Biomarker identification through spatial proteomics for the characterization of indeterminate thyroid nodules

Area of Science:

• Biochemistry
• Proteomics
• Molecular Biology

Background:

• Indeterminate thyroid nodules present diagnostic challenges.
• Novel molecular biomarkers are needed for accurate characterization.
• Proteomic analysis offers a promising approach for biomarker discovery.

Purpose of the Study:

• To explore proteomic analyses for biomarker discovery in challenging thyroid lesions.
• To identify molecular features for classifying thyroid tumor histologies.
• To distinguish between NRAS-mutant (mNRAS) and NRAS-wild-type (wtNRAS) thyroid tumors.

Main Methods:

• Linear Discriminant Analysis (LDA) applied to Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) data.
• Selection of impactful molecular features for tumor classification and NRAS mutation status discrimination.
• Identification of relevant peaks using nanoscale liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS).

Main Results:

• LDA identified nine markers distinguishing noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTPs) from other histologies (73% accuracy).
• Nineteen markers were selected to identify mNRAS cases (84% accuracy).
• Nine differentially expressed proteins were putatively identified, including DDX42 and Histone H4 with specific distribution patterns; Protein disulfide-isomerase A1 and Complement C4-B were overexpressed in wtNRAS cases.

Conclusions:

• LDA-selected features effectively distinguish NIFTPs and discriminate between mNRAS and wtNRAS cases.
• Identified protein markers may complement genetic analyses for thyroid nodule characterization.
• These findings provide insights into pathogenic drivers of mNRAS versus wtNRAS thyroid lesions.