhancement was associated with a low proteasome gene expression in the breast cancer. Low proteasome tumor gene expression was associated with improved survival in an independent patient cohort.
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Affiliation(s)
- Max A A Ragusi
- Department of Radiology / Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Radiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis - Oncode Institute, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bas H M van der Velden
- Department of Radiology / Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Claudette E Loo
- Department of Radiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sander Canisius
- Division of Molecular Carcinogenesis - Oncode Institute, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis - Oncode Institute, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Mekelweg 5, 2628 CD Delft, the Netherlands
| | - Sjoerd G Elias
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Kenneth G A Gilhuijs
- Department of Radiology / Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
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25
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Siefert JC, Cioni B, Muraro MJ, Alshalalfa M, Vivié J, van der Poel HG, Schoots IG, Bekers E, Feng FY, Wessels LFA, Zwart W, Bergman AM. The Prognostic Potential of Human Prostate Cancer-Associated Macrophage Subtypes as Revealed by Single-Cell Transcriptomics. Mol Cancer Res 2021; 19:1778-1791. [PMID: 34131070 PMCID: PMC9398107 DOI: 10.1158/1541-7786.mcr-20-0740] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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] [Received: 08/26/2020] [Revised: 12/18/2020] [Accepted: 06/07/2021] [Indexed: 01/07/2023]
Abstract
Macrophages in the tumor microenvironment are causally linked with prostate cancer development and progression, yet little is known about their composition in neoplastic human tissue. By performing single cell transcriptomic analysis of human prostate cancer resident macrophages, three distinct populations were identified in the diseased prostate. Unexpectedly, no differences were observed between macrophages isolated from the tumorous and nontumorous portions of the prostatectomy specimens. Markers associated with canonical M1 and M2 macrophage phenotypes were identifiable, however these were not the main factors defining unique subtypes. The genes selectively associated with each macrophage cluster were used to develop a gene signature which was highly associated with both recurrence-free and metastasis-free survival. These results highlight the relevance of tissue-specific macrophage subtypes in the tumor microenvironment for prostate cancer progression and demonstrates the utility of profiling single-cell transcriptomics in human tumor samples as a strategy to design gene classifiers for patient prognostication. IMPLICATIONS: The specific macrophage subtypes present in a diseased human prostate have prognostic value, suggesting that the relative proportions of these populations are related to patient outcome. Understanding the relative contributions of these subtypes will not only inform patient prognostication, but will enable personalized immunotherapeutic strategies to increase beneficial populations or reduce detrimental populations.
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Affiliation(s)
- Joseph C Siefert
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bianca Cioni
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mauro J Muraro
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Judith Vivié
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Henk G van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ivo G Schoots
- Department of Radiology and Nuclear Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elise Bekers
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Felix Y Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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26
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van de Haar J, Hoes LR, Roepman P, Lolkema MP, Verheul HMW, Gelderblom H, de Langen AJ, Smit EF, Cuppen E, Wessels LFA, Voest EE. Limited evolution of the actionable metastatic cancer genome under therapeutic pressure. Nat Med 2021; 27:1553-1563. [PMID: 34373653 DOI: 10.1038/s41591-021-01448-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 03/06/2021] [Accepted: 06/23/2021] [Indexed: 11/08/2022]
Abstract
Genomic profiling is critical for the identification of treatment options for patients with metastatic cancer, but it remains unclear how frequently this procedure should be repeated during the course of the disease. To address this, we analyzed whole-genome sequencing (WGS) data of 250 biopsy pairs, longitudinally collected over the treatment course of 231 adult patients with a representative variety of metastatic solid malignancies. Within the biopsy interval (median, 6.4 months), patients received one or multiple lines of (mostly) standard-of-care (SOC) treatments, with all major treatment modalities being broadly represented. SOC biomarkers and biomarkers for clinical trial enrollment could be identified in 23% and 72% of biopsies, respectively. For SOC genomic biomarkers, we observed full concordance between the first and the second biopsy in 99% of pairs. Of the 219 biomarkers for clinical trial enrollment that were identified in the first biopsies, we recovered 94% in the follow-up biopsies. Furthermore, a second WGS analysis did not identify additional biomarkers for clinical trial enrollment in 91% of patients. More-frequent genomic evolution was observed when considering specific genes targeted by small-molecule inhibitors or hormonal therapies (21% and 22% of cases, respectively). Together, our data demonstrate that there is limited evolution of the actionable genome of treated metastases. A single WGS analysis of a metastatic biopsy is generally sufficient to identify SOC genomic biomarkers and to identify investigational treatment opportunities.
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Affiliation(s)
- Joris van de Haar
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Louisa R Hoes
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Adrianus J de Langen
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Egbert F Smit
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Amsterdam, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands
| | - Emile E Voest
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Oncode Institute, Amsterdam, the Netherlands.
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands.
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27
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Jochems F, Thijssen B, De Conti G, Jansen R, Pogacar Z, Groot K, Wang L, Schepers A, Wang C, Jin H, Beijersbergen RL, Leite de Oliveira R, Wessels LFA, Bernards R. The Cancer SENESCopedia: A delineation of cancer cell senescence. Cell Rep 2021; 36:109441. [PMID: 34320349 PMCID: PMC8333195 DOI: 10.1016/j.celrep.2021.109441] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 12/21/2020] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in cancer. We report here a comprehensive analysis of the transcriptome and senolytic responses in a panel of 13 cancer cell lines rendered senescent by two distinct compounds. We show that in cancer cells, the response to senolytic agents and the composition of the senescence-associated secretory phenotype are more influenced by the cell of origin than by the senescence trigger. Using machine learning, we establish the SENCAN gene expression classifier for the detection of senescence in cancer cell samples. The expression profiles and senescence classifier are available as an interactive online Cancer SENESCopedia. Senescent cancer cells respond differently to senolytic ABT-263 SASP expression in cancer is heterogeneous and influenced by cell origin The SENCAN classifier detects cancer cell senescence in vitro The Cancer SENESCopedia contains transcriptome data from 37 senescence models
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Affiliation(s)
- Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Robin Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
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28
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Almekinders MMM, Schaapveld M, Thijssen B, Visser LL, Bismeijer T, Sanders J, Isnaldi E, Hofland I, Mertz M, Wessels LFA, Broeks A, Hooijberg E, Zwart W, Lips EH, Desmedt C, Wesseling J. Breast adipocyte size associates with ipsilateral invasive breast cancer risk after ductal carcinoma in situ. NPJ Breast Cancer 2021; 7:31. [PMID: 33753731 PMCID: PMC7985299 DOI: 10.1038/s41523-021-00232-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/03/2021] [Indexed: 12/25/2022] Open
Abstract
Although ductal carcinoma in situ (DCIS) is a non-obligate precursor to ipsilateral invasive breast cancer (iIBC), most DCIS lesions remain indolent. Hence, overdiagnosis and overtreatment of DCIS is a major concern. There is an urgent need for prognostic markers that can distinguish harmless from potentially hazardous DCIS. We hypothesised that features of the breast adipose tissue may be associated with risk of subsequent iIBC. We performed a case-control study nested in a population-based DCIS cohort, consisting of 2658 women diagnosed with primary DCIS between 1989 and 2005, uniformly treated with breast conserving surgery (BCS) alone. We assessed breast adipose features with digital pathology (HALO®, Indica Labs) and related these to iIBC risk in 108 women that developed subsequent iIBC (cases) and 168 women who did not (controls) by conditional logistic regression, accounting for clinicopathological and immunohistochemistry variables. Large breast adipocyte size was significantly associated with iIBC risk (odds ratio (OR) 2.75, 95% confidence interval (95% CI) = 1.25-6.05). High cyclooxygenase (COX)-2 protein expression in the DCIS cells was also associated with subsequent iIBC (OR 3.70 (95% CI = 1.59-8.64). DCIS with both high COX-2 expression and large breast adipocytes was associated with a 12-fold higher risk (OR 12.0, 95% CI = 3.10-46.3, P < 0.001) for subsequent iIBC compared with women with smaller adipocyte size and low COX-2 expression. Large breast adipocytes combined with high COX-2 expression in DCIS is associated with a high risk of subsequent iIBC. Besides COX-2, adipocyte size has the potential to improve clinical management in patients diagnosed with primary DCIS.
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Affiliation(s)
- Mathilde M M Almekinders
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Michael Schaapveld
- Division of Psychosocial Research, Epidemiology and Biostatistics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lindy L Visser
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joyce Sanders
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Edoardo Isnaldi
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Internal Medicine and Medical Specialties, Università degli Studi di Genova, IT-16132, Genova, Italy
| | - Ingrid Hofland
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjolijn Mertz
- Bio-Imaging Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Erik Hooijberg
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, Utrecht, The Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jelle Wesseling
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
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29
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Šuštić T, van Wageningen S, Bosdriesz E, Reid RJD, Dittmar J, Lieftink C, Beijersbergen RL, Wessels LFA, Rothstein R, Bernards R. Correction to: A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers. Genome Med 2021; 13:24. [PMID: 33568196 PMCID: PMC7877087 DOI: 10.1186/s13073-020-00815-5] [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: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Tonći Šuštić
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Sake van Wageningen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Evert Bosdriesz
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Robert J D Reid
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - John Dittmar
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Rodney Rothstein
- Department Genetics and Development, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, 10032, USA.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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30
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Puppe J, Liu X, Ratz L, Bartke L, van de Ven M, Vliet MH, Wientjes E, van der Gulden H, Zevenhoven J, Hahnen E, Malter W, Wessels LFA, Schmutzler R, Mallmann P, Reinhardt C, Linn S, Jonkers J. Double BRCA1 and BRCA2 inactivation is epistatic in mammary tumorigenesis and treatment response to PARP-inhibition and platinum drugs. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1717868] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- J Puppe
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | - X Liu
- Netherlands Cancer Institute
| | - L Ratz
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | - L Bartke
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | | | | | | | | | - E Hahnen
- Zentrum Familiärer Brust- und Eierstockkrebs, Uniklinik Köln
| | - W Malter
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | - R Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Uniklinik Köln
| | - P Mallmann
- Klinik und Poliklinik für Frauenheilkunde, Uniklinik Köln
| | | | - S Linn
- Netherlands Cancer Institute
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31
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van der Vos KE, Vis DJ, Nevedomskaya E, Kim Y, Choi W, McConkey D, Wessels LFA, van Rhijn BWG, Zwart W, van der Heijden MS. Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer. Sci Rep 2020; 10:10952. [PMID: 32616859 PMCID: PMC7331601 DOI: 10.1038/s41598-020-67850-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 08/15/2019] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease that often recurs despite aggressive treatment with neoadjuvant chemotherapy and (radical) cystectomy. Basal and luminal molecular subtypes have been identified that are linked to clinical characteristics and have differential sensitivities to chemotherapy. While it has been suggested that epigenetic mechanisms play a role in defining these subtypes, a thorough understanding of the biological mechanisms is lacking. This report details the first genome-wide analysis of histone methylation patterns of human primary bladder tumours by chromatin immunoprecipitations and next-generation sequencing (ChIP-seq). We profiled multiple histone marks: H3K27me3, a marker for repressed genes, and H3K4me1 and H3K4me3, which are indicators of active enhancers and active promoters. Integrated analysis of ChIP-seq data and RNA sequencing revealed that H3K4 mono-methylation demarcates MIBC subtypes, while no association was found for the other two histone modifications in relation to basal and luminal subtypes. Additionally, we identified differentially methylated H3K4me1 peaks in basal and luminal tumour samples, suggesting that active enhancers play a role in defining subtypes. Our study is the first analysis of histone modifications in primary bladder cancer tissue and provides an important resource for the bladder cancer community.
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Affiliation(s)
- K E van der Vos
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D J Vis
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E Nevedomskaya
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Y Kim
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - W Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - D McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - B W G van Rhijn
- Department of Surgical Oncology (Urology), The Netherlands Cancer Institute, Antoni Van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - W Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M S van der Heijden
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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32
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Bouwman P, van der Heijden I, van der Gulden H, de Bruijn R, Braspenning ME, Moghadasi S, Wessels LFA, Vreeswijk MPG, Jonkers J. Functional Categorization of BRCA1 Variants of Uncertain Clinical Significance in Homologous Recombination Repair Complementation Assays. Clin Cancer Res 2020; 26:4559-4568. [PMID: 32546644 DOI: 10.1158/1078-0432.ccr-20-0255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/29/2020] [Accepted: 06/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Because BRCA1 is a high-risk breast/ovarian cancer susceptibility gene, BRCA1 sequence variants of uncertain clinical significance (VUS) complicate genetic counseling. As most VUS are rare, reliable classification based on clinical and genetic data is often impossible. However, all pathogenic BRCA1 variants analyzed result in defective homologous recombination DNA repair (HRR). Thus, BRCA1 VUS may be categorized based on their functional impact on this pathway. EXPERIMENTAL DESIGN Two hundred thirty-eight BRCA1 VUS-comprising most BRCA1 VUS known in the Netherlands and Belgium-were tested for their ability to complement Brca1-deficient mouse embryonic stem cells in HRR, using cisplatin and olaparib sensitivity assays and a direct repeat GFP (DR-GFP) HRR assay. Assays were validated using 25 known benign and 25 known pathogenic BRCA1 variants. For assessment of pathogenicity by a multifactorial likelihood analysis method, we collected clinical and genetic data for functionally deleterious VUS and VUS occurring in three or more families. RESULTS All three assays showed 100% sensitivity and specificity (95% confidence interval, 83%-100%). Out of 238 VUS, 45 showed functional defects, 26 of which were deleterious in all three assays. For 13 of these 26 variants, we could calculate the probability of pathogenicity using clinical and genetic data, resulting in the identification of 7 (likely) pathogenic variants. CONCLUSIONS We have functionally categorized 238 BRCA1 VUS using three different HRR-related assays. Classification based on clinical and genetic data alone for a subset of these variants confirmed the high sensitivity and specificity of our functional assays.
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Affiliation(s)
- Peter Bouwman
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Ingrid van der Heijden
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hanneke van der Gulden
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute and Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Merel E Braspenning
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute and Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jos Jonkers
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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33
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Mourragui S, Loog M, van de Wiel MA, Reinders MJT, Wessels LFA. PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors. Bioinformatics 2020; 35:i510-i519. [PMID: 31510654 PMCID: PMC6612899 DOI: 10.1093/bioinformatics/btz372] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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] [Indexed: 11/25/2022] Open
Abstract
Motivation Cell lines and patient-derived xenografts (PDXs) have been used extensively to understand the molecular underpinnings of cancer. While core biological processes are typically conserved, these models also show important differences compared to human tumors, hampering the translation of findings from pre-clinical models to the human setting. In particular, employing drug response predictors generated on data derived from pre-clinical models to predict patient response remains a challenging task. As very large drug response datasets have been collected for pre-clinical models, and patient drug response data are often lacking, there is an urgent need for methods that efficiently transfer drug response predictors from pre-clinical models to the human setting. Results We show that cell lines and PDXs share common characteristics and processes with human tumors. We quantify this similarity and show that a regression model cannot simply be trained on cell lines or PDXs and then applied on tumors. We developed PRECISE, a novel methodology based on domain adaptation that captures the common information shared amongst pre-clinical models and human tumors in a consensus representation. Employing this representation, we train predictors of drug response on pre-clinical data and apply these predictors to stratify human tumors. We show that the resulting domain-invariant predictors show a small reduction in predictive performance in the pre-clinical domain but, importantly, reliably recover known associations between independent biomarkers and their companion drugs on human tumors. Availability and implementation PRECISE and the scripts for running our experiments are available on our GitHub page (https://github.com/NKI-CCB/PRECISE). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Soufiane Mourragui
- Computational Cancer Biology, Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam CX, The Netherlands.,Department of Intelligent Systems, Faculty of EEMCS, Delft University of Technology, Delft CD, The Netherlands
| | - Marco Loog
- Department of Intelligent Systems, Faculty of EEMCS, Delft University of Technology, Delft CD, The Netherlands.,Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Marcel J T Reinders
- Department of Intelligent Systems, Faculty of EEMCS, Delft University of Technology, Delft CD, The Netherlands.,Computational Biology Center, Leiden University Medical Center, Leiden ZC, The Netherlands
| | - Lodewyk F A Wessels
- Computational Cancer Biology, Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam CX, The Netherlands.,Department of Intelligent Systems, Faculty of EEMCS, Delft University of Technology, Delft CD, The Netherlands
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Bismeijer T, van der Velden BHM, Canisius S, Lips EH, Loo CE, Viergever MA, Wesseling J, Gilhuijs KGA, Wessels LFA. Radiogenomic Analysis of Breast Cancer by Linking MRI Phenotypes with Tumor Gene Expression. Radiology 2020; 296:277-287. [PMID: 32452738 DOI: 10.1148/radiol.2020191453] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Better understanding of the molecular biology associated with MRI phenotypes may aid in the diagnosis and treatment of breast cancer. Purpose To discover the associations between MRI phenotypes of breast cancer and their underlying molecular biology derived from gene expression data. Materials and Methods This is a secondary analysis of the Multimodality Analysis and Radiologic Guidance in Breast-Conserving Therapy, or MARGINS, study. MARGINS included patients eligible for breast-conserving therapy between November 2000 and December 2008 for preoperative breast MRI. Tumor RNA was collected for sequencing from surgical specimen. Twenty-one computer-generated MRI features of tumors were condensed into seven MRI factors related to tumor size, shape, initial enhancement, late enhancement, smoothness of enhancement, sharpness, and sharpness variation. These factors were associated with gene expression levels from RNA sequencing by using gene set enrichment analysis. Statistical significance of these associations was evaluated by using a sample permutation test and the false discovery rate. Results Gene expression and MRI data were obtained for 295 patients (mean age, 56 years ± 10.3 [standard deviation]). Larger and more irregular tumors showed increased expression of cell cycle and DNA damage checkpoint genes (false discovery rate <0.25; normalized enrichment statistic [NES], 2.15). Enhancement and sharpness of the tumor margin were associated with expression of ribosomal proteins (false discovery rate <0.25; NES, 1.95). Smoothness of enhancement, tumor size, and tumor shape were associated with expression of genes involved in the extracellular matrix (false discovery rate <0.25; NES, 2.25). Conclusion Breast cancer MRI phenotypes were related to their underlying molecular biology revealed by using RNA sequencing. The association between enhancements and sharpness of the tumor margin with the ribosome suggests that these MRI features may be imaging biomarkers for drugs targeting the ribosome. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Cho in this issue.
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Affiliation(s)
- Tycho Bismeijer
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Bas H M van der Velden
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Sander Canisius
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Esther H Lips
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Claudette E Loo
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Max A Viergever
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Jelle Wesseling
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Kenneth G A Gilhuijs
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
| | - Lodewyk F A Wessels
- From the Division of Molecular Carcinogenesis, Oncode Institute (T.B., S.C., L.F.A.W.), Division of Molecular Pathology (S.C., E.H.L., J.W.), Department of Radiology (C.E.L.), and Department of Pathology (J.W.), the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Image Sciences Institute, University Medical Center Utrecht, Utrecht, the Netherlands (B.H.M.v.d.V., M.A.V., K.G.A.G.); and Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, the Netherlands (L.F.A.W.)
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Slagter M, Rozeman EA, Ding H, Versluis JM, Valenti M, Peters D, Broeks A, Rooijen CV, Horlings H, Haanen JBAG, Hooijberg E, Wessels LFA, Blank CU, Schumacher TN. Spatial proximity of CD8 T cells to tumor cells as an independent biomarker for response to anti-PD-1 therapy. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.10038] [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
10038 Background: Only a subset of advanced melanoma patients respond to anti-PD-1 (aPD1) monotherapy. Upfront identification of (non-)responsiveness would help guide first-line treatment decisions, prevent overtreatment and unnecessary risk for toxicities. T cell density and expression of T cell related genes have been associated with response to aPD1, but are imperfect predictors. We investigated whether spatial proximity of CD8 T cells to tumor cells improves upon the predictive value of T cell density alone. Methods: Pretreatment tumor specimens from melanoma patients treated with aPD1 in the Netherlands Cancer Institute were stained for DAPI, SOX10/Melan-A, CD4, CD8, FOXP3 and PD-1 by multiplex immunofluorescence. Sections were imaged on Vectra and analyzed using HALO to optimize marker thresholds and demarcate tumor and stroma. T cell proximity to tumor cells was evaluated as difference in area under the curve between i) a spatial G-function quantifying T cell density around tumor cells in tumor areas and ii) analogous null distributions obtained by random permutation of cell labels. This assessment of co-clustering is independent of cell density and heterogeneity therein and does not reflect repulsion of T cells to stromal/marginal areas. Clinical characteristics, RECIST response and survival were collected from patient records. Associations between T cell density, T cell proximity to Sox10/Melan-A+ tumor cells, other clinical biomarkers (LDH, M stage and WHO performance status) and response were examined in a Bayesian hierarchical logistic regression. Results: Tumor specimens of 98 patients were included, of whom 45 were treated with aPD1 as first-line therapy and 33 had an objective response. CD8 T cell proximity to tumor cells was associated with response in an independent, comparatively strong, and tissue dependent manner (cutaneous tissue: 2.78 [2.45, 3.17], visceral: 2.30 [1.95, 2.72], lymphoid: 2.12 [1.88, 2.40], format: maximal posteriori odds ratio [89% equal-tailed credibility interval]), in a multivariate model correcting for CD8 T cell density (1.74 [1.62, 1.88]), LDH (1.93 [1.72, 2.16]), M stage (0.92 [0.87, 0.98]) and WHO performance status (0.79 [0.72, 0.88]). Our model achieved an area under the ROC curve of 77.7%, whereas an analogous model omitting the proximity variable achieved 73.1%. Conclusions: Our analyses show that spatial proximity of CD8 T cells to tumor cells functions as an independent biomarker for response to aPD1 and suggests that preexisting CD8 T cell tumor reactivity is reflected by this spatial proximity.
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Affiliation(s)
| | | | - Huiwen Ding
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Dennis Peters
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Hugo Horlings
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Lodewyk F. A. Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
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36
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van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell 2020; 177:1375-1383. [PMID: 31150618 DOI: 10.1016/j.cell.2019.05.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 10/16/2018] [Revised: 03/04/2019] [Accepted: 04/30/2019] [Indexed: 12/30/2022]
Abstract
Recent studies of the tumor genome seek to identify cancer pathways as groups of genes in which mutations are epistatic with one another or, specifically, "mutually exclusive." Here, we show that most mutations are mutually exclusive not due to pathway structure but to interactions with disease subtype and tumor mutation load. In particular, many cancer driver genes are mutated preferentially in tumors with few mutations overall, causing mutations in these cancer genes to appear mutually exclusive with numerous others. Researchers should view current epistasis maps with caution until we better understand the multiple cause-and-effect relationships among factors such as tumor subtype, positive selection for mutations, and gross tumor characteristics including mutational signatures and load.
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Affiliation(s)
- Joris van de Haar
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands; Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sander Canisius
- Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michael K Yu
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emile E Voest
- Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft, 2628 CD, the Netherlands.
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative, University of California, San Diego, La Jolla, CA 92093, USA.
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37
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Flach KD, Periyasamy M, Jadhav A, Dorjsuren D, Siefert JC, Hickey TE, Opdam M, Patel H, Canisius S, Wilson DM, Donaldson Collier M, Prekovic S, Nieuwland M, Kluin RJC, Zakharov AV, Wesseling J, Wessels LFA, Linn SC, Tilley WD, Simeonov A, Ali S, Zwart W. Endonuclease FEN1 Coregulates ERα Activity and Provides a Novel Drug Interface in Tamoxifen-Resistant Breast Cancer. Cancer Res 2020; 80:1914-1926. [PMID: 32193286 DOI: 10.1158/0008-5472.can-19-2207] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/30/2020] [Accepted: 03/09/2020] [Indexed: 11/16/2022]
Abstract
Estrogen receptor α (ERα) is a key transcriptional regulator in the majority of breast cancers. ERα-positive patients are frequently treated with tamoxifen, but resistance is common. In this study, we refined a previously identified 111-gene outcome prediction-classifier, revealing FEN1 as the strongest determining factor in ERα-positive patient prognostication. FEN1 levels were predictive of outcome in tamoxifen-treated patients, and FEN1 played a causal role in ERα-driven cell growth. FEN1 impacted the transcriptional activity of ERα by facilitating coactivator recruitment to the ERα transcriptional complex. FEN1 blockade induced proteasome-mediated degradation of activated ERα, resulting in loss of ERα-driven gene expression and eradicated tumor cell proliferation. Finally, a high-throughput 465,195 compound screen identified a novel FEN1 inhibitor, which effectively blocked ERα function and inhibited proliferation of tamoxifen-resistant cell lines as well as ex vivo-cultured ERα-positive breast tumors. Collectively, these results provide therapeutic proof of principle for FEN1 blockade in tamoxifen-resistant breast cancer. SIGNIFICANCE: These findings show that pharmacologic inhibition of FEN1, which is predictive of outcome in tamoxifen-treated patients, effectively blocks ERα function and inhibits proliferation of tamoxifen-resistant tumor cells.
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Affiliation(s)
- Koen D Flach
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, the Netherlands.,Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Ajit Jadhav
- National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Joseph C Siefert
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia
| | - Mark Opdam
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hetal Patel
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sander Canisius
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David M Wilson
- Laboratory of Molecular Gerontology, Intramural Research Program, National Institute on Aging, NIH, Baltimore, Maryland
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, the Netherlands
| | - Marja Nieuwland
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, the Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, NIH, Bethesda, Maryland
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands.,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
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38
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Klarenbeek S, Doornebal CW, Kas SM, Bonzanni N, Bhin J, Braumuller TM, van der Heijden I, Opdam M, Schouten PC, Kersten K, de Bruijn R, Zingg D, Yemelyanenko J, Wessels LFA, de Visser KE, Jonkers J. Response of metastatic mouse invasive lobular carcinoma to mTOR inhibition is partly mediated by the adaptive immune system. Oncoimmunology 2020; 9:1724049. [PMID: 32117586 PMCID: PMC7028325 DOI: 10.1080/2162402x.2020.1724049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/03/2019] [Revised: 11/14/2019] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Effective treatment of invasive lobular carcinoma (ILC) of the breast is hampered by late detection, invasive growth, distant metastasis, and poor response to chemotherapy. Phosphoinositide 3-kinase (PI3K) signaling, one of the major druggable oncogenic signaling networks, is frequently activated in ILC. We investigated treatment response and resistance to AZD8055, an inhibitor of mammalian target of rapamycin (mTOR), in the K14-cre;Cdh1Flox/Flox;Trp53Flox/Flox (KEP) mouse model of metastatic ILC. Inhibition of mTOR signaling blocked the growth of primary KEP tumors as well as the progression of metastatic disease. However, primary tumors and distant metastases eventually acquired resistance after long-term AZD8055 treatment, despite continued effective suppression of mTOR signaling in cancer cells. Interestingly, therapeutic responses were associated with increased expression of genes related to antigen presentation. Consistent with this observation, increased numbers of tumor-infiltrating major histocompatibility complex class II-positive (MHCII+) immune cells were observed in treatment-responsive KEP tumors. Acquisition of treatment resistance was associated with loss of MHCII+ cells and reduced expression of genes related to the adaptive immune system. The therapeutic efficacy of mTOR inhibition was reduced in Rag1−/- mice lacking mature T and B lymphocytes, compared to immunocompetent mice. Furthermore, therapy responsiveness could be partially rescued by transplanting AZD8055-resistant KEP tumors into treatment-naïve immunocompetent hosts. Collectively, these data indicate that the PI3K signaling pathway is an attractive therapeutic target in invasive lobular carcinoma, and that part of the therapeutic effect of mTOR inhibition is mediated by the adaptive immune system.
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Affiliation(s)
- Sjoerd Klarenbeek
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Chris W Doornebal
- Oncode Institute, Utrecht, The Netherlands.,Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Anesthesiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sjors M Kas
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Nicola Bonzanni
- Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,ENPICOM, 's-Hertogenbosch, The Netherlands
| | - Jinhyuk Bhin
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tanya M Braumuller
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelly Kersten
- Oncode Institute, Utrecht, The Netherlands.,Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Zingg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Julia Yemelyanenko
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Karin E de Visser
- Oncode Institute, Utrecht, The Netherlands.,Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
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Stelloo S, Linder S, Nevedomskaya E, Valle-Encinas E, de Rink I, Wessels LFA, van der Poel H, Bergman AM, Zwart W. Androgen modulation of XBP1 is functionally driving part of the AR transcriptional program. Endocr Relat Cancer 2020; 27:67-79. [PMID: 31804970 DOI: 10.1530/erc-19-0181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 11/08/2022]
Abstract
Prostate cancer development and progression is largely dependent on androgen receptor (AR) signaling. AR is a hormone-dependent transcription factor, which binds to thousands of sites throughout the human genome to regulate expression of directly responsive genes, including pro-survival genes that enable tumor cells to cope with increased cellular stress. ERN1 and XBP1 - two key players of the unfolded protein response (UPR) - are among such stress-associated genes. Here, we show that XBP1 levels in primary prostate cancer are associated with biochemical recurrence in five independent cohorts. Patients who received AR-targeted therapies had significantly lower XBP1 expression, whereas expression of the active form of XBP1 (XBP1s) was elevated. In vitro results show that AR-induced ERN1 expression led to increased XBP1s mRNA and protein levels. Furthermore, ChIP-seq analysis revealed that XBP1s binds enhancers upon stress stimuli regulating genes involved in UPR processes, eIF2 signaling and protein ubiquitination. We further demonstrate genomic overlap of AR- and XBP1s-binding sites, suggesting genomic conversion of the two signaling cascades. Transcriptomic effects of XBP1 were further studied by knockdown experiments, which lead to decreased expression of androgen-responsive genes and UPR genes. These results suggest a two-step mechanism of gene regulation, which involves androgen-induced expression of ERN1, thereby enhancing XBP1 splicing and transcriptional activity. This signaling cascade may prepare the cells for the increased protein folding, mRNA decay and translation that accompanies AR-regulated tumor cell proliferation.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ekaterina Nevedomskaya
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Eider Valle-Encinas
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris de Rink
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Henk van der Poel
- Division of Urology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. Nat Commun 2020; 11:312. [PMID: 31949161 PMCID: PMC6965101 DOI: 10.1038/s41467-019-14100-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 01/31/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.
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Affiliation(s)
- Maria Escala-Garcia
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Jean Abraham
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, University of Cambridge NHS Foundation Hospitals, Cambridge, UK
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Javier Benitez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, University of Tübingen, Tübingen, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Breast Cancer Programme, CRUK Cambridge Cancer Centre and NIHR Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Janet A Dunn
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Helena M Earl
- Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, University of Cambridge NHS Foundation Hospitals, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carolina Ellberg
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - D Gareth Evans
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Genomic Medicine, St Mary's Hospital, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Edinburgh, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Angela George
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), University Paris-Saclay, INSERM, University Paris-Sud, Villejuif, France
| | - Qi Guo
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Louise Hiller
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Esther M John
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Linetta B Koppert
- Department of Surgical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Diether Lambrechts
- VIB, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Flavio Lejbkowicz
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Pathology, Imaging Center, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Genomic Medicine, St Mary's Hospital, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew F Olshan
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Ireland, UK
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Christos Petridis
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Ross L Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Kevin Punie
- Department of Oncology, Leuven Multidisciplinary Breast Center, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | | | - Gad Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | | | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Lukas Schwentner
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jacques Simard
- Genomics Center, Research Center, Centre Hospitalier Universitaire de Québec - Université Laval, Québec City, QC, Canada
| | - Christof Sohn
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Heather Thorne
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Melissa A Troester
- Department of Epidemiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), University Paris-Saclay, INSERM, University Paris-Sud, Villejuif, France
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Biocenter Oulu, Cancer and Translational Medicine Research Unit, Laboratory of Cancer Genetics and Tumor Biology, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
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Šuštić T, Bosdriesz E, van Wageningen S, Wessels LFA, Bernards R. RUNX2/CBFB modulates the response to MEK inhibitors through activation of receptor tyrosine kinases in KRAS-mutant colorectal cancer. Transl Oncol 2019; 13:201-211. [PMID: 31865182 PMCID: PMC6931198 DOI: 10.1016/j.tranon.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 10/26/2022] Open
Abstract
Intrinsic and acquired resistances are major hurdles preventing the effective use of MEK inhibitors for treatment of colorectal cancer (CRC). Some 35-45% of colorectal cancers are KRAS-mutant and their treatment remains challenging as these cancers are refractory to MEK inhibitor treatment, because of feedback activation of receptor tyrosine kinases (RTKs). We reported previously that loss of ERN1 sensitizes a subset of KRAS-mutant colon cancer cells to MEK inhibition. Here we show that the loss of RUNX2 or its cofactor CBFB can confer MEK inhibitor resistance in CRC cells. Mechanistically, we find that cells with genetically ablated RUNX2 or CBFB activate multiple RTKs, which coincides with high SHP2 phosphatase activity, a phosphatase that relays signals from the cell membrane to downstream pathways governing growth and proliferation. Moreover, we show that high activity of SHP2 is causal to loss of RUNX2-induced MEK inhibitor resistance, as a small molecule SHP2 inhibitor reinstates sensitivity to MEK inhibitor in RUNX2 knockout cells. Our results reveal an unexpected role for loss of RUNX2/CBFB in regulating RTK activity in colon cancer, resulting in reduced sensitivity to MEK inhibitors.
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Affiliation(s)
- Tonći Šuštić
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066, CX, the Netherlands
| | - Evert Bosdriesz
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066, CX, the Netherlands
| | - Sake van Wageningen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066, CX, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066, CX, the Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066, CX, the Netherlands.
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42
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Kim Y, Bismeijer T, Zwart W, Wessels LFA, Vis DJ. Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo. Nat Commun 2019; 10:5034. [PMID: 31695042 PMCID: PMC6834616 DOI: 10.1038/s41467-019-13027-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 07/26/2018] [Accepted: 10/10/2019] [Indexed: 01/20/2023] Open
Abstract
Integrative analyses that summarize and link molecular data to treatment sensitivity are crucial to capture the biological complexity which is essential to further precision medicine. We introduce Weighted Orthogonal Nonnegative parallel factor analysis (WON-PARAFAC), a data integration method that identifies sparse and interpretable factors. WON-PARAFAC summarizes the GDSC1000 cell line compendium in 130 factors. We interpret the factors based on their association with recurrent molecular alterations, pathway enrichment, cancer type, and drug-response. Crucially, the cell line derived factors capture the majority of the relevant biological variation in Patient-Derived Xenograft (PDX) models, strongly suggesting our factors capture invariant and generalizable aspects of cancer biology. Furthermore, drug response in cell lines is better and more consistently translated to PDXs using factor-based predictors as compared to raw feature-based predictors. WON-PARAFAC efficiently summarizes and integrates multiway high-dimensional genomic data and enhances translatability of drug response prediction from cell lines to patient-derived xenografts.
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Affiliation(s)
- Yongsoo Kim
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. .,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.
| | - Daniel J Vis
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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43
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Dorel M, Klinger B, Gross T, Sieber A, Prahallad A, Bosdriesz E, Wessels LFA, Blüthgen N. Modelling signalling networks from perturbation data. Bioinformatics 2019; 34:4079-4086. [PMID: 29931053 DOI: 10.1093/bioinformatics/bty473] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation Intracellular signalling is realized by complex signalling networks, which are almost impossible to understand without network models, especially if feedbacks are involved. Modular Response Analysis (MRA) is a convenient modelling method to study signalling networks in various contexts. Results We developed the software package STASNet (STeady-STate Analysis of Signalling Networks) that provides an augmented and extended version of MRA suited to model signalling networks from incomplete perturbation schemes and multi-perturbation data. Using data from the Dialogue on Reverse Engineering Assessment and Methods challenge, we show that predictions from STASNet models are among the top-performing methods. We applied the method to study the effect of SHP2, a protein that has been implicated in resistance to targeted therapy in colon cancer, using a novel dataset from the colon cancer cell line Widr and a SHP2-depleted derivative. We find that SHP2 is required for mitogen-activated protein kinase signalling, whereas AKT signalling only partially depends on SHP2. Availability and implementation An R-package is available at https://github.com/molsysbio/STASNet. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mathurin Dorel
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Bertram Klinger
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Torsten Gross
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Anja Sieber
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Anirudh Prahallad
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands
| | - Evert Bosdriesz
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands
| | - Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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44
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Abstract
Motivation In biology, we are often faced with multiple datasets recorded on the same set of objects, such as multi-omics and phenotypic data of the same tumors. These datasets are typically not independent from each other. For example, methylation may influence gene expression, which may, in turn, influence drug response. Such relationships can strongly affect analyses performed on the data, as we have previously shown for the identification of biomarkers of drug response. Therefore, it is important to be able to chart the relationships between datasets. Results We present iTOP, a methodology to infer a topology of relationships between datasets. We base this methodology on the RV coefficient, a measure of matrix correlation, which can be used to determine how much information is shared between two datasets. We extended the RV coefficient for partial matrix correlations, which allows the use of graph reconstruction algorithms, such as the PC algorithm, to infer the topologies. In addition, since multi-omics data often contain binary data (e.g. mutations), we also extended the RV coefficient for binary data. Applying iTOP to pharmacogenomics data, we found that gene expression acts as a mediator between most other datasets and drug response: only proteomics clearly shares information with drug response that is not present in gene expression. Based on this result, we used TANDEM, a method for drug response prediction, to identify which variables predictive of drug response were distinct to either gene expression or proteomics. Availability and implementation An implementation of our methodology is available in the R package iTOP on CRAN. Additionally, an R Markdown document with code to reproduce all figures is provided as Supplementary Material. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nanne Aben
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Yipeng Song
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk A L Kiers
- Heymans Institute, University of Groningen, Groningen, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Age K Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
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45
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Bosdriesz E, Prahallad A, Klinger B, Sieber A, Bosma A, Bernards R, Blüthgen N, Wessels LFA. Comparative Network Reconstruction using mixed integer programming. Bioinformatics 2019; 34:i997-i1004. [PMID: 30423075 PMCID: PMC6129277 DOI: 10.1093/bioinformatics/bty616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/21/2022] Open
Abstract
Motivation Signal-transduction networks are often aberrated in cancer cells, and new anti-cancer drugs that specifically target oncogenes involved in signaling show great clinical promise. However, the effectiveness of such targeted treatments is often hampered by innate or acquired resistance due to feedbacks, crosstalks or network adaptations in response to drug treatment. A quantitative understanding of these signaling networks and how they differ between cells with different oncogenic mutations or between sensitive and resistant cells can help in addressing this problem. Results Here, we present Comparative Network Reconstruction (CNR), a computational method to reconstruct signaling networks based on possibly incomplete perturbation data, and to identify which edges differ quantitatively between two or more signaling networks. Prior knowledge about network topology is not required but can straightforwardly be incorporated. We extensively tested our approach using simulated data and applied it to perturbation data from a BRAF mutant, PTPN11 KO cell line that developed resistance to BRAF inhibition. Comparing the reconstructed networks of sensitive and resistant cells suggests that the resistance mechanism involves re-establishing wild-type MAPK signaling, possibly through an alternative RAF-isoform. Availability and implementation CNR is available as a python module at https://github.com/NKI-CCB/cnr. Additionally, code to reproduce all figures is available at https://github.com/NKI-CCB/CNR-analyses. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evert Bosdriesz
- Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anirudh Prahallad
- Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bertram Klinger
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Anja Sieber
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany.,IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands
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46
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Wellenstein MD, Coffelt SB, Duits DEM, van Miltenburg MH, Slagter M, de Rink I, Henneman L, Kas SM, Prekovic S, Hau CS, Vrijland K, Drenth AP, de Korte-Grimmerink R, Schut E, van der Heijden I, Zwart W, Wessels LFA, Schumacher TN, Jonkers J, de Visser KE. Loss of p53 triggers WNT-dependent systemic inflammation to drive breast cancer metastasis. Nature 2019; 572:538-542. [PMID: 31367040 PMCID: PMC6707815 DOI: 10.1038/s41586-019-1450-6] [Citation(s) in RCA: 279] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/26/2019] [Indexed: 11/09/2022]
Abstract
Cancer-associated systemic inflammation is strongly linked to poor disease outcome in patients with cancer1,2. For most human epithelial tumour types, high systemic neutrophil-to-lymphocyte ratios are associated with poor overall survival3, and experimental studies have demonstrated a causal relationship between neutrophils and metastasis4,5. However, the cancer-cell-intrinsic mechanisms that dictate the substantial heterogeneity in systemic neutrophilic inflammation between tumour-bearing hosts are largely unresolved. Here, using a panel of 16 distinct genetically engineered mouse models for breast cancer, we uncover a role for cancer-cell-intrinsic p53 as a key regulator of pro-metastatic neutrophils. Mechanistically, loss of p53 in cancer cells induced the secretion of WNT ligands that stimulate tumour-associated macrophages to produce IL-1β, thus driving systemic inflammation. Pharmacological and genetic blockade of WNT secretion in p53-null cancer cells reverses macrophage production of IL-1β and subsequent neutrophilic inflammation, resulting in reduced metastasis formation. Collectively, we demonstrate a mechanistic link between the loss of p53 in cancer cells, secretion of WNT ligands and systemic neutrophilia that potentiates metastatic progression. These insights illustrate the importance of the genetic makeup of breast tumours in dictating pro-metastatic systemic inflammation, and set the stage for personalized immune intervention strategies for patients with cancer.
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Affiliation(s)
- Max D Wellenstein
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Seth B Coffelt
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.,Cancer Research UK Beatson Institute, Glasgow, UK
| | - Danique E M Duits
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martine H van Miltenburg
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten Slagter
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris de Rink
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Linda Henneman
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sjors M Kas
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cheei-Sing Hau
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim Vrijland
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne Paulien Drenth
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Eva Schut
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Karin E de Visser
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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47
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Song Y, Westerhuis JA, Aben N, Michaut M, Wessels LFA, Smilde AK. Principal component analysis of binary genomics data. Brief Bioinform 2019; 20:317-329. [PMID: 30657888 DOI: 10.1093/bib/bbx119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 07/22/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Genome-wide measurements of genetic and epigenetic alterations are generating more and more high-dimensional binary data. The special mathematical characteristics of binary data make the direct use of the classical principal component analysis (PCA) model to explore low-dimensional structures less obvious. Although there are several PCA alternatives for binary data in the psychometric, data analysis and machine learning literature, they are not well known to the bioinformatics community. Results: In this article, we introduce the motivation and rationale of some parametric and nonparametric versions of PCA specifically geared for binary data. Using both realistic simulations of binary data as well as mutation, CNA and methylation data of the Genomic Determinants of Sensitivity in Cancer 1000 (GDSC1000), the methods were explored for their performance with respect to finding the correct number of components, overfit, finding back the correct low-dimensional structure, variable importance, etc. The results show that if a low-dimensional structure exists in the data, that most of the methods can find it. When assuming a probabilistic generating process is underlying the data, we recommend to use the parametric logistic PCA model, while when such an assumption is not valid and the data are considered as given, the nonparametric Gifi model is recommended. Availability The codes to reproduce the results in this article are available at the homepage of the Biosystems Data Analysis group (www.bdagroup.nl).
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Affiliation(s)
- Yipeng Song
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Nanne Aben
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Age K Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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48
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Brana I, Massard C, Baird RD, Opdam F, Schlenk RF, De Petris L, Vernieri C, Chavarria E, Garralda E, van der Noll R, Vivancos A, Wessels LFA, Martin JE, Tamborero D, Dienstmann R, Meijer GA, Muñoz S, Piris-Giménez A, Calvo F, Rodon J. Basket of baskets (BoB): A modular, open label, phase II, multicenter study to evaluate targeted agents in molecularly selected populations with advanced solid tumors. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.tps3151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
TPS3151 Background: Basket trials with targeted agents can show high response rates for tumors with specific molecular profiles, granting extension of the label of some drugs. In other cases, study results were disappointing, likely due to the rarity of molecular alterations, limits in trial design and the difficulties in applying molecular tumor profiling in the clinical setting. Methods: Basket of Baskets (BoB), NCT03767075, aims to bridge the gap between Academic Genomics and clinical applications (ready-to market multi-marker Companion Diagnostics) by providing a sustainable and adaptable (to new technologies, markers, and therapeutic agents) platform for co-development of drug/companion diagnostic. BoB is a novel platform trial from Cancer Core Europe, a recently established sustainable European network for innovative cancer research. This protocol has two parts: (1) Part A includes a molecular profiling program for subjects with advanced solid tumors (iPROFILER), a variant annotation tool, and a molecular tumor board to select the most appropriate treatment. It also enables testing/developing companion diagnostics linked with the therapeutic part (part B). (2) Part B includes iBASKET, a modular multi-arm basket trial for subjects with tumors harboing selected molecular alterations. Each module is focused on a certain molecular pathway or on certain molecular alterations that may confer sensitivity to the study drug or study drug combination evaluated in that module/arm. The current version of iBASKET (Module 1- Atezolizumab in genomically-selected patients) is open for enrollment for patients with advanced neoplasms bearing one of the following alterations: Arm 1A: BRCA1 or BRCA2; Arm 1B: MLH1, MSH2, MSH6, PMS2; Arm 1C: POLE, POLD1 mutations; Arm 1D: hypermutated tumors; Arm 1E: other mutations in DNA-repair genes; Arm 1F: PDL1 gene amplification. All patients enrolled in Module 1 will receive single-agent atezolizumab. New Modules for genomically selected populations can be added through amendments. Our final aim is to achieve drug repurposing of treatments, co-develop multi-marker companion diagnostics and a large database of knowledge in Precision Medicine. Clinical trial information: NCT03767075.
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Affiliation(s)
- Irene Brana
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Christophe Massard
- Gustave Roussy Cancer Campus and University Paris-Sud, Villejuif, France
| | | | | | - Richard F. Schlenk
- National Center of Tumor Diseases Heidelberg, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Luigi De Petris
- Dep of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Claudio Vernieri
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | | | - Elena Garralda
- Hospital Universitari Vall d’Hebron, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ruud van der Noll
- The Netherlands Cancer Institute, Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Ana Vivancos
- Cancer Genomics Lab and Molecular Pathology Lab, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Lodewyk F. A. Wessels
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Susana Muñoz
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Jordi Rodon
- Vall d’Hebron University Hospital Institute of Oncology (VHIO), Barcelona, Spain
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49
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Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Nat Commun 2019; 10:1598. [PMID: 30962441 PMCID: PMC6453899 DOI: 10.1038/s41467-019-09551-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
- Data & Translational Sciences Group, UCB Biosciences GmbH, Alfred-Nobel-Straße 10, Monheim am Rhein, 40789, Germany
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Division of Gene Regulation, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands.
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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50
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Nagel R, Avelar AT, Aben N, Proost N, van de Ven M, van der Vliet J, Cozijnsen M, de Vries H, Wessels LFA, Berns A. Inhibition of the Replication Stress Response Is a Synthetic Vulnerability in SCLC That Acts Synergistically in Combination with Cisplatin. Mol Cancer Ther 2019; 18:762-770. [PMID: 30872379 DOI: 10.1158/1535-7163.mct-18-0972] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 08/27/2018] [Revised: 10/20/2018] [Accepted: 02/22/2019] [Indexed: 12/20/2022]
Abstract
Small cell lung cancer (SCLC) is generally regarded as very difficult to treat, mostly due to the development of metastases early in the disease and a quick relapse with resistant disease. SCLC patients initially show a good response to treatment with the DNA damaging agents cisplatin and etoposide. This is, however, quickly followed by the development of resistant disease, which urges the development of novel therapies for this type of cancer. In this study, we set out to compile a comprehensive overview of the vulnerabilities of SCLC. A functional genome-wide screen where all individual genes were knocked out was performed to identify novel vulnerabilities of SCLC. By analysis of the knockouts that were lethal to these cancer cells, we identified several processes to be synthetic vulnerabilities in SCLC. We were able to validate the vulnerability to inhibition of the replication stress response machinery by use of Chk1 and ATR inhibitors. Strikingly, SCLC cells were more sensitive to these inhibitors than nontransformed cells. In addition, these inhibitors work synergistically with either etoposide and cisplatin, where the interaction is largest with the latter. ATR inhibition by VE-822 treatment in combination with cisplatin also outperforms the combination of cisplatin with etoposide in vivo Altogether, our study uncovered a critical dependence of SCLC on the replication stress response and urges the validation of ATR inhibitors in combination with cisplatin in a clinical setting.
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Affiliation(s)
- Remco Nagel
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ana Teresa Avelar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nanne Aben
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Natalie Proost
- Preclinical Intervention Unit of the Mouse Clinic for Cancer and Ageing, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marieke van de Ven
- Preclinical Intervention Unit of the Mouse Clinic for Cancer and Ageing, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jan van der Vliet
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Miranda Cozijnsen
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hilda de Vries
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anton Berns
- Oncode Institute, Amsterdam, the Netherlands.
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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