Genetic Landscape of Somatic Mutations in a Large Cohort of Sporadic Medullary Thyroid Carcinomas Studied by Next-Generation Targeted Sequencing

Raffaele Ciampi, Cristina Romei, Teresa Ramone, Alessandro Prete, Alessia Tacito, Virginia Cappagli, Valeria Bottici, David Viola, Liborio Torregrossa, Clara Ugolini, Fulvio Basolo, Rossella Elisei, Raffaele Ciampi, Cristina Romei, Teresa Ramone, Alessandro Prete, Alessia Tacito, Virginia Cappagli, Valeria Bottici, David Viola, Liborio Torregrossa, Clara Ugolini, Fulvio Basolo, Rossella Elisei

Abstract

Sporadic Medullary Thyroid Carcinoma (sMTC) is a rare but aggressive thyroid tumor. RET and RAS genes are present in about 50%-80% of cases, but most of the remaining cases are still orphan of a genetic driver. We studied the largest series of sMTC by deep sequencing to define the mutational landscape. With this methodology we greatly reduced the number of RET- or RAS-negative cases and we confirmed the central role of RET and RAS mutations. Moreover, we highlighted the bad prognostic role of RET mutations in sMTC and consolidated the favorable prognostic role of RAS mutations. For the first time, we showed that the variant allele frequency represents an additional prognostic marker inside the group of RET-mutated sMTC.

Keywords: Biological Sciences; Cancer; Genomics.

Conflict of interest statement

The authors declare that there are no conflicts of interest that could affect the impartiality of the reported research.

Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.

Figures

Graphical abstract
Graphical abstract
Figure 1
Figure 1
Mutational Landscape of sMTC Mutational profile of the 168 informative sMTC cases identified by NGS analysis. Each column corresponds to a single case. Genetic variations are listed on the left. The colored squares correspond to somatic mutations, whereas the black squares correspond to germline mutations, all validated by Sanger sequencing. Squares with a point-pattern represent mutations that were not validated by Sanger or not confirmed to be somatic or germline. See also Table S1.
Figure 2
Figure 2
Survival in RET- and RAS-Mutated sMTC Cases Kaplan-Meier curves showing survival in patients with sMTC harboring RET mutations or RAS mutations. The difference in the curves was statistically significant (log rank = 4.41; p = 0.035) and demonstrated that RET-positive cases have a higher probability to die of the disease.
Figure 3
Figure 3
Correlation of the Variant Allele Frequency with Tumor Size and Outcome of Patients with sMTC (A) Correlation between the tumor size (cm) and VAF of the driver mutation in sMTC. The comparison considered all mutations (A1), only RET mutations (A2), only the RET M918T mutation (A3), and only RAS mutations (A4). In all cases, except RAS-mutated cases, a statistically significant difference was observed (A1: p < 0.0001; A2: p < 0.0001; A3: p = 0.0013; A4: p = ns). (B) Correlation between the VAF value (%) of the driver mutations and outcome of patients when considering all mutations (B1), only RET mutations (B2), and only RAS mutations (B3). The differences between the outcome categories were significant between disease-free and metastatic patients in the former two cases (B1: p = 0.003; B2: p = 0.0047; ANOVA), whereas no difference was observed considering only RAS mutations (B3: p = ns). Data are represented as mean ± SEM.

References

    1. Agrawal N., Jiao Y., Sausen M., Leary R., Bettegowda C., Roberts N.J., Bhan S., Ho A.S., Khan Z., Bishop J. Exomic sequencing of medullary thyroid cancer reveals dominant and mutually exclusive oncogenic mutations in RET and RAS. J. Clin. Endocrinol. Metab. 2013;98:E364–E369.
    1. Alzahrani A.S., Alsaadi R., Murugan A.K., Sadiq B.B. TERT promoter mutations in thyroid cancer. Horm. Cancer. 2016;7:165–177.
    1. Berger M.F., Mardis E.R. The emerging clinical relevance of genomics in cancer medicine. Nat. Rev. Clin. Oncol. 2018;15:353–365.
    1. Boichard A., Croux L., Al Ghuzlan A., Broutin S., Dupuy C., Leboulleux S., Schlumberger M., Bidart J.M., Lacroix L. Somatic RAS mutations occur in a large proportion of sporadic RET-negative medullary thyroid carcinomas and extend to a previously unidentified exon. J. Clin. Endocrinol. Metab. 2012;97:E2031–E2035.
    1. Camidge D.R., Pao W., Sequist L.V. Acquired resistance to TKIs in solid tumours: learning from lung cancer. Nat. Rev. Clin. Oncol. 2014;11:473–481.
    1. Cancer Genome Atlas Research Network Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014;159:676–690.
    1. Cerrato A., De Falco V., Santoro M. Molecular genetics of medullary thyroid carcinoma: the quest for novel therapeutic targets. J. Mol. Endocrinol. 2009;43:143–155.
    1. Chang Y.-S., Chang C.-C., Huang H.-Y., Lin C.-Y., Yeh K.-T., Chang J.-G. Detection of molecular alterations in Taiwanese patients with medullary thyroid cancer using whole-exome sequencing. Endocr. Pathol. 2018;29:324–331.
    1. Chen Y., Fu L. Mechanisms of acquired resistance to tyrosine kinase inhibitors. Acta Pharm. Sin. B. 2011;1:197–207.
    1. Ciampi R., Mian C., Fugazzola L., Cosci B., Romei C., Barollo S., Cirello V., Bottici V., Marconcini G., Rosa P.M. Evidence of a low prevalence of RAS mutations in a large medullary thyroid cancer series. Thyroid. 2013;23:50–57.
    1. Ciampi R., Romei C., Cosci B., Vivaldi A., Bottici V., Renzini G., Ugolini C., Tacito A., Basolo F., Pinchera A., Elisei R. Chromosome 10 and RET gene copy number alterations in hereditary and sporadic Medullary Thyroid Carcinoma. Mol. Cell. Endocrinol. 2012;348:176–182.
    1. Comoglio P.M., Trusolino L., Boccaccio C. Known and novel roles of the MET oncogene in cancer: a coherent approach to targeted therapy. Nat. Rev. Cancer. 2018;18:341–358.
    1. Drosten M., Putzer B.M. Mechanisms of Disease: cancer targeting and the impact of oncogenic RET for medullary thyroid carcinoma therapy. Nat. Clin. Pr. Oncol. 2006;3:564–574.
    1. Elisei R., Cosci B., Romei C., Bottici V., Renzini G., Molinaro E., Agate L., Vivaldi A., Faviana P., Basolo F. Prognostic significance of somatic RET oncogene mutations in sporadic medullary thyroid cancer: a 10-year follow-up study. J. Clin. Endocrinol. Metab. 2008;93:682–687.
    1. Elisei R., Molinaro E., Agate L., Bottici V., Viola D., Biagini A., Matrone A., Tacito A., Ciampi R., Vivaldi A., Romei C. Ret oncogene and thyroid carcinoma. J. Genet. Syndr. Gene Ther. 2014;5:10.
    1. Elisei R., Schlumberger M.J., Müller S.P., Schöffski P., Brose M.S., Shah M.H., Licitra L., Jarzab B., Medvedev V., Kreissl M.C. Cabozantinib in progressive medullary thyroid cancer. J. Clin. Oncol. 2013;31:3639–3646.
    1. Eng C., Smith D.P., Mulligan L.M., Nagai M.A., Healey C.S., Ponder M.A., Gardner E., Scheumann G.F., Jackson C.E., Tunnacliffe A. Point mutation within the tyrosine kinase domain of the RET proto-oncogene in multiple endocrine neoplasia type 2B and related sporadic tumours. Hum. Mol. Genet. 1994;3:237–241.
    1. Guerra A., Fugazzola L., Marotta V., Cirillo M., Rossi S., Cirello V., Forno I., Moccia T., Budillon A., Vitale M. A high percentage of BRAFV600E alleles in papillary thyroid carcinoma predicts a poorer outcome. J. Clin. Endocrinol. Metab. 2012;97:2333–2340.
    1. Heilmann A.M., Subbiah V., Wang K., Sun J.X., Elvin J.A., Chmielecki J., Sherman S.I., Murthy R., Busaidy N.L., Subbiah I. Comprehensive genomic profiling of clinically advanced medullary thyroid carcinoma. Oncology. 2016;90:339–346.
    1. Höppner W., Dralle H., Brabant G. Duplication of 9 base pairs in the critical cysteine rich domain of the ret proto-oncogene causes multiple endocrine neoplasia type 2A. Hum. Mutat. 1998;(Suppl 1):S128–S130. doi: 10.1002/humu.1380110143.
    1. Ji J.H., Oh Y.L., Hong M., Yun J.W., Lee H.-W., Kim D., Ji Y., Kim D.-H., Park W.-Y., Shin H.-T. Identification of driving ALK fusion genes and genomic landscape of medullary thyroid cancer. PLoS Genet. 2015;11:e1005467.
    1. Kamps R., Brandão R.D., van den Bosch B.J., Paulussen A.D.C., Xanthoulea S., Blok M.J., Romano A. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int. J. Mol. Sci. 2017;18 doi: 10.3390/ijms18020308.
    1. Kouvaraki M.A., Shapiro S.E., Perrier N.D., Cote G.J., Gagel R.F., Hoff A.O., Sherman S.I., Lee J.E., Evans D.B. RET proto-oncogene: a review and update of genotype-phenotype correlations in hereditary medullary thyroid cancer and associated endocrine tumors. Thyroid. 2005;15:531–544.
    1. Li M.M., Datto M., Duncavage E.J., Kulkarni S., Lindeman N.I., Roy S., Tsimberidou A.M., Vnencak-Jones C.L., Wolff D.J., Younes A., Nikiforova M.N. Standards and guidelines for the interpretation and reporting of sequence variants in cancer. J. Mol. Diagn. 2017;19:4–23.
    1. Moura M.M., Cavaco B.M., Leite V. RAS proto-oncogene in medullary thyroid carcinoma. Endocr. Relat. Cancer. 2015;22:R235–R252.
    1. Moura M.M., Cavaco B.M., Pinto A.E., Leite V. High prevalence of RAS mutations in RET-negative sporadic medullary thyroid carcinomas. J. Clin. Endocrinol. Metab. 2011;96:E863–E868.
    1. Neklason D.W., Done M.W., Sargent N.R., Schwartz A.G., Anton-Culver H., Griffin C.A., Ahnen D.J., Schildkraut J.M., Tomlinson G.E., Strong L.C. Activating mutation in MET oncogene in familial colorectal cancer. BMC Cancer. 2011;11:424.
    1. Nikiforov Y.E., Carty S.E., Chiosea S.I., Coyne C., Duvvuri U., Ferris R.L., Gooding W.E., Hodak S.P., LeBeau S.O., Ohori N.P. Highly accurate diagnosis of cancer in thyroid nodules with follicular neoplasm/suspicious for a follicular neoplasm cytology by thyroseq V2 next-generation sequencing assay. Cancer. 2014;120:3627–3634.
    1. Nikiforova M.N., Wald A.I., Roy S., Durso M.B., Nikiforov Y.E. Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J. Clin. Endocrinol. Metab. 2013;98:1852–1860.
    1. Persani L., de Filippis T., Colombo C., Gentilini D. GENETICS IN ENDOCRINOLOGY: genetic diagnosis of endocrine diseases by NGS: novel scenarios and unpredictable results and risks. Eur. J. Endocrinol. 2018;179:R111–R123.
    1. Romei C., Ciampi R., Elisei R. A comprehensive overview of the role of the RET proto-oncogene in thyroid carcinoma. Nat. Rev. Endocrinol. 2016;12:192–202.
    1. Romei C., Cosci B., Renzini G., Bottici V., Molinaro E., Agate L., Passannanti P., Viola D., Biagini A., Basolo F. RET genetic screening of sporadic medullary thyroid cancer (MTC) allows the preclinical diagnosis of unsuspected gene carriers and the identification of a relevant percentage of hidden familial MTC (FMTC) Clin. Endocrinol. 2011;74:241–247.
    1. Romei C., Ugolini C., Cosci B., Torregrossa L., Vivaldi A., Ciampi R., Tacito A., Basolo F., Materazzi G., Miccoli P. Low prevalence of the somatic M918T RET mutation in micro-medullary thyroid cancer. Thyroid. 2012;22:476–481.
    1. Ruark E., Snape K., Humburg P., Loveday C., Bajrami I., Brough R., Rodrigues D.N., Renwick A., Seal S., Ramsay E. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature. 2013;493:406–410.
    1. Simbolo M., Mian C., Barollo S., Fassan M., Mafficini A., Neves D., Scardoni M., Pennelli G., Rugge M., Pelizzo M.R. High-throughput mutation profiling improves diagnostic stratification of sporadic medullary thyroid carcinomas. Virchows Arch. 2014;465:73–78.
    1. Vigna E., Gramaglia D., Longati P., Bardelli A., Comoglio P.M. Loss of the exon encoding the juxtamembrane domain is essential for the oncogenic activation of TPR-MET. Oncogene. 1999;18:4275–4281.
    1. Viola D., Valerio L., Molinaro E., Agate L., Bottici V., Biagini A., Lorusso L., Cappagli V., Pieruzzi L., Giani C. Treatment of advanced thyroid cancer with targeted therapies: ten years of experience. Endocr. Relat. Cancer. 2016;23:R185–R205.
    1. Vuong H.G., Odate T., Ngo H.T.T., Pham T.Q., Tran T.T.K., Mochizuki K., Nakazawa T., Katoh R., Kondo T. Clinical significance of RET and RAS mutations in sporadic medullary thyroid carcinoma: a meta-analysis. Endocr. Relat. Cancer. 2018;25:633–641. doi: 10.1530/ERC-18-0056.
    1. Wang Q., Mehmood A., Wang H., Xu Q., Xiong Y., Wei D.Q. Computational screening and analysis of lung cancer related non-synonymous single nucleotide polymorphisms on the human kirsten rat sarcoma gene. Molecules. 2019;24 doi: 10.3390/molecules24101951.
    1. Wasenius V.M., Hemmer S., Karjalainen-Lindsberg M.L., Nupponen N.N., Franssila K., Joensuu H. MET receptor tyrosine kinase sequence alterations in differentiated thyroid carcinoma. Am. J. Surg. Pathol. 2005;29:544–549.
    1. Wei S., LiVolsi V.A., Montone K.T., Morrissette J.J.D., Baloch Z.W. Detection of molecular alterations in medullary thyroid carcinoma using next-generation sequencing: an institutional experience. Endocr. Pathol. 2016;27:359–362.
    1. Wells S.A., Jr., Gosnell J.E., Gagel R.F., Moley J., Pfister D., Sosa J.A., Skinner M., Krebs A., Vasselli J., Schlumberger M. Vandetanib for the treatment of patients with locally advanced or metastatic hereditary medullary thyroid cancer. J. Clin. Oncol. 2010;28:767–772.

Source: PubMed

Sponsorer og samarbeidspartnere

Medisinsk tilstand

Legemiddelintervensjoner

3
Abonnere