Publications

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In Preparation/Under Review

Gomez, A.E., Alvarado, K., Yase, R. A., Hsu, Y-H., Hulleman, J.D., and Kwon, R.Y. (2025) Dominant nonsense mutations in efemp1 alter vertebral and craniofacial characteristics in adult zebrafish. Published as a preprint

2025

Ortega, A.J., Daniel, S., Renwick, M.A., Kambhampati, P., Thompson, K.N., Collier, G.E., Baker, E.L., Zaki, H., and Hulleman, J.D. Ω (2025) Nlrp3 inflammasome deficiency protects against sporadic and R345W Efemp1-induced basal laminar deposit formation. Cell Death and Disease. (Ω - corresponding author). PMID 41198612
Hulleman, J.D. Ω, Jeon, S., Bali, S., DiCesare, S.M., Abbas, A., Daniel, S., Ortega, A.J., Collier, G.E., Yang, J., Bhattacharyaa, A., McCoy, M.K., Joachimiak, L.A., and Posner, B.A. (2025) Select azo compounds post-translationally modulate HTRA1 abundance and activity potentially through interactions at the trimer interface. ACS Chemical Biology (Ω - corresponding author). PMID 40735939
Collier, G.E., Roovers, A.L., and Hulleman, J.D. Ω (2025) A spectrum of population based cysteine mutations in fibulin-3 (EFEMP1) highlight its disulfide bonding complexity and potential to induce ER stress. Scientific Reports (Ω - corresponding author). PMID 40819107
Daniel, S., Ortega, A.J., and Hulleman, J.D. Ω RPE basal lamina biology and pathophysiology relevant to age- related macular degeneration. Advances in Experimental Medicine and Biology. 2025;1468:15-19 (Ω - corresponding author) PMID: 39930166
Youngblood, H.A., Harris, E.F., Lankford, K.P., Garfinkel, V., Hulleman, J.D. Ω, and Lieberman, R.L.Ω (2025) Monitoring mutant myocilin secretion and localization in trabecular meshwork cultures using a protein complementation-based luminescence assay. Experimental Eye Research. 11;255:110333 (Ω co-corresponding author). PMID: 40081751

2024

Miron-Mendoza M, Poole K, DiCesare S, Nakahara E, Bhatt MP, Hulleman JD, Petroll WM. The Role of Vimentin in Human Corneal Fibroblast Spreading and Myofibroblast Transformation. Cells. 2024 Jun 25;13(13):1094. PMID: 38994947
Daniel S, Hulleman JD. Exploring ocular fibulin-3 (EFEMP1): Anatomical, age-related, and species perspectives. Biochim Biophys Acta Mol Basis Dis. 2024 Aug;1870(6):167239. (Ω - corresponding author). PMID: 38750770
DiCesare SM, Ortega AJ, Collier GE, Daniel S, Thompson KN, McCoy MK, Posner BA, Hulleman JD. GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology. JCI Insight. 2024 Aug 8;9(15):e178050. (Ω - corresponding author). PMID: 39114980
Lankford, K.P., and Hulleman, J.D. Ω Protocol for HiBiT tagging endogenous proteins using CRISPR/Cas9 gene editing. STAR Protocols. 5(2):103000 ( Ω - corresponding author). PMID: 38598333
Zegeye, Y., Aredo, B., Yuksel, S., He, Y-G., Tang, M., Li, X., DiCesare, S.M., Hulleman, J.D., Gautron, L., Ludwig, S., Moresco, E.M., Beutler, B.A., Ufret-Vincenty, R.L. (2024) Deficiency of Herc3, an E3 ubiquitin ligase, leads to accumulation of subretinal microglia and retinal degeneration. Scientific Reports. 14(1):3010. PMID: 38321224

2023

Hayes, M.H., Woodard, D.R., and Hulleman, J.D. Ω. Ocular amyloid, condensates, and aggregates – higher-order protein assemblies participate in both retinal degeneration and function. Advances in Experimental Medicine and Biology. 1415: 263-267 PMID: 37440043
Yuksel, S., Aredo, B., Zegeye, Y., Zhao, C., Tang, M., Li, X., Hulleman, J.D., Gautron, L., Ludwig, S., Moresco, E.M., Butovich, I.A., Beutler, B.A., and Ufret-Vincenty, R.L. (2023). Forward genetic screening using fundus spot scale identifies an essential role for Lipe in retinal homeostasis. Communications Biology. 6(533) PMID: 37198396

2022

Burdon, K.P., Graham, P., Hadler, J., Hulleman, J.D., Prasutto, F., Boese, E.A., Craig, J.E., Fingert, J., Hewitt, A.W., J.D. Hulleman 4 Siggs, O.M., Whisenhunt, K., Young, T.L., Mackey, D.A., Dubowsky, A., and Souzeau, E. (2022). Specifications of the ACMG/AMP variant curation guidelines for MYOC: recommendations from the ClinGen Glaucoma Expert Panel. Human Mutation. 43(12):2170-2186. Selected as an Editor’s Choice article. PMID: 36217948
Nakahara, E., Mullapudi, V., Collier, G.E., Joachimiak, L.A., and Hulleman, J.D. Ω. A new DHFR-based destabilizing domain with enhanced turnover and broader flexibility. ACS Chemical Biology. 17(10):2877-2889 ( Ω - corresponding author). PMID: 36122928
Woodard, D.R., Daniel, S., Nakahara, E., Abbas, A., DiCesare, S.M., Collier, G.E., and Hulleman, J.D. Ω. A loss-of- function cysteine mutant in fibulin-3 (EFEMP1) forms aberrant extracellular disulfide-linked homodimers and alters extracellular matrix composition. Human Mutation. 43(12):1945-1955 ( Ω - corresponding author). Selected as an Editor’s Choice article. PMID: 35998264
Peng, H.*, Ramadurgum, P.*, Woodard, D.R.*, Daniel, S., Renwick, M., Nakahara, E., Datta, S., Chen, B., Aredo, B., Ufret-Vincenty, R.L. and Hulleman, J.D. Ω. Utility of the DHFR-based destabilizing domain across mouse models of retinal degeneration. iScience. 25(5):104206 (*- equal contribution, Ω - corresponding author). PMID: 35521529
Nakahara, E., and Hulleman, J.D. Ω. A simple secretion assay for assessing new and existing myocilin variants. Current Eye Research. Mar. 25; 1-5 ( Ω - corresponding author). PMID: 35196929

2021

Manna, M.S., Tamer, Y.T., Gaszek, I., Poulides, N., Ahmed, A., Wang, X., Toprak, F.C.R., Woodard, D.R., Koh, A.Y., Williams, N., Borek, D., Atilgan, A.R., Hulleman, J.D., Atilgan, C., Tambar, U.K., and Toprak, E. A trimethoprim derivative impedes antibiotic resistance evolution. Nature Communications. 12(1): 2949. Featured Article in Nat. Comm. PMID: 34011959
Woodard, D.R., Xing, C., Ganne, P., Liang, H., Mahindrakar, A., Sankurathri, C., Hulleman, J.D. # , and Mootha, V.V. # A novel homozygous P388S mutation in TULP1 causes protein instability and retinitis pigmentosa. Molecular Vision 27: 179-190 ( # - co-corresponding author) PMID: 33907372
Woodard, D.R., Nakahara, E., and Hulleman, J.D. Ω. Clinically-identified C-terminal mutations in fibulin-3 are prone to misfolding and destabilization. Scientific Reports. 11(1): 2998. ( Ω -corresponding author) PMID: 33542268

2020

Daniel, S., Renwick, M., Datta, S., Chau, V.Q., Zode, G.S., Wade, E.M., Robertson, S.P., Petroll, W.M., and Hulleman, J.D. Ω Fibulin-3 knockout mice demonstrate corneal dysfunction but maintain normal retinal integrity. Journal of Molecular Medicine, 98(11): 1639-1656 ( Ω -corresponding author) PMID: 32964303
Ramadurgum, P., Daniel, S., and Hulleman, J.D. Ω Protocol for in vivo evaluation and use of destabilizing domains in the eye, liver and beyond. Invited article. STAR Protocols, 1(2): 100094 ( Ω -corresponding author) PMID: 32995756
Rong, Z., Gong, X., Hulleman, J.D., Corey, D.R., and Mootha, V.V. (2020) Trinucleotide repeat-targeting dCas9 as a therapeutic strategy for Fuchs’ endothelial corneal dystrophy. Translation Vision Science and Technology, 9(9): 47 PMID: 32934897
Landeck, N., Strathearn, K.E., Ysselstein, D., Buck, K., Dutta, S., Banerjee, S., Lu, Z., Hulleman, J.D., Hindupur, J., Lin, L-K., Padalkar, S., McCabe, G.P., Stanciu, L.A., Lyubchenko, Y.L., Kirik, D., and Rochet, J-C. (2020) Two C-terminal sequence variations determine differential neurotoxicity between human and mouse α-synuclein. Molecular Neurodegeneration, 15(1): 49. PMID: 32900375
Ramadurgum, P., and Hulleman, J.D. Ω Protocol for designing small molecule-regulated destabilizing domains for in vitro use. Invited article. STAR Protocols, 1(2): 100069 ( Ω -corresponding author) PMID: 32995752
Zhou, M., Weber, S.R., Zhao, Y., Chen, H., Barber, A., Grillo, S.L., Wilis, C.A., Wang, H.G., Hulleman, J.D., and Sundstrom, J.M. (2020) Expression of R345W-Fibulin-3 induces epithelial-mesenchymal transition in retinal pigment epithelial cells. Frontiers in Cell and Developmental Biology, 8: 469 PMID: 32637411
Ramadurgum, P., Woodard, D.R., Daniel, S.N., Peng, H., Mallipeddi, P.L., Niederstrasser, H., Mihelakis, M., Chau, V.Q., Douglas, P.M., Posner, B.A., and Hulleman, J.D. Ω. Simultaneous control of endogenous and user-defined genetic pathways using new ecDHFR pharmacological chaperones. Cell Chemical Biology, 27(5): 622-634. ( Ω - corresponding author). PMID: 32330442
Chau, V.Q., Hu, J., Gong, X., Hulleman, J.D., Ufret-Vincenty, R.L., Rigo, F., Prakash, T.P., Corey, D., and Mootha, V.V. Delivery of antisense oligonucleotides to the corneal endothelium. Nucleic Acid Therapeutics, 30(4): 207-214. Featured Article in Nuc. Acid Ther. PMID: 32202944

2019

Datta, S., Peng, H., and Hulleman, J.D. Ω. Small molecule-based inducible gene therapies for retinal degeneration. Advances in Experimental Medicine and Biology, 1185: 65-69. ( Ω - corresponding author) PMID: 31884590
Peng, H.*, Chau, V.Q.*, Phetsang, W., Sebastian, R.L., Stone, M.R.L., Datta, S., Renwick, M., Tamer, Y.T., Toprak, E., Koh, A.Y., Blaskovich, M.A.T. and Hulleman, J.D. Ω. Non-antibiotic small-molecule regulation of DHFR-based destabilizing domains in vivo. Molecular Therapy – Methods and Clinical Development, 15: 27-39. (* - equal contribution, Ω - corresponding author) PMID: 31649953
Peng, H., and Hulleman, J.D. Ω. Prospective application of activity-based protein profiling in eye research – Insights into ocular protease biology and pathology. Invited review. International Journal of Molecular Science, 20(16): 3855. ( Ω - corresponding author) PMID: 31398819

2018

Datta, S., Renwick, M., Chau, V.Q., Zhang, F., Nettesheim, E., Lipinski, D.M., and Hulleman, J.D. Ω. A destabilizing domain allows for fast, non-invasive, conditional control of protein abundance in the mouse eye – Implications for ocular gene therapy*. 58(12): 4909-4920. Investigative Ophthalmology and Vision Science. ( Ω - corresponding author) *article chosen as a Featured Article, included in the Hot Topic 2017 Collection in IOVS and top 5 viewed paper of 2018 (Silverchair analytics). PMID: 30347085
Bamberger, C., Martínez­Bartolomé, S., Montgomery, M., Pankow, S. Hulleman, J.D., Kelly, J.W., and Yates, J.R. Deducing missing proteins and proteoforms in quantitative proteomics. Nature Communications, 9(1): 2320 PMID: 29899466
Wong, M.Y., Doan, N.D., DiChiara, Papa, L., A.S., Cheah, J.H., Soule, C.K., Watson, N., Hulleman, J.D., and Shoulders, M.D. A high-throughput assay for collagen secretion suggests an unanticipated role for Hsp90 in collagen production. Biochemistry, 57(19): 2814-2827. PMID: 29676157

2017

Vu, K.T., Zhang, F., and Hulleman, J.D. Ω Conditional, genetically-encoded, small molecule-regulated inhibition of NFB signaling in RPE cells*. Investigative Ophthalmology and Vision Science, 58(10): 4126-4137 ( Ω - corresponding author). *article chosen as a Featured Article, Most Viewed and an Editor’s Top Pick. PMID: 28829844
Vu, K.T., and Hulleman, J.D. Ω An inducible form of Nrf2 confers enhanced protection against acute oxidative stresses in RPE cells. Experimental Eye Research, 164: 31-36 ( Ω - corresponding author). PMID: 28782506

2016

Hulleman, J.D. *Ω , Genereux, J.C. * , and Nguyen, A. Mapping wild-type and R345W fibulin-3 intracellular interactomes. Experimental Eye Research, 153: 165-169 (* - equal contribution, Ω - corresponding author). PMID: 27777122
Zadoo, S., Nguyen, A., Zode, G., and Hulleman, J.D. Ω A novel luciferase assay for sensitively monitoring myocilin variants in cell culture. Investigative Ophthalmology and Vision Science 57(4): 1939-1950 ( Ω - corresponding author). PMID: 27092720
Nguyen, A. and Hulleman, J.D. Ω Evidence of alternative cystatin c signal sequence cleavage which is influenced by the A25T polymorphism. PLoS One. 11(2) ( Ω - corresponding author). PMID: 26845025
Hulleman, J.D., Nguyen, A., Ramprasad, V.L., Murugan, S., Gupta, R., Mahindrakar, A., Angara, R., Sankurathri, C., and Mootha, V.V. (2016) A novel H395R mutation in MKKS/BBS6 causes retinitis pigmentosa and polydactyly without other findings of Bardet-Biedl or McKusick-Kaufman syndrome. Molecular Vision, 22: 73-81. PMID: 26900326
Hulleman, J.D. Ω Malattia Leventinese/Doyne Honeycomb Retinal Dystrophy: Similarities to age-related macular degeneration and potential therapies. Advances in Experimental Medicine and Biology, 854: 153-158. ( Ω - corresponding author). PMID: 26427406

2015

Nguyen, A. and Hulleman, J.D. Ω Differential tolerance of ‘pseudo-pathogenic’ tryptophan residues in calcium- binding EGF domains of short fibulin proteins. Experimental Eye Research, 130: 66-72. ( Ω - corresponding author). PMID: 25481286
Hulleman, J.D. # and Kelly, J.W. # (2015) Genetic ablation of N-linked glycosylation reveals two important folding pathways for mutant fibulin-3, a protein associated with retinal degeneration. FASEB Journal, 29(2): 565-75 ( # - co- corresponding author). PMID: 25389134

2014

Chen, J.J., Genereux, J.G., Qu, S., Hulleman, J.D., Shoulders, M.D., and Wiseman, R.L. Increasing ER quality control stringency through ATF6 activation reduces the secretion and extracellular aggregation of destabilized variants of an amyloidogenic protein. Chemistry and Biology 21(11): 1–11. PMID: 25444553
Cooley, C.B., Ryno, L.M., Plate, L., Morgan, G.J., Hulleman, J.D., Kelly, J.W., and Wiseman, R.L. Unfolded protein response activation reduces secretion and extracellular aggregation of amyloidogenic immunoglobulin light chain. Proceedings of the National Academy of Science, U.S.A. 111(36): 13046-13051. PMID: 25157167
Wang, X., Cattaneo, F., Ryno, L.M., Hulleman, J.D., Reixach, N., and Buxbaum, J.N. (2014) The systemic amyloid precursor transthyretin (TTR) behaves as a neuronal stress protein regulated by HSF1 in SH-SY5Y human neuroblastoma cells and APP23 Alzheimer's disease model mice. Journal of Neuroscience, 34(21): 7253-65. PMID: 24849358

2013

Hulleman, J.D. # , Brown, S.J., Rosen, H., and Kelly, J.W. # A high-throughput cell-based Gaussia luciferase reporter assay for identifying modulators of fibulin-3 secretion. Journal of Biomolecular Screening, 18(6): 647-658 ( # - co- corresponding author). PMID: 23230284

2012

Hulleman, J.D. # , Balch, W.E., and Kelly, J.W. # Translational attenuation differentially alters the fate of disease- associated fibulin proteins. FASEB Journal, 26 (11): 4548-4560 ( # - co-corresponding author). PMID: 22872678
Madian, A.G., Hindupur, J., Hulleman, J.D., Diaz-Maldonado, N., Guigard, E., Kay, C.M., Rochet, J-C., and Regnier, F.E. Effect of single amino acid substitution on oxidative modifications of the Parkinson’s disease-related protein, DJ-1. Molecular & Cellular Proteomics, 11 (2): M111.010892. PMID: 22104028

2011

Hulleman, J.D.# , Kaushal, S., Balch, W.E., and Kelly, J.W. # Compromised mutant EFEMP1 secretion remedied by proteostasis network alteration. Molecular Biology of the Cell, 22 (24): 4765-4775 ( # - co-corresponding author). PMID: 22031286

2009

Usui, K.*, Hulleman, J.D.*, Paulsson, J.F., Siegel, S.S., Powers, E.T., and Kelly, J.W. Site-specific modification of Alzheimer's peptides by cholesterol oxidation products enhances aggregation energetics and neurotoxicity. Proceedings of the National Academy of Science, U.S.A., 106 (44): 18563-18568 (* - equal contribution). PMID: 19841277
Padalkar, S., Hulleman, J.D., Kim, S.M., Tumkur, T., Rochet, J-C., Stach, E., and Stanciu, L.A. Fabrication of ZnS nanoparticle chains on a protein template. Journal of Nanoparticle Research (doi: 10.1007/s11051-009-9689-8 ). PMID: 21804765
Rochet, J-C. and Hulleman, J.D. α-Synuclein self-assembly in Parkinson’s disease: insights from biophysical analyses. In T.F. Outeiro (Ed.), Protein Misfolding in Biology and Disease. Trivandrum, India: Research Signpost.

2008

Liu, F., Nguyen, J.L., Hulleman, J.D., Li, L., Rochet, J-C. Neuroprotective function of DJ-1 and MsrA in a cellular model of Parkinson’s disease. Journal of Neurochemistry, 105 (6): 2435-2453. PMID: 18331584
Padalkar, S., Hulleman, J.D., Rochet, J-C., Stach, E., Stanciu, L. Protein-templated semiconductor nanoparticle chains. Nanotechnology, 19 (27) (doi: 10.1088/0957-4484/19/27/275602 ). PMID: 21828709
Colby, R., Hulleman, J.D., Padalkar, S., Rochet, J-C., Stanciu, L. Biotemplated synthesis of metallic nanoparticle chains on an α-synuclein fiber scaffold. Journal of Nanoscience and Nanotechnology, 8 (2): 973–978. PMID: 18464436

2007

Zakharov, S., Hulleman, J.D., Dutseva, E., Antonenko, Y., Rochet, J-C., Cramer, W.A. (2007) Helical α-synuclein forms highly conductive ion channels. Biochemistry, 46 (50): 14369-14379. PMID: 18031063
Hulleman, J.D., Mirzaei, H., Guigard, E., Taylor, K.L., Ray, S.S., Kay, C.M., Regnier, F.E., Rochet, J-C. Destabilization of DJ-1 by a familial substitution and oxidative modifications: implications for Parkinson’s disease. Biochemistry, 46 (19): 5776-5789. PMID: 17451229
Padalkar, S., Hulleman, J.D., Colby, R., Cunzeman, K., Rochet, J-C., Stach, E., Stanciu, L. (2007) α-synuclein as a template for the synthesis of metallic nanowires. Nanotechnology, 18 (5) (doi: 10.1088/0957- 4484/18/5/055609 ).