Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jun 29;17(6):e87001.
doi: 10.7759/cureus.87001. eCollection 2025 Jun.

Gene Expression Analysis of Papillary Thyroid Carcinoma With Lymph Node Metastasis and Radioiodine Refractivity

Nur Fadhlina Mohamad Pakarulrazy  1 , Nadiah Abu  1 , Shahrun Niza Abdullah Suhaimi  2 , Nadzlee Harith Paisol  3 , Reena Rahayu Md Zin  4 , Nani H MdLatar  5 , Nurul Syakima Ab Mutalib  1
Affiliations

Gene Expression Analysis of Papillary Thyroid Carcinoma With Lymph Node Metastasis and Radioiodine Refractivity

Nur Fadhlina Mohamad Pakarulrazy et al. Cureus. .

Abstract

Background/aim: Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer (TC) and is generally associated with a favorable prognosis. Nevertheless, aggressive variants of PTC that exhibit metastasis and resistance to radioiodine (RAI) therapy present significant clinical challenges. This study sought to generate a preliminary dataset on gene expression in RAI-refractory PTC using microarray analysis.

Materials and methods: Fresh frozen thyroid tissues were collected from PTC patients without lymph node metastasis and RAI avidity (n = 5), PTC patients with lymph node metastasis and RAI refractoriness (n = 5), and adjacent normal thyroid tissues (n = 4). The samples were cryosectioned, stained with hematoxylin and eosin, and confirmed by a pathologist. Nucleic acids were extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Germany), and RNA quantity, purity, and integrity were assessed. RNA samples were amplified, labelled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, US), and purified using the RNeasy Mini Kit (Qiagen). Cy3-labelled cRNA was fragmented and hybridized to Agilent SurePrint G3 Human GE v3 8 × 60 K microarray slides. Data were analyzed using AltAnalyze software and the iDEP web application.

Results: Our results revealed distinct expression patterns between RAI-avid and RAI-refractory PTC, with significant downregulation observed in key thyroid hormone synthesis genes, such as TPO, DIO1, and SLC26A4, across both groups. Notably, TG showed a variable expression pattern, suggesting its complex role in PTC pathophysiology. Pathway analysis highlighted the disruption of metabolic and immune-related pathways, emphasizing the altered physiological state of RAI-refractory PTC.

Conclusion: This study provides essential insights into the molecular underpinnings of RAI resistance in PTC and offers a foundation for future research aimed at developing targeted therapies that could enhance treatment efficacy and patient outcomes.

Keywords: cancer biomarker; microarray; papillary thyroid carcinoma; precision medicine; radioiodine; refractory.

PubMed Disclaimer

Conflict of interest statement

Human subjects: Informed consent for treatment and open access publication was obtained or waived by all participants in this study. Universiti Kebangsaan Malaysia Research Ethics Committee issued approval UKM PPI/111/8/JEP-2020-677. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: This research was funded by the Fundamental Research Grant Scheme (FRGS) of the Ministry of Higher Education Malaysia (FRGS/1/2019/SKK04/UKM/03/1). Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work.

Figures

Figure 1
Figure 1. Differential gene expression profiles in radioactive iodine-avid (RAI-A) and radioactive iodine-refractory (RAI-R) papillary thyroid carcinoma (PTC).
Differential gene expression profiles in RAI-A and RAI-R PTC. (A) Venn diagram showing the number of DEGs between adjacent normal thyroid tissues and PTC tissues with RAI-A or RAI-R. DEGs were identified using the limma statistical method in iDEP v2.0, with a false discovery rate < 0.05 and a fold change ≥ 2. (B) Heatmap of the top 100 upregulated and downregulated DEGs in RAI-A compared to adjacent normal thyroid tissues. (C) Heatmap of the top 100 upregulated and downregulated DEGs in RAI-R compared to adjacent normal thyroid tissue. The color scale represents the log2 fold change, with red indicating upregulated DEGs and green indicating downregulated DEGs. (D, E) Volcano plots showing the distribution of DEGs between RAI-A (D) and RAI-R (E) compared with adjacent normal thyroid tissues. Significantly upregulated DEGs are highlighted in red, whereas those significantly downregulated DEGs are marked in green. DEGs: differentially expressed genes.
Figure 2
Figure 2. Heatmaps and pathway analysis of differentially expressed genes (DEGs) involved in thyroid hormone synthesis in RAI-A.
(A) Heatmap representing the expression patterns of genes involved in thyroid hormone synthesis in RAI-A compared with normal thyroid tissues. Each row represents a gene, and each column represents a sample, with green indicating downregulation and red indicating upregulation. A clear distinction in expression patterns was observed between RAI-A samples and normal tissues. (B) KEGG pathway analysis illustrating the involvement of DEGs in the thyroid hormone synthesis pathway in RAI-A. Upregulated genes are shown in red, and downregulated genes are shown in green, indicating significant changes in the pathway regulation in RAI-A samples. RAI-A: radioactive iodine-avid; KEGG: Kyoto Encyclopedia of Genes and Genomes. The figure was originally created by the authors and developed specifically for this manuscript.
Figure 3
Figure 3. Heatmaps and pathway analysis of differentially expressed genes (DEGs) involved in thyroid hormone synthesis in RAI-R.
(A) Heatmap representing the expression patterns of genes involved in thyroid hormone synthesis in RAI-R compared with normal thyroid tissues. Each row represents a gene, and each column represents a sample, with green indicating downregulation and red indicating upregulation. A clear distinction in expression patterns was observed between normal tissues and RAI-R samples. (B) KEGG pathway analysis illustrating the involvement of DEGs in the thyroid hormone synthesis pathway in RAI-R. Upregulated genes are shown in red, and downregulated genes are shown in green, indicating significant changes in the pathway regulation in RAI-R samples. RAI-R: radioactive iodine-refractory; KEGG: Kyoto Encyclopedia of Genes and Genomes. The figure was originally created by the authors and developed specifically for this manuscript.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Temporal trends of thyroid cancer between 2010 and 2019 in Asian countries by geographical region and SDI, comparison with global data. Rezaei F, Mazidimoradi A, Pasokh Z, Dehghani SP, Allahqoli L, Salehiniya H. Aging Med (Milton) 2023;6:386–426. - PMC - PubMed
    1. Global burden of thyroid cancer in 2022: incidence and mortality estimates from GLOBOCAN. Lyu Z, Zhang Y, Sheng C, Huang Y, Zhang Q, Chen K. Chin Med J (Engl) 2024;137:2567–2576. - PMC - PubMed
    1. Overall survival of papillary thyroid carcinoma patients: a single-institution long-term follow-up of 5897 patients. Ito Y, Miyauchi A, Kihara M, Fukushima M, Higashiyama T, Miya A. World J Surg. 2018;42:615–622. - PMC - PubMed
    1. Radioiodine refractoriness score: a multivariable prediction model for postoperative radioiodine-refractory differentiated thyroid carcinomas. Li G, Lei J, Song L, et al. Cancer Med. 2018;7:5448–5456. - PMC - PubMed
    1. Associations between pathological features and radioactive iodine-refractory recurrent papillary thyroid carcinoma: with mutation analysis using recurrent samples. Nguyen TN, Mussazhanova Z, Kurohama H, et al. BMC Endocr Disord. 2025;25:134. - PMC - PubMed

LinkOut - more resources