Construction and Validation of an Immune-Related lncRNA Prognosis Model for Thyroid Cancer

Li, Zheng; Wang, Hui; Deng, Xia; Zhang, Jing; Tang, Wanyan; You, Wenxin; Nian, Weiqi

doi:10.21203/rs.3.rs-722174/v2

Cited by 1 publication

(1 citation statement)

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“…Epigenetic pro les, such as DNA methylation [19], histone modi cations [20], and noncoding RNA [21,22] have been characterized in thyroid cancer. Chromosomal accessibility is a powerful method for mapping genome-wide open chromatin patterns in multiple tumors [23,24] and provides valuable insights into the regulatory mechanisms of TC [25].…”

Section: Introductionmentioning

confidence: 99%

Different genetic landscapes of papillary thyroid carcinoma and paired benign nodules revealed by integrated multi-omics analysis

Yuan

Yang

chen

et al. 2023

Preprint

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Background: Alterations in the genetic landscape of papillary thyroid carcinoma (PTC) compared with coincidental benign thyroid nodules, especially adenomatoid nodules, remain to be demonstrated. Methods: Multi-omics profiling of whole-exome sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), and transcriptome sequencing were used for analysis. Results: Chromatin accessibility in the PTC was lower than that in the benign nodules around the transcription start sites (distance <1 kb) with high interpatient heterogeneity of chromatin profiles and distinct open chromatin accessibility. The gene regions around the mutation loci that were only detected in PTC exhibited altered chromatin accessibility between the PTC and benign nodules. Through integrated ATAC-Seq and RNA-Seq analysis, ARHGEF28 and ARHGEF24, genes not previously related to PTC or adenomatoid nodules, were identified. They were overexpressed and hyperaccessible in adenomatoid nodules compared to those in PTC. They were regulated by TEAD4, and hyperaccessible binding sites were enriched in differentially accessible regions in benign nodules. In addition, extrachromosomal circular DNA (eccDNA) analysis derived from ATAC-sequencing showed indolent character, but no PTC-diver genes in the eccDNA was found. Conclusions: This compendium of multi-omics data provides valuable insights and a resource for understanding the landscape of open chromatin features and regulatory networks in PTC and benign nodule pathogeneses.

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