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Eide PW, Moosavi SH, Eilertsen IA, Brunsell TH, Langerud J, Berg KCG, Røsok BI, Bjørnbeth BA, Nesbakken A, Lothe RA, Sveen A. Metastatic heterogeneity of the consensus molecular subtypes of colorectal cancer. NPJ Genom Med 2021; 6:59. [PMID: 34262039 PMCID: PMC8280229 DOI: 10.1038/s41525-021-00223-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023] Open
Abstract
Gene expression-based subtypes of colorectal cancer have clinical relevance, but the representativeness of primary tumors and the consensus molecular subtypes (CMS) for metastatic cancers is not well known. We investigated the metastatic heterogeneity of CMS. The best approach to subtype translation was delineated by comparisons of transcriptomic profiles from 317 primary tumors and 295 liver metastases, including multi-metastatic samples from 45 patients and 14 primary-metastasis sets. Associations were validated in an external data set (n = 618). Projection of metastases onto principal components of primary tumors showed that metastases were depleted of CMS1-immune/CMS3-metabolic signals, enriched for CMS4-mesenchymal/stromal signals, and heavily influenced by the microenvironment. The tailored CMS classifier (available in an updated version of the R package CMScaller) therefore implemented an approach to regress out the liver tissue background. The majority of classified metastases were either CMS2 or CMS4. Nonetheless, subtype switching and inter-metastatic CMS heterogeneity were frequent and increased with sampling intensity. Poor-prognostic value of CMS1/3 metastases was consistent in the context of intra-patient tumor heterogeneity.
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Affiliation(s)
- Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tuva H Brunsell
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bård I Røsok
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Bjørn A Bjørnbeth
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway. .,Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
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Flatin BTB, Vedeld HM, Pinto R, Langerud J, Lind GE, Lothe RA, Sveen A, Jeanmougin M. Multiregional assessment of CIMP in primary colorectal cancers: Phenotype concordance but marker variability. Int J Cancer 2020; 148:1652-1657. [PMID: 33284993 PMCID: PMC7898891 DOI: 10.1002/ijc.33425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/03/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Intratumor heterogeneity of colorectal cancers (CRCs) is manifested both at the genomic and epigenomic levels. Early genetic aberrations in carcinogenesis are clonal and present throughout the tumors, but less is known about the heterogeneity of the epigenetic CpG island methylator phenotype (CIMP). CIMP characterizes a subgroup of CRCs thought to originate from specific precursor lesions, and it is defined by widespread DNA methylation within promoter regions. In this work, we investigated CIMP in two to four multiregional samples from 30 primary tumors (n = 86 samples) using the consensus Weisenberger gene panel (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1). Twenty‐nine of 30 tumors (97%) showed concordant CIMP status in all samples, and percent methylated reference (PMR) values of all five markers had higher intertumor than intratumor variation (P value = 1.5e−09). However, a third of the CIMP+ tumors exhibited discrepancies in methylation status in at least one of the five gene markers. To conclude, CIMP status was consistent within primary CRCs, and it is likely a clonal phenotype. However, spatial discordances of the individual genes suggest that large‐scale analysis of multiregional samples could be of interest for identifying CIMP markers that are robust to intratumor heterogeneity. What's new? Colorectal cancers (CRCs) exhibit significant intratumoral genetic and epigenetic heterogeneity. A subgroup of CRCs is characterized in particular by the epigenetic CpG island methylator phenotype (CIMP), though the extent to which CIMP contributes to intratumoral heterogeneity in these tumors is unknown. Here, investigation of CIMP in multiregional samples from primary CRCs shows that CIMP status is highly homogenous within tumors. In one‐third of CIMP‐positive primary CRCs, methylation status differed in at least one of five gene markers investigated. The findings suggest that inclusion of multiregional CRC samples could aid the development of more robust marker panels for CIMP assessment.
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Affiliation(s)
- Bjørnar T B Flatin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Rita Pinto
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Division for Cancer Medicine, K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
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Kryeziu K, Bruun J, Eide PW, Moosavi SH, Eilertsen IA, Langerud J, Røsok B, Brunsell TH, Guren MG, Abildgaard A, Nesbakken A, Bjørnbeth BA, Sveen A, Lothe RA. Abstract A19: Modeling intrapatient pharmacotranscriptomic heterogeneity with organoids derived from colorectal cancer liver metastases. Cancer Res 2020. [DOI: 10.1158/1538-7445.camodels2020-a19] [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
Patients with metastatic colorectal cancer (CRC) have few targeted treatment options compared with other major malignancies, and both over- and undertreatment with cytostatic drugs remain a challenge. Recent studies show that patient-derived organoids (PDOs) can predict clinical responses to systemic therapies in a personalized manner, but tumor heterogeneity may limit the clinical benefit of anticancer therapies, as well as the accuracy of preclinical predictions. PDO lineage establishment from multiple distinct lesions per patient presents a novel opportunity for preclinical investigation of intrapatient pharmacotranscriptomic heterogeneity. From September 2017 until November 2019, we have established a living biobank of 107 PDOs from 53 patients who underwent resection of CRC liver metastases at Oslo University Hospital, Norway, 31 of whom had multiple (2-5) metastases. All PDOs were screened for sensitivity to 40 anticancer agents, including clinically relevant targeted drugs and conventional chemotherapies. Molecular profiling by gene expression and mutation analyses is ongoing and currently completed for 27 PDOs. Recapitulation of known pharmacogenomic/transcriptomic associations was confirmed in PDOs for EGFR inhibition and RAS/BRAFV600E mutation status, as well as TP53-MDM2 inhibition and TP53 mutation status and TP53 transcriptional activity. Antimetabolites such as gemcitabine and methotrexate, or small-molecule inhibitors in late-stage clinical development targeting Aurora A, PLK1, and HSP90, showed strong differential activities, enabling identification of sensitive subgroups. Strong sensitivity to HSP90 inhibition was associated with low protein expression of Heat Shock Transcription Factor 1, which had a homogenous intrapatient intermetastatic expression pattern. Principal component analyses revealed a clear patient-wise separation of PDOs based on both their pharmacologic and transcriptomic profiles separately, indicating only modest intrapatient heterogeneity among distinct metastatic lesions. Accurate prediction of clinical responses to 5-FU and oxaliplatin was shown in PDOs from one patient treated for recurrent liver metastases. Additionally, PDOs from recurrent liver metastases showed an increased sensitivity to off-label drugs compared to PDOs from the first liver resection, supporting therapy repurposing in later lines of treatment. In summary, patient-derived models of CRC liver metastases reveal modest intrapatient pharmacotranscriptomic heterogeneity—an encouraging result for further efforts to develop personalized drug repurposing strategies for this poor-prognosis patient group.
Citation Format: Kushtrim Kryeziu, Jarle Bruun, Peter W. Eide, Seyed H. Moosavi, Ina A. Eilertsen, Jonas Langerud, Bård Røsok, Tuva H. Brunsell, Marianne G. Guren, Andreas Abildgaard, Arild Nesbakken, Bjørn Atle Bjørnbeth, Anita Sveen, Ragnhild A. Lothe. Modeling intrapatient pharmacotranscriptomic heterogeneity with organoids derived from colorectal cancer liver metastases [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr A19.
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Affiliation(s)
- Kushtrim Kryeziu
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Jarle Bruun
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Peter W. Eide
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Seyed H. Moosavi
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Ina A. Eilertsen
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Jonas Langerud
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Bård Røsok
- 2Department of Hepato-Pancreato-Biliary Surgery and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Tuva H. Brunsell
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Marianne G. Guren
- 3Department of Oncology and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Andreas Abildgaard
- 4Department of Radiology and Nuclear Medicine and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Arild Nesbakken
- 5Department of Gastrointestinal Surgery, Ullevål Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjørn Atle Bjørnbeth
- 2Department of Hepato-Pancreato-Biliary Surgery and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Anita Sveen
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
| | - Ragnhild A. Lothe
- 1Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital and K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway,
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Bruun J, Kryeziu K, Eide PW, Moosavi SH, Eilertsen IA, Langerud J, Røsok B, Totland MZ, Brunsell TH, Pellinen T, Saarela J, Bergsland CH, Palmer HG, Brudvik KW, Guren T, Dienstmann R, Guren MG, Nesbakken A, Bjørnbeth BA, Sveen A, Lothe RA. Patient-Derived Organoids from Multiple Colorectal Cancer Liver Metastases Reveal Moderate Intra-patient Pharmacotranscriptomic Heterogeneity. Clin Cancer Res 2020; 26:4107-4119. [PMID: 32299813 DOI: 10.1158/1078-0432.ccr-19-3637] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/02/2020] [Accepted: 04/10/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Molecular tumor heterogeneity may have important implications for the efficacy of targeted therapies in metastatic cancers. Inter-metastatic heterogeneity of sensitivity to anticancer agents has not been well explored in colorectal cancer. EXPERIMENTAL DESIGN We established a platform for ex vivo pharmacogenomic profiling of patient-derived organoids (PDO) from resected colorectal cancer liver metastases. Drug sensitivity testing (n = 40 clinically relevant agents) and gene expression profiling were performed on 39 metastases from 22 patients. RESULTS Three drug-response clusters were identified among the colorectal cancer metastases, based primarily on sensitivities to EGFR and/or MDM2 inhibition, and corresponding with RAS mutations and TP53 activity. Potentially effective therapies, including off-label use of drugs approved for other cancer types, could be nominated for eighteen patients (82%). Antimetabolites and targeted agents lacking a decisive genomic marker had stronger differential activity than most approved chemotherapies. We found limited intra-patient drug sensitivity heterogeneity between PDOs from multiple (2-5) liver metastases from each of ten patients. This was recapitulated at the gene expression level, with a highly proportional degree of transcriptomic and pharmacological variation. One PDO with a multi-drug resistance profile, including resistance to EGFR inhibition in a RAS-mutant background, showed sensitivity to MEK plus mTOR/AKT inhibition, corresponding with low-level PTEN expression. CONCLUSIONS Intra-patient inter-metastatic pharmacological heterogeneity was not pronounced and ex vivo drug screening may identify novel treatment options for metastatic colorectal cancer. Variation in drug sensitivities was reflected at the transcriptomic level, suggesting potential to develop gene expression-based predictive signatures to guide experimental therapies.
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Affiliation(s)
- Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Kushtrim Kryeziu
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Seyed H Moosavi
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Jonas Langerud
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Bård Røsok
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Max Z Totland
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Tuva H Brunsell
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.,Department of Gastrointestinal Surgery, Ullevål Hospital-Oslo University Hospital, Oslo, Norway
| | - Teijo Pellinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Christian H Bergsland
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Hector G Palmer
- Stem Cells and Cancer Group, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Barcelona, Spain. CIBERONC, Madrid, Spain
| | - Kristoffer W Brudvik
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Tormod Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Rodrigo Dienstmann
- Stem Cells and Cancer Group, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Barcelona, Spain. CIBERONC, Madrid, Spain
| | - Marianne G Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.,Department of Gastrointestinal Surgery, Ullevål Hospital-Oslo University Hospital, Oslo, Norway
| | - Bjørn Atle Bjørnbeth
- K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Clinic for Cancer Medicine, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
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Langerud J, Jarhelle E, Van Ghelue M, Ariansen SL, Iversen N. Trans-activation-based risk assessment of BRCA1 BRCT variants with unknown clinical significance. Hum Genomics 2018; 12:51. [PMID: 30458859 PMCID: PMC6247502 DOI: 10.1186/s40246-018-0183-1] [Citation(s) in RCA: 2] [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: 08/31/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022] Open
Abstract
Background Deleterious variants in the tumour suppressor BRCA1 are known to cause hereditary breast and ovarian cancer syndrome (HBOC). Missense variants in BRCA1 pose a challenge in clinical care, as their effect on protein functionality often remains unknown. Many of the pathogenic missense variants found in BRCA1 are located in the BRCA1 C-terminal (BRCT) domains, domains that are known to be vital for key functions such as homologous recombination repair, protein-protein interactions and trans-activation (TA). We investigated the TA activity of 12 BRCA1 variants of unknown clinical significance (VUSs) located in the BRCT domains to aid in the classification of these variants. Results Twelve BRCA1 VUSs were investigated using a modified version of the dual luciferase TA activity assay (TA assay) that yielded increased sensitivity and sample throughput. Variants were classified according to American College of Medical Genetics and Genomics (ACMG) criteria using TA assay results and available data. In combining our TA-assay results and available data, in accordance with the ACMG guidelines for variant classification, we proposed the following variant classifications: c.5100A>G, c.5326C>T, c.5348T>C and c.5477A>T as likely benign (class 2) variants. c.5075A>C, c.5116G>A and c.5513T>G were likely pathogenic (class 4), whereas c.5096G>A likely represents a likely pathogenic variant with moderate penetrance. Variants c.5123C>T, c.5125G>A, c.5131A>C and c.5504G>A remained classified as VUSs (class 3). Conclusions The modified TA assay provides efficient risk assessment of rare missense variants found in the BRCA1 BRCT-domains. We also report that increased post-transfection incubation time yielded a significant increase in TA assay sensitivity. Electronic supplementary material The online version of this article (10.1186/s40246-018-0183-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonas Langerud
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | | | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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