Classification of follicular-patterned thyroid lesions using a minimal set of epigenetic biomarkers

in European Journal of Endocrinology
View More View Less
  • 1 Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Asturias, Spain
  • | 2 Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Asturias, Spain
  • | 3 Spanish Biomedical Research Network in Rare Diseases (CIBERER), Madrid, Spain
  • | 4 Central University Hospital of Asturias (HUCA), Endocrinology and Nutrition Department, Endocrinology, Nutrition, Diabetes and Obesity Unit (ENDO-ISPA), ISPA, Oviedo, Asturias, Spain
  • | 5 Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Asturias, Spain
  • | 6 Central University Hospital of Asturias, HUCA Otorhinolaryngology Service, Oviedo, Asturias, Spain
  • | 7 Department of Pathology, University Hospital of Asturias (HUCA), Oviedo, Asturias, Spain
  • | 8 University Hospital of Asturias (HUCA), Laboratory of Molecular Oncology, Oviedo, Asturias, Spain
  • | 9 IdiPAZ Biobank, La Paz University Hospital (IdiPAZ), Madrid, Spain
  • | 10 General Surgery, Innovation in Surgery, Transplants and Health Technologies Service, Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, Barakaldo, Bizkaia, Spain
  • | 11 Department of Pathology, University Hospital La Paz, Madrid, Spain
  • | 12 Arnau de Vilanova University Hospital, IRBLleida, Lleida, Spain

Correspondence should be addressed to E Delgado or M F Fraga; Email: eliasdelga@gmail.com or mffraga@cinn.es

*(S Rodríguez-Rodero, P Morales-Sánchez and J Ramón Tejedor contributed equally to this work)

Restricted access

USD  $0.00
USD  $0.00

USD  $0.00
USD  $0.00

USD  $0.00
USD  $0.00

Objective

The minimally invasive fine-needle aspiration cytology (FNAC) is the current gold standard for the diagnosis of thyroid nodule malignancy. However, the correct discrimination of follicular neoplasia often requires more invasive diagnostic techniques. The lack of suitable immunohistochemical markers to distinguish between follicular thyroid carcinoma and other types of follicular-derived lesions complicates diagnosis, and despite most of these tumours being surgically resected, only a small number will test positive for malignancy. As such, the development of new orthogonal diagnostic approaches may improve the accuracy of diagnosing thyroid nodules.

Design

This study includes a retrospective, multi-centre training cohort including 54 fresh-frozen follicular-patterned thyroid samples and two independent, multi-centre validation cohorts of 103 snap-frozen biopsies and 33 FNAC samples, respectively.

Methods

We performed a genome-wide genetic and epigenetic profiling of 54 fresh-frozen follicular-patterned thyroid samples using exome sequencing and the Illumina Human DNA Methylation EPIC platform. An extensive validation was performed using the bisulfite pyrosequencing technique.

Results

Using a random forest approach, we developed a three-CpG marker-based diagnostic model that was subsequently validated using bisulfite pyrosequencing experiments. According to the validation cohort, this cost-effective method discriminates between benign and malignant nodules with a sensitivity and specificity of 97 and 88%, respectively (positive predictive value (PPV): 0.85, negative predictive value (NPV): 0.98).

Conclusions

Our classification system based on a minimal set of epigenetic biomarkers can complement the potential of the diagnostic techniques currently available and would prioritize a considerable number of surgical interventions that are often performed due to uncertain cytology.

Significance statement

In recent years, there has been a significant increase in the number of people diagnosed with thyroid nodules. The current challenge is their etiological diagnosis to discount malignancy without resorting to thyroidectomy. The method proposed here, based on DNA pyrosequencing assays, has high sensitivity (0.97) and specificity (0.88) for the identification of malignant thyroid nodules. This simple and cost-effective approach can complement expert pathologist evaluation to prioritize the classification of difficult-to-diagnose follicular-patterned thyroid lesions and track tumor evolution, including real-time monitoring of treatment efficacy, thereby stimulating adherence to health promotion programs.

 

     European Society of Endocrinology

Sept 2018 onwards Past Year Past 30 Days
Abstract Views 2299 2299 727
Full Text Views 136 136 49
PDF Downloads 167 167 55
  • 1

    Hoda RS, Rao R, Scognamiglio T. Atlas of Thyroid Cytopathology on Liquid-Based Preparations: Correlation with Clinical, Radiological, Molecular Tests and Histopathology. Cham: Springer, 2020. (https://doi.org/10.1007/978-3-030-25066-9)

    • Search Google Scholar
    • Export Citation
  • 2

    Vuong HG, Ngo HTT, Bychkov A, Jung CK, Vu TH, Lu KB, Kakudo K, Kondo T. Differences in surgical resection rate and risk of malignancy in thyroid cytopathology practice between Western and Asian countries: a systematic review and meta-analysis. Cancer Cytopathology 2020 128 238249. (https://doi.org/10.1002/cncy.22228)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 3

    Cibas ES, Ali SZ. The 2017 Bethesda system for reporting thyroid cytopathology. Thyroid 2017 27 13411346. (https://doi.org/10.1089/thy.2017.0500)

  • 4

    Haugen BR, Alexander EK, Bible KC, Doherty GM, Mandel SJ, Nikiforov YE, Pacini F, Randolph GW, Sawka AM & Schlumberger M et al.2015 American Thyroid Association management guidelines for adult patients with thyroid nodules and differentiated thyroid cancer: the American Thyroid Association guidelines task force on thyroid nodules and differentiated thyroid cancer. Thyroid 2016 26 1133. (https://doi.org/10.1089/thy.2015.0020)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 5

    Enomoto K, Uchino S, Watanabe S, Enomoto Y, Noguchi S. Recurrent laryngeal nerve palsy during surgery for benign thyroid diseases: risk factors and outcome analysis. Surgery 2014 155 522528. (https://doi.org/10.1016/j.surg.2013.11.005)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 6

    Sitges-Serra A Etiology and diagnosis of permanent hypoparathyroidism after total thyroidectomy. Journal of Clinical Medicine 2021 10 543. (https://doi.org/10.3390/jcm10030543)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 7

    Steward DL, Carty SE, Sippel RS, Yang SP, Sosa JA, Sipos JA, Figge JJ, Mandel S, Haugen BR & Burman KD et al.Performance of a multigene genomic classifier in thyroid nodules with indeterminate cytology: a prospective blinded multicenter study. JAMA Oncology 2019 5 204212. (https://doi.org/10.1001/jamaoncol.2018.4616)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 8

    Nikiforova MN, Mercurio S, Wald AI, Barbi de Moura M, Callenberg K, Santana-Santos L, Gooding WE, Yip L, Ferris RL, Nikiforov YE. Analytical performance of the ThyroSeq v3 genomic classifier for cancer diagnosis in thyroid nodules. Cancer 2018 124 16821690. (https://doi.org/10.1002/cncr.31245)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 9

    Alexander EK, Kennedy GC, Baloch ZW, Cibas ES, Chudova D, Diggans J, Friedman L, Kloos RT, LiVolsi VA & Mandel SJ et al. Preoperative diagnosis of benign thyroid nodules with indeterminate cytology. New England Journal of Medicine 2012 367 705715. (https://doi.org/10.1056/NEJMoa1203208)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 10

    Alexander EK, Schorr M, Klopper J, Kim C, Sipos J, Nabhan F, Parker C, Steward DL, Mandel SJ, Haugen BR. Multicenter clinical experience with the afirma gene expression classifier. Journal of Clinical Endocrinology and Metabolism 2014 99 119125. (https://doi.org/10.1210/jc.2013-2482)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 11

    Labourier E, Shifrin A, Busseniers AE, Lupo MA, Manganelli ML, Andruss B, Wylie D, Beaudenon-Huibregtse S. Molecular testing for miRNA, mRNA, and DNA on fine-needle aspiration improves the preoperative diagnosis of thyroid nodules with indeterminate cytology. Journal of Clinical Endocrinology and Metabolism 2015 100 27432750. (https://doi.org/10.1210/jc.2015-1158)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 12

    Jug RC, Datto MB, Jiang XS. Molecular testing for indeterminate thyroid nodules: performance of the afirma gene expression classifier and ThyroSeq panel. Cancer Cytopathology 2018 126 471480. (https://doi.org/10.1002/cncy.21993)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 13

    Harrell RMK, Bimston DN. Surgical utility of afirma: effects of high cancer prevalence and oncocytic cell types in patients with indeterminate thyroid cytology. Endocrine Practice 2014 20 364369. (https://doi.org/10.4158/EP13330.OR)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 14

    Wang J, Yang J, Li D, Li J. Technologies for targeting DNA methylation modifications: basic mechanism and potential application in cancer. Biochimica et Biophysica Acta: Reviews on Cancer 2021 1875 188454. (https://doi.org/10.1016/j.bbcan.2020.188454)

    • Search Google Scholar
    • Export Citation
  • 15

    Zafon C, Gil J, Pérez-González B, Jordà M. DNA methylation in thyroid cancer. Endocrine-Related Cancer 2019 26 R415R439. (https://doi.org/10.1530/ERC-19-0093)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 16

    Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Angel Del G, Rivas MA & Hanna M et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 2011 43 491498. (https://doi.org/10.1038/ng.806)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 17

    Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 2016 8 389399. (https://doi.org/10.2217/epi.15.114)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 18

    Tejedor JR, Bueno C, Cobo I, Bayón GF, Prieto C, Mangas C, Pérez RF, Santamarina P, Urdinguio RG & Menéndez P et al. Epigenome-wide analysis reveals specific DNA hypermethylation of T cells during human hematopoietic differentiation. Epigenomics 2018 10 903923. (https://doi.org/10.2217/epi-2017-0163)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 19

    ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA & Dobin A et al.Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020 583 699710. (https://doi.org/10.1038/s41586-020-2493-4)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 20

    Park JL, Jeon S, Seo EH, Bae DH, Jeong YM, Kim Y, Bae JS, Kim SK, Jung CK, Kim YS. Comprehensive DNA methylation profiling identifies novel diagnostic biomarkers for thyroid cancer. Thyroid 2020 30 192203. (https://doi.org/10.1089/thy.2019.0011)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 21

    Guth S, Theune U, Aberle J, Galach A, Bamberger CM. Very high prevalence of thyroid nodules detected by high frequency (13 MHz) ultrasound examinationNo. European Journal of Clinical Investigation 2009 39 699706. (https://doi.org/10.1111/j.1365-2362.2009.02162.x)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 22

    Erinjeri NJ, Nicolson NG, Deyholos C, Korah R, Carling T. Whole-exome sequencing identifies two discrete druggable signaling pathways in follicular thyroid cancer. Journal of the American College of Surgeons 2018 226 950959.e5. (https://doi.org/10.1016/j.jamcollsurg.2018.01.059)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 23

    Fang Y, Ma X, Zeng J, Jin Y, Hu Y, Wang J, Liu R, Cao C. The profile of genetic mutations in papillary thyroid cancer detected by whole exome sequencing. Cellular Physiology and Biochemistry 2018 50 179195. (https://doi.org/10.1159/000493966)

    • Search Google Scholar
    • Export Citation
  • 24

    Cancer Genome Atlas Research Network, Akbani R, Aksoy BA, Ally A, Arachchi H, Asa SL. Integrated genomic characterization of papillary thyroid carcinoma. Cell 2014 159 676690. (https://doi.org/10.1016/j.cell.2014.09.050)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 25

    Fukahori M, Yoshida A, Hayashi H, Yoshihara M, Matsukuma S, Sakuma Y, Koizume S, Okamoto N, Kondo T & Masuda M et al. The associations between ras mutations and clinical characteristics in follicular thyroid tumors: new insights from a single center and a large patient cohort. Thyroid 2012 22 683689. (https://doi.org/10.1089/thy.2011.0261)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 26

    An JH, Song KH, Kim SK, Park KS, Yoo YB, Yang JH, Hwang TS, Kim DL. RAS mutations in indeterminate thyroid nodules are predictive of the follicular variant of papillary thyroid carcinoma. Clinical Endocrinology 2015 82 760766. (https://doi.org/10.1111/cen.12579)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 27

    Borowczyk M, Szczepanek-Parulska E, Dębicki S, Budny B, Verburg FA, Filipowicz D, Więckowska B, Janicka-Jedyńska M, Gil L & Ziemnicka K et al. Differences in mutational profile between follicular thyroid carcinoma and follicular thyroid adenoma identified using next generation sequencing. International Journal of Molecular Sciences 2019 20. (https://doi.org/10.3390/ijms20133126) .

    • Search Google Scholar
    • Export Citation
  • 28

    Jung SH, Kim MS, Jung CK, Park HC, Kim SY, Liu J, Bae JS, Lee SH, Kim TM & Lee SH et al. Mutational burdens and evolutionary ages of thyroid follicular adenoma are comparable to those of follicular carcinoma. Oncotarget 2016 7 6963869648. (https://doi.org/10.18632/oncotarget.11922)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 29

    Puzziello A, Guerra A, Murino A, Izzo G, Carrano M, Angrisani E, Zeppa P, Marotta V, Faggiano A, Vitale M. Benign thyroid nodules with RAS mutation grow faster. Clinical Endocrinology 2016 84 736740. (https://doi.org/10.1111/cen.12875)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 30

    Joseph B, Ji M, Liu D, Hou P, Xing MM. Lack of mutations in the thyroid hormone receptor (TR) α and β genes but frequent hypermethylation of the TRβ gene in differentiated thyroid tumors. Journal of Clinical Endocrinology and Metabolism 2007 92 47664770. (https://doi.org/10.1210/jc.2007-0812)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 31

    Cimino PJ, Gonzalez-Cuyar LF, Perry A, Dahiya S. Lack of BRAF-V600E mutation in papillary tumor of the pineal region. Neurosurgery 2015 77 621628. (https://doi.org/10.1227/NEU.0000000000000877)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 32

    Khan MS, Pandith AA, Ul Hussain M, Iqbal M, Khan NP, Wani KA, Masoodi SR, Mudassar S. Lack of mutational events of RAS genes in sporadic thyroid cancer but high risk associated with HRAS T81C single nucleotide polymorphism (case-control study). Tumour Biology 2013 34 521529. (https://doi.org/10.1007/s13277-012-0577-y)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 33

    Valderrabano P, Khazai L, Leon ME, Thompson ZJ, Ma Z, Chung CH, Hallanger-Johnson JE, Otto KJ, Rogers KD & Centeno BA et al.Evaluation of ThyroSeq v2 performance in thyroid nodules with indeterminate cytology. Endocrine-Related Cancer 2017 24 127136. (https://doi.org/10.1530/ERC-16-0512)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 34

    Nikiforov YE, Carty SE, Chiosea SI, Coyne C, Duvvuri U, Ferris RL, Gooding WE, LeBeau SO, Ohori NP & Seethala RR et al.Impact of the multi-gene ThyroSeq next-generation sequencing assay on cancer diagnosis in thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance cytology. Thyroid 2015 25 12171223. (https://doi.org/10.1089/thy.2015.0305)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 35

    Rivas AM, Nassar A, Zhang J, Casler JD, Chindris AM, Smallridge R, Bernet V. ThyroSeq®V2.0 Molecular testing: a cost-effective approach for the evaluation of indeterminate thyroid nodules. Endocrine Practice 2018 24 780788. (https://doi.org/10.4158/EP-2018-0212)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 36

    Parente DN, Kluijfhout WP, Bongers PJ, Verzijl R, Devon KM, Rotstein LE, Goldstein DP, Asa SL, Mete O, Pasternak JD. Clinical safety of renaming encapsulated follicular variant of papillary thyroid carcinoma: is NIFTP truly benign? World Journal of Surgery 2018 42 321326. (https://doi.org/10.1007/s00268-017-4182-5)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 37

    Jiang XS, Harrison GP, Datto MB. Young investigator challenge: molecular testing in noninvasive follicular thyroid neoplasm with papillary-like nuclear features. Cancer Cytopathology 2016 124 893900. (https://doi.org/10.1002/cncy.21802)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 38

    Nikiforov YE, Seethala RR, Tallini G, Baloch ZW, Basolo F, Thompson LDR, Barletta JA, Wenig BM, Ghuzlan AAl & Kakudo K et al. Nomenclature revision for encapsulated follicular variant of papillary thyroid carcinoma a paradigm shift to reduce overtreatment of indolent tumors. JAMA Oncology 2016 2 10231029. (https://doi.org/10.1001/jamaoncol.2016.0386)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 39

    Giannini R, Ugolini C, Poma AM, Urpì M, Niccoli C, Elisei R, Chiarugi M, Vitti P, Miccoli P, Basolo F. Identification of two distinct molecular subtypes of non-invasive follicular neoplasm with papillary-like nuclear features by digital RNA counting. Thyroid 2017 27 12671276. (https://doi.org/10.1089/thy.2016.0605)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 40

    Yim JH, Choi AH, Li AX, Qin H, Chang S, Tong ST, Chu P, Kim BW, Schmolze D & Lew R et al. Identification of tissue-specific DNA methylation signatures for thyroid nodule diagnostics. Clinical Cancer Research 2019 25 544551. (https://doi.org/10.1158/1078-0432.CCR-18-0841)

    • Crossref
    • Search Google Scholar
    • Export Citation
  • 41

    Carmona JJ, Accomando WP, Binder AM, Hutchinson JN, Pantano L, Izzi B, Just AC, Lin X, Schwartz J & Vokonas PS et al. Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans. NPJ Genomic Medicine 2017 2 13. (https://doi.org/10.1038/s41525-017-0012-9)

    • Crossref
    • Search Google Scholar
    • Export Citation