A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates.
Alexandra S RebakIvo A HendriksJonas Damgaard ElsborgSara C Buch-LarsenClaus H NielsenLene TerslevRebecca KirschDres DamgaardNadezhda T DonchevaCaroline LennartssonMartin RykærLars J JensenMaria A ChristophorouMichael Lund NielsenPublished in: Nature structural & molecular biology (2024)
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
Keyphrases
- rheumatoid arthritis
- mass spectrometry
- high resolution
- cancer therapy
- gene expression
- disease activity
- acute myeloid leukemia
- transcription factor
- liquid chromatography
- drug delivery
- oxidative stress
- interstitial lung disease
- health information
- induced pluripotent stem cells
- social media
- high performance liquid chromatography
- tandem mass spectrometry