Photo-Catalyzed Labeling of Amyloid Deposits in Human Tissue to Proteotype Amyloidosis Diseases

Abstract

Over 40 amyloidogenic proteins have been identified to cause amyloidosis diseases in clinics. Tissue deposition of amyloid proteins entangled with interacting partners is a characteristic pathological hallmark of amyloidosis diseases. However, the proteomic complexity of co-aggregated amyloid deposits poses a clinical challenge to diagnose the exact disease-causing pathogenic proteins in patients’ biopsied tissue. Herein, we present a photocatalytic proteomic method, named Amyloid-ID, as a promising approach to identify the composition of amyloid deposits for clinical proteotyping of amyloidosis diseases. Amyloid-ID is enabled by a photosensitized probe analogous to a pan-amyloid sensor, Thioflavin T. We show this probe photocatalyzes protein labeling via reactive oxygen species and demonstrate its applicability in both AD mouse models and human laryngeal samples. Next, we exemplify its utility by proteotyping the pathogenic protein underlying the rare laryngeal amyloidosis (LA). Using patients’ biopsied tissue sections, we label, enrich, and profile the amyloid deposits. Proteomics analysis top-ranks fibrinogen as a potential pathogenic protein. Biochemical and biophysical characterizations confirm that fibrinogen can aggregate into amyloid fibrils. Intriguingly, we observe that fibrinogen's fibrillation is sensitive to mechanical forces, particularly impacted by sonication. Such observation coincides with its primary larynx deposition, where frequent vocal cord friction occurs. Overall, given the photocatalytic properties, our Amyloid-ID serves as a promising clinical proteotyping method for amyloidosis diseases.

Keywords

amyloid / photocatalytic chemistry / proximity labeling / amyloidosis disease / proteomics

References

[1] G. Merlini and V. Bellotti, “Molecular Mechanisms of Amyloidosis,” The New England Journal of Medicine 349 (2003): 583-596.

[2] M. Clerico, A. K. Pozhidaeva, R. M. Jansen, et al., “Selective Promiscuity in the Binding of E. coli Hsp70 to an Unfolded Protein,” Proceedings of the National Academy of Sciences of the United States of America 118 (2021): e2016962118.

[3] Q. Xu, Y. Ma, Y. Sun, et al., “Protein Amyloid Aggregate: Structure and Function,” Aggregate 4 (2023): e333.

[4] N. Buxbaum, D. S. Eisenberg, M. Fändrich, et al., “Amyloid Nomenclature 2024: Update, Novel Proteins, and Recommendations by the International Society of Amyloidosis (ISA) Nomenclature Committee,” Amyloid 31 (2024): 249-256.

[5] I. Sulatsky, O. V. Stepanenko, O. V. Stepanenko, et al., “Solving the Amyloid Paradox: Unveiling the Complex Pathogenicity of Amyloid Fibrils,” Aggregate 6 (2025): e70078.

[6] C. M. Lim, A. González Díaz, M. Fuxreiter, et al., “Multiomic Prediction of Therapeutic Targets for Human Diseases Associated With Protein Phase Separation,” Proceedings of the National Academy of Sciences of the United States of America 120 (2023): e2300215120.

[7] G. J. Morgan, N. L. Yan, D. E. Mortenson, et al., “Stabilization of Amyloidogenic Immunoglobulin Light Chains by Small Molecules,” Proceedings of the National Academy of Sciences of the United States of America 116 (2019): 8360-8369.

[8] Y. Cao, J. Adamcik, M. Diener, J. R. Kumita, et al., “Different Folding States From the Same Protein Sequence Determine Reversible vs Irreversible Amyloid Fate,” Journal of the American Chemical Society 143 (2021): 11473-11481.

[9] D. Adams, H. Koike, M. Slama, et al., “Hereditary Transthyretin Amyloidosis: A Model of Medical Progress for a Fatal Disease,” Nature Reviews Neurology 15 (2019): 387-404.

[10] A. Martinez-Naharro, A. J. Baksi, P. N. Hawkins, et al., “Diagnostic Imaging of Cardiac Amyloidosis,” Nature Reviews Cardiology 17 (2020): 413-426.

[11] K. Hou, H. Pan, H. Shahpasand-Kroner, C. Hu, et al., “D-peptide-magnetic Nanoparticles Fragment Tau Fibrils and Rescue Behavioral Deficits in a Mouse Model of Alzheimer's Disease,” Science Advances 10 (2024): eadl2991.

[12] L. D. Aubrey, N. Ninkina, S. M. Ulamec, et al., “Substitution of Met-38 to Ile in γ-Synuclein Found in Two Patients With Amyotrophic Lateral Sclerosis Induces Aggregation Into Amyloid,” Proceedings of the National Academy of Sciences of the United States of America 121 (2024): e2309700120.

[13] D. Ogasawara, D. B. Konrad, Z. Y. Tan, et al., “Chemical Tools to Expand the Ligandable Proteome: Diversity-Oriented Synthesis-Based Photoreactive Stereoprobes,” Cell Chemical Biology 31 (2024): 2138-2155.e32.

[14] M. Z. Chen, N. S. Moily, J. L. Bridgford, et al., “A Thiol Probe for Measuring Unfolded Protein Load and Proteostasis in Cells,” Nature Communications 8 (2017): 474.

[15] S. Zhang, T. C. Owyong, O. Sanislav, et al., “Global Analysis of Endogenous Protein Disorder in Cells,” Nature Methods 22 (2025): 124-134.

[16] W. K. Self and D. M. Holtzman, “Emerging Diagnostics and Therapeutics for Alzheimer Disease,” Nature Medicine 29 (2023): 2187-2199.

[17] M. Rodrigues, P. Bhattacharjee, and A. Brinkmalm, “Structure-Specific Amyloid Precipitation in Biofluids,” Nature Chemistry 14 (2022): 1045-1053.

[18] J. Yang, B. Zhu, J. Zhang, and S. H. Liang, “Half-Curcumin-Based Chemiluminescence Probes and Their Applications in Detecting Quasi-Stable Oxidized Proteins,” Angewandte Chemie International Edition 63 (2024): e202409896.

[19] M. Ji, M. Arbel, L. Zhang, et al., “Label-Free Imaging of Amyloid Plaques in Alzheimer's Disease With Stimulated Raman Scattering Microscopy,” Science Advances 4 (2018): eaat7715.

[20] Y. Tao, W. Xia, Q. Zhao, et al., “Structural Mechanism for Specific Binding of Chemical Compounds to Amyloid Fibrils,” Nature Chemical Biology 19 (2023): 1235-1245.

[21] W. Qin, K. F. Cho, P. E. Cavanagh, et al., “Deciphering Molecular Interactions by Proximity Labeling,” Nature Methods 18 (2021): 133-143.

[22] M. G. Kang and H. W. Rhee, “Molecular Spatiomics by Proximity Labeling,” Accounts of Chemical Research 55 (2022): 1411-1422.

[23] S. Zhang, Q. Tang, X. Zhang, et al., “Proximitomics by Reactive Species,” ACS Central Science 10 (2024): 1135-1147.

[24] C. A. Lutomski, T. J. El-Baba, J. D. Hinkle, et al., “Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors,” Angewandte Chemie International Edition 62 (2023): e202305694.

[25] D. C. McCutcheon, G. Lee, A. Carlos, et al., “Photoproximity Profiling of Protein-Protein Interactions in Cells,” Journal of the American Chemical Society 142 (2020): 146-153.

[26] Y. Liu, Y. Ge, R. Zeng, et al., “Proximity Chemistry in Living Systems,” CCS Chemistry 5 (2023): 802-813.

[27] H. Jia, J. Han, Y. Qi, et al., “Small-Molecule Benzo-Phenoselenazine Derivatives for Multi-Subcellular Biomolecule Profiling,” Angewandte Chemie International Edition 64 (2025): e202419904.

[28] Z. Lin, X. Wang, K. A. Bustin, et al., “Activity-Based Hydrazine Probes for Protein Profiling of Electrophilic Functionality in Therapeutic Targets,” ACS Central Science 7 (2021): 1524-1534.

[29] W. Qin, S. A. Myers, D. K. Carey, et al., “Spatiotemporally-Resolved Mapping of RNA Binding Proteins via Functional Proximity Labeling Reveals a Mitochondrial mRNA Anchor Promoting Stress Recovery,” Nature Communications 12 (2021): 4980.

[30] S. W. Huth, J. B. Geri, J. V. Oakley, et al., “µMap-Interface: Temporal Photoproximity Labeling Identifies F11R as a Functional Member of the Transient Phagocytic Surfaceome,” Journal of the American Chemical Society 146 (2024): 32255-32262.

[31] H. Zhu, J. H. Oh, Y. Matsuda, et al., “Tyrosinase-Based Proximity Labeling in Living Cells and in Vivo,” Journal of the American Chemical Society 146 (2024): 7515-7523.

[32] Y. Zhai, X. Zhang, Z. Chen, et al., “Global Profiling of Functional Histidines in Live Cells Using Small-Molecule Photosensitizer and Chemical Probe Relay Labelling,” Nature Chemistry 16 (2024): 1546-1557.

[33] A. Taniguchi, Y. Shimizu, K. Oisaki, et al., “Switchable Photooxygenation Catalysts That Sense Higher-Order Amyloid Structures,” Nature Chemistry 8 (2016): 974-982.

[34] M. Furuta, S. Arii, H. Umeda, et al., “Leuco Ethyl Violet as Self-Activating Prodrug Photocatalyst for In Vivo Amyloid-Selective Oxygenation,” Advanced Science 11 (2024): 2401346.

[35] Z. Lin, K. Schaefer, I. Lui, et al., “Multiscale Photocatalytic Proximity Labeling Reveals Cell Surface Neighbors on and Between Cells,” Science 385 (2024): eadl5763.

[36] M. Takato, S. Sakamoto, H. Nonaka, et al., “Photoproximity Labeling of Endogenous Receptors in the Live Mouse Brain in Minutes,” Nature Chemical Biology 21 (2025): 109-119.

[37] C. Loynd, S. J. Singha Roy, and V. J. Ovalle, “Electrochemical Labelling of Hydroxyindoles With Chemoselectivity for Site-Specific Protein Bioconjugation,” Nature Chemistry 16 (2024): 389-397.

[38] H. Feng, Q. Zhao, N. Zhao, et al., “A Cell-Permeable Photosensitizer for Selective Proximity Labeling and Crosslinking of Aggregated Proteome,” Advanced Science 11 (2024): 2306950.

[39] P. Wang, W. Tang, Z. Li, et al., “Mapping Spatial Transcriptome With Light-Activated Proximity-Dependent RNA Labeling,” Nature Chemical Biology 15 (2019): 1110-1119.

[40] H. Feng, Q. Zhao, B. Zhang, et al., “Enabling Photo-Crosslinking and Photo-Sensitizing Properties for Synthetic Fluorescent Protein Chromophores,” Angewandte Chemie International Edition 62 (2023): e202215215.

[41] F. Zheng, C. Yu, X. Zhou, et al., “Genetically Encoded Photocatalytic Protein Labeling Enables Spatially-Resolved Profiling of Intracellular Proteome,” Nature Communications 14 (2023): 2978.

[42] M. A. Arnanz, M. Ferrer, M. T. Grande, et al., “Fatty Acid Amide Hydrolase Gene Inactivation Induces Hetero-Cellular Potentiation of Microglial Function in the 5xFAD Mouse Model of Alzheimer's Disease,” Glia 73 (2025): 352-367.

[43] F. Galluzzi and W. Garavello, “Surgical Treatment of Laryngeal Amyloidosis: A Systematic Review,” European Archives of Oto-Rhino-Laryngology 280 (2023): 3065-3074.

[44] N. M. Phillips, E. Matthews, C. Altmann, et al., “Laryngeal Amyloidosis: Diagnosis, Pathophysiology and Management,” The Journal of Laryngology and Otology 131 (2017): S41-S47.

[45] J. W. Jackson, J. S. Foster, E. B. Martin, et al., “Collagen Inhibits Phagocytosis of Amyloid In Vitro and In Vivo and May Act as a ‘Don't Eat Me’ Signal,” Amyloid 30 (2023): 249-260.

[46] S. A. Bondarev, M. V. Uspenskaya, J. Leclercq, et al., “AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-Aggregation,” Journal of Molecular Biology 436 (2024): 168437.

[47] M. A. Petersen, J. K. Ryu, and K. Akassoglou, “Fibrinogen in Neurological Diseases: Mechanisms, Imaging and Therapeutics,” Nature Reviews Neuroscience 19 (2018): 283-301.

[48] S. Ye, A. P. Latham, Y. Tang, et al., “Micropolarity Governs the Structural Organization of Biomolecular Condensates,” Nature Chemical Biology 20 (2024): 443-451.

[49] Y. Wang, J. Guo, M. Chen, et al., “Ultrabright and Ultrafast Afterglow Imaging in Vivo via Nanoparticles Made of Trianthracene Derivatives,” Nature Biomedical Engineering 9 (2025): 656-670.

[50] X. Li, F. Han, X. Zhou, et al., “Aggregation-Induced Triplet Symmetry-Breaking Charge Separation Drives Electron Transfer for Autophagy Blockade-Enhanced Type-I Photodynamic Therapy,” Aggregate 6 (2025): e70208.

[51] E. W. Deutsch, N. Bandeira, Y. Perez-Riverol, et al., “The ProteomeX-change Consortium at 10 Years: 2023 Update,” Nucleic Acids Research 51 (2023): D1539-D1548.

RIGHTS & PERMISSIONS

2026 The Author(s). Aggregate published by SCUT, AIEI, and John Wiley & Sons Australia, Ltd.