Publications by authors named "Lynnette Fernandez-Cuesta"

31 Publications

Challenges in lung and thoracic pathology: molecular advances in the classification of pleural mesotheliomas.

Virchows Arch 2021 Jan 7;478(1):73-80. Epub 2021 Jan 7.

Section of Genetics, International Agency for Research on Cancer (IARC/WHO), Lyon, France.

The diagnosis and classification of malignant pleural mesothelioma (MPM) is extremely challenging; obtaining an accurate histopathological diagnosis of the different types and subtypes requires expert assessment and suitable biopsies that are not always available, which can leave doctors uncertain about the patient's diagnosis, sometimes resulting in a delay in the start of treatment. In this review, we discuss recent major advances in the molecular characterisation of MPM and their implications for histological classification. We detail what is known of the molecular landscape of MPM at the genomic, transcriptomic, and epigenomic levels, describe the similarities and dissimilarities of the multiple molecular classifications that have been proposed, and provide an overview of the current state of knowledge regarding inter- and intra-tumour heterogeneity. We also highlight the current gaps in knowledge and how addressing them would benefit classification, as well as the patients in general.
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http://dx.doi.org/10.1007/s00428-020-02980-9DOI Listing
January 2021

New molecular classification of large cell neuroendocrine carcinoma and small cell lung carcinoma with potential therapeutic impacts.

Transl Lung Cancer Res 2020 Oct;9(5):2233-2244

Université Grenoble Alpes, Grenoble, France.

Large cell neuroendocrine carcinoma (LCNECs) and small cell lung carcinomas (SCLCs) are high-grade neuroendocrine carcinomas of the lung with very aggressive behavior and poor prognosis. Their histological classification as well as their therapeutic management has not changed much in recent years, but genomic and transcriptomic analyses have revealed different molecular subtypes raising hopes for more personalized treatment. Indeed, four subtypes of SCLCs have been recently described, SCLC-A driven by the master gene ASCL1, SCLC-N driven by NEUROD1, SCLC-Y by YAP1 and SCLC-P by POU2F3. Whereas SCLC standard of care is based on concurrent chemoradiation for limited stages and on chemotherapy alone or chemotherapy combined with anti-PD-L1 checkpoint inhibitors for extensive stage SCLC, SCLC-A variants could benefit from DLL3 or BCL2 inhibitors, and SCLC-N variants from Aurora kinase inhibitors combined with chemotherapy, or PI3K/mTOR or HSP90 inhibitors. In addition, a new SCLC variant (SCLC-IM) with high-expression of immune checkpoints has been also reported, which could benefit from immunotherapies. PARP inhibitors also gave promising results in combination with chemotherapy in a subset of SCLCs. Regarding LCNECs, they represent a heterogeneous group of tumors, some of them exhibiting mutations also found in SCLC but with a pattern of expression of NSCLC, while others harbor mutations also found in NSCLC but with a pattern of expression of SCLC, questioning their clinical management as NSCLCs or SCLCs. Overall, we are probably entering a new area, which, if personalized treatments are effective, will also lead to the implementation in practice of molecular testing or biomarkers detection for the selection of patients who can benefit from them.
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http://dx.doi.org/10.21037/tlcr-20-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653155PMC
October 2020

A molecular map of lung neuroendocrine neoplasms.

Gigascience 2020 10;9(11)

Section of Genetics, International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69372 Lyon CEDEX 08, France.

Background: Lung neuroendocrine neoplasms (LNENs) are rare solid cancers, with most genomic studies including a limited number of samples. Recently, generating the first multi-omic dataset for atypical pulmonary carcinoids and the first methylation dataset for large-cell neuroendocrine carcinomas led us to the discovery of clinically relevant molecular groups, as well as a new entity of pulmonary carcinoids (supra-carcinoids).

Results: To promote the integration of LNENs molecular data, we provide here detailed information on data generation and quality control for whole-genome/exome sequencing, RNA sequencing, and EPIC 850K methylation arrays for a total of 84 patients with LNENs. We integrate the transcriptomic data with other previously published data and generate the first comprehensive molecular map of LNENs using the Uniform Manifold Approximation and Projection (UMAP) dimension reduction technique. We show that this map captures the main biological findings of previous studies and can be used as reference to integrate datasets for which RNA sequencing is available. The generated map can be interactively explored and interrogated on the UCSC TumorMap portal (https://tumormap.ucsc.edu/?p=RCG_lungNENomics/LNEN). The data, source code, and compute environments used to generate and evaluate the map as well as the raw data are available, respectively, in a Nextjournal interactive notebook (https://nextjournal.com/rarecancersgenomics/a-molecular-map-of-lung-neuroendocrine-neoplasms/) and at the EMBL-EBI European Genome-phenome Archive and Gene Expression Omnibus data repositories.

Conclusions: We provide data and all resources needed to integrate them with future LNENs transcriptomic studies, allowing meaningful conclusions to be drawn that will eventually lead to a better understanding of this rare understudied disease.
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http://dx.doi.org/10.1093/gigascience/giaa112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596803PMC
October 2020

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data.

NAR Genom Bioinform 2020 Jun 20;2(2):lqaa021. Epub 2020 Apr 20.

Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyon, France.

The emergence of next-generation sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations, such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accurately call mutations. Needlestack is based on the idea that the sequencing error rate can be dynamically estimated from analysing multiple samples together. We show that the sequencing error rate varies across alterations, illustrating the need to precisely estimate it. We evaluate the performance of needlestack for various types of variations, and we show that needlestack is robust among positions and outperforms existing state-of-the-art method for low abundance mutations. Needlestack, along with its source code is freely available on the GitHub platform: https://github.com/IARCbioinfo/needlestack.
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http://dx.doi.org/10.1093/nargab/lqaa021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182099PMC
June 2020

Comprehensive Molecular and Pathologic Evaluation of Transitional Mesothelioma Assisted by Deep Learning Approach: A Multi-Institutional Study of the International Mesothelioma Panel from the MESOPATH Reference Center.

J Thorac Oncol 2020 06 9;15(6):1037-1053. Epub 2020 Mar 9.

MESOPATH, MESONAT, MESOBANK Department of BioPathology Centre Leon Berard, Lyon, France; CHU Cochin-Hotel Dieu, Department of Pathology, Paris, France.

Introduction: Histologic subtypes of malignant pleural mesothelioma are a major prognostic indicator and decision denominator for all therapeutic strategies. In an ambiguous case, a rare transitional mesothelioma (TM) pattern may be diagnosed by pathologists either as epithelioid mesothelioma (EM), biphasic mesothelioma (BM), or sarcomatoid mesothelioma (SM). This study aimed to better characterize the TM subtype from a histological, immunohistochemical, and molecular standpoint. Deep learning of pathologic slides was applied to this cohort.

Methods: A random selection of 49 representative digitalized sections from surgical biopsies of TM was reviewed by 16 panelists. We evaluated BAP1 expression and CDKN2A (p16) homozygous deletion. We conducted a comprehensive, integrated, transcriptomic analysis. An unsupervised deep learning algorithm was trained to classify tumors.

Results: The 16 panelists recorded 784 diagnoses on the 49 cases. Even though a Kappa value of 0.42 is moderate, the presence of a TM component was diagnosed in 51%. In 49% of the histological evaluation, the reviewers classified the lesion as EM in 53%, SM in 33%, or BM in 14%. Median survival was 6.7 months. Loss of BAP1 observed in 44% was less frequent in TM than in EM and BM. p16 homozygous deletion was higher in TM (73%), followed by BM (63%) and SM (46%). RNA sequencing unsupervised clustering analysis revealed that TM grouped together and were closer to SM than to EM. Deep learning analysis achieved 94% accuracy for TM identification.

Conclusion: These results revealed that the TM pattern should be classified as non-EM or at minimum as a subgroup of the SM type.
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http://dx.doi.org/10.1016/j.jtho.2020.01.025DOI Listing
June 2020

Molecular studies of lung neuroendocrine neoplasms uncover new concepts and entities.

Transl Lung Cancer Res 2019 Dec;8(Suppl 4):S430-S434

International Agency for Research on Cancer (IARC/WHO), Section of Genetics, 150 Cours Albert Thomas, Lyon, France.

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http://dx.doi.org/10.21037/tlcr.2019.11.08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6987337PMC
December 2019

Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions.

EBioMedicine 2019 Oct 21;48:191-202. Epub 2019 Oct 21.

Toulouse University Hospital, Toulouse, France.

Background: Malignant Pleural Mesothelioma (MPM) is an aggressive disease related to asbestos exposure, with no effective therapeutic options.

Methods: We undertook unsupervised analyses of RNA-sequencing data of 284 MPMs, with no assumption of discreteness. Using immunohistochemistry, we performed an orthogonal validation on a subset of 103 samples and a biological replication in an independent series of 77 samples.

Findings: A continuum of molecular profiles explained the prognosis of the disease better than any discrete model. The immune and vascular pathways were the major sources of molecular variation, with strong differences in the expression of immune checkpoints and pro-angiogenic genes; the extrema of this continuum had specific molecular profiles: a "hot" bad-prognosis profile, with high lymphocyte infiltration and high expression of immune checkpoints and pro-angiogenic genes; a "cold" bad-prognosis profile, with low lymphocyte infiltration and high expression of pro-angiogenic genes; and a "VEGFR2+/VISTA+" better-prognosis profile, with high expression of immune checkpoint VISTA and pro-angiogenic gene VEGFR2. We validated the gene expression levels at the protein level for a subset of five selected genes belonging to the immune and vascular pathways (CD8A, PDL1, VEGFR3, VEGFR2, and VISTA), in the validation series, and replicated the molecular profiles as well as their prognostic value in the replication series.

Interpretation: The prognosis of MPM is best explained by a continuous model, which extremes show specific expression patterns of genes involved in angiogenesis and immune response.
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http://dx.doi.org/10.1016/j.ebiom.2019.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838392PMC
October 2019

EURACAN/IASLC Proposals for Updating the Histologic Classification of Pleural Mesothelioma: Towards a More Multidisciplinary Approach.

J Thorac Oncol 2020 01 20;15(1):29-49. Epub 2019 Sep 20.

Department of Pathology, New York University Langone Health, New York, New York.

Introduction: Molecular and immunologic breakthroughs are transforming the management of thoracic cancer, although advances have not been as marked for malignant pleural mesothelioma where pathologic diagnosis has been essentially limited to three histologic subtypes.

Methods: A multidisciplinary group (pathologists, molecular biologists, surgeons, radiologists, and oncologists), sponsored by European Network for Rare Adult Solid Cancers/International Association for the Study of Lung Cancer, met in 2018 to critically review the current classification.

Results: Recommendations include: (1) classification should be updated to include architectural patterns and stromal and cytologic features that refine prognostication; (2) subject to data accrual, malignant mesothelioma in situ could be an additional category; (3) grading of epithelioid malignant pleural mesotheliomas should be routinely undertaken; (4) favorable/unfavorable histologic characteristics should be routinely reported; (5) clinically relevant molecular data (programmed death ligand 1, BRCA 1 associated protein 1 [BAP1], and cyclin dependent kinase inhibitor 2A) should be incorporated into reports, if undertaken; (6) other molecular data should be accrued as part of future trials; (7) resection specimens (i.e., extended pleurectomy/decortication and extrapleural pneumonectomy) should be pathologically staged with smaller specimens being clinically staged; (8) ideally, at least three separate areas should be sampled from the pleural cavity, including areas of interest identified on pre-surgical imaging; (9) image-acquisition protocols/imaging terminology should be standardized to aid research/refine clinical staging; (10) multidisciplinary tumor boards should include pathologists to ensure appropriate treatment options are considered; (11) all histologic subtypes should be considered potential candidates for chemotherapy; (12) patients with sarcomatoid or biphasic mesothelioma should not be excluded from first-line clinical trials unless there is a compelling reason; (13) tumor subtyping should be further assessed in relation to duration of response to immunotherapy; and (14) systematic screening of all patients for germline mutations is not recommended, in the absence of a family history suspicious for BAP1 syndrome.

Conclusions: These multidisciplinary recommendations for pathology classification and application will allow more informative pathologic reporting and potential risk stratification, to support clinical practice, research investigation and clinical trials.
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http://dx.doi.org/10.1016/j.jtho.2019.08.2506DOI Listing
January 2020

Highlights of the 14th international mesothelioma interest group meeting: Pathologic separation of benign from malignant mesothelial proliferations and histologic/molecular analysis of malignant mesothelioma subtypes.

Lung Cancer 2018 10 30;124:95-101. Epub 2018 Jul 30.

Centre National Référent MESOPATHm Centre Leon Berard, Lyon, France.

Objectives: The separation of benign from malignant mesothelial proliferations and exact subclassification of mesothelioma subtypes is crucial to determining patient care and prognosis but morphologically can be very difficult.

Methods: This session of the 2018 IMIG meeting addressed these problems.

Results: A new immunohistochemical marker, methylthioadenosine phosphorylase, was shown to correlate well with CDKN2A FISH and is cheaper and faster to run. A 117 gene expression panel also provided good separation on both tissue biopsy and cytology samples. Review of a series of mesotheliomas thought to be biphasic produced only a moderate level of agreement among expert pathologists with some cases being classified as purely epithelioid or sarcomatoid; these classifications had prognostic significance. The entity called transitional mesothelioma was found to behave exactly like sarcomatoid mesothelioma. RNA-seq analysis of a large series of mesotheliomas from a public database showed that, genetically, the morphologic breakdown into epithelioid, sarcomatoid, or biphasic mesotheliomas is artificial because there is a continuous spectrum of genomic changes. There are now criteria for the diagnosis of mesothelioma in situ and this is potentially important, since such cases might be curable.

Conclusions: This session documented new morphological and molecular approaches to separating benign from malignant mesothelial proliferations and to subclassifying malignant mesoteheliomas in clinical relevant ways.
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http://dx.doi.org/10.1016/j.lungcan.2018.07.041DOI Listing
October 2018

A common classification framework for neuroendocrine neoplasms: an International Agency for Research on Cancer (IARC) and World Health Organization (WHO) expert consensus proposal.

Mod Pathol 2018 12 23;31(12):1770-1786. Epub 2018 Aug 23.

International Agency for Research on Cancer (IARC), World Health Organization (WHO), Lyon, France.

The classification of neuroendocrine neoplasms (NENs) differs between organ systems and currently causes considerable confusion. A uniform classification framework for NENs at any anatomical location may reduce inconsistencies and contradictions among the various systems currently in use. The classification suggested here is intended to allow pathologists and clinicians to manage their patients with NENs consistently, while acknowledging organ-specific differences in classification criteria, tumor biology, and prognostic factors. The classification suggested is based on a consensus conference held at the International Agency for Research on Cancer (IARC) in November 2017 and subsequent discussion with additional experts. The key feature of the new classification is a distinction between differentiated neuroendocrine tumors (NETs), also designated carcinoid tumors in some systems, and poorly differentiated NECs, as they both share common expression of neuroendocrine markers. This dichotomous morphological subdivision into NETs and NECs is supported by genetic evidence at specific anatomic sites as well as clinical, epidemiologic, histologic, and prognostic differences. In many organ systems, NETs are graded as G1, G2, or G3 based on mitotic count and/or Ki-67 labeling index, and/or the presence of necrosis; NECs are considered high grade by definition. We believe this conceptual approach can form the basis for the next generation of NEN classifications and will allow more consistent taxonomy to understand how neoplasms from different organ systems inter-relate clinically and genetically.
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http://dx.doi.org/10.1038/s41379-018-0110-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265262PMC
December 2018

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.

Nat Commun 2018 03 13;9(1):1048. Epub 2018 Mar 13.

Genetic Cancer Susceptibility Group, Section of Genetics, International Agency for Research on Cancer (IARC-WHO), Lyon, 69008, France.

Pulmonary large-cell neuroendocrine carcinomas (LCNECs) have similarities with other lung cancers, but their precise relationship has remained unclear. Here we perform a comprehensive genomic (n = 60) and transcriptomic (n = 69) analysis of 75 LCNECs and identify two molecular subgroups: "type I LCNECs" with bi-allelic TP53 and STK11/KEAP1 alterations (37%), and "type II LCNECs" enriched for bi-allelic inactivation of TP53 and RB1 (42%). Despite sharing genomic alterations with adenocarcinomas and squamous cell carcinomas, no transcriptional relationship was found; instead LCNECs form distinct transcriptional subgroups with closest similarity to SCLC. While type I LCNECs and SCLCs exhibit a neuroendocrine profile with ASCL1/DLL3/NOTCH, type II LCNECs bear TP53 and RB1 alterations and differ from most SCLC tumors with reduced neuroendocrine markers, a pattern of ASCL1/DLL3/NOTCH, and an upregulation of immune-related pathways. In conclusion, LCNECs comprise two molecularly defined subgroups, and distinguishing them from SCLC may allow stratified targeted treatment of high-grade neuroendocrine lung tumors.
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http://dx.doi.org/10.1038/s41467-018-03099-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849599PMC
March 2018

New Insights into the Molecular Characteristics of Pulmonary Carcinoids and Large Cell Neuroendocrine Carcinomas, and the Impact on Their Clinical Management.

J Thorac Oncol 2018 06 14;13(6):752-766. Epub 2018 Feb 14.

Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, IARC-WHO, Lyon, France. Electronic address:

Carcinoids and large cell neuroendocrine carcinomas (LCNECs) are rare neuroendocrine lung tumors. Here we provide an overview of the most updated data on the molecular characteristics of these diseases. Recent genomic studies showed that carcinoids generally contain a low mutational burden and few recurrently mutated genes. Most of the reported mutations occur in chromatin-remodeling genes (e.g., menin 1 gene [MEN1]), and few affect genes of the phosphoinositide 3-kinase (PI3K)-AKT-mechanistic target of rapamycin gene pathway. Aggressive disease has been related to chromothripsis, DNA-repair gene mutations, loss of orthopedia homeobox/CD44, and upregulation of ret proto-oncogene gene (RET) gene expression. In the case of LCNECs, which present with a high mutation burden, two major molecular subtypes have been identified: one with biallelic inactivation of tumor protein p53 gene (TP53) and retinoblastoma gene (RB1), a hallmark of SCLC; and the other one with biallelic inactivation of TP53 and serine/threonine kinase 11 gene (STK11)/kelch like ECH associated protein 1 gene (KEAP1), genes that are frequently mutated in NSCLC. These data, together with the identification of common mutations in the different components of combined LCNEC tumors, provide further evidence of the close molecular relation of LCNEC with other lung tumor types. In terms of therapeutic options, future studies should explore the association between mechanistic target of rapamycin pathway mutations and response to mechanistic target of rapamycin inhibitors in carcinoids. For LCNEC, preliminary data suggest that the two molecular subtypes might have a predictive value for chemotherapy response, but this observation needs to be validated in randomized prospective clinical trials. Finally, delta like Notch canonical ligand 3 inhibitors and immunotherapy may provide alternative options for patient-tailored therapy in LCNEC.
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http://dx.doi.org/10.1016/j.jtho.2018.02.002DOI Listing
June 2018

Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome.

Clin Cancer Res 2018 01 24;24(1):33-42. Epub 2017 Oct 24.

Department of Pulmonary Diseases, GROW School for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands.

Previous genomic studies have identified two mutually exclusive molecular subtypes of large-cell neuroendocrine carcinoma (LCNEC): the mutated (mostly comutated with ) and the wild-type groups. We assessed whether these subtypes have a predictive value on chemotherapy outcome. Clinical data and tumor specimens were retrospectively obtained from the Netherlands Cancer Registry and Pathology Registry. Panel-consensus pathology revision confirmed the diagnosis of LCNEC in 148 of 232 cases. Next-generation sequencing (NGS) for and genes, as well as IHC for RB1 and P16 was performed on 79 and 109 cases, respectively, and correlated with overall survival (OS) and progression-free survival (PFS), stratifying for non-small cell lung cancer type chemotherapy including platinum + gemcitabine or taxanes (NSCLC-GEM/TAX) and platinum-etoposide (SCLC-PE). mutation and protein loss were detected in 47% ( = 37) and 72% ( = 78) of the cases, respectively. Patients with wild-type LCNEC treated with NSCLC-GEM/TAX had a significantly longer OS [9.6; 95% confidence interval (CI), 7.7-11.6 months] than those treated with SCLC-PE [5.8 (5.5-6.1); = 0.026]. Similar results were obtained for patients expressing RB1 in their tumors ( = 0.001). RB1 staining or P16 loss showed similar results. The same outcome for chemotherapy treatment was observed in LCNEC tumors harboring an mutation or lost RB1 protein. Patients with LCNEC tumors that carry a wild-type gene or express the RB1 protein do better with NSCLC-GEM/TAX treatment than with SCLC-PE chemotherapy. However, no difference was observed for mutated or with lost protein expression. .
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http://dx.doi.org/10.1158/1078-0432.CCR-17-1921DOI Listing
January 2018

BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas.

J Thorac Oncol 2017 04 27;12(4):724-733. Epub 2016 Dec 27.

Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Pathology, University Hospital of Lyon and Lyon1 University, Lyon, France.

Introduction: Malignant mesothelioma is a deadly disease that is strongly associated with asbestos exposure. Peritoneal mesotheliomas account for 10% of all the cases. BRCA1 associated protein 1 (BAP1) is a deubiquitinating hydrolase that plays a key role in various cellular processes. Germline and somatic inactivation of BRCA1 associated protein 1 gene (BAP1) is frequent in pleural mesothelioma; however, little is known about its status in peritoneal mesothelioma.

Methods: Taking advantage of the extensive French National Network for the Diagnosis of Malignant Pleural Mesothelioma and Rare Peritoneal Tumors and the French National Network for the Treatment of Rare Peritoneal Surface Malignancies, we collected biological material and clinical and epidemiological data for 46 patients with peritoneal mesothelioma. The status of BAP1 was evaluated at the mutational and protein expression levels and combined with our previous data on copy number alterations assessed in the same samples.

Results: We detected mutations in 32% of the malignant peritoneal mesotheliomas analyzed. In addition, we have previously reported that copy number losses occurred in 42% of the samples included in this series. Overall, 73% of the malignant peritoneal mesotheliomas analyzed carried at least one inactivated BAP1 allele, but only 57% had a complete loss of its protein nuclear expression. Better overall survival was observed for patients with BAP1 mutations (p = 0.04), protein expression loss (p = 0.016), or at least one of these alterations (p = 0.007) independently of tumor histological subtype, age, and sex.

Conclusions: As in pleural mesothelioma, inactivation of BAP1 is frequent in peritoneal mesotheliomas. We found that BAP1 protein nuclear expression is a good prognostic factor and a more reliable marker for the complete loss of BAP1 activity than mutation or copy number loss.
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http://dx.doi.org/10.1016/j.jtho.2016.12.019DOI Listing
April 2017

Shared Oncogenic Pathways Implicated in Both Virus-Positive and UV-Induced Merkel Cell Carcinomas.

J Invest Dermatol 2017 01 1;137(1):197-206. Epub 2016 Sep 1.

Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain; IBBTEC-UC-CSIC-SODERCAN Instituto de Biomedicina y Biotecnología de Cantabria, Santander, Spain. Electronic address:

Merkel cell carcinoma (MCC) is a highly malignant neuroendocrine tumor of the skin whose molecular pathogenesis is not completely understood, despite the role that Merkel cell polyomavirus can play in 55-90% of cases. To study potential mechanisms driving this disease in clinically characterized cases, we searched for somatic mutations using whole-exome sequencing, and extrapolated our findings to study functional biomarkers reporting on the activity of the mutated pathways. Confirming previous results, Merkel cell polyomavirus-negative tumors had higher mutational loads with UV signatures and more frequent mutations in TP53 and RB compared with their Merkel cell polyomavirus-positive counterparts. Despite important genetic differences, the two Merkel cell carcinoma etiologies both exhibited nuclear accumulation of oncogenic transcription factors such as NFAT or nuclear factor of activated T cells (NFAT), P-CREB, and P-STAT3, indicating commonly deregulated pathogenic mechanisms with the potential to serve as targets for therapy. A multivariable analysis identified phosphorylated CRE-binding protein as an independent survival factor with respect to clinical variables and Merkel cell polyomavirus status in our cohort of Merkel cell carcinoma patients.
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http://dx.doi.org/10.1016/j.jid.2016.08.015DOI Listing
January 2017

Identification of Circulating Tumor DNA for the Early Detection of Small-cell Lung Cancer.

EBioMedicine 2016 Aug 25;10:117-23. Epub 2016 Jun 25.

International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France. Electronic address:

Circulating tumor DNA (ctDNA) is emerging as a key potential biomarker for post-diagnosis surveillance but it may also play a crucial role in the detection of pre-clinical cancer. Small-cell lung cancer (SCLC) is an excellent candidate for early detection given there are no successful therapeutic options for late-stage disease, and it displays almost universal inactivation of TP53. We assessed the presence of TP53 mutations in the cell-free DNA (cfDNA) extracted from the plasma of 51 SCLC cases and 123 non-cancer controls. We identified mutations using a pipeline specifically designed to accurately detect variants at very low fractions. We detected TP53 mutations in the cfDNA of 49% SCLC patients and 11.4% of non-cancer controls. When stratifying the 51 initial SCLC cases by stage, TP53 mutations were detected in the cfDNA of 35.7% early-stage and 54.1% late-stage SCLC patients. The results in the controls were further replicated in 10.8% of an independent series of 102 non-cancer controls. The detection of TP53 mutations in 11% of the 225 non-cancer controls suggests that somatic mutations in cfDNA among individuals without any cancer diagnosis is a common occurrence, and poses serious challenges for the development of ctDNA screening tests.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036515PMC
http://dx.doi.org/10.1016/j.ebiom.2016.06.032DOI Listing
August 2016

Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors.

Clin Cancer Res 2016 Oct 1;22(19):4837-4847. Epub 2016 Jun 1.

Institute for Theoretical Physics. University of Cologne, Cologne, Germany.

Purpose: To identify novel mechanisms of resistance to third-generation EGFR inhibitors in patients with lung adenocarcinoma that progressed under therapy with either AZD9291 or rociletinib (CO-1686).

Experimental Design: We analyzed tumor biopsies from seven patients obtained before, during, and/or after treatment with AZD9291 or rociletinib (CO-1686). Targeted sequencing and FISH analyses were performed, and the relevance of candidate genes was functionally assessed in in vitro models.

Results: We found recurrent amplification of either MET or ERBB2 in tumors that were resistant or developed resistance to third-generation EGFR inhibitors and show that ERBB2 and MET activation can confer resistance to these compounds. Furthermore, we identified a KRAS mutation in a patient with acquired resistance to AZD9291 as a potential driver of acquired resistance. Finally, we show that dual inhibition of EGFR/MEK might be a viable strategy to overcome resistance in EGFR-mutant cells expressing mutant KRAS CONCLUSIONS: Our data suggest that heterogeneous mechanisms of resistance can drive primary and acquired resistance to third-generation EGFR inhibitors and provide a rationale for potential combination strategies. Clin Cancer Res; 22(19); 4837-47. ©2016 AACR.
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http://dx.doi.org/10.1158/1078-0432.CCR-15-1915DOI Listing
October 2016

Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations.

Oncotarget 2016 Feb;7(5):5273-88

Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.

In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies.
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http://dx.doi.org/10.18632/oncotarget.6567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868685PMC
February 2016

Genomic architecture of lung cancers.

Curr Opin Oncol 2016 Jan;28(1):52-7

Group of Genetic Cancer Susceptibility, Section of Genetics, International Agency for Research on Cancer (IARC-WHO), Lyon, France.

Purpose Of Review: Lung cancer remains the most frequent cancer worldwide and the leading cause of cancer death in most countries. The molecular characteristics of lung tumors play an important role in clinical decisions, which ultimately affect patients' survival. This review aims to summarize the most recent genomic discoveries made on lung cancer.

Recent Findings: A relatively comprehensive molecular characterization has been achieved for the three major types of lung cancer: adenocarcinoma, squamous-cell carcinoma, and small-cell carcinoma. Little is still known about large-cell neuroendocrine carcinoma and carcinoid tumors. A major finding has been the nonnegligible inter and intratumor heterogeneity of lung cancer and their impact in the clinical management of this disease.

Summary: The high load of mutations, the frequent inactivation of major tumor suppressor genes, and the huge heterogeneity of lung cancer tumors may complicate long-lasting therapeutic responses. The development of strategies for the early detection of lung cancer might translate into an increase of the number of surgical resectable tumors, and therefore contribute to improve the survival rate of these patients.
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http://dx.doi.org/10.1097/CCO.0000000000000251DOI Listing
January 2016

Comprehensive genomic profiles of small cell lung cancer.

Nature 2015 Aug 13;524(7563):47-53. Epub 2015 Jul 13.

Department of Internal Medicine, University Hospital of Cologne, 50931 Cologne, Germany.

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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http://dx.doi.org/10.1038/nature14664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861069PMC
August 2015

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.

Genome Biol 2015 Jan 5;16. Epub 2015 Jan 5.

Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.
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http://dx.doi.org/10.1186/s13059-014-0558-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300615PMC
January 2015

Molecular Pathways: Targeting NRG1 Fusions in Lung Cancer.

Clin Cancer Res 2015 May 11;21(9):1989-94. Epub 2014 Dec 11.

Department of Translational Genomics and Pathology, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.

The four members of the ERBB (HER) family of transmembrane receptor tyrosine kinases are frequently activated in cancer by several mechanisms, such as mutation, amplification, or autocrine ligand-receptor stimulation. We recently identified gene fusions involving the ERBB ligand gene, NRG1, which represent a novel mechanism for ERBB pathway deregulation. These fusions lead to expression and presentation of the EGF-like domain of NRG1 on the cell surface, which binds to ERBB3 in an autocrine and juxtacrine manner, thus inducing the formation of ERBB2-ERBB3 heterodimers, and subsequent activation of the PI3K-AKT and MAPK signaling pathways. These fusion genes were exclusively detected in lung adenocarcinomas of never smokers of the invasive mucinous subtype, which usually presents as a multifocal and unresectable disease, for which no effective treatment exists. Considering the large amount of drugs that target ERBB2 (HER2) and ERBB3 (HER3), and which are currently in different stages of clinical development, detecting and targeting NRG1 fusions in invasive mucinous lung adenocarcinomas may represent a therapeutic opportunity for this aggressive disease.
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http://dx.doi.org/10.1158/1078-0432.CCR-14-0854DOI Listing
May 2015

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.

Nat Commun 2014 Mar 27;5:3518. Epub 2014 Mar 27.

University of Melbourne Department of Surgery, St Vincent's Hospital, Melbourne, 3065 Victoria, Australia.

Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n=44) and transcriptome (n=69) sequencing of pulmonary carcinoids and observe frequent mutations in chromatin-remodelling genes. Covalent histone modifiers and subunits of the SWI/SNF complex are mutated in 40 and 22.2% of the cases, respectively, with MEN1, PSIP1 and ARID1A being recurrently affected. In contrast to small-cell lung cancer and large-cell neuroendocrine lung tumours, TP53 and RB1 mutations are rare events, suggesting that pulmonary carcinoids are not early progenitor lesions of the highly aggressive lung neuroendocrine tumours but arise through independent cellular mechanisms. These data also suggest that inactivation of chromatin-remodelling genes is sufficient to drive transformation in pulmonary carcinoids.
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http://dx.doi.org/10.1038/ncomms4518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132974PMC
March 2014

CD74-NRG1 fusions in lung adenocarcinoma.

Cancer Discov 2014 Apr 27;4(4):415-22. Epub 2014 Jan 27.

1Department of Translational Genomics; 2Department I of Internal Medicine; 3Laboratory of Translational Cancer Genomics; 4Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne-Bonn; 5Center for Molecular Medicine Cologne (CMMC); 6Cologne Center for Genomics (CCG); 7Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); 8Department of Pathology, University Hospital Medical Center, University of Cologne; 9Blackfield AG; 10Max Planck Institute for Neurological Research; 11Thoracic Surgery, Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH; 12Institute of Human Genetics, Cologne; 13Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin; 14Department of Prostate Cancer Research, Institute of Pathology; 15Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn; 16Institute of Pathology; 17Department of Internal Medicine II, Jena University Hospital, Friedrich-Schiller-University, Jena; 18Institute for Pathology Bad Berka, Bad Berka, Germany;19Division of Molecular Oncology, Aichi Cancer Center Research Institute; 20Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan; Departments of 21Surgery and22Pathology, St. Vincent's Hospital; 23Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia;24Department of Pathology, 25CHU Grenoble Institut National de la Santé et de la Recherche Medicale (INSERM) U823, Institute Albert Bonniot, Grenoble-Alpes University, Grenoble, France; 26Laboratory of Oncology IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo; 27Laboratory for Molecular Medicine and Biotechnology, University Campus Bio-Medico, Rome, Italy; 28Center for the Biology of Disease, VIB, Leuven; and 29Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium.

Unlabelled: We discovered a novel somatic gene fusion, CD74-NRG1, by transcriptome sequencing of 25 lung adenocarcinomas of never smokers. By screening 102 lung adenocarcinomas negative for known oncogenic alterations, we found four additional fusion-positive tumors, all of which were of the invasive mucinous subtype. Mechanistically, CD74-NRG1 leads to extracellular expression of the EGF-like domain of NRG1 III-β3, thereby providing the ligand for ERBB2-ERBB3 receptor complexes. Accordingly, ERBB2 and ERBB3 expression was high in the index case, and expression of phospho-ERBB3 was specifically found in tumors bearing the fusion (P < 0.0001). Ectopic expression of CD74-NRG1 in lung cancer cell lines expressing ERBB2 and ERBB3 activated ERBB3 and the PI3K-AKT pathway, and led to increased colony formation in soft agar. Thus, CD74-NRG1 gene fusions are activating genomic alterations in invasive mucinous adenocarcinomas and may offer a therapeutic opportunity for a lung tumor subtype with, so far, no effective treatment.

Significance: CD74–NRG1 fusions may represent a therapeutic opportunity for invasive mucinous lung adenocarcinomas, a tumor with no effective treatment that frequently presents with multifocal unresectable disease.
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http://dx.doi.org/10.1158/2159-8290.CD-13-0633DOI Listing
April 2014

Cell-autonomous and non-cell-autonomous mechanisms of transformation by amplified FGFR1 in lung cancer.

Cancer Discov 2014 Feb 3;4(2):246-57. Epub 2013 Dec 3.

1Department of Translational Genomics, University of Cologne; 2Max-Planck-Institute for Neurological Research; Institutes of 3Pathology and 4Virology, University of Cologne;5Department I of Internal Medicine and Center for Integrated Oncology, University Hospital of Cologne; 6Blackfield AG, Cologne; 7Technical University Dortmund, Dortmund, Germany; 8Medical Oncology and 9Institute of Pathology, Cantonal Hospital, Luzern; 10Novartis Pharma AG, Basel, Switzerland; and 11Division of Natural Products Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India.

Unlabelled: The 8p12 locus (containing the FGFR1 tyrosine kinase gene) is frequently amplified in squamous cell lung cancer. However, it is currently unknown which of the 8p12-amplified tumors are also sensitive to fibroblast growth factor receptor (FGFR) inhibition. We found that, in contrast with other recurrent amplifications, the 8p12 region included multiple centers of amplification, suggesting marked genomic heterogeneity. FGFR1-amplified tumor cells were dependent on FGFR ligands in vitro and in vivo. Furthermore, ectopic expression of FGFR1 was oncogenic, which was enhanced by expression of MYC. We found that MYC was coexpressed in 40% of FGFR1-amplified tumors. Tumor cells coexpressing MYC were more sensitive to FGFR inhibition, suggesting that patients with FGFR1-amplified and MYC-overexpressing tumors may benefit from FGFR inhibitor therapy. Thus, both cell-autonomous and non-cell-autonomous mechanisms of transformation modulate FGFR dependency in FGFR1-amplified lung cancer, which may have implications for patient selection for treatment with FGFR inhibitors.

Significance: Amplification of FGFR1 is one of the most frequent candidate targets in lung cancer. Here, we show that multiple factors affect the tumorigenic potential of FGFR1, thus providing clinical hypotheses for refinement of patient selection.
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http://dx.doi.org/10.1158/2159-8290.CD-13-0323DOI Listing
February 2014

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.

Nat Genet 2012 Oct 2;44(10):1104-10. Epub 2012 Sep 2.

Department of Translational Genomics, University of Cologne, Cologne, Germany.

Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor prognosis. We sequenced 29 SCLC exomes, 2 genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million base pairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases, we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in the CREBBP, EP300 and MLL genes that encode histone modifiers. Furthermore, we observed mutations in PTEN, SLIT2 and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from Tp53 and Rb1 double knockout mice. Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genomic alterations and provides a generalizable framework for the identification of biologically relevant genes in the context of high mutational background.
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http://dx.doi.org/10.1038/ng.2396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915822PMC
October 2012

Lung cancers with acquired resistance to EGFR inhibitors occasionally harbor BRAF gene mutations but lack mutations in KRAS, NRAS, or MEK1.

Proc Natl Acad Sci U S A 2012 Jul 6;109(31):E2127-33. Epub 2012 Jul 6.

Division of Hematology-Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Acquired resistance to EGF receptor (EGFR) tyrosine kinase inhibitors (TKIs) is inevitable in metastatic EGFR-mutant lung cancers. Here, we modeled disease progression using EGFR-mutant human tumor cell lines. Although five of six models displayed alterations already found in humans, one harbored an unexpected secondary NRAS Q61K mutation; resistant cells were sensitive to concurrent EGFR and MEK inhibition but to neither alone. Prompted by this finding and because RAS/RAF/MEK mutations are known mediators of acquired resistance in other solid tumors (colon cancers, gastrointestinal stromal tumors, and melanomas) responsive to targeted therapies, we analyzed the frequency of secondary KRAS/NRAS/BRAF/MEK1 gene mutations in the largest collection to date of lung cancers with acquired resistance to EGFR TKIs. No recurrent NRAS, KRAS, or MEK1 mutations were found in 212, 195, or 146 patient samples, respectively, but 2 of 195 (1%) were found to have mutations in BRAF (G469A and V600E). Ectopic expression of mutant NRAS or BRAF in drug-sensitive EGFR-mutant cells conferred resistance to EGFR TKIs that was overcome by addition of a MEK inhibitor. Collectively, these positive and negative results provide deeper insight into mechanisms of acquired resistance to EGFR TKIs in lung cancer and inform ongoing clinical trials designed to overcome resistance. In the context of emerging knowledge about mechanisms of acquired resistance to targeted therapies in various cancers, our data highlight the notion that, even though solid tumors share common signaling cascades, mediators of acquired resistance must be elucidated for each disease separately in the context of treatment.
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http://dx.doi.org/10.1073/pnas.1203530109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411967PMC
July 2012

Prognostic and predictive value of TP53 mutations in node-positive breast cancer patients treated with anthracycline- or anthracycline/taxane-based adjuvant therapy: results from the BIG 02-98 phase III trial.

Breast Cancer Res 2012 May 2;14(3):R70. Epub 2012 May 2.

Molecular Carcinogenesis Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon Cedex 8, France.

Introduction: Pre-clinical data suggest p53-dependent anthracycline-induced apoptosis and p53-independent taxane activity. However, dedicated clinical research has not defined a predictive role for TP53 gene mutations. The aim of the current study was to retrospectively explore the prognosis and predictive values of TP53 somatic mutations in the BIG 02-98 randomized phase III trial in which women with node-positive breast cancer were treated with adjuvant doxorubicin-based chemotherapy with or without docetaxel.

Methods: The prognostic and predictive values of TP53 were analyzed in tumor samples by gene sequencing within exons 5 to 8. Patients were classified according to p53 protein status predicted from TP53 gene sequence, as wild-type (no TP53 variation or TP53 variations which are predicted not to modify p53 protein sequence) or mutant (p53 nonsynonymous mutations). Mutations were subcategorized according to missense or truncating mutations. Survival analyses were performed using the Kaplan-Meier method and log-rank test. Cox-regression analysis was used to identify independent predictors of outcome.

Results: TP53 gene status was determined for 18% (520 of 2887) of the women enrolled in BIG 02-98. TP53 gene variations were found in 17% (90 of 520). Nonsynonymous p53 mutations, found in 16.3% (85 of 520), were associated with older age, ductal morphology, higher grade and hormone-receptor negativity. Of the nonsynonymous mutations, 12.3% (64 of 520) were missense and 3.6% were truncating (19 of 520). Only truncating mutations showed significant independent prognostic value, with an increased recurrence risk compared to patients with non-modified p53 protein (hazard ratio = 3.21, 95% confidence interval = 1.740 to 5.935, P = 0.0002). p53 status had no significant predictive value for response to docetaxel.

Conclusions: p53 truncating mutations were uncommon but associated with poor prognosis. No significant predictive role for p53 status was detected.

Trial Registration: ClinicalTrials.gov NCT00174655.
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http://dx.doi.org/10.1186/bcr3179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446332PMC
May 2012

p53-Dependent repression of focal adhesion kinase in response to estradiol in breast cancer cell-lines.

Cancer Lett 2011 Jan 10;300(2):215-24. Epub 2010 Nov 10.

International Agency for Research on Cancer, Lyon, France.

Mutations in the TP53 suppressor gene are frequent in breast cancers. These mutations are associated with poor prognosis, thought to be due to proliferative advantage and poor response to chemotherapy associated with loss of p53 function. The focal adhesion kinase (FAK/PTK2), a tyrosine kinase, is over-expressed in a variety of human tumors including breast cancers. FAK is a critical regulator of adhesion and motility and its over-expression is associated with increased metastatic potential. Recently, FAK promoter has been shown to contain p53 responsive elements and to be down-regulated by DNA-damage in a p53-dependent manner. Here, we have used five estrogen-dependent breast cancer cells lines with different p53 status, including an isogenic model, to show that FAK expression was regulated in a p53-dependent manner in response to estradiol. FAK protein and mRNA expression were down-regulated by estradiol in wild-type but not mutant p53 cells. Moreover, silencing wild-type p53 increased FAK expression, while over expressing p53 repressed FAK expression. ChIP experiment showed that p53 bound to FAK promoter in the presence of estradiol in p53 wild-type but not in mutant p53 cells, suggesting a direct role of p53 in down regulating FAK mRNA expression. FAK mRNA expression was also found to correlate with TP53 mutation status in a series of breast tumors. Finally, loss of FAK down-regulation in p53 mutant cells was correlated with increased proliferation and invasion upon estradiol stimulation, while FAK silencing reduced invasion. These results suggest that p53 is an important down regulator of FAK and that loss of p53 function in breast cancer may contribute to the metastatic potential of estrogen-responsive tumors through uncontrolled FAK expression upon estrogens stimulation.
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http://dx.doi.org/10.1016/j.canlet.2010.10.008DOI Listing
January 2011

p53 status influences response to tamoxifen but not to fulvestrant in breast cancer cell lines.

Int J Cancer 2011 Apr;128(8):1813-21

International Agency for Research on Cancer, Lyon, France.

Mutations in the tumor suppressor gene TP53 are associated with poor prognosis in breast cancer. This prognostic value may rely in part on the fact that p53 plays a role in the antiproliferative and apoptotic activities of chemotherapy regimens used to treat breast tumors. However, some studies suggested that p53 may also influence response to antihormone treatments. Here we investigate how p53 may affect response to antihormonal treatments, using estrogen-dependent breast cancer cell-lines with different p53 status. We show that p53 mutated cells were more resistant to cytotoxic effects of 4-hydroxy-tamoxifen (OHT) compared to p53 wild-type cells. In contrast, p53 status did not significantly impact on response to fulvestrant. p53 mutated cells were also hypersensitive to proliferative effects of estradiol. Interestingly, OHT at doses in the low range had proliferative activities in p53 mutated cells (120-150% proliferation rate under 1 μM OHT treatment in low estrogen conditions). Using gene silencing or specific tyrosine kinase inhibitors, we show that the proliferative effects of OHT were estrogen receptor dependent and could be abrogated by the inhibition of EGFR and/or HER2 kinases. These findings suggest that loss of p53 function may increase cross-talks between estrogen receptor and EGFR/HER2 pathways, contributing to a proliferative effect of OHT. These results bring new insights into the prognostic role of p53 in breast cancer and into possible mechanisms underlying tamoxifen resistance.
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http://dx.doi.org/10.1002/ijc.25512DOI Listing
April 2011