Mapping the IMiD‐dependent cereblon interactome using BioID‐proximity labelling

• Published in: The FEBS journal Vol. 291; no. 22; pp. 4892 - 4912
• Main Authors: Costacurta, Matteo, Sandow, Jarrod J., Maher, Belinda, Susanto, Olivia, Vervoort, Stephin J., Devlin, Jennifer R., Garama, Daniel, Condina, Mark R., Steele, Joel R., Kahrood, Hossein V., Gough, Daniel, Johnstone, Ricky W., Shortt, Jake
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.11.2024
• Subjects: BioID2; Biotinylation; Bortezomib; cereblon; Drugs; IMiDs; Immunomodulation; Labeling; Multiple myeloma; Myosin; Proteasome inhibitors; Proteasomes; Proteomics; Substrate specificity; Toxicity; Transcription factors; Ubiquitin-protein ligase; myosin; cereblon; BioID2; bortezomib; IMiDs
• ISSN: 1742-464X; 1742-4658; 1742-4658
• DOI: 10.1111/febs.17196

Immunomodulatory imide drugs (IMiDs) are central components of therapy for multiple myeloma (MM). IMiDs bind cereblon (CRBN), an adaptor for the CUL4‐DDB1‐RBX1 E3 ligase to change its substrate specificity and induce degradation of ‘neosubstrate’ transcription factors that are essential to MM cells. Mechanistic studies to date have largely focussed on mediators of therapeutic activity and insight into clinical IMiD toxicities is less developed. We adopted BioID2‐dependent proximity labelling (BioID2‐CRBN) to characterise the CRBN interactome in the presence and absence of various IMiDs and the proteasome inhibitor, bortezomib. We aimed to leverage this technology to further map CRBN interactions beyond what has been achieved by conventional proteomic techniques. In support of this approach, analysis of cells expressing BioID2‐CRBN following IMiD treatment displayed biotinylation of known CRBN interactors and neosubstrates. We observed that bortezomib alone significantly modifies the CRBN interactome. Proximity labelling also suggested that IMiDs augment the interaction between CRBN and proteins that are not degraded, thus designating ‘neointeractors’ distinct from previously disclosed ‘neosubstrates’. Here we identify Non‐Muscle Myosin Heavy Chain IIA (MYH9) as a putative CRBN neointeractor that may contribute to the haematological toxicity of IMiDs. These studies provide proof of concept for proximity labelling technologies in the mechanistic profiling of IMiDs and related E3‐ligase‐modulating drugs. Immunomodulatory imide drugs (IMiDs) are central components of multiple myeloma therapies. IMiDs bind cereblon (CRBN), an adaptor for the CUL4‐DDB1‐RBX1 E3 ubiquitin ligase. BioID2 proximity labelling maps the CRBN interactome in myeloma cells treated with anti‐myeloma drugs via purification and mass spectrometry analysis of biotinylated proteins. After IMiD exposure, neosubstrates IKZF1 and CK1α that are protected from proteasomal degradation by bortezomib, are purified. Bortezomib alone induces interactions of CRBN with other regulators of protein homeostasis. IMiDs increase the interaction of CRBN with MYH9, but MHY9 is not degraded, even in the absence of bortezomib.