4D-DIA proteomics and transcriptomics of thyroid cancer subtypes

Formalin-fixed paraffin-embedded (FFPE) tissue samples were obtained from 120 patients, including anaplastic thyroid carcinoma (ATC, n=35), poorly differentiated thyroid carcinoma (PDTC, n=18), papillary thyroid carcinoma (PTC, n=37), and adjacent normal tissues (N, n=30). All samples were confirmed histologically using hematoxylin and eosin (HE) staining and classified according to the 2022 WHO Classification of Thyroid Tumors. For 4D-DIA proteomics analysis, 34 ATC samples, 18 PDTC samples, 36 PTC samples, and 30 N samples passed quality control for further examination. Shanghai OE Biotech Company provided services in micro-proteomics. Proteins were extracted from FFPE sections after dewaxing and rehydration, using the iST Sample Preparation Kit 8x. ue to RNA degradation and occasionally sample contamination in some of the FFPE samples, 10 ATC samples, 5 PDTC samples, 31 PTC samples, and 23 N samples passed quality control for further examination. Shanghai OE Biotech Company offered total transcriptome sequencing services, covering mRNA, lncRNA, and circRNA. Total RNA was isolated from FFPE samples using the RecoverAll Total Nucleic Acid Isolation Kit. Libraries were constructed from fragmented RNA and sequenced on the Illumina NovaSeq 6000 platform. Clean reads were obtained by trimming adapters and filtering low-quality sequences using Fastq. Reads were aligned to the human genome with HISAT2, and gene expression levels were quantified as FPKM.