1
|
Spiekman IAC, Geurts BS, Zeverijn LJ, de Wit GF, van der Noort V, Roepman P, de Leng WWJ, Jansen AML, Kusters B, Beerepoot LV, de Vos FYFL, de Groot DJA, de Groot JWB, Hoeben A, Buter J, Gelderblom HAJ, Voest EE, Verheul HMW. Efficacy and Safety of Panitumumab in Patients With RAF/RAS-Wild-Type Glioblastoma: Results From the Drug Rediscovery Protocol. Oncologist 2024; 29:431-440. [PMID: 38109296 PMCID: PMC11067815 DOI: 10.1093/oncolo/oyad320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/02/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The prognosis of malignant primary high-grade brain tumors, predominantly glioblastomas, is poor despite intensive multimodality treatment options. In more than 50% of patients with glioblastomas, potentially targetable mutations are present, including rearrangements, altered splicing, and/or focal amplifications of epidermal growth factor receptor (EGFR) by signaling through the RAF/RAS pathway. We studied whether treatment with the clinically available anti-EGFR monoclonal antibody panitumumab provides clinical benefit for patients with RAF/RAS-wild-type (wt) glioblastomas in the Drug Rediscovery Protocol (DRUP). METHODS Patients with progression of treatment refractory RAF/RASwt glioblastoma were included for treatment with panitumumab in DRUP when measurable according to RANO criteria. The primary endpoints of this study are clinical benefit (CB: defined as confirmed objective response [OR] or stable disease [SD] ≥ 16 weeks) and safety. Patients were enrolled using a Simon-like 2-stage model, with 8 patients in stage 1 and up to 24 patients in stage 2 if at least 1 in 8 patients had CB in stage 1. RESULTS Between 03-2018 and 02-2022, 24 evaluable patients were treated. CB was observed in 5 patients (21%), including 2 patients with partial response (8.3%) and 3 patients with SD ≥ 16 weeks (12.5%). After median follow-up of 15 months, median progression-free survival and overall survival were 1.7 months (95% CI 1.6-2.1 months) and 4.5 months (95% CI 2.9-8.6 months), respectively. No unexpected toxicities were observed. CONCLUSIONS Panitumumab treatment provides limited CB in patients with recurrent RAF/RASwt glioblastoma precluding further development of this therapeutic strategy.
Collapse
Affiliation(s)
- Ilse A C Spiekman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Birgit S Geurts
- Oncode Institute, Utrecht, The Netherlands
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Laurien J Zeverijn
- Oncode Institute, Utrecht, The Netherlands
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gijs F de Wit
- Oncode Institute, Utrecht, The Netherlands
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Cancer Center Utrecht, Utrecht, The Netherlands
| | - Anne M L Jansen
- Department of Pathology, University Medical Cancer Center Utrecht, Utrecht, The Netherlands
| | - Benno Kusters
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens V Beerepoot
- Department of Internal Medicine, ETZ Hospital (Elisabeth-TweeSteden Ziekenhuis), Tilburg, The Netherlands
| | - Filip Y F L de Vos
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Derk-Jan A de Groot
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Ann Hoeben
- Division of Medical Oncology, Department of Internal Medicine, GROW School of Oncology and Development Biology, Maastricht University Center+, Maastricht, The Netherlands
| | - Jan Buter
- Department of Medical Oncology, Amsterdam University Medical Center, Location VuMC, Amsterdam, The Netherlands
| | - Hans A J Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Emile E Voest
- Oncode Institute, Utrecht, The Netherlands
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam,The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| |
Collapse
|
2
|
Spiekman IAC, Zeverijn LJ, Geurts BS, Verkerk K, Haj Mohammad SF, van der Noort V, Roepman P, de Leng WWJ, Jansen AML, Gootjes EC, de Groot DJA, Kerver ED, van Voorthuizen T, Roodhart JML, Valkenburg-van Iersel LBJ, Gelderblom H, Voest EE, Verheul HMW. Trastuzumab plus pertuzumab for HER2-amplified advanced colorectal cancer: Results from the drug rediscovery protocol (DRUP). Eur J Cancer 2024; 202:113988. [PMID: 38471288 DOI: 10.1016/j.ejca.2024.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND In 2-5% of patients with colorectal cancer (CRC), human epidermal growth factor 2 (HER2) is amplified or overexpressed. Despite prior evidence that anti-HER2 therapy confers clinical benefit (CB) in one-third of these patients, it is not approved for this indication in Europe. In the Drug Rediscovery Protocol (DRUP), patients are treated with off-label drugs based on their molecular profile. Here, we present the results of the cohort 'trastuzumab/pertuzumab for treatment-refractory patients with RAS/BRAF-wild-type HER2amplified metastatic CRC (HER2+mCRC)'. METHODS Patients with progressive treatment-refractory RAS/BRAF-wild-type HER2+mCRC with measurable disease were included for trastuzumab plus pertuzumab treatment. Primary endpoints of DRUP are CB (defined as confirmed objective response (OR) or stable disease (SD) ≥ 16 weeks) and safety. Patients were enrolled using a Simon-like 2-stage model, with 8 patients in stage 1 and 24 patients in stage 2 if at least 1/8 patients had CB. To identify biomarkers for response, whole genome sequencing (WGS) was performed on pre-treatment biopsies. RESULTS CB was observed in 11/24 evaluable patients (46%) with HER2+mCRC, seven patients achieved an OR (29%). Median duration of response was 8.4 months. Patients had undergone a median of 3 prior treatment lines. Median progression-free survival and overall survival were 4.3 months (95% CI 1.9-10.3) and 8.2 months (95% CI 7.2-14.7), respectively. No unexpected toxicities were observed. WGS provided potential explanations for resistance in 3/10 patients without CB, for whom WGS was available. CONCLUSIONS The results of this study confirm a clinically significant benefit of trastuzumab plus pertuzumab treatment in patients with HER2+mCRC.
Collapse
Affiliation(s)
- Ilse A C Spiekman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, the Netherlands
| | - Laurien J Zeverijn
- Oncode Institute, Utrecht, the Netherlands; Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Birgit S Geurts
- Oncode Institute, Utrecht, the Netherlands; Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Karlijn Verkerk
- Oncode Institute, Utrecht, the Netherlands; Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Soemeya F Haj Mohammad
- Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anne M L Jansen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elske C Gootjes
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Derk-Jan A de Groot
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Emile D Kerver
- Department of Medical Oncology, OLVG, Amsterdam, the Netherlands
| | | | - Jeanine M L Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Liselot B J Valkenburg-van Iersel
- Division of Medical Oncology, Department of Internal Medicine, GROW school of Oncology and Development Biology, Maastricht University Center+, Maastricht, the Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emile E Voest
- Oncode Institute, Utrecht, the Netherlands; Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, the Netherlands.
| |
Collapse
|
3
|
Geurts BS, Zeverijn LJ, Leek LVM, van Berge Henegouwen JM, Hoes LR, van der Wijngaart H, van der Noort V, van de Haar J, van Ommen-Nijhof A, Kok M, Roepman P, Jansen AML, de Leng WWJ, de Jonge MJA, Hoeben A, van Herpen CML, Westgeest HM, Wessels LFA, Verheul HMW, Gelderblom H, Voest EE. Efficacy of pembrolizumab and biomarker analysis in patients with WGS-based intermediate to high tumor mutational load: results from the Drug Rediscovery Protocol. Clin Cancer Res 2024:743079. [PMID: 38630551 DOI: 10.1158/1078-0432.ccr-24-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/25/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
PURPOSE To evaluate efficacy of pembrolizumab across multiple cancer types harboring different levels of Whole-Genome Sequencing (WGS)-based tumor mutational load (TML; total of non-synonymous mutations across the genome) in patients included in the Drug Rediscovery Protocol (NCT02925234). PATIENTS AND METHODS Patients with solid, treatment-refractory, microsatellite-stable tumors were enrolled in cohort A: breast cancer TML 140-290, cohort B: tumor-agnostic cohort TML 140-290, and cohort C: tumor-agnostic cohort TML >290. Patients received pembrolizumab 200 mg every three weeks. Primary endpoint was clinical benefit (CB: objective response or stable disease (SD) ≥16 weeks). Pre-treatment tumor biopsies were obtained for WGS and RNA-sequencing. RESULTS Seventy-two evaluable patients with 26 different histotypes were enrolled. CB rate was 13% in cohort A (3/24 with partial response (PR)), 21% in cohort B (3/24 with SD, 2/24 with PR), and 42% in cohort C (4/24 with SD, 6/24 with PR). In cohort C, neoantigen burden estimates and expression of inflammation and innate immune biomarkers were significantly associated with CB. Similar associations were not identified in cohort A and B. In cohort A, CB was significantly associated with mutations in the chromatin remodeling gene PBRM1, while in cohort B, CB was significantly associated with expression of MICA/MICB and butyrophilins. CB and clonal TML were not significantly associated. CONCLUSION While in cohort A pembrolizumab lacked activity, cohort B and cohort C met the study's primary endpoint. Further research is warranted to refine selection of patients with tumors harboring lower TMLs and may benefit from a focus on innate immunity.
Collapse
Affiliation(s)
| | | | | | | | - Louisa R Hoes
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Joris van de Haar
- The Netherlands Cancer Institute, Amsterdam, Noord-Holland, Netherlands
| | | | - Marleen Kok
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Anne M L Jansen
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | | | | | - Ann Hoeben
- Maastricht University Medical Centre, Maastricht, Netherlands
| | | | | | | | | | | | - Emile E Voest
- Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
4
|
Zeverijn LJ, Looze EJ, Thavaneswaran S, van Berge Henegouwen JM, Simes RJ, Hoes LR, Sjoquist KM, van der Wijngaart H, Sebastian L, Geurts BS, Lee CK, de Wit GF, Espinoza D, Roepman P, Lin FP, Jansen AML, de Leng WWJ, van der Noort V, Leek LVM, de Vos FYFL, van Herpen CML, Gelderblom H, Verheul HMW, Thomas DM, Voest EE. Limited clinical activity of palbociclib and ribociclib monotherapy in advanced cancers with cyclin D-CDK4/6 pathway alterations in the Dutch DRUP and Australian MoST trials. Int J Cancer 2023; 153:1413-1422. [PMID: 37424386 DOI: 10.1002/ijc.34649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023]
Abstract
The Dutch Drug Rediscovery Protocol (DRUP) and the Australian Cancer Molecular Screening and Therapeutic (MoST) Program are similar nonrandomized, multidrug, pan-cancer trial platforms that aim to identify signals of clinical activity of molecularly matched targeted therapies or immunotherapies outside their approved indications. Here, we report results for advanced or metastatic cancer patients with tumors harboring cyclin D-CDK4/6 pathway alterations treated with CDK4/6 inhibitors palbociclib or ribociclib. We included adult patients that had therapy-refractory solid malignancies with the following alterations: amplifications of CDK4, CDK6, CCND1, CCND2 or CCND3, or complete loss of CDKN2A or SMARCA4. Within MoST, all patients were treated with palbociclib, whereas in DRUP, palbociclib and ribociclib were assigned to different cohorts (defined by tumor type and alteration). The primary endpoint for this combined analysis was clinical benefit, defined as confirmed objective response or stable disease ≥16 weeks. We treated 139 patients with a broad variety of tumor types; 116 with palbociclib and 23 with ribociclib. In 112 evaluable patients, the objective response rate was 0% and clinical benefit rate at 16 weeks was 15%. Median progression-free survival was 4 months (95% CI: 3-5 months), and median overall survival 5 months (95% CI: 4-6 months). In conclusion, only limited clinical activity of palbociclib and ribociclib monotherapy in patients with pretreated cancers harboring cyclin D-CDK4/6 pathway alterations was observed. Our findings indicate that monotherapy use of palbociclib or ribociclib is not recommended and that merging data of two similar precision oncology trials is feasible.
Collapse
Affiliation(s)
- Laurien J Zeverijn
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Eleonora J Looze
- Division of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Subotheni Thavaneswaran
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - J Maxime van Berge Henegouwen
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert J Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Louisa R Hoes
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Katrin M Sjoquist
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Hanneke van der Wijngaart
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Lucille Sebastian
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Birgit S Geurts
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Chee K Lee
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Gijsbrecht F de Wit
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David Espinoza
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Frank P Lin
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Anne M L Jansen
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Lindsay V M Leek
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Filip Y F L de Vos
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carla M L van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Emile E Voest
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| |
Collapse
|
5
|
Geurts BS, Battaglia TW, van Berge Henegouwen JM, Zeverijn LJ, de Wit GF, Hoes LR, van der Wijngaart H, van der Noort V, Roepman P, de Leng WWJ, Jansen AML, Opdam FL, de Jonge MJA, Cirkel GA, Labots M, Hoeben A, Kerver ED, Bins AD, Erdkamp FGL, van Rooijen JM, Houtsma D, Hendriks MP, de Groot JWB, Verheul HMW, Gelderblom H, Voest EE. Efficacy, safety and biomarker analysis of durvalumab in patients with mismatch-repair deficient or microsatellite instability-high solid tumours. BMC Cancer 2023; 23:205. [PMID: 36870947 PMCID: PMC9985217 DOI: 10.1186/s12885-023-10663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND In this study we aimed to evaluate the efficacy and safety of the PD-L1 inhibitor durvalumab across various mismatch repair deficient (dMMR) or microsatellite instability-high (MSI-H) tumours in the Drug Rediscovery Protocol (DRUP). This is a clinical study in which patients are treated with drugs outside their labeled indication, based on their tumour molecular profile. PATIENTS AND METHODS Patients with dMMR/MSI-H solid tumours who had exhausted all standard of care options were eligible. Patients were treated with durvalumab. The primary endpoints were clinical benefit ((CB): objective response (OR) or stable disease ≥16 weeks) and safety. Patients were enrolled using a Simon like 2-stage model, with 8 patients in stage 1, up to 24 patients in stage 2 if at least 1/8 patients had CB in stage 1. At baseline, fresh frozen biopsies were obtained for biomarker analyses. RESULTS Twenty-six patients with 10 different cancer types were included. Two patients (2/26, 8%) were considered as non-evaluable for the primary endpoint. CB was observed in 13 patients (13/26, 50%) with an OR in 7 patients (7/26, 27%). The remaining 11 patients (11/26, 42%) had progressive disease. Median progression-free survival and median overall survival were 5 months (95% CI, 2-not reached) and 14 months (95% CI, 5-not reached), respectively. No unexpected toxicity was observed. We found a significantly higher structural variant (SV) burden in patients without CB. Additionally, we observed a significant enrichment of JAK1 frameshift mutations and a significantly lower IFN-γ expression in patients without CB. CONCLUSION Durvalumab was generally well-tolerated and provided durable responses in pre-treated patients with dMMR/MSI-H solid tumours. High SV burden, JAK1 frameshift mutations and low IFN-γ expression were associated with a lack of CB; this provides a rationale for larger studies to validate these findings. TRIAL REGISTRATION Clinical trial registration: NCT02925234. First registration date: 05/10/2016.
Collapse
Affiliation(s)
- Birgit S Geurts
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Thomas W Battaglia
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - J Maxime van Berge Henegouwen
- Oncode Institute, Utrecht, the Netherlands.,Department of Medical Oncology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Laurien J Zeverijn
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Gijs F de Wit
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Louisa R Hoes
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Hanneke van der Wijngaart
- Oncode Institute, Utrecht, the Netherlands.,Department of Medical Oncology, Amsterdam University Medical Centre, location VUMC, Amsterdam, the Netherlands
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Cancer Centre Utrecht, Utrecht, the Netherlands
| | - Anne M L Jansen
- Department of Pathology, University Medical Cancer Centre Utrecht, Utrecht, the Netherlands
| | - Frans L Opdam
- Department of Clinical Pharmacology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maja J A de Jonge
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Geert A Cirkel
- Department of Medical Oncology, Meander, Amersfoort, the Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam University Medical Centre, location VUMC, Amsterdam, the Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, Department of Internal Medicine, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Emile D Kerver
- Department of Medical Oncology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Adriaan D Bins
- Department of Medical Oncology, Amsterdam University Medical Centre, location AUMC, Amsterdam, the Netherlands
| | - Frans G L Erdkamp
- Department of Medical Oncology, Zuyderland Hospital, Sittard-Geelen, the Netherlands
| | - Johan M van Rooijen
- Department of Medical Oncology, Martini Hospital, Groningen, the Netherlands
| | - Danny Houtsma
- Department of Medical Oncology, Haga Hospital, The Hague, the Netherlands
| | - Mathijs P Hendriks
- Department of Medical Oncology, Northwest Clinics, Alkmaar, the Netherlands
| | | | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Emile E Voest
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, Utrecht, the Netherlands.
| |
Collapse
|
6
|
van Not OJ, Blokx WAM, van den Eertwegh AJM, de Meza MM, Haanen JB, Blank CU, Aarts MJB, van den Berkmortel FWPJ, de Groot JWB, Hospers GAP, Kapiteijn E, Piersma D, van Rijn RS, Stevense-den Boer M, van der Veldt AAM, Boers-Sonderen MJ, Jansen AML, Wouters MWJM, Suijkerbuijk KPM. BRAF and NRAS Mutation Status and Response to Checkpoint Inhibition in Advanced Melanoma. JCO Precis Oncol 2022; 6:e2200018. [PMID: 36130145 DOI: 10.1200/po.22.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Little is known about the effect of specific gene mutations on efficacy of immune checkpoint inhibitors in patients with advanced melanoma. MATERIALS AND METHODS All patients with advanced melanoma treated with first-line anti-PD-1 or ipilimumab-nivolumab between 2012 and 2021 in the nationwide Dutch Melanoma Treatment Registry were included in this cohort study. Objective response rate, progression-free survival (PFS), and overall survival (OS) were analyzed according to BRAF and NRAS status. A multivariable Cox model was used to analyze prognostic factors associated with PFS and OS. RESULTS In total, 1764 patients received anti-PD-1 and 759 received ipilimumab-nivolumab. No significant differences in PFS were found in the anti-PD-1 cohort. In the ipilimumab-nivolumab cohort, median PFS was significantly higher for BRAF-mutant melanoma (9.9 months; 95% CI, 6.8 to 17.2) compared with NRAS-mutant (4.8 months; 95% CI, 3.0 to 7.5) and double wild-type (5.3 months; 95% CI, 3.6 to 7.1). In multivariable analysis, BRAF-mutant melanoma was significantly associated with a lower risk of progression or death in the ipilimumab-nivolumab cohort. Median OS was significantly higher for BRAF-mutant melanoma compared with NRAS-mutant and double wild-type melanoma for both immune checkpoint inhibitor regimens. CONCLUSION Ipilimumab-nivolumab-treated patients with BRAF-mutant melanoma display improved PFS and OS compared with patients with NRAS-mutant and double wild-type melanoma. BRAF mutation status is a factor to consider while choosing between mono and dual checkpoint inhibition in advanced melanoma.
Collapse
Affiliation(s)
- Olivier J van Not
- Scientific Bureau, Dutch Institute for Clinical Auditing, Leiden, the Netherlands.,Department of Medical Oncology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Willeke A M Blokx
- Department of Pathology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Alfons J M van den Eertwegh
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Melissa M de Meza
- Scientific Bureau, Dutch Institute for Clinical Auditing, Leiden, the Netherlands.,Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - John B Haanen
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christian U Blank
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Medical Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maureen J B Aarts
- Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | | | | | - Geke A P Hospers
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Ellen Kapiteijn
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Djura Piersma
- Department of Internal Medicine, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Rozemarijn S van Rijn
- Department of Internal Medicine, Medical Centre Leeuwarden, Leeuwarden, the Netherlands
| | | | - Astrid A M van der Veldt
- Department of Medical Oncology and Radiology and Nuclear Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marye J Boers-Sonderen
- Department of Medical Oncology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Anne M L Jansen
- Department of Pathology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Michel W J M Wouters
- Scientific Bureau, Dutch Institute for Clinical Auditing, Leiden, the Netherlands.,Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | |
Collapse
|
7
|
van Berge Henegouwen JM, Jebbink M, Hoes LR, van der Wijngaart H, Zeverijn LJ, van der Velden DL, Roepman P, de Leng WWJ, Jansen AML, van Werkhoven E, van der Noort V, van der Wekken AJ, de Langen AJ, Voest EE, Verheul HMW, Smit EF, Gelderblom H. Trastuzumab and pertuzumab combination therapy for advanced pre-treated HER2 exon 20-mutated non-small cell lung cancer. Eur J Cancer 2022; 171:114-123. [PMID: 35716537 DOI: 10.1016/j.ejca.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/23/2022] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
INTRODUCTION In 1-3% of non-small cell lung cancer (NSCLC) human epidermal growth factor 2 (HER2) mutations are identified as a genomic driver. Nevertheless, no HER2-targeted treatment is approved for NSCLC. In the Drug Rediscovery Protocol (DRUP), patients are treated with off-label drugs based on their molecular profile. Here, we present the results of the cohort 'trastuzumab/pertuzumab for HER2 exon20 mutation positive (HER2m+) NSCLC'. METHODS Patients with treatment refractory, advanced HER2m+ NSCLC with measurable disease (RECISTv1.1) were eligible. Treatment with intravenous trastuzumab combined with pertuzumab every 3 weeks was administered. The primary end-point was clinical benefit (CB: either objective response or stable disease ≥ 16 weeks). Patients were enrolled using a Simon-like 2-stage design, with 8 patients in stage 1 and up to 24 patients in stage 2 if at least 1 patient had CB in stage 1. At baseline, a biopsy for biomarker analysis, including whole genome sequencing, was obtained. RESULTS Twenty-four evaluable patients were enrolled and treated between May 2017 and August 2020. CB was observed in 9 patients (38%); including an objective response rate of 8.3% (2 patients had a partial response) and 7 patients with stable disease ≥ 16 weeks. The most frequently observed HER2 mutation was p.Y772_A775dup (71%, n = 20). Median follow-up was 13 months, median progression-free survival and overall survival 4 (95% CI 3-6) and 10 months (95% CI 4 - not reached), respectively. Whole genome sequencing data (available for 67% of patients) confirmed the inclusion mutation in all cases. No unexpected toxicity was observed. CONCLUSION Despite the fact that the study did meet its primary end-point, trastuzumab/pertuzumab was only marginally active in a subset of patients with heavily pre-treated HER2m+ NSCLC.
Collapse
Affiliation(s)
- J M van Berge Henegouwen
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands; Oncode Institute, the Netherlands
| | - M Jebbink
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - L R Hoes
- Oncode Institute, the Netherlands; Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - H van der Wijngaart
- Oncode Institute, the Netherlands; Department of Medical Oncology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - L J Zeverijn
- Oncode Institute, the Netherlands; Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - D L van der Velden
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - P Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - W W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A M L Jansen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - E van Werkhoven
- Biometrics Department, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - V van der Noort
- Biometrics Department, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - A J van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - A J de Langen
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - E E Voest
- Oncode Institute, the Netherlands; Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - H M W Verheul
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - E F Smit
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - H Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands.
| |
Collapse
|
8
|
van der Velde KJ, Singh G, Kaliyaperumal R, Liao X, de Ridder S, Rebers S, Kerstens HHD, de Andrade F, van Reeuwijk J, De Gruyter FE, Hiltemann S, Ligtvoet M, Weiss MM, van Deutekom HWM, Jansen AML, Stubbs AP, Vissers LELM, Laros JFJ, van Enckevort E, Stemkens D, 't Hoen PAC, Beliën JAM, van Gijn ME, Swertz MA. FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Sci Data 2022; 9:169. [PMID: 35418585 PMCID: PMC9008059 DOI: 10.1038/s41597-022-01265-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org .
Collapse
Affiliation(s)
- K Joeri van der Velde
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gurnoor Singh
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Rajaram Kaliyaperumal
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - XiaoFeng Liao
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Sander de Ridder
- Amsterdam University Medical Center, University of Amsterdam, Department of Pathology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Susanne Rebers
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hindrik H D Kerstens
- Prinses Máxima Center for Pediatric Oncology, Kemmeren group, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Fernanda de Andrade
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jeroen van Reeuwijk
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Fini E De Gruyter
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Saskia Hiltemann
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Maarten Ligtvoet
- Nictiz - Dutch competence centre for electronic exchange of health and care information, Oude Middenweg 55, 2491 AC, The Hague, The Netherlands
| | - Marjan M Weiss
- Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hanneke W M van Deutekom
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Anne M L Jansen
- University Medical Center Utrecht, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Andrew P Stubbs
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisenka E L M Vissers
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen F J Laros
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Leiden University Medical Center, Department of Clinical Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Esther van Enckevort
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Daphne Stemkens
- VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands, Koninginnelaan 23, 3762 DA, Soest, The Netherlands
| | - Peter A C 't Hoen
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen A M Beliën
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Mariëlle E van Gijn
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| |
Collapse
|
9
|
van der Wijngaart H, Hoes LR, van Berge Henegouwen JM, van der Velden DL, Zeverijn LJ, Roepman P, van Werkhoven E, de Leng WWJ, Jansen AML, Mehra N, Robbrecht DGJ, Labots M, de Groot DJA, Hoeben A, Hamberg P, Gelderblom H, Voest EE, Verheul HMW. Patients with Biallelic BRCA1/2 Inactivation Respond to Olaparib Treatment Across Histologic Tumor Types. Clin Cancer Res 2021; 27:6106-6114. [PMID: 34475104 DOI: 10.1158/1078-0432.ccr-21-1104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/20/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE To assess the efficacy of olaparib, a PARP inhibitor (PARPi) in patients with tumors with BRCA1/2 mutations, regardless of histologic tumor type. PATIENTS AND METHODS Patients with treatment-refractory BRCA1/2-mutated cancer were included for treatment with off-label olaparib 300 mg twice daily until disease progression or unacceptable toxicity. In Drug Rediscovery Protocol (DRUP), patients with treatment-refractory solid malignancies receive off-label drugs based on tumor molecular profiles while whole-genome sequencing (WGS) is performed on baseline tumor biopsies. The primary endpoint was clinical benefit (CB; defined as objective response or stable disease ≥ 16 weeks according to RECIST 1.1). Per protocol patients were enrolled using a Simon-like two-stage model. RESULTS Twenty-four evaluable patients with nine different tumor types harboring BRCA1/2 mutations were included, 58% had CB from treatment with olaparib. CB was observed in patients with complete loss of function (LoF) of BRCA1/2, while 73% of patients with biallelic BRCA LoF had CB. In 17 patients with and seven without current labeled indication, 10 and four patients had CB, respectively. Treatment resistance in four patients with biallelic loss might be explained by an additional oncogenic driver which was discovered by WGS, including Wnt pathway activation, FGFR amplification, and CDKN2A loss, in three tumor types. CONCLUSIONS These data indicate that using PARPis is a promising treatment strategy for patients with non-BRCA-associated histologies harboring biallelic BRCA LoF. WGS allows to accurately detect complete LoF of BRCA and homologous repair deficiency (HRD) signature as well as oncogenic drivers that may contribute to resistance, using a single assay.
Collapse
Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Louisa R Hoes
- Oncode Institute, Utrecht, the Netherlands.,Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - J Maxime van Berge Henegouwen
- Oncode Institute, Utrecht, the Netherlands.,Department of Medical Oncology, Leiden University Medical Center, Rapenburg, Leiden, the Netherlands
| | - Daphne L van der Velden
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurien J Zeverijn
- Oncode Institute, Utrecht, the Netherlands.,Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Erik van Werkhoven
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anne M L Jansen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Debbie G J Robbrecht
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Derk Jan A de Groot
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Paul Hamberg
- Department of Internal Medicine, Franciscus Gasthuis and Vlietland, Rotterdam, the Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Rapenburg, Leiden, the Netherlands
| | - Emile E Voest
- Oncode Institute, Utrecht, the Netherlands.,Department of Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
10
|
Ebbelaar CF, Jansen AML, Bloem LT, Blokx WAM. Genome-wide copy number variations as molecular diagnostic tool for cutaneous intermediate melanocytic lesions: a systematic review and individual patient data meta-analysis. Virchows Arch 2021; 479:773-783. [PMID: 33851238 PMCID: PMC8516778 DOI: 10.1007/s00428-021-03095-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/08/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Cutaneous intermediate melanocytic neoplasms with ambiguous histopathological features are diagnostically challenging. Ancillary cytogenetic techniques to detect genome-wide copy number variations (CNVs) might provide a valuable tool to allow accurate classification as benign (nevus) or malignant (melanoma). However, the CNV cut-off value to distinguish intermediate lesions from melanoma is not well defined. We performed a systematic review and individual patient data meta-analysis to evaluate the use of CNVs to classify intermediate melanocytic lesions. A total of 31 studies and 431 individual lesions were included. The CNV number in intermediate lesions (median 1, interquartile range [IQR] 0-2) was significantly higher (p<0.001) compared to that in benign lesions (median 0, IQR 0-1) and lower (p<0.001) compared to that in malignant lesions (median 6, IQR 4-11). The CNV number displayed excellent ability to differentiate between intermediate and malignant lesions (0.90, 95% CI 0.86-0.94, p<0.001). Two CNV cut-off points demonstrated a sensitivity and specificity higher than 80%. A cut-off of ≥3 CNVs corresponded to 85% sensitivity and 84% specificity, and a cut-off of ≥4 CNVs corresponded to 81% sensitivity and 91% specificity, respectively. This individual patient data meta-analysis provides a comprehensive overview of CNVs in cutaneous intermediate melanocytic lesions, based on the largest pooled cohort of ambiguous melanocytic neoplasms to date. Our meta-analysis suggests that a cut-off of ≥3 CNVs might represent the optimal trade-off between sensitivity and specificity in clinical practice to differentiate intermediate lesions from melanoma.
Collapse
Affiliation(s)
- Chiel F Ebbelaar
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, P.O. Box 85500, 3508, Utrecht, GA, Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Anne M L Jansen
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, P.O. Box 85500, 3508, Utrecht, GA, Netherlands
| | - Lourens T Bloem
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Willeke A M Blokx
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, P.O. Box 85500, 3508, Utrecht, GA, Netherlands.
| |
Collapse
|
11
|
Kerckhoffs KGP, Aallali T, Ambarus CA, Sigurdsson V, Jansen AML, Blokx WAM. Expanding spectrum of "spitzoid" lesions: a small series of 4 cases with MAP2K1 mutations. Virchows Arch 2020; 479:195-202. [PMID: 33040161 PMCID: PMC8298358 DOI: 10.1007/s00428-020-02940-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/10/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
The molecular background of a significant proportion of spitzoid neoplasms is still unknown. Recently, activating mutations in MAP2K1 have been described in a few spitzoid lesions, but not in benign Spitz nevi. We report four cases of melanocytic tumors with spitzoid features in which a MAP2K1 mutation was detected. The lesions did not show a single distinct phenotype and ranged from benign to malignant. Two cases resembled desmoplastic Spitz nevi. Based on the combination of morphological, immunohistochemical, and molecular findings, one case was classified as benign, one as probably benign, possibly intermediate low-grade (MELTUMP—melanocytic tumor of unknown malignant potential), one case was classified as intermediate (MELTUMP), and one case was considered a superficial spreading melanoma with spitzoid features. Based on this, we conclude that MAP2K1 mutations can indicate a spitzoid genetic signature and can be found in both benign and malignant spitzoid neoplasms.
Collapse
Affiliation(s)
- K G P Kerckhoffs
- Department of Pathology, Maastricht University Medical Center+, Maastricht, The Netherlands.
| | - T Aallali
- Symbiant Pathology Expert Center, Hoorn/Zaandam, The Netherlands
| | - C A Ambarus
- Department of Pathology, Sint Antonius Hospital, Nieuwegein, The Netherlands
| | - V Sigurdsson
- Department of Dermatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A M L Jansen
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - W A M Blokx
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
12
|
Jansen AML, Tops CMJ, Ruano D, van Eijk R, Wijnen JT, Ten Broeke S, Nielsen M, Hes FJ, van Wezel T, Morreau H. The complexity of screening PMS2 in DNA isolated from formalin-fixed paraffin-embedded material. Eur J Hum Genet 2019; 28:333-338. [PMID: 31616036 DOI: 10.1038/s41431-019-0527-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 11/09/2022] Open
Abstract
Germline variants in the DNA mismatch repair (MMR) gene PMS2 cause 1-14% of all Lynch Syndrome cancers. Correct variant analysis of PMS2 is complex due to the presence of multiple pseudogenes and the occurrence of gene conversion. The analysis complexity increases in highly fragmented DNA from formalin-fixed paraffin-embedded (FFPE) tissue. Here we describe a reliable approach to detect true PMS2 variants in fragmented DNA. A custom NGS panel designed for FFPE tissue was used targeting four MMR genes, POLE and POLD1. Amplicon design for PMS2 was based on the position of paralogous sequence variants (PSVs) that distinguish PMS2 from its pseudogenes. PMS2 variants in exons 1-11 can be correctly curated based on this information. For exons 12-15 this is less reliable as these undergo gene conversion. Using this method, we screened PMS2 variants in 125 MMR-deficient tumors. Of the 125 tumors tested, six were unexplained MMR-deficient tumors with solitary PMS2 protein expression loss. In these six tumors two unclassified variants (class 3) and five variants likely affecting function (class 4/5) were detected in PMS2. One microsatellite unstable tumor with positive staining for all MMR proteins was found to carry a frameshift PMS2 variant (class 5). No class 4 or class 5 PMS2 variants were detected in tumors with other patterns of MMR protein expression loss.
Collapse
Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanne Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
13
|
Jansen AML, Ghosh P, Dakal TC, Slavin TP, Boland CR, Goel A. Novel candidates in early-onset familial colorectal cancer. Fam Cancer 2019; 19:1-10. [PMID: 31555933 DOI: 10.1007/s10689-019-00145-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022]
Abstract
In 20-30% of patients suspected of a familial colorectal cancer (CRC) syndrome, no underlying genetic cause is detected. Recent advances in whole exome sequencing have generated evidence for new CRC-susceptibility genes including POLE, POLD1 and NTHL1¸ but many patients remain unexplained. Whole exome sequencing was performed on DNA from nine patients from five different families with familial clusters of CRC in which traditional genetic testing failed to yield a diagnosis. Variants were filtered by minor allele frequencies, followed by prioritization based on in silico prediction tools, and the presence in cancer susceptibility genes or genes in cancer-associated pathways. Effects of frameshift variants on protein structure were modeled using I-Tasser. One known pathogenic variant in POLD1 was detected (p.S478N), together with variants in 17 candidate genes not previously associated with CRC. Additional in silico analysis using SIFT, PROVEAN and PolyPhen on the 14 missense variants indicated a possible damaging effect in nine of 14 variants. Modeling of the insertions/deletions showed a damaging effect of two variants in NOTCH2 and CYP1B1. One family was explained by a mutation in a known familial CRC gene. In the remaining four families, the most promising candidates found are a frameshift NOTCH2 and a missense RAB25 variant. This study provides potential novel candidate variants in unexplained familial CRC patients, however, functional validation is imperative to confirm the role of these variants in CRC tumorigenesis. Additionally, while whole exome sequencing enables detection of variants throughout the exome, other causes explaining the familial phenotype such as multiple single nucleotide polymorphisms accumulating to a polygenic risk or epigenetic events, might be missed with this approach.
Collapse
Affiliation(s)
- Anne M L Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tikam C Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Thomas P Slavin
- Division of Clinical Cancer Genomics City of Hope, Department of Medical Oncology, National Medical Center, Duarte, CA, USA
| | - C Richard Boland
- Departments of Medicine and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, TX, USA.
- Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91016, USA.
| |
Collapse
|
14
|
Ten Broeke SW, van Bavel TC, Jansen AML, Gómez-García E, Hes FJ, van Hest LP, Letteboer TGW, Olderode-Berends MJW, Ruano D, Spruijt L, Suerink M, Tops CM, van Eijk R, Morreau H, van Wezel T, Nielsen M. Molecular Background of Colorectal Tumors From Patients With Lynch Syndrome Associated With Germline Variants in PMS2. Gastroenterology 2018; 155:844-851. [PMID: 29758216 DOI: 10.1053/j.gastro.2018.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Germline variants in mismatch repair genes MLH1, MSH2 (EPCAM), MSH6, or PMS2 cause Lynch syndrome. Patients with these variants have an increased risk of developing colorectal cancers (CRCs) that differ from sporadic CRCs in genetic and histologic features. It has been a challenge to study CRCs associated with PMS2 variants (PMS2-associated CRCs) because these develop less frequently and in older patients than CRCs with variants in other mismatch repair genes. METHODS We analyzed 20 CRCs associated with germline variants in PMS2, 22 sporadic CRCs, 18 CRCs with germline variants in MSH2, and 24 CRCs from patients with germline variants in MLH1. Tumor tissue blocks were collected from Dutch pathology departments in 2017. After extraction of tumor DNA, we used a platform designed to detect approximately 3,000 somatic hotspot variants in 55 genes (including KRAS, APC, CTNNB1, and TP53). Somatic variant frequencies were compared using the Fisher exact test. RESULTS None of the PMS2-associated CRCs contained any somatic variants in the catenin-β1 gene (CTNNB1), which encodes β-catenin, whereas 14 of 24 MLH1-associated CRCs (58%) contained variants in CTNNB1. Half the PMS2-associated CRCs contained KRAS variants, but only 20% of these were in hotspots that encoded G12D or G13D. These hotspot variants occurred more frequently in CRCs associated with variants in MLH1 (37.5%; P = .44) and MSH2 (71.4%; P = .035) than in those associated with variants in PMS2. CONCLUSIONS In a genetic analysis of 84 colorectal tumors, we found tumors from patients with PMS2-associated Lynch syndrome to be distinct from colorectal tumors associated with defects in other mismatch repair genes. This might account for differences in development and less frequent occurrence.
Collapse
Affiliation(s)
- Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Tom C van Bavel
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne M L Jansen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Encarnca Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Liselot P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Tom G W Letteboer
- Department of Clinical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Liesbeth Spruijt
- Department of Clinical Genetics, Radboud University Medical Center, Radboud, the Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
15
|
Jansen AML, Crobach S, Geurts-Giele WRR, van den Akker BEWM, Garcia MV, Ruano D, Nielsen M, Tops CMJ, Wijnen JT, Hes FJ, van Wezel T, Dinjens WNM, Morreau H. Distinct Patterns of Somatic Mosaicism in the APC Gene in Neoplasms From Patients With Unexplained Adenomatous Polyposis. Gastroenterology 2017; 152:546-549.e3. [PMID: 27816598 DOI: 10.1053/j.gastro.2016.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 12/02/2022]
Abstract
We investigated the presence and patterns of mosaicism in the APC gene in patients with colon neoplasms not associated with any other genetic variants; we performed deep sequence analysis of APC in at least 2 adenomas or carcinomas per patient. We identified mosaic variants in APC in adenomas from 9 of the 18 patients with 21 to approximately 100 adenomas. Mosaic variants of APC were variably detected in leukocyte DNA and/or non-neoplastic intestinal mucosa of these patients. In a comprehensive sequence analysis of 1 patient, we found no evidence for mosaicism in APC in non-neoplastic intestinal mucosa. One patient was found to carry a mosaic c.4666dupA APC variant in only 10 of 16 adenomas, indicating the importance of screening 2 or more adenomas for genetic variants.
Collapse
Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | | | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
| |
Collapse
|
16
|
van der Klift HM, Jansen AML, van der Steenstraten N, Bik EC, Tops CMJ, Devilee P, Wijnen JT. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med 2015; 3:327-45. [PMID: 26247049 PMCID: PMC4521968 DOI: 10.1002/mgg3.145] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants.
Collapse
Affiliation(s)
- Heleen M van der Klift
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Anne M L Jansen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands
| | | | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Pathology, Leiden University Medical Center Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| |
Collapse
|