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Verschoor N, Smid M, Jager A, Sleijfer S, Wilting SM, Martens JWM. Integrative whole-genome and transcriptome analysis of HER2-amplified metastatic breast cancer. Breast Cancer Res 2023; 25:145. [PMID: 37968696 PMCID: PMC10648326 DOI: 10.1186/s13058-023-01743-z] [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: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND In breast cancer, the advent of anti-HER2 therapies has made HER2+ tumors a highly relevant subgroup. However, the exact characteristics which prohibit clinical response to anti-HER2 therapies and drive disease progression are not yet fully known. Integrative whole-genome and transcriptomic sequencing data from both primary and metastatic HER2-positive breast cancer will enhance our understanding of underlying biological processes. METHODS Here, we used WGS and RNA sequencing data of 700 metastatic breast tumors, of which 68 being HER2+, to search for specific genomic features of HER2+ disease and therapy resistance. Furthermore, we integrated results with transcriptomic data to associate tumors exhibiting a HER2+-specific gene expression profile with ERBB2 mutation status, prior therapy and relevant gene expression signatures. RESULTS Overall genomic profiles of primary and metastatic HER2+ breast cancers were similar, and no specific acquired genomics traits connected to prior anti-HER2 treatment were observed. However, specific genomic features were predictive of progression-free survival on post-biopsy anti-HER2 treatment. Furthermore, a HER2-driven expression profile grouped HER2-amplified tumors with ERBB2-mutated cases and cases without HER2 alterations. The latter were reported as ER positive in primary disease, but the metastatic biopsy showed low ESR1 expression and upregulation of the MAPK pathway, suggesting transformation to ER independence. CONCLUSIONS In summary, although the quantity of variants increased throughout HER2-positive breast cancer progression, the genomic composition remained largely consistent, thus yielding no new major processes beside those already operational in primary disease. Our results suggest that integrated genomic and transcriptomic analyses may be key in establishing therapeutic options.
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Affiliation(s)
- Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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2
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Angus L, Smid M, Wilting SM, Bos MK, Steeghs N, Konings IRHM, Tjan-Heijnen VCG, van Riel JMGH, van de Wouw AJ, Cuppen E, Lolkema MP, Jager A, Sleijfer S, Martens JWM. Genomic Alterations Associated with Estrogen Receptor Pathway Activity in Metastatic Breast Cancer Have a Differential Impact on Downstream ER Signaling. Cancers (Basel) 2023; 15:4416. [PMID: 37686693 PMCID: PMC10487136 DOI: 10.3390/cancers15174416] [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: 07/30/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Mutations in the estrogen receptor gene (ESR1), its transcriptional regulators, and the mitogen-activated protein kinase (MAPK) pathway are enriched in patients with endocrine-resistant metastatic breast cancer (MBC). Here, we integrated whole genome sequencing with RNA sequencing data from the same samples of 101 ER-positive/HER2-negative MBC patients who underwent a tumor biopsy prior to the start of a new line of treatment for MBC (CPCT-02 study, NCT01855477) to analyze the downstream effects of DNA alterations previously linked to endocrine resistance, thereby gaining a better understanding of the associated mechanisms. Hierarchical clustering was performed using expression of ESR1 target genes. Genomic alterations at the DNA level, gene expression levels, and last administered therapy were compared between the identified clusters. Hierarchical clustering revealed two distinct clusters, one of which was characterized by increased expression of ESR1 and its target genes. Samples in this cluster were significantly enriched for mutations in ESR1 and amplifications in FGFR1 and TSPYL. Patients in the other cluster showed relatively lower expression levels of ESR1 and its target genes, comparable to ER-negative samples, and more often received endocrine therapy as their last treatment before biopsy. Genes in the MAPK-pathway, including NF1, and ESR1 transcriptional regulators were evenly distributed. In conclusion, RNA sequencing identified a subgroup of patients with clear expression of ESR1 and its downstream targets, probably still benefiting from ER-targeting agents. The lower ER expression in the other subgroup might be partially explained by ER activity still being blocked by recently administered endocrine treatment, indicating that biopsy timing relative to endocrine treatment needs to be considered when interpreting transcriptomic data.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Manouk K. Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Inge R. H. M. Konings
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Vivianne C. G. Tjan-Heijnen
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
- Department of Medical Oncology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | | | - Agnes J. van de Wouw
- Department of Medical Oncology, VieCuri Medical Center, 5912 BL Venlo, The Netherlands;
| | - CPCT Consortium
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
- Hartwig Medical Foundation, 1098 XH Amsterdam, The Netherlands
| | - Martijn P. Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
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3
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Verschoor N, de Weerd V, Van MN, Kraan J, Smid M, Heijns JB, Drooger JC, Zuetenhorst JM, van der Padt-Pruijsten A, Jager A, Sleijfer S, Martens JWM, Wilting SM. Tumor-agnostic ctDNA levels by mFAST-SeqS in first-line HR-positive, HER2 negative metastatic breast cancer patients as a biomarker for survival. NPJ Breast Cancer 2023; 9:61. [PMID: 37452019 PMCID: PMC10349058 DOI: 10.1038/s41523-023-00563-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
This prospective cohort study reports aneuploidy score by mFast-SeqS as a strong prognostic marker in MBC patients. mFAST-SeqS is an affordable and easily implementable method for the assessment of total ctDNA levels and, as such, provides an alternative prognostic tool. One mixed cohort (cohort A, n = 45) starting any type of treatment in any line of therapy and one larger cohort (cohort B, n = 129) consisting of patients starting aromatase inhibitors (AI) as first-line therapy were used. mFAST-SeqS was performed using plasma of blood in which CTCs (CellSearch) were enumerated. The resulting aneuploidy score was correlated with categorized CTC count and associated with outcome. The aneuploidy score was significantly correlated with CTC count, but discordance was observed in 31.6% when applying cut-offs of 5. In both cohorts, aneuploidy score was a significant prognostic marker for both PFS and OS. In the Cox regression models, the HR for aneuploidy score for PFS was 2.52 (95% CI: 1.56-4.07), and the HR for OS was 2.37 (95% CI: 1.36-4.14). Results presented here warrant further investigations into the clinical utility of this marker in MBC patients.
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Affiliation(s)
- Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mai N Van
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joan B Heijns
- Department of Medical Oncology, Amphia, Breda, The Netherlands
| | - Jan C Drooger
- Department of Medical Oncology, Breast Cancer Center South Holland South, Ikazia Hospital, Rotterdam, The Netherlands
| | - Johanna M Zuetenhorst
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, Rotterdam/ Schiedam, the Netherlands
| | | | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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4
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Smid M, Schmidt MK, Prager-van der Smissen WJC, Ruigrok-Ritstier K, Schreurs MAC, Cornelissen S, Garcia AM, Broeks A, Timmermans AM, Trapman-Jansen AMAC, Collée JM, Adank MA, Hooning MJ, Martens JWM, Hollestelle A. Breast cancer genomes from CHEK2 c.1100delC mutation carriers lack somatic TP53 mutations and display a unique structural variant size distribution profile. Breast Cancer Res 2023; 25:53. [PMID: 37161532 PMCID: PMC10169359 DOI: 10.1186/s13058-023-01653-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND CHEK2 c.1100delC was the first moderate-risk breast cancer (BC) susceptibility allele discovered. Despite several genomic, transcriptomic and functional studies, however, it is still unclear how exactly CHEK2 c.1100delC promotes tumorigenesis. Since the mutational landscape of a tumor reflects the processes that have operated on its development, the aim of this study was to uncover the somatic genomic landscape of CHEK2-associated BC. METHODS We sequenced primary BC (pBC) and normal genomes of 20 CHEK2 c.1100delC mutation carriers as well as their pBC transcriptomes. Including pre-existing cohorts, we exhaustively compared CHEK2 pBC genomes to those from BRCA1/2 mutation carriers, those that displayed homologous recombination deficiency (HRD) and ER- and ER+ pBCs, totaling to 574 pBC genomes. Findings were validated in 517 metastatic BC genomes subdivided into the same subgroups. Transcriptome data from 168 ER+ pBCs were used to derive a TP53-mutant gene expression signature and perform cluster analysis with CHEK2 BC transcriptomes. Finally, clinical outcome of CHEK2 c.1100delC carriers was compared with BC patients displaying somatic TP53 mutations in two well-described retrospective cohorts totaling to 942 independent pBC cases. RESULTS BC genomes from CHEK2 mutation carriers were most similar to ER+ BC genomes and least similar to those of BRCA1/2 mutation carriers in terms of tumor mutational burden as well as mutational signatures. Moreover, CHEK2 BC genomes did not show any evidence of HRD. Somatic TP53 mutation frequency and the size distribution of structural variants (SVs), however, were different compared to ER+ BC. Interestingly, BC genomes with bi-allelic CHEK2 inactivation lacked somatic TP53 mutations and transcriptomic analysis indicated a shared biology with TP53 mutant BC. Moreover, CHEK2 BC genomes had an increased frequency of > 1 Mb deletions, inversions and tandem duplications with peaks at specific sizes. The high chromothripsis frequency among CHEK2 BC genomes appeared, however, not associated with this unique SV size distribution profile. CONCLUSIONS CHEK2 BC genomes are most similar to ER+ BC genomes, but display unique features that may further unravel CHEK2-driven tumorigenesis. Increased insight into this mechanism could explain the shorter survival of CHEK2 mutation carriers that is likely driven by intrinsic tumor aggressiveness rather than endocrine resistance.
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Affiliation(s)
- Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maartje A C Schreurs
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Aida Marsal Garcia
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - A Mieke Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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5
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Wang Z, Coban B, Wu H, Chouaref J, Daxinger L, Paulsen MT, Ljungman M, Smid M, Martens JWM, Danen EHJ. GRHL2-controlled gene expression networks in luminal breast cancer. Cell Commun Signal 2023; 21:15. [PMID: 36691073 PMCID: PMC9869538 DOI: 10.1186/s12964-022-01029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/24/2022] [Indexed: 01/24/2023] Open
Abstract
Grainyhead like 2 (GRHL2) is an essential transcription factor for development and function of epithelial tissues. It has dual roles in cancer by supporting tumor growth while suppressing epithelial to mesenchymal transitions (EMT). GRHL2 cooperates with androgen and estrogen receptors (ER) to regulate gene expression. We explore genome wide GRHL2 binding sites conserved in three ER⍺/GRHL2 positive luminal breast cancer cell lines by ChIP-Seq. Interaction with the ER⍺/FOXA1/GATA3 complex is observed, however, only for a minor fraction of conserved GRHL2 peaks. We determine genome wide transcriptional dynamics in response to loss of GRHL2 by nascent RNA Bru-seq using an MCF7 conditional knockout model. Integration of ChIP- and Bru-seq pinpoints candidate direct GRHL2 target genes in luminal breast cancer. Multiple connections between GRHL2 and proliferation are uncovered, including transcriptional activation of ETS and E2F transcription factors. Among EMT-related genes, direct regulation of CLDN4 is corroborated but several targets identified in other cells (including CDH1 and ZEB1) are ruled out by both ChIP- and Bru-seq as being directly controlled by GRHL2 in luminal breast cancer cells. Gene clusters correlating positively (including known GRHL2 targets such as ErbB3, CLDN4/7) or negatively (including TGFB1 and TGFBR2) with GRHL2 in the MCF7 knockout model, display similar correlation with GRHL2 in ER positive as well as ER negative breast cancer patients. Altogether, this study uncovers gene sets regulated directly or indirectly by GRHL2 in luminal breast cancer, identifies novel GRHL2-regulated genes, and points to distinct GRHL2 regulation of EMT in luminal breast cancer cells. Video Abstract.
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Affiliation(s)
- Zi Wang
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bircan Coban
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik H J Danen
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, 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George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Smid M, Schmidt MK, Prager - van der Smissen WJ, Ruigrok - Ritstier K, Cornelissen S, Schreurs MA, Collee JM, Adank MA, Hooning MJ, Martens JW, Hollestelle A. Abstract 3627: The genomic landscape of breast cancers from CHEK2 c.1100delC mutation carriers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3627] [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
Women who carry the germline CHEK2 c.1100delC mutation have a 2.3-fold increased life-time risk to develop breast cancer (BC). Their BCs are mostly of the luminal/ER+ subtype and diagnosed at a younger age than BCs in sporadic patients. BC patients carrying a CHEK2 c.1100delC mutation are at an increased risk of developing a contralateral BC and have a worse survival compared to sporadic BC patients although resistance to either endocrine or chemotherapy does not appear to play a role herein. To unravel the biological mechanism by which CHEK2 c.1100delC exerts its tumorigenic potential, whole genome sequencing was performed of matching normal and primary BC (pBC) DNA from twenty female CHEK2 c.1100delC mutation carriers at Hartwig Medical Foundation (HMF). We compared the somatic pBC genomes of these twenty patients to 560 pBC genomes from the International Cancer Genome Consortium including 30 BRCA1 and 25 BRCA2 mutation carriers and 329 sporadic ER+ pBC patients. The validation cohort consisted of 517 metastatic BC (mBC) genomes from the Center for Personalized Cancer Treatment that were sequenced at HMF and included 24 mBC genomes from CHEK2 c.1100delC mutation carriers. We found that CHEK2 pBC and mBC genomes were dissimilar to pBC and mBC genomes of BRCA1 and BRCA2 mutation carriers and did not show evidence of a homologous recombination deficiency (HRD) phenotype. Instead, CHEK2 pBC and mBC genomes were very similar to genomes of sporadic ER+ pBC and mBC patients in terms of tumor mutational burden, single and double base substitution signatures as well as small insertion/deletion signatures. The size distribution of structural variants (SVs), however, was different for CHEK2 pBCs and mBCs compared with ER+ as well as BRCA1 and BRCA2 pBCs and mBCs. Importantly, the CHEK2 c.1100delC mutation was associated with an increased frequency of larger (> 1Mb) deletions, inversions and tandem duplications (TDs) with peaks at specific sizes. Although CHEK2 mBC genomes more frequently harbored chromothripsis compared with other mBC subtypes, this did not explain the CHEK2-specific SV size distribution pattern. Moreover, increased chromothripsis in CHEK2 mBC genomes was not associated with a higher frequency of somatic TP53 mutations. In fact, we did not observe any somatic TP53 mutations among CHEK2 pBC and mBC genomes. This mutual exclusiveness suggests CHEK2-driven tumorigenesis could act through the TP53 signaling pathway. To conclude, CHEK2 BC genomes do not harbor somatic TP53 mutations and display a unique SV size distribution profile. Moreover, the absence of an HRD phenotype among CHEK2 BC genomes suggests PARP inhibitors will not be effective for treatment of BC in CHEK2 c.1100delC mutation carriers. Increasing knowledge of the mechanisms of CHEK2-driven tumorigenesis may ultimately lead to the development of tailored strategies for treatment and prevention of BC for CHEK2 mutation carriers.
Citation Format: Marcel Smid, Marjanka K. Schmidt, Wendy J. Prager - van der Smissen, Kirsten Ruigrok - Ritstier, Sten Cornelissen, Maartje A. Schreurs, J. Margriet Collee, Muriel A. Adank, Maartje J. Hooning, John W. Martens, Antoinette Hollestelle. The genomic landscape of breast cancers from CHEK2 c.1100delC mutation carriers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3627.
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Affiliation(s)
- Marcel Smid
- 1Erasmus MC Cancer Institute, Rotterdam, Netherlands
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9
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Bos MK, Smid M, Sleijfer S, Martens JWM. Apolipoprotein B mRNA-Editing Catalytic Polypeptide-Like-Induced Protein Changes in Estrogen Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer Throughout Disease Progression. JCO Precis Oncol 2022; 6:e2100190. [PMID: 35050709 PMCID: PMC8789213 DOI: 10.1200/po.21.00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Apolipoprotein B mRNA-Editing Catalytic Polypeptide-like (APOBEC) enzymes are mutagenic factors contributing to tumor progression and therapy resistance. However, the effects of APOBEC-induced protein changes have not been systematically assessed. Here, we describe the effects of APOBEC on the coding sequence in primary and metastatic estrogen receptor–positive (ER+)/human epidermal growth factor receptor 2–negative (HER2–) breast cancer (BC). METHODS We determined the enrichment of amino acid (AA) changes resulting from APOBEC mutagenesis in 323 primary BC tumors and 424 metastatic breast cancer (mBC) lesions via comparison with a simulated mutational genomic landscape not under selection pressure. We subsequently explored genes with recurrent APOBEC-associated AA changes and investigated the clonality of individual APOBEC-associated mutations. Using public sequencing data from an independent primary BC and mBC cohort, we further confirm our findings by reporting genes having these enriched AA changes in an APOBEC context. RESULTS Our analysis demonstrated that several APOBEC-derived AA changes are significantly enriched compared with a simulated AA change distribution drawn at random. Among the enriched AA changes, Glutamate(E)>Lysine(K) and Glutamate(E)>Glutamine(Q) were mostly found at hotspots in oncogenes, whereas termination codons (Glutamine[Q]>STOP[X] and Serine[S]>STOP[X]) occurred in tumor suppressor genes and, mostly, not at hotspot locations. These mutations are found in genes contributing to BC initiation, eg, introduction of termination codons in TP53, MAP3K1, and CDH1 (in lobular BC) and two oncogenic hotspots in PIK3CA (p.E542K and p.E545K). In endocrine-resistant BC, we observed APOBEC-induced termination codons at ER-modulating genes, KMT2C, ARID1A, NF1, and ZFHX3. Finally, in mBC, compared with single PIK3CA mutations, dual PIK3CA mutations occurred more frequently in an APOBEC context (Fisher's exact P < .001). CONCLUSION Our results show that APOBEC mutagenesis recurrently targets various known drivers of BC initiation, progression, and endocrine resistance. APOBEC drives early, metastatic and endocrine resistant disease in ER+/HER2- breast cancer![]()
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Affiliation(s)
- Manouk K Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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10
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Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW. Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data. Gigascience 2021; 10:6458609. [PMID: 34891161 PMCID: PMC8673554 DOI: 10.1093/gigascience/giab080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/05/2021] [Revised: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non-poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA-minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG-positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION By using the full potential of non-poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
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Affiliation(s)
- Youri Hoogstrate
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Malgorzata A Komor
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - René Böttcher
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
| | - Job van Riet
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Cancer Computational Biology Center, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | - Evert van den Broek
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands.,Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen 9713GZ, The Netherlands
| | - Anne S Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Daoud Sie
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | | | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | | | | | - Andrew P Stubbs
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
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11
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Hammerl D, Martens JWM, Timmermans M, Smid M, Trapman-Jansen AM, Foekens R, Isaeva OI, Voorwerk L, Balcioglu HE, Wijers R, Nederlof I, Salgado R, Horlings H, Kok M, Debets R. Spatial immunophenotypes predict response to anti-PD1 treatment and capture distinct paths of T cell evasion in triple negative breast cancer. Nat Commun 2021; 12:5668. [PMID: 34580291 PMCID: PMC8476574 DOI: 10.1038/s41467-021-25962-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [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: 06/02/2020] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Only a subgroup of triple-negative breast cancer (TNBC) responds to immune checkpoint inhibitors (ICI). To better understand lack of response to ICI, we analyze 681 TNBCs for spatial immune cell contextures in relation to clinical outcomes and pathways of T cell evasion. Excluded, ignored and inflamed phenotypes can be captured by a gene classifier that predicts prognosis of various cancers as well as anti-PD1 response of metastatic TNBC patients in a phase II trial. The excluded phenotype, which is associated with resistance to anti-PD1, demonstrates deposits of collagen-10, enhanced glycolysis, and activation of TGFβ/VEGF pathways; the ignored phenotype, also associated with resistance to anti-PD1, shows either high density of CD163+ myeloid cells or activation of WNT/PPARγ pathways; whereas the inflamed phenotype, which is associated with response to anti-PD1, revealed necrosis, high density of CLEC9A+ dendritic cells, high TCR clonality independent of neo-antigens, and enhanced expression of T cell co-inhibitory receptors.
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Affiliation(s)
- Dora Hammerl
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Renée Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Olga I Isaeva
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leonie Voorwerk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Rebecca Wijers
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Iris Nederlof
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Center, Melbourne, Australia
| | - Hugo Horlings
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marleen Kok
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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van den Berg I, Smid M, Coebergh van den Braak RRJ, van de Wiel MA, van Deurzen CHM, de Weerd V, Martens JWM, IJzermans JNM, Wilting SM. A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer. Mol Oncol 2021; 15:3348-3362. [PMID: 34510716 PMCID: PMC8637568 DOI: 10.1002/1878-0261.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/09/2021] [Revised: 08/04/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). We aim to identify methylation markers to distinguish between CMS2 and CMS3 in patients with CRC, for which an easy test is currently lacking. To this aim, fresh‐frozen tumor tissue of 239 patients with stage I‐III CRC was analyzed. Methylation profiles were obtained using the Infinium HumanMethylation450 BeadChip. We performed adaptive group‐regularized logistic ridge regression with post hoc group‐weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3. The Cancer Genome Atlas (TCGA) data were used for validation. Group regularization of the probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier, resulting in two different prediction models and subsequently different marker panels. For both panels, even when using only five markers, accuracies were > 90% in our cohort and in the TCGA validation set. Our methylation marker panel accurately distinguishes between CMS2 and CMS3. This enables development of a targeted assay to provide a robust and clinically relevant classification tool for CRC patients.
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Affiliation(s)
- Inge van den Berg
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | | | - Mark A van de Wiel
- Department of Epidemiology & Data Science, Amsterdam University Medical Center, Amsterdam Public Health research institute, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
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13
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Klaver Y, Rijnders M, Oostvogels A, Wijers R, Smid M, Grünhagen D, Verhoef C, Sleijfer S, Lamers C, Debets R. Differential quantities of immune checkpoint-expressing CD8 T cells in soft tissue sarcoma subtypes. J Immunother Cancer 2021; 8:jitc-2019-000271. [PMID: 32792357 PMCID: PMC7430493 DOI: 10.1136/jitc-2019-000271] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
Introduction Local T-cell immunity is recognized for its contribution to the evolution and therapy response of various carcinomas. Here, we investigated characteristics of tumor-infiltrating lymphocytes (TILs), as well as T-cell evasive mechanisms in different soft tissue sarcoma (STS) subtypes. Methods Liposarcoma, gastrointestinal stromal tumor (GIST), leiomyosarcoma, myxofibrosarcoma and pleomorphic sarcomas were assessed for T-cell numbers and phenotypes using flow cytometry. Next-generation sequencing was used to analyze T-cell receptor repertoire, mutational load, immune cell frequencies, and expression of immune-related genes. Results GIST, myxofibrosarcoma and pleomorphic sarcoma showed high numbers of CD8+ TILs, with GIST having the lowest fraction of effector memory T cells. These TILs coexpress the immune checkpoints PD1, TIM3, and LAG3 in myxofibrosarcoma and pleomorphic sarcoma, yet TILs coexpressing these checkpoints were near negligible in GIST. Fractions of dominant T-cell clones among STS subtypes were lowest in GIST and liposarcoma, whereas mutational load was relatively low in all STS subtypes. Furthermore, myeloid-derived cells and expression of the costimulatory ligands CD86, ICOS-L and 41BB-L were lowest in GIST when compared with other STS subtypes. Conclusion STS subtypes differ with respect to number and phenotypical signs of antitumor responsiveness of CD8+ TILs. Notably, GIST, myxofibrosarcoma and pleomorphic sarcoma harbor high numbers of CD8+ T cells, yet in the GIST microenvironment, these T cells are less differentiated and non-exhausted, which is accompanied with a relatively low expression of costimulatory ligands.
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Affiliation(s)
- Yarne Klaver
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Maud Rijnders
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Astrid Oostvogels
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Rebecca Wijers
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Marcel Smid
- Medical Oncology, Erasmus MC, Rotterdam, Zuid-Holland, The Netherlands
| | - Dirk Grünhagen
- General Surgery, Erasmus MC, Rotterdam, Zuid-Holland, The Netherlands
| | - Cornelis Verhoef
- General Surgery, Erasmus MC, Rotterdam, Zuid-Holland, The Netherlands
| | - Stefan Sleijfer
- Medical Oncology, Erasmus MC, Rotterdam, Zuid-Holland, The Netherlands
| | - Cor Lamers
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Reno Debets
- Medical Oncology, Laboratory of Tumor Immunology, Erasmus MC, Rotterdam, The Netherlands
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14
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Agahozo MC, Smid M, van Marion R, Hammerl D, van den Bosch TPP, Timmermans MAM, Heijerman CJ, Westenend PJ, Debets R, Martens JWM, van Deurzen CHM. Transcriptomic Properties of HER2+ Ductal Carcinoma In Situ of the Breast Associate with Absence of Immune Cells. Biology (Basel) 2021; 10:768. [PMID: 34440000 PMCID: PMC8389698 DOI: 10.3390/biology10080768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
The identification of transcriptomic alterations of HER2+ ductal carcinoma in situ (DCIS) that are associated with the density of tumor-infiltrating lymphocytes (TILs) could contribute to optimizing choices regarding the potential benefit of immune therapy. We compared the gene expression profile of TIL-poor HER2+ DCIS to that of TIL-rich HER2+ DCIS. Tumor cells from 11 TIL-rich and 12 TIL-poor DCIS cases were micro-dissected for RNA isolation. The Ion AmpliSeq Transcriptome Human Gene Expression Kit was used for RNA sequencing. After normalization, a Mann-Whitney rank sum test was used to analyze differentially expressed genes between TIL-poor and TIL-rich HER2+ DCIS. Whole tissue sections were immunostained for validation of protein expression. We identified a 29-gene expression profile that differentiated TIL-rich from TIL-poor HER2+ DCIS. These genes included CCND3, DUSP10 and RAP1GAP, which were previously described in breast cancer and cancer immunity and were more highly expressed in TIL-rich DCIS. Using immunohistochemistry, we found lower protein expression in TIL-rich DCIS. This suggests regulation of protein expression at the posttranslational level. We identified a gene expression profile of HER2+ DCIS cells that was associated with the density of TILs. This classifier may guide towards more rationalized choices regarding immune-mediated therapy in HER2+ DCIS, such as targeted vaccine therapy.
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Affiliation(s)
- Marie Colombe Agahozo
- Department of Pathology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.C.A.); (R.v.M.); (T.P.P.v.d.B.)
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.C.A.); (R.v.M.); (T.P.P.v.d.B.)
| | - Dora Hammerl
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | - Thierry P. P. van den Bosch
- Department of Pathology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.C.A.); (R.v.M.); (T.P.P.v.d.B.)
| | - Mieke A. M. Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | - Chayenne J. Heijerman
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | | | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.S.); (D.H.); (M.A.M.T.); (C.J.H.); (R.D.); (J.W.M.M.)
| | - Carolien H. M. van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands; (M.C.A.); (R.v.M.); (T.P.P.v.d.B.)
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Mendelaar PAJ, Smid M, van Riet J, Angus L, Labots M, Steeghs N, Hendriks MP, Cirkel GA, van Rooijen JM, Ten Tije AJ, Lolkema MP, Cuppen E, Sleijfer S, Martens JWM, Wilting SM. Author Correction: Whole genome sequencing of metastatic colorectal cancer reveals prior treatment effects and specific metastasis features. Nat Commun 2021; 12:3269. [PMID: 34039979 PMCID: PMC8155047 DOI: 10.1038/s41467-021-23629-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Pauline A J Mendelaar
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.,Department of Medical Oncology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Mathijs P Hendriks
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.,Department of Medical Oncology, Northwest Clinics, Alkmaar, The Netherlands
| | - Geert A Cirkel
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.,Department of Medical Oncology, Meander Medical Center, Amersfoort, The Netherlands
| | - Johan M van Rooijen
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.,Department of Medical Oncology, Martini Hospital, Groningen, The Netherlands
| | - Albert J Ten Tije
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.,Department of Medical Oncology, Amphia Hospital, Breda, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.,Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.
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16
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van Den Berg I, Smid M, Coebergh van den Braak RR, van de Wiel MA, Van Deurzen CHM, de Weerd V, Martens JW, IJzermans JN, Wilting SM. A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.3545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3545 Background: Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). Currently available assays can identify CMS1 and CMS4 cases well, while a dedicated test to distinguish CMS2 and 3 is lacking. This study aimed to identify a panel of methylation markers to distinguish between CMS2 and 3 in patients with CRC. Methods: Fresh-frozen tumor tissue of 239 patients with stage I-III CRC was included. CMS classification was performed on RNA-seq data using the single-sample-prediction parameter from the “CMSclassifier” package. Methylation profiles were obtained using the Infinium HumanMethylation450 BeadChip. We performed adaptive group-regularised logistic ridge-regression with post-hoc group-weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3 based on 15, 10 or 5 markers. Data from TCGAwas used for validation. Results: Overall methylation profiles differed between CMS2 and CMS3. Group-regularisation of the probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier resulting in two different prediction models and subsequently different marker panels. For both panels, even when using only 5 markers, sensitivity, specificity, and accuracy were > 90%. Validation showed comparable performances. Conclusions: Our highly sensitive and specific methylation marker panel can be used to distinguish CMS2 and 3. This enables development of a qPCR DNA methylation assay in patients with CRC to provide a specific and non-invasive classification tool.
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Affiliation(s)
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics and Department of Mathematics, VU University Medical Center, Amsterdam, Netherlands
| | | | - Vanja de Weerd
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
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17
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van den Berg I, Smid M, Coebergh van den Braak RRJ, van Deurzen CHM, de Weerd V, Foekens JA, IJzermans JNM, Martens JWM, Wilting SM. Circular RNA in Chemonaive Lymph Node Negative Colon Cancer Patients. Cancers (Basel) 2021; 13:1903. [PMID: 33920880 PMCID: PMC8071322 DOI: 10.3390/cancers13081903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) appear important in tumor progression of colon cancer (CC). We identified an extensive catalog of circRNAs in 181 chemonaive stage I/II colon tumors, who underwent curative surgery between 2007 and 2014. We identified circRNAs from RNAseq data, investigated common biology related to circRNA expression, and studied the association between circRNAs and relapse status, tumor stage, consensus molecular subtypes (CMS), tumor localization and microsatellite instability (MSI). We identified 2606 unique circRNAs. 277 circRNAs (derived from 260 genes) were repeatedly occurring in at least 20 patients of which 153 showed a poor or even negative (R < 0.3) correlation with the expression level of their linear gene. The circular junctions for circSATB2, circFGD6, circKMT2C and circPLEKHM3 were validated by Sanger sequencing. Multiple correspondence analysis showed that circRNAs were often co-expressed and that high diversity in circRNAs was associated with favorable disease-free survival (DFS), which was confirmed by Cox regression analysis (Hazard Ratio (HR) 0.60, 95% CI 0.38-0.97, p = 0.036). Considering individual circRNAs, absence of circMGA was significantly associated with relapse, whereas circSATB2, circNAB1, and circCEP192 were associated with both MSI and CMS. This study represents a showcase of the potential clinical utility of circRNAs for prognostic stratification in patients with stage I-II colon cancer and demonstrated that high diversity in circRNAs is associated with favorable DFS.
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Affiliation(s)
- Inge van den Berg
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (I.v.d.B.); (R.R.J.C.v.d.B.); (J.N.M.I.)
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (M.S.); (V.d.W.); (J.A.F.); (J.W.M.M.)
| | - Robert R. J. Coebergh van den Braak
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (I.v.d.B.); (R.R.J.C.v.d.B.); (J.N.M.I.)
| | - Carolien H. M. van Deurzen
- Department of Pathology, Erasmus MC-University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (M.S.); (V.d.W.); (J.A.F.); (J.W.M.M.)
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (M.S.); (V.d.W.); (J.A.F.); (J.W.M.M.)
| | - Jan N. M. IJzermans
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (I.v.d.B.); (R.R.J.C.v.d.B.); (J.N.M.I.)
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (M.S.); (V.d.W.); (J.A.F.); (J.W.M.M.)
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (M.S.); (V.d.W.); (J.A.F.); (J.W.M.M.)
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18
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Desa DE, Strawderman RL, Wu W, Hill RL, Smid M, Martens JWM, Turner BM, Brown EB. Intratumoral heterogeneity of second-harmonic generation scattering from tumor collagen and its effects on metastatic risk prediction. BMC Cancer 2020; 20:1217. [PMID: 33302909 PMCID: PMC7731482 DOI: 10.1186/s12885-020-07713-4] [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: 08/27/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Background Metastases are the leading cause of breast cancer-related deaths. The tumor microenvironment impacts cancer progression and metastatic ability. Fibrillar collagen, a major extracellular matrix component, can be studied using the light scattering phenomenon known as second-harmonic generation (SHG). The ratio of forward- to backward-scattered SHG photons (F/B) is sensitive to collagen fiber internal structure and has been shown to be an independent prognostic indicator of metastasis-free survival time (MFS). Here we assess the effects of heterogeneity in the tumor matrix on the possible use of F/B as a prognostic tool. Methods SHG imaging was performed on sectioned primary tumor excisions from 95 untreated, estrogen receptor-positive, lymph node negative invasive ductal carcinoma patients. We identified two distinct regions whose collagen displayed different average F/B values, indicative of spatial heterogeneity: the cellular tumor bulk and surrounding tumor-stroma interface. To evaluate the impact of heterogeneity on F/B’s prognostic ability, we performed SHG imaging in the tumor bulk and tumor-stroma interface, calculated a 21-gene recurrence score (surrogate for OncotypeDX®, or S-ODX) for each patient and evaluated their combined prognostic ability. Results We found that F/B measured in tumor-stroma interface, but not tumor bulk, is prognostic of MFS using three methods to select pixels for analysis: an intensity threshold selected by a blinded observer, a histogram-based thresholding method, and an adaptive thresholding method. Using both regression trees and Random Survival Forests for MFS outcome, we obtained data-driven prediction rules that show F/B from tumor-stroma interface, but not tumor bulk, and S-ODX both contribute to predicting MFS in this patient cohort. We also separated patients into low-intermediate (S-ODX < 26) and high risk (S-ODX ≥26) groups. In the low-intermediate risk group, comprised of patients not typically recommended for adjuvant chemotherapy, we find that F/B from the tumor-stroma interface is prognostic of MFS and can identify a patient cohort with poor outcomes. Conclusions These data demonstrate that intratumoral heterogeneity in F/B values can play an important role in its possible use as a prognostic marker, and that F/B from tumor-stroma interface of primary tumor excisions may provide useful information to stratify patients by metastatic risk. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07713-4.
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Affiliation(s)
- Danielle E Desa
- Department of Biomedical Engineering, Hajim School of Engineering and Applied Sciences, University of Rochester, Rochester, New York, USA
| | - Robert L Strawderman
- Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, New York, USA
| | - Wencheng Wu
- Goergen Institute for Data Science, University of Rochester, Rochester, New York, USA
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - J W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bradley M Turner
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward B Brown
- Department of Biomedical Engineering, Hajim School of Engineering and Applied Sciences, University of Rochester, Rochester, New York, USA.
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19
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20
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Coebergh van den Braak RRJ, Ten Hoorn S, Sieuwerts AM, Tuynman JB, Smid M, Wilting SM, Martens JWM, Punt CJA, Foekens JA, Medema JP, IJzermans JNM, Vermeulen L. Interconnectivity between molecular subtypes and tumor stage in colorectal cancer. BMC Cancer 2020; 20:850. [PMID: 32887573 PMCID: PMC7473811 DOI: 10.1186/s12885-020-07316-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND There are profound individual differences in clinical outcomes between colorectal cancers (CRCs) presenting with identical stage of disease. Molecular stratification, in conjunction with the traditional TNM staging, is a promising way to predict patient outcomes. We investigated the interconnectivity between tumor stage and tumor biology reflected by the Consensus Molecular Subtypes (CMSs) in CRC, and explored the possible value of these insights in patients with stage II colon cancer. METHODS We performed a retrospective analysis using clinical records and gene expression profiling in a meta-cohort of 1040 CRC patients. The interconnectivity of tumor biology and disease stage was assessed by investigating the association between CMSs and TNM classification. In order to validate the clinical applicability of our findings we employed a meta-cohort of 197 stage II colon cancers. RESULTS CMS4 was significantly more prevalent in advanced stages of disease (stage I 9.8% versus stage IV 38.5%, p < 0.001). The observed differential gene expression between cancer stages is at least partly explained by the biological differences as reflected by CMS subtypes. Gene signatures for stage III-IV and CMS4 were highly correlated (r = 0.77, p < 0.001). CMS4 cancers showed an increased progression rate to more advanced stages (CMS4 compared to CMS2: 1.25, 95% CI: 1.08-1.46). Patients with a CMS4 cancer had worse survival in the high-risk stage II tumors compared to the total stage II cohort (5-year DFS 41.7% versus 100.0%, p = 0.008). CONCLUSIONS Considerable interconnectivity between tumor biology and tumor stage in CRC exists. This implies that the TNM stage, in addition to the stage of progression, might also reflect distinct biological disease entities. These insights can potentially be utilized to optimize identification of high-risk stage II colon cancers.
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Affiliation(s)
- R R J Coebergh van den Braak
- Department of Surgery, Erasmus MC University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - S Ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - A M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Cancer Genomics Center Netherlands, Amsterdam, The Netherlands
| | - J B Tuynman
- Department of Surgery, Amsterdam UMC, Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - M Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - S M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.,Cancer Genomics Center Netherlands, Amsterdam, The Netherlands
| | - C J A Punt
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Universiteitsweg 100, 3584 CX, Utrecht, The Netherlands
| | - J A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J P Medema
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - J N M IJzermans
- Department of Surgery, Erasmus MC University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - L Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Amsterdam UMC, University of Amsterdam and Cancer Center Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. .,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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21
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Mendelaar P, Smid M, Van Riet J, Angus L, Van de Werken H, Labots M, Steeghs N, Hendriks M, Cirkel G, van Rooijen J, Tije AT, Lolkema M, Cuppen E, Sleijfer S, Martens J, Wilting S. 472P Whole genome sequencing of metastatic CRC reveals footprints from the past and present with future clinical relevance. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.583] [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: 10/23/2022] Open
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22
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White MG, Baumann E, Vayshenker I, Ruiz ZE, Stephens MS, Smid M, Lehman JH. Nature of fiber-coupled detector responsivity measurements at 0.1% using a primary standard. Opt Express 2020; 28:15331-15346. [PMID: 32403563 DOI: 10.1364/oe.393064] [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] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
We demonstrate the capability to measure the absolute power responsivity of optical fiber-coupled detectors at an expanded uncertainty of 0.1%, by direct comparison with a cryogenic primary standard. To facilitate synchronous power measurements, commercial all-fiber beam-splitters direct laser diode light simultaneously to the device under test and the primary standard. We investigate the use of single-mode, polarisation maintaining, and photonic crystal fibers to access the cryogenic standard, and report a reduction in the temperature dependent effective refractive index of these fibers of 0.1%, 0.15% and 0.3% respectively in going from room temperature to 5 K. We also evaluate the polarisation dependent loss of the beam-splitters, the stability of the beam-splitter ratio between the cryogenic detector and the device under test and the temporal and modal stability of the Fabry-Pérot laser diode sources. It is shown that the stability of the optical fiber beam-splitters limits the overall performance of the measurement system to an expanded uncertainty of 0.1%.
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23
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Rypens C, Bertucci F, Viens P, Martens JWM, Smid M, Schröder C, Ueno NT, Cristofanilli M, Dirix P, Vermeulen P, Dirix L, Van Laere S. Abstract P3-03-03: Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p3-03-03] [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
Inflammatory breast cancer (IBC) is an aggressive and poorly characterized breast cancer subtype with few targets available for molecular therapy. Several attempts aimed at characterizing the disease at the genomic, transcriptomic and proteomic level. Together, these studies suggest that MYC is central to the biology of IBC. Here, we analyzed data sets from patient samples and preclinical models to corroborate this hypothesis.
Genomic and transcriptomic profiles were obtained using next-generation sequencing and Affymetrix GeneChip analysis on a series of 101 and 137 samples from patients with IBC. In addition, non-IBC (nIBC) control samples were included from our own repositories (N=252) as well as from publicly available data sets (i.e. TCGA and METABRIC). Finally, RNA-sequencing and peptide phosphorylation data from preclinical IBC and nIBC models, both with and without TGFβ treatment, were explored.
Apart from TP53 and ERBB2, MYC is the 3rd most frequently mutated gene with single nucleotide variants, indels and amplifications found in 22% of 101 patients. Furthermore, MYC mutations are mutually exclusive with alterations in the NOTCH genes (i.e. NOTCH1, -2, -3, and -4 and CREBBP). At the gene expression level, a MYC activation score is elevated in IBC as compare to nIBC and correlates with a NOTCH activation signature. Genes overexpressed in IBC are enriched for various sets of MYC target genes and are associated with MYC amplifications in TCGA and METABRIC samples. In preclinical models, MYC target genes are particularly responsive to TGFβ treatment in IBC cells but not in nIBC cells and analysis of peptide phosphorylation patterns suggest this interaction may be regulated via PTK2B.
The present data suggest that MYC could be an important driver of IBC biology, which corroborates with the recent observation that MYC is an important hub in the signal transduction network of SUM149 and -190 cells. Furthermore, our data reveal that MYC activation is linked to NOCTH and TGFβ signaling. In earlier studies it was demonstrated that lymphovascular tumor emboli in the Mary-X mouse model of IBC exhibit NOTCH3 addition with downstream MYC overexpression, indicating that NOTCH/MYC signaling could be crucial for metastatic progression in IBC. In this context, it should be noted that an allele associated with metastatic risk in IBC patients resides at the 8q24 locus that harbors the MYC gene.
Citation Format: Charlotte Rypens, François Bertucci, Patrice Viens, John WM Martens, Marcel Smid, Carolien Schröder, Naoto T Ueno, Massimo Cristofanilli, Piet Dirix, Peter Vermeulen, Luc Dirix, Steven Van Laere. Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-03-03.
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Affiliation(s)
- Charlotte Rypens
- 1University of Antwerp & GZA Hospitals Sint-Augustinus, Wilrijk, Belgium
| | | | | | | | - Marcel Smid
- 3Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | | | - Naoto T Ueno
- 5The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Piet Dirix
- 1University of Antwerp & GZA Hospitals Sint-Augustinus, Wilrijk, Belgium
| | | | - Luc Dirix
- 7GZA Hospitals Sint-Augustinus, Wilrijk, Belgium
| | - Steven Van Laere
- 1University of Antwerp & GZA Hospitals Sint-Augustinus, Wilrijk, Belgium
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Nederlof I, De Bortoli D, Bareche Y, Nguyen B, de Maaker M, Hooijer GKJ, Buisseret L, Kok M, Smid M, Van den Eynden GGGM, Brinkman AB, Hudecek J, Koster J, Sotiriou C, Larsimont D, Martens JWM, van de Vijver MJ, Horlings HM, Salgado R, Biganzoli E, Desmedt C. Comprehensive evaluation of methods to assess overall and cell-specific immune infiltrates in breast cancer. Breast Cancer Res 2019; 21:151. [PMID: 31878981 PMCID: PMC6933637 DOI: 10.1186/s13058-019-1239-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/16/2019] [Indexed: 12/23/2022] Open
Abstract
Background Breast cancer (BC) immune infiltrates play a critical role in tumor progression and response to treatment. Besides stromal tumor infiltrating lymphocytes (sTILs) which have recently reached level 1B evidence as a prognostic marker in triple negative BC, a plethora of methods to assess immune infiltration exists, and it is unclear how these compare to each other and if they can be used interchangeably. Methods Two experienced pathologists scored sTIL, intra-tumoral TIL (itTIL), and 6 immune cell types (CD3+, CD4+, CD8+, CD20+, CD68+, FOXP3+) in the International Cancer Genomics Consortium breast cancer cohort using hematoxylin and eosin-stained (n = 243) and immunohistochemistry-stained tissue microarrays (n = 254) and whole slides (n = 82). The same traits were evaluated using transcriptomic- and methylomic-based deconvolution methods or signatures. Results The concordance correlation coefficient (CCC) between pathologists for sTIL was very good (0.84) and for cell-specific immune infiltrates slightly lower (0.63–0.66). Comparison between tissue microarray and whole slide pathology scores revealed systematically higher values in whole slides (ratio 2.60–5.98). The Spearman correlations between microscopic sTIL and transcriptomic- or methylomic-based assessment of immune infiltrates were highly variable (r = 0.01–0.56). Similar observations were made for cell type-specific quantifications (r = 0.001–0.54). We observed a strong inter-method variability between the omics-derived estimations, which is further cell type dependent. Finally, we demonstrated that most methods more accurately identify highly infiltrated (sTIL ≥ 60%; area under the curve, AUC, 0.64–0.99) as compared to lowly infiltrated tumors (sTIL ≤ 10%; AUC 0.52–0.82). Conclusions There is a lower inter-pathologist concordance for cell-specific quantification as compared to overall infiltration quantification. Microscopic assessments are underestimated when considering small cores (tissue microarray) instead of whole slides. Results further highlight considerable differences between the microscopic-, transcriptomic-, and methylomic-based methods in the assessment of overall and cell-specific immune infiltration in BC. We therefore call for extreme caution when assessing immune infiltrates using current methods and emphasize the need for standardized immune characterization beyond TIL.
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Affiliation(s)
- Iris Nederlof
- Department of Pathology, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Davide De Bortoli
- Unit of Medical Statistics, Biometry and Bioinformatics "Giulio A. Maccacaro," Department of Clinical Sciences and Community Health and DSRC, University of Milan, Campus Cascina Rosa, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Yacine Bareche
- J.C. Heuson Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000, Brussels, Belgium
| | - Bastien Nguyen
- J.C. Heuson Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000, Brussels, Belgium
| | - Michiel de Maaker
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Gerrit K J Hooijer
- Department of Pathology, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Laurence Buisseret
- J.C. Heuson Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000, Brussels, Belgium
| | - Marleen Kok
- Departments of Medical Oncology and Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Centre Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | | | - Arie B Brinkman
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Faculty of Science, Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Jan Hudecek
- Department of Research IT, The Netherlands Cancer Institute - Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Christos Sotiriou
- J.C. Heuson Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000, Brussels, Belgium
| | - Denis Larsimont
- Pathology Department, Institut Jules Bordet, 1000, Brussels, Belgium
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Centre Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Amsterdam University Medical Centre, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Hugo M Horlings
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Wilrijk, Belgium.,Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Bioinformatics "Giulio A. Maccacaro," Department of Clinical Sciences and Community Health and DSRC, University of Milan, Campus Cascina Rosa, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Christine Desmedt
- Department of Oncology, Laboratory for Translational Breast Cancer Research, KU Leuven, Leuven, Belgium.
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Smid M, Wilting SM. A tale on rabbit ears and pan-handles, the rings that rule all. EBioMedicine 2019; 49:17-18. [PMID: 31676388 PMCID: PMC6945197 DOI: 10.1016/j.ebiom.2019.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands.
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Hammerl D, Massink MPG, Smid M, van Deurzen CHM, Meijers-Heijboer HEJ, Waisfisz Q, Debets R, Martens JWM. Clonality, Antigen Recognition, and Suppression of CD8 + T Cells Differentially Affect Prognosis of Breast Cancer Subtypes. Clin Cancer Res 2019; 26:505-517. [PMID: 31649042 DOI: 10.1158/1078-0432.ccr-19-0285] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/24/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE In breast cancer, response rates to immune therapies are generally low and differ significantly across molecular subtypes, urging a better understanding of immunogenicity and immune evasion. EXPERIMENTAL DESIGN We interrogated large gene-expression data sets including 867 node-negative, treatment-naïve breast cancer patients (microarray data) and 347 breast cancer patients (whole-genome sequencing and transcriptome data) according to parameters of T cells as well as immune microenvironment in relation to patient survival. RESULTS We developed a 109-immune gene signature that captures abundance of CD8 tumor-infiltrating lymphocytes (TIL) and is prognostic in basal-like, her2, and luminal B breast cancer, but not in luminal A or normal-like breast cancer. Basal-like and her2 are characterized by highest CD8 TIL abundance, highest T-cell clonality, highest frequencies of memory T cells, and highest antigenicity, yet only the former shows highest expression level of immune and metabolic checkpoints and highest frequency of myeloid suppressor cells. Also, luminal B shows a high antigenicity and T-cell clonality, yet a low abundance of CD8 TILs. In contrast, luminal A and normal-like both show a low antigenicity, and notably, a low and high abundance of CD8 TILs, respectively, which associates with T-cell influx parameters, such as expression of adhesion molecules. CONCLUSIONS Collectively, our data argue that not only CD8 T-cell presence itself, but rather T-cell clonality, T-cell subset distribution, coinhibition, and antigen presentation reflect occurrence of a CD8 T-cell response in breast cancer subtypes, which have been aborted by distinct T-cell-suppressive mechanisms, providing a rationale for subtype-specific combination immune therapies.
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Affiliation(s)
- Dora Hammerl
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Maarten P G Massink
- Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | | | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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Angus L, Smid M, Wilting SM, van Riet J, Van Hoeck A, Nguyen L, Nik-Zainal S, Steenbruggen TG, Tjan-Heijnen VCG, Labots M, van Riel JMGH, Bloemendal HJ, Steeghs N, Lolkema MP, Voest EE, van de Werken HJG, Jager A, Cuppen E, Sleijfer S, Martens JWM. The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies. Nat Genet 2019; 51:1450-1458. [PMID: 31570896 PMCID: PMC6858873 DOI: 10.1038/s41588-019-0507-7] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [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: 01/17/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023]
Abstract
The whole-genome sequencing of prospectively collected tissue biopsies from 442 patients with metastatic breast cancer reveals that, compared to primary breast cancer, tumor mutational burden doubles, the relative contributions of mutational signatures shift and the mutation frequency of six known driver genes increases in metastatic breast cancer. Significant associations with pretreatment are also observed. The contribution of mutational signature 17 is significantly enriched in patients pretreated with fluorouracil, taxanes, platinum and/or eribulin, whereas the de novo mutational signature I identified in this study is significantly associated with pretreatment containing platinum-based chemotherapy. Clinically relevant subgroups of tumors are identified, exhibiting either homologous recombination deficiency (13%), high tumor mutational burden (11%) or specific alterations (24%) linked to sensitivity to FDA-approved drugs. This study provides insights into the biology of metastatic breast cancer and identifies clinically useful genomic features for the future improvement of patient management.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - Tessa G Steenbruggen
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Johanna M G H van Riel
- Department of Internal Medicine, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Haiko J Bloemendal
- Department of Medical Oncology, Meander Medical Center, Amersfoort, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Emile E Voest
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.
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Ren J, Smid M, Iaria J, Salvatori DCF, van Dam H, Zhu HJ, Martens JWM, Ten Dijke P. Cancer-associated fibroblast-derived Gremlin 1 promotes breast cancer progression. Breast Cancer Res 2019; 21:109. [PMID: 31533776 PMCID: PMC6751614 DOI: 10.1186/s13058-019-1194-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
Background Bone morphogenetic proteins (BMPs) have been reported to maintain epithelial integrity and to antagonize the transforming growth factor β (TGFβ)-induced epithelial to mesenchymal transition. The expression of soluble BMP antagonists is dysregulated in cancers and interrupts proper BMP signaling in breast cancer. Methods In this study, we mined the prognostic role of BMP antagonists GREMLIN 1 (GREM1) in primary breast cancer tissues using in-house and publicly available datasets. We determined which cells express GREM1 RNA using in situ hybridization (ISH) on a breast cancer tissue microarray. The effects of Grem1 on the properties of breast cancer cells were assessed by measuring the mesenchymal/stem cell marker expression and functional cell-based assays for stemness and invasion. The role of Grem1 in breast cancer-associated fibroblast (CAF) activation was measured by analyzing the expression of fibroblast markers, phalloidin staining, and collagen contraction assays. The role of Grem1 in CAF-induced breast cancer cell intravasation and extravasation was studied by utilizing xenograft zebrafish breast cancer (co-) injection models. Results Expression analysis of clinical breast cancer datasets revealed that high expression of GREM1 in breast cancer stroma is correlated with a poor prognosis regardless of the molecular subtype. The large majority of human breast cancer cell lines did not express GREM1 in vitro, but breast CAFs did express GREM1 both in vitro and in vivo. Transforming growth factor β (TGFβ) secreted by breast cancer cells, and also inflammatory cytokines, stimulated GREM1 expression in CAFs. Grem1 abrogated bone morphogenetic protein (BMP)/SMAD signaling in breast cancer cells and promoted their mesenchymal phenotype, stemness, and invasion. Moreover, Grem1 production by CAFs strongly promoted the fibrogenic activation of CAFs and promoted breast cancer cell intravasation and extravasation in co-injection xenograft zebrafish models. Conclusions Our results demonstrated that Grem1 is a pivotal factor in the reciprocal interplay between breast cancer cells and CAFs, which promotes cancer cell invasion. Targeting Grem1 could be beneficial in the treatment of breast cancer patients with high Grem1 expression. Electronic supplementary material The online version of this article (10.1186/s13058-019-1194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiang Ren
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Josephine Iaria
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Australia
| | - Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans van Dam
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Hong Jian Zhu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Australia
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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de Kruijff IE, Sieuwerts AM, Onstenk W, Kraan J, Smid M, Van MN, van der Vlugt-Daane M, Hoop EOD, Mathijssen RHJ, Lolkema MP, de Wit R, Hamberg P, Meulenbeld HJ, Beeker A, Creemers GJ, Martens JWM, Sleijfer S. Circulating Tumor Cell Enumeration and Characterization in Metastatic Castration-Resistant Prostate Cancer Patients Treated with Cabazitaxel. Cancers (Basel) 2019; 11:cancers11081212. [PMID: 31434336 PMCID: PMC6721462 DOI: 10.3390/cancers11081212] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
(1) Background: Markers identifying which patients with metastatic, castration-resistant prostate cancer (mCRPC) will benefit from cabazitaxel therapy are currently lacking. Therefore, the aim of this study was to identify markers associated with outcome to cabazitaxel therapy based on counts and gene expression profiles of circulating tumor cells (CTCs). (2) Methods: From 120 mCRPC patients, CellSearch enriched CTCs were obtained at baseline and after 6 weeks of cabazitaxel therapy. Furthermore, 91 genes associated with prostate cancer were measured in mRNA of these CTCs. (3) Results: In 114 mCRPC patients with an evaluable CTC count, the CTC count was independently associated with poor progression-free survival (PFS) and overall survival (OS) in multivariable analysis with other commonly used variables associated with outcome in mCRPC (age, prostate specific antigen (PSA), alkaline phosphatase, lactate dehydrogenase (LDH), albumin, hemoglobin), together with alkaline phosphatase and hemoglobin. A five-gene expression profile was generated to predict for outcome to cabazitaxel therapy. However, even though this signature was associated with OS in univariate analysis, this was not the case in the multivariate analysis for OS nor for PFS. (4) Conclusion: The established five-gene expression profile in CTCs was not independently associated with PFS nor OS. However, along with alkaline phosphatase and hemoglobin, CTC-count is independently associated with PFS and OS in mCRPC patients who are treated with cabazitaxel.
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Affiliation(s)
- Ingeborg E de Kruijff
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Wendy Onstenk
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Mai N Van
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Esther Oomen-de Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Paul Hamberg
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, 3045 PM Rotterdam, The Netherlands
| | - Hielke J Meulenbeld
- Department of Medical Oncology, Gelre Ziekenhuizen, 7334 DZ Apeldoorn, The Netherlands
| | - Aart Beeker
- Department of Medical Oncology, Spaarne Gasthuis, 2134 TM Hoofddorp, The Netherlands
| | - Geert-Jan Creemers
- Department of Medical Oncology, Catharina Ziekenhuis, 5623 EJ Eindhoven, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands.
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
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Post AE, Bussink J, Smid M, Sweep FC, Span PN. Downregulation of matrix Gla protein is a biomarker for tamoxifen-resistant and radioresistant breast cancer. Biomark Med 2019; 13:841-850. [PMID: 31317787 DOI: 10.2217/bmm-2019-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: To establish downregulated biomarkers for cross-resistance for radiotherapy (RT) in tamoxifen (TAM)-resistant breast cancer cells. Materials & methods: RNA sequencing was performed on TAM and RT-resistant breast cancer cells. Breast cancer patient cohorts were queried in silico for associations between genes of interest and outcome after TAM treatment or irradiation. Results: 20 genes showed decreased expression in both TAM-resistant and RT-resistant breast cancer cells. Only matrix Gla protein in the primary tumor was associated with outcome after TAM treatment or RT in breast cancer patients. Conclusion: Matrix Gla protein is a biomarker for therapy sensitivity in breast cancer.
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Affiliation(s)
- Annemarie Em Post
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Laboratory Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Johan Bussink
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology & Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3008 AE, Rotterdam, The Netherlands
| | - Fred Cgj Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Paul N Span
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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McLaughlin RP, He J, van der Noord VE, Redel J, Foekens JA, Martens JWM, Smid M, Zhang Y, van de Water B. A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy. Breast Cancer Res 2019; 21:77. [PMID: 31262335 PMCID: PMC6604188 DOI: 10.1186/s13058-019-1161-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 10/05/2018] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The effective treatment of triple-negative breast cancer (TNBC) remains a profound clinical challenge. Despite frequent epidermal growth factor receptor (EGFR) overexpression and reliance on downstream signalling pathways in TNBC, resistance to EGFR-tyrosine kinase inhibitors (TKIs) remains endemic. Therefore, the identification of targeted agents, which synergise with current therapeutic options, is paramount. METHODS Compound-based, high-throughput, proliferation screening was used to profile the response of TNBC cell lines to EGFR-TKIs, western blotting and siRNA transfection being used to examine the effect of inhibitors on EGFR-mediated signal transduction and cellular dependence on such pathways, respectively. A kinase inhibitor combination screen was used to identify compounds that synergised with EGFR-TKIs in TNBC, utilising sulphorhodamine B (SRB) assay as read-out for proliferation. The impact of drug combinations on cell cycle arrest, apoptosis and signal transduction was assessed using flow cytometry, automated live-cell imaging and western blotting, respectively. RNA sequencing was employed to unravel transcriptomic changes elicited by this synergistic combination and to permit identification of the signalling networks most sensitive to co-inhibition. RESULTS We demonstrate that a dual cdc7/CDK9 inhibitor, PHA-767491, synergises with multiple EGFR-TKIs (lapatinib, erlotinib and gefitinib) to overcome resistance to EGFR-targeted therapy in various TNBC cell lines. Combined inhibition of EGFR and cdc7/CDK9 resulted in reduced cell proliferation, accompanied by induction of apoptosis, G2-M cell cycle arrest, inhibition of DNA replication and abrogation of CDK9-mediated transcriptional elongation, in contrast to mono-inhibition. Moreover, high expression of cdc7 and RNA polymerase II Subunit A (POLR2A), the direct target of CDK9, is significantly correlated with poor metastasis-free survival in a cohort of breast cancer patients. RNA sequencing revealed marked downregulation of pathways governing proliferation, transcription and cell survival in TNBC cells treated with the combination of an EGFR-TKI and a dual cdc7/CDK9 inhibitor. A number of genes enriched in these downregulated pathways are associated with poor metastasis-free survival in TNBC. CONCLUSIONS Our results highlight that dual inhibition of cdc7 and CDK9 by PHA-767491 is a potential strategy for targeting TNBC resistant to EGFR-TKIs.
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Affiliation(s)
- Ronan P. McLaughlin
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jichao He
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Vera E. van der Noord
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jevin Redel
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yinghui Zhang
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Bob van de Water
- Department of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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Uhr K, Prager-van der Smissen WJC, Heine AAJ, Ozturk B, van Jaarsveld MTM, Boersma AWM, Jager A, Wiemer EAC, Smid M, Foekens JA, Martens JWM. MicroRNAs as possible indicators of drug sensitivity in breast cancer cell lines. PLoS One 2019; 14:e0216400. [PMID: 31063487 PMCID: PMC6504094 DOI: 10.1371/journal.pone.0216400] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 11/06/2018] [Accepted: 04/20/2019] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression post-transcriptionally. In this way they might influence whether a cell is sensitive or resistant to a certain drug. So far, only a limited number of relatively small scale studies comprising few cell lines and/or drugs have been performed. To obtain a broader view on miRNAs and their association with drug response, we investigated the expression levels of 411 miRNAs in relation to drug sensitivity in 36 breast cancer cell lines. For this purpose IC50 values of a drug screen involving 34 drugs were associated with miRNA expression data of the same breast cancer cell lines. Since molecular subtype of the breast cancer cell lines is considered a confounding factor in drug association studies, multivariate analysis taking subtype into account was performed on significant miRNA-drug associations which retained 13 associations. These associations consisted of 11 different miRNAs and eight different drugs (among which Paclitaxel, Docetaxel and Veliparib). The taxanes, Paclitaxel and Docetaxel, were the only drugs having miRNAs in common: hsa-miR-187-5p and hsa-miR-106a-3p indicative of drug resistance while Paclitaxel sensitivity alone associated with hsa-miR-556-5p. Tivantinib was associated with hsa-let-7d-5p and hsa-miR-18a-5p for sensitivity and hsa-miR-637 for resistance. Drug sensitivity was associated with hsa-let-7a-5p for Bortezomib, hsa-miR-135a-3p for JNJ-707 and hsa-miR-185-3p for Panobinostat. Drug resistance was associated with hsa-miR-182-5p for Veliparib and hsa-miR-629-5p for Tipifarnib. Pathway analysis for significant miRNAs was performed to reveal biological roles, aiding to find a potential mechanistic link for the observed associations with drug response. By doing so hsa-miR-187-5p was linked to the cell cycle G2-M checkpoint in line with this checkpoint being the target of taxanes. In conclusion, our study shows that miRNAs could potentially serve as biomarkers for intrinsic drug resistance and that pathway analyses can provide additional information in this context.
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Affiliation(s)
- Katharina Uhr
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wendy J. C. Prager-van der Smissen
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anouk A. J. Heine
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bahar Ozturk
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marijn T. M. van Jaarsveld
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Antonius W. M. Boersma
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik A. C. Wiemer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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Meijer TG, Verkaik NS, Sieuwerts AM, van Riet J, Naipal KAT, van Deurzen CHM, den Bakker MA, Sleddens HFBM, Dubbink HJ, den Toom TD, Dinjens WNM, Lips E, Nederlof PM, Smid M, van de Werken HJG, Kanaar R, Martens JWM, Jager A, van Gent DC. Correction: Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects. Clin Cancer Res 2019; 25:2935. [PMID: 31043383 DOI: 10.1158/1078-0432.ccr-19-0936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG, Martens JWM, Foekens JA, Stratton MR, Stunnenberg HG. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nat Commun 2019; 10:1749. [PMID: 30988298 PMCID: PMC6465362 DOI: 10.1038/s41467-019-09828-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 11/08/2018] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.
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Affiliation(s)
- Arie B Brinkman
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands.
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Femke Simmer
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
- Department of Pathology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - F Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Ludmil B Alexandrov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, SE-223 81, Sweden
| | - Anieta Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Anthony Ferrari
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316, Norway
- Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, 1478, Norway
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, 08028, Spain
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, Amsterdam, AZ 1105, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, 0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, 0316, Norway
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, 08028, Spain
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - John A Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | | | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, PO Box 9101, Nijmegen, 6500 HB, The Netherlands.
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Smid M, Wilting SM, Uhr K, Rodríguez-González FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A, Martin S, Davies HR, Staaf J, van de Vijver MJ, Richardson AL, MacGrogan G, Salgado R, van den Eynden GGGM, Purdie CA, Thompson AM, Caldas C, Span PN, Sweep FCGJ, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Paradiso A, Eyfjord J, Broeks A, Vincent-Salomon A, Futreal AP, Knappskog S, King T, Viari A, Børresen-Dale AL, Stunnenberg HG, Stratton M, Foekens JA, Sieuwerts AM, Martens JWM. The circular RNome of primary breast cancer. Genome Res 2019; 29:356-366. [PMID: 30692147 PMCID: PMC6396421 DOI: 10.1101/gr.238121.118] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [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: 04/05/2018] [Accepted: 01/23/2019] [Indexed: 11/25/2022]
Abstract
Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.
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Affiliation(s)
- Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Saskia M Wilting
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Katharina Uhr
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - F Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Vanja de Weerd
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Wendy J C Prager-Van der Smissen
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Michelle van der Vlugt-Daane
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Anne van Galen
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, United Kingdom
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Helen R Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Gaëten MacGrogan
- Département de Biopathologie, Institut Bergonié, CS 61283 33076 Bordeaux, France
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, B-1000 Brussels, Belgium
- Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium
| | - Gert G G M van den Eynden
- Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium
- Molecular Immunology Unit, Jules Bordet Institute, B-1000 Brussels, Belgium
| | - Colin A Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Alastair M Thompson
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Paul N Span
- Department of Radiation Oncology, and Department of Laboratory Medicine, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Fred C G J Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, 4029 Brisbane, Australia
| | - Sunil R Lakhani
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, 4029 Brisbane, Australia
- Pathology Queensland, The Royal Brisbane and Women's Hospital, 4029 Brisbane, Australia
| | - Steven Van Laere
- Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, B-1000 Brussels, Belgium
| | | | - Jorunn Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Annegien Broeks
- The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 75248 Paris Cedex 05, France
| | - Andrew P Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Tari King
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Alain Viari
- Synergie Lyon Cancer, Centre Léon Bérard, Lyon Cedex 08, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 38330 Montbonnot-Saint Martin, France
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radiumhospital, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - John A Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Anieta M Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
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37
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Hussein AE, Senabulya N, Ma Y, Streeter MJV, Kettle B, Dann SJD, Albert F, Bourgeois N, Cipiccia S, Cole JM, Finlay O, Gerstmayr E, González IG, Higginbotham A, Jaroszynski DA, Falk K, Krushelnick K, Lemos N, Lopes NC, Lumsdon C, Lundh O, Mangles SPD, Najmudin Z, Rajeev PP, Schlepütz CM, Shahzad M, Smid M, Spesyvtsev R, Symes DR, Vieux G, Willingale L, Wood JC, Shahani AJ, Thomas AGR. Laser-wakefield accelerators for high-resolution X-ray imaging of complex microstructures. Sci Rep 2019; 9:3249. [PMID: 30824838 PMCID: PMC6397215 DOI: 10.1038/s41598-019-39845-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/29/2019] [Indexed: 12/19/2022] Open
Abstract
Laser-wakefield accelerators (LWFAs) are high acceleration-gradient plasma-based particle accelerators capable of producing ultra-relativistic electron beams. Within the strong focusing fields of the wakefield, accelerated electrons undergo betatron oscillations, emitting a bright pulse of X-rays with a micrometer-scale source size that may be used for imaging applications. Non-destructive X-ray phase contrast imaging and tomography of heterogeneous materials can provide insight into their processing, structure, and performance. To demonstrate the imaging capability of X-rays from an LWFA we have examined an irregular eutectic in the aluminum-silicon (Al-Si) system. The lamellar spacing of the Al-Si eutectic microstructure is on the order of a few micrometers, thus requiring high spatial resolution. We present comparisons between the sharpness and spatial resolution in phase contrast images of this eutectic alloy obtained via X-ray phase contrast imaging at the Swiss Light Source (SLS) synchrotron and X-ray projection microscopy via an LWFA source. An upper bound on the resolving power of 2.7 ± 0.3 μm of the LWFA source in this experiment was measured. These results indicate that betatron X-rays from laser wakefield acceleration can provide an alternative to conventional synchrotron sources for high resolution imaging of eutectics and, more broadly, complex microstructures.
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Affiliation(s)
- A E Hussein
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, MI, 48109-2099, USA.
| | - N Senabulya
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-2099, USA
| | - Y Ma
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, MI, 48109-2099, USA.,Physics Department, Lancaster University, Lancaster, LA1 4YB, UK.,The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK
| | - M J V Streeter
- Physics Department, Lancaster University, Lancaster, LA1 4YB, UK.,The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK.,The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - B Kettle
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - S J D Dann
- Physics Department, Lancaster University, Lancaster, LA1 4YB, UK.,The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK
| | - F Albert
- Lawrence Livermore National Laboratory, NIF and Photon Sciences, Livermore, CA, 94550, USA
| | - N Bourgeois
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - S Cipiccia
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot, OX11 0DE, UK
| | - J M Cole
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - O Finlay
- Physics Department, Lancaster University, Lancaster, LA1 4YB, UK.,The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK
| | - E Gerstmayr
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | | | - A Higginbotham
- York Plasma Institute, Department of Physics, University of York, York, YO10 5DD, UK
| | - D A Jaroszynski
- The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK.,SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK
| | - K Falk
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.,Technische Universität Dresden, 01062, Dresden, Germany.,Institute of Physics of the ASCR, 182 21, Prague, Czech Republic
| | - K Krushelnick
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, MI, 48109-2099, USA
| | - N Lemos
- Lawrence Livermore National Laboratory, NIF and Photon Sciences, Livermore, CA, 94550, USA
| | - N C Lopes
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK.,GoLP/Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, U.L., Lisboa, 1049-001, Portugal
| | - C Lumsdon
- York Plasma Institute, Department of Physics, University of York, York, YO10 5DD, UK
| | - O Lundh
- Department of Physics, Lund University, P.O. Box 118, S-22100, Lund, Sweden
| | - S P D Mangles
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - Z Najmudin
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - P P Rajeev
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - C M Schlepütz
- Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland
| | - M Shahzad
- The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK.,SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK
| | - M Smid
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.,ELI Beamlines, Institute of Physics of the ASCR, 182 21, Prague, Czech Republic
| | - R Spesyvtsev
- The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK.,SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK
| | - D R Symes
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - G Vieux
- The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK.,SUPA, Department of Physics, University of Strathclyde, Glasgow, G4 0NG, UK
| | - L Willingale
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, MI, 48109-2099, USA
| | - J C Wood
- The John Adams Institute for Accelerator Science, Imperial College London, London, SW7 2AZ, UK
| | - A J Shahani
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-2099, USA
| | - A G R Thomas
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, MI, 48109-2099, USA.,Physics Department, Lancaster University, Lancaster, LA1 4YB, UK.,The Cockcroft Institute, Keckwick Lane, Daresbury, WA4 4AD, UK
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Klaver Y, Lamers C, Rijnders M, Oostvogels A, Wijers R, Smid M, Grunhagen D, Verhoef K, Sleijfer S, Debets R. In contrast to other soft tissue sarcomas, GIST shows enhanced numbers of immune checkpoint-negative CD8 T cells. Eur J Cancer 2019. [DOI: 10.1016/j.ejca.2019.01.043] [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: 11/30/2022]
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de Kruijff IE, Sieuwerts AM, Onstenk W, Jager A, Hamberg P, de Jongh FE, Smid M, Kraan J, Timmermans MA, Martens JWM, Sleijfer S. Androgen receptor expression in circulating tumor cells of patients with metastatic breast cancer. Int J Cancer 2019; 145:1083-1089. [PMID: 30761532 DOI: 10.1002/ijc.32209] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/28/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
The androgen receptor (AR) has potential clinical relevance in metastatic breast cancer (mBC) since it might be a treatment target and has been associated with endocrine resistance. A minimal-invasive way to determine AR expression on metastatic tumor cells is by characterization of circulating tumor cells (CTCs). Here, we assessed AR mRNA expression in CTCs (CTC-AR) and in matched primary tumor samples from mBC patients representing different breast cancer subtypes. In addition, we explored CTC-AR-status in relation to outcome on endocrine therapy. AR, and 92 AR or estrogen receptor (ER) related genes, were measured in CellSearch-enriched CTCs from 124 mBC patients and in 52 matched FFPE primary tissues using quantitative reverse-transcriptase PCR. AR in CTCs was considered positive if the expression was 1 standard deviation higher than the expression measured in 11 healthy blood donors. A total of 31% of the mBC patients had AR-positive (AR+) CTCs. 58% of the matched CTC and primary tumor samples were discordant with respect to AR status, observing both switches from AR+ to AR-negative (AR-) and vice versa. There was no statistically significant difference in progression-free survival for patients treated with ER-targeting drugs and CTC-AR-status (13 AR+/ 37 AR- cases, p = 0.28). Thus, AR can be determined in RNA isolated from CTCs, with in our set 31% AR-positive samples. Given the discordance between AR status in CTC samples and corresponding primary tumors, determination of AR expression in CTCs might be a promising tool to select mBC patients for AR inhibiting agents.
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Affiliation(s)
- Ingeborg E de Kruijff
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wendy Onstenk
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Paul Hamberg
- Department of Medical Oncology, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Felix E de Jongh
- Department of Medical Oncology, Ikazia Ziekenhuis, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jaco Kraan
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mieke A Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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40
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 2019; 566:E1. [DOI: 10.1038/s41586-019-0883-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Weerts MJA, Smid M, Foekens JA, Sleijfer S, Martens JWM. Mitochondrial RNA Expression and Single Nucleotide Variants in Association with Clinical Parameters in Primary Breast Cancers. Cancers (Basel) 2018; 10:cancers10120500. [PMID: 30544876 PMCID: PMC6318759 DOI: 10.3390/cancers10120500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 11/10/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022] Open
Abstract
The human mitochondrial DNA (mtDNA) encodes 37 genes, including thirteen proteins essential for the respiratory chain, and RNAs functioning in the mitochondrial translation apparatus. The total number of mtDNA molecules per cell (mtDNA content) is variable between tissue types and also between tumors and their normal counterparts. For breast cancer, tumors tend to be depleted in their mtDNA content compared to adjacent normal mammary tissue. Various studies have shown that primary breast tumors harbor somatic mtDNA variants. A decrease in mtDNA content or the presence of somatic variants could indicate a reduced mitochondrial function within breast cancer. In this explorative study we aimed to further understand genomic changes and expression of the mitochondrial genome within breast cancer, by analyzing RNA sequencing data of primary breast tumor specimens of 344 cases. We demonstrate that somatic variants detected at the mtRNA level are representative for somatic variants in the mtDNA. Also, the number of somatic variants within the mitochondrial transcriptome is not associated with mutational processes impacting the nuclear genome, but is positively associated with age at diagnosis. Finally, we observe that mitochondrial expression is related to ER status. We conclude that there is a large heterogeneity in somatic mutations of the mitochondrial genome within primary breast tumors, and differences in mitochondrial expression among breast cancer subtypes. The exact impact on metabolic differences and clinical relevance deserves further study.
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Affiliation(s)
- Marjolein J A Weerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands.
| | - John A Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands.
| | - Stefan Sleijfer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands.
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands.
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Meijer TG, Verkaik NS, Sieuwerts AM, van Riet J, Naipal KA, van Deurzen CH, den Bakker MA, Sleddens HF, Dubbink HJ, den Toom TD, Dinjens WN, Lips E, Nederlof PM, Smid M, van de Werken HJ, Kanaar R, Martens JW, Jager A, van Gent DC. Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects. Clin Cancer Res 2018; 24:6277-6287. [DOI: 10.1158/1078-0432.ccr-18-0063] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/17/2018] [Accepted: 08/17/2018] [Indexed: 11/16/2022]
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Lagendijk M, Saadatmand S, Koppert LB, Tilanus-Linthorst MM, de Weerd V, Ramírez-Moreno R, Smid M, Sieuwerts AM, Martens JW. Correction: MicroRNA expression in pre-treatment plasma of patients with benign breast diseases and breast cancer. Oncotarget 2018; 9:32096. [PMID: 30174799 PMCID: PMC6112841 DOI: 10.18632/oncotarget.25979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Mirelle Lagendijk
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Sepideh Saadatmand
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Linetta B. Koppert
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Raquel Ramírez-Moreno
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
- Cancer Genomics Centre Netherlands, Erasmus University MC, CN 3015, Rotterdam, The Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
- Cancer Genomics Centre Netherlands, Erasmus University MC, CN 3015, Rotterdam, The Netherlands
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Smid M, Weerd VD, Wilting S, Sieuwerts A, Nik-Zainal S, Martens J. Abstract 4978: On circular RNAs in breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4978] [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
Introduction Circular RNA was already discovered many decades ago and circRNAs were long considered idiosyncrasies of the splicing machinery processing precursor mRNA to mature mRNA. A much more recent take on this phenomenon showed an unanticipated abundance of circRNA isoforms in human cells. In breast cancer some work has already been done on publicly available TCGA data, but this analysis has a big limitation since the RNA-seq data were prepared using a poly(A) selection step, thereby missing most circRNAs (which lack a poly(A) tail). Here we describe the identification of circRNAs in a large cohort of 348 primary breast tumors, using RNA-seq data obtained without using a poly(A) selection step in the generation of the sequence libraries. We developed a method that, in contrast to previous identification methods, does not rely on unmapped reads or known splice-junctions.
Methods RNA-seq data were generated, using total RNA and removing ribosomal RNA using Ribo Zero (Illumina, USA). Paired-end (75 bases) sequencing was performed on an Illumina HiSeq 2000. The resulting fastq files were mapped to GRCh38 using STAR (version 2.4.2a) and the resulting bam files were sorted and indexed. CircRNAs were identified directly on the bam file generated by STAR; assuming a circular RNA molecule is present, the sequence read that aligns over the crossing of the non-canonical junction would, on a linear reference, get two different mapped locations. The read-mate aligns somewhere in between these two locations with the head of the read-mate pointing toward the head of the junction read, as would be expected in a properly paired read. Finding additional read-pairs showing this configuration, but always with a breakpoint at the exact same location, strengthens the evidence for circular transcripts.
Results In our cohort of 348 primary breast cancer cases we identified 25,783 circRNAs having a junction over exons of a gene. Of these, 13,853 (54%) were identified in at least 2 samples, and 426 circRNAs were found in at least 150 samples. The top recurrent circRNA was CDR1, a known circRNA that functions as a miR-7 sponge. Other previously described circRNAs were also present in our list. Of the circRNAs with sufficient data, 668 (41%) showed a poor (R<0.2) and 210 (13%) showed a negative correlation with the expression level of the linear gene. We validated several circRNAs by PCR and sequencing, including CNOT2 and CREBBP, the former showing prognostic value, the latter a known breast cancer driver gene. Additional analyses are ongoing and will be presented at the annual meeting.
Conclusion circRNAs are an abundant RNA species in breast cancer, several of which may just be a remnant of the splicing machinery. However, several circRNAs have characteristics of being regulated and thus may have a functional role in breast cancer. Due to their structural stability, candidate circRNAs may serve as good biomarkers for diagnosis and therapy-monitoring in liquid biopsies.
Citation Format: Marcel Smid, Vanja de Weerd, Saskia Wilting, Anieta Sieuwerts, Serena Nik-Zainal, John Martens. On circular RNAs in breast cancer [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 4978.
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Affiliation(s)
- Marcel Smid
- 1Erasmus Medical Ctr., Rotterdam, Netherlands
| | | | | | | | - Serena Nik-Zainal
- 2University of Cambridge, on Behalf of the BASIS consortium, Cambridge, United Kingdom
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Amirnasr A, Gits CM, Kuijk PF, Smid M, Debiec-Rychter M, Sleijfer S, Wiemer EA. Abstract 4345: Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background and aim: Gastrointestinal stromal tumors (GISTs) are rare mesenchymal tumors of the gastrointestinal tract. Gain-of-function mutations in KIT or, less frequently, PDGFRA underlie the pathogenesis of the majority of these tumors. The introduction of imatinib mesylate, a selective tyrosine kinase inhibitor, has dramatically improved the outcome for GIST patients. However, half of the advanced patients treated with imatinib eventually progress and acquire resistance within two years of treatment, underscoring the need to get better insight into the resistance mechanisms. In this context we examined the miRNA and mRNA expression profiles in primary (imatinib-naïve) and imatinib resistant GIST samples.
Material and Methods: Fifty-three frozen GIST samples derived from various anatomical sites (small intestine, stomach, colon) harboring a KIT mutation including exon 9 (n=11), exon 11 (n=41) and exon 17 (n=1), were analyzed. Total RNA was isolated from imatinib naïve (IM-n; n=33) and resistant (IM-r; n=20) tumors. The resistant tumors bearing secondary mutations in exon 13 (n=3), exon 17 (n=6) or no secondary mutations (n=11). The miRNA expression profiles were determined using LNA™ oligonucleotide arrays (Exiqon) capable of detecting 725 human miRNAs. Furthermore, from a subset of samples (IM-n; n=14; IM-r; n=15) the mRNA expression profile was established using Affymetrix U133A oligonucleotide arrays. Using the mRNA expression data and the Biocarta and KEGG databases, global testing identified a number of biochemical pathways containing genes that are differentially expressed between the primary and progressive tumors.
Results: Thirty-five differentially expressed miRNAs (P<0.009, FDR<20%) between IM-n and IM-r GIST samples were identified. MiR-30c, miR-181a and miR-144 were among the most significantly different, with p values of 0.006, 0.006 and 0.003, respectively. Analysis of the mRNA data has revealed the up-regulation of genes (P <0002, FDR<30%) involved in cell cycle, DNA replication and cancer related pathways (i.e. proliferation, genomic instability, resistance to chemotherapy, evading apoptosis, etc.) in IM-r samples. To further elucidate the possible involvement of the deregulated miRNAs in the regulation of the indicated genes, the most significantly differentially expressed genes were correlated to miRNA expression. Negative correlations indicate miRNA mediated gene regulation, and were further examined in target prediction programs.
Conclusion: A molecular comparison between primary, IM-n and IM-r GIST samples revealed significant differentially expressed miRNAs and mRNAs. Bioinformatic analyses provided insight into biochemical pathways, and their putative regulation by miRNAs, that may contribute to imatinib resistance as observed in GIST patients.
Citation Format: Azadeh Amirnasr, Caroline M. Gits, Patricia F. Kuijk, Marcel Smid, Maria Debiec-Rychter, Stefan Sleijfer, Erik A. Wiemer. Molecular comparison of imatinib-naïve and resistant gastrointestinal stromal tumors: Differentially expressed microRNAs and mRNAs [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 4345.
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Affiliation(s)
| | | | | | - Marcel Smid
- 1Erasmus Medical Center, Rotterdam, Netherlands
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Uhr K, Sieuwerts AM, de Weerd V, Smid M, Hammerl D, Foekens JA, Martens JWM. Association of microRNA-7 and its binding partner CDR1-AS with the prognosis and prediction of 1 st-line tamoxifen therapy in breast cancer. Sci Rep 2018; 8:9657. [PMID: 29941867 PMCID: PMC6018428 DOI: 10.1038/s41598-018-27987-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The large number of non-coding RNAs (ncRNAs) and their breadth of functionalities has fuelled many studies on their roles in cancer. We previously linked four microRNAs to breast cancer prognosis. One of these microRNAs, hsa-miR-7, was found to be regulated by another type of ncRNA, the circular non-coding RNA (circRNA) CDR1-AS, which contains multiple hsa-miR-7 binding sites. Based on this finding, we studied the potential clinical value of this circRNA on breast cancer prognosis in a cohort based on a cohort that was previously analysed for hsa-miR-7 and in an adjuvant hormone-naïve cohort for 1st-line tamoxifen treatment outcomes, in which we also analysed hsa-miR-7. A negative correlation was observed between hsa-miR-7 and CDR1-AS in both cohorts. Despite associations with various clinical metrics (e.g., tumour grade, tumour size, and relapse location), CDR1-AS was neither prognostic nor predictive of relevant outcomes in our cohorts. However, we did observe stromal CDR1-AS expression, suggesting a possible cell-type specific interaction. Next to the known association of hsa-miR-7 expression with poor prognosis in primary breast cancer, we found that high hsa-miR-7 expression was predictive of an adverse response to tamoxifen therapy and poor progression-free and post-relapse overall survival in patients with recurrent disease.
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Affiliation(s)
- K Uhr
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - A M Sieuwerts
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - V de Weerd
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - M Smid
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - D Hammerl
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J A Foekens
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J W M Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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Smid M, Coebergh van den Braak RRJ, van de Werken HJG, van Riet J, van Galen A, de Weerd V, van der Vlugt-Daane M, Bril SI, Lalmahomed ZS, Kloosterman WP, Wilting SM, Foekens JA, IJzermans JNM, Martens JWM, Sieuwerts AM. Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons. BMC Bioinformatics 2018; 19:236. [PMID: 29929481 PMCID: PMC6013957 DOI: 10.1186/s12859-018-2246-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 09/25/2017] [Accepted: 06/14/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of gene signatures. Most studies on optimization of normalization methods typically use simulated data to validate methodologies. We describe a new method, GeTMM, which allows for both inter- and intrasample analyses with the same normalized data set. We used actual (i.e. not simulated) RNA-seq data from 263 colon cancers (no biological replicates) and used the same read count data to compare GeTMM with the most commonly used normalization methods (i.e. TMM (used by edgeR), RLE (used by DESeq2) and TPM) with respect to distributions, effect of RNA quality, subtype-classification, recurrence score, recall of DE genes and correlation to RT-qPCR data. RESULTS We observed a clear benefit for GeTMM and TPM with regard to intrasample comparison while GeTMM performed similar to TMM and RLE normalized data in intersample comparisons. Regarding DE genes, recall was found comparable among the normalization methods, while GeTMM showed the lowest number of false-positive DE genes. Remarkably, we observed limited detrimental effects in samples with low RNA quality. CONCLUSIONS We show that GeTMM outperforms established methods with regard to intrasample comparison while performing equivalent with regard to intersample normalization using the same normalized data. These combined properties enhance the general usefulness of RNA-seq but also the comparability to the many array-based gene expression data in the public domain.
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Affiliation(s)
- Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands.
| | | | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands.,Department of Urology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands.,Department of Urology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Anne van Galen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Sandra I Bril
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Zarina S Lalmahomed
- Department of Surgery, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Wigard P Kloosterman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands
| | | | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands.,Cancer Genomics Center, 3584 CG, Utrecht, The Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, 3015 CE, Rotterdam, The Netherlands.,Cancer Genomics Center, 3584 CG, Utrecht, The Netherlands
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Kolijn K, Verhoef EI, Smid M, Böttcher R, Jenster GW, Debets R, van Leenders GJLH. Epithelial-Mesenchymal Transition in Human Prostate Cancer Demonstrates Enhanced Immune Evasion Marked by IDO1 Expression. Cancer Res 2018; 78:4671-4679. [PMID: 29921693 DOI: 10.1158/0008-5472.can-17-3752] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/16/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022]
Abstract
Cancer invasion and metastasis are driven by epithelial-mesenchymal transition (EMT), yet the exact mechanisms that account for EMT in clinical prostate cancer are not fully understood. Expression of N-cadherin is considered a hallmark of EMT in clinical prostate cancer. In this study, we determined the molecular mechanisms associated with N-cadherin expression in patients with prostate cancer. We performed laser capture microdissection of matched N-cadherin-positive and -negative prostate cancer areas from patient samples (n = 8), followed by RNA sequencing. N-cadherin expression was significantly associated with an immune-regulatory signature including profound upregulation of indoleamine 2,3-dioxygenase (IDO1; log2-fold change = 5.1; P = 2.98E-04). Fluorescent immunostainings of patient samples confirmed expression of IDO1 protein and also its metabolite kynurenine in primarily N-cadherin-positive areas. N-cadherin-positive areas also exhibited a local decrease of intraepithelial cytotoxic (CD8+) T cells and an increase of immunosuppressive regulatory T cells (CD4+/FOXP3+). In conclusion, EMT in clinical prostate cancer is accompanied by upregulated expression of IDO1 and an increased number of regulatory T cells. These data indicate that EMT, which is an important step in tumor progression, can be protected from effective immune control in patients with prostate cancer.Significance: These findings demonstrate EMT is linked to an immunosuppressive environment in clinical prostate cancer, suggesting that patients with prostate cancer can potentially benefit from combinatorial drug therapy. Cancer Res; 78(16); 4671-9. ©2018 AACR.
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Affiliation(s)
- Kimberley Kolijn
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Esther I Verhoef
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - René Böttcher
- Department of Urology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
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de Kruijff IE, Sieuwerts AM, Onstenk W, Jager A, Hamberg P, De Jongh F, Smid M, Timmermans MA, Martens JW, Sleijfer S. Androgen receptor expression in circulating tumor cells of metastatic breast cancer patients. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.1087] [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: 11/20/2022] Open
Affiliation(s)
- Ingeborg Elisabeth de Kruijff
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wendy Onstenk
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - A. Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Paul Hamberg
- Department of Internal Medicine, Franciscus Gasthuis & Vlietland, Rotterdam, Netherlands
| | - Felix De Jongh
- Department of Internal Medicine, Ikazia Hospital, Rotterdam, Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mieke A. Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
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50
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Lagendijk M, Sadaatmand S, Koppert LB, Tilanus-Linthorst MMA, de Weerd V, Ramírez-Moreno R, Smid M, Sieuwerts AM, Martens JWM. MicroRNA expression in pre-treatment plasma of patients with benign breast diseases and breast cancer. Oncotarget 2018; 9:24335-24346. [PMID: 29849944 PMCID: PMC5966243 DOI: 10.18632/oncotarget.25262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNAs (miRs) are small RNA molecules, influencing messenger RNA (mRNA) expression and translation, and are readily detectable in blood. Some have been reported as potential breast cancer biomarkers. This study aimed to identify and validate miRs indicative of breast cancer. Results Based on the discovery and literature, 18 potentially informative miRs were quantified in the validation cohort. Irrespective of patient and tumour characteristics, hsa-miR-652-5p was significantly upregulated in the malignant compared to benign patients (1.26 fold, P = 0.005) and therefore validated as potential biomarker. In the validation cohort literature-based hsa-let-7b levels were higher in malignant patients as well (1.53 fold, P = 0.011). Two miRs differentiated benign wildtype from benign BRCA1 mutation carriers and an additional 8 miRs differentiated metastastic (n = 8) from non-metastatic (n = 41) cases in the validation cohort. Methods Pre-treatment plasma samples were collected of patients with benign breast disease and breast cancer and divided over a discovery (n = 31) and validation (n = 84) cohort. From the discovery cohort miRs differentially expressed between benign and malignant cases were identified using a 2,000-miR microarray. Literature-based miRs differentiating benign from malignant disease were added. Using RT-qPCR, their expression was investigated in a validation cohort consisting of pre-treatment benign, malignant and metastatic samples. Additionally, benign and malignant cases were compared to benign and malignant cases of BRCA1-mutation carriers. Conclusions Plasma microRNA levels differed between patients with and without breast cancer, between benign disease from wildtype and BRCA1-mutation carriers and between breast cancer with and without metastases. Hsa-miR-652-5p was validated as a potential biomarker for breast cancer.
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Affiliation(s)
- Mirelle Lagendijk
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Sepideh Sadaatmand
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Linetta B Koppert
- Department of Surgical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Raquel Ramírez-Moreno
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands.,Cancer Genomics Centre Netherlands, Erasmus University MC, CN 3015, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, EA 3075, Rotterdam, The Netherlands.,Cancer Genomics Centre Netherlands, Erasmus University MC, CN 3015, Rotterdam, The Netherlands
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