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AmyloGram reveals amyloidogenic potential in stroke thrombus proteomes
Open accessPublished version of a preprint
Abstract
Amyloidogenic proteins play a central role in a range of pathological conditions, yet their presence in thrombi has only recently been recognized. Whether computational prediction tools can identify amyloid- forming potential in thrombus proteomes remains unclear. AmyloGram is a computational tool that estimates amyloid-forming potential based on n-gram sequence encoding and random forest classification. Using AmyloGram, we analyzed 204 proteins in UniProt that were tagged by humans as amyloidogenic. We then applied the same approach to proteins identified in thrombi retrieved using mechanical thrombectomy from patients with cardioembolic and atherothrombotic stroke. In addition, we used AmyloGram to analyze the amyloidogenicity of 83,567 canonical human protein sequences. Among the UniProt-annotated ‘amyloid’ set, nearly all proteins received AmyloGram scores above 0.7, including 23 of the 24 human proteins. Even the lowest-scoring human protein, lysozyme (scoring 0.675), is known to form amyloid under certain conditions. In thrombi from both stroke subtypes in four different studies, all detected proteins (with a single exception) had AmyloGram scores above 0.7, suggesting a high likelihood of amyloid content. A majority of unannotated proteins also achieve AmyloGram scores exceeding 0.7. AmyloGram reliably identifies known amyloid-forming proteins and reveals that stroke thrombi are enriched for proteins with high amyloidogenic potential. These findings support the hypothesis that thrombus formation in stroke involves amyloid-related mechanisms and warrant further investigation using histological and functional validation.
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“Amyloidogenic proteins, long studied in the context of neurodegeneration and systemic amyloidoses [3,13–18], are increasingly recognized for their roles in vascular and thrombotic pathologies [19–25].”
Self-citationEcology and Biogenesis of Functional Amyloids in Pseudomonas
Rouse, S., Matthews, S., & Dueholm, M. S. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.05.004 · Cited by 65
β2-microglobulin: from physiology to amyloidosis
Heegaard, N. (2009) · Amyloid: Journal of Protein Folding Disorders · doi:10.1080/13506120903151775 · Cited by 60
Radford, S. E., Gosal, W. S., & Platt, G. W. (2005) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2005.07.006 · Cited by 59 · cited 1×
“Other high-scoring proteins included serum amyloid P [71–73], β2-microglobulin [31,74– 77], protein phosphatase 5, the major prion protein [78–80], and transforming growth factor β1 [81].”
Levy-Sakin, M., Shreberk, M., Daniel, Y., & Gazit, E. (2009) · Islets · doi:10.4161/isl.1.3.9609 · Cited by 58
Breakdown of supersaturation barrier links protein folding to amyloid formation
Noji, M., Samejima, T., Yamaguchi, K.-I., So, M., Yuzu, K., Chatani, E., Akazawa-Ogawa, Y., Hagihara, Y., Kawata, Y., Ikenaka, K., et al. (2021) · Communications Biology · doi:10.1038/s42003-020-01641-6 · Cited by 57
Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes
Bhardwaj, T., Gadhave, K., Kapuganti, S. K., Kumar, P., Brotzakis, Z. F., Saumya, K. U., Nayak, N., Kumar, A., Joshi, R., Mukherjee, B., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36234-4 · Cited by 52
Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification
Bondarev, S. A., Antonets, K. S., Kajava, A. V., Nizhnikov, A. A., & Zhouravleva, G. A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19082292 · Cited by 49 · cited 1×
“This further reinforces the view that the proteins contained in such clots tend to be highly amyloidogenic in nature, whatever their biochemical or enzymatic functions, and likely because they are cross-seeding each other’s amyloidogenesis [24,25,94].”
Risman, R., Belcher, H. A., Ramanujam, R., Weisel, J., Hudson, N., & Tutwiler, V. (2024) · Biomolecules · doi:10.3390/biom14020230 · Cited by 49 · cited 1×
“Laboratory studies have also shown that clot shrinkage and compression can increase the clot’s resistance to breakdown [112–116], including by enhancing strong crosslinks between fibrin and other molecules.”
Activation of innate immunity by lysozyme fibrils is critically dependent on cross-β sheet structure
Gustot, A., Raussens, V., Dehousse, M., Dumoulin, M., Bryant, C., Ruysschaert, J., & Lonez, C. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-1245-5 · Cited by 48 · cited 1×
“Indeed, mutant forms of lysozyme are naturally amyloidogenic [117–119], and lysozymes are widely studied as an amyloidogenic model [118–126], albeit some require a rather acidic pH to create stable amyloid conformations [127].”
Amyloid Fibrillation of Insulin: Amelioration Strategies and Implications for Translation
Fagihi, M. H. A., & Bhattacharjee, S. (2022) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.2c00174 · Cited by 47 · cited 1×
“…that a majority of proteins can potentially form amyloid under suitable conditions [42,44,138,139]; insulin is another well-known human example [140–146], and the existence of a great many well-established amyloidogenic proteins above our nominal threshold of 0.7 is seen as sufficient…”
InfluentialPuchtler, H., & Sweat, F. (1966) · Journal of Histochemistry and Cytochemistry · doi:10.1177/14.2.123 · Cited by 44
Grobbelaar, L., Kruger, A., Venter, C., Burger, E. M., Laubscher, G. J., Maponga, T. G., Kotze, M., Kwaan, H., Miller, J. B., Fulkerson, D., et al. (2022) · Seminars in Thrombosis and Hemostasis · doi:10.21203/rs.3.rs-1970823/v1 · Cited by 43 · cited 1×
“The SARS-CoV-2 spike protein provides a highly pertinent example [47–49], with its demonstrated ability both to form amyloid and to cross-seed amyloid formation [50], including during blood clotting [51,52].”
Self-citationdel Blanco, B. G., Ruiz‐Meana, M., Pascual, J. F., Barrabés, J. A., Figueras, J., Bañeras, J., Otaegui, I., Rojas, A., Vilardosa, Ú., Montaner, J., et al. (2016) · Thrombosis and Haemostasis · doi:10.1160/th15-12-0985 · Cited by 43 · cited 1×
“These results align with prior histological evidence of amyloid deposition in stroke thrombi, as detected by thioflavin T [26,27], and provide a straightforward explanation for the comparative resistance [153,154] of these clots towards fibrinolytics such as tissue plasmin(ogen activator).”
Amyloid Aggregation of Insulin: An Interaction Study of Green Tea Constituents
Gančár, M., Kurin, E., Bednarikova, Z., Marek, J., Mučaji, P., Nagy, M., & Gažová, Z. (2020) · Scientific Reports · doi:10.1038/s41598-020-66033-6 · Cited by 42
In vitro and in vivo insulin amyloid degradation mediated by Serratiopeptidase.
Metkar, S., Girigoswami, A., Murugesan, R., & Girigoswami, K. (2017) · Materials Science and Engineering C: Materials for Biological Applications · doi:10.1016/j.msec.2016.09.049 · Cited by 40
Baral, P. K., Yin, J., Aguzzi, A., & James, M. (2019) · Protein Science · doi:10.1002/pro.3735 · Cited by 39 · cited 1×
“Other high-scoring proteins included serum amyloid P [71–73], β2-microglobulin [31,74– 77], protein phosphatase 5, the major prion protein [78–80], and transforming growth factor β1 [81].”
Aitken, J., Loomes, K., Riba-Garcia, I., Unwin, R., Prijic, G., Phillips, A. S., Phillips, A., Wu, D.-H., Poppitt, S., Ding, K., et al. (2017) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2016.11.083 · Cited by 37 · cited 1×
“The highest-scoring proteins included amyloid precursor protein (APP, part of whose sequence forms the highly amyloidogenic Aβ protein [65]) and islet amyloid polypeptide (IAPP or amylin [66–70]), both exceeding 0.95.”
InfluentialFibrinolytic Enzymes for Thrombolytic Therapy.
Kumar, S. S., & Sabu, A. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-981-13-7709-9_15 · Cited by 34
The PrP-like proteins Shadoo and Doppel.
Westaway, D., Daude, N., Wohlgemuth, S. L., & Harrison, P. M. (2011) · Topics in current chemistry · doi:10.1007/128_2011_190 · Cited by 34 · cited 1×
“The four lowest-scoring human proteins that were tagged as amyloid were cystatin C, lysozyme, protein shadoo [86,87], and transthyretin, with lysozyme scoring 0.675 and transthyretin scoring 0.74 (Figure 3).”
InfluentialRibonuclease A suggests how proteins self‐chaperone against amyloid fiber formation
Teng, P. K., Anderson, N., Goldschmidt, L., Sawaya, M., Sambashivan, S., & Eisenberg, D. (2012) · Protein Science · doi:10.1002/pro.754 · Cited by 33
Recent Advances in Understanding Mammalian Prion Structure: A Mini Review
Terry, C., & Wadsworth, J. (2019) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2019.00169 · Cited by 31 · cited 1×
“Other high-scoring proteins included serum amyloid P [71–73], β2-microglobulin [31,74– 77], protein phosphatase 5, the major prion protein [78–80], and transforming growth factor β1 [81].”
Dargazanli, C., Zub, E., Deverdun, J., Decourcelle, M., de Bock, F., Labreuche, J., Lefèvre, P.-H., Gascou, G., Derraz, I., Bareiro, C. R., et al. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.575376 · Cited by 31 · cited 1×
“Data from Dargazanli et al. [96], who analyzed the thrombus proteome in 32 cardioembolic and 28 atherothrombotic stroke cases, identified 2455 proteins in total, of which 438 were detected in all samples.”
Wechalekar, A., Antoni, G., Al-Azzam, W. A., Bergström, M., Biswas, S., Chen, C.-G., Cheriyan, J., Cleveland, M., Cookson, L., Galette, P., et al. (2022) · BMC Cardiovascular Disorders · doi:10.1186/s12872-021-02407-6 · Cited by 30 · cited 1×
“Other high-scoring proteins included serum amyloid P [71–73], β2-microglobulin [31,74– 77], protein phosphatase 5, the major prion protein [78–80], and transforming growth factor β1 [81].”
Rossi, R., Fitzgerald, S., Gil, S., Mereuta, O., Douglas, A., Pandit, A., Brennan, P., Power, S., Alderson, J., O'Hare, A., et al. (2021) · European Stroke Journal · doi:10.1177/23969873211024777 · Cited by 28
Self-citationFunctional amyloid proteins confer defence against predatory bacteria
Ledvina, H. E., Sayegh, R., Carale, R. O., Burroughs, A. M., Macklin, A. R., Azadeh, A. L., Najera, L. D. B., Aravind, L., & Whiteley, A. T. (2025) · Nature · doi:10.1038/s41586-025-09204-7 · Cited by 27 · cited 1×
“Interestingly, even bacterial species produce proteins with strong amyloidogenic potential [147–151], where these structures may serve physiological roles such as defense or biofilm reinforcement [152].”
Biological properties of the PrP-like Shadoo protein
Daude, N. (2010) · Frontiers in bioscience · doi:10.2741/3801 · Cited by 27 · cited 1×
“The four lowest-scoring human proteins that were tagged as amyloid were cystatin C, lysozyme, protein shadoo [86,87], and transthyretin, with lysozyme scoring 0.675 and transthyretin scoring 0.74 (Figure 3).”
InfluentialThe amyloid proteome: a systematic review and proposal of a protein classification system
Gottwald, J., & Röcken, C. (2021) · Critical reviews in biochemistry and molecular biology · doi:10.1080/10409238.2021.1937926 · Cited by 26 · cited 1×
“One important family of such conformations is represented by amyloids, which differ markedly from the native structures synthesized on the ribosome [1–12].”
Human cystatin C monomer, dimer, oligomer, and amyloid structures are related to health and disease
Jurczak, P., Groves, P., Szymańska, A., & Rodziewicz-Motowidło, S. (2016) · FEBS Letters · doi:10.1002/1873-3468.12463 · Cited by 26
Rossi, R., Mereuta, O. M., Silva, M. B. E., Gil, S. M., Douglas, A., Pandit, A. S., Gilvarry, M., McCarthy, R., O’Connell, S., Tierney, C., et al. (2022) · Frontiers in Neurology · doi:10.3389/fneur.2022.854846 · Cited by 26 · cited 2×
“The first included 14 proteins found to be enriched in thrombi from patients with cardioembolic stroke [88].”
Self-citationFlow affects the structural and mechanical properties of the fibrin network in plasma clots
Eyisoylu, H., Hazekamp, E. D., Cruts, J., Koenderink, G., & de Maat, M. D. (2024) · Journal of materials science. Materials in medicine · doi:10.1007/s10856-024-06775-1 · Cited by 25
Molecular foundations of prion strain diversity.
Carta, M. C., & Aguzzi, A. (2021) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2021.07.010 · Cited by 25
Sabaté, R., & Ventura, S. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-065-6_15 · Cited by 25 · cited 1×
“These properties are conferred by a defining structural feature, the cross-β motif [8,37–41], which consists of β-sheets aligned perpendicular to the fibril axis.”
Lysozyme Amyloid Fibril Structural Variability Dependence on Initial Protein Folding State
Mikalauskaitė, K., Žiaunys, M., & Smirnovas, V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105421 · Cited by 21
Roy, S., Srinivasan, V. R., Arunagiri, S., Mishra, N., Bhatia, A., Shejale, K. P., Prajapati, K. P., Kar, K., & Anand, B. G. (2024) · Advances in Colloid and Interface Science · doi:10.1016/j.cis.2024.103205 · Cited by 21 · cited 1×
“Indeed, mutant forms of lysozyme are naturally amyloidogenic [117–119], and lysozymes are widely studied as an amyloidogenic model [118–126], albeit some require a rather acidic pH to create stable amyloid conformations [127].”
Arutyunyan, A., Seuma, M., Faure, A. J., Bolognesi, B., & Lehner, B. (2025) · Science Advances · doi:10.1126/sciadv.adv1422 · Cited by 21 · cited 2×
“Although ‘irreversibly’ formed amyloids (see [28]) are typically separated from native forms by a high energy barrier [29–34], they are often significantly more stable [30,32,35,36] and tend to form insoluble fibrils that can oligomerize.”
Pretorius, E., & Kell, D. (2023) · Seminars in Thrombosis and Hemostasis · doi:10.1055/s-0043-1774796 · Cited by 20
Self-citationLópez-Pedrera, C., Oteros, R., Ibáñez-Costa, A., Luque-Tévar, M., Muñoz-Barrera, L., Barbarroja, N., Chicano-Gálvez, E., Marta-Enguita, J., Orbe, J., Velasco, F., et al. (2023) · Journal of Thrombosis and Haemostasis · doi:10.1016/j.jtha.2023.04.015 · Cited by 20 · cited 2×
“The second included six proteins reported to be more abundant in thrombi from patients with atherothrombotic stroke compared with those with cardioembolic stroke [89].”
Amyloidosis: review and imaging findings.
Loizos, S., Chrysa, T. S., & Christos, G. S. (2014) · Seminars in ultrasound, CT, and MR · doi:10.1053/j.sult.2013.12.006 · Cited by 19
Increased fibrinaloid microclot counts in platelet-poor plasma are associated with Long COVIDPreprint
Dalton, C., Oliveira, M., Stafford, P., Peake, N., Kane, B., Higham, A., Singh, D., Jackson, N. A., Davies, H. E., Price, D. A., et al. (2024) · medRxiv · doi:10.1101/2024.04.04.24305318 · Cited by 19
ISCHAEMIC STROKE, THROMBOEMBOLISM AND CLOT STRUCTURE.
Stanton, K., Philippou, H., & Ariëns, R. (2024) · Neuroscience · doi:10.1016/j.neuroscience.2024.02.024 · Cited by 18
Singh, P., Simões‐Pires, E. N., Chen, Z.-L., Torrente, D., Calvano, M., Sharma, A., Strickland, S., & Norris, E. (2024) · bioRxiv · doi:10.1101/2024.01.20.576458 · Cited by 18 · cited 1×
“Such interactions have been observed in other settings [23,156–161] and may link clot composition to post-stroke inflammation or neurodegeneration.”
Exploring critical determinants of protein amyloidogenesis: a review
Sarkar, N., & Dubey, V. (2013) · Journal of Peptide Science · doi:10.1002/psc.2539 · Cited by 18
Muthu, S. A., Sharma, R., Qureshi, A., Parvez, S., & Ahmad, B. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.12.166 · Cited by 17
Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots
Kell, D. B., & Pretorius, E. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910809 · Cited by 17 · cited 5×
“Given the diversity of sequences capable of forming amyloid, numerous computational tools (31 were recently summarized in [24]) have been developed to predict amyloidogenic potential based on sequence features.”
InfluentialSelf-citationDoche, E., Sulowski, C., Guigonis, J., Graslin, F., Casolla, B., Hak, J., Carle, X., Brunel, H., Lindenthal, S., Martin, J.-C., et al. (2024) · Stroke · doi:10.1161/strokeaha.124.047156 · Cited by 16 · cited 1×
“We also used AmyloGram to analyze the nine proteins listed as being enriched in high-fibrin clots thrombectomized from (mainly cardioembolic) ischemic strokes in a paper by Doche and colleagues ([90]; their Figure 1).”
Schofield, J., Abrams, S., Jenkins, R. E., Lane, S., Wang, G.-Z., & Toh, C.-H. (2024) · Blood Advances · doi:10.1182/bloodadvances.2023012473 · Cited by 16 · cited 2×
“The complex proteomes observed in these (and other [23,84,85]) clots are only realistically accounted for by a rather widespread cross-seeding (many papers are summarized in [24,25]).”
SARS-CoV‑2 Spike Protein Amyloid Fibrils Impair Fibrin Formation and Fibrinolysis
Westman, H., Hammarström, P., & Nyström, S. (2025) · bioRxiv · doi:10.1101/2025.06.30.661938 · Cited by 15 · cited 1×
“The SARS-CoV-2 spike protein provides a highly pertinent example [47–49], with its demonstrated ability both to form amyloid and to cross-seed amyloid formation [50], including during blood clotting [51,52].”
Multiscale hierarchical perspectives on food protein amyloid fibrils: A review
Miao, L., Zhu, J.-Y., Wu, C., Li, D., Wang, H., Jiang, L.-Z., Guo, Q.-B., & Zhu, B.-W. (2025) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2025.111577 · Cited by 15 · cited 1×
“This is because it is considered that a majority of proteins can potentially form amyloid under suitable conditions [42,44,138,139]; insulin is another well-known human example [140–146], and the existence of a great many well-established amyloidogenic proteins above our nominal threshold of 0.7 is…”
InfluentialOne- and Two-Photon Excited Autofluorescence of Lysozyme Amyloids
Grelich-Mucha, M., Lipok, M., Różycka, M., Samoć, M., & Olesiak-Bańska, J. (2022) · Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c00570 · Cited by 15
Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy.
Louros, N. N., Tsiolaki, P. L., Baltoumas, F. A., Chryssikos, G., Gionis, V., Hamodrakas, S., & Iconomidou, V. A. (2017) · Journal of Structural Biology · doi:10.1016/j.jsb.2017.06.002 · Cited by 15
Cheng, Y., Ho, E., Weıntraub, S., Rentz, D. M., Gershon, R. C., Das, S., & Dodge, H. H. (2024) · The Journal of Prevention of Alzheimer s Disease · doi:10.14283/jpad.2024.77 · Cited by 14
The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil
Rouse, S. L., Stylianou, F., Wu, H. Y. G., Berry, J.-L., Sewell, L., Morgan, R. M. L., Sauerwein, A. C., & Matthews, S. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.06.007 · Cited by 14 · cited 1×
“Interestingly, even bacterial species produce proteins with strong amyloidogenic potential [147–151], where these structures may serve physiological roles such as defense or biofilm reinforcement [152].”
Lysozyme Fibrils Alter the Mechanism of Insulin Amyloid Aggregation
Žiaunys, M., Sakalauskas, A., Šneideris, T., & Smirnovas, V. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041775 · Cited by 13 · cited 1×
“Indeed, mutant forms of lysozyme are naturally amyloidogenic [117–119], and lysozymes are widely studied as an amyloidogenic model [118–126], albeit some require a rather acidic pH to create stable amyloid conformations [127].”
ASTRAL-R score predicts non-recanalisation after intravenous thrombolysis in acute ischaemic stroke
Vanacker, P., Heldner, M., Seiffge, D., Mueller, H., Eskandari, A., Traenka, C., Ntaios, G., Mosimann, P., Sztajzel, R., Pereira, V., et al. (2015) · Thrombosis and Haemostasis · doi:10.1160/th14-06-0482 · Cited by 13 · cited 1×
“Thrombi responsible for large vessel occlusion (LVO) in the setting of AIS are commonly characterized by a low recanalization rate, even after intravenous thrombolysis (e.g. [99–108]).”
AlphaFold2's training set powers its predictions of some fold‐switched conformations
Schafer, J. W., & Porter, L. L. (2025) · Protein Science · doi:10.1002/pro.70105 · Cited by 12
Kell, D., & Pretorius, E. (2024) · bioRxiv · doi:10.3390/molecules30030668 · Cited by 11 · cited 4×
“Amyloidogenic proteins, long studied in the context of neurodegeneration and systemic amyloidoses [3,13–18], are increasingly recognized for their roles in vascular and thrombotic pathologies [19–25].”
InfluentialSelf-citationSzulc, N., Burdukiewicz, M., Gąsior-Głogowska, M., Wojciechowski, J. W., Chilimoniuk, J., Mackiewicz, P., Šneideris, T., Smirnovas, V., & Kotulska, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-86530-6 · Cited by 9 · cited 2×
“In this study, we focus on AmyloGram [53,54], a predictive algorithm that uses n-gram encoding of amino acid sequences and a random forest [55] classifier to assign a single score between 0 and 1, reflecting overall amyloid-forming potential.”
(2020) · Because Sadness is Beautiful? · doi:10.2307/j.ctv1b74264.44 · Cited by 9 · cited 1×
“Given its known tendency to form amyloid blood clots [32,82,83] that are rather resistant to fibrinolysis [84,85], fibrinogen A, with a score of 0.8276, is also of notable interest (and see below).”
InfluentialRoberts, L., Coutts, G., Dickie, B. R., Smith, C. J., South, K., & Allan, S. (2025) · Stroke · doi:10.1161/strokeaha.125.050848 · Cited by 8 · cited 1×
“These results align with prior histological evidence of amyloid deposition in stroke thrombi, as detected by thioflavin T [26,27], and provide a straightforward explanation for the comparative resistance [153,154] of these clots towards fibrinolytics such as tissue plasmin(ogen activator).”
Exploring the occurrence of thioflavin-T-positive insulin amyloid aggregation intermediates
Žiaunys, M., Sakalauskas, A., Mikalauskaitė, K., & Smirnovas, V. (2021) · PeerJ · doi:10.7717/peerj.10918 · Cited by 8 · cited 1×
“…that a majority of proteins can potentially form amyloid under suitable conditions [42,44,138,139]; insulin is another well-known human example [140–146], and the existence of a great many well-established amyloidogenic proteins above our nominal threshold of 0.7 is seen as sufficient…”
InfluentialMeasuring the Energy Barrier of the Structural Change that Initiates Amyloid Formation
Arden, B. G., Borotto, N. B., Burant, B., Warren, W., Akiki, C., & Vachet, R. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00368 · Cited by 8
Chong, X., Lu, X., Wang, Y., Chang, A., Xu, L., Wang, N., Sun, Y., Jones, G. W., Song, Y.-T., Song, Y.-B., et al. (2016) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1126796 · Cited by 8
Grixti, J., Chandran, A., Pretorius, J., Walker, M., Sekhar, A., Pretorius, E., & Kell, D. (2025) · Stroke · doi:10.1161/strokeaha.124.050033 · Cited by 7 · cited 7×
“However, subtle differences likely exist, since the observed amyloid dispositions were highly heterogeneous both within and between clots [26,27].”
InfluentialSelf-citationSnorradottir, A. O., Hakonarson, H., & Palsdottir, A. (2024) · Brain Pathology · doi:10.1111/bpa.13291 · Cited by 7 · cited 1×
“Cystatin C [128–131], with an AmyloGram score of just 0.73, and transthyretin [132–137] (0.74) are directly responsible for two well-known amyloidoses.”
InfluentialThe clots removed from ischaemic stroke patients by mechanical thrombectomy are amyloid in nature
Grixti, J. M., Chandran, A., Pretorius, J., Walker, M., Sekhar, A., Pretorius, E., & Kell, D. (2024) · medRxiv · doi:10.1101/2024.11.01.24316555 · Cited by 6 · cited 7×
“However, subtle differences likely exist, since the observed amyloid dispositions were highly heterogeneous both within and between clots [26,27].”
InfluentialSelf-citationInfluence of Centrifugation and Shaking on the Self-Assembly of Lysozyme Fibrils
Krzek, M., Stroobants, S., Gelin, P., de Malsche, W., & Maes, D. (2022) · Biomolecules · doi:10.3390/biom12121746 · Cited by 6
Seth, P., & Sarkar, N. (2022) · 3 Biotech · doi:10.1007/s13205-022-03390-1 · Cited by 6
Rouse, S., Hawthorne, W. J., Lambert, S., Morgan, M., Hare, S., & Matthews, S. (2016) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x16017921 · Cited by 6
Schartz, D., Akkipeddi, S., Rahmani, R., Ellens, N., Houk, C., Kohli, G., Worley, L., Welle, K., Bhalla, T., Mattingly, T., et al. (2023) · American Journal of Neuroradiology · doi:10.3174/ajnr.a8069 · Cited by 5 · cited 1×
“We next analyzed the data for 19 proteins tabulated in a paper by Schartz and colleagues [95], who were interested in the proteome content of variably porous thrombi.”
Singh, P., Berk-Rauch, H. E., Soplop, N., Uryu, K., Strickland, S., & Ahn, H. (2018) · Journal of Visualized Experiments · doi:10.3791/58475 · Cited by 5
Kuriata, A., Badaczewska-Dawid, A. E., Pujols, J., Ventura, S., & Kmiecik, S. (2020) · bioRxiv · doi:10.1101/2020.09.09.276915 · Cited by 4 · cited 1×
“A sequence-based predictive approach was selected rather than a structure-based method such as Aggrescan 3D [56,57].”
The Importance of Macrophages, Lipid Membranes and Seeding in Experimental AA Amyloidosis
Shariatpanahi, A. V. (2019) · Linköping University medical dissertations · doi:10.3384/diss.diva-159658 · Cited by 4 · cited 1×
“Adapted from a CC-BY 4.0 publication [43] using Biorender.com.”
Influential
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Research works printed but not linked: 17
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Cited by
Sorted by citations
Booyens, R. M., Vlok, M., Bester, C., Hira, R., Khan, M. A., Kell, D., Raj, S. R., & Pretorius, E. (2025) · bioRxiv · doi:10.64898/2025.12.29.696828 · Cited by 2
“We note, too, that the proteome of FMCs differs substantially from that of normal clots, being highly enriched in amyloid(ogenic) proteins 27,28 ; the same is true for 29 the macroclots observed in ischaemic stroke 30 .”
Self-citationUncovering the hidden biology of fibrinaloid microclot complexes in complex, inflammatory diseases
Grixti, J., Pretorius, E., & Kell, D. (2026) · QRB Discovery · doi:10.1017/qrd.2026.10022
“Wehaveused the Amylogram programme (Burdukiewicz et al. , 2017; Szulc et al. , 2021) to assess the amyloidogenicity of individual proteins (the output is a score between 0 and 1, with anything over ca 0.75 being significantly and experimentally amyloidogenic (Kell et al. , 2025).”
InfluentialSelf-citationBooyens, R. M., Vlok, M., Bester, C., Hira, R., Khan, M. A., Kell, D., Raj, S. R., & Pretorius, E. (2026) · Cardiovascular Diabetology · doi:10.1186/s12933-026-03296-9
“We note, too, that the proteome of FMCs differs substantially from that of normal clots, being highly enriched in amyloid(ogenic) proteins [28, 29]; the same is true for [30] the macroclots observed in [31] ischaemic stroke.”
Self-citationRoberts, I., Tan, X., Moore, J. B., Pretorius, E., & Kell, D. (2026) · Biochemical Journal · doi:10.1042/bcj20250336
Self-citationSurface cues shape procoagulant properties of amyloidogenic microclots
Pretorius, E., Venter, C., Nunes, M., Thierry, A., & Kell, D. (2026) · Cell Death and Disease · doi:10.1038/s41419-026-08884-x
“Strikingly, the fi rst three of these have also been found in heterogenous deposits or FMCs [62, 145, 147], consistent with their appearance in and contributions to a variety of thrombotic diseases [160] and the general biophysics underlying cross-seeding [148, 149].”
Self-citation
Metadata
- Authors
- Kell, D. B., Doyle, K. M., Salcedo-Sora, J. E., Sekhar, A., Walker, M., & Pretorius, E.
- Affiliations
- University of Liverpool (GB)
- Ollscoil na Gaillimhe – University of Galway (IE)
- Walton Centre (GB)
- University of Washington (US)
- Corresponding author
- Kell, Douglas B.
- Pretorius, Etheresia
- ORCID
- Venue
- Biochemical Journal
- Publisher
- Portland Press Ltd.
- Published
- 2025-11
- Volume
- 482
- Issue
- 22
- Pages
- 1689-1706
- ISSN
- 0264-6021 (ISSN-L)
- 1470-8728
- PMC
- PMC12751076
- OpenAlex
- W4415242890
- Cited by
- 4
- References
- 160
- Citations by year
- 2026: 2 · 2025: 2
- FWCI
- 2.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Biochemical Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- Funders
- National Research Foundation (142142)
- South African Medical Research Council
- Novo Nordisk (NNF20CC0035580)
- Novo Nordisk Fonden (NNF20CC0035580)
- Medical Research Council
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- amylogram, amyloidogenic proteins, amyloid fibril formation, mechanical thrombectomy, cardioembolic stroke, atherothrombotic stroke, random forest classification, protein sequence prediction, lysozyme
- MeSH terms
- Amyloid, Humans, Thrombosis, Stroke, Proteome, Amyloidogenic Proteins
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