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Paromov V, Uversky VN, Cooley A, Liburd LE, Mukherjee S, Na I, Dayhoff GW, Pratap S. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci 2024; 25:1552. [PMID: 38338831 PMCID: PMC10855131 DOI: 10.3390/ijms25031552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.
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Affiliation(s)
- Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Ayorinde Cooley
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Lincoln E. Liburd
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Shyamali Mukherjee
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Insung Na
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33613, USA;
| | - Siddharth Pratap
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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