1
|
Lebret T, Bonastre J, Fraslin A, Neuzillet Y, Droupy S, Rebillard X, Vordos D, Guy L, Villers A, Schneider M, Coloby P, Lacoste J, Méjean A, Lacoste J, Descotes JL, Eschwege P, Loison G, Blanché H, Mariani O, Ghaleh B, Mangin A, Sirab N, Groussard K, Radvanyi F, Allory Y, Benhamou S. Cohort profile: COBLAnCE: a French prospective cohort to study prognostic and predictive factors in bladder cancer and to generate real-world data on treatment patterns, resource use and quality of life. BMJ Open 2023; 13:e075942. [PMID: 38128940 DOI: 10.1136/bmjopen-2023-075942] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
PURPOSE Bladder cancer is a complex disease with a wide range of outcomes. Clinicopathological factors only partially explain the variability between patients in prognosis and treatment response. There is a need for large cohorts collecting extensive data and biological samples to: (1) investigate gene-environment interactions, pathological/molecular classification and biomarker discovery; and (2) describe treatment patterns, outcomes, resource use and quality of life in a real-world setting. PARTICIPANTS COBLAnCE (COhort to study BLAdder CancEr) is a French national prospective cohort of patients with bladder cancer recruited between 2012 and 2018 and followed for 6 years. Data on patient and tumour characteristics, treatments, outcomes and biological samples are collected at enrolment and during the follow-up. FINDINGS TO DATE We describe the cohort at enrolment according to baseline surgery and tumour type. In total, 1800 patients were included: 1114 patients with non-muscle-invasive bladder cancer (NMIBC) and 76 patients with muscle-invasive bladder cancer (MIBC) had transurethral resection of a bladder tumour without cystectomy, and 610 patients with NMIBC or MIBC underwent cystectomy. Most patients had a solitary lesion (56.3%) without basement membrane invasion (71.7% of Ta and/or Tis). Half of the patients with cystectomy were stage ≤T2 and 60% had non-continent diversion. Surgery included local (n=298) or super-extended lymph node dissections (n=11) and prostate removal (n=492). Among women, 16.5% underwent cystectomy and 81.4% anterior pelvectomy. FUTURE PLANS COBLAnCE will be used for long-term studies of bladder cancer with focus on clinicopathological factors and molecular markers. It will lead to a much-needed improvement in the understanding of the disease. The cohort provides valuable real-world data, enabling researchers to study various research questions, assess routine medical practices and guide medical decision-making.
Collapse
Affiliation(s)
| | - Julia Bonastre
- Biostatistics and Epidemiology, Gustave Roussy, Villejuif, France
| | - Aldéric Fraslin
- Biostatistics and Epidemiology, Gustave Roussy, Villejuif, France
| | | | - Stéphane Droupy
- Urology, Centre Hospitalier Universitaire de Nimes, Nimes, France
| | | | - Dimitri Vordos
- Clinical Investigation Center 1430, INSERM, Créteil, France
| | - Laurent Guy
- Urology, University Hospital Centre Gabriel Montpied, Clermont-Ferrand, France
| | | | | | - Patrick Coloby
- Urology, University Hospital Center René Dubos, Cergy-Pontoise, France
| | - Jean Lacoste
- Urology, Private Hospital of Provence, Aix-en-Provence, France
| | - Arnaud Méjean
- Urology, Hopital Europeen Georges Pompidou, Paris, France
| | | | | | - Pascal Eschwege
- Urology, CHU de Nancy Hôpital de Brabois Adultes, Vandoeuvre-les-Nancy, France
| | | | | | - Odette Mariani
- Biological Resources Center, Curie Institute Hospital Group, Paris, France
| | - Bijan Ghaleh
- Biological Resources Platform, Hôpital Henri Mondor, Creteil, France
| | - Anthony Mangin
- Biostatistics and Epidemiology, Gustave Roussy, Villejuif, France
| | | | | | | | - Yves Allory
- Patholgy, Curie Institute Saint Cloud, Saint-Cloud, France
| | | |
Collapse
|
2
|
Passeri T, Gutman T, Hamza A, Adle-Biassette H, Girard E, Beaurepere R, Tariq Z, Mariani O, Dahmani A, Bourneix C, Abbritti R, Driouch K, Bohec M, Servant N, Baulande S, Decaudin D, Guichard JP, Calugaru V, Feuvret L, Guinebretière JM, Champion L, Bièche I, Froelich S, Mammar H, Masliah-Planchon J. The mutational landscape of skull base and spinal chordomas and the identification of potential prognostic and theranostic biomarkers. J Neurosurg 2023; 139:1270-1280. [PMID: 37029667 DOI: 10.3171/2023.1.jns222180] [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: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 04/09/2023]
Abstract
OBJECTIVE Chordomas are rare bone neoplasms characterized by a high recurrence rate and no benefit from any approved medical treatment to date. However, the investigation of molecular alterations in chordomas could be essential to prognosticate, guide clinical decision-making, and identify theranostic biomarkers. The aim of this study was to provide a detailed genomic landscape of a homogeneous series of 64 chordoma samples, revealing driver events, theranostic markers, and outcome-related genomic features. METHODS The authors conducted whole-exome sequencing (WES), targeted next-generation sequencing, and RNA sequencing of 64 skull base and spinal chordoma samples collected between December 2006 and September 2020. Clinical, histological, and radiological data were retrospectively analyzed and correlated to genetic findings. RESULTS The authors identified homozygous deletions of CDKN2A/2B, PIK3CA mutations, and alterations affecting genes of SWI/SNF chromatin remodeling complexes (PBRM1 and ARID1A) as potential theranostic biomarkers. Using matched germline WES, they observed a higher frequency of a common genetic variant (rs2305089; p.(Gly177Asp)) in TBXT (97.8%, p < 0.001) compared to its distribution in the general population. PIK3CA mutation was identified as an independent biomarker of short progression-free survival (HR 10.68, p = 0.0008). Loss of CDKN2A/2B was more frequently observed in spinal tumors and recurrent tumors. CONCLUSIONS In the current study, the authors identified driver events such as PBRM1 and PIK3CA mutations, TBXT alterations, or homozygous deletions of CDKN2A/2B, which could, for some, be considered potential theranostic markers and could allow for identifying novel therapeutic approaches. With the aim of a future biomolecular prognostication classification, alterations affecting PIK3CA and CDKN2A/2B could be considered as poor prognostic biomarkers.
Collapse
Affiliation(s)
- Thibault Passeri
- Departments of1Genetics and
- Departments of2Neurosurgery
- 3Department of Translational Research, Laboratory of Preclinical Investigation, Institut Curie, Paris-Saclay University, Paris
| | | | | | | | | | | | | | | | - Ahmed Dahmani
- 3Department of Translational Research, Laboratory of Preclinical Investigation, Institut Curie, Paris-Saclay University, Paris
| | | | | | | | | | | | | | - Didier Decaudin
- 3Department of Translational Research, Laboratory of Preclinical Investigation, Institut Curie, Paris-Saclay University, Paris
| | - Jean-Pierre Guichard
- 8Radiology, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, Paris
| | - Valentin Calugaru
- 9Department of Radiotherapy, Proton Therapy Center, Institut Curie, Paris-Saclay University, Orsay
| | - Loïc Feuvret
- 10Department of Radiotherapy, Pitié-Salpêtrière Hospital, Assistance Publique des Hôpitaux de Paris, Paris
| | | | - Laurence Champion
- 12Department of Nuclear Medicine, Institut Curie, Paris-Saclay University, Saint-Cloud, France
| | | | | | - Hamid Mammar
- 9Department of Radiotherapy, Proton Therapy Center, Institut Curie, Paris-Saclay University, Orsay
| | | |
Collapse
|
3
|
Nemati F, de Koning L, Gentien D, Assayag F, Henry E, Ait Rais K, Pierron G, Mariani O, Nijnikoff M, Champenois G, Nicolas A, Meseure D, Gardrat S, Servant N, Hupé P, Kamal M, Le Tourneau C, Piperno-Neumann S, Rodrigues M, Roman-Roman S, Decaudin D, Mariani P, Cassoux N. Patient Derived Xenografts (PDX) Models as an Avatar to Assess Personalized Therapy Options in Uveal Melanoma: A Feasibility Study. Curr Oncol 2023; 30:9090-9103. [PMID: 37887557 PMCID: PMC10604955 DOI: 10.3390/curroncol30100657] [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: 08/14/2023] [Revised: 09/13/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Uveal melanoma is the most common primary intraocular malignancy in adults. Up to 50% of UM patients develop metastatic disease, usually in the liver. When metastatic, the prognosis is poor, and few treatment options exist. Here, we investigated the feasibility of establishing patient-derived xenografts (PDXs) from a patient's tumor in order to screen for therapies that the patient could benefit from. Samples obtained from 29 primary tumors and liver metastases of uveal melanoma were grafted into SCID mice. PDX models were successfully established for 35% of primary patient tumors and 67% of liver metastases. The tumor take rate was proportional to the risk of metastases. PDXs showed the same morphology, the same GNAQ/11, BAP1, and SF3B1 mutations, and the same chromosome 3 and 8q status as the corresponding patient samples. Six PDX models were challenged with two compounds for 4 weeks. We show that, for 31% of patients with high or intermediate risk of metastasis, the timing to obtain efficacy results on PDX models derived from their primary tumors was compatible with the selection of the therapy to treat the patient after relapse. PDXs could thus be a valid tool ("avatar") to select the best personalized therapy for one third of patients that are most at risk of relapse.
Collapse
Affiliation(s)
- Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University Paris, 26 rue d’Ulm, CEDEX 05, 75248 Paris, France
| | - Leanne de Koning
- Translational Research Department, Institut Curie, PSL University Paris, 75248 Paris, France; (L.d.K.)
| | - David Gentien
- Genomics Platform, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Franck Assayag
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University Paris, 26 rue d’Ulm, CEDEX 05, 75248 Paris, France
| | - Emilie Henry
- Genomics Platform, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Khadija Ait Rais
- Department of Genetics, Institut Curie, PSL Research University, 75248 Paris, France
| | - Gaelle Pierron
- Department of Genetics, Institut Curie, PSL Research University, 75248 Paris, France
| | - Odette Mariani
- Biological Resource Center, Department of Pathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Michèle Nijnikoff
- Biological Resource Center, Department of Pathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Gabriel Champenois
- Department of Biopathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - André Nicolas
- Department of Biopathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Didier Meseure
- Department of Biopathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Nicolas Servant
- Institut Curie, INSERM U900, CBIO-Centre for Computational Biology, Mines Paris Tech, PSL-Research University, 75248 Paris, France
| | - Philippe Hupé
- Institut Curie, INSERM U900, CBIO-Centre for Computational Biology, Mines Paris Tech, PSL-Research University, 75248 Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, 75248 Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, 75248 Paris, France
- INSERM U900 Research Unit, Institut Curie, 92064 Saint-Cloud, France
- Paris-Saclay University, 75248 Paris, France
| | - Sophie Piperno-Neumann
- Department of Medical Oncology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, PSL University Paris, 75248 Paris, France; (L.d.K.)
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University Paris, 26 rue d’Ulm, CEDEX 05, 75248 Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Pascale Mariani
- Department of Surgical Oncology, Institut Curie, PSL Research University, 75248 Paris, France
| | - Nathalie Cassoux
- Department of Oncological Ophthalmology, Institut Curie, Université Paris Cité, 75248 Paris, France
| |
Collapse
|
4
|
Gruel N, Quignot C, Vibert J, Bonvalot S, Zein SE, Tzanis D, Baulande S, Mariani O, Waterfall J, Delattre O, Watson S. Abstract 96: Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-96] [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: 04/07/2023]
Abstract
Abstract
Introduction: Dedifferentiated liposarcomas (DDLPS) are the most frequent high-grade soft tissue sarcoma in adults. From a pathological point of view, these tumors are composed of high-grade undifferentiated tumor cells (DD), often showing an abrupt transition from a compartment of well-differentiated adipocytic tumor cells (WD). Tumor cells from both WD and DD compartments are characterized by recurrent MDM2 amplification, but their cellular origin and the molecular mechanisms associated with dedifferentiation are poorly understood.
Methods: We performed an integrated molecular analysis of tumors collected from 11 patients undergoing surgery for primary untreated DDLPS. DDLPS tumors were analyzed by single-cell RNA sequencing (scRNAseq) and bulk RNA sequencing on paired WD and DD samples from the same tumors. Results were validated in vitro and in vivo in an additional cohort of human tumors, patient-derived xenografts and DDLPS cell lines.
Results: Through RNA-sequencing of 102,753 individual cells from 11 primary DDLPS lesions, major cell clusters were identified based on unsupervised clustering of gene expression profiles and canonical markers. They include 31 tumor microenvironment clusters and 11 tumor cell clusters. A cluster of tumor cells from the WD compartment is characterized by signatures of early adipocytic progenitors, previously identified as TGFβ-dependent, DPP4-positive stromal progenitors. We show that these cells harbor specifically the truncal genomic alterations of the cancer, with further subclonal mutations identifiable in both WD and DD compartments of DDLPS. Furthermore, these cells have multipotent properties and their differentiation towards the adipocytic lineage is inhibited by TGFβ. Treatment of DD tumor cells with TGFβ inhibitors restores their adipocytic phenotype in vitro and in vivo.
Conclusion: We provide the first single-cell atlas of human DDLPS tumor and microenvironment and identify a population of adipocytic tumor progenitors at the origin of both WD and DD compartments. This study provides rationale for the development of therapeutic strategies based on TGFβ inhibition in advanced DDLPS.
Citation Format: Nadège Gruel, Chloé Quignot, Julien Vibert, Sylvie Bonvalot, Sophie El Zein, Dimitri Tzanis, Sylvain Baulande, Odette Mariani, Joshua Waterfall, Olivier Delattre, Sarah Watson. Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 96.
Collapse
|
5
|
Watson S, Gruel N, Quignot C, Vibert J, Bonvalot S, El Zein S, Tzanis D, Baulande S, Mariani O, Waterfall J, Delattre O. 46O Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of tumoral progenitors vulnerable to TGF beta inhibition. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.101083] [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: 04/05/2023] Open
|
6
|
Hamy AS, Abécassis J, Driouch K, Darrigues L, Vandenbogaert M, Laurent C, Zaccarini F, Sadacca B, Delomenie M, Laas E, Mariani O, Lam T, Grandal B, Laé M, Bieche I, Vacher S, Pierga JY, Brain E, Vallot C, Hotton J, Richer W, Rocha D, Tariq Z, Becette V, Meseure D, Lesage L, Vincent-Salomon A, Filmann N, Furlanetto J, Loibl S, Dumas E, Waterfall JJ, Reyal F. Evolution of synchronous female bilateral breast cancers and response to treatment. Nat Med 2023; 29:646-655. [PMID: 36879128 PMCID: PMC10033420 DOI: 10.1038/s41591-023-02216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 01/10/2023] [Indexed: 03/08/2023]
Abstract
Synchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics and environmental exposures. Little evidence exists regarding immune infiltration and response to treatment in sBBCs. Here we show that the impact of the subtype of breast cancer on levels of tumor infiltrating lymphocytes (TILs, n = 277) and on pathologic complete response (pCR) rates (n = 140) differed according to the concordant or discordant subtype of breast cancer of the contralateral tumor: luminal breast tumors with a discordant contralateral tumor had higher TIL levels and higher pCR rates than those with a concordant contralateral tumor. Tumor sequencing revealed that left and right tumors (n = 20) were independent regarding somatic mutations, copy number alterations and clonal phylogeny, whereas primary tumor and residual disease were closely related both from the somatic mutation and from the transcriptomic point of view. Our study indicates that tumor-intrinsic characteristics may have a role in the association of tumor immunity and pCR and demonstrates that the characteristics of the contralateral tumor are also associated with immune infiltration and response to treatment.
Collapse
Affiliation(s)
- Anne-Sophie Hamy
- Department of Medical Oncology, Institut Curie, Université Paris Cité, Paris, France
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
| | - Judith Abécassis
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
- INRIA, Université Paris-Saclay, CEA, Palaiseau, France
| | - Keltouma Driouch
- Pharmacogenomics Unit, Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Lauren Darrigues
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
| | - Mathias Vandenbogaert
- Translational Research Department, Institut Curie Research Center, PSL University, Paris, France
- INSERM U830, Institut Curie, PSL University, Paris, France
| | - Cecile Laurent
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
| | - Francois Zaccarini
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
| | - Benjamin Sadacca
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
- INSERM U830, Institut Curie, PSL University, Paris, France
| | - Myriam Delomenie
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
| | - Enora Laas
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
| | - Odette Mariani
- Biological Resource Center, Department of Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie, PSL University, Paris, France
| | - Thanh Lam
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
- Department of Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Beatriz Grandal
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France
| | - Marick Laé
- Biological Resource Center, Department of Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie, PSL University, Paris, France
- Department of Pathology, Centre Henri Becquerel, INSERM U1245, UNIROUEN, University of Normandie, Rouen, France
| | - Ivan Bieche
- Pharmacogenomics Unit, Department of Genetics, PSL University, Institut Curie, Paris, France
- INSERM U1016, Faculty of Pharmaceutical and Biological Sciences, Université de Paris Cité, Paris, France
| | - Sophie Vacher
- Pharmacogenomics Unit, Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, Université Paris Cité, Paris, France
| | - Etienne Brain
- Department of Medical Oncology, Institut Curie, Université Paris Cité, Paris, France
| | - Celine Vallot
- Translational Research Department, Institut Curie Research Center, PSL University, Paris, France
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
| | - Judicael Hotton
- Department of Surgical Oncology, Institut Godinot, Reims, France
| | - Wilfrid Richer
- Translational Research Department, Institut Curie Research Center, PSL University, Paris, France
- Translational Immunotherapy Team, INSERM U932, Institut Curie, PSL University, Paris, France
| | - Dario Rocha
- Translational Immunotherapy Team, INSERM U932, Institut Curie, PSL University, Paris, France
| | - Zakia Tariq
- Pharmacogenomics Unit, Department of Genetics, PSL University, Institut Curie, Paris, France
| | - Veronique Becette
- Biological Resource Center, Department of Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie, PSL University, Paris, France
| | - Didier Meseure
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | - Laetitia Lesage
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, University Paris-Sciences et Lettres, Paris, France
| | | | | | - Sibylle Loibl
- German Breast Group, Neu-Isenburg, Germany
- Centre for Haematology and Oncology/Bethanien, Frankfurt am Main, Germany
| | - Elise Dumas
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France
| | - Joshua J Waterfall
- Translational Research Department, Institut Curie Research Center, PSL University, Paris, France.
- INSERM U830, Institut Curie, PSL University, Paris, France.
| | - Fabien Reyal
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, Paris, INSERM, U932 Immunity and Cancer, Institut Curie, Université de Paris, Paris, France.
- Department of Breast, Gynecological and Reconstructive Surgery, Institut Curie, Université de Paris Cité, Paris, France.
| |
Collapse
|
7
|
Morretton JP, Simon A, Herbette A, Barbazan J, Pérez-González C, Cosson C, Mboup B, Latouche A, Popova T, Kieffer Y, Macé AS, Gestraud P, Bataillon G, Becette V, Meseure D, Nicolas A, Mariani O, Vincent-Salomon A, Stern MH, Mechta-Grigoriou F, Roman Roman S, Vignjevic DM, Rouzier R, Sastre-Garau X, Goundiam O, Basto R. A catalog of numerical centrosome defects in epithelial ovarian cancers. EMBO Mol Med 2022; 14:e15670. [PMID: 36069081 PMCID: PMC9449595 DOI: 10.15252/emmm.202215670] [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: 01/03/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Centrosome amplification, the presence of more than two centrosomes in a cell is a common feature of most human cancer cell lines. However, little is known about centrosome numbers in human cancers and whether amplification or other numerical aberrations are frequently present. To address this question, we have analyzed a large cohort of primary human epithelial ovarian cancers (EOCs) from 100 patients. We found that rigorous quantitation of centrosome number in tumor samples was extremely challenging due to tumor heterogeneity and extensive tissue disorganization. Interestingly, even if centrosome clusters could be identified, the incidence of centrosome amplification was not comparable to what has been described in cultured cancer cells. Surprisingly, centrosome loss events where a few or many nuclei were not associated with centrosomes were clearly noticed and overall more frequent than centrosome amplification. Our findings highlight the difficulty of characterizing centrosome numbers in human tumors, while revealing a novel paradigm of centrosome number defects in EOCs.
Collapse
Affiliation(s)
- Jean-Philippe Morretton
- Biology of Centrosomes and Genetic Instability, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| | - Anthony Simon
- Biology of Centrosomes and Genetic Instability, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| | - Aurélie Herbette
- Department of Translational Research, Institut Curie, PSL University, Paris Cedex 05, France
| | - Jorge Barbazan
- Migration and Invasion Laboratory, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| | - Carlos Pérez-González
- Migration and Invasion Laboratory, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| | - Camille Cosson
- Department of Translational Research, Institut Curie, PSL University, Paris Cedex 05, France
| | - Bassirou Mboup
- Statistical Methods for Precision Medicine, INSERM U900, Institut Curie, Saint-Cloud, France
| | - Aurélien Latouche
- Statistical Methods for Precision Medicine, INSERM U900, Institut Curie, Saint-Cloud, France
| | - Tatiana Popova
- DNA Repair & Uveal Melanoma (D.R.U.M.), INSERM U830, Institut Curie, PSL Research University, Paris Cedex 05, France
| | - Yann Kieffer
- Stress and Cancer Laboratory, INSERM U830, Institut Curie, Team Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Anne-Sophie Macé
- Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Paris, France
| | - Pierre Gestraud
- Bioinformatics and Computational Systems Biology of Cancer, Mines Paristech, INSERM U900, Institut Curie, PSL University, Paris Cedex 05, France
| | | | | | - Didier Meseure
- Department of Pathology, Institut Curie, Paris Cedex 05, France
| | - André Nicolas
- Department of Pathology, Institut Curie, Paris Cedex 05, France
| | - Odette Mariani
- Department of Pathology, Institut Curie, Paris Cedex 05, France.,Biological Resource Center, Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | | | - Marc-Henri Stern
- DNA Repair & Uveal Melanoma (D.R.U.M.), INSERM U830, Institut Curie, PSL Research University, Paris Cedex 05, France
| | - Fatima Mechta-Grigoriou
- Stress and Cancer Laboratory, INSERM U830, Institut Curie, Team Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Sergio Roman Roman
- Department of Translational Research, Institut Curie, PSL University, Paris Cedex 05, France
| | - Danijela Matic Vignjevic
- Migration and Invasion Laboratory, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| | - Roman Rouzier
- Statistical Methods for Precision Medicine, INSERM U900, Institut Curie, Saint-Cloud, France.,Department of Surgery, Institut Curie, Saint-Cloud, France.,UFR Simone Veil - Santé, Université Versailles Saint Quentin, Université Paris Saclay, Montigny le Bretonneux, France
| | | | - Oumou Goundiam
- Department of Translational Research, Institut Curie, PSL University, Paris Cedex 05, France
| | - Renata Basto
- Biology of Centrosomes and Genetic Instability, Institut Curie, PSL Research University, CNRS UMR 144, Paris, France
| |
Collapse
|
8
|
Fimereli D, Venet D, Rediti M, Boeckx B, Maetens M, Majjaj S, Rouas G, Marchio C, Bertucci F, Mariani O, Capra M, Bonizzi G, Contaldo F, Galant C, Van den Eynden G, Salgado R, Biganzoli E, Vincent-Salomon A, Pruneri G, Larsimont D, Lambrechts D, Desmedt C, Brown DN, Rothé F, Sotiriou C. Timing evolution of lobular breast cancer through phylogenetic analysis. EBioMedicine 2022; 82:104169. [PMID: 35882101 PMCID: PMC9309404 DOI: 10.1016/j.ebiom.2022.104169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Danai Fimereli
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - David Venet
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Mattia Rediti
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marion Maetens
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium; Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samira Majjaj
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ghizlane Rouas
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Caterina Marchio
- Department of Medical Sciences, University of Turin, Turin, Italy; FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Francois Bertucci
- Predictive Oncology Laboratory, Institut Paoli-Calmettes, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille Université Marseille, France
| | - Odette Mariani
- Department of Pathology, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Maria Capra
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppina Bonizzi
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Contaldo
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Christine Galant
- Department of Pathology, Cliniques Universitaires Saint Luc, Brussels, Belgium; IREC, Université Catholique de Louvain, Brussels, Belgium
| | | | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium; Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Elia Biganzoli
- Department of Biomedical and Clinical Sciences (DIBIC) "L. Sacco" & DSRC, LITA Vialba campus, University of Milan, Milan, Italy
| | - Anne Vincent-Salomon
- Department of Pathology, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Giancarlo Pruneri
- Division of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; School of Medicine, University of Milan, Milano, Milan, Italy
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Brussels, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - David N Brown
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Françoise Rothé
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Christos Sotiriou
- J.-C. Heuson Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
| |
Collapse
|
9
|
Liu J, Ottaviani D, Sefta M, Desbrousses C, Chapeaublanc E, Aschero R, Sirab N, Lubieniecki F, Lamas G, Tonon L, Dehainault C, Hua C, Fréneaux P, Reichman S, Karboul N, Biton A, Mirabal-Ortega L, Larcher M, Brulard C, Arrufat S, Nicolas A, Elarouci N, Popova T, Némati F, Decaudin D, Gentien D, Baulande S, Mariani O, Dufour F, Guibert S, Vallot C, Rouic LLL, Matet A, Desjardins L, Pascual-Pasto G, Suñol M, Catala-Mora J, Llano GC, Couturier J, Barillot E, Schaiquevich P, Gauthier-Villars M, Stoppa-Lyonnet D, Golmard L, Houdayer C, Brisse H, Bernard-Pierrot I, Letouzé E, Viari A, Saule S, Sastre-Garau X, Doz F, Carcaboso AM, Cassoux N, Pouponnot C, Goureau O, Chantada G, de Reyniès A, Aerts I, Radvanyi F. A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression. Nat Commun 2021; 12:5578. [PMID: 34552068 PMCID: PMC8458383 DOI: 10.1038/s41467-021-25792-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma is the most frequent intraocular malignancy in children, originating from a maturing cone precursor in the developing retina. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using multi-omics data, we demonstrate the existence of two retinoblastoma subtypes. Subtype 1, of earlier onset, includes most of the heritable forms. It harbors few genetic alterations other than the initiating RB1 inactivation and corresponds to differentiated tumors expressing mature cone markers. By contrast, subtype 2 tumors harbor frequent recurrent genetic alterations including MYCN-amplification. They express markers of less differentiated cone together with neuronal/ganglion cell markers with marked inter- and intra-tumor heterogeneity. The cone dedifferentiation in subtype 2 is associated with stemness features including low immune and interferon response, E2F and MYC/MYCN activation and a higher propensity for metastasis. The recognition of these two subtypes, one maintaining a cone-differentiated state, and the other, more aggressive, associated with cone dedifferentiation and expression of neuronal markers, opens up important biological and clinical perspectives for retinoblastomas.
Collapse
Affiliation(s)
- Jing Liu
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013, Paris, France
| | - Daniela Ottaviani
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Meriem Sefta
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Céline Desbrousses
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Elodie Chapeaublanc
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Rosario Aschero
- Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Nanor Sirab
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | | | - Gabriela Lamas
- Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de Bioinformatique "Gilles Thomas", Centre Léon Bérard, 69008, Lyon, France
| | - Catherine Dehainault
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Service de Génétique, Institut Curie, 75005, Paris, France
| | - Clément Hua
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Paul Fréneaux
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
| | - Sacha Reichman
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012, Paris, France
| | - Narjesse Karboul
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Anne Biton
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Institut Curie, PSL Research University, INSERM, U900, 75005, Paris, France
- Ecole des Mines ParisTech, 77305, Fontainebleau, France
- Institut Pasteur - Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, 75015, Paris, France
| | - Liliana Mirabal-Ortega
- Institut Curie, CNRS, UMR3347, PSL Research University, 91405, Orsay, France
- Institut Curie, PSL Research University, INSERM, U1021, 91405, Orsay, France
- Université Paris-Saclay, 91405, Orsay, France
| | - Magalie Larcher
- Institut Curie, CNRS, UMR3347, PSL Research University, 91405, Orsay, France
- Institut Curie, PSL Research University, INSERM, U1021, 91405, Orsay, France
- Université Paris-Saclay, 91405, Orsay, France
| | - Céline Brulard
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- INSERM U930, CHU Bretonneau, 37000, Tours, France
| | - Sandrine Arrufat
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
| | - André Nicolas
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013, Paris, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, INSERM U830, 75005, Paris, France
| | - Fariba Némati
- Département de Recherche Translationnelle, Institut Curie, 75005, Paris, France
| | - Didier Decaudin
- Département de Recherche Translationnelle, Institut Curie, 75005, Paris, France
| | - David Gentien
- Département de Recherche Translationnelle, Institut Curie, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, NGS Platform, 75005, Paris, France
| | - Odette Mariani
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
| | - Florent Dufour
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | | | - Céline Vallot
- GeCo Genomics Consulting, Integragen, 91000, Evry, France
| | | | - Alexandre Matet
- Département de Chirurgie, Service d'Ophtalmologie, Institut Curie, 75005, Paris, France
- Université de Paris, Paris, France
| | - Laurence Desjardins
- Département de Chirurgie, Service d'Ophtalmologie, Institut Curie, 75005, Paris, France
| | - Guillem Pascual-Pasto
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
| | - Mariona Suñol
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Department of Pathology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
| | - Jaume Catala-Mora
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Department of Ophthalmology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
| | - Genoveva Correa Llano
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
| | - Jérôme Couturier
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, INSERM, U900, 75005, Paris, France
- Ecole des Mines ParisTech, 77305, Fontainebleau, France
| | - Paula Schaiquevich
- Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Marion Gauthier-Villars
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Service de Génétique, Institut Curie, 75005, Paris, France
- Institut Curie, PSL Research University, INSERM U830, 75005, Paris, France
| | - Dominique Stoppa-Lyonnet
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Service de Génétique, Institut Curie, 75005, Paris, France
- Université de Paris, Paris, France
| | - Lisa Golmard
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Service de Génétique, Institut Curie, 75005, Paris, France
- Institut Curie, PSL Research University, INSERM U830, 75005, Paris, France
| | - Claude Houdayer
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Service de Génétique, Institut Curie, 75005, Paris, France
- Institut Curie, PSL Research University, INSERM U830, 75005, Paris, France
- Department of Genetics, Rouen University Hospital, 76000, Rouen, France
| | - Hervé Brisse
- Département d'Imagerie Médicale, Institut Curie, 75005, Paris, France
| | - Isabelle Bernard-Pierrot
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Eric Letouzé
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, 75006, Paris, France
- Functional Genomics of Solid Tumors, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de Bioinformatique "Gilles Thomas", Centre Léon Bérard, 69008, Lyon, France
| | - Simon Saule
- Institut Curie, CNRS, UMR3347, PSL Research University, 91405, Orsay, France
- Institut Curie, PSL Research University, INSERM, U1021, 91405, Orsay, France
- Université Paris-Saclay, 91405, Orsay, France
| | - Xavier Sastre-Garau
- Département de Biologie des Tumeurs, Institut Curie, 75005, Paris, France
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 94000, Créteil, France
| | - François Doz
- Université de Paris, Paris, France
- SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005, Paris, France
| | - Angel M Carcaboso
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
| | - Nathalie Cassoux
- Département de Chirurgie, Service d'Ophtalmologie, Institut Curie, 75005, Paris, France
- Université de Paris, Paris, France
| | - Celio Pouponnot
- Institut Curie, CNRS, UMR3347, PSL Research University, 91405, Orsay, France
- Institut Curie, PSL Research University, INSERM, U1021, 91405, Orsay, France
- Université Paris-Saclay, 91405, Orsay, France
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012, Paris, France
| | - Guillermo Chantada
- Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina
- Institut de Recerca Sant Joan de Déu, 08950, Barcelona, Spain
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950, Barcelona, Spain
- National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013, Paris, France
| | - Isabelle Aerts
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005, Paris, France
| | - François Radvanyi
- Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005, Paris, France.
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France.
| |
Collapse
|
10
|
Vibert J, Pierron G, Benoist C, Gruel N, Guillemot D, Vincent-Salomon A, Le Tourneau C, Livartowski A, Mariani O, Baulande S, Bidard FC, Delattre O, Waterfall JJ, Watson S. Identification of Tissue of Origin and Guided Therapeutic Applications in Cancers of Unknown Primary Using Deep Learning and RNA Sequencing (TransCUPtomics). J Mol Diagn 2021; 23:1380-1392. [PMID: 34325056 DOI: 10.1016/j.jmoldx.2021.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/14/2021] [Accepted: 07/14/2021] [Indexed: 01/04/2023] Open
Abstract
Cancers of unknown primary (CUP) are metastatic cancers for which the primary tumor is not found despite thorough diagnostic investigations. Multiple molecular assays have been proposed to identify the tissue of origin (TOO) and inform clinical care; however, none has been able to combine accuracy, interpretability, and easy access for routine use. We developed a classifier tool based on the training of a variational autoencoder to predict tissue of origin based on RNA-sequencing data. We used as training data 20,918 samples corresponding to 94 different categories, including 39 cancer types and 55 normal tissues. The TransCUPtomics classifier was applied to a retrospective cohort of 37 CUP patients and 11 prospective patients. TransCUPtomics exhibited an overall accuracy of 96% on reference data for TOO prediction. The TOO could be identified in 38 (79%) of 48 CUP patients. Eight of 11 prospective CUP patients (73%) could receive first-line therapy guided by TransCUPtomics prediction, with responses observed in most patients. The variational autoencoder added further utility by enabling prediction interpretability, and diagnostic predictions could be matched to detection of gene fusions and expressed variants. TransCUPtomics confidently predicted TOO for CUP and enabled tailored treatments leading to significant clinical responses. The interpretability of our approach is a powerful addition to improve the management of CUP patients.
Collapse
Affiliation(s)
- Julien Vibert
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
| | - Gaëlle Pierron
- Somatic Genetics Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | - Camille Benoist
- Clinical Bioinformatic Unit, Department of Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Nadège Gruel
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Delphine Guillemot
- Somatic Genetics Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation, INSERM U900, Paris-Saclay University, Institut Curie Hospital and Research Center, Paris and Saint-Cloud
| | - Alain Livartowski
- Department of Medical Oncology, Institut Curie Hospital, Paris, France
| | - Odette Mariani
- Department of Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie Hospital, Paris, France; INSERM CIC-BT 1428, UVSQ, Paris-Saclay University, Saint-Cloud, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Somatic Genetics Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | - Joshua J Waterfall
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France; INSERM U830, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe Labellisée Ligue Nationale Contre le Cancer, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Medical Oncology, Institut Curie Hospital, Paris, France.
| |
Collapse
|
11
|
Petak I, Kamal M, Dirner A, Bieche I, Doczi R, Mariani O, Filotas P, Salomon A, Vodicska B, Servois V, Varkondi E, Gentien D, Tihanyi D, Tresca P, Lakatos D, Servant N, Deri J, du Rusquec P, Hegedus C, Bello Roufai D, Schwab R, Dupain C, Valyi-Nagy IT, Le Tourneau C. A computational method for prioritizing targeted therapies in precision oncology: performance analysis in the SHIVA01 trial. NPJ Precis Oncol 2021; 5:59. [PMID: 34162980 PMCID: PMC8222375 DOI: 10.1038/s41698-021-00191-2] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/13/2021] [Indexed: 01/25/2023] Open
Abstract
Precision oncology is currently based on pairing molecularly targeted agents (MTA) to predefined single driver genes or biomarkers. Each tumor harbors a combination of a large number of potential genetic alterations of multiple driver genes in a complex system that limits the potential of this approach. We have developed an artificial intelligence (AI)-assisted computational method, the digital drug-assignment (DDA) system, to prioritize potential MTAs for each cancer patient based on the complex individual molecular profile of their tumor. We analyzed the clinical benefit of the DDA system on the molecular and clinical outcome data of patients treated in the SHIVA01 precision oncology clinical trial with MTAs matched to individual genetic alterations or biomarkers of their tumor. We found that the DDA score assigned to MTAs was significantly higher in patients experiencing disease control than in patients with progressive disease (1523 versus 580, P = 0.037). The median PFS was also significantly longer in patients receiving MTAs with high (1000+ <) than with low (<0) DDA scores (3.95 versus 1.95 months, P = 0.044). Our results indicate that AI-based systems, like DDA, are promising new tools for oncologists to improve the clinical benefit of precision oncology.
Collapse
Affiliation(s)
- Istvan Petak
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, USA.
- Oncompass Medicine, Budapest, Hungary.
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France
| | | | - Ivan Bieche
- Pharmacogenomics unit, Institut Curie, Paris, France
| | | | - Odette Mariani
- Department of Biopathology, Institut Curie, Paris, France
| | | | - Anne Salomon
- Department of Biopathology, Institut Curie, Paris, France
| | | | | | | | - David Gentien
- Translational Research Department, Institut Curie, Paris, France
| | | | - Patricia Tresca
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France
| | | | | | | | - Pauline du Rusquec
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France
| | | | - Diana Bello Roufai
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France
| | | | - Celia Dupain
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France
| | - Istvan T Valyi-Nagy
- Central Hospital of Southern Pest-National Institute for Hematology and Infectious Diseases, Budapest, Hungary.
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institute Curie, Paris & Saint-Cloud, France.
- INSERM U900 Research Unit, Paris & Saint-Cloud, France.
- Paris-Saclay University, Paris, France.
| |
Collapse
|
12
|
Derrien AC, Rodrigues M, Eeckhoutte A, Dayot S, Houy A, Mobuchon L, Gardrat S, Lequin D, Ballet S, Pierron G, Alsafadi S, Mariani O, El-Marjou A, Matet A, Colas C, Cassoux N, Stern MH. Germline MBD4 Mutations and Predisposition to Uveal Melanoma. J Natl Cancer Inst 2021; 113:80-87. [PMID: 32239153 PMCID: PMC7781447 DOI: 10.1093/jnci/djaa047] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Uveal melanoma (UM) arises from malignant transformation of melanocytes in the uveal tract of the eye. This rare tumor has a poor outcome with frequent chemo-resistant liver metastases. BAP1 is the only known predisposing gene for UM. UMs are generally characterized by low tumor mutation burden, but some UMs display a high level of CpG>TpG mutations associated with MBD4 inactivation. Here, we explored the incidence of germline MBD4 variants in a consecutive series of 1093 primary UM case patients and a series of 192 UM tumors with monosomy 3 (M3). Methods We performed MBD4 targeted sequencing on pooled germline (n = 1093) and tumor (n = 192) DNA samples of UM patients. MBD4 variants (n = 28) were validated by Sanger sequencing. We performed whole-exome sequencing on available tumor samples harboring MBD4 variants (n = 9). Variants of unknown pathogenicity were further functionally assessed. Results We identified 8 deleterious MBD4 mutations in the consecutive UM series, a 9.15-fold (95% confidence interval = 4.24-fold to 19.73-fold) increased incidence compared with the general population (Fisher exact test, P = 2.00 × 10–5, 2-sided), and 4 additional deleterious MBD4 mutations in the M3 cohort, including 3 germline and 1 somatic mutations. Tumors carrying deleterious MBD4 mutations were all associated with high tumor mutation burden and a CpG>TpG hypermutator phenotype. Conclusions We demonstrate that MBD4 is a new predisposing gene for UM associated with hypermutated M3 tumors. The tumor spectrum of this predisposing condition will likely expand with the addition of MBD4 to diagnostic panels. Tumors arising in such a context should be recognized because they may respond to immunotherapy.
Collapse
Affiliation(s)
- Anne-Céline Derrien
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Manuel Rodrigues
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Eeckhoutte
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Stéphane Dayot
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Lenha Mobuchon
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Sophie Gardrat
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Delphine Lequin
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Stelly Ballet
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Samar Alsafadi
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Odette Mariani
- Biological Resource Center, Institut Curie, PSL Research University, Paris, France
| | - Ahmed El-Marjou
- Institut Curie, PSL Research University, UMR144, Recombinant Protein Facility, Paris, France
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, Paris, France.,Faculty of Medicine, University of Paris Descartes, Paris, France
| | | | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France.,Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Genetics, Institut Curie, Paris, France
| |
Collapse
|
13
|
Moreira A, Poulet A, Masliah-Planchon J, Lecerf C, Vacher S, Larbi Chérif L, Dupain C, Marret G, Girard E, Syx L, Hoffmann C, Jeannot E, Klijanienko J, Guillou I, Mariani O, Dubray-Vautrin A, Badois N, Lesnik M, Choussy O, Calugaru V, Borcoman E, Baulande S, Legoix P, Albaud B, Servant N, Bieche I, Le Tourneau C, Kamal M. Prognostic value of tumor mutational burden in patients with oral cavity squamous cell carcinoma treated with upfront surgery. ESMO Open 2021; 6:100178. [PMID: 34118772 PMCID: PMC8207209 DOI: 10.1016/j.esmoop.2021.100178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/15/2021] [Revised: 04/19/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022] Open
Abstract
Background Oral cavity is the most prevalent site of head and neck squamous cell carcinomas (HNSCCs). Most often diagnosed at a locally advanced stage, treatment is multimodal with surgery as the cornerstone. The aim of this study was to explore the molecular landscape of a homogenous cohort of oral cavity squamous cell carcinomas (OCSCCs), and to assess the prognostic value of tumor mutational burden (TMB), along with classical molecular and clinical parameters. Patients and methods One hundred and fifty-one consecutive patients with OCSCC treated with upfront surgery at the Institut Curie were analyzed. Sequencing of tumor DNA from frozen specimens was carried out using an in-house targeted next-generation sequencing panel (571 genes). The impact of molecular alterations and TMB on disease-free survival (DFS) and overall survival (OS) was evaluated in univariate and multivariate analyses. Results Pathological tumor stage, extranodal spread, vascular emboli, and perineural invasion were associated with both DFS and OS. TP53 was the most mutated gene (71%). Other frequent molecular alterations included the TERT promoter (50%), CDKN2A (25%), FAT1 (17%), PIK3CA (14%), and NOTCH1 (15%) genes. Transforming growth factor-β pathway alterations (4%) were associated with poor OS (P = 0.01) and DFS (P = 0.02) in univariate and multivariate analyses. High TMB was associated with prolonged OS (P = 0.01 and P = 0.02, in the highest 10% and 20% TMB values, respectively), but not with DFS. Correlation of TMB with OS remained significant in multivariate analysis (P = 0.01 and P = 0.005 in the highest 10% and 20% TMB values, respectively). Pathological tumor stage combined with high TMB was associated with good prognosis. Conclusion Our results suggest that a high TMB is associated with a favorable prognosis in patients with OCSCC treated with upfront surgery. High TMB is associated with a favorable prognosis in patients with OCSCC treated with upfront surgery Pathological tumor stage combined with high TMB is associated with good prognosis TP53 was the most mutated gene (71%). Other frequent molecular alterations included the TERT promoter (50%) TGFβ pathway alterations were associated with poor outcomes, although it was only observed in 4% of the patients
Collapse
Affiliation(s)
- A Moreira
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - A Poulet
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - J Masliah-Planchon
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - C Lecerf
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - S Vacher
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - L Larbi Chérif
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - C Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - G Marret
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - E Girard
- INSERM U900 Research Unit, Institut Curie, Paris and Saint-Cloud, France
| | - L Syx
- INSERM U900 Research Unit, Institut Curie, Paris and Saint-Cloud, France
| | - C Hoffmann
- INSERM U932 Research Unit, Institut Curie, PSL Research University, Paris, France; Department of Oncologic Surgery, Institut Curie, PSL Research University, Paris, France
| | - E Jeannot
- Department of Genetics, Institut Curie, PSL Research University, Paris, France; Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - J Klijanienko
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - I Guillou
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - O Mariani
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - A Dubray-Vautrin
- Department of Oncologic Surgery, Institut Curie, PSL Research University, Paris, France
| | - N Badois
- Department of Oncologic Surgery, Institut Curie, PSL Research University, Paris, France
| | - M Lesnik
- Department of Oncologic Surgery, Institut Curie, PSL Research University, Paris, France
| | - O Choussy
- Department of Oncologic Surgery, Institut Curie, PSL Research University, Paris, France
| | - V Calugaru
- Department of Oncologic Radiotherapy, Institut Curie, PSL Research University, Paris, France
| | - E Borcoman
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - S Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Paris, France
| | - P Legoix
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Paris, France
| | - B Albaud
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Paris, France
| | - N Servant
- INSERM U900 Research Unit, Institut Curie, Paris and Saint-Cloud, France
| | - I Bieche
- Department of Genetics, Institut Curie, PSL Research University, Paris, France; INSERM U1016, Paris Descartes University, Faculty of Pharmaceutical and Biological Sciences, Paris, France
| | - C Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France; INSERM U900 Research Unit, Institut Curie, Paris and Saint-Cloud, France; Paris-Saclay University, Paris, France
| | - M Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France.
| |
Collapse
|
14
|
Tu Z, Schmoellerl J, Mariani O, Zheng Y, Hu Y, Vincent-Salomon A, Karnoub AE. The LINC01119-SOCS5 axis as a critical theranostic in triple-negative breast cancer. NPJ Breast Cancer 2021; 7:69. [PMID: 34059683 PMCID: PMC8166834 DOI: 10.1038/s41523-021-00259-z] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 04/09/2021] [Indexed: 02/04/2023] Open
Abstract
The development of triple-negative breast cancer (TNBC) is critically regulated by certain tumor-microenvironment-associated cells called mesenchymal stem/stromal cells (MSCs), which we and others have shown promote TNBC progression by activating pro-malignant signaling in neighboring cancer cells. Characterization of these cascades would better our understanding of TNBC biology and bring about therapeutics that eliminate the morbidity and mortality associated with advanced disease. Here, we focused on the emerging class of RNAs called long non-coding RNAs or lncRNAs and utilized a MSC-supported TNBC progression model to identify specific family members of functional relevance to TNBC pathogenesis. Indeed, although some have been described to play functional roles in TNBC, activities of lncRNAs as mediators of tumor-microenvironment-driven TNBC development remain to be fully explored. We report that MSCs stimulate robust expression of LINC01119 in TNBC cells, which in turn induces suppressor of cytokine signaling 5 (SOCS5), leading to accelerated cancer cell growth and tumorigenesis. We show that LINC01119 and SOCS5 exhibit tight correlation across multiple breast cancer gene sets and that they are highly enriched in TNBC patient cohorts. Importantly, we present evidence that the LINC01119-SOCS5 axis represents a powerful prognostic indicator of adverse outcomes in TNBC patients, and demonstrate that its repression severely impairs cancer cell growth. Altogether, our findings identify LINC01119 as a major driver of TNBC development and delineate critical non-coding RNA theranostics of potential translational utility in the management of advanced TNBC, a class of tumors in most need of effective and targeted therapy.
Collapse
Affiliation(s)
- Zhenbo Tu
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Johannes Schmoellerl
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Yurong Zheng
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yi Hu
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Antoine E Karnoub
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
15
|
Dupain C, Masliah‐Planchon J, Gu C, Girard E, Gestraud P, Du Rusquec P, Borcoman E, Bello D, Ricci F, Hescot S, Sablin M, Tresca P, de Moura A, Loirat D, Frelaut M, Vincent‐Salomon A, Lecerf C, Callens C, Antonio S, Franck C, Mariani O, Bièche I, Kamal M, Le Tourneau C, Servois V. Fine-needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next-generation sequencing in cancer patients included in the SHIVA02 trial. Mol Oncol 2021; 15:104-115. [PMID: 32750212 PMCID: PMC7782085 DOI: 10.1002/1878-0261.12776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
High-throughput molecular profiling of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations, with around 70% success rate. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of the less invasive fine-needle aspiration (FNA) compared to CNB to detect molecular alterations. We aimed to prospectively evaluate the potential of FNA to detect such alterations in various tumour types as compared to CNB in cancer patients included in the SHIVA02 trial. An in-house amplicon-based targeted sequencing panel (Illumina TSCA 99.3 kb panel covering 87 genes) was used to identify pathogenic variants and gene copy number variations (CNV) in concomitant CNB and FNA samples obtained from 61 patients enrolled in the SHIVA02 trial (NCT03084757). The main tumour types analysed were breast (38%), colon (15%), pancreas (11%), followed by cervix and stomach (7% each). We report 123 molecular alterations (85 variants, 23 amplifications and 15 homozygous deletions) among which 98 (80%) were concordant between CNB and FNA. The remaining discordances were mainly related to deletions status, yet undetected alterations were not exclusively specific to FNA. Comparative analysis of molecular alterations in CNB and FNA showed high concordance in terms of variants as well as CNVs identified. We conclude FNA could therefore be used in routine diagnostics workflow and clinical trials for tumour molecular profiling with the advantages of being minimally invasive and preserve tissue material needed for diagnostic, prognostic or theranostic purposes.
Collapse
Affiliation(s)
- Célia Dupain
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | | | - Céline Gu
- Department of PathologyInstitut CuriePSL Research UniversityParisFrance
| | - Elodie Girard
- INSERM U900 Research UnitInstitut CurieSaint‐CloudFrance
| | | | - Pauline Du Rusquec
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Edith Borcoman
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Diana Bello
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Francesco Ricci
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Ségolène Hescot
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Marie‐Paule Sablin
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Patricia Tresca
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Alexandre de Moura
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Delphine Loirat
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Maxime Frelaut
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | | | - Charlotte Lecerf
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Céline Callens
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Samantha Antonio
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Coralie Franck
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Odette Mariani
- Department of PathologyInstitut CuriePSL Research UniversityParisFrance
| | - Ivan Bièche
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
- INSERM U1016Faculty of Pharmaceutical and Biological SciencesParis Descartes UniversityParisFrance
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
- INSERM U900 Research UnitInstitut CurieSaint‐CloudFrance
- Paris‐Saclay UniversityParisFrance
| | - Vincent Servois
- Department of RadiologyInstitut CuriePSL Research UniversityParis & Saint‐CloudFrance
| |
Collapse
|
16
|
Richard F, Majjaj S, Venet D, Rothé F, Pingitore J, Boeckx B, Marchio C, Clatot F, Bertucci F, Mariani O, Galant C, Eynden GVD, Salgado R, Biganzoli E, Lambrechts D, Vincent-Salomon A, Pruneri G, Larsimont D, Sotiriou C, Desmedt C. Characterization of Stromal Tumor-infiltrating Lymphocytes and Genomic Alterations in Metastatic Lobular Breast Cancer. Clin Cancer Res 2020; 26:6254-6265. [PMID: 32943456 DOI: 10.1158/1078-0432.ccr-20-2268] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/12/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Invasive lobular carcinoma (ILC) represents the second most common histologic breast cancer subtype after invasive ductal carcinoma (IDC). While primary ILC has been extensively studied, metastatic ILC has been poorly characterized at the genomic and immune level. EXPERIMENTAL DESIGN We retrospectively assembled the multicentric EuroILC series of matched primary and metastatic samples from 94 patients with estrogen receptor (ER)-positive ILC. Stromal tumor-infiltrating lymphocytes (sTILs) were assessed by experienced pathologists. Targeted sequencing and low pass whole-genome sequencing were conducted to detect mutations and copy-number aberrations (CNAs). We compared the frequencies of the alterations in EuroILC with those from patients with ER-positive metastatic ILC (n = 135) and IDC (n = 563) from MSK-IMPACT. RESULTS Low sTIL levels were observed in ILC metastases, with higher levels in the mixed nonclassic histology. Considering ILC metastases from EuroILC and MSK-IMPACT, we observed that >50% of tumors harbor genomic alterations that have previously been associated with endocrine resistance. A matched primary/metastasis comparison in EuroILC revealed mutations (AKT1, ARID1A, ESR1, ERBB2, or NF1) and CNAs (PTEN or NF1 deletion, CYP19A1 amplification) associated with endocrine resistance that were private to the metastasis in 22% (7/32) and 19% (4/21) of patients, respectively. An increase in CDH1, ERBB2, FOXA1, and TBX3 mutations, in CDH1 deletions and a decrease in TP53 mutations was observed in ILC as compared with IDC metastases. CONCLUSIONS ILC metastases harbor genomic alterations that may potentially explain endocrine resistance in a large proportion of patients, and present genomic differences as compared with IDC metastases.
Collapse
Affiliation(s)
- François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samira Majjaj
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, U-CRC, Brussels, Belgium
| | - David Venet
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, U-CRC, Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, U-CRC, Brussels, Belgium
| | - Julien Pingitore
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, U-CRC, Brussels, Belgium
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Caterina Marchio
- Department of Medical Sciences, University of Turin, Turin, Italy.,FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Florian Clatot
- Department of Medical Oncology, Centre Henri-Becquerel, Rouen, France.,Rouen University Hospital, IRON/Inserm U1245, Rouen, France
| | - François Bertucci
- Predictive Oncology Laboratory, Institut Paoli-Calmettes, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille Université, Marseille, France
| | - Odette Mariani
- Department of Pathology, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Christine Galant
- Department of Pathology, Cliniques Universitaires Saint Luc, Brussels, Belgium
| | | | | | - Elia Biganzoli
- Unit of Medical Statistics, Biometry and Bioinformatics "Giulio A. Maccacaro," Department of Clinical Sciences and Community Health, University of Milan, Campus Cascina Rosa, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Anne Vincent-Salomon
- Department of Pathology, Institut Curie, Paris Sciences Lettres Research University, Paris, France
| | - Giancarlo Pruneri
- Division of Pathology, European Institute of Oncology, University of Milan, Milan, Italy.,Division of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,School of Medicine, University of Milan, Milan, Italy
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, U-CRC, Brussels, Belgium.
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium.
| |
Collapse
|
17
|
Pareja F, Lee JY, Brown DN, Piscuoglio S, Gularte-Mérida R, Selenica P, Da Cruz Paula A, Arunachalam S, Kumar R, Geyer FC, Silveira C, da Silva EM, Li A, Marchiò C, Ng CKY, Mariani O, Fuhrmann L, Wen HY, Norton L, Vincent-Salomon A, Brogi E, Reis-Filho JS, Weigelt B. The Genomic Landscape of Mucinous Breast Cancer. J Natl Cancer Inst 2020; 111:737-741. [PMID: 30649385 DOI: 10.1093/jnci/djy216] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/18/2018] [Accepted: 11/19/2018] [Indexed: 12/13/2022] Open
Abstract
Mucinous carcinoma of the breast (MCB) is a rare histologic form of estrogen receptor (ER)-positive/HER2-negative breast cancer (BC) characterized by tumor cells floating in lakes of mucin. We assessed the genomic landscape of 32 MCBs by whole-exome sequencing and/or RNA-sequencing. GATA3 (23.8%), KMT2C (19.0%), and MAP3K1 (14.3%) were the most frequently mutated genes in pure MCBs. In addition, two recurrent but not pathognomonic fusion genes, OAZ1-CSNK1G2 and RFC4-LPP, were detected in 3/31 (9.7%) and 2/31 (6.5%) samples, respectively. Compared with ER-positive/HER2-negative common forms of BC, MCBs displayed lower PIK3CA and TP53 mutation rates and fewer concurrent 1q gains and 16q losses. Clonal decomposition analysis of the mucinous and ductal components independently microdissected from five mixed MCBs revealed that they are clonally related and evolve following clonal selection or parallel evolution. Our findings indicate that MCB represents a genetically distinct ER-positive/HER2-negative form of BC.
Collapse
Affiliation(s)
- Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sasi Arunachalam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Catarina Silveira
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,GenoMed SA, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caterina Marchiò
- Department of Medical Sciences, FPO-Canndiolo Cancer Institute, University of Turin, Turin, Italy
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Odette Mariani
- Départment de Médecine Diagnostique et Théranostique, Institute Curie, Paris, France
| | - Laetitia Fuhrmann
- Départment de Médecine Diagnostique et Théranostique, Institute Curie, Paris, France
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anne Vincent-Salomon
- Départment de Médecine Diagnostique et Théranostique, Institute Curie, Paris, France
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
18
|
Morretton JP, Herbette A, Cosson C, Mboup B, Latouche A, Gestraud P, Popova T, Stern MH, Nemati F, Decaudin D, Bataillon G, Becette V, Meseure D, Nicolas A, Mariani O, Bonneau C, Barbazan J, Vincent-Salomon A, Mechta-Grigoriou F, Roman-Roman S, Rouzier R, Sastre-Garau X, Goundiam O, Basto R. Abstract A43: Centrosome amplification favors survival and impairs ovarian cancer progression. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-a43] [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
Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. The most common subtype of EOC is high-grade serous (HGSOC), which responds at least initially to chemotherapy but has a worse overall prognosis. Genomic, transcriptomic, and proteogenomic profiling of HGSOC suggested a whole spectrum of molecular diversity, including homologous recombination pathway deficiencies (HRD). The centrosome is the main microtubule (MT)-organizing center of animal cells. It facilitates the accuracy of chromosome segregation during mitosis and influences cell polarity and migration. The presence of more than two centrosomes in a cell, centrosome amplification, has long been associated with tumorigenesis. However, little is known about the real status of centrosome numbers in human cancers and whether numerical alterations are solely associated with poor prognosis. We screened 100 samples of primary EOCs including 88 HGSOC, using immunofluorescence and state-of-the-art microscopy, to determine the centrosome-nucleus index (CNI). We integrated these data with genomic alterations, HRD status, and patient outcome. We found that EOCs are highly heterogeneous, with infrequent but strong centrosome amplifications leading to higher CNI than in healthy tissues. Strikingly, while a correlation between CNI and genomic alterations, such as aneuploidy or chromosome rearrangements, could not be established, we found that high CNI correlates with increased patient survival and sensitivity to chemotherapy, independently of HRD status. Using ovarian cancer cellular models to manipulate centrosome numbers and patient-derived xenografts (PDXs), we found that higher CNIs can positively impact the response to chemotherapy and inhibit peritoneal cell dissemination.
Citation Format: Jean-Philippe Morretton, Aurelie Herbette, Camille Cosson, Bassirou Mboup, Aurelien Latouche, Pierre Gestraud, Tatiana Popova, Marc-Henri Stern, Fariba Nemati, Didier Decaudin, Guillaume Bataillon, Veronique Becette, Didier Meseure, Andre Nicolas, Odette Mariani, Claire Bonneau, Jorge Barbazan, Anne Vincent-Salomon, Fatima Mechta-Grigoriou, Sergio Roman-Roman, Roman Rouzier, Xavier Sastre-Garau, Oumou Goundiam, Renata Basto. Centrosome amplification favors survival and impairs ovarian cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A43.
Collapse
|
19
|
Hoffmann C, Vacher S, Sirven P, Lecerf C, Massenet L, Moreira A, Surun A, Schnitzler A, Klijanienko J, Mariani O, Jeannot E, Badois N, Lesnik M, Choussy O, Le Tourneau C, Guillot-Delost M, Kamal M, Bieche I, Soumelis V. MMP2 as an independent prognostic stratifier in oral cavity cancers. Oncoimmunology 2020; 9:1754094. [PMID: 32934875 PMCID: PMC7466851 DOI: 10.1080/2162402x.2020.1754094] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Around 25% of oral cavity squamous cell carcinoma (OCSCC) are not controlled by the standard of care, but there is currently no validated biomarker to identify those patients. Our objective was to determine a robust biomarker for severe OCSCC, using a biology-driven strategy. Patients and methods Tumor and juxtatumor secretome were analyzed in a prospective discovery cohort of 37 OCSCC treated by primary surgery. Independent biomarker validation was performed by RTqPCR in a retrospective cohort of 145 patients with similar clinical features. An 18-gene signature (18 G) predictive of the response to PD-1 blockade was evaluated in the same cohort. Results Among 29 deregulated molecules identified in a secretome analysis, including chemokines, cytokines, growth factors, and molecules related to tumor growth and tissue remodeling, only soluble MMP2 was a prognostic biomarker. In our validation cohort, high levels of MMP2 and CD276, and low levels of CXCL10 and STAT1 mRNA were associated with poor prognosis in univariate analysis (Kaplan-Meier). MMP2 (p = .001) and extra-nodal extension (ENE) (p = .006) were independent biomarkers of disease-specific survival (DSS) in multivariate analysis and defined prognostic groups with 5-year DSS ranging from 36% (MMP2highENE+) to 88% (MMP2lowENE-). The expression of 18 G was similar in the different prognostic groups, suggesting comparable responsiveness to anti-PD-1. Conclusion High levels of MMP2 were an independent and validated prognostic biomarker, surpassing other molecules of a large panel of the tumor and immune-related processes, which may be used to select poor prognosis patients for intensified neoadjuvant or adjuvant regimens.
Collapse
Affiliation(s)
- Caroline Hoffmann
- Paris Sciences and Letters (PSL) University, Paris, France
- INSERM U932 Research Unit, Immunity and Cancer, Paris, France
- Department of Surgical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Sophie Vacher
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Genetics, Institut Curie, Paris, France
| | - Philémon Sirven
- Paris Sciences and Letters (PSL) University, Paris, France
- INSERM U932 Research Unit, Immunity and Cancer, Paris, France
| | - Charlotte Lecerf
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Lucile Massenet
- Paris Sciences and Letters (PSL) University, Paris, France
- INSERM U932 Research Unit, Immunity and Cancer, Paris, France
| | - Aurélie Moreira
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Aurore Surun
- SIREDO Cancer Center (Care, Innovation and Research in Pediatric, Adolescents and Young Adults Oncology), Institut Curie, Paris, France
- Paris Descartes University, Paris, France
| | - Anne Schnitzler
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Genetics, Institut Curie, Paris, France
| | - Jerzy Klijanienko
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Odette Mariani
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Pathology, Institut Curie, Paris, France
- Biological Resources Center, Institut Curie, Paris, France
| | - Emmanuelle Jeannot
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Nathalie Badois
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Surgical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Maria Lesnik
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Surgical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Olivier Choussy
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Surgical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Christophe Le Tourneau
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
- INSERM U900 Research Unit, Saint-Cloud, France
| | - Maude Guillot-Delost
- Paris Sciences and Letters (PSL) University, Paris, France
- INSERM U932 Research Unit, Immunity and Cancer, Paris, France
- Center of Clinical Investigation, CIC IGR-Curie, Paris, France
| | - Maud Kamal
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris & Saint-Cloud, France
| | - Ivan Bieche
- Paris Sciences and Letters (PSL) University, Paris, France
- Department of Genetics, Institut Curie, Paris, France
- Faculty of Pharmaceutical and Biological Sciences, INSERM U1016 Research Unit, Paris Descartes University, Paris, France
| | - Vassili Soumelis
- Paris Sciences and Letters (PSL) University, Paris, France
- INSERM U932 Research Unit, Immunity and Cancer, Paris, France
- Clinical Immunology Department, Institut Curie, Paris, France
| |
Collapse
|
20
|
Morel A, Neuzillet C, Wack M, Lameiras S, Vacher S, Deloger M, Servant N, Veyer D, Péré H, Mariani O, Baulande S, Rouzier R, Kamal M, El Alam E, Jeannot E, Nicolas A, Bièche I, Cacheux W. Mechanistic Signatures of Human Papillomavirus Insertions in Anal Squamous Cell Carcinomas. Cancers (Basel) 2019; 11:cancers11121846. [PMID: 31766658 PMCID: PMC6966520 DOI: 10.3390/cancers11121846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 10/21/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 01/26/2023] Open
Abstract
The role of human papillomavirus (HPV) in anal squamous cell carcinoma (ASCC) carcinogenesis has been clearly established, involving the expression of viral oncoproteins and optional viral DNA integration into the host genome. In this article, we describe the various mechanisms and sites of HPV DNA insertion and assess their prognostic and predictive value in a large series of patients with HPV-positive ASCC with long-term follow-up. We retrospectively analyzed 96 tumor samples from 93 HPV-positive ASCC patients using the Capture-HPV method followed by Next-Generation Sequencing, allowing determination of HPV genotype and identification of the mechanisms and sites of viral genome integration. We identified five different mechanistic signatures of HPV insertions. The distribution of HPV signatures differed from that previously described in HPV-positive cervical carcinoma (p < 0.001). In ASCC samples, the HPV genome more frequently remained in episomal form (45.2%). The most common signature of HPV insertion was MJ-SC (26.9%), i.e., HPV–chromosomal junctions scattered at different loci. Functionally, HPV integration signatures were not associated with survival or response to treatment, but were associated with viral load (p = 0.022) and PIK3CA mutation (p = 0.0069). High viral load was associated with longer survival in both univariate (p = 0.044) and multivariate (p = 0.011) analyses. Finally, HPV integration occurred on most human chromosomes, but intragenic integration into the NFIX gene was recurrently observed (n = 4/51 tumors). Overall, the distribution of mechanistic signatures of HPV insertions in ASCC was different from that observed in cervical carcinoma and was associated with viral load and PIK3CA mutation. We confirmed recurrent targeting of NFIX by HPV integration, suggesting a role for this gene in ASCC carcinogenesis.
Collapse
Affiliation(s)
- Adeline Morel
- Institut Curie, Pharmacogenomic Unit, 26 rue d’Ulm, 75248 Paris, France; (A.M.); (S.V.); (I.B.)
| | - Cindy Neuzillet
- Institut Curie, Medical Oncology Department, Versailles Saint-Quentin University, 35 rue Dailly, 92210 Saint-Cloud, France; (R.R.); (W.C.)
- Correspondence: or ; Tel.: +33-147-111-515 or +33-682-550-492
| | - Maxime Wack
- Département d’Informatique Médicale, Biostatistiques et Santé Publique, Hôpital Européen Georges Pompidou, and Assistance Publique-Hôpitaux de Paris, 75015 Paris, France;
- Centre de Recherche des Cordeliers, INSERM UMRS1138, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Sonia Lameiras
- Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University, 26 rue d’Ulm, 75248 Paris CEDEX 05, France; (S.L.); (S.B.)
| | - Sophie Vacher
- Institut Curie, Pharmacogenomic Unit, 26 rue d’Ulm, 75248 Paris, France; (A.M.); (S.V.); (I.B.)
| | - Marc Deloger
- Institut Curie, Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75248 Paris, France; (M.D.); (N.S.)
| | - Nicolas Servant
- Institut Curie, Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, 75248 Paris, France; (M.D.); (N.S.)
| | - David Veyer
- Laboratoire de virologie, Hôpital Européen Georges Pompidou, and Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; (D.V.); (H.P.)
| | - Hélène Péré
- Laboratoire de virologie, Hôpital Européen Georges Pompidou, and Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; (D.V.); (H.P.)
| | - Odette Mariani
- Institut Curie, Centre de Ressources Biologiques, 26 rue d’Ulm, 75248 Paris, France;
| | - Sylvain Baulande
- Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University, 26 rue d’Ulm, 75248 Paris CEDEX 05, France; (S.L.); (S.B.)
| | - Roman Rouzier
- Institut Curie, Medical Oncology Department, Versailles Saint-Quentin University, 35 rue Dailly, 92210 Saint-Cloud, France; (R.R.); (W.C.)
| | - Maud Kamal
- Institut Curie, Department of Drug Development and Innovation (D3i), Institut Curie Paris & Saint Cloud, 75248 Paris, France;
| | - Elsy El Alam
- Institut Curie, Pathology Department, 35 rue Dailly, 92210 Saint-Cloud, France;
| | - Emmanuelle Jeannot
- Institut Curie, Pathology Department, 26 rue d’Ulm, 75248 Paris, France;
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS UMR3244, 75248 Paris, France;
| | - Ivan Bièche
- Institut Curie, Pharmacogenomic Unit, 26 rue d’Ulm, 75248 Paris, France; (A.M.); (S.V.); (I.B.)
- INSERM U1016, Université Paris Descartes University, 75006 Paris, France
| | - Wulfran Cacheux
- Institut Curie, Medical Oncology Department, Versailles Saint-Quentin University, 35 rue Dailly, 92210 Saint-Cloud, France; (R.R.); (W.C.)
- Hôpital Privé Pays de Savoie, Service d’oncologie Médicale, 19 Avenue Pierre Mendès France, 74100 Annemasse, France
| |
Collapse
|
21
|
Masliah-Planchon J, Kamal M, Borcoman E, Girard E, Gestraud P, Bataillon G, Vincent-Salomon A, Lecerf C, Callens C, Antonio S, Franck C, Mariani O, Bieche I, Le Tourneau C, Servois V. Prospective comparative study of next-generation sequencing on fine needle aspirations versus core needle biopsies in cancer patients included in SHIVA02 trial. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.014] [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: 11/12/2022] Open
|
22
|
Rodrigues M, Mobuchon L, Houy A, Alsafadi S, Baulande S, Mariani O, Marande B, Ait Rais K, Van der Kooij MK, Kapiteijn E, Gassama S, Gardrat S, Barnhill RL, Servois V, Dendale R, Putterman M, Tick S, Piperno-Neumann S, Cassoux N, Pierron G, Waterfall JJ, Roman-Roman S, Mariani P, Stern MH. Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations. Clin Cancer Res 2019; 25:5513-5524. [DOI: 10.1158/1078-0432.ccr-19-1215] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/29/2019] [Accepted: 06/18/2019] [Indexed: 11/16/2022]
|
23
|
Borcoman E, Ngo C, Rapinat A, Simaga F, Mariani O, Fuhrmann L, Jeannot E, Laé M, Pierga JY, Gentien D, Pierron G, Morel P, Brauer HA, Vincent-Salomon A. Abstract P6-17-25: PAM50 and CGH-array genomic characterization of HER2-equivocal breast cancers defined by the ASCO/CAP2013 recommendations and response to treatment. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p6-17-25] [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
HER2 breast cancer status determines patients' eligibility for targeted therapy. HER2 level of amplification is associated with a better response to anti-HER2 therapy (Arnould CCR 2007, Singer CCR 2017). Benefit of anti-HER2 therapy for equivocal cases remains debated.
Objectives
We aimed to better characterize HER2-equivocal breast cancers by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) according to 2013 ASCO/CAP guidelines using PAM50 gene expression-based molecular subtyping. We then investigated genome-wide copy number alterations of HER2-equivocal cases, assessing agreement between genomic alterations of the chromosome (chr) 17 and molecular subtypes.
Methods
PAM50 (nCounter assay; Nanostring) was performed on RNA from formalin-fixed paraffin-embedded samples of 40 HER2-equivocal cases. These cases were subsequently analyzed by Agilent 60-mer oligonucleotide microarrays for array-based comparative genomic hybridization (aCGH).
Results
The 40 HER2-equivocal cases were classified as Luminal B in 16 cases (40%), HER2-Enriched in 14 cases (35%), Luminal A in 9 cases (22.5%) and Basal-like in 1 case (2.5%) using PAM50.
By IHC, 34 cases (85%) were ER+, 24 (60%) were also PgR+, 26 (65%) were grade III and 33 (82.5%) showed a high Ki67 > 20%.
Using aCGH, 10 cases (25%) presented chr 17q large copy number gain, 10 (25%) showed segmental copy number gains including HER2, 9 (22.5%) showed HER2 amplification, one (2.5%) showed a large copy number loss and 10 cases (25%) didn't show any copy number alteration of the chr 17.
Out of the 14 PAM50 HER2-Enriched cases, only 5 (35.7%) showed HER2 genomic amplification (Table 1). Four HER2 amplified cases at the genomic level were classified as Luminal B (3 cases, Ki67 > 20%, ER+, PgR- by IHC) or Luminal A (1 case, Ki67<20%, ER+, PgR>10% by IHC) using PAM50, although these luminal B tumors presented strong correlation with the HER2-Enriched centroid. In total, 13 cases (32.5%) were discordant between molecular classification and genomic alteration status of the chr 17.
Among patients with early stage HER2-equivocal breast cancers (n=37), 2 received neo-adjuvant chemotherapy (5.4%), 25 received adjuvant chemotherapy (67.6%) and 2 received adjuvant trastuzumab (5.4%). With a median follow up of 5.8 years (3.8-6.9), one controlateral recurrence (2.7%), four metastatic recurrences (10.8%) and three deaths were observed (8.1%).
Conclusion
Using PAM50, the majority of HER2-equivocal cases were classified as Luminal tumors.
At the genomic level, HER2-equivocal cases harbored mostly chr 17 segmental or large copy number gains. These results emphasized the need of HER2 status genomic determination. In line with the new ASCO 2018 recommendations intending to decrease the number of cases considered as HER2 equivocal, we showed that these tumors were mainly HER2 not amplified, ER positive and grade 3. There is no evidence of benefit of anti-HER2 therapy in these cases.
Table 1Genomic alterations of chromosome 17Basal-likeHER2-EnrichedLuminal ALuminal BTotalHER2 amplified05139Large copy number gain013610Segmental copy number gain153110No alteration032510Large copy number loss00011Total11491640
Citation Format: Borcoman E, Ngo C, Rapinat A, Simaga F, Mariani O, Fuhrmann L, Jeannot E, Laé M, Pierga J-Y, Gentien D, Pierron G, Morel P, Brauer HA, Vincent-Salomon A. PAM50 and CGH-array genomic characterization of HER2-equivocal breast cancers defined by the ASCO/CAP2013 recommendations and response to treatment [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-17-25.
Collapse
Affiliation(s)
- E Borcoman
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - C Ngo
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - A Rapinat
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - F Simaga
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - O Mariani
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - L Fuhrmann
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - E Jeannot
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - M Laé
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - J-Y Pierga
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - D Gentien
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - G Pierron
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - P Morel
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - HA Brauer
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| | - A Vincent-Salomon
- Institut Curie, Paris, Ile de France, France; Nanostring Technologies, Seattle, WA
| |
Collapse
|
24
|
Lièvre A, Ouine B, Canet J, Cartier A, Amar Y, Cacheux W, Mariani O, Guimbaud R, Selves J, Lecomte T, Guyetant S, Bieche I, Berger F, de Koning L. Correction: Protein biomarkers predictive for response to anti-EGFR treatment in RAS wild-type metastatic colorectal carcinoma. Br J Cancer 2018; 119:387. [PMID: 29899390 PMCID: PMC6079395 DOI: 10.1038/s41416-018-0130-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Astrid Lièvre
- Service des maladies de l'appareil digestif, CHU Pontchaillou, 2 rue Henri Le Guilloux, Rennes Cedex, 09 35033, France.,Faculté de médecine, Université Rennes 1, 2 Avenue du Prof. Léon Bernard, Rennes, 35043, France.,Inserm ER440-Oncogenesis, Stress and Signaling, Rue Bataille Flandres-Dunkerque, Rennes, 35042, France
| | - Bérèngere Ouine
- Department of Translational Research, Institut Curie, PSL Research University, 26 rue d'Ulm, Paris, 75005, France
| | - Jim Canet
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d'Ulm, Paris, 75005, France
| | - Aurélie Cartier
- Department of Translational Research, Institut Curie, PSL Research University, 26 rue d'Ulm, Paris, 75005, France
| | - Yael Amar
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d'Ulm, Paris, 75005, France
| | - Wulfran Cacheux
- Department of Medical Oncology, Institut Curie, René Huguenin Hospital, 35 rue Dailly, Saint-Cloud, 92210, France.,Department of Genetics, Institut Curie, Unit of Pharmacogenomics, 26 rue d'Ulm, Paris, 75005, France
| | - Odette Mariani
- Biological Resource Center, Institut Curie, PSL Research University, 26 rue d'Ulm, Paris, 75005, France
| | - Rosine Guimbaud
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM-Université Toulouse III, Toulouse, 31062, France.,Service d'oncologie médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, 31059, France
| | - Janick Selves
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM-Université Toulouse III, Toulouse, 31062, France.,Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse, 31059, France
| | - Thierry Lecomte
- Hôpital Trousseau-CHRU de TOURS, Service d'Hépato-Gastro-Entérologie, Tours, 37000, France.,UMR CNRS 7292 (GICC), Université François Rabelais, Tours, 37000, France
| | - Serge Guyetant
- Hôpital Trousseau-CHRU de TOURS, Service d'Anatomie et Cytologie Pathologiques-Tumorothèque, Tours, 37000, France
| | - Ivan Bieche
- Department of Genetics, Institut Curie, Unit of Pharmacogenomics, 26 rue d'Ulm, Paris, 75005, France
| | - Frédérique Berger
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d'Ulm, Paris, 75005, France.,Institut Curie, PSL Research University, INSERM U900, 26 rue d'Ulm, Paris, 75005, France
| | - Leanne de Koning
- Department of Translational Research, Institut Curie, PSL Research University, 26 rue d'Ulm, Paris, 75005, France.
| |
Collapse
|
25
|
Cacheux W, Tsantoulis P, Briaux A, Vacher S, Mariani P, Richard-Molard M, Buecher B, Richon S, Jeannot E, Lazartigues J, Rouleau E, Mariani O, El Alam E, Cros J, Roman-Roman S, Mitry E, Girard E, Dangles-Marie V, Lièvre A, Bièche I. Array comparative genomic hybridization identifies high level of PI3K/Akt/mTOR pathway alterations in anal cancer recurrences. Cancer Med 2018; 7:3213-3225. [PMID: 29804324 PMCID: PMC6051172 DOI: 10.1002/cam4.1533] [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: 02/07/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/31/2023] Open
Abstract
Genomic alterations of anal squamous cell carcinoma (ASCC) remain poorly understood due to the rarity of this tumor. Array comparative genomic hybridization and targeted gene sequencing were performed in 49 cases of ASCC. The most frequently altered regions (with a frequency greater than 25%) were 10 deleted regions (2q35, 2q36.3, 3p21.2, 4p16.3, 4p31.21, 7q36.1, 8p23.3, 10q23.2, 11q22.3, and 13q14.11) and 8 gained regions (1p36.33, 1q21.1, 3q26.32, 5p15.33, 8q24.3, 9q34.3, 16p13.3, and 19p13.3). The most frequent minimal regions of deletion (55%) encompassed the 11q22.3 region containing ATM, while the most frequent minimal regions of gain (57%) encompassed the 3q26.32 region containing PIK3CA. Recurrent homozygous deletions were observed for 5 loci (ie, TGFR2 in 4 cases), and recurrent focal amplifications were observed for 8 loci (ie, DDR2 and CCND1 in 3 cases, respectively). Several of the focal amplified genes are targets for specific therapies. Integrated analysis showed that the PI3K/Akt/mTOR signaling pathway was the pathway most extensively affected, particularly in recurrences compared to treatment‐naive tumors (64% vs 30%; P = .017). In patients with ASCC recurrences, poor overall survival (OS) was significantly correlated with a large number of altered regions (P = .024). These findings provide insight into the somatic genomic alterations in ASCC and highlight the key role of the druggable PI3K/Akt/mTOR signaling pathway.
Collapse
Affiliation(s)
- Wulfran Cacheux
- Département d'oncologie médicale, Institut Curie, Ensemble hospitalier, Hôpital René Huguenin, Saint-Cloud, France.,Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Petros Tsantoulis
- Centre d'oncologie, Hôpitaux universitaires de Genève, Genève, Switzerland
| | - Adrien Briaux
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Sophie Vacher
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Pascale Mariani
- Département de chirurgie oncologique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Marion Richard-Molard
- Département de radio-oncologie, Institut Curie, Ensemble hospitalier, Hôpital René Huguenin, Saint-Cloud, France
| | - Bruno Buecher
- Département d'oncologie médicale, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Sophie Richon
- Centre de recherche, Institut Curie, UMR144, Paris Cedex 05, France
| | - Emmanuelle Jeannot
- Département d'anatomopathologie, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Julien Lazartigues
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Etienne Rouleau
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Odette Mariani
- Département d'anatomopathologie, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Elsy El Alam
- Département d'anatomopathologie, Institut Curie, Ensemble hospitalier, Hôpital René Huguenin, Saint-Cloud, France
| | - Jérôme Cros
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| | - Sergio Roman-Roman
- Recherche translationnelle, Centre de recherche, Institut Curie, Paris Cedex 05, France
| | - Emmanuel Mitry
- Département d'oncologie médicale, Institut Curie, Ensemble hospitalier, Hôpital René Huguenin, Saint-Cloud, France
| | - Elodie Girard
- Département de bio-informatiques, Centre de recherche, Institut Curie, Paris Cedex 05, France
| | - Virginie Dangles-Marie
- Recherche translationnelle, Centre de recherche, Institut Curie, Paris Cedex 05, France.,IFR71, Faculté des sciences biologique et pharmacologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Astrid Lièvre
- Département d'oncologie médicale, Institut Curie, Ensemble hospitalier, Hôpital René Huguenin, Saint-Cloud, France.,Département de gastroentérologie, Hôpital universitaire de Rennes, Université de Rennes 1, Rennes, France
| | - Ivan Bièche
- Unité de pharmacogénomique, Département de génétique, Institut Curie, Ensemble hospitalier, Paris Cedex 05, France
| |
Collapse
|
26
|
Basse C, Morel C, Alt M, Sablin MP, Franck C, Pierron G, Callens C, Melaabi S, Masliah-Planchon J, Bataillon G, Gardrat S, Lavigne M, Bonsang B, Vaflard P, Pons Tostivint E, Dubot C, Loirat D, Marous M, Geiss R, Clément N, Schleiermacher G, Kamoun C, Girard E, Ardin M, Benoist C, Bernard V, Mariani O, Rouzier R, Tresca P, Servois V, Vincent-Salomon A, Bieche I, Le Tourneau C, Kamal M. Relevance of a molecular tumour board (MTB) for patients' enrolment in clinical trials: experience of the Institut Curie. ESMO Open 2018; 3:e000339. [PMID: 29636991 PMCID: PMC5890857 DOI: 10.1136/esmoopen-2018-000339] [Citation(s) in RCA: 30] [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: 02/08/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/27/2022] Open
Abstract
Background High throughput molecular screening techniques allow the identification of multiple molecular alterations, some of which are actionable and can be targeted by molecularly targeted agents (MTA). We aimed at evaluating the relevance of using this approach in the frame of Institut Curie Molecular Tumor Board (MTB) to guide patients with cancer to clinical trials with MTAs. Patients and methods We included all patients presented at Institut Curie MTB from 4 October 2014 to 31 October 2017. The following information was extracted from the chart: decision to perform tumour profiling, types of molecular analyses, samples used, molecular alterations identified and those which are actionable, and inclusion in a clinical trial with matched MTA. Results 736 patients were presented at the MTB. Molecular analyses were performed in 442 patients (60%). Techniques used included next-generation sequencing, comparative genomic hybridisation array and/or other techniques including immunohistochemistry in 78%, 51% and 58% of patients, respectively. Analyses were performed on a fresh frozen biopsy in 91 patients (21%), on archival tissue (fixed or frozen) in 326 patients (74%) and on both archival and fresh frozen biopsy in 25 patients (6%). At least one molecular alteration was identified in 280 analysed patients (63%). An actionable molecular alteration was identified in 207 analysed patients (47%). Forty-five analysed patients (10%) were enrolled in a clinical trial with matched MTA and 29 additional patients were oriented and included in a clinical trial based on a molecular alteration identified prior to the MTB analysis. Median time between date of specimen reception and molecular results was 28 days (range: 5–168). Conclusions The implementation of an MTB at Institut Curie enabled the inclusion of 10% of patients into a clinical trial with matched therapy.
Collapse
Affiliation(s)
- Clémence Basse
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Claire Morel
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Marie Alt
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Marie Paule Sablin
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Coralie Franck
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Céline Callens
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | | | - Guillaume Bataillon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Marion Lavigne
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Benjamin Bonsang
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Pauline Vaflard
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | | | - Coraline Dubot
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Delphine Loirat
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Miguelle Marous
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Romain Geiss
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Nathalie Clément
- Department of Pediatric Oncology, Institut Curie, PSL Research University, Paris, France
| | - Gudrun Schleiermacher
- Department of Pediatric Oncology, Institut Curie, PSL Research University, Paris, France
| | | | - Elodie Girard
- INSERM U900 Research Unit, Institut Curie, Paris, France
| | - Maude Ardin
- INSERM U900 Research Unit, Institut Curie, Paris, France
| | - Camille Benoist
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Virginie Bernard
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Odette Mariani
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Roman Rouzier
- INSERM U900 Research Unit, Institut Curie, Paris, France.,Department of Surgery, Institut Curie, PSL Research University, Paris, France
| | - Patricia Tresca
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| | - Vincent Servois
- Department of Radiology and Nuclear Medicine, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Ivan Bieche
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France.,EA7331, University of Paris-Descartes, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation, Institut Curie, Paris, France.,INSERM U900 Research Unit, Institut Curie, Paris, France.,Versailles-Saint-Quentin-en-Yvelines University, Montigny-le-Bretonneux, France
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, Paris, France
| |
Collapse
|
27
|
Laé M, Gardrat S, Rondeau S, Richardot C, Caly M, Chemlali W, Vacher S, Couturier J, Mariani O, Terrier P, Bièche I. MED12 mutations in breast phyllodes tumors: evidence of temporal tumoral heterogeneity and identification of associated critical signaling pathways. Oncotarget 2018; 7:84428-84438. [PMID: 27806318 PMCID: PMC5356671 DOI: 10.18632/oncotarget.12991] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/13/2016] [Indexed: 01/08/2023] Open
Abstract
Exome sequencing has recently identified highly recurrent MED12 somatic mutations in fibroadenomas (FAs) and phyllodes tumors (PTs). In the present study, based on a large series, we confirmed the presence of MED12 exon 1 and 2 mutations in 49% (41/83) of PTs, 70% (7/10) of FAs and 9.1% (1/11) of fibromatoses. We show that MED12 mutations are associated with benign behavior of phyllodes tumors, as they are detected less frequently in malignant PTs (27.6%) compared to benign (58.3%) and borderline (63.3%) PTs, respectively (p = 0.0036). Phyllodes tumors presented marked temporal heterogeneity of MED12 mutation status, as 50% (3/6) of primary and recurrent phyllodes tumor pairs with MED12 mutation presented different MED12 mutations between the primary and recurrent tumors. There was no correlation between MED12 status and genomic profiles obtained by array-CGH. MED12 mutations are associated with altered expressions of the genes involved in the WNT (PAX3, WNT3A, AXIN2), TGFB (TAGLN, TGFBR2, CTGF) and THRA (RXRA, THRA) signaling pathways. In conclusion, this study confirmed that MED12 plays a central oncogenic role in breast fibroepithelial tumorigenesis and identified a limited number of altered signaling pathways that maybe associated with MED12 mutations. MED12 exon 1 and 2 mutation status and some of the altered genes identified in this study could constitute useful diagnostic or prognostic markers, and form the basis for novel therapeutic strategies for PTs.
Collapse
Affiliation(s)
- Marick Laé
- Service de Pathologie, Institut Curie, 75248 Paris Cedex 05, France
| | - Sophie Gardrat
- Service de Pathologie, Institut Curie, 75248 Paris Cedex 05, France.,Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| | - Sophie Rondeau
- Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| | | | - Martial Caly
- Service de Pathologie, Institut Curie, 75248 Paris Cedex 05, France
| | - Walid Chemlali
- Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| | - Sophie Vacher
- Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| | - Jérôme Couturier
- Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| | - Odette Mariani
- Service de Pathologie, Institut Curie, 75248 Paris Cedex 05, France
| | - Philippe Terrier
- Service de Pathologie, Institut Gustave Roussy, 94805, Villejuif Cedex, France
| | - Ivan Bièche
- Service de Génétique, Unité de pharmacogénomique, Institut Curie, 75248 Paris Cedex 05, France
| |
Collapse
|
28
|
Ngo C, Borcoman E, Simaga F, Mariani O, Fuhrmann L, Jeannot E, Loirat D, Lae M, Pierga JY, Pierron G, Vincent-Salomon A. Abstract P2-05-11: Not presented. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-05-11] [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
This abstract was not presented at the symposium.
Collapse
Affiliation(s)
- C Ngo
- Institut Curie, Paris, France
| | | | | | | | | | | | | | - M Lae
- Institut Curie, Paris, France
| | | | | | | |
Collapse
|
29
|
Pareja F, Geyer FC, Piscuoglio S, Selenica P, Kumar R, Lim RS, Guerini-Rocco E, Marchio C, Mariani O, Ng CKY, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Abstract P2-05-08: Mucinous breast carcinomas: A genomically distinct subtype of estrogen receptor-positive invasive breast cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-05-08] [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: Mucinous carcinoma of the breast (MCB) is a rare histologic form of estrogen receptor (ER)-positive invasive carcinoma, accounting for up to 2% of breast cancers. MCBs are characterized by clusters of tumor cells floating in lakes of extracellular mucin, and are classified into mucinous A (paucicellular) and mucinous B (hypercellular) subtypes. Some MCBs are found admixed with invasive ductal carcinoma components, and then classified as mixed MCBs. The aims of this study were to determine the repertoire of somatic mutations of MCBs and to ascertain whether these genetic alterations are distinct from those identified in common forms of ER+/HER2- invasive breast cancers (IBCs). We also sought to determine whether the mucinous and ductal components of mixed MCBs would be clonally related.
Materials and methods: Thirty MCBs including 25 pure MCBs (n=13 mucinous A, n=12 mucinous B) and five mixed MCBs were microdissected and subjected to whole exome sequencing. Each tumor component of mixed cases was microdissected and analyzed separately. Somatic mutations, copy number alterations and mutational signatures were defined using state-of-the-art bioinformatics methods. The mutational repertoire of MCBs was compared with that of ER+/HER2- IBCs (n = 240) from The Cancer Genome Atlas (TCGA) breast cancer study.
Results: The genes most frequently mutated in MCBs were GATA3 (27%, 8/30, all frameshift mutations), KMT2C (13%, 4/30) and MAP3K1 (10%, 3/30). No significant differences were identified in single gene comparisons between mucinous A and mucinous B MCBs or between pure MCBs and the mucinous component of mixed MCBs (Fisher's exact tests, p>0.05). As compared to common forms of ER+/HER2- IBC, MCBs had a lower frequency of PIK3CA mutations (7% vs 42%, p<0.001) and a higher frequency of GATA3 mutations (27% vs 12%, p=0.04). Mucinous B MCBs had a higher frequency of KMT2C mutations than ER+/HER2- IBCs (25% vs 6%, p=0.04). Most MCBs displayed the mutational signature 1 (aging-related; 20/30, 67%), and no differences in the frequency of specific mutational signatures according to the type of MCBs were observed. Concurrent 1q gains and 16q losses, which are the hallmark genetic alterations of low-grade ER+/HER2- breast cancers, were not observed in pure MCBs, but were found in three of the five mixed MCBs analyzed. The mucinous and ductal components of all five mixed MCBs shared a median of 58% of somatic mutations (range 42%-64%), including clonal GATA3 frameshift mutations in two of them, as well as a similar pattern of copy number alterations, supporting their clonal relatedness. Additional somatic mutations found to be restricted to the ductal or mucinous components of all mixed MCBs analyzed were identified, including clonal missense mutations in PIK3C2B and PIK3R2 in the ductal component of one case, and a PIK3R5 missense mutation in the mucinous component of another case.
Conclusions: The repertoire of somatic mutations in MCBs is distinct from that of common forms of ER+/HER2- IBCs. These differences include the lack of concurrent 1q gains/16q losses, a lower frequency of PIK3CA mutations and a higher frequency of GATA3 mutations in pure MCBs.
Citation Format: Pareja F, Geyer FC, Piscuoglio S, Selenica P, Kumar R, Lim RS, Guerini-Rocco E, Marchio C, Mariani O, Ng CKY, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Mucinous breast carcinomas: A genomically distinct subtype of estrogen receptor-positive invasive breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-08.
Collapse
Affiliation(s)
- F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - P Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - R Kumar
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - E Guerini-Rocco
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - C Marchio
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Turin, Turin, Italy; Instiut Curie, Paris, France
| |
Collapse
|
30
|
Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. Abstract P2-05-03: Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-05-03] [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
Introduction: Breast adenoid cystic carcinoma (AdCC) is a rare type of triple-negative breast cancer associated with an indolent clinical behavior. AdCCs provide a clear example of genotypic-phenotypic correlation with the majority harboring the MYB-NFIB fusion gene. In this study, we sought to identify alternative driver genetic alterations in breast AdCCs lacking the MYB-NFIB fusion gene.
Methods: Nucleic acids obtained from four breast AdCCs lacking the MYB-NFIB fusion gene as defined by reverse transcription (RT)-PCR and/or fluorescence in situ hybridization (FISH) were subjected to RNA-sequencing (n=3), whole-genome (n=2) and/or targeted (n=1) massively parallel sequencing. Sequencing data were analyzed using state-of-the-art bioinformatics algorithms, and potential alternative driver genetic alterations were validated using orthogonal sequencing and molecular pathology methods.
Results: RNA-sequencing revealed the presence of MYBL1-ACTN1 or MYBL1-NFIB fusion genes in two breast AdCCs, which were validated by whole-genome sequencing and/or MYBL1 FISH analysis. Both MYBL1 fusion gene-positive cases were found to overexpress MYBL1 as defined by quantitative RT-PCR analysis. In the third MYB-NFIB-negative breast AdCC studied, a high-level MYB gene amplification coupled with overexpression of MYB at the mRNA and protein levels was identified. In the fourth breast AdCC, which expressed high levels of MYB, whole-genome and RNA-sequencing revealed no definite alternative driver alteration, however, a MYBL2 intronic mutation was found in this case, which was associated with high levels of MYBL2 mRNA expression. In this case, single sample gene set enrichment analysis revealed activation of pathways similar to those activated in AdCCs harboring the MYB-NFIB or MYBL1 fusions genes.
Conclusion: We demonstrate that in breast AdCCs lacking the MYB-NFIB fusion gene MYBL1 rearrangements and MYB amplification are likely alternative driver genetic events. Given that activation of MYB/MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification or other yet to be validated mechanisms (e.g. MYBL2 non-coding mutations), our findings further suggest that breast AdCCs constitute a convergent phenotype.
Citation Format: Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-03.
Collapse
Affiliation(s)
- J Kim
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - P Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - A Li
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - N Fusco
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - M Edelweiss
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - S Badve
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| |
Collapse
|
31
|
Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Kumar R, Gularte-Merida R, Forbes AN, Khurana E, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene. J Pathol 2018; 244:143-150. [PMID: 29149504 PMCID: PMC5839480 DOI: 10.1002/path.5006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 06/02/2017] [Revised: 11/03/2017] [Accepted: 11/11/2017] [Indexed: 01/14/2023]
Abstract
Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer, has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression. A third AdCC harboured a high-level MYB amplification, which resulted in MYB overexpression at the mRNA and protein levels. RNA-sequencing and whole-genome sequencing revealed no definite alternative driver in the fourth AdCC studied, despite high levels of MYB expression and the activation of pathways similar to those activated in MYB-NFIB-positive AdCCs. In this case, a deletion encompassing the last intron and part of exon 15 of MYB, including the binding site of ERG-1, a transcription factor that may downregulate MYB, and the exon 15 splice site, was detected. In conclusion, we demonstrate that MYBL1 rearrangements and MYB amplification probably constitute alternative genetic drivers of breast AdCCs, functioning through MYBL1 or MYB overexpression. These observations emphasize that breast AdCCs probably constitute a convergent phenotype, whereby activation of MYB and MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification, or other yet to be identified mechanisms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Jisun Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Department of Surgery, Ulsan University, College of Medicine, Asan
Medical Center, Seoul, Korea
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Institute of Pathology, University Hospital Basel and Department of
Biomedicine, University of Basel, Basel, Switzerland
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Division of Pathology, Fondazione IRCCS Ca’Granda Ospedale
Maggiore Policlinico, University of Milan, Milan, Italy
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | | | - Andre N Forbes
- Institute for Computational Medicine and Department of Physiology
and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Ekta Khurana
- Institute for Computational Medicine and Department of Physiology
and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | | | - Sunil Badve
- IU Health Pathology Laboratory, Indiana University, Indianapolis,
IN, USA
| | | | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| |
Collapse
|
32
|
Dubot C, Bernard V, Sablin MP, Vacher S, Chemlali W, Schnitzler A, Pierron G, Ait Rais K, Bessoltane N, Jeannot E, Klijanienko J, Mariani O, Jouffroy T, Calugaru V, Hoffmann C, Lesnik M, Badois N, Berger F, Le Tourneau C, Kamal M, Bieche I. Comprehensive genomic profiling of head and neck squamous cell carcinoma reveals FGFR1 amplifications and tumour genomic alterations burden as prognostic biomarkers of survival. Eur J Cancer 2018; 91:47-55. [PMID: 29331751 DOI: 10.1016/j.ejca.2017.12.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/25/2017] [Accepted: 12/09/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis. Univariate and multivariate analyses were performed to assess the prognostic value of altered genes. RESULTS A median of 2 (range: 0-10) genomic alterations per sample was observed. Most frequently altered genes involved the cell cycle pathway (TP53 [60%], CCND1 [30%], CDKN2A [25%]), the PI3K/AKT/MTOR pathway (PIK3CA [12%]), tyrosine kinase receptors (EGFR [9%], FGFR1 [5%]) and cell differentiation (FAT1 [7%], NOTCH1 [4%]). TP53 mutations (p = 0.003), CCND1 amplifications (p = 0.04), CDKN2A alterations (p = 0.02) and FGFR1 amplifications (p = 0.003), correlated with shorter overall survival (OS). The number of genomic alterations was significantly higher in the HPV-negative population (p = 0.029) and correlated with a shorter OS (p < 0.0001). Only TP53 mutation and FGFR1 amplification status remained statistically significant in the multivariate analysis. CONCLUSION These results suggest that genomic alterations involving the cell cycle (TP53, CCND1, CDKN2A), as well as FGFR1 amplifications and tumour genomic alterations burden are prognostic biomarkers and might be therapeutic targets for patients with HNSCC.
Collapse
Affiliation(s)
- C Dubot
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France; Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France.
| | - V Bernard
- Unit of Bioinformatics, Next Generation Sequencing Platform-ICGex, Institut Curie, Paris, France
| | - M P Sablin
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France
| | - S Vacher
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - W Chemlali
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - A Schnitzler
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - G Pierron
- Unit of Somatic Genomics, Department of Genetics, Institut Curie, Paris, France
| | - K Ait Rais
- Unit of Somatic Genomics, Department of Genetics, Institut Curie, Paris, France
| | - N Bessoltane
- Unit of Bioinformatics, Next Generation Sequencing Platform-ICGex, Institut Curie, Paris, France
| | - E Jeannot
- Department of Biopathology, Institut Curie, Paris, France
| | - J Klijanienko
- Department of Biopathology, Institut Curie, Paris, France
| | - O Mariani
- Department of Biopathology, Institut Curie, Paris, France
| | - T Jouffroy
- Department of Surgery, Institut Curie, Paris, France
| | - V Calugaru
- Department of Radiotherapy, Institut Curie, Paris, France
| | - C Hoffmann
- Department of Surgery, Institut Curie, Paris, France
| | - M Lesnik
- Department of Surgery, Institut Curie, Paris, France
| | - N Badois
- Department of Surgery, Institut Curie, Paris, France
| | - F Berger
- Department of Biostatistics, Institut Curie, Paris, France
| | - C Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France; INSERM U900 Research Unit, Saint-Cloud, France
| | - M Kamal
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France
| | - I Bieche
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France; EA7331, Paris Descartes University, Faculty of Pharmaceutical and Biological Sciences, Paris, France
| |
Collapse
|
33
|
Lièvre A, Ouine B, Canet J, Cartier A, Amar Y, Cacheux W, Mariani O, Guimbaud R, Selves J, Lecomte T, Guyetant S, Bieche I, Berger F, de Koning L. Protein biomarkers predictive for response to anti-EGFR treatment in RAS wild-type metastatic colorectal carcinoma. Br J Cancer 2017; 117:1819-1827. [PMID: 29024937 PMCID: PMC5729470 DOI: 10.1038/bjc.2017.353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/02/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Metastatic colorectal cancer (mCRC) patients with mutant KRAS or NRAS are ineligible for anti-epidermal growth factor receptor (anti-EGFR) therapy, as RAS mutations activate downstream pathways independently of EGFR and induce primary resistance. However, even among RAS wild-type (WT) patients, only a fraction responds to anti-EGFR therapy, suggesting that other mechanisms of resistance exist. We hypothesise that different (epi)genetic alterations can lead to primary anti-EGFR resistance and that the crucial end point is the activation of protein signalling pathways. METHODS We analysed the expression and activation of proteins involved in cell signalling, using reverse phase protein arrays, on a multicentre French cohort of RAS WT mCRC treated with anti-EGFR treatment. RESULTS We identify activated EGFR and HER3 as protein biomarkers predictive for better overall survival. Active EGFR signalling and downstream PI3K, but not MAPK, pathway activation are associated with response to anti-EGFR treatment. Left-sided mCRC displays active ErbB2/3 and Wnt pathways and a better response to anti-EGFR therapy compared to right-sided mCRC. CONCLUSIONS We identify active EGFR and PI3K signalling as a key factor for response to anti-EGFR treatment in mCRC and highlight the importance of developing these biomarkers in clinical practice for the selection of RAS WT mCRC patients that would benefit from anti-EGFR treatment.
Collapse
Affiliation(s)
- Astrid Lièvre
- Service des maladies de l’appareil digestif, CHU Pontchaillou, 2 rue Henri Le Guilloux, Rennes cedex 09 35033, France
- Université Rennes 1, Faculté de médecine, 2 Avenue du Prof. Léon Bernard, Rennes 35043, France
- Inserm ER440-Oncogenesis, Stress and Signaling, Rue Bataille Flandres-Dunkerque, Rennes 35042, France
| | - Bérèngere Ouine
- Institut Curie, PSL Research University, Department of Translational Research, 26 rue d’Ulm, Paris 75005, France
| | - Jim Canet
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d’Ulm, Paris 75005, France
| | - Aurélie Cartier
- Institut Curie, PSL Research University, Department of Translational Research, 26 rue d’Ulm, Paris 75005, France
| | - Yael Amar
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d’Ulm, Paris 75005, France
| | - Wulfran Cacheux
- Institut Curie, Department of Medical Oncology, René Huguenin Hospital, 35 rue Dailly, Saint-Cloud 92210, France
- Institut Curie, Unit of Pharmacogenomics, Department of Genetics, 26 rue d’Ulm, Paris 75005, France
| | - Odette Mariani
- Institut Curie, PSL Research University, Biological Resource Center, 26 rue d’Ulm, Paris 75005, France
| | - Rosine Guimbaud
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM—Université Toulouse III, Toulouse 31062, France
- Service d’oncologie médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse 31059, France
| | - Janick Selves
- Centre de Recherche en Cancérologie de Toulouse, Unité Mixte de Recherche, 1037 INSERM—Université Toulouse III, Toulouse 31062, France
- Department of Pathology, Centre Hospitalier Universitaire de Toulouse, Toulouse 31059, France
| | - Thierry Lecomte
- Hôpital Trousseau—CHRU de TOURS, Service d'Hépato-Gastro-Entérologie, Tours 37000, France
- UMR CNRS 7292 (GICC), Université François Rabelais, Tours 37000, France
| | - Serge Guyetant
- Hôpital Trousseau—CHRU de TOURS, Service d'Anatomie et Cytologie Pathologiques—Tumorothèque, Tours 37000, France
| | - Ivan Bieche
- Institut Curie, Unit of Pharmacogenomics, Department of Genetics, 26 rue d’Ulm, Paris 75005, France
| | - Frédérique Berger
- Institut Curie, PSL Research University, Unit of Biostatistics, 26 rue d’Ulm, Paris 75005, France
- Institut Curie, PSL Research University, INSERM U900, 26 rue d’Ulm, Paris 75005, France
| | - Leanne de Koning
- Institut Curie, PSL Research University, Department of Translational Research, 26 rue d’Ulm, Paris 75005, France
| |
Collapse
|
34
|
Cabantous S, Hou X, Louis L, He H, Mariani O, Sastre X, Daujat-Chavanieu M, Li Y, Dessein A. Evidence for an important role of host microRNAs in regulating hepatic fibrosis in humans infected with Schistosoma japonicum. Int J Parasitol 2017; 47:823-830. [PMID: 28739251 DOI: 10.1016/j.ijpara.2017.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 03/20/2017] [Revised: 05/12/2017] [Accepted: 05/18/2017] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that repress the translation of target gene transcripts. They have been implicated in various activities such as cell proliferation, survival, differentiation, migration and metabolism. We report here the first known miRNome and transcriptome analysis of human livers displaying advanced fibrosis due to Schistosoma japonicum infection. We present evidence that hsa-miR-150-5p, hsa-miR-10a-5p, hsa-miR-199a-3p, hsa-miR-4521, hsa-miR-222/221, hsa-miR-663b and hsa-miR-143-3p (associated without correction) play an important role in hepatic fibrosis by acting on metabolism, organization of the extracellular matrix proteins, lipid mobilization and limitation of oxidative damage stress.
Collapse
Affiliation(s)
- Sandrine Cabantous
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR906, GIMP, Labex ParaFrap, Aix-Marseille Université, 13005 Marseille, France.
| | - Xunya Hou
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | - Laurence Louis
- INSERM UMR910, GMGF, Aix Marseille Université, 13005 Marseille, France
| | - Hongbin He
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | | | | | | | - Yuesheng Li
- Queensland Institute of Medical Research, Brisbane, Australia
| | - Alain Dessein
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR906, GIMP, Labex ParaFrap, Aix-Marseille Université, 13005 Marseille, France.
| |
Collapse
|
35
|
Prieur A, Mazard T, Assenat E, Ychou M, Gourgou S, Mariani O, Bronzini T, Salomon AV, Joubert D. Progastrin: A new specific early cancer screening biomarker. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.11545] [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
11545 Background: One in two people will be diagnosed with cancer during his/her lifetime. Because we are lacking effective screening tests, most cancers are detected in late stages, when survival rates are very low. Here, we show the development of the first early cancer screening test for multiple cancers using progastrin (PG) as biomarker. The gene coding for PG is a target gene of the Wnt oncogenic pathway that is activated in almost all type of cancers, at the earliest stages of development. We showed that the neutralization of PG by a specific humanized antibody could be used for colorectal cancer treatment. Moreover, as PG is secreted by cancer cells, we can specifically detect it in the blood of persons having a cancer at early stage. Methods: Antibodies directed against PG were produced and selected for target specificity and affinity. ELISA is the most reliable assay to detect biomarker on the blood. Hence, selected antibodies were used to set up an ELISA sandwich to detect PG in the blood of patients with various types of cancers and at various stages. Results: We first set up a prototype ELISA using polyclonal antibodies. We validated our test using 223 blood samples from patients with polyps and colorectal cancers at various stages for which we observed an increased levels of PG. Then, we showed the presence of PG in the blood of 212 patients with other types of cancer, including liver, pancreatic and breast cancers, confirming that PG could be used as a biomarker for multiple types of cancers. Next, we set up our industrial ELISA using polyclonal and monoclonal antibodies called DECODE Lab and tested 245 new blood samples from patients with various types of cancer including early stages. Strikingly, using our test we were able to detect breast (AUC = 0.9638; sensitivity 70%), colorectal (AUC = 0.9635; sensitivity 73%), melanoma (AUC = 0.9882; sensitivity 87%) and cervix utery (AUC = 0.9827; sensitivity 84%) all stages combined with a high specificity of 97.5%. Finally, for early stage patients with melanoma and breast cancer, we had a sensitivity of 68% and 81% respectively. Conclusions: Taken together, the results presented here show that PG is a reliable biomarker for early cancer screening. The ELISA test that we developed is very efficient and now available for the clinic.
Collapse
Affiliation(s)
| | - Thibault Mazard
- Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Eric Assenat
- Institut du Cancer de Montpellier, Montpellier, France
| | - Marc Ychou
- Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Sophie Gourgou
- Biostatistics Unit, CTD INCa, ICM-Montpellier Cancer Institute, Montpellier, France
| | | | | | | | | |
Collapse
|
36
|
Geyer FC, Ng CK, Piscuoglio S, Wen YH, Wen HC, Pareja F, Eberle CA, Burke KA, Lim RS, Natrajan R, Mariani O, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Abstract P1-05-03: The genomic landscape of breast metaplastic carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-05-03] [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
Introduction: Metaplastic breast carcinoma (MBC) is a rare histologic type of triple-negative breast cancer (TNBC), characterized by the presence of cells displaying squamous and/or mesenchymal differentiation. The transcriptomic profiles of MBCs have been reported to vary according to the type of metaplastic elements. The somatic genetic alterations that underpin this breast cancer subtype remain to be fully characterized. Here we sought to define the genomic landscape of MBCs, whether different subtypes of MBC would be driven by distinct constellations of genetic alterations, and to investigate functionally the impact of mutations affecting WNT pathway genes using non-malignant breast epithelial cells.
Methods: Thirty-five MBCs were retrieved from the pathology department of the authors' institutions and classified into the MBC histologic subtypes. All but one of the MBCs were of triple-negative phenotype. DNA was extracted from microdissected tumor-normal pairs and subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. The genomic profiles of MBCs were compared to those of 69 common type TNBCs from The Cancer Genome Atlas. Overall mutation rates were compared using the Mann Whitney U test, and the frequency of mutations in each gene was compared using Fisher's exact test. RNA was extracted from a subset of MBCs and subjected to WNT signaling pathway activation analysis with the RT2 Profiler PCR Array. Triple-negative non-malignant breast epithelial cells (MCF10A and MCF12A) and cancer cell lines were utilized for 2D and 3D functional studies.
Results: Whole-exome analysis revealed that MBCs displayed a median of 103 (15-344) somatic mutations, which did not differ from the median number of somatic mutations in common type TNBCs (76, range 14-233). The most frequent recurrently mutated cancer genes included TP53 (69%) and PIK3CA (29%). MBCs more frequently harbored mutations in PI3K pathway genes than common type TNBCs (57% vs 22%, P<0.05), including mutations affecting PIK3CA (29% vs 7%), PIK3R1 (11% vs 0) and PTEN (11% vs 1%). MBCs also more frequently harbored mutations affecting WNT signaling pathway genes (46% vs 26%, P<0.05), including AXIN1 (6% vs 1%), WNT5A (6% vs 0) and APC (3% vs 0). MBC subtype analysis revealed that PIK3CA mutations were only detected in non-chondroid MBCs (53% vs 0), CHERP mutations were only found in chondroid MBCs (25% vs 0), whereas USP5 mutations only found in squamous MBCs (33% vs 0). MBCs with somatic mutations in WNT pathway genes had significantly higher WNT pathway activation than MBCs lacking mutations in these genes (P=0.0244). Consistent with the mesenchymal phenotype frequently exhibited by MBCs, in vitro experiments provided functional evidence that aberrant WNT pathway activation induces an epithelial-to-mesenchymal transition (EMT) phenotype, with downregulation of epithelial markers and upregulation of EMT transcriptional inducers.
Conclusions: MBCs are significantly enriched for mutations affecting PI3K and WNT pathways, highlighting the importance of the dysregulation of the WNT pathway in MBC carcinogenesis. Moreover, our findings suggest that specific mutations are significantly associated with distinct histologic subtypes of MBCs.
Citation Format: Geyer FC, Ng CK, Piscuoglio S, Wen YH, Wen H-C, Pareja F, Eberle CA, Burke KA, Lim RS, Natrajan R, Mariani O, Brogi E, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS. The genomic landscape of breast metaplastic carcinoma [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-03.
Collapse
Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - CK Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - YH Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - H-C Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - CA Eberle
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - R Natrajan
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; The Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| |
Collapse
|
37
|
Ng CKY, Piscuoglio S, Geyer FC, Burke KA, Pareja F, Eberle CA, Lim RS, Natrajan R, Riaz N, Mariani O, Norton L, Vincent-Salomon A, Wen YH, Weigelt B, Reis-Filho JS. The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas. Clin Cancer Res 2017; 23:3859-3870. [PMID: 28153863 DOI: 10.1158/1078-0432.ccr-16-2857] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/04/2017] [Accepted: 01/23/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Metaplastic breast carcinoma (MBC) is a rare and aggressive histologic type of breast cancer, predominantly of triple-negative phenotype, and characterized by the presence of malignant cells showing squamous and/or mesenchymal differentiation. We sought to define the repertoire of somatic genetic alterations and the mutational signatures of MBCs.Experimental Design: Whole-exome sequencing was performed in 35 MBCs, with 16, 10, and 9 classified as harboring chondroid, spindle, and squamous metaplasia as the predominant metaplastic component. The genomic landscape of MBCs was compared with that of triple-negative invasive ductal carcinomas of no special type (IDC-NST) from The Cancer Genome Atlas. Wnt and PI3K/AKT/mTOR pathway activity was assessed using a qPCR assay.Results: MBCs harbored complex genomes with frequent TP53 (69%) mutations. In contrast to triple-negative IDC-NSTs, MBCs more frequently harbored mutations in PIK3CA (29%), PIK3R1 (11%), ARID1A (11%), FAT1 (11%), and PTEN (11%). PIK3CA mutations were not found in MBCs with chondroid metaplasia. Compared with triple-negative IDC-NSTs, MBCs significantly more frequently harbored mutations in PI3K/AKT/mTOR pathway-related (57% vs. 22%) and canonical Wnt pathway-related (51% vs. 28%) genes. MBCs with somatic mutations in PI3K/AKT/mTOR or Wnt pathway-related genes displayed increased activity of the respective pathway.Conclusions: MBCs are genetically complex and heterogeneous, and are driven by a repertoire of somatic mutations distinct from that of triple-negative IDC-NSTs. Our study highlights the genetic basis and the importance of PI3K/AKT/mTOR and Wnt pathway dysregulation in MBCs and provides a rationale for the metaplastic phenotype and the reported responses to PI3K/AKT/mTOR inhibitors in these tumors. Clin Cancer Res; 23(14); 3859-70. ©2017 AACR.
Collapse
Affiliation(s)
- Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carey A Eberle
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Y Hannah Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
38
|
Curtit E, Benhamo V, Gruel N, Popova T, Manie E, Cottu P, Mariani O, Stoppa-Lyonnet D, Pivot X, Stern MH, Vincent-Salomon A. First description of a sporadic breast cancer in a woman with BRCA1 germline mutation. Oncotarget 2016; 6:35616-24. [PMID: 26426992 PMCID: PMC4742129 DOI: 10.18632/oncotarget.5348] [Citation(s) in RCA: 8] [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: 06/22/2015] [Accepted: 09/17/2015] [Indexed: 12/04/2022] Open
Abstract
We describe the case of a woman carrying a germline pathogenic BRCA1 mutation diagnosed with a breast cancer overexpressing HER2. Clinical presentation of the tumor, HER2-positivity, genomic profile and loss of the mutated BRCA1 allele in tumor evidence that BRCA1 is not inactivated in this breast cancer. It represents the first biological demonstration for the existence of a sporadic HER2-positive breast cancer independent from BRCA loss of function in a woman carrier of a deleterious BRCA1 mutation. In a context where targeted therapies based on BRCA loss of function in the tumor are developed, such case could have direct implications.
Collapse
Affiliation(s)
- Elsa Curtit
- Department of Medical Oncology, Institut Curie, 75248 Paris, France.,Department of Medical Oncology, University Hospital, 25000 Besançon, France.,Medical Department, University of Franche-Comté, 25000 Besançon, France.,Medical Oncology Department, INSERM U1098, 25000 Besançon, France.,Present affiliations: 2-4; affiliation when working on this case: 1
| | - Vanessa Benhamo
- Université Paris Sciences Lettres, Medical Department, INSERM U934, Institut Curie, 75248 Paris, France
| | - Nadège Gruel
- Université Paris Sciences Lettres, Medical Department, INSERM U830, Institut Curie, 75248 Paris, France.,Department of Translational Research, Institut Curie, 75248 Paris, France
| | - Tatiana Popova
- Université Paris Sciences Lettres, Medical Department, INSERM U830, Institut Curie, 75248 Paris, France
| | - Elodie Manie
- Université Paris Sciences Lettres, Medical Department, INSERM U830, Institut Curie, 75248 Paris, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, 75248 Paris, France
| | - Odette Mariani
- Department of Pathology, Genetics and Immunology, Institut Curie, 75248 Paris, France
| | | | - Xavier Pivot
- Department of Medical Oncology, University Hospital, 25000 Besançon, France.,Medical Department, University of Franche-Comté, 25000 Besançon, France.,Medical Oncology Department, INSERM U1098, 25000 Besançon, France
| | - Marc-Henri Stern
- Université Paris Sciences Lettres, Medical Department, INSERM U830, Institut Curie, 75248 Paris, France
| | - Anne Vincent-Salomon
- Université Paris Sciences Lettres, Medical Department, INSERM U934, Institut Curie, 75248 Paris, France.,Department of Pathology, Genetics and Immunology, Institut Curie, 75248 Paris, France
| |
Collapse
|
39
|
Shlien A, Raine K, Fuligni F, Arnold R, Nik-Zainal S, Dronov S, Mamanova L, Rosic A, Ju YS, Cooke SL, Ramakrishna M, Papaemmanuil E, Davies HR, Tarpey PS, Van Loo P, Wedge DC, Jones DR, Martin S, Marshall J, Anderson E, Hardy C, Barbashina V, Aparicio SAJR, Sauer T, Garred Ø, Vincent-Salomon A, Mariani O, Boyault S, Fatima A, Langerød A, Borg Å, Thomas G, Richardson AL, Børresen-Dale AL, Polyak K, Stratton MR, Campbell PJ. Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer. Cell Rep 2016; 16:2032-46. [PMID: 27498871 PMCID: PMC4987284 DOI: 10.1016/j.celrep.2016.07.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/03/2016] [Accepted: 07/14/2016] [Indexed: 12/02/2022] Open
Abstract
Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation. Greater transcriptional activity in cancer than stromal cells, particularly when ER-ve Intron mutations only infrequently affect splicing, even at essential splice sites Distinctive RNA effects of sense-to-antisense and gene-to-intergenic rearrangements Exhaustive pipeline for identifying aberrant transcripts from RNA-sequencing data
Collapse
Affiliation(s)
- Adam Shlien
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Fabio Fuligni
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Roland Arnold
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Serge Dronov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lira Mamanova
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrej Rosic
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Young Seok Ju
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Susanna L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Helen R Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David R Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - John Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Elizabeth Anderson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Claire Hardy
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Violetta Barbashina
- Breakthrough Breast Cancer, The Institute of Cancer Research, London SM2 5NG, UK
| | | | - Torill Sauer
- Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | - Øystein Garred
- Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | | | | | | | | | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
| | - Åke Borg
- Department of Oncology, Lund University, SE-221 00 Lund, Sweden
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 69008 Lyon, France
| | | | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Haematology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK.
| |
Collapse
|
40
|
Sablin MP, Dubot C, Klijanienko J, Vacher S, Ouafi L, Chemlali W, Caly M, Sastre-Garau X, Lappartient E, Mariani O, Rodriguez J, Jouffroy T, Girod A, Calugaru V, Hoffmann C, Lidereau R, Berger F, Kamal M, Bieche I, Le Tourneau C. Identification of new candidate therapeutic target genes in head and neck squamous cell carcinomas. Oncotarget 2016; 7:47418-47430. [PMID: 27329726 PMCID: PMC5216951 DOI: 10.18632/oncotarget.10163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/01/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We aimed at identifying druggable molecular alterations at the RNA level from untreated HNSCC patients, and assessing their prognostic significance. METHODS We retrieved 96 HNSCC patients who underwent primary surgery. Real-time quantitative RT-PCR was used to analyze a panel of 42 genes coding for major druggable proteins. Univariate and multivariate analyses were performed to assess the prognostic significance of overexpressed genes. RESULTS Median age was 56 years [35-78]. Most of patients were men (80%) with a history of alcohol (70.4%) and/or tobacco consumption (72.5%). Twelve patients (12%) were HPV-positive. Most significantly overexpressed genes involved cell cycle regulation (CCND1 [27%], CDK6 [21%]), tyrosine kinase receptors (MET [18%], EGFR [14%]), angiogenesis (PGF [301%], VEGFA [14%]), and immune system (PDL1/CD274 [28%]). PIK3CA expression was an independent prognostic marker, associated with shorter disease-free survival. CONCLUSIONS We identified druggable overexpressed genes associated with a poor outcome that might be of interest for personalizing treatment of HNSCC patients.
Collapse
Affiliation(s)
- Marie-Paule Sablin
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Coraline Dubot
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | | | - Sophie Vacher
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - Lamia Ouafi
- Department of Biopathology, Institut Curie, Paris, France
| | - Walid Chemlali
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - Martial Caly
- Department of Biopathology, Institut Curie, Paris, France
| | | | | | - Odette Mariani
- Department of Biopathology, Institut Curie, Paris, France
| | | | | | | | | | | | - Rosette Lidereau
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - Frédérique Berger
- Department of Surgery, Institut Curie, Paris, France
- Department of Biostatistics, Institut Curie, Paris, France
| | - Maud Kamal
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
| | - Ivan Bieche
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
- EA7331, Paris Descartes University, Sorbonne Paris Cité, Faculty of Pharmaceutical and Biological Sciences, Paris, France
| | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
- EA7285, Versailles-Saint-Quentin-en-Yvelines University, Versailles, France
| |
Collapse
|
41
|
Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G. A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. Nat Commun 2016; 7:12222. [PMID: 27406316 PMCID: PMC4947184 DOI: 10.1038/ncomms12222] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/12/2016] [Indexed: 02/06/2023] Open
Abstract
HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism.
Collapse
Affiliation(s)
- Anthony Ferrari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Anne Vincent-Salomon
- Institut Curie, PSL Research University, Département de Pathologie, INSERM U934, 26 rue d'Ulm, 75248 Paris, France
| | - Xavier Pivot
- Centre Hospitalier Universitaire de Minjoz, UMR INSERM 1098, Boulevard A. Fleming, Besançon 25000, France
| | - Anne-Sophie Sertier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Emilie Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Sandrine Boyault
- Plateforme de génomique des cancers, Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Eskeatnaf Mulugeta
- Institut Curie, UMR 3215 CNRS, Génétique et biologie du développement, Epigénèse et développement des mammifères, U934 Inserm, 26 rue d'Ulm, 75248 Paris, France
| | - Isabelle Treilleux
- Centre Léon Bérard, Département de Pathologie, 28 rue Laënnec, 69008 Lyon, France
| | - Gaëtan MacGrogan
- Département de Biopathologie, Unité Inserm U916, Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux, France
| | - Laurent Arnould
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Vincent Le Texier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Hélène Blanché
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jean-François Deleuze
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jocelyne Jacquemier
- Institut Paoli-Calmettes, Département de Pathologie, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Marie-Christine Mathieu
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Frédérique Penault-Llorca
- Centre Jean Perrin, Département de Biopathologie, EA 4677 ERTICa, Université d'Auvergne, 58 rue Montalembert, 63000 Clermont-Ferrand, France
| | - Frédéric Bibeau
- Institut Régional du Cancer de Montpellier (ICM), Département de Pathologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Odette Mariani
- Institut Curie, PSL Research University, Service de Pathologie, Centre de Ressources Biologiques, BRIF BB-0033-00048, 26 rue d'Ulm, 75248 Paris, France
| | - Cécile Mannina
- Département de Pathologie, Institut Bergonié, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Jean-Yves Pierga
- Institut Curie, PSL Research University, Département d'Oncologie Médicale, Université Paris Descartes, 26 rue d'Ulm, 75248 Paris, France
| | - Olivier Trédan
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Thomas Bachelot
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Hervé Bonnefoi
- Department of Medical Oncology, Institut Bergonié Unicancer, University of Bordeaux, INSERM U916, CIC1401, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Gilles Romieu
- Institut Régional du Cancer de Montpellier (ICM), Oncologie Sénologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Pierre Fumoleau
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Suzette Delaloge
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Maria Rios
- Centre Alexis Vautrin, Département d'Oncologie Médicale, 6 Avenue de Bourgogne, 54511 Vandoeuvre Les Nancy, France
| | - Jean-Marc Ferrero
- Centre Antoine Lacassagne, Département d'Oncologie Médicale, 33 Avenue de Valombrose, 06189 Nice, France
| | - Carole Tarpin
- Institut Paoli-Calmettes, Département d'Oncologie Médicale, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Catherine Bouteille
- Clinique Mutualiste de Bellevue, Chirurgie Gynécologique et Mammaire, 3 rue le Verrier, 42100 Saint-Etienne, France
| | - Fabien Calvo
- Institut Gustave Roussy, Cancer Core Europe, 39 rue Camille Desmoulins, Villejuif 94805, France
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | | | - Iris Pauporté
- Institut National du Cancer, Département de Recherche Clinique, 52 Avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Pierre Saintigny
- INSERM U1052-CNRS 5286, Cancer Research Center of Lyon, F-69008 Lyon, France
- Université de Lyon, F-69622 Lyon, France
- Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Daniel Birnbaum
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Aix-Marseille Université, 232 boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, 38330 Montbonnot-Saint Martin, France
| | - Gilles Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| |
Collapse
|
42
|
Popova T, Manié E, Boeva V, Battistella A, Goundiam O, Smith NK, Mueller CR, Raynal V, Mariani O, Sastre-Garau X, Stern MH. Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications. Cancer Res 2016; 76:1882-91. [PMID: 26787835 DOI: 10.1158/0008-5472.can-15-2128] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/08/2016] [Indexed: 11/16/2022]
Abstract
CDK12 is a recurrently mutated gene in serous ovarian carcinoma, whose downregulation is associated with impaired expression of DNA damage repair genes and subsequent hypersensitivity to DNA-damaging agents and PARP1/2 inhibitors. In this study, we investigated the genomic landscape associated with CDK12 inactivation in patients with serous ovarian carcinoma. We show that CDK12 loss was consistently associated with a particular genomic instability pattern characterized by hundreds of tandem duplications of up to 10 megabases (Mb) in size. Tandem duplications were characterized by a bimodal (∼0.3 and ∼3 Mb) size distribution and overlapping microhomology at the breakpoints. This genomic instability, denoted as the CDK12 TD-plus phenotype, is remarkably distinct from other alteration patterns described in breast and ovarian cancers. The CDK12 TD-plus phenotype was associated with a greater than 10% gain in genomic content and occurred at a 3% to 4% rate in The Cancer Genome Atlas-derived and in-house cohorts of patients with serous ovarian carcinoma. Moreover, CDK12-inactivating mutations together with the TD-plus phenotype were also observed in prostate cancers. Our finding provides new insight toward deciphering the function of CDK12 in genome maintenance and oncogenesis. Cancer Res; 76(7); 1882-91. ©2016 AACR.
Collapse
Affiliation(s)
- Tatiana Popova
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France.
| | - Elodie Manié
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France
| | - Valentina Boeva
- Institut Curie, Centre de Recherche, Paris, France. PSL Research University, Paris, France. INSERM U900, Paris, France
| | - Aude Battistella
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France
| | - Oumou Goundiam
- Institut Curie, Centre de Recherche, Paris, France. PSL Research University, Paris, France. EA4340-BCOH, Versailles Saint-Quentin-en-Yvelines University, Guyancourt, France. Institut Curie, Département de Biopathologie, Paris, France. Institut Curie, Département de Recherche Translationnelle, Paris, France
| | - Nicholas K Smith
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France
| | | | - Virginie Raynal
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France
| | - Odette Mariani
- PSL Research University, Paris, France. Institut Curie, Département de Biopathologie, Paris, France. Institut Curie, Centre de Ressources Biologiques, Paris, France
| | - Xavier Sastre-Garau
- PSL Research University, Paris, France. EA4340-BCOH, Versailles Saint-Quentin-en-Yvelines University, Guyancourt, France. Institut Curie, Département de Biopathologie, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Centre de Recherche, Paris, France. INSERM U830, Paris, France. PSL Research University, Paris, France
| |
Collapse
|
43
|
Gruel N, Fuhrmann L, Lodillinsky C, Benhamo V, Mariani O, Cédenot A, Arnould L, Macgrogan G, Sastre-Garau X, Chavrier P, Delattre O, Vincent-Salomon A. LIN7A is a major determinant of cell-polarity defects in breast carcinomas. Breast Cancer Res 2016; 18:23. [PMID: 26887652 PMCID: PMC4756502 DOI: 10.1186/s13058-016-0680-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 12/18/2015] [Accepted: 01/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background Polarity defects are a hallmark of most carcinomas. Cells from invasive micropapillary carcinomas (IMPCs) of the breast are characterized by a striking cell polarity inversion and represent an interesting model for the analysis of polarity abnormalities. Methods In-depth investigation of polarity proteins in 24 IMPCs and a gene expression profiling, comparing IMPC (n = 73) with invasive carcinomas of no special type (ICNST) (n = 51) have been performed. Results IMPCs showed a profound disorganization of the investigated polarity proteins and revealed major abnormalities in their subcellular localization. Gene expression profiling experiments highlighted a number of deregulated genes in the IMPCs that have a role in apico-basal polarity, adhesion and migration. LIN7A, a Crumbs-complex polarity gene, was one of the most differentially over-expressed genes in the IMPCs. Upon LIN7A over-expression, we observed hyperproliferation, invasion and a complete absence of lumen formation, revealing strong polarity defects. Conclusion This study therefore shows that LIN7A has a crucial role in the polarity abnormalities associated with breast carcinogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0680-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nadège Gruel
- Institut Curie, PSL Research University, INSERM U830, 26 rue d'Ulm, 75248, Paris cédex 05, France. .,Département de Recherche Translationnelle, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Laetitia Fuhrmann
- Institut Curie, PSL Research University, CNRS UMR144, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Catalina Lodillinsky
- Institut Curie, PSL Research University, CNRS UMR144, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Vanessa Benhamo
- Institut Curie, PSL Research University, INSERM U830, 26 rue d'Ulm, 75248, Paris cédex 05, France. .,Département de Recherche Translationnelle, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Odette Mariani
- Department of Pathology, Institut Curie, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Aurélie Cédenot
- Department of Pathology, Institut Curie, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Laurent Arnould
- Département de Pathologie and Centre de Ressources Biologiques Ferdinand Cabanne, Centre Georges François Leclerc, 1 rue Professeur Marion, BP 77980, 21079, Dijon cédex, France.
| | - Gaëtan Macgrogan
- Institut Bergonié, Service de Biopathologie, 229 cours de l'Argonne, 33076, Bordeaux, France.
| | - Xavier Sastre-Garau
- Department of Pathology, Institut Curie, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Philippe Chavrier
- Institut Curie, PSL Research University, CNRS UMR144, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Olivier Delattre
- Institut Curie, PSL Research University, INSERM U830, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| | - Anne Vincent-Salomon
- Institut Curie, PSL Research University, INSERM U830, 26 rue d'Ulm, 75248, Paris cédex 05, France. .,Department of Pathology, Institut Curie, 26 rue d'Ulm, 75248, Paris cédex 05, France.
| |
Collapse
|
44
|
Piscuoglio S, Ng CKY, Marchio C, Eberle CA, Guerini-Rocco E, Mariani O, Vincent-Salomon A, Reis-Filho JS, Weigelt B. Abstract P6-07-04: Distinct repertoires of somatic mutations affecting driver genes in mucinous and neuroendocrine carcinomas of the breast. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-07-04] [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: Mucinous carcinoma of the breast (MCB) is a rare histologic type, which accounts for approximately 2% of all invasive breast cancers (IBCs) and is characterized by clusters of tumor cells floating in large amounts of extracellular mucin. MCB comprises two main subtypes based on architectural and cytologic features: mucinous A (paucicellular) and mucinous B (hypercellular). Although MCBs are low-grade ER-positive/HER2-negative tumors of luminal molecular subtype, these cancers lack concurrent losses of 16q and gains of 1q, the hallmark genetic features of low-grade ER+/HER2- breast cancers, and have low levels of genetic instability. Neuroendocrine carcinoma of the breast (NCB) accounts for 2% - 5% of IBCs and displays morphologic features similar to those of neuroendocrine tumors of other organs. Previous transcriptomic analyses have revealed that NCBs and mucinous B, but not mucinous A, breast cancers display similar gene expression profiles. The aims of this study were to determine whether MCBs and NCBs share a similar repertoire of somatic genetic alterations and if these aberrations are distinct from those reported in common forms of ER+/HER2- IBCs.
Material and methods: DNA extracted from microdissected MCBs (n=7 mucinous A, n=6 mucinous B), NCBs (n=14) and adjacent normal tissues were subjected to massively parallel sequencing targeting all exons of 254 genes most frequently mutated in IBC or related to DNA repair. Somatic point mutations were identified using MuTect and somatic insertions and deletions (indels) were defined using Strelka and Varscan2. We retrieved mutations in the same 254 genes in common forms of ER+/HER2- IBC (n=252) from The Cancer Genome Atlas (TCGA).
Results: The most frequently mutated genes in MCBs were GATA3 (31% of cases, 4/13, all frame-shift indels), followed by KMT2C (MLL3) and MAP3K1 (both 23%). GATA3 and KMT2C (29%) were the most frequently mutated genes in mucinous A cancers, whereas MAP3K1 (33%) was the most frequently mutated gene in mucinous B cancers. ARID1A mutations were found in three of 14 (21%) NCBs, of which 2 were truncating mutations. A comparative analysis of the repertoire of somatic mutations found in mucinous A, mucinous B and NCBs did not reveal any statistically significant differences. As compared to common forms of ER+/HER2- IBCs, MCBs were found to have a significantly lower frequency of PIK3CA (8% vs 42%, p=0.02) mutations, which was particularly evident in mucinous A cancers (0% vs 42%, p=0.04). NCBs displayed significantly higher frequencies of somatic mutations affecting ARID1A (21% vs 2%, respectively, p=0.006), FOXA1 (14% vs 2%, respectively, p<0.05) and a lower frequency of PIK3CA somatic mutations (14% vs 42%, respectively, p<0.05) than common forms of ER+/HER2- IBCs.
Conclusion: The frequency of mutations affecting bona fide breast cancer genes differed among mucinous A, mucinous B and NCBs. The repertoire of somatic mutations found in MCBs and NCBs differed from that of common forms of ER+/HER2- IBCs, in particular by the low frequency of somatic mutations affecting PIK3CA.
Citation Format: Piscuoglio S, Ng CKY, Marchio C, Eberle CA, Guerini-Rocco E, Mariani O, Vincent-Salomon A, Reis-Filho JS, Weigelt B. Distinct repertoires of somatic mutations affecting driver genes in mucinous and neuroendocrine carcinomas of the breast. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-04.
Collapse
Affiliation(s)
- S Piscuoglio
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - C Marchio
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - CA Eberle
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - E Guerini-Rocco
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, NY, NY; School of Pathology, University of Milan, Milan, Italy; Institut Curie, Paris, France
| |
Collapse
|
45
|
Piscuoglio S, Ng CKY, Cowell CF, Mariani O, Martelotto L, Natrajan R, Lim RS, Maher CA, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Abstract P6-03-10: Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-03-10] [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: Metaplastic breast carcinoma (MBC) is a rare form of triple-negative breast cancer (TNBC), accounting for approximately 0.2%-5% of all invasive breast cancers. These tumors are characterized by the presence of neoplastic cells displaying differentiation towards squamous epithelium or mesenchymal elements. MBCs are reported to have an aggressive clinical behavior, to exhibit a worse prognosis and to respond less frequently to conventional chemotherapy regimens than common forms of TNBCs. In this study, we sought to define whether morphologically distinct subgroups of MBCs would be underpinned by distinct gene expression or copy number profiles, and whether MBCs, akin to other special histologic types of TNBC (e.g. secretory carcinoma and adenoid cystic carcinoma), would be underpinned by a highly recurrent fusion gene.
Methods: RNA and DNA samples were extracted from microdissected frozen MBCs (5 squamous, 5 spindle and 7 chondroid) and subjected to gene expression profiling using the Illumina Human HT-12 v4 platform and gene copy number profiling using the Affymetrix Human SNP 6.0 arrays, respectively. Genes differentially expressed between MBC subtypes were identified using SAM, and functional annotation of these genes was performed using Ingenuity Pathway Analysis. Intrinsic molecular subtypes were determined using the PAM50 and claudin-low intrinsic gene lists. In addition, all cases were subjected to paired-end massively parallel RNA-sequencing (Illumina GAIIx). Putative expressed fusion transcripts were identified using a validated algorithm (i.e. ChimeraScan), and confirmed by means of RT-PCR.
Results: MBCs with spindle cell morphology were all classified as of claudin-low intrinsic subtype, whereas MBCs with chondroid or squamous cell metaplasia were classified as of normal breast-like, basal-like or claudin-low subtypes, suggesting that these morphologic subgroups are heterogeneous. Unsupervised analysis of microarray and RNA-sequencing gene expression data further demonstrated that MBCs with spindle cell differentiation displayed distinctive transcriptomic profiles, and formed clusters distinct from those enriched for MBCs with chondroid and squamous cell metaplasia. MBCs with spindle cell morphology preferentially expressed regulators of epithelial-to-mesenchymal transition including lower expression of E-cadherin and EpCAM. At the genomic level, MBC subtypes displayed patterns of gene copy number alterations similar to those of common forms of TNBCs from The Cancer Genome Atlas, and no significant differences were found among the distinct MBC subtypes. Nine in-frame fusion genes, TBL1XR1-PIK3CA, WAPL-CDHR1, MAP2K3-HMGCLL, PARG-BMS1, FN1-ICAM1, TNKS1BP1-SPARC, AAK1-ARNT2, MBTPS1-TCEANC2 and PSMA6-SHMT1 were identified and validated in the index cases, however none of these was found to be recurrent in the cases analyzed in this study.
Conclusion: MBC subtypes, despite harboring similar patterns of gene copy number alterations, display significant transcriptomic differences, which may account for their distinct histologic features. Our findings also demonstrate that unlike other histologic special types of TNBC, MBCs are not underpinned by a highly recurrent expressed fusion gene.
Citation Format: Piscuoglio S, Ng CKY, Cowell CF, Mariani O, Martelotto L, Natrajan R, Lim RS, Maher CA, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Genomic and transcriptomic heterogeneity in metaplastic breast carcinomas. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-10.
Collapse
Affiliation(s)
- S Piscuoglio
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - CF Cowell
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - L Martelotto
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - R Natrajan
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - CA Maher
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, NY, NY; Institut Curie, Paris, France; The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom; The Genome Institute, Washington University School of Medicine, St Louis, MO
| |
Collapse
|
46
|
Comte A, Sigal-Zafrani B, Belin L, Bièche I, Callens C, Diéras V, Bidard FC, Mariani O, Servois V, Szwarc D, Vincent-Salomon A, Brain ECG, Cottu PH. Abstract P2-05-06: Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p2-05-06] [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: Cumulative evidence for phenotypic and molecular heterogeneity between primary breast cancer (BC) site and matched metastasis (mets) has been obtained in retrospective studies. Current expert consensus suggests performing biopsies of mets, but clinical utility and cost are unknown. The primary objective of the ESOPE study (NCT01956552) was to compare the phenotype and genotype of the primary tumor (PT) with those of matched mets at time of first distant relapse, before the start of any treatment, in order to optimize the treatment of mets
PATIENTS and METHODS: Between Nov. 2010 and Sept. 2013, we conducted a prospective multicenter study on BC patients (pts) with diagnosis of first mets. All pts were to have available Formalin-Fixed Paraffin-Embedded (FFPE) PT sample and mets accessible to either percutaneous or surgical sampling. All tissue samples were centrally analyzed with immunohistochemistry (ER, PgR, HER2, and Ki67) and FISH when indicated. Frozen samples were stored for further analyses. We recorded intended therapeutic decision before and after biopsy.
RESULTS: Of 93 pts included, 89 were eligible for biopsy. Median age was 57 years (28-81); median interval between PT and mets was 42 months (0-211), including 14 pts with novo metastatic breast cancer. Mets biopsy was performed in 85 pts (96%, refusal n=2, not feasible n=2). Toxicity was limited to only 1 grade 1 hemorrhage. Sampled sites were liver (44%), lung (16%), bone (13%), lymph node (13%), skin/muscle/chest wall (9%), ovary/peritoneum (4%), and adrenal gland (1%). PT was not available in 4 pts; mets biopsy was non contributive in 6 pts but led to a diagnosis of second primary cancer in 3 pts.
In 72 pts with matched PT and mets, PT were luminal A (n=11), luminal B (n=33), triple negative (n=13), HER2 (n=13), non-evaluable (n=2). Mets were luminal A (n=6), luminal B (n=30), triple negative (n=16), HER2 (n=14), non-evaluable (n=6). Discrepancy rates were: ER 18% [kappa for concordance =0.6, CI 95 % (0.42-0.77)], PgR: 39% [kappa=0.19, CI 95% (0.01-0.39)], Her2: 4% [kappa=0.86, CI 95% (0.7-1)], Ki67: 25% [kappa=0.19, CI 95% (-0.09; 0.49)].
The most frequent discrepancy rate was observed in pts with lum A PT, as only 3/10 developed Lum A mets. HER2 and triple negative were the most stable subtypes (12/13 and 12/12 respectively). Most importantly, mets biopsy led to a change in therapeutic decision in 25 pts (independent evaluation by 2 oncologists). Additional comparative targeted NGS analyses are ongoing on a first subset of 54 FFPE paired samples, and parallel whole exome sequencing is planned on 38 paired samples with available constitutional DNA.
CONCLUSION: Comparative analysis of breast cancer PT and first mets is routinely feasible, with very low morbidity and a significant impact for patients' management: 29% had a second cancer diagnosis or were proposed a therapeutic change. Furthermore, this study will provide additional data on quality and quantity of tissue available for molecular analysis, and ultimately in terms of cost-efficacy.
Citation Format: Comte A, Sigal-Zafrani B, Belin L, Bièche I, Callens C, Diéras V, Bidard F-C, Mariani O, Servois V, Szwarc D, Vincent-Salomon A, Brain ECG, Cottu PH. Clinical utility of systematic biopsy of first metastatic event in breast cancer: Results from a prospective multicenter trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-05-06.
Collapse
Affiliation(s)
- A Comte
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - B Sigal-Zafrani
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - L Belin
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - I Bièche
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - C Callens
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - V Diéras
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - F-C Bidard
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - O Mariani
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - V Servois
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - D Szwarc
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | | | - ECG Brain
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| | - PH Cottu
- Institut Curie, Paris, France; Institut Curie, Saint Cloud, France
| |
Collapse
|
47
|
Romano A, Hou X, Sertorio M, Dessein H, Cabantous S, Oliveira P, Li J, Oyegue S, Arnaud V, Luo X, Daujat-Chavanieu M, Mariani O, Sastre X, Dombey AM, He H, Li Y, Dessein A. Correction: FOXP3+ Regulatory T Cells in Hepatic Fibrosis and Splenomegaly Caused by Schistosoma japonicum: The Spleen May Be a Major Source of Tregs in Subjects with Splenomegaly. PLoS Negl Trop Dis 2016; 10:e0004454. [PMID: 26849557 PMCID: PMC4743961 DOI: 10.1371/journal.pntd.0004454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
48
|
Romano A, Hou X, Sertorio M, Dessein H, Cabantous S, Oliveira P, Li J, Oyegue S, Arnaud V, Luo X, Chavanieu M, Mariani O, Sastre X, Dombey AM, He H, Li Y, Dessein A. FOXP3+ Regulatory T Cells in Hepatic Fibrosis and Splenomegaly Caused by Schistosoma japonicum: The Spleen May Be a Major Source of Tregs in Subjects with Splenomegaly. PLoS Negl Trop Dis 2016; 10:e0004306. [PMID: 26731721 PMCID: PMC4701139 DOI: 10.1371/journal.pntd.0004306] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Schistosoma eggs cause chronic liver inflammation and a complex disease characterized by hepatic fibrosis (HF) and splenomegaly (SplM). FOXP3+ Tregs could regulate inflammation, but it is unclear where these cells are produced and what roles they play in human schistosomiasis. We investigated blood and spleen FOXP3+ Tregs in Chinese fishermen with lifelong exposure to Schistosoma japonicum and various degrees of liver and spleen disease. FOXP3+ Tregs accounted for 4.3% of CD4+ T cells and 41.2% of FOXP3+CD4+ T cells; they could be divided into CD45RA-FOXP3hi effector (eTregs) and CD45RA+FOXP3low naive Tregs. Blood Treg levels were high in severe HF (+1.3; p = 0.004) and in SplM (+1.03, p = 0.03). Multivariate regression showed that severe HF (+0.85, p = 0.01) and SplM (+0.97; p = 0.05) were independently associated with the higher proportion of Tregs in the blood. This effect was mostly due to an increase in the proportion of eTregs in the blood of HF+++ (+0.9%; p = 0.04) and SplM (+0.9%; p = 0.04) patients. The proportion of eTregs expressing CXCR3 in the blood was lower in the HF+++ patients (37.4 +/- 5.9%) than in those with milder fibrosis (51.7 ± 2%; p = 0.009), whereas proportion were similar for cells expressing CD25hi, CCR7, and CTLA-4. Splenectomy improves symptoms and was associated with decreases in blood FOXP3+ Treg (-2.5; p<0.001) and eTreg (-1.3; p = 0.03) levels. SplM spleens contained a high proportion of eTregs with CXCR3, CCR5 and CTLA4 upregulation and CCR7 downregulation. This, and the strong expression of ligands of CXCR3 and CCR5 in the liver (n = 8) but not in the spleen suggested that spleen eTregs migrated to Th1-infiltrated liver tissues. Such migration may be attenuated in hepatosplenic patients due to lower levels of CXCR3 expression on Tregs (p = 0.009). Thus, higher blood Treg levels are associated with severe liver disease and splenomegaly. Our data are consistent with the hypothesis that the spleen is a major source of Tregs in subjects with splenomegaly. In most cases, Tregs migrate to the Th1-infiltrated liver and the lower levels of CXCR3+ Tregs in the blood of patients with severe schistosomiasis suggest that decreases in Treg migration sites of inflammation may aggravate the disease.
Collapse
Affiliation(s)
- Audrey Romano
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Xunya Hou
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | - Mathieu Sertorio
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Hélia Dessein
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Sandrine Cabantous
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Pablo Oliveira
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Jun Li
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | - Sandrine Oyegue
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Violaine Arnaud
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
| | - Xinsong Luo
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | | | | | | | | | - Hongbin He
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | - Yuesheng Li
- Hunan Institute of Parasitic Diseases, Yueyang, China
| | - Alain Dessein
- INSERM, UMR-906, Marseille, France
- Université Aix-Marseille, Faculté de Médecine, Marseille, France
- Assistance Publique, Hôpitaux de Marseille, Marseille, France
- * E-mail:
| |
Collapse
|
49
|
Manié E, Popova T, Battistella A, Tarabeux J, Caux-Moncoutier V, Golmard L, Smith NK, Mueller CR, Mariani O, Sigal-Zafrani B, Dubois T, Vincent-Salomon A, Houdayer C, Stoppa-Lyonnet D, Stern MH. Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. Int J Cancer 2015; 138:891-900. [DOI: 10.1002/ijc.29829] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 06/25/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Elodie Manié
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Tatiana Popova
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Aude Battistella
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Julien Tarabeux
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | | | - Lisa Golmard
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
| | - Nicholas K. Smith
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| | - Christopher R. Mueller
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Queen's Cancer Research Institute, Queen's University, Kingston; Ontario K7L 3N6 Canada
| | - Odette Mariani
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
- Centre De Ressources Biologiques; Institut Curie; Paris F-75248 France
| | | | - Thierry Dubois
- Centre De Recherche; Institut Curie; Paris F-75248 France
- Département De Recherche Translationnelle; Institut Curie; Paris F-75248 France
| | | | - Claude Houdayer
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
| | - Dominique Stoppa-Lyonnet
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
- Département De Biologie Des Tumeurs; Institut Curie; Paris F-75248 France
- Sorbonne Paris Cité; University Paris-Descartes; Paris F-75270 France
| | - Marc-Henri Stern
- Centre De Recherche; Institut Curie; Paris F-75248 France
- INSERM U830; Paris F-75248 France
| |
Collapse
|
50
|
Sablin M, Dubot C, Kamal M, Rodriguez J, Jouffroy T, Girod A, Calugaru V, Klijanienko J, Caly M, Sastre-Garau X, Lappartient E, Mariani O, Berger F, Vacher S, Biáche I, Tourneau CL. 2878 Identification of actionable genes in head and neck squamous cell carcinoma (HNSCC) using gene expression analyses. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31615-x] [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: 10/22/2022]
|