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Middelburg J, Sluijter M, Schaap G, Göynük B, Lloyd K, Ovcinnikovs V, Zom GG, Marijnissen RJ, Groeneveldt C, Griffioen L, Sandker GGW, Heskamp S, van der Burg SH, Arakelian T, Ossendorp F, Arens R, Schuurman J, Kemper K, van Hall T. T-cell stimulating vaccines empower CD3 bispecific antibody therapy in solid tumors. Nat Commun 2024; 15:48. [PMID: 38167722 PMCID: PMC10761684 DOI: 10.1038/s41467-023-44308-6] [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: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
CD3 bispecific antibody (CD3 bsAb) therapy is clinically approved for refractory hematological malignancies, but responses in solid tumors have been limited so far. One of the main hurdles in solid tumors is the lack of sufficient T-cell infiltrate. Here, we show that pre-treatment vaccination, even when composed of tumor-unrelated antigens, induces CXCR3-mediated T-cell influx in immunologically 'cold' tumor models in male mice. In the absence of CD3 bsAb, the infiltrate is confined to the tumor invasive margin, whereas subsequent CD3 bsAb administration induces infiltration of activated effector CD8 T cells into the tumor cell nests. This combination therapy installs a broadly inflamed Th1-type tumor microenvironment, resulting in effective tumor eradication. Multiple vaccination formulations, including synthetic long peptides and viruses, empower CD3 bsAb therapy. Our results imply that eliciting tumor infiltration with vaccine-induced tumor-(un)related T cells can greatly improve the efficacy of CD3 bsAbs in solid tumors.
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Affiliation(s)
- Jim Middelburg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Gaby Schaap
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Büşra Göynük
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | | | | | - Christianne Groeneveldt
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Lisa Griffioen
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Gerwin G W Sandker
- Department of Medical Imaging, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Sandra Heskamp
- Department of Medical Imaging, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Tsolere Arakelian
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Thorbald van Hall
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands.
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Kemper K, Gielen E, Boross P, Houtkamp M, Plantinga TS, de Poot SAH, Burm SM, Janmaat ML, Koopman LA, van den Brink EN, Rademaker R, Verzijl D, Engelberts PJ, Satijn D, Sasser AK, Breij ECW. Mechanistic and pharmacodynamic studies of DuoBody-CD3x5T4 in preclinical tumor models. Life Sci Alliance 2022; 5:5/11/e202201481. [PMID: 36271507 PMCID: PMC9458754 DOI: 10.26508/lsa.202201481] [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] [Received: 04/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
CD3 bispecific antibodies (bsAbs) show great promise as anticancer therapeutics. Here, we show in-depth mechanistic studies of a CD3 bsAb in solid cancer, using DuoBody-CD3x5T4. Cross-linking T cells with tumor cells expressing the oncofetal antigen 5T4 was required to induce cytotoxicity. Naive and memory CD4+ and CD8+ T cells were equally effective at mediating cytotoxicity, and DuoBody-CD3x5T4 induced partial differentiation of naive T-cell subsets into memory-like cells. Tumor cell kill was associated with T-cell activation, proliferation, and production of cytokines, granzyme B, and perforin. Genetic knockout of FAS or IFNGR1 in 5T4+ tumor cells abrogated tumor cell kill. In the presence of 5T4+ tumor cells, bystander kill of 5T4− but not of 5T4−IFNGR1− tumor cells was observed. In humanized xenograft models, DuoBody-CD3x5T4 antitumor activity was associated with intratumoral and peripheral blood T-cell activation. Lastly, in dissociated patient-derived tumor samples, DuoBody-CD3x5T4 activated tumor-infiltrating lymphocytes and induced tumor-cell cytotoxicity, even when most tumor-infiltrating lymphocytes expressed PD-1. These data provide an in-depth view on the mechanism of action of a CD3 bsAb in preclinical models of solid cancer.
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3
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Ven RVD, Ganzevles S, Veth M, Franken P, Breij E, Brakenhoff R, Kemper K. 889 DuoBody®-CD3x5T4 induces efficient T-cell activation and killing of patient-derived head and neck cancer cells in vitro and ex vivo. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Background5T4, also known as trophoblast glycoprotein, is expressed in many solid cancers, including non-small cell lung cancer, triple-negative breast cancer, bladder, esophageal, prostate, uterine and head and neck squamous cell carcinomas (HNSCCs). DuoBody-CD3x5T4 is a CD3 bispecific antibody that efficiently induces T-cell mediated cytotoxicity of 5T4-positive tumor cells. Currently, DuoBody-CD3x5T4 is being evaluated in a first-in-human clinical trial (NCT04424641) in solid cancers in partnership between Genmab and AbbVie. In this study we explored the preclinical mechanism-of-action of DuoBody-CD3x5T4 in vitro and ex vivo, using HNSCC as a case study.Methods5T4 protein expression in HNSCC tumor specimens was determined by immunohistochemistry (IHC) and flow cytometry. T-cell mediated cytotoxicity and T-cell activation induced by DuoBody-CD3x5T4 were studied in co-cultures of healthy donor T cells and patient-derived HNSCC cell lines in vitro. Lastly, the capacity of DuoBody-CD3x5T4 to activate tumor-infiltrating lymphocytes (TILs) was analyzed in freshly dissociated 5T4-expressing HNSCC tumor specimens ex vivo.ResultsIHC analysis confirmed expression of 5T4 in HNSCC oral biopsies, including specimens from primary tumors, recurrent tumors and lymph node metastases. Patient-derived HNSCC cell lines (n=22) demonstrated 5T4 expression on the plasma membrane, ranging from 10,000 - 61,000 5T4 molecules per cell. Moreover, 5T4 expression was evident on EGFR+CD45- tumor cells in single-cell suspensions from freshly dissociated HNSCC biopsies, independent of the tumor site. DuoBody-CD3x5T4 demonstrated potent, target-dependent cytotoxicity in vitro in co-cultures of healthy donor T cells and patient-derived HNSCC cell lines across the range of 5T4 expression levels tested. Tumor cell kill was associated with CD4+ and CD8+ T-cell activation and granzyme B secretion. Importantly, DuoBody-CD3x5T4 induced potent activation of autologous TILs in single-cell suspensions from freshly dissociated HNSCC biopsies. Notably, T-cell activation (as assessed by expression of CD69, CD25 and CD137) was also observed in PD-1+ TILs, suggesting that DuoBody-CD3x5T4 was able to engage antigen-experienced T cells in the tumor microenvironment. In this autologous assay, preliminary data showed that 5T4-expressing HNSCC tumor cells were specifically eradicated.Conclusions5T4 was broadly expressed in HNSCC cell lines, tumor biopsies and primary tumor cell suspensions. DuoBody-CD3x5T4 activated healthy donor T cells in co-cultures with patient-derived HNSCC cell lines, resulting in secretion of granzyme B and efficient tumor cell kill. In single-cell suspensions from freshly dissociated 5T4+ HNSCC biopsies, DuoBody-CD3x5T4 activated autologous CD4+ and CD8+ TILs, including PD-1+ TILs. This dataset adds to the preclinical evidence for targeting 5T4-expressing solid cancers with DuoBody-CD3x5T4.Ethics ApprovalWritten informed consent was obtained from all patients from whom fresh tumor biopsies were used for research, as part of the HNcol protocol at the Department of Otolaryngology|Head and Neck Surgery of Amsterdam UMC (VUmc) as approved by the Institutional Review Board (2008.071|A2016.035). Archival FFPE specimens were used for scientific research in agreement with the medical ethical guidelines described in the Code of Conduct for Proper Secondary Use of Human Tissue of the Dutch Federation of Biomedical Scientific Societies (Federa) in accordance with the Declaration of Helsinki and after Biobank approval (BUP2019-74).
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Merrell K, Ochieng P, Osei - Bonsu E, Seife E, Kemper K, Begna K, Bussman S, Leavitt T, Acheamfour O, Vanderpuye V, Manirakiza A, DeWees T, Addison E. 1622P The impact of COVID-19 on cancer treatment delivery in Sub-Saharan Africa. Ann Oncol 2021. [PMCID: PMC8454350 DOI: 10.1016/j.annonc.2021.08.1615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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5
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Krijgsman O, Kemper K, Boshuizen J, Vredevoogd DW, Rozeman EA, Ibanez Molero S, de Bruijn B, Cornelissen-Steijger P, Shahrabi A, Del Castillo Velasco-Herrera M, Song JY, Ligtenberg MA, Kluin RJC, Kuilman T, Ross-Macdonald P, Haanen JBAG, Adams DJ, Blank CU, Peeper DS. Predictive Immune-Checkpoint Blockade Classifiers Identify Tumors Responding to Inhibition of PD-1 and/or CTLA-4. Clin Cancer Res 2021; 27:5389-5400. [PMID: 34230026 DOI: 10.1158/1078-0432.ccr-20-4218] [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: 10/29/2020] [Revised: 12/01/2020] [Accepted: 06/25/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Combining anti-PD-1 + anti-CTLA-4 immune-checkpoint blockade (ICB) shows improved patient benefit, but it is associated with severe immune-related adverse events and exceedingly high cost. Therefore, there is a dire need to predict which patients respond to monotherapy and which require combination ICB treatment. EXPERIMENTAL DESIGN In patient-derived melanoma xenografts (PDX), human tumor microenvironment (TME) cells were swiftly replaced by murine cells upon transplantation. Using our XenofilteR deconvolution algorithm we curated human tumor cell RNA reads, which were subsequently subtracted in silico from bulk (tumor cell + TME) patients' melanoma RNA. This produced a purely tumor cell-intrinsic signature ("InTumor") and a signature comprising tumor cell-extrinsic RNA reads ("ExTumor"). RESULTS We show that whereas the InTumor signature predicts response to anti-PD-1, the ExTumor predicts anti-CTLA-4 benefit. In PDX, InTumorLO, but not InTumorHI, tumors are effectively eliminated by cytotoxic T cells. When used in conjunction, the InTumor and ExTumor signatures identify not only patients who have a substantially higher chance of responding to combination treatment than to either monotherapy, but also those who are likely to benefit little from anti-CTLA-4 on top of anti-PD-1. CONCLUSIONS These signatures may be exploited to distinguish melanoma patients who need combination ICB blockade from those who likely benefit from either monotherapy.
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Affiliation(s)
- Oscar Krijgsman
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kristel Kemper
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Julia Boshuizen
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David W Vredevoogd
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elisa A Rozeman
- Medical Oncology Department, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sofia Ibanez Molero
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Beaunelle de Bruijn
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paulien Cornelissen-Steijger
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Aida Shahrabi
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Ji-Ying Song
- Animal Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thomas Kuilman
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - John B A G Haanen
- Medical Oncology Department, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Christian U Blank
- Medical Oncology Department, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniel S Peeper
- Department of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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6
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Middelburg J, Kemper K, Engelberts P, Labrijn AF, Schuurman J, van Hall T. Overcoming Challenges for CD3-Bispecific Antibody Therapy in Solid Tumors. Cancers (Basel) 2021; 13:287. [PMID: 33466732 PMCID: PMC7829968 DOI: 10.3390/cancers13020287] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy of cancer with CD3-bispecific antibodies is an approved therapeutic option for some hematological malignancies and is under clinical investigation for solid cancers. However, the treatment of solid tumors faces more pronounced hurdles, such as increased on-target off-tumor toxicities, sparse T-cell infiltration and impaired T-cell quality due to the presence of an immunosuppressive tumor microenvironment, which affect the safety and limit efficacy of CD3-bispecific antibody therapy. In this review, we provide a brief status update of the CD3-bispecific antibody therapy field and identify intrinsic hurdles in solid cancers. Furthermore, we describe potential combinatorial approaches to overcome these challenges in order to generate selective and more effective responses.
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Affiliation(s)
- Jim Middelburg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| | - Kristel Kemper
- Genmab, 3584 CT Utrecht, The Netherlands; (K.K.); (P.E.); (A.F.L.); (J.S.)
| | - Patrick Engelberts
- Genmab, 3584 CT Utrecht, The Netherlands; (K.K.); (P.E.); (A.F.L.); (J.S.)
| | - Aran F. Labrijn
- Genmab, 3584 CT Utrecht, The Netherlands; (K.K.); (P.E.); (A.F.L.); (J.S.)
| | - Janine Schuurman
- Genmab, 3584 CT Utrecht, The Netherlands; (K.K.); (P.E.); (A.F.L.); (J.S.)
| | - Thorbald van Hall
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
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7
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Sanchez IM, Purwin TJ, Chervoneva I, Erkes DA, Nguyen MQ, Davies MA, Nathanson KL, Kemper K, Peeper DS, Aplin AE. In Vivo ERK1/2 Reporter Predictively Models Response and Resistance to Combined BRAF and MEK Inhibitors in Melanoma. Mol Cancer Ther 2019; 18:1637-1648. [PMID: 31270153 PMCID: PMC6726573 DOI: 10.1158/1535-7163.mct-18-1056] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/02/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023]
Abstract
Combined BRAF and MEK inhibition is a standard of care in patients with advanced BRAF-mutant melanoma, but acquired resistance remains a challenge that limits response durability. Here, we quantitated in vivo ERK1/2 activity and tumor response associated with resistance to combined BRAF and MEK inhibition in mutant BRAF xenografts. We found that ERK1/2 pathway reactivation preceded the growth of resistant tumors. Moreover, we detected a subset of cells that not only persisted throughout long-term treatment but restored ERK1/2 signaling and grew upon drug removal. Cell lines derived from combination-resistant tumors (CRT) exhibited elevated ERK1/2 phosphorylation, which were sensitive to ERK1/2 inhibition. In some CRTs, we detected a tandem duplication of the BRAF kinase domain. Monitoring ERK1/2 activity in vivo was efficacious in predicting tumor response during intermittent treatment. We observed maintained expression of the mitotic regulator, polo-like kinase 1 (Plk1), in melanoma resistant to BRAF and MEK inhibitors. Plk1 inhibition induced apoptosis in CRTs, leading to slowed growth of BRAF and MEK inhibitor-resistant tumors in vivo These data demonstrate the utility of in vivo ERK1/2 pathway reporting as a tool to optimize clinical dosing schemes and establish suppression of Plk1 as potential salvage therapy for BRAF inhibitor and MEK inhibitor-resistant melanoma.
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Affiliation(s)
- Ileine M Sanchez
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Timothy J Purwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Inna Chervoneva
- Division of Biostatistics, Sidney Kimmel Cancer Center at Jefferson, Philadelphia, Pennsylvania
| | - Dan A Erkes
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Mai Q Nguyen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael A Davies
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Katherine L Nathanson
- Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristel Kemper
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.
- Department of Pharmacology and Experimental Therapeutics, Sidney Kimmel Cancer Center at Jefferson, Philadelphia, Pennsylvania
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8
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Coppé JP, Mori M, Pan B, Yau C, Wolf DM, Ruiz-Saenz A, Brunen D, Prahallad A, Cornelissen-Steijger P, Kemper K, Posch C, Wang C, Dreyer CA, Krijgsman O, Lee PRE, Chen Z, Peeper DS, Moasser MM, Bernards R, van 't Veer LJ. Mapping phospho-catalytic dependencies of therapy-resistant tumours reveals actionable vulnerabilities. Nat Cell Biol 2019; 21:778-790. [PMID: 31160710 DOI: 10.1038/s41556-019-0328-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/09/2019] [Indexed: 12/21/2022]
Abstract
Phosphorylation networks intimately regulate mechanisms of response to therapies. Mapping the phospho-catalytic profile of kinases in cells or tissues remains a challenge. Here, we introduce a practical high-throughput system to measure the enzymatic activity of kinases using biological peptide targets as phospho-sensors to reveal kinase dependencies in tumour biopsies and cell lines. A 228-peptide screen was developed to detect the activity of >60 kinases, including ABLs, AKTs, CDKs and MAPKs. Focusing on BRAFV600E tumours, we found mechanisms of intrinsic resistance to BRAFV600E-targeted therapy in colorectal cancer, including targetable parallel activation of PDPK1 and PRKCA. Furthermore, mapping the phospho-catalytic signatures of melanoma specimens identifies RPS6KB1 and PIM1 as emerging druggable vulnerabilities predictive of poor outcome in BRAFV600E patients. The results show that therapeutic resistance can be caused by the concerted upregulation of interdependent pathways. Our kinase activity-mapping system is a versatile strategy that innovates the exploration of actionable kinases for precision medicine.
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Affiliation(s)
- Jean-Philippe Coppé
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| | - Miki Mori
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Breast Surgical Oncology, Showa University, Tokyo, Japan
| | - Bo Pan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Christina Yau
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Denise M Wolf
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ana Ruiz-Saenz
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Diede Brunen
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anirudh Prahallad
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Kristel Kemper
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christian Posch
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany.,School of Medicine, Sigmund Freud University, Vienna, Austria
| | - Changjun Wang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Courtney A Dreyer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pei Rong Evelyn Lee
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Zhongzhong Chen
- The State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel S Peeper
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mark M Moasser
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - René Bernards
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laura J van 't Veer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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9
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Kluin RJC, Kemper K, Kuilman T, de Ruiter JR, Iyer V, Forment JV, Cornelissen-Steijger P, de Rink I, Ter Brugge P, Song JY, Klarenbeek S, McDermott U, Jonkers J, Velds A, Adams DJ, Peeper DS, Krijgsman O. XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data. BMC Bioinformatics 2018; 19:366. [PMID: 30286710 PMCID: PMC6172735 DOI: 10.1186/s12859-018-2353-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/30/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from the murine host. The reads of murine origin result in false positives in mutation analysis of DNA samples and obscure gene expression levels when sequencing RNA. However, currently available algorithms are limited and improvements in accuracy and ease of use are necessary. RESULTS We developed the R-package XenofilteR, which separates mouse from human sequence reads based on the edit-distance between a sequence read and reference genome. To assess the accuracy of XenofilteR, we generated sequence data by in silico mixing of mouse and human DNA sequence data. These analyses revealed that XenofilteR removes > 99.9% of sequence reads of mouse origin while retaining human sequences. This allowed for mutation analysis of xenograft samples with accurate variant allele frequencies, and retrieved all non-synonymous somatic tumor mutations. CONCLUSIONS XenofilteR accurately dissects RNA and DNA sequences from mouse and human origin, thereby outperforming currently available tools. XenofilteR is open source and available at https://github.com/PeeperLab/XenofilteR .
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Affiliation(s)
- Roelof J C Kluin
- Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kristel Kemper
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivek Iyer
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Josep V Forment
- The Wellcome Trust/Cancer Research UK (CRUK) Gurdon Institute, University of Cambridge, Cambridge, UK
- Present address: DNA Damage Response Biology, Bioscience Oncology IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Paulien Cornelissen-Steijger
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Iris de Rink
- Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra Ter Brugge
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sjoerd Klarenbeek
- Division of Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ultan McDermott
- Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David J Adams
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
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10
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Krijgsman O, Kluin RJC, Kemper K, Kuilman T, Ruiter JRD, Iyer V, Forment JV, Cornelissen-Steijger P, Rink ID, Brugge PT, Song JY, Klarenbeek S, McDermott U, Jonkers J, Velds A, Adams DJ, Peeper DS. Abstract 1041: XenofilteR: Computational dissection of mouse and human reads in PDX and xenograft sequence data. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analysis of their RNA and DNA profiles is challenging, because they comprise reads not only from the grafted human cancer but also from the murine host. The reads of murine origin can result both in the generation of false positives in mutation analysis of DNA samples and obscure gene expression levels when sequencing RNA. Therefore, we developed the open-source R-package XenofilteR, which separates mouse from human sequence reads based on the number of discordant base pairs between each read and the reference genomes. To assess the accuracy of XenofilteR, we generated sequence data by in silico mixing of mouse and human whole genome and whole exome DNA sequence data. This analysis revealed that XenofilteR removes >99.9% of sequence reads of mouse origin while retaining sequence reads of human origin. The filtering allowed for mutation analysis of PDX samples with accurate variant allele frequencies, and retrieved all non-synonymous somatic mutations present in the original tumor. These findings were further validated in breast cancer and melanoma PDX samples, confirming the retrieval of accurate variant allele frequencies and somatic mutations. In conclusion, XenofilteR accurately dissects sequence reads from mouse and human origin in PDX sequence data, thereby outperforming currently available tools.
Citation Format: Oscar Krijgsman, Roelof JC Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji-Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper. XenofilteR: Computational dissection of mouse and human reads in PDX and xenograft sequence data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1041.
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Affiliation(s)
| | | | | | | | | | - Vivek Iyer
- 2Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | | | - Iris de Rink
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Ji-Ying Song
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Jos Jonkers
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Arno Velds
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David J. Adams
- 2Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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11
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Krijgsman O, Kemper K, Rozeman E, Cornelissen-Steijger P, Shahrabi A, Haanen J, Adams D, Blank C, Peeper D. PO-512 Gene expression signature comprising distinct stromal and tumor-intrinsic signals predicts response to combined anti-PD1 and anti-CTLA4 checkpoint inhibition. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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12
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Yu Y, Schleich K, Yue B, Ji S, Lohneis P, Kemper K, Silvis MR, Qutob N, van Rooijen E, Werner-Klein M, Li L, Dhawan D, Meierjohann S, Reimann M, Elkahloun A, Treitschke S, Dörken B, Speck C, Mallette FA, Zon LI, Holmen SL, Peeper DS, Samuels Y, Schmitt CA, Lee S. Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma. Cancer Cell 2018; 33:785. [PMID: 29634951 DOI: 10.1016/j.ccell.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, Maddalo G. Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors. Mol Syst Biol 2018; 14:e7858. [PMID: 29507054 PMCID: PMC5836539 DOI: 10.15252/msb.20177858] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/15/2018] [Accepted: 02/01/2018] [Indexed: 12/19/2022] Open
Abstract
Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors for the treatment of therapy-resistant melanomas. Unfortunately, our data show that this combination elicits a heterogeneous response in a panel of melanoma cell lines including PDX-derived models. We sought to understand the mechanisms underlying the differential responses and suggest a patient stratification strategy. Thermal proteome profiling (TPP) identified the protein targets of XL888 in a pair of sensitive and unresponsive cell lines. Unbiased proteomics and phosphoproteomics analyses identified CDK2 as a driver of resistance to both BRAF and Hsp90 inhibitors and its expression is regulated by the transcription factor MITF upon XL888 treatment. The CDK2 inhibitor, dinaciclib, attenuated resistance to both classes of inhibitors and combinations thereof. Notably, we found that MITF expression correlates with CDK2 upregulation in patients; thus, dinaciclib would warrant consideration for treatment of patients unresponsive to BRAF-MEK and/or Hsp90 inhibitors and/or harboring MITF amplification/overexpression.
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Affiliation(s)
- Alireza Azimi
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Stefano Caramuta
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Boström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan L Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rainer Tuominen
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristel Kemper
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Suzanne Egyhazi Brage
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Altun
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Gianluca Maddalo
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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14
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Yu Y, Schleich K, Yue B, Ji S, Lohneis P, Kemper K, Silvis MR, Qutob N, van Rooijen E, Werner-Klein M, Li L, Dhawan D, Meierjohann S, Reimann M, Elkahloun A, Treitschke S, Dörken B, Speck C, Mallette FA, Zon LI, Holmen SL, Peeper DS, Samuels Y, Schmitt CA, Lee S. Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma. Cancer Cell 2018; 33:322-336.e8. [PMID: 29438700 PMCID: PMC5977991 DOI: 10.1016/j.ccell.2018.01.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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: 12/26/2015] [Revised: 10/16/2017] [Accepted: 01/04/2018] [Indexed: 12/23/2022]
Abstract
Oncogene-induced senescence, e.g., in melanocytic nevi, terminates the expansion of pre-malignant cells via transcriptional silencing of proliferation-related genes due to decoration of their promoters with repressive trimethylated histone H3 lysine 9 (H3K9) marks. We show here that structurally distinct H3K9-active demethylases-the lysine-specific demethylase-1 (LSD1) and several Jumonji C domain-containing moieties (such as JMJD2C)-disable senescence and permit Ras/Braf-evoked transformation. In mouse and zebrafish models, enforced LSD1 or JMJD2C expression promoted Braf-V600E-driven melanomagenesis. A large subset of established melanoma cell lines and primary human melanoma samples presented with a collective upregulation of related and unrelated H3K9 demethylase activities, whose targeted inhibition restored senescence, even in Braf inhibitor-resistant melanomas, evoked secondary immune effects and controlled tumor growth in vivo.
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Affiliation(s)
- Yong Yu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Kolja Schleich
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Bin Yue
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Sujuan Ji
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Philipp Lohneis
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, 10117 Berlin, Germany
| | - Kristel Kemper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mark R Silvis
- Department of Surgery, University of Utah Health Sciences Center & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Nouar Qutob
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot 7610001, Israel
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Melanie Werner-Klein
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, 93053 Regensburg, Germany; Experimental Medicine and Therapy Research, University of Regensburg, 93053 Regensburg, Germany
| | - Lianjie Li
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Dhriti Dhawan
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Svenja Meierjohann
- University of Würzburg, Physiological Chemistry, Biocenter, 97074 Würzburg, Germany
| | - Maurice Reimann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany
| | - Abdel Elkahloun
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Steffi Treitschke
- Fraunhofer-Institute for Toxicology and Experimental Medicine, 93053 Regensburg, Germany
| | - Bernd Dörken
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany
| | - Christian Speck
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, and MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
| | - Frédérick A Mallette
- Department of Medicine, Université de Montréal, Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4, Canada
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sheri L Holmen
- Department of Surgery, University of Utah Health Sciences Center & Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Yardena Samuels
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot 7610001, Israel
| | - Clemens A Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany.
| | - Soyoung Lee
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medical Department of Hematology, Oncology and Tumor Immunology, Virchow Campus, and Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Deutsches Konsortium für Translationale Krebsforschung (German Cancer Consortium), Partner Site Berlin, Germany
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15
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Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Cancer Res 2017; 77:e62-e66. [PMID: 29092942 PMCID: PMC5738926 DOI: 10.1158/0008-5472.can-17-0582] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/20/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
Abstract
Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62-66. ©2017 AACR.
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Affiliation(s)
- Terrence F Meehan
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom.
| | - Nathalie Conte
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom
| | - Theodore Goldstein
- Institute for Computational Health Sciences, University of California, San Francisco, California
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Mark A Murakami
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Sebastian Brabetz
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Zhiping Gu
- Northrop Grumman Information Systems Health IT, Rockville, Maryland
| | - Jeffrey A Wiser
- Northrop Grumman Information Systems Health IT, Rockville, Maryland
| | - Patrick Dunn
- Northrop Grumman Information Systems Health IT, Rockville, Maryland
| | | | | | - Andrea Bertotti
- Candiolo Cancer Institute, FPO-IRCC, Department of Oncology, University of Torino, Torino, Italy
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge, United Kingdom
| | - Matthew H Brush
- Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health and Science University, Portland, Oregon
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge, United Kingdom
| | - Amanda L Christie
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Dominic A Clark
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom
| | - Heidi Dowst
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Jonathan R Dry
- Oncology Innovative Medicines and Early Development, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - James H Doroshow
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | - Yvonne A Evrard
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Stephane Ferretti
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Switzerland
| | - Kristopher K Frese
- Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | | | | | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health and Science University, Portland, Oregon
| | - Els Hermans
- Katholieke Universiteit Leuven, Leuven, Belgium
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Jos Jonkers
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kristel Kemper
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tin O Khor
- Institute for Applied Cancer Science, Center for Co-Clinical Trial, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Lewis
- The Lester and Sue Smith Breast Center, Departments of Molecular and Cellular Biology and Radiology, Baylor College of Medicine, Houston, Texas
| | - K C Kent Lloyd
- Department of Surgery, School of Medicine, and Mouse Biology Program, University of California Davis, Davis, California
| | - Jeremy Mason
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom
| | - Enzo Medico
- Candiolo Cancer Institute, FPO-IRCC, Department of Oncology, University of Torino, Torino, Italy
| | | | - James M Olson
- Fred Hutchinson Cancer Research Center, Seattle Children's Hospital, Seattle, Washington
| | - Daniel S Peeper
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge, United Kingdom
| | - Je Kyung Seong
- Research Institute for Veterinary Science and Korea Mouse Phenotyping Center, Seoul, Republic of Korea
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO-IRCC, Department of Oncology, University of Torino, Torino, Italy
| | | | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, La Jolla, California
| | - David M Weinstock
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Alana Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - S John Weroha
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Frédéric Amant
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
- University of Leuven, Leuven, Belgium
| | - Stefan M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California
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16
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Kong X, Kuilman T, Shahrabi A, Boshuizen J, Kemper K, Song JY, Niessen HWM, Rozeman EA, Geukes Foppen MH, Blank CU, Peeper DS. Cancer drug addiction is relayed by an ERK2-dependent phenotype switch. Nature 2017; 550:270-274. [PMID: 28976960 PMCID: PMC5640985 DOI: 10.1038/nature24037] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/25/2017] [Indexed: 12/29/2022]
Abstract
Drug addiction denotes the dependency of tumors on the same therapeutic
drugs to which they have acquired resistance. Observations from cultured
cells1–3, animal models4 and
patients5–7 raise the possibility that cancer drug addiction can
instigate a potential cancer vulnerability, which may be used therapeutically.
However, for this trait to become of clinical interest, it is imperative to
first define the underlying mechanism. Therefore, we performed an unbiased
CRISPR-Cas9 knockout screen to functionally mine the genome of melanoma cells
that are both resistant and addicted to BRAF inhibition for “addiction
genes”. Here, we describe a signaling pathway comprising ERK2, JUNB and
FRA1, disruption of which allows tumor cells to reverse addiction and survive
upon treatment discontinuation. This occurred both in culture and mice, and was
irrespective of the acquired drug resistance mechanism. In melanoma and lung
cancer cells, death induced by drug withdrawal was preceded by a specific
ERK2-dependent phenotype switch, alongside transcriptional reprogramming
reminiscent of EMT. In melanoma, this caused shutdown of the lineage survival
oncoprotein MITF, restoration of which reversed both phenotype switching and
drug addiction-associated lethality. In melanoma patients who had progressed on
BRAF inhibition, treatment cessation was followed by increased expression of the
phenotype switch-associated receptor tyrosine kinase AXL. Drug discontinuation
synergized with the melanoma chemotherapeutic dacarbazine by further suppressing
MITF and its prosurvival target BCL2 while inducing DNA damage. Our results
uncover a pathway driving cancer drug addiction, which may guide alternating
therapeutic strategies for enhanced clinical responses of drug-resistant
cancers.
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Affiliation(s)
- Xiangjun Kong
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Aida Shahrabi
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Kristel Kemper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans W M Niessen
- Department of Pathology and Cardiac Surgery, VU University Medical Center, ACS, 1007 MB Amsterdam, The Netherlands
| | - Elisa A Rozeman
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marnix H Geukes Foppen
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Christian U Blank
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L. Interrogating open issues in cancer medicine with patient-derived xenografts. Nat Rev Cancer 2017; 17:632. [PMID: 28912576 DOI: 10.1038/nrc.2017.85] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This corrects the article DOI: 10.1038/nrc.2016.140.
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Ranzani M, Kemper K, Michaut M, Krijgsman O, Iyer V, Speak A, Nsengimana J, Wong K, Grinkevich V, Aben N, Velasco-Herrera MDC, Alsinet C, Sjoberg M, Rashid M, Turner G, Behan F, Supper E, Thompson N, Bignell G, Dutton-Regester K, Pritchard A, Wong C, McDermott U, Hayward NK, Yusa K, Newton-Bishop J, Wessels L, Garnett M, Peeper D, Adams D. Abstract 3717: New therapies for the treatment of BRAF/NRAS wild type melanoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma represents the common tumor whose incidence has increased the most in the last 30 years and causes more than one death every hour in the US alone. Despite significant advances in targeted and immunotherapies, most patients cannot still be cured. Our aim is to identify new drug combinations that are synergistic in BRAF/NRAS wild type melanoma, a sub-type representing 30% of cases for which targeted therapies are not currently available. We high-throughput screened a collection of 20 BRAF/NRAS wild type melanoma cell lines with 180 drug combinations (60 library drugs used at 5 different concentrations combined with 3 clinically relevant anchor drugs) and generated over 8000 survival curves . We found that 25% of cell lines are highly sensitive to a combination of nilotinib plus trametinib and confirmed this finding with 2 independent assays. We further validated the drug synergy firstly using an independent collection of BRAF/NRAS wild type melanoma cell lines (n=7), then a collection of BRAF/NRAS wild type patient derived xenotransplant cultures (n=3), and finally with a collection of BRAFV600E and NRASQ61 melanoma cell lines (n=12). Further, we generated a gene expression signature of cell lines that display synergy for the nilotinib/trametinib combination, and used it to classify human melanomas from Leeds Melanoma Project (N=171) and TCGA (n=470) cohorts. Tumors classified as “synergistic-like” (27.9 and 36.7%, respectively) are associated to decreased overall and recurrence free survival (P<0.05), suggesting that our combination might be effective in a relevant fraction of aggressive tumors. In order to identify drug resistance mechanisms we deployed a genome-wide CRISPR/Cas9 screen. We found that loss of the tuberous sclerosis complex can confer resistance to nilotinib/trametinib, and validated this mechanism using clonal engineered lines. Since tuberous sclerosis complex genes are mutated in 10% of melanomas, this approach can help to identify patients potentially refractory to the treatment. We also investigated the molecular mechanism of nilotinib/trametinib synergy by analysing the level of several phosphoproteins upon treatment. We discovered that the nilotinib/trametinib combination synergistically reduce the level of P-ERK in synergistic cell lines but not in cell lines resistant to the drug combination, thus pointing out the MAPK pathway dependence of the synergy. This finding provides a putative marker to identify tumors responsive to the treatment. Finally, we tested in vivo the nilotinib/trametinib combination in a patient derived xenotransplant mouse model and showed that the combination is well tolerated and significantly more effective than the 2 drugs alone (P<0.01). These data suggest a strong clinical translation potential for nilotinib/trametinib combination and pave the way to the development of clinical trials for BRAF/NRAS wild type melanoma.
Citation Format: Marco Ranzani, Kristel Kemper, Magali Michaut, Oscar Krijgsman, Vivek Iyer, Anneliese Speak, Jeremie Nsengimana, Kim Wong, Vera Grinkevich, Nanne Aben, Martin Del Castillo Velasco-Herrera, Clara Alsinet, Marcela Sjoberg, Mamunur Rashid, Gemma Turner, Fiona Behan, Emmanuelle Supper, Nicola Thompson, Graham Bignell, Ken Dutton-Regester, Antonia Pritchard, Chi Wong, Ultan McDermott, Nicholas K. Hayward, Kosuke Yusa, Julia Newton-Bishop, Lodewyk Wessels, Mathew Garnett, Daniel Peeper, David Adams. New therapies for the treatment of BRAF/NRAS wild type melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3717. doi:10.1158/1538-7445.AM2017-3717
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Affiliation(s)
- Marco Ranzani
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | - Kristel Kemper
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Magali Michaut
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Vivek Iyer
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | | | - Kim Wong
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | - Nanne Aben
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Clara Alsinet
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | | | - Gemma Turner
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | - Fiona Behan
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | | | | | | | | | - Chi Wong
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | | | - Kosuke Yusa
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
| | | | | | | | - Daniel Peeper
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David Adams
- 1Wellcome Trust Sanger Inst., Cambridge, United Kingdom
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Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L. Interrogating open issues in cancer precision medicine with patient-derived xenografts. Nat Rev Cancer 2017; 17:254-268. [PMID: 28104906 DOI: 10.1038/nrc.2016.140] [Citation(s) in RCA: 450] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Patient-derived xenografts (PDXs) have emerged as an important platform to elucidate new treatments and biomarkers in oncology. PDX models are used to address clinically relevant questions, including the contribution of tumour heterogeneity to therapeutic responsiveness, the patterns of cancer evolutionary dynamics during tumour progression and under drug pressure, and the mechanisms of resistance to treatment. The ability of PDX models to predict clinical outcomes is being improved through mouse humanization strategies and the implementation of co-clinical trials, within which patients and PDXs reciprocally inform therapeutic decisions. This Opinion article discusses aspects of PDX modelling that are relevant to these questions and highlights the merits of shared PDX resources to advance cancer medicine from the perspective of EurOPDX, an international initiative devoted to PDX-based research.
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Affiliation(s)
- Annette T Byrne
- EurOPDX Consortium and are at the Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Denis G Alférez
- EurOPDX Consortium and are at the Breast Cancer Now Research Unit, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, University of Manchester, Manchester M20 4QL, UK
| | - Frédéric Amant
- EurOPDX Consortium and are at the Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Daniela Annibali
- EurOPDX Consortium and are at the Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Joaquín Arribas
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology, 08035 Barcelona, the Universitat Autònoma de Barcelona, 08193 Bellaterra, and the Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CIBERONC, 08035 Barcelona, Spain
| | - Andrew V Biankin
- EurOPDX Consortium and are at the Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Alejandra Bruna
- EurOPDX Consortium and are at Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Eva Budinská
- EurOPDX Consortium and is at the Institute of Biostatistics and Analyses, Faculty of Medicine, and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masarykova Univerzita, 625 00 Brno, Czech Republic
| | - Carlos Caldas
- EurOPDX Consortium and are at Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - David K Chang
- EurOPDX Consortium and are at the Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Robert B Clarke
- EurOPDX Consortium and are at the Breast Cancer Now Research Unit, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, University of Manchester, Manchester M20 4QL, UK
| | - Hans Clevers
- Hubrecht Institute, University Medical Centre Utrecht, and Princess Maxima Center for Pediatric Oncology, 3584CT Utrecht, The Netherlands
| | - George Coukos
- EurOPDX Consortium and are at Lausanne Branch, Ludwig Institute for Cancer Research at the University of Lausanne, 1066 Lausanne, Switzerland
| | - Virginie Dangles-Marie
- EurOPDX Consortium and is at the Institut Curie, PSL Research University, Translational Research Department, 75005 Paris, and Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, 75006 Paris, France
| | - S Gail Eckhardt
- University of Colorado Cancer Center, Aurora, Colorado 80045, USA
| | - Eva Gonzalez-Suarez
- EurOPDX Consortium and is at the Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Els Hermans
- EurOPDX Consortium and are at the Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Manuel Hidalgo
- EurOPDX Consortium and is at Beth Israel Deaconess Medical Center, Boston, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Monika A Jarzabek
- EurOPDX Consortium and are at the Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Steven de Jong
- EurOPDX Consortium and is at the University Medical Centre Groningen, University of Groningen, 9713GZ Groningen, The Netherlands
| | - Jos Jonkers
- EurOPDX Consortium and are at The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kristel Kemper
- EurOPDX Consortium and are at The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Luisa Lanfrancone
- EurOPDX Consortium and are at the Department of Experimental Oncology, European Institiute of Oncology, 20139 Milan, Italy
| | - Gunhild Mari Mælandsmo
- EurOPDX Consortium and are at Oslo University Hospital, Institute for Cancer Research, 0424 Oslo, Norway
| | - Elisabetta Marangoni
- EurOPDX Consortium and are at Institut Curie, PSL Research University, Translational Research Department, 75005 Paris, France
| | - Jean-Christophe Marine
- EurOPDX Consortium and is at the Laboratory for Molecular Cancer Biology, Department of Oncology, Katholieke Universiteit Leuven, and the Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Enzo Medico
- EurOPDX Consortium and are at the Candiolo Cancer Institute IRCCS and Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
| | - Jens Henrik Norum
- EurOPDX Consortium and are at Oslo University Hospital, Institute for Cancer Research, 0424 Oslo, Norway
| | - Héctor G Palmer
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology and CIBERONC, 08035 Barcelona, Spain
| | - Daniel S Peeper
- EurOPDX Consortium and are at The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Pier Giuseppe Pelicci
- EurOPDX Consortium and are at the Department of Experimental Oncology, European Institiute of Oncology, 20139 Milan, Italy
| | - Alejandro Piris-Gimenez
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology and CIBERONC, 08035 Barcelona, Spain
| | - Sergio Roman-Roman
- EurOPDX Consortium and are at Institut Curie, PSL Research University, Translational Research Department, 75005 Paris, France
| | - Oscar M Rueda
- EurOPDX Consortium and are at Cancer Research UK Cambridge Institute, Cambridge Cancer Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joan Seoane
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology, 08035 Barcelona, the Universitat Autònoma de Barcelona, 08193 Bellaterra, and the Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CIBERONC, 08035 Barcelona, Spain
| | - Violeta Serra
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology and CIBERONC, 08035 Barcelona, Spain
| | - Laura Soucek
- EurOPDX Consortium and are at the Vall d'Hebron Institute of Oncology, 08035 Barcelona, the Universitat Autònoma de Barcelona, 08193 Bellaterra, and the Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Dominique Vanhecke
- EurOPDX Consortium and are at Lausanne Branch, Ludwig Institute for Cancer Research at the University of Lausanne, 1066 Lausanne, Switzerland
| | - Alberto Villanueva
- EurOPDX Consortium and is at the Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology ICO, Bellvitge Biomedical Research Institute IDIBELL, 08098 L'Hospitalet de Llobregat, Barcelona, and Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Andrea Bertotti
- EurOPDX Consortium and are at the Candiolo Cancer Institute IRCCS and Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- EurOPDX Consortium and are at the Candiolo Cancer Institute IRCCS and Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
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20
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Kemper K, Krijgsman O, Kong X, Cornelissen-Steijger P, Shahrabi A, Weeber F, van der Velden DL, Bleijerveld OB, Kuilman T, Kluin RJC, Sun C, Voest EE, Ju YS, Schumacher TNM, Altelaar AFM, McDermott U, Adams DJ, Blank CU, Haanen JB, Peeper DS. BRAF(V600E) Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts. Cell Rep 2016; 16:263-277. [PMID: 27320919 PMCID: PMC4929150 DOI: 10.1016/j.celrep.2016.05.064] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 04/08/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022] Open
Abstract
The therapeutic landscape of melanoma is improving rapidly. Targeted inhibitors show promising results, but drug resistance often limits durable clinical responses. There is a need for in vivo systems that allow for mechanistic drug resistance studies and (combinatorial) treatment optimization. Therefore, we established a large collection of patient-derived xenografts (PDXs), derived from BRAFV600E, NRASQ61, or BRAFWT/NRASWT melanoma metastases prior to treatment with BRAF inhibitor and after resistance had occurred. Taking advantage of PDXs as a limitless source, we screened tumor lysates for resistance mechanisms. We identified a BRAFV600E protein harboring a kinase domain duplication (BRAFV600E/DK) in ∼10% of the cases, both in PDXs and in an independent patient cohort. While BRAFV600E/DK depletion restored sensitivity to BRAF inhibition, a pan-RAF dimerization inhibitor effectively eliminated BRAFV600E/DK-expressing cells. These results illustrate the utility of this PDX platform and warrant clinical validation of BRAF dimerization inhibitors for this group of melanoma patients. Patient-derived xenograft (PDX) platform comprises 89 metastatic melanoma tumors Platform includes several pre-vemurafenib and vemurafenib-resistant PDXs Duplication of the BRAFV600E kinase domain is identified as a resistance mechanism Pan-RAF dimerization inhibitor LY3009120 eliminates melanoma cells with this duplication
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Affiliation(s)
- Kristel Kemper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Xiangjun Kong
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paulien Cornelissen-Steijger
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Aida Shahrabi
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fleur Weeber
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Daphne L van der Velden
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Roel J C Kluin
- Central Genomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Chong Sun
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Emile E Voest
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Young Seok Ju
- Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ton N M Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - A F Maarten Altelaar
- Mass Spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ultan McDermott
- Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
| | - Christian U Blank
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - John B Haanen
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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21
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Kemper K, Krijgsman O, Cornelissen-Steijger P, Shahrabi A, Weeber F, Song JY, Kuilman T, Vis DJ, Wessels LF, Voest EE, Schumacher TN, Blank CU, Adams DJ, Haanen JB, Peeper DS. Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts. EMBO Mol Med 2016; 7:1104-18. [PMID: 26105199 PMCID: PMC4568946 DOI: 10.15252/emmm.201404914] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The development of targeted inhibitors, like vemurafenib, has greatly improved the clinical outcome of BRAFV600E metastatic melanoma. However, resistance to such compounds represents a formidable problem. Using whole-exome sequencing and functional analyses, we have investigated the nature and pleiotropy of vemurafenib resistance in a melanoma patient carrying multiple drug-resistant metastases. Resistance was caused by a plethora of mechanisms, all of which reactivated the MAPK pathway. In addition to three independent amplifications and an aberrant form of BRAFV600E, we identified a new activating insertion in MEK1. This MEK1T55delinsRT mutation could be traced back to a fraction of the pre-treatment lesion and not only provided protection against vemurafenib but also promoted local invasion of transplanted melanomas. Analysis of patient-derived xenografts (PDX) from therapy-refractory metastases revealed that multiple resistance mechanisms were present within one metastasis. This heterogeneity, both inter- and intra-tumorally, caused an incomplete capture in the PDX of the resistance mechanisms observed in the patient. In conclusion, vemurafenib resistance in a single patient can be established through distinct events, which may be preexisting. Furthermore, our results indicate that PDX may not harbor the full genetic heterogeneity seen in the patient’s melanoma.
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Affiliation(s)
- Kristel Kemper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Aida Shahrabi
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Weeber
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel J Vis
- Computational Cancer Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F Wessels
- Computational Cancer Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton Nm Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian U Blank
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - John B Haanen
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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22
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Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol 2015; 16:49. [PMID: 25887352 PMCID: PMC4396974 DOI: 10.1186/s13059-015-0617-1] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022] Open
Abstract
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
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Affiliation(s)
- Thomas Kuilman
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Arno Velds
- Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Kristel Kemper
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Marco Ranzani
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Lorenzo Bombardelli
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Marlous Hoogstraat
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Ekaterina Nevedomskaya
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Guotai Xu
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Julian de Ruiter
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Martijn P Lolkema
- Center for Personalized Cancer Treatment, Amsterdam, The Netherlands.
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Sven Rottenberg
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
- Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Bern, Switzerland.
| | - Lodewyk F Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Daniel S Peeper
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Oscar Krijgsman
- Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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24
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Müller J, Krijgsman O, Tsoi J, Robert L, Hugo W, Song C, Kong X, Possik PA, Cornelissen-Steijger PDM, Geukes Foppen MH, Kemper K, Goding CR, McDermott U, Blank C, Haanen J, Graeber TG, Ribas A, Lo RS, Peeper DS. Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma. Nat Commun 2014; 5:5712. [PMID: 25502142 DOI: 10.1038/ncomms6712] [Citation(s) in RCA: 427] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 10/30/2014] [Indexed: 02/07/2023] Open
Abstract
Increased expression of the Microphthalmia-associated transcription factor (MITF) contributes to melanoma progression and resistance to BRAF pathway inhibition. Here we show that the lack of MITF is associated with more severe resistance to a range of inhibitors, while its presence is required for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlate with the expression of several activated receptor tyrosine kinases, most frequently AXL. The MITF-low/AXL-high/drug-resistance phenotype is common among mutant BRAF and NRAS melanoma cell lines. The dichotomous behaviour of MITF in drug response is corroborated in vemurafenib-resistant biopsies, including MITF-high and -low clones in a relapsed patient. Furthermore, drug cocktails containing AXL inhibitor enhance melanoma cell elimination by BRAF or ERK inhibition. Our results demonstrate that a low MITF/AXL ratio predicts early resistance to multiple targeted drugs, and warrant clinical validation of AXL inhibitors to combat resistance of BRAF and NRAS mutant MITF-low melanomas.
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Affiliation(s)
- Judith Müller
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jennifer Tsoi
- Division of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-1750, USA
| | - Lidia Robert
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA
| | - Willy Hugo
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA
| | - Chunying Song
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA
| | - Xiangju Kong
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA
| | - Patricia A Possik
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | | | - Marnix H Geukes Foppen
- Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kristel Kemper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK
| | - Ultan McDermott
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Christian Blank
- Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - John Haanen
- Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Thomas G Graeber
- 1] Division of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-1750, USA [2] UCLA Metabolomics Center, Crump Institute for Molecular Imaging, California Nanosystems Institute, UCLA, 570 Westwood Plaza, Building 114, Los Angeles, California 90095-7227, USA [3] Jonsson Comprehensive Cancer Center (JCCC), 8-684 Factor Building, Los Angeles, California 90095-1781, USA
| | - Antoni Ribas
- 1] Division of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-1750, USA [2] Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA [3] Jonsson Comprehensive Cancer Center (JCCC), 8-684 Factor Building, Los Angeles, California 90095-1781, USA
| | - Roger S Lo
- 1] Division of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-1750, USA [2] Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, California 90095-7227, USA [3] Jonsson Comprehensive Cancer Center (JCCC), 8-684 Factor Building, Los Angeles, California 90095-1781, USA
| | - Daniel S Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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Possik P, Müller J, Gerlach C, Kenski J, Huang X, Shahrabi A, Krijgsman O, Song JY, Smit M, Gerritsen B, Lieftink C, Kemper K, Michaut M, Beijersbergen R, Wessels L, Schumacher T, Peeper D. Parallel In Vivo and In Vitro Melanoma RNAi Dropout Screens Reveal Synthetic Lethality between Hypoxia and DNA Damage Response Inhibition. Cell Rep 2014; 9:1375-86. [DOI: 10.1016/j.celrep.2014.10.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 08/12/2014] [Accepted: 10/10/2014] [Indexed: 12/25/2022] Open
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Abstract
Mutations in BRAF are present in the majority of patients with melanoma, rendering these tumors sensitive to targeted therapy with BRAF and MEK inhibitors. Unfortunately, resistance almost invariably develops. Recently, a phenomenon called "phenotype switching" has been identified as an escape route. By switching from a proliferative to an invasive state, melanoma cells can acquire resistance to these targeted therapeutics. Interestingly, phenotype switching bears a striking resemblance to the epithelial-to-mesenchymal-like transition that has been described to occur in cancer stem cells in other tumor types. We propose that these changes are manifestations of one and the same underlying feature, namely a dynamic and reversible phenotypic tumor cell plasticity that renders a proportion of cells both more invasive and resistant to therapy. At the same time, the specific characteristics of these tumor cell populations offer potential for being explored as target for therapeutic intervention.
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Affiliation(s)
- Kristel Kemper
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pauline L de Goeje
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Renée van Amerongen
- Section of Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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Fortes MRS, Kemper K, Sasazaki S, Reverter A, Pryce JE, Barendse W, Bunch R, McCulloch R, Harrison B, Bolormaa S, Zhang YD, Hawken RJ, Goddard ME, Lehnert SA. Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle. Anim Genet 2013; 44:636-47. [PMID: 23909810 DOI: 10.1111/age.12075] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2013] [Indexed: 02/03/2023]
Abstract
A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10(-4) ). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.
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Affiliation(s)
- M R S Fortes
- Cooperative Research Centre for Beef Genetic Technologies Armidale, Armidale, NSW, 2351, Australia; Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Gatton, QLD, 4343, Australia; CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, Brisbane, QLD, 4067, Australia
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Bolormaa S, Pryce JE, Kemper K, Savin K, Hayes BJ, Barendse W, Zhang Y, Reich CM, Mason BA, Bunch RJ, Harrison BE, Reverter A, Herd RM, Tier B, Graser HU, Goddard ME. Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. J Anim Sci 2013; 91:3088-104. [PMID: 23658330 DOI: 10.2527/jas.2012-5827] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction [BayesR and genomic BLUP (GBLUP)] either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identified many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.
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Affiliation(s)
- S Bolormaa
- Victorian Department of Primary Industries, Bundoora, VIC 3083, Australia.
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Kemper K, Prasetyanti PR, De Lau W, Rodermond H, Clevers H, Medema JP. Monoclonal antibodies against Lgr5 identify human colorectal cancer stem cells. Stem Cells 2013; 30:2378-86. [PMID: 22969042 DOI: 10.1002/stem.1233] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In colorectal cancer (CRC), a subpopulation of tumor cells, called cancer stem cell (CSC) fraction, is suggested to be responsible for tumor initiation, growth, and metastasis. The search for a reliable marker to identify these CSCs is ongoing as current markers, like CD44 and CD133, are more broadly expressed and therefore are not highly selective and currently also lack function in CSC biology. Here, we analyzed whether the Wnt target Lgr5, which has earlier been identified as a marker for murine intestinal stem cells, could potentially serve as a functional marker for CSCs. Fluorescence-activated cell sorting-based detection of Lgr5, using three newly developed antibodies, on primary colorectal tumor cells revealed a clear subpopulation of Epcam+ Lgr5+ cells. Similarly, primary CRC-derived spheroid cultures, known to be enriched for CSCs, contain high levels of Lgr5+ cells, which decrease upon in vitro differentiation of these CSCs. Selection of the Lgr5(high) CRC cells identified the clonogenic fraction in vitro as well as the tumorigenic population in vivo. Finally, we confirm that Lgr5 expression is dependent on the Wnt pathway and show that Lgr5 overexpression induces clonogenic growth. We thus provide evidence that Lgr5 is, next to a functional intestinal stem cell marker, a selective marker for human colorectal CSCs.
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Affiliation(s)
- Kristel Kemper
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Amsterdam, The Netherlands
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Kemper K, Medema JP. Prognostic Value of CD133 Caused by Mutant K-Ras and B-Raf—Response. Clin Cancer Res 2012. [DOI: 10.1158/1078-0432.ccr-12-1816] [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: 11/16/2022]
Affiliation(s)
- Kristel Kemper
- Authors' Affiliation: Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - Jan Paul Medema
- Authors' Affiliation: Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
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Abstract
Colorectal cancer stem cells (CSCs) drive tumor growth and are suggested to initiate distant metastases. Moreover, colon CSCs are reportedly more resistant to conventional chemotherapy, which is in part due to upregulation of anti-apoptotic Bcl-2 family members. To determine whether we could circumvent this apoptotic blockade, we made use of an inducible active caspase-9 (iCasp9) construct to target CSCs. Dimerization of iCasp9 with AP20187 in HCT116 colorectal cancer cells resulted in massive and rapid induction of apoptosis. In contrast to fluorouracil (5-FU)-induced apoptosis, iCasp9-induced apoptosis was independent of the mitochondrial pathway as evidenced by Bax/Bak double deficient HCT116 cells. Dimerizer treatment of colon CSCs transduced with iCasp9 (CSC-iCasp9) also rapidly induced high levels of apoptosis, while these cells were unresponsive to 5-FU in vitro. More importantly, injection of the dimerizer into mice that developed a colon CSC-iCasp9-induced tumor resulted in a strong decrease in tumor size, an increase in tumor cell apoptosis and a clear loss of CD133+ CSCs. Taken together, our data indicate that dimerization of iCasp9 circumvents the apoptosis block in CSCs, which results in effective tumor regression in vivo.
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Affiliation(s)
- Kristel Kemper
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hans Rodermond
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Selçuk Colak
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Catarina Grandela
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Centre for Molecular Medicine, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Kemper K, Shaltout H, Tooze J, Rosenberger E. P05.11. Time, touch, and compassion: effects on autonomic nervous system and well-being. BMC Complement Altern Med 2012. [PMCID: PMC3373814 DOI: 10.1186/1472-6882-12-s1-p371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kemper K, Banasiewicz B. P02.162. Parental interest in integrative care for children with attentional concerns. Altern Ther Health Med 2012. [PMCID: PMC3373557 DOI: 10.1186/1472-6882-12-s1-p218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kemper K, Shaltout H. P02.28. Non-verbal communication of compassion: feasibility of measuring psychophysiological effects of blind exposure. BMC Complement Altern Med 2012. [PMCID: PMC3373914 DOI: 10.1186/1472-6882-12-s1-p84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Kemper K, Versloot M, Cameron K, Colak S, de Sousa e Melo F, de Jong JH, Bleackley J, Vermeulen L, Versteeg R, Koster J, Medema JP. Mutations in the Ras-Raf Axis underlie the prognostic value of CD133 in colorectal cancer. Clin Cancer Res 2012; 18:3132-41. [PMID: 22496204 DOI: 10.1158/1078-0432.ccr-11-3066] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE High expression of cancer stem cell (CSC) marker CD133 has been used as a predictor for prognosis in colorectal cancer (CRC), suggesting that enumeration of CSCs, using CD133, is predictive for disease progression. However, we showed recently that both CD133 mRNA and protein are not downregulated during differentiation of colon CSCs, pointing to an alternative reason for the prognostic value of CD133. We therefore set out to delineate the relation between CD133 expression and prognosis. EXPERIMENTAL DESIGN A CRC patient series was studied for expression of CD133 and other CSC markers by microarray and quantitative PCR analysis. In addition, several common mutations were analyzed to determine the relation with CD133 expression. RESULTS CD133 mRNA expression predicted relapse-free survival in our patient series, whereas several other CSC markers could not. Moreover, no correlation was found between expression of other CSC markers and CD133. Interestingly, high CD133 expression was related to mutations in K-Ras and B-Raf, and inhibition of mutant K-Ras or downstream mitogen-activated protein kinase kinase (MEK) signaling decreases CD133 expression. In addition, an activated K-Ras gene expression signature could predict CD133 expression in our patient set as well as data sets of other tumor types. CONCLUSION CD133 expression is upregulated in CRC tumors that have a hyperactivated Ras-Raf-MEK-ERK pathway and is therefore related to mutations in K-Ras or B-Raf. As mutations in either gene have been related to poor prognosis, we conclude that CD133 expression is not indicative for CSC numbers but rather related to the mutation or activity status of the Ras-Raf pathway.
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Affiliation(s)
- Kristel Kemper
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
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Abstract
Tumor initiating or cancer stem cells (CSCs) are suggested to be responsible for tumor initiation and growth. Moreover, therapy resistance and minimal residual disease are thought to result from selective resistance of CSCs. Isolation of CSCs from colon carcinomas can be accomplished by selection of a subpopulation of tumor cells based on expression of one or multiple cell surface markers associated with cancer stemness, like CD133, CD44, CD24, CD29, CD166 and Lgr5. Identification of colon CSCs will lead to a better rational for new therapies that aim to target this fraction specifically. In this review, we analyze known markers used for selection of colon CSCs and their potential function in CSC biology. Moreover, we discuss potential targeting strategies for eradicating CSCs specifically in order to develop more effective therapeutic strategies as well as to address more fundamental questions like the actual role of CSCs in tumor growth.
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Affiliation(s)
- Kristel Kemper
- LEXOR (Lab for Experimental Oncology and Radiobiology), Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands.
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Kemper K, Grandela C, Medema JP. Molecular identification and targeting of colorectal cancer stem cells. Oncotarget 2010; 1. [PMID: 21311095 PMCID: PMC3248116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Tumor initiating or cancer stem cells (CSCs) are suggested to be responsible for tumor initiation and growth. Moreover, therapy resistance and minimal residual disease are thought to result from selective resistance of CSCs. Isolation of CSCs from colon carcinomas can be accomplished by selection of a subpopulation of tumor cells based on expression of one or multiple cell surface markers associated with cancer stemness, like CD133, CD44, CD24, CD29, CD166 and Lgr5. Identification of colon CSCs will lead to a better rational for new therapies that aim to target this fraction specifically. In this review, we analyze known markers used for selection of colon CSCs and their potential function in CSC biology. Moreover, we discuss potential targeting strategies for eradicating CSCs specifically in order to develop more effective therapeutic strategies as well as to address more fundamental questions like the actual role of CSCs in tumor growth.
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Abstract
Prominin-1, a heavily glycosylated pentaspan membrane protein, is mainly known for its function as a marker for (cancer) stem cells, although it can also be detected on differentiated cells. Mouse prominin-1 expression is heavily regulated by splicing in eight different variants. The function or the expression pattern of prominin-1 and its splice variants (SVs) is thus far unknown. In this study, we analyzed the expression of the prominin-1 splice variants on mRNA level in several mouse tissues and found a broad tissue expression of the majority of SVs, but a specific set of SVs had a much more restricted expression profile. For instance, the testis expressed only SV3 and SV7. Moreover, SV8 was solely detected in the eye. Intriguingly, prominin-1 knockout mice do not suffer from gross abnormalities, but do show signs of blindness, which suggest that SV8 has a specific function in this tissue. In addition, databases searches for putative promoter regions in the mouse prominin-1 gene revealed three potential promoter regions that could be linked to specific SVs. Interestingly, for both SV7 and SV8, a specific potential promoter region could be identified. To conclude, the majority of mouse prominin-1 splice variants are widely expressed in mouse tissues. However, specific expression of a few variants, likely driven by specific promoters, suggests distinct regulation and a potential important function for these variants in certain tissues.
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Affiliation(s)
- Kristel Kemper
- Lab for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands.
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Vermeulen L, De Sousa E Melo F, van der Heijden M, Cameron K, de Jong JH, Borovski T, Tuynman JB, Todaro M, Merz C, Rodermond H, Sprick MR, Kemper K, Richel DJ, Stassi G, Medema JP. Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nat Cell Biol 2010; 12:468-76. [DOI: 10.1038/ncb2048] [Citation(s) in RCA: 1412] [Impact Index Per Article: 100.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/26/2010] [Indexed: 11/09/2022]
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Kemper K, Sprick MR, de Bree M, Scopelliti A, Vermeulen L, Hoek M, Zeilstra J, Pals ST, Mehmet H, Stassi G, Medema JP. The AC133 epitope, but not the CD133 protein, is lost upon cancer stem cell differentiation. Cancer Res 2010; 70:719-29. [PMID: 20068153 DOI: 10.1158/0008-5472.can-09-1820] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colon cancer stem cells (CSC) can be identified with AC133, an antibody that detects an epitope on CD133. However, recent evidence suggests that expression of CD133 is not restricted to CSCs, but is also expressed on differentiated tumor cells. Intriguingly, we observed that detection of the AC133 epitope on the cell surface decreased upon differentiation of CSC in a manner that correlated with loss of clonogenicity. However, this event did not coincide with a change in CD133 promoter activity, mRNA, splice variant, protein expression, or even cell surface expression of CD133. In contrast, we noted that with CSC differentiation, a change occured in CD133 glycosylation. Thus, AC133 may detect a glycosylated epitope, or differential glycosylation may cause CD133 to be retained inside the cell. We found that AC133 could effectively detect CD133 glycosylation mutants or bacterially expressed unglycosylated CD133. Moreover, cell surface biotinylation experiments revealed that differentially glycosylated CD133 could be detected on the membrane of differentiated tumor cells. Taken together, our results argue that CD133 is a cell surface molecule that is expressed on both CSC and differentiated tumor cells, but is probably differentially folded as a result of differential glycosylation to mask specific epitopes. In summary, we conclude that AC133 can be used to detect cancer stem cells, but that results from the use of this antibody should be interpreted with caution.
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Affiliation(s)
- Kristel Kemper
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, and Department of Pathology, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
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Tuynman JB, Vermeulen L, Boon EM, Kemper K, Zwinderman AH, Peppelenbosch MP, Richel DJ. Cyclooxygenase-2 inhibition inhibits c-Met kinase activity and Wnt activity in colon cancer. Cancer Res 2008; 68:1213-20. [PMID: 18281498 DOI: 10.1158/0008-5472.can-07-5172] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Activity of receptor tyrosine kinases (RTK) in colorectal cancer (CRC) is associated with enhanced tumor growth and a poorer prognosis. In addition, cyclooxygenase-2 (COX-2) expression contributes to tumor growth and invasion. COX-2 inhibitors exhibit important anticarcinogenic potential against CRC, but the molecular mechanism underlying this effect and the relation with RTK signaling remain the subject of intense research effort. Therefore, the rapid effects of COX-2 inhibition in CRC on the complement of all cellular kinases were investigated using a kinase substrate peptide array, Western blotting, transfection, small interfering RNA assays, and CRC cell lines. The resulting alterations in the kinome profile revealed that celecoxib, a selective COX-2 inhibitor, impairs phosphorylation of substrates for the RTKs c-Met and insulin-like growth factor receptor, resulting in decreased downstream signaling. The decrease in c-Met activation is accompanied with an increase in glycogen synthase kinase 3beta kinase activity together with a rapid increase in phosphorylation of beta-catenin. In agreement, a significant reduction of beta-catenin-T-cell factor-dependent transcription is observed both with celecoxib and selective inhibition of c-Met phosphorylation by small molecules. Hence, corepression of c-Met-related and beta-catenin-related oncogenic signal transduction seems a major effector of celecoxib in CRC, which provides a rationale to use c-Met inhibitors and celecoxib analogous to target c-Met and Wnt signaling in a therapeutic setting for patients with CRC.
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Affiliation(s)
- Jurriaan B Tuynman
- Laboratory of Experimental Oncology, Department of Surgery, Academic Medical Center, Amsterdam, the Netherlands.
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Abstract
Cancer has long been viewed as an exclusively genetic disorder. The model of carcinogenesis, postulated by Nowell and Vogelstein, describes the formation of a tumor by the sequential accumulation of mutations in oncogenes and tumor suppressor genes. In this model, tumors are thought to consist of a heterogeneous population of cells that continue to acquire new mutations, resulting in a highly dynamic process, with clones that out compete others due to increased proliferative or survival capacity. However, novel insights in cancer stem cell research suggest another layer of complexity in the process of malignant transformation and preservation. It has been reported that only a small fraction of the cancer cells in a malignancy have the capacity to propagate the tumor upon transplantation into immuno-compromised mice. Those cells are termed 'cancer stem cells' (CSC) and can be selected based on the expression of cell surface markers associated with immature cell types. In this review, we will critically discuss these novel insights in CSC-related research. Where possible we integrate these results within the genetic model of cancer and illustrate that the CSC model can be considered an extension of the classic genetic model rather than a contradictory theory. Finally, we discuss some of the most controversial issues in this field.
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Affiliation(s)
- L Vermeulen
- LEXOR (Laboratory for Experimental Oncology and Radiobiology), Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
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Al-Haik MS, Trinkle S, Momotyuk O, Roeder BT, Kemper K, Hussaini MY, Malloy KJ. Nanocharacterization of Proton Radiation Damage on Magnetically Oriented Epoxy. International Journal of Polymer Analysis and Characterization 2007. [DOI: 10.1080/10236660701551638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Tuynman JB, Buskens CJ, Kemper K, ten Kate FJW, Offerhaus GJA, Richel DJ, van Lanschot JJB. Neoadjuvant selective COX-2 inhibition down-regulates important oncogenic pathways in patients with esophageal adenocarcinoma. Ann Surg 2006; 242:840-9, discussion 849-50. [PMID: 16327494 PMCID: PMC1409886 DOI: 10.1097/01.sla.0000189546.77520.ef] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVES To evaluate the effects of neoadjuvant therapy with the selective cyclooxygenase-2 (COX-2) inhibitor celecoxib in vitro and in patients with esophageal adenocarcinoma on COX-2 and MET expression. SUMMARY BACKGROUND DATA High COX-2 and/or MET expression levels are negative prognostic factors for adenocarcinoma of the esophagus. Nonsteroidal anti-inflammatory drugs (NSAIDs) and selective COX-2 inhibitors exert anticancer mechanisms as is evident from epidemiologic studies and from experimental models for esophageal cancer. The mechanisms and the significance of these findings in patients with adenocarcinoma of the esophagus are unknown. METHODS Esophageal adenocarcinoma cell lines were used to asses the effects in vitro. To study the clinical effects 12 patients with esophageal adenocarcinoma were included for neoadjuvant treatment (4 weeks) with celecoxib at 400 mg twice daily. Fifteen patients not receiving NSAIDs or celecoxib were included as a control. Effects were evaluated using the MTT-cell viability test, Western blot analysis, immunohistochemistry, and RT-PCR. RESULTS In vitro celecoxib administration resulted in decreased cell viability, increased apoptosis, and decreased COX-2 and MET expression levels. In patients, neoadjuvant treatment with celecoxib significantly down-regulated COX-2 and MET expression in the tumor when compared with the nontreated control group and when compared with pretreatment measurements. CONCLUSIONS This is the first study to show in vitro and in patients with esophageal adenocarcinoma that selective COX-2 inhibition down-regulates COX-2 and MET expression, both important proteins involved in cancer progression and dissemination. Therefore, (neo)adjuvant therapy with celecoxib might have clinical potential for patients with esophageal adenocarcinoma.
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Affiliation(s)
- Jurriaan B Tuynman
- Departments of Surgery, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
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Wiedl KH, Kemper K, Uhlhorn S, Schöttke H. [Which schizophrenic patients improve under work therapy, which ones don't?]. Fortschr Neurol Psychiatr 2005; 73:674-80. [PMID: 16283611 DOI: 10.1055/s-2004-830247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This investigation is part of a multicenter study, where only small effects and no superiority compared to creative ergotherapy was found for four weeks of inpatient work therapy. The criteria were three scales of the Osnabrück-Working Capabilities Profile (O-AFP) assessing basic learning ability, social communication ability and adaptation at the work place. The goal of this investigation is to identify subgroups of patients within the work therapy group, which differ in their course of ability level during the intervention. Three subgroups were identified for each scale. Subgroups with improvements comprise 24 % (learning ability) and 15 % (social communication) of the sample. Adaptation level decreases in a group of 9 % of the patients. The remaining clusters show constancy of abilities at different levels. Comparison of the clusters with neurocognitive, symptom and motivational variables shows that for learning ability mainly neurocognitive variables yield salient differences, whereas for social communication abilities, symptoms and motivation, together with a specific aspect of memory, seem to be characteristic. Only positive symptoms are related to adaptation. Also, there are hints for variables that specifically characterize patients with improvement of ability level. The discussion deals with issues of assessment and prognosis in rehabilitation, contributions to the neurocognitive theory of schizophrenia and to the development of person-centered interventions.
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Affiliation(s)
- K H Wiedl
- Universität Osnabrück, Fachbereich Humanwissenschaften, Lehreinheit Klinische Psychologie und Psychotherapie.
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Kemper K, Begemann P, Regier M, Stork A, Adam G, Nolte-Ernsting C. Mehrschicht-CT-Urographie (MSCTU): Experimentelle Dosisoptimierung am Schweinemodell. ROFO-FORTSCHR RONTG 2005. [DOI: 10.1055/s-2005-867520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
A direct continuous spectrophotometric assay to measure pyrethroid-cleaving enzymes in human serum was developed using cis- and trans-alpha-naphthyl-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane carboxylate (cis- and trans-naphthyl-Cl2CA). These substrates show a structure very similar to the pyrethroids most often used (e.g. permethrin, cyfluthrin). The method is based on an increase in absorbance at 321 nm which occurs with the hydrolysis of the alpha-naphthyl esters to alpha-naphthol. The assay was optimised regarding type of buffer, pH and substrate concentrations, it was linear for at least 10 min at 37 degrees C. These esterases were completely inhibited by bis-(4-nitrophenylphosphate), a specific carboxyesterase inhibitor. They displayed a great individual variability in human serum, activities were between less than 40 and 1000 U/l for cis-naphthyl-Cl2CA, between less than 40 and 2000 U/l for trans-naphthyl-Cl2CA, respectively. However, a correlation of enzyme activity to sex or age could not be observed. Furthermore, the activity of pyrethroid-cleaving esterases did not correspond to the activities of acylesterase, arylesterase, acetylcholinesterase or butyrylcholinesterase.
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Affiliation(s)
- W Butte
- Carl von Ossietzky Universität Oldenburg, Fachbereich Chemie, Germany.
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Abstract
A large and increasing number of patients use medicinal herbs or seek the advice of their physician regarding their use. More than one third of Americans use herbs for health purposes, yet patients (and physicians) often lack accurate information about the safety and efficacy of herbal remedies. Burgeoning interest in medicinal herbs has increased scientific scrutiny of their therapeutic potential and safety, thereby providing physicians with data to help patients make wise decisions about their use. This article provides a review of the data on 12 of the most commonly used herbs in the United States. In addition, we provide practical information and guidelines for the judicious use of medicinal herbs.
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Affiliation(s)
- M O'Hara
- Robert Wood Johnson Clinical Scholars Program, University of Washington Health Sciences Center, Seattle 98195, USA.
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