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Open AccessArticle

Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes

1
Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
2
Department of Surgery, University of California, San Diego, La Jolla, CA 92093, USA
3
Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
4
Surgery Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
5
Department of Radiology, University of California, San Diego, California CA 92093, USA
6
Radiology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
7
Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
8
Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Cancers 2019, 11(8), 1179; https://doi.org/10.3390/cancers11081179
Received: 4 July 2019 / Revised: 8 August 2019 / Accepted: 8 August 2019 / Published: 15 August 2019
(This article belongs to the Special Issue Thyroid Cancer)
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PDF [5111 KB, uploaded 15 August 2019]
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Abstract

Papillary thyroid carcinoma (PTC) variants exhibit different prognosis, but critical characteristics of PTC variants that contribute to differences in pathogenesis are not well-known. This study aims to characterize dysregulated immune-associated and cancer-associated genes in three PTC subtypes to explore how the interplay between cancer and immune processes causes differential prognosis. RNA-sequencing data from The Cancer Genome Atlas (TCGA) were used to identify dysregulated genes in each variant. The dysregulation profiles of the subtypes were compared using functional pathways clustering and correlations to relevant clinical variables, genomic alterations, and microRNA regulation. We discovered that the dysregulation profiles of classical PTC (CPTC) and the tall cell variant (TCPTC) are similar and are distinct from that of the follicular variant (FVPTC). However, unique cancer or immune-associated genes are associated with clinical variables for each subtype. Cancer-related genes MUC1, FN1, and S100-family members were the most clinically relevant in CPTC, while APLN and IL16, both immune-related, were clinically relevant in FVPTC. RAET-family members, also immune-related, were clinically relevant in TCPTC. Collectively, our data suggest that dysregulation of both cancer and immune associated genes defines the gene expression landscapes of PTC variants, but different cancer or immune related genes may drive the phenotype of each variant. View Full-Text
Keywords: papillary thyroid carcinoma; cancer immunology; microRNA papillary thyroid carcinoma; cancer immunology; microRNA
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Chakladar, J.; Li, W.T.; Bouvet, M.; Chang, E.Y.; Wang-Rodriguez, J.; Ongkeko, W.M. Papillary Thyroid Carcinoma Variants are Characterized by Co-dysregulation of Immune and Cancer Associated Genes. Cancers 2019, 11, 1179.

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