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Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP. Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells. Nat Chem Biol 2017; 13:12-14. [PMID: 27820796 PMCID: PMC5164930 DOI: 10.1038/nchembio.2226] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022]
Abstract
In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.
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Affiliation(s)
- Josep V. Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mareike Herzog
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tomasz Konopka
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bianca V. Gapp
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sebastian M. Nijman
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Stephen P. Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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4
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Le Pennec S, Konopka T, Gacquer D, Fimereli D, Tarabichi M, Tomás G, Savagner F, Decaussin-Petrucci M, Trésallet C, Andry G, Larsimont D, Detours V, Maenhaut C. Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases. Endocr Relat Cancer 2015; 22:205-16. [PMID: 25691441 DOI: 10.1530/erc-14-0351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The contribution of intratumor heterogeneity to thyroid metastatic cancers is still unknown. The clonal relationships between the primary thyroid tumors and lymph nodes (LN) or distant metastases are also poorly understood. The objective of this study was to determine the phylogenetic relationships between matched primary thyroid tumors and metastases. We searched for non-synonymous single-nucleotide variants (nsSNVs), gene fusions, alternative transcripts, and loss of heterozygosity (LOH) by paired-end massively parallel sequencing of cDNA (RNA-Seq) in a patient diagnosed with an aggressive papillary thyroid cancer (PTC). Seven tumor samples from a stage IVc PTC patient were analyzed by RNA-Seq: two areas from the primary tumor, four areas from two LN metastases, and one area from a pleural metastasis (PLM). A large panel of other thyroid tumors was used for Sanger sequencing screening. We identified seven new nsSNVs. Some of these were early events clonally present in both the primary PTC and the three matched metastases. Other nsSNVs were private to the primary tumor, the LN metastases and/or the PLM. Three new gene fusions were identified. A novel cancer-specific KAZN alternative transcript was detected in this aggressive PTC and in dozens of additional thyroid tumors. The PLM harbored an exclusive whole-chromosome 19 LOH. We have presented the first, to our knowledge, deep sequencing study comparing the mutational spectra in a PTC and both LN and distant metastases. This study has yielded novel findings concerning intra-tumor heterogeneity, clonal evolution and metastases dissemination in thyroid cancer.
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Affiliation(s)
- Soazig Le Pennec
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Tomasz Konopka
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - David Gacquer
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Danai Fimereli
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Maxime Tarabichi
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Gil Tomás
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Frédérique Savagner
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Myriam Decaussin-Petrucci
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Christophe Trésallet
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Guy Andry
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Denis Larsimont
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Vincent Detours
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
| | - Carine Maenhaut
- IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium IRIBHMWELBIOUniversité libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, 1070 Brussels, BelgiumCHU d'AngersBâtiment IRIS, 4 rue Larrey, Angers F-49033, FranceEA 3143Université d'Angers, F-49033 Angers, FranceService d'Anatomie et Cytologie PathologiquesCentre de Biologie Sud - Bâtiment 3D, Centre Hospitalier Lyon Sud, 69495 Pierre Bénite Cedex, FranceHôpital Pitié-SalpêtrièreUniversité Pierre et Marie Curie, 47 Boulevard de l'Hôpital, 75013 Paris, FranceInstitut Jules Bordet121 Boulevard de Waterloo, 1000 Brussels, Belgium
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5
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Fimereli D, Gacquer D, Fumagalli D, Salgado R, Rothé F, Larsimont D, Sotiriou C, Detours V. No significant viral transcription detected in whole breast cancer transcriptomes. BMC Cancer 2015; 15:147. [PMID: 25884932 PMCID: PMC4374178 DOI: 10.1186/s12885-015-1176-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/06/2015] [Indexed: 02/07/2023] Open
Abstract
Background Studies evaluating the presence of viral sequences in breast cancer (BC), including various strains of human papillomavirus and human herpes virus, have yielded conflicting results. Most were based on RT-PCR and in situ hybridization. Methods In this report we searched for expressed viral sequences in 58 BC transcriptomes using five distinct in silico methods. In addition, we complemented our RNA sequencing results with exome sequencing, PCR and immunohistochemistry (IHC) analyses. A control sample was used to test our in silico methods. Results All of the computational methods correctly detected viral sequences in the control sample. We identified a small number of viral sequences belonging to human herpesvirus 4 and 6 and Merkel cell polyomavirus. The extremely low expression levels—two orders of magnitude lower than in a typical hepatitis B virus infection in hepatocellular carcinoma—did not suggest active infections. The presence of viral elements was confirmed in sample-matched exome sequences, but could not be confirmed by PCR or IHC. Conclusions Our results show that no viral sequences are expressed in significant amounts in the BC investigated. The presence of non-transcribed viral DNA cannot be excluded.
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Affiliation(s)
- Danai Fimereli
- IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium.
| | - David Gacquer
- IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium.
| | - Debora Fumagalli
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium.
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium. .,Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium.
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium.
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium.
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Bld de Waterloo, 125-1000, Brussels, Belgium.
| | - Vincent Detours
- IRIBHM - Université Libre de Bruxelles, ULB, Campus Erasme CP602, 808 route de Lennik, 1070, Brussels, Belgium. .,WELBIO, 808 route de Lennik, 1070, Brussels, Belgium.
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