Use of mutation profiles to refine the classification of endometrial carcinomas

The classification of endometrial carcinomas is based on pathological assessment of tumour cell type; the different cell types (endometrioid, serous, carcinosarcoma, mixed, undifferentiated, and clear cell) are associated with distinct molecular alterations. This current classification system for high‐grade subtypes, in particular the distinction between high‐grade endometrioid (EEC‐3) and serous carcinomas (ESC), is limited in its reproducibility and prognostic abilities. Therefore, a search for specific molecular classifiers to improve endometrial carcinoma subclassification is warranted. We performed target enrichment sequencing on 393 endometrial carcinomas from two large cohorts, sequencing exons from the following nine genes: ARID1A, PPP2R1A, PTEN, PIK3CA, KRAS, CTNNB1, TP53, BRAF, and PPP2R5C. Based on this gene panel, each endometrial carcinoma subtype shows a distinct mutation profile. EEC‐3s have significantly different frequencies of PTEN and TP53 mutations when compared to low‐grade endometrioid carcinomas. ESCs and EEC‐3s are distinct subtypes with significantly different frequencies of mutations in PTEN, ARID1A, PPP2R1A, TP53, and CTNNB1. From the mutation profiles, we were able to identify subtype outliers, ie cases diagnosed morphologically as one subtype but with a mutation profile suggestive of a different subtype. Careful review of these diagnostically challenging cases suggested that the original morphological classification was incorrect in most instances. The molecular profile of carcinosarcomas suggests two distinct mutation profiles for these tumours: endometrioid‐type (PTEN, PIK3CA, ARID1A, KRAS mutations) and serous‐type (TP53 and PPP2R1A mutations). While this nine‐gene panel does not allow for a purely molecularly based classification of endometrial carcinoma, it may prove useful as an adjunct to morphological classification and serve as an aid in the classification of problematic cases. If used in practice, it may lead to improved diagnostic reproducibility and may also serve to stratify patients for targeted therapeutics. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

[1]  M. Köbel,et al.  High-Grade Endometrial Carcinoma: Serous and Grade 3 Endometrioid Carcinomas Have Different Immunophenotypes and Outcomes , 2010, International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists.

[2]  A. Mes-Masson,et al.  Subtype‐specific mutation of PPP2R1A in endometrial and ovarian carcinomas , 2011, The Journal of pathology.

[3]  C Blake Gilks,et al.  Poor Interobserver Reproducibility in the Diagnosis of High-grade Endometrial Carcinoma , 2013, The American journal of surgical pathology.

[4]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[5]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[6]  G. Mills,et al.  High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability. , 2011, Cancer discovery.

[7]  E. Oliva,et al.  Clinicopathologic Analysis of 187 High-grade Endometrial Carcinomas of Different Histologic Subtypes: Similar Outcomes Belie Distinctive Biologic Differences , 2007, The American journal of surgical pathology.

[8]  G. Schaller,et al.  Should grade 3 endometrioid endometrial carcinoma be considered a type 2 cancer-a clinical and pathological evaluation. , 2012, Gynecologic oncology.

[9]  Kathleen R. Cho,et al.  Mutations in PTEN are frequent in endometrial carcinoma but rare in other common gynecological malignancies. , 1997, Cancer research.

[10]  F. Bray,et al.  Endometrial Cancer Incidence Trends in Europe: Underlying Determinants and Prospects for Prevention , 2005, Cancer Epidemiology Biomarkers & Prevention.

[11]  Gholamreza Haffari,et al.  Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data , 2011, Bioinform..

[12]  I. Shih,et al.  Mutation and Loss of Expression of ARID1A in Uterine Low-grade Endometrioid Carcinoma , 2011, The American journal of surgical pathology.

[13]  M. Hendrickson,et al.  Uterine papillary serous and clear cell carcinomas predict for poorer survival compared to grade 3 endometrioid corpus cancers , 2006, British Journal of Cancer.

[14]  G. Scambia,et al.  Does high-grade endometrioid carcinoma (grade 3 FIGO) belong to type I or type II endometrial cancer? A clinical–pathological and immunohistochemical study , 2010, Virchows Archiv.

[15]  G. Fleuren,et al.  Molecular genetic evidence for the conversion hypothesis of the origin of malignant mixed Müllerian tumours , 1997, Journal of Pathology.

[16]  T. Okai,et al.  Genetics of Endometrial Cancers , 2010, Obstetrics and gynecology international.

[17]  Frank McCormick,et al.  High frequency of coexistent mutations of PIK3CA and PTEN genes in endometrial carcinoma. , 2005, Cancer research.

[18]  T Nakamura,et al.  Mutational analysis of the PTEN gene in endometrial carcinoma and hyperplasia. , 2001, American journal of clinical pathology.

[19]  Matt van de Rijn,et al.  Identification of prognostically relevant and reproducible subsets of endometrial adenocarcinoma based on clustering analysis of immunostaining data , 2007, Modern Pathology.

[20]  R. Soslow.  Endometrial carcinomas with ambiguous features. , 2010, Seminars in diagnostic pathology.

[21]  I. Yeh,et al.  Molecular Profiling of Endometrial Malignancies , 2010, Obstetrics and gynecology international.

[22]  Jaime Prat,et al.  Prognostic parameters of endometrial carcinoma. , 2004, Human pathology.

[23]  P. Pollock,et al.  FGFR2 Point Mutations in 466 Endometrioid Endometrial Tumors: Relationship with MSI, KRAS, PIK3CA, CTNNB1 Mutations and Clinicopathological Features , 2012, PloS one.

[24]  M. Post.  Mutation and Loss of Expression of ARID1A in Uterine Low-grade Endometrioid Carcinoma , 2012 .

[25]  J. Prat,et al.  Pathology of mixed Müllerian tumours. , 2011, Best practice & research. Clinical obstetrics & gynaecology.

[26]  X. Matías-Guiu,et al.  PIK3CA gene mutations in endometrial carcinoma: correlation with PTEN and K-RAS alterations. , 2006, Human pathology.

[27]  Samuel Leung,et al.  Diagnosis of Ovarian Carcinoma Cell Type is Highly Reproducible: A Transcanadian Study , 2010, The American journal of surgical pathology.

[28]  Richard A. Moore,et al.  ARID1A mutations in endometriosis-associated ovarian carcinomas. , 2010, The New England journal of medicine.

[29]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[30]  M. Dimopoulos,et al.  Low frequency of somatic mutations in uterine sarcomas: a molecular analysis and review of the literature. , 2010, Mutation research.

[31]  Mingming Jia,et al.  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..

[32]  H. Saya,et al.  Expression profiles of carcinosarcoma of the uterine corpus—are these similar to carcinoma or sarcoma? , 2012, Genes, chromosomes & cancer.

[33]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[34]  Steven J. M. Jones,et al.  Frequent mutation of histone modifying genes in non-Hodgkin lymphoma , 2011, Nature.

[35]  B. Clarke,et al.  Endometrial carcinoma: controversies in histopathological assessment of grade and tumour cell type , 2010, Journal of Clinical Pathology.

[36]  H. Thaler,et al.  Serous Endometrial Cancers That Mimic Endometrioid Adenocarcinomas: A Clinicopathologic and Immunohistochemical Study of a Group of Problematic Cases , 2004, The American journal of surgical pathology.

[37]  D. Sgroi,et al.  PIK3R1 (p85α) is somatically mutated at high frequency in primary endometrial cancer. , 2011, Cancer research.

[38]  P. Goodfellow,et al.  Prevalence of defective DNA mismatch repair and MSH6 mutation in an unselected series of endometrial cancers , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Mari Mino-Kenudson,et al.  EGFR-mediated re-activation of MAPK signaling contributes to insensitivity of BRAF mutant colorectal cancers to RAF inhibition with vemurafenib. , 2012, Cancer discovery.

[40]  P. Neven,et al.  Endometrial carcinosarcomas have a different prognosis and pattern of spread compared to high-risk epithelial endometrial cancer. , 2005, Gynecologic oncology.

[41]  Andrea J. O'Hara,et al.  The genomics and genetics of endometrial cancer. , 2012, Advances in genomics and genetics.

[42]  V. Velculescu,et al.  Somatic mutations of PPP2R1A in ovarian and uterine carcinomas. , 2011, The American journal of pathology.

[43]  C. Bandera,et al.  The molecular genetics of endometrial carcinoma. , 1997, Progress in clinical and biological research.

[44]  J. V. Bokhman.  Two pathogenetic types of endometrial carcinoma. , 1983, Gynecologic oncology.

[45]  A. Blann,et al.  Differential trends in the rising incidence of endometrial cancer by type: data from a UK population-based registry from 1994 to 2006 , 2011, British Journal of Cancer.

[46]  R. Bernards,et al.  Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR , 2012, Nature.

[47]  E. Pirog,et al.  Mutational Analysis of the CTNNB1 and APC Genes in Uterine Endometrioid Carcinoma , 2000, Modern Pathology.

[48]  H. Mackay,et al.  Clear cell carcinoma of the ovary: a report from the first Ovarian Clear Cell Symposium, June 24th, 2010. , 2011, Gynecologic oncology.

[49]  Ryan D. Morin,et al.  Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution , 2009, Nature.

[50]  Patrick Neven,et al.  Endometrial cancer. , 2005, Lancet.

[51]  M. Goluda,et al.  Assessment of the quality and frequency of mutations occurrence in PTEN gene in endometrial carcinomas and hyperplasias. , 2002, Cancer letters.

[52]  P. Pollock,et al.  Frequent activating FGFR2 mutations in endometrial carcinomas parallel germline mutations associated with craniosynostosis and skeletal dysplasia syndromes , 2007, Oncogene.

[53]  T. Eberlein,et al.  Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation , 2012 .

[54]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .