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Research

Publications

  • 2025
    • T2 Hyperintensities in Gracile Tracts of Cervical Spinal Cord in Giant Axonal Neuropathy (GAN)
      Armao D, Bouldin TW, Bharucha-Goebel DX, Hartman TS, Gray SJ, Bailey RM, Saade D, Todd JJ, Jain M, Waite M, Bönnemann CG, Smith JK., Muscle Nerve. 2025 Nov;72(5):1152-1155. doi: 10.1002/mus.70004. Epub 2025 Aug 16. PMID: 40878963
    • Correlative light and electron microscopy for human brain and other biological models
      Shafiei N, Stӓhli D, Burger D, Di Fabrizio M, van den Heuvel L, Daraspe J, Böing C, Shahmoradian SH, van de Berg WDJ, Genoud C, Stahlberg H, Lewis AJ., Nat Protoc. 2025 Oct;20(10):2994-3023. doi: 10.1038/s41596-025-01153-9. Epub 2025 Mar 31. PMID: 40164750
    • Structural and molecular homogeneity of ATTRv-T60A amyloid fibrils across patients and organs
      Fernandez-Ramirez MDC, Nguyen BA, Afrin S, Singh V, Evers B, Shelton JM, Escobar CL, Bassett P, Wang L, Pękała M, Ahmed Y, Cabrera Hernandez LO, Pedretti R, Singh P, Canepa J, Wosztyl A, Li Y, Boyer DR, Cao Q, Saelices L., Structure. 2025 Oct 16:S0969-2126(25)00374-0. doi: 10.1016/j.str.2025.09.008. Epub ahead of print. PMID: 41106377
    • Spontaneous pathology in PS19 tauopathy mice progresses via brain networks
      Ramirez DMO, Whitesell JD, Bhagwat N, Thomas TL, Ajay AD, Nawaby A, Delatour B, Bay S, LaFaye P, Harris JA, Meeks JP, Diamond MI., Neurobiol Dis. 2025 Oct 15;215:107072. doi: 10.1016/j.nbd.2025.107072. Epub 2025 Aug 29. PMID: 40886860
    • AXZ viewer: a web application to visualize unprocessed AFM-IR data
      Duverger W, Ramer G, Louros N, Schymkowitz J, Rousseau F., Bioinformatics. 2025 Oct 2;41(10):btaf513. doi: 10.1093/bioinformatics/btaf513. PMID: 40973685
    • Toward a thermodynamic taxonomy of amyloid fibrils
      Louros N, Schymkowitz J, Rousseau F., Structure. 2025 Oct 2;33(10):1628-1630. doi: 10.1016/j.str.2025.08.010. PMID: 41043396
    • A Rare Unusually Aggressive Form of Hereditary Transthyretin Amyloidosis
      Zhang J, Roth LR, Wees I, Phillips L, Pedretti R, Nguyen P, Saelices L, Grodin JL., JACC Case Rep. 2025 Oct 1;30(30):105309. doi: 10.1016/j.jaccas.2025.105309. PMID: 41043930
    • β-Amyloid induces microglial expression of GPC4 and APOE leading to increased neuronal tau pathology and toxicity
      Holmes BB, Weigel TK, Chung JM, Kaufman SK, Apresa BI, Byrnes JR, Kumru KS, Vaquer-Alicea J, Gupta A, Rose IVL, Zhang Y, Nana AL, Alter D, Grinberg LT, Spina S, Leung KK, Miller BL, Condello C, Kampmann M, Seeley WW, Coutinho-Budd JC, Wells JA., Mol Neurodegener. 2025 Aug 29;20(1):96. doi: 10.1186/s13024-025-00883-4. PMID: 40883746
    • High-density brush-shaped polymer lipids reduce anti-PEG antibody binding for repeated administration of mRNA therapeutics.
      Xiao Y, Lian X, Sun Y, Sung YC, Vaidya A, Chen Z, Gupta A, Chatterjee S, Zheng L, Guerrero E, Wang X, Farbiak L, Yang Y, Diamond MI, Leal C, McDonald JG, Siegwart DJ., Nat Mater. 2025 Aug;24(8):1320. doi: 10.1038/s41563-025-02270-2. Erratum for: Nat Mater. 2025 Nov;24(11):1840-1851. doi: 10.1038/s41563-024-02116-3. PMID: 40467735
    • Risk for Heart Failure and Atrial Fibrillation Across the Lifespan for Carriers of the Amyloidogenic p.V142I TTR Variant
      Grodin JL, Gupta A, Rison I Jr, Kozlitina J, Saelices-Gomez L, Girotra S, Shah AM, Roth LR, Griffin JM, Drazner MH, Tang WHW, Maurer MS, de Lemos JA., Circ Genom Precis Med. 2025 Aug;18(4):e004911. doi: 10.1161/CIRCGEN.124.004911. Epub 2025 Jul 23. PMID: 40698407
    • Select Azo Compounds Post-translationally Modulate HTRA1 Abundance and Activity Potentially through Interactions at the Trimer Interface
      Hulleman JD, Jeon S, Bali S, DiCesare SM, Abbas A, Daniel S, Ortega AJ, Collier GE, Yang J, Bhattacharyaa A, McCoy MK, Joachimiak LA, Posner BA., ACS Chem Biol. 2025 Aug 15;20(8):1849-1862. doi: 10.1021/acschembio.4c00818. Epub 2025 Jul 30. PMID: 40735939
    • Mechanism of inhibition of acid-mediated transthyretin aggregation by designed peptides
      Sun X, Pedretti R, Dyson HJ, Saelices L, Wright PE. J Biol Chem. 2025 Aug 13;301(10):110594. doi: 10.1016/j.jbc.2025.110594. Epub ahead of print. PMID: 40816471
    • A Shared Amyloid Architecture in Cardiac Fibrils from Three Neuropathy-Associated ATTR Variants
      Fernandez-Ramirez MDC, Afrin S, An Nguyen B, Singh V, Pekala M, Singh P, Ahmed Y, Pedretti R, Lemoff A, Kluve-Beckerman B, Chhapra F, Eisenberg D, Saelices L., bioRxiv [Preprint]. 2025 Aug 7:2025.08.05.667944. doi: 10.1101/2025.08.05.667944. PMID: 40799554
    • Structural polymorphism of ex-vivo ALECT2 amyloid fibrils revealed by cryo-EM
      Afrin S, Nguyen BA, Singh V, Singh P, Bassett P, Pekala M, Evers B, Lopez C, Ahmed Y, Li L, Kallem RR, Lemoff A, Argyropoulos C, Kluve-Beckerman B, Saelices L., bioRxiv [Preprint]. 2025 Jul 18:2025.07.15.664973. doi: 10.1101/2025.07.15.664973. PMID: 40791318
    • Structural variability of apolipoprotein A-I amyloid fibrils across organs, mutations, and clinical presentations, revealed by cryo-EM
      An Nguyen B, Del Carmen Fernandez-Ramirez M, Bassett P, Singh V, Singh P, Pękała M, Villalon L, Ahmed Y, Lemoff A, Evers B, Lopez C, Kluve-Beckerman B, Saelices L., bioRxiv [Preprint]. 2025 Jul 11:2025.07.08.663734. doi: 10.1101/2025.07.08.663734. PMID: 40672337
    • Developmental phenotype and quality of life in SLC13A5 citrate transporter disorder
      Ozlu C, Adams RM, Solidum RM, Cooper S, Best CR, Elacio J, Kavanaugh BC, Spelbrink EM, Brown TL, Nye K, Liu JS, Bailey RM, Goodspeed K, Porter BE., Dev Med Child Neurol. 2025 Jul;67(7):930-940. doi: 10.1111/dmcn.16218. Epub 2024 Dec 22. PMID: 39710583
    • Nitrous oxide enhances MR-guided focused ultrasound delivery of gene therapy to the murine hippocampus
      Bhardwaj D, Youssef I, Imphean D, Holmes SK, Krishnan V, Estill-Terpack SJ, Diamond M, Chopra R, Bailey RM, Shah BR., Gene Ther. 2025 Jul;32(4):376-384. doi: 10.1038/s41434-025-00530-z. Epub 2025 May 6. PMID: 40328971
    • Interactions between pathological and functional amyloid: A match made in Heaven or Hell?
      Otzen DE, Peña-Díaz S, Widmann J, Daugberg AOH, Zhang Z, Jiang Y, Mittal C, Dueholm MKD, Louros N, Wang H, Javed I., Mol Aspects Med. 2025 Jun;103:101351. doi: 10.1016/j.mam.2025.101351. Epub 2025 Mar 1. PMID: 40024004
    • Expression and distribution of rAAV9 intrathecally administered in juvenile to adolescent mice
      Garza IT, Eller MM, Holmes SK, Schackmuth MK, Bailey RM., Gene Ther. 2025 May;32(3):189-196. doi: 10.1038/s41434-024-00498-2. Epub 2024 Nov 5. PMID: 39501094
    • A preliminary study on plasma markers across cognitive stages and links to a history of mild traumatic brain injury
      LoBue C, Stopschinski BE, Calveras NS, Salter A, Galasko D, Giza C, Cullum CM, Douglas PM, Hart J., J Alzheimers Dis. 2025 May;105(1):49-55. doi: 10.1177/13872877251325757. Epub 2025 Mar 21. PMID: 40116680
    • Direct Vagus Nerve Injection Protocol For Rats
      Regmi NL, Chen X, Bailey RM, Gray SJ., J Vis Exp. 2025 Mar 14;(217). doi: 10.3791/67820. PMID: 40163378
    • Plasma glialfibrillary acidic protein as a biomarker of acute focal brain injury after high intensity focused ultrasound thalamotomy.
      Saez-Calveras N, Asturias A, Yu J, Stopschinski B, Vaquer-Alicea J, O'Suilleabhain P, McKenzie L, Viera J, Diamond MI, Shah BR., Brain Commun. 2025 Mar 3;7(1):fcaf054. doi: 10.1093/braincomms/fcaf054. PMID: 40236997
    • Mapping Hsp104 interactions using cross-linking mass spectrometry
      Westphal K, Michalska K, Joachimiak A, Joachimiak LA., FEBS Open Bio. 2025
      Jun;15(6):922-939. doi: 10.1002/2211-5463.70007. Epub 2025 Feb 24. PMID: 39992796
    • Biomarkers in Subclinical Transthyretin Cardiac Amyloidosis
      Gulati JS, Pedretti R, Hendren N, Kozlitina J, Saelices L, Roth LR, Grodin JL. Curr Heart Fail Rep. 2025 Feb 13;22(1):8. doi: 10.1007/s11897-025-00696-y. PMID: 39945945
    • Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context
      Bali S, Singh R, Wydorski PM, Van Nuland NE, Wosztyl A, Perez VA, Chen D, Chen J, Rizo J, Joachimiak LA., bioRxiv [Preprint]. 2025 Feb 13:2023.12.13.571598. doi: 10.1101/2023.12.13.571598. PMID: 38168322
    • TDP-43 Aggregate Seeding Impairs Autoregulation and Causes TDP-43 Dysfunction
      Mamede LD, Hu M, Titus AR, Vaquer-Alicea J, French RL, Diamond MI, Miller TM,
      Ayala YM., bioRxiv [Preprint]. 2025 Feb 12:2025.02.11.637743. doi: 10.1101/2025.02.11.637743. PMID: 39990366
    • Preclinical use of a clinically-relevant scAAV9/SUMF1 vector for the treatment of multiple sulfatase deficiency
      Presa M, Bailey RM, Ray S, Bailey L, Tata S, Murphy T, Piec PA, Combs H, Gray SJ, Lutz C., Commun Med (Lond). 2025 Jan 27;5(1):29. doi: 10.1038/s43856-025-00734-9. PMID: 39870870
    • Functional classification of tauopathy strains reveals the role of protofilament core residues
      Vaquer-Alicea J, Manon VA, Bommareddy V, Kunach P, Gupta A, Monistrol J,
      Perez VA, Tran HT, Saez-Calveras N, Du S, Batra S, Stoddard D, White CL 3rd,
      Joachimiak LA, Shahmoradian SH, Diamond MI., Sci Adv. 2025 Jan 24;11(4): eadp5978. doi: 10.1126/sciadv.adp5978. Epub 2025 Jan 22. PMID: 39841851
    • Essential tremor with tau pathology features seeds indistinguishable in conformation from Alzheimer's disease and primary age-related tauopathy
      Saez-Calveras N, Vaquer-Alicea J, White CL 3rd, Tak Y, Cosentino S, Faust PL, Louis ED, Diamond MI., Acta Neuropathol. 2025 Jan 8;149(1):6. doi: 10.1007/s00401-024-02843-6. PMID: 39775287
    • VCP regulates early tau seed amplification via specific cofactors
      Batra S, Vaquer-Alicea J, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM,
      Kolay S, Lemoff A, Cairns NJ, White CL 3rd, Diamond MI., Mol Neurodegener. 2025 Jan 7;20(1):2. doi: 10.1186/s13024-024-00783-z. PMID: 39773263; PMCID: PMC11707990.
  • 2024
    • ATTRv-V30M Type A amyloid fibrils from the heart and nerves exhibit structural homogeneity
      Nguyen, B.A., Afrin, S., Yakubovska, A., Singh, V., Vaquer-Alicea, J., Kunach, P., Singh, P., Pekala, M., Ahmed, Y., Fernandez-Ramirez, M.D.C. and Cabrera Hernandez, L. & Saelices, L. , bioRxiv:the preprint server for biology, 2024.05. 14.594028. https://doi.org/10.1101/2024.05.14.594028 bioRxiv
    • Intrathecal gene therapy for giant axonal neuropathy
      Bharucha-Goebel D, Saade D, Todd JJ, Norato G, Jain M, Lehky T, Rybin D, Bailey RM, Zein W, Averion G, Chichester J, Calcedo del Hoyo R, Hu Y, Foley AR, Waite M, Huryn L, Hooper J, Crawford T, Mohassel P, Sumner C, Kang E, Donkervoort S, Hoke A, Armao D, Gray SJ, Bonnemann CG. New England Journal of Medicine. 390:1092-1104
    • Valine and Inflammation Drive Epilepsy in a Mouse Model of ECHS1 Deficiency
      Eller MM, Zuberi AR, Fu X, Burgess SC, Lutz CM, Bailey RM. doi: 10.1101/2024.06.13.598697 bioRxiv
    • Radiologic-pathologic correlation of the spinal MRI findings in Giant Axonal Neuropathy
      Armao D, Bouldin TW, Gray SJ, Bailey RM, Bharucha-Goebel DX, Bönnemann CG, JK Smith.
    • Sleep abnormalities in SLC13A5 citrate transporter disorder
      Adams R, Ozlu C, Bailey LE, Solidum RM, Cooper S, Best CR, Elacio J, Kavanaugh BC, Brown T, Nye K, Liu J, Porter BE, Goodspeed K, Bailey RM.
    • Developmental Phenotype and Quality of Life in SLC13A5 Citrate Transporter Disorder
      Ozlu C, Adams R, Solidum RM, Cooper S, Best CR, Elacio J, Kavanaugh BC, Brown T, Nye K, Liu J, Bailey RM, Goodspeed K, Porter BE.
    • Age affects the brain transduction of intrathecal-delivered rAAV9 in mice
      Garza IT, Holmes S, Eller M, Schackmuth M, Bailey RM.
    • Preclinical use of a new scAAV9/SUMF1 vector for the treatment of multiple sulfatase deficiency
      Presa M*, Bailey RM*, Ray S, Bailey L, Tata S, Murphy T, Combs H, Gray SJ, Lutz C.
    • An end-to-end approach for single-cell infrared absorption spectroscopy of bacterial inclusion bodies: from AFM-IR measurement to data interpretation of large sample sets
      Duverger W, Tsaka G, Khodaparast L, Khodaparast L, Louros N, Rousseau F, et al. 2024;22(1):406. Journal of Nanobiotechnology
    • CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences
      Louros N, Rousseau F, Schymkowitz J. 2024;40(5):btae279. Bioinformatics.
    • Pharmacological modulation of septins restores calcium homeostasis and is neuroprotective in models of Alzheimer's disease
      Princen K, Van Dooren T, van Gorsel M, Louros N, Yang X, Dumbacher M, et al. 2024;384(6699):eadd6260. Science.
    • Modeling late-onset Alzheimer's disease neuropathology via direct neuronal reprogramming
      Sun Z, Kwon JS, Ren Y, Chen S, Walker CK, Lu X, Cates K, Karahan H, Sviben S, Fitzpatrick JAJ, Valdez C, Houlden H, Karch CM, Bateman RJ, Sato C, Mennerick SJ, Diamond MI, Kim J, Tanzi RE, Holtzman DM, Yoo AS. 10.1126/science.adl2992. Science
    • VCP regulates early tau seed amplification via specific cofactors
      Batra S, Vaquer-Alicea JI, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. 10.21203/rs.3.rs-4307848/v1 Res Sq
    • DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity
      Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska MI, Wydorski PM, Macierzyńska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak LA. 10.1016/j.str.2024.02.015. Structure
    • Docking for Molecules That Bind in a Symmetric Stack with SymDOCK
      Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. 10.1021/acs.jcim.3c01749. J Chem Inf Model
    • Hairpin trimer transition state of amyloid fibril
      Sari L, Bali S, Joachimiak LA, Lin MM. 10.1038/s41467-024-46446-x. Nat Commun
    • Multivalent coiled-coil interactions enable full-scale centrosome assembly and strength
      Rios MU, Bagnucka MA, Ryder BD, Ferreira Gomes B, Familiari NE, Yaguchi K, Amato M, Stachera WE, Joachimiak ŁA, Woodruff JB. 10.1083/jcb.202306142. J Cell Biol
    • J-domain proteins: From molecular mechanisms to diseases
      Marszalek J, De Los Rios P, Cyr D, Mayer MP, Adupa V, Andréasson C, Blatch GL, Braun JEA, Brodsky JL, Bukau B, Chapple JP, Conz C, Dementin S, Genevaux P, Genest O, Goloubinoff P, Gestwicki J, Hammond CM, Hines JK, Ishikawa K, Joachimiak LA, Kirstein J, Liberek K, Mokranjac D, Nillegoda N, Ramos CHI, Rebeaud M, Ron D, Rospert S, Sahi C, Shalgi R, Tomiczek B, Ushioda R, Ustyantseva E, Ye Y, Zylicz M, Kampinga HH. 10.1016/j.cstres.2023.12.002. Cell Stress Chaperones
    • Ensemble-based design of tau to inhibit aggregation while preserving biological activity
      Bali S, Singh R, Wydorski PM, Wosztyl A, Perez VA, Chen D, Rizo J, Joachimiak LA. 10.21203/rs.3.rs-3796916/v1. Res Sq
    • TorsinA is essential for neuronal nuclear pore complex localization and maturation
      Kim S, Phan S, Tran HT, Shaw TR, Shahmoradian SH, Ellisman MH, Veatch SL, Barmada SJ, Pappas SS, Dauer WT. 10.1038/s41556-024-01480-1. Nat Cell Biol
    • Detection of ATTR aggregates in the plasma of polyneuropathic patients with ATTR-V30M amyloidosis
      Pedretti R, Wang L, Grodin JL, Masri A, Kelly J, Saelices L. 10.1080/13506129.2024.2404073
    • Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis
      Nguyen BA, Singh V, Afrin S, Singh P, Pekala M, Ahmed Y, Pedretti R, Canepa J, Lemoff A, Kluve-Beckerman B, Wydorski PM, Chhapra F, Saelices L. 10.1038/s42003-024-06588-6
    • Multi-organ structural homogeneity of amyloid fibrils in ATTRv-T60A amyloidosis patients, revealed by Cryo-EM
      Fernandez-Ramirez MDC, Nguyen BA, Singh V, Afrin S, Evers B, Basset P, Wang L, Pękała M, Ahmed Y, Singh P, Canepa J, Wosztyl A, Li Y, Saelices L. 10.1101/2024.05.14.594218
    • Amyloid fibril polymorphism in the heart of an ATTR amyloidosis patient with polyneuropathy attributed to the V122Δ variant
      Ahmed Y, Nguyen BA, Afrin S, Singh V, Evers B, Singh P, Pedretti R, Wang L, Bassett P, Del Carmen Fernandez-Ramirez M, Pekala M, Kluve-Beckerman B, Saelices L.
    • Circulating transthyretin and retinol binding protein 4 levels among middle-age V122I TTR carriers in the general population
      Hendren NS, De Lemos JA, Berry JD, Kozlitina J, Saelices L, Ji AX, Shao Z, Liu CF, Garg S, Farr MA, Drazner MH, Tang WHW, Grodin JL.
    • O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology
      Balana AT, Mahul-Mellier AL, Nguyen BA, Horvath M, Javed A, Hard ER, Jasiqi Y, Singh P, Afrin S, Pedretti R, Singh V, Lee VM, Luk KC, Saelices L, Lashuel HA, Pratt MR.
    • Author Correction: O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology
      Balana AT, Mahul-Mellier AL, Nguyen BA, Horvath M, Javed A, Hard ER, Jasiqi Y, Singh P, Afrin S, Pedretti R, Singh V, Lee VM, Luk KC, Saelices L, Lashuel HA, Pratt MR.
    • Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy
      Nguyen BA, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y, Pedretti R, Fernandez-Ramirez MDC, Singh P, Pękała M, Cabrera Hernandez LO, Kumar S, Lemoff A, Gonzalez-Prieto R, Sawaya MR, Eisenberg DS, Benson MD, Saelices L.
    • Condensate interfaces can accelerate protein aggregation
      Choi CH, Lee DSW, Sanders DW, Brangwynne CP.
  • 2023
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