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Retrospective analysis of cancer-specific gene expression panel for thyroid fine needle aspiration specimens

  • Original Article – Cancer Research
  • Published:
Journal of Cancer Research and Clinical Oncology Aims and scope Submit manuscript

Abstract

Background

While molecular testing is a promising strategy for preoperative assessment of cytologically indeterminate thyroid nodules, thyroid fine needle aspiration biopsy (FNA) presents unique challenges for molecular assays, including contaminating peripheral blood mononuclear cells (PBMC) and variable numbers of evaluable epithelial thyroid cells. Moreover, the newly recognized entity, noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), has added an additional challenge to the currently available molecular diagnostic platforms. New diagnostic tools are still needed to correctly distinguish benign and malignant thyroid nodules preoperatively.

Methods

Twenty-two transcript splice variants from 12 genes we previously identified as discriminating benign from malignant thyroid nodules were characterized in 80 frozen thyroid tumors from 8 histological subtypes. Isoforms detectable in PBMC were excluded, and the 5 most discriminating isoforms were further validated by real-time quantitative PCR (qPCR) on intraoperative FNA samples from 59 malignant tumors, 55 benign nodules, and 23 NIFTP samples. The qPCR threshold cycle values for each transcript were normalized to the thyrocyte-specific thyroid peroxidase isoform 1 (TPO1) and z-transformed. Receiver operating characteristic (ROC) analyses of the composite transcript scores were used to evaluate classification of thyroid FNAs by the 5-gene isoform expression panel.

Results

A molecular signature was developed by combining expression levels of specific isoforms of CDH3, FNDC4, HMGA2, KLK7, and PLAG1. FNAs containing at least 12–36 thyrocytes were sufficient for this assay. The 5-gene composite score achieved an area under the ROC curve (AUC) of 0.86 for distinguishing malignant from benign nodules, with a specificity of 91%, sensitivity of 75%, negative predictive value of 91%, and positive predictive value of 74%.

Conclusion

Our newly developed 5-gene isoform expression panel distinguishes benign from malignant thyroid tumors and, may help distinguish benign from malignant thyroid nodules in the context of the new NIFTP subtype.

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Availability of Data and Material

The datasets used during the current study are available from the corresponding author on reasonable request.

Abbreviations

FNA:

Fine needle aspiration biopsy

PBMC:

Peripheral blood mononuclear cells

AN:

Adenomatoid nodules

FA:

Follicular adenomas

HA:

HÜRTHLE cell adenomas

NIFTP:

Noninvasive follicular thyroid neoplasm with papillary-like nuclear features

FVPTC:

Follicular variant of papillary thyroid carcinoma

PTC:

Papillary thyroid carcinoma

FC:

Follicular carcinomas

HC:

Hürthle cell carcinomas

qPCR:

Real-time quantitative PCR

Ct:

Threshold cycle

ROC:

Receiver operating characteristic

AUC:

Area under the ROC curve

PPV:

Positive predictive value

NPV:

Negative predictive value

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Funding

This work was supported by a grant from the TEDCO-Maryland Innovation Initiative #2016-MII-3379, awarded to CBU.

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Authors and Affiliations

  1. Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Yongchun Wang, Brittany A. McKelvey, Zhiyang Liu & Christopher B. Umbricht

  2. Department of Oncology Biostatistics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Leslie M. Cope

  3. Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Lisa Rooper & Christopher B. Umbricht

  4. Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Christopher B. Umbricht

  5. Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

    Martha A. Zeiger

Authors
  1. Yongchun Wang
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  2. Brittany A. McKelvey
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  3. Zhiyang Liu
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  4. Lisa Rooper
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  5. Leslie M. Cope
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  6. Martha A. Zeiger
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  7. Christopher B. Umbricht
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Contributions

MZ and CU planned and designed the study. YW, BM, and ZL performed and analyzed the experiments. LR was the study pathologist and LC the study bioinformatician. All participated in writing and editing the manuscript.

Corresponding author

Correspondence to Christopher B. Umbricht.

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Conflict of interest

None of the authors declare any conflicts of interest or competing financial interests.

Ethical approval

Under Johns Hopkins Institutional Review Board approval, thyroid tumor tissue, intraoperative FNA, and blood specimens were collected from patients undergoing thyroid surgery at Johns Hopkins Hospital.

Consent to participate

This manuscript does not contain individual patient data.

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Supplementary Information

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Supplementary file1 (DOCX 19 KB)

Supplementary file2 (DOCX 19 KB)

Fig. S1. Study Workflow Diagram

432_2021_3706_MOESM4_ESM.tif

Fig. S2. Expression of the 5 gene transcripts and internal control in PBMC samples. Lane 1–5: PBMCs from different patients. Center lane: 50-bp DNA ladder. The representative gel image shows that in contrast to the general house-keeping gene GapDH, none of the 5 isoforms were detectable in patient PBMCs

432_2021_3706_MOESM5_ESM.tif

Fig. S3. The expression of different TPO1 and Thyroglobulin isoforms in PBMC samples. The representative gel image shows TPO1 was the only isoform not detectable in PBMCs

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Wang, Y., McKelvey, B.A., Liu, Z. et al. Retrospective analysis of cancer-specific gene expression panel for thyroid fine needle aspiration specimens. J Cancer Res Clin Oncol 147, 2983–2991 (2021). https://doi.org/10.1007/s00432-021-03706-3

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  • DOI: https://doi.org/10.1007/s00432-021-03706-3

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