Publications

Selected Publications

For a complete list of our publications, please refer to PubMed

2025   Oshima Y, Nagidi Y, Moorthy ME, Heier J, Matsubara JA, Hardin J, Flajnik M, Vogel BE. TEP-1, a glial thioester protein is required for cilia organization and intraflagellar transport in ensheathed sensory neurons in Caenorhabditis elegans. Mol Biol Cell. 2026 Mar 1;37(3):ar24. doi: 10.1091/mbc.E25-11-0547. Epub 2026 Jan 28. PMID: 41604455.

2025   Yoo HS, Chakravarthy H, Xi J, Cui J, Ai Z, Hosseini A, Song J, Tan N, Ma N, Zhou C, Li B, Bell R, Haegert A, Le Bihan S, Ju MJ, Granville DJ, Matsubara JA. Granzyme B contributes to subretinal fibrosis in neovascular age-related macular degeneration by modulating inflammation and epithelial-mesenchymal transition. J Neuroinflammation. 2025 Nov 27;23(1):1. doi: 10.1186/s12974-025-03619-9. PMID: 41310732; PMCID: PMC12764018.

2025   Oshima Y, Hussey KA, Hagen J, Smit-McBride Z, Moorthy M, Matsubara JA, Flajnik M, Johnston RJ Jr, Vogel BE. Complement Factor H and its C. elegans homolog regulate IFT52/OSM-6 and CNG channel localization in sensory neurons. bioRxiv [Preprint]. 2025 Oct 13:2025.10.10.681644. doi: 10.1101/2025.10.10.681644. PMID: 41278837; PMCID: PMC12632885.

2025   Oshima Y, Nagidi Y, Moorthy ME, Heier J, Matsubara JA, Hardin J, Flajnik M, Vogel BE. TEP-1, a glial thioester protein is required for cilia organization and intraflagellar transport in ensheathed sensory neurons. bioRxiv [Preprint]. 2025 Oct 24:2025.10.23.684198. doi: 10.1101/2025.10.23.684198. Update in: Mol Biol Cell. 2026 Mar 1;37(3):ar24. doi: 10.1091/mbc.E25-11-0547. PMID: 41278702; PMCID: PMC12633222.

2025    Rajagopalan S, Chen A, Song J, Matsubara J, Yeung SN, Lane PM, Makita S, Yasuno Y, Ju MJ. Enhanced visualization of ex-vivo ocular tissues using spatial-phase-resolved optical coherence microscopy. Opt Lett. 2025 Nov 15;50(22):6959-6962. doi: 10.1364/OL.569766. PMID: 41236954.

2025   Wijesinghe P, Hosseini A, Campbell M, Tejpal S, Haynes J, Xi J, Mackenzie IR, Hirsch-Reinshagen V, Hsiung GR, Spiller BW, Wadzinski BE, Pham W, Matsubara JA. Decoding amyloid beta clearance systems at inner blood-retina barrier using three-dimensional ex vivo retinal imaging in Alzheimer’s disease. Alzheimers Dement. 2025 Sep;21(9):e70592. doi: 10.1002/alz.70592. PMID: 41047467; PMCID: PMC12497512.

2025   Hosseini A, Yoo HS, Wagen C, Iovieno A, Matsubara JA, Yeung SN. Potential roles of extracellular granzyme B in corneal and conjunctival diseases: A narrative review. Exp Eye Res. 2025 Oct;259:110566. doi: 10.1016/j.exer.2025.110566. Epub 2025 Jul 31. PMID: 40752881.

2025   Glashutter M, Wijesinghe P, Matsubara JA. TDP-43 as a potential retinal biomarker for neurodegenerative diseases. Front Neurosci. 2025 Feb 12;19:1533045. doi: 10.3389/fnins.2025.1533045. PMID: 40012679; PMCID: PMC11861351.

2024  Wijesinghe P, Li HR, Ai Z, Campbell M, Chen SX, Xi J, Pham W, Matsubara JA. Apolipoprotein E dysfunction in Alzheimer’s disease: a study on miRNA regulation, glial markers, and amyloid pathology. Front Aging Neurosci. 2024 Dec 18;16:1495615. doi: 10.3389/fnagi.2024.1495615. PMID: 39744521; PMCID: PMC11688329.

2024  Chakravarthy H, Georgyev V, Wagen C, Hosseini A, Matsubara J. Blue light-induced phototoxicity in retinal cells: implications in age-related macular degeneration. Front Aging Neurosci. 2024 Dec 17;16:1509434. doi: 10.3389/fnagi.2024.1509434. PMID: 39741521; PMCID: PMC11685196.

2024  Nassrallah WB, Li HR, Irani L, Wijesinghe P, Hogg PW, Hui L, Oh J, Mackenzie IR, Hirsch-Reinshagen V, Hsiung GR, Pham W, Lee S, Matsubara JA. 3-Dimensional morphological characterization of neuroretinal microglia in Alzheimer’s disease via machine learning. Acta Neuropathol Commun. 2024 Dec 24;12(1):202. doi: 10.1186/s40478-024-01898-6. PMID: 39719599; PMCID: PMC11669245.

2024  Lee S, Matsubara JA. Editorial: Retinal biomarkers of neurodegenerative diseases. Front Ophthalmol (Lausanne). 2024 Oct 7;4:1479755. doi: 10.3389/fopht.2024.1479755. PMID: 39434764; PMCID: PMC11491430.

2024  Choi Y, Samad I, Chakravarthy H, Matsubara J, Granville DJ, Yeung SN. Granzyme B Expression in Conjunctiva of Patients with Pterygium. Int J Mol Sci. 2024 Aug 9;25(16):8679. doi: 10.3390/ijms25168679. PMID: 39201366; PMCID: PMC11354738.

2024  Richardson KC, Jung K, Matsubara JA, Choy JC, Granville DJ. Granzyme B in aging and age-related pathologies. Trends Mol Med. 2024 Dec;30(12):1165-1179. doi: 10.1016/j.molmed.2024.07.010. Epub 2024 Aug 23. PMID: 39181801.

2024  Gill K, Yoo HS, Chakravarthy H, Granville DJ, Matsubara JA. Exploring the role of granzyme B in subretinal fibrosis of age-related macular degeneration. Front Immunol. 2024 Jul 18;15:1421175. doi: 10.3389/fimmu.2024.1421175. PMID: 39091492; PMCID: PMC11291352.

2024  Song J, Hu Y, Chen A, Yoo HS, Zawadzki RJ, Matsubara JA, Ju MJ. In vivo multi-contrast depth-resolved choroidal imaging of a mouse using polarization-diversity optical coherence tomography. Opt Lett. 2024 Aug 1;49(15):4314-4317. doi: 10.1364/OL.529146. PMID: 39090922.

2024  Haynes JR, Whitmore CA, Behof WJ, Landman CA, Ong HH, Feld AP, Suero IC, Greer CB, Gore JC, Wijesinghe P, Matsubara JA, Wadzinski BE, Spiller BW, Pham W. Targeting soluble amyloid-beta oligomers with a novel nanobody. Sci Rep. 2024 Jul 12;14(1):16086. doi: 10.1038/s41598-024-66970-6. PMID: 38992064; PMCID: PMC11239946.

2024  Bandara NA, Burgos-Blasco B, Zhou XR, Khaira A, Iovieno A, Matsubara JA, Yeung SN. The Impact of Vaping on the Ocular Surface: A Systematic Review of the Literature. J Clin Med. 2024 Apr 29;13(9):2619. doi: 10.3390/jcm13092619. PMID: 38731149; PMCID: PMC11084645.

2024  Behof WJ, Haynes JR, Whitmore CA, Cheung YY, Tantawy MN, Peterson TE, Wijesinghe P, Matsubara JA, Pham W. Synthesis and Evaluation of a Novel PET Radioligand for Imaging Glutaminyl Cyclase Activity as a Biomarker for Detecting Alzheimer’s Disease. ACS Sens. 2024 May 24;9(5):2605-2613. doi: 10.1021/acssensors.4c00313. Epub 2024 May 8. PMID: 38718161; PMCID: PMC11129349.

2024  Obasanmi G, Uppal M, Cui JZ, Xi J, Ju MJ, Song J, To E, Li S, Khan W, Cheng D, Zhu J, Irani L, Samad I, Zhu J, Yoo HS, Aubert A, Stoddard J, Neuringer M, Granville DJ, Matsubara JA. Correction: Granzyme B degrades extracellular matrix and promotes inflammation and choroidal neovascularization. Angiogenesis. 2024 Aug;27(3):375-377. doi: 10.1007/s10456-024-09919-7. Erratum for: Angiogenesis. 2024 Aug;27(3):351-373. doi: 10.1007/s10456-024-09909-9. PMID: 38700585; PMCID: PMC11303458.

2024  Haynes JR, Whitmore CA, Behof WJ, Landman CA, Ong HH, Feld AP, Suero IC, Greer CB, Gore JC, Wijesinghe P, Matsubara JA, Wadzinski BE, Spiller BW, Pham W. TARGETING SOLUBLE AMYLOID-BETA OLIGOMERS WITH A NOVEL NANOBODY. Res Sq [Preprint]. 2024 Mar 15:rs.3.rs-3944211. doi: 10.21203/rs.3.rs-3944211/v1. Update in: Sci Rep. 2024 Jul 12;14(1):16086. doi: 10.1038/s41598-024-66970-6. PMID: 38559050; PMCID: PMC10980145.

2024  Obasanmi G, Uppal M, Cui JZ, Xi J, Ju MJ, Song J, To E, Li S, Khan W, Cheng D, Zhu J, Irani L, Samad I, Zhu J, Yoo HS, Aubert A, Stoddard J, Neuringer M, Granville DJ, Matsubara JA. Granzyme B degrades extracellular matrix and promotes inflammation and choroidal neovascularization. Angiogenesis. 2024 Aug;27(3):351-373. doi: 10.1007/s10456-024-09909-9. Epub 2024 Mar 18. Erratum in: Angiogenesis. 2024 Aug;27(3):375-377. doi: 10.1007/s10456-024-09919-7. PMID: 38498232; PMCID: PMC11303490.

2024   Ma D, Deng W, Khera Z, Sajitha TA, Wang X, Wollstein G, Schuman JS, Lee S, Shi H, Ju MJ, Matsubara J, Beg MF, Sarunic M, Sappington RM, Chan KC. Early inner plexiform layer thinning and retinal nerve fiber layer thickening in excitotoxic retinal injury using deep learning-assisted optical coherence tomography. Acta Neuropathol Commun. 2024 Feb 1;12(1):19. doi: 10.1186/s40478-024-01732-z. PubMed PMID: 38303097; PubMed Central PMCID: PMC10835918.

2023   Duan Y, Wu W, Cui J, Matsubara JA, Kazlauskas A, Ma G, Li X, Lei H. Ligand-independent activation of platelet-derived growth factor receptor β promotes vitreous-induced contraction of retinal pigment epithelial cells. BMC Ophthalmol. 2023 Aug 3;23(1):344. doi: 10.1186/s12886-023-03089-8. PubMed PMID: 37537538; PubMed Central PMCID: PMC10401781.

2023   Molcak H, Jiang K, Campbell CJ, Matsubara JA. Purinergic signaling via P2X receptors and mechanisms of unregulated ATP release in the outer retina and age-related macular degeneration. Front Neurosci. 2023;17:1216489. doi: 10.3389/fnins.2023.1216489. eCollection 2023. Review. PubMed PMID: 37496736; PubMed Central PMCID: PMC10366617.

2023   Wijesinghe P, Xi J, Cui J, Campbell M, Pham W, Matsubara JA. MicroRNAs in tear fluids predict underlying molecular changes associated with Alzheimer’s disease. Life Sci Alliance. 2023 Jun;6(6). doi: 10.26508/lsa.202201757. Print 2023 Jun. PubMed PMID: 36941055; PubMed Central PMCID: PMC10027899.

2023   Wijesinghe P, Whitmore CA, Campbell M, Li C, Tsuyuki M, To E, Haynes J, Pham W, Matsubara JA. Ergothioneine, a dietary antioxidant improves amyloid beta clearance in the neuroretina of a mouse model of Alzheimer’s disease. Front Neurosci. 2023;17:1107436. doi: 10.3389/fnins.2023.1107436. eCollection 2023. PubMed PMID: 36998724; PubMed Central PMCID: PMC10043244.

2023   Obasanmi G, Zeglinski MR, Hardie E, Wilhelm AC, Turner CT, Hiroyasu S, Boivin WA, Tian Y, Zhao H, To E, Cui JZ, Xi J, Yoo HS, Uppal M, Granville DJ, Matsubara JA. Granzyme B Contributes to Choroidal Neovascularization and Age-Related Macular Degeneration Through Proteolysis of Thrombospondin-1. Lab Invest. 2023 Feb 26;103(6):100123. doi: 10.1016/j.labinv.2023.100123. PubMed PMID: 36849037.

2023   Wu W, Ma G, Qi H, Dong L, Chen F, Wang Y, Mao X, Guo X, Cui J, Matsubara JA, Vanhaesebroeck B, Yan X, Zhao G, Zhang S, Lei H. Genome Editing of Pik3cd Impedes Abnormal Retinal Angiogenesis. Hum Gene Ther. 2023 Jan;34(1-2):30-41. doi: 10.1089/hum.2022.079. PubMed PMID: 36515172.

2022   Cardoen B, Wong T, Alan P, Lee S, Matsubara JA, Nabi IR, Hamarneh G. SPECHT: Self-tuning Plausibility based object detection Enables quantification of Conflict in Heterogeneous multi-scale microscopy. PLoS One. 2022;17(12):e0276726. doi: 10.1371/journal.pone.0276726. eCollection 2022. PubMed PMID: 36580473; PubMed Central PMCID: PMC9799313.

2022   Xu QA, Boerkoel P, Hirsch-Reinshagen V, Mackenzie IR, Hsiung GR, Charm G, To EF, Liu AQ, Schwab K, Jiang K, Sarunic M, Beg MF, Pham W, Cui J, To E, Lee S, Matsubara JA. Müller cell degeneration and microglial dysfunction in the Alzheimer’s retina. Acta Neuropathol Commun. 2022 Oct 5;10(1):145. doi: 10.1186/s40478-022-01448-y. PubMed PMID: 36199154; PubMed Central PMCID: PMC9533552.

2022   Behof WJ, Whitmore CA, Haynes JR, Rosenberg AJ, Tantawy MN, Peterson TE, Harrison FE, Beelman RB, Wijesinghe P, Matsubara JA, Pham W. Improved synthesis of an ergothioneine PET radioligand for imaging oxidative stress in Alzheimer’s disease. FEBS Lett. 2022 Jan 31;. doi: 10.1002/1873-3468.14303. [Epub ahead of print] PubMed PMID: 35100442.

2021   Zhao M, Li S, Matsubara JA. Targeting Pyroptotic Cell Death Pathways in Retinal Disease. Front Med (Lausanne). 2021;8:802063. doi: 10.3389/fmed.2021.802063. eCollection 2021. Review. PubMed PMID: 35047535; PubMed Central PMCID: PMC8763245.

2021   Acker N, Smith H, Devine C, Oltjen SL, Tsiropoulou S, Smit-McBride Z, Lange K, Blacque OE, Matsubara JA, Gordus A, Golden A, Vogel BE. A complement factor H homolog, heparan sulfation, and syndecan maintain inversin compartment boundaries in C. elegans cilia. Proc Natl Acad Sci U S A. 2021 Apr 20;118(16). doi: 10.1073/pnas.2016698118. PubMed PMID: 33859044; PubMed Central PMCID: PMC8072366.

2021   Barton SM, To E, Rogers BP, Whitmore C, Uppal M, Matsubara JA, Pham W. Inhalable Thioflavin S for the Detection of Amyloid Beta Deposits in the Retina. Molecules. 2021 Feb 5;26(4). doi: 10.3390/molecules26040835. PubMed PMID: 33562625; PubMed Central PMCID: PMC7915734.

2020   Ma D, Cardoso MJ, Zuluaga MA, Modat M, Powell NM, Wiseman FK, Cleary JO, Sinclair B, Harrison IF, Siow B, Popuri K, Lee S, Matsubara JA, Sarunic MV, Beg MF, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Substantially thinner internal granular layer and reduced molecular layer surface in the cerebellar cortex of the Tc1 mouse model of down syndrome – a comprehensive morphometric analysis with active staining contrast-enhanced MRI. Neuroimage. 2020 Dec;223:117271. doi: 10.1016/j.neuroimage.2020.117271. Epub 2020 Aug 22. PubMed PMID: 32835824.

2020   Raman KS, Matsubara JA. Dysregulation of the NLRP3 Inflammasome in Diabetic Retinopathy and Potential Therapeutic Targets. Ocul Immunol Inflamm. 2020 Oct 7;:1-9. doi: 10.1080/09273948.2020.1811350. [Epub ahead of print] PubMed PMID: 33026924.

2020   Lee S, Jiang K, McIlmoyle B, To E, Xu QA, Hirsch-Reinshagen V, Mackenzie IR, Hsiung GR, Eadie BD, Sarunic MV, Beg MF, Cui JZ, Matsubara JA. Amyloid Beta Immunoreactivity in the Retinal Ganglion Cell Layer of the Alzheimer’s Eye. Front Neurosci. 2020;14:758. doi: 10.3389/fnins.2020.00758. eCollection 2020. PubMed PMID: 32848548; PubMed Central PMCID: PMC7412634.

2020   Sidiqi A, Wahl D, Lee S, Ma D, To E, Cui J, To E, Beg MF, Sarunic M, Matsubara JA. In vivo Retinal Fluorescence Imaging With Curcumin in an Alzheimer Mouse Model. Front Neurosci. 2020;14:713. doi: 10.3389/fnins.2020.00713. eCollection 2020. PubMed PMID: 32719582; PubMed Central PMCID: PMC7350785.

2020   Matsubara JA, Tian Y, Cui JZ, Zeglinski MR, Hiroyasu S, Turner CT, Granville DJ. Retinal Distribution and Extracellular Activity of Granzyme B: A Serine Protease That Degrades Retinal Pigment Epithelial Tight Junctions and Extracellular Matrix Proteins. Front Immunol. 2020;11:574. doi: 10.3389/fimmu.2020.00574. eCollection 2020. PubMed PMID: 32318066; PubMed Central PMCID: PMC7155911.

2020   Wu W, Zhou G, Han H, Huang X, Jiang H, Mukai S, Kazlauskas A, Cui J, Matsubara JA, Vanhaesebroeck B, Xia X, Wang J, Lei H. PI3Kδ as a Novel Therapeutic Target in Pathological Angiogenesis. Diabetes. 2020 Apr;69(4):736-748. doi: 10.2337/db19-0713. Epub 2020 Jan 8. PubMed PMID: 31915155; PubMed Central PMCID: PMC7085248.

2020   Xin T, Han H, Wu W, Huang X, Cui J, Matsubara JA, Song J, Wang F, Colyer M, Lei H. Idelalisib inhibits vitreous-induced Akt activation and proliferation of retinal pigment epithelial cells from epiretinal membranes. Exp Eye Res. 2020 Jan;190:107884. doi: 10.1016/j.exer.2019.107884. Epub 2019 Nov 29. PubMed PMID: 31786159.

2019   Liu B, Song J, Han H, Hu Z, Chen N, Cui J, Matsubara JA, Zhong J, Lei H. Blockade of MDM2 with inactive Cas9 prevents epithelial to mesenchymal transition in retinal pigment epithelial cells. Lab Invest. 2019 Dec;99(12):1874-1886. doi: 10.1038/s41374-019-0307-9. Epub 2019 Aug 22. PubMed PMID: 31439892.

2019   Gao J, Cui JZ, Wang A, Chen HHR, Fong A, Matsubara JA.  The reduction of XIAP is associated with inflammasome activation in RPE: implications for AMD pathogenesis. J Neuroinflammation. 2019 Aug 22;16(1):171. doi: 10.1186/s12974-019-1558-5.

2019   Barton SM, Janve VA, McClure R, Anderson A, Matsubara JA, Gore JC, Pham W. Lipopolysaccharide Induced Opening of the Blood Brain Barrier on Aging 5XFAD Mouse Model. J Alzheimers Dis. 2019;67(2):503-513. doi: 10.3233/JAD-180755.

2018   Ukalovic K, Cao S, Lee S, Tang Q, Beg MF, Sarunic MV, Hsiung GR, Mackenzie IR, Hirsch-Reinshagen V, Cui JZ, Matsubara JA. Drusen in the Peripheral Retina of the Alzheimer’s Eye. Curr Alzheimer Res. 2018 Jan 23. doi: 10.2174/1567205015666180123122637.

2018   Gao J, Cui JZ, To E, Cao S, Matsubara JA. Evidence for the activation of pyroptotic and apoptotic pathways in RPE cells associated with NLRP3 inflammasome in the rodent eye. J Neuroinflammation. 2018 Jan 12;15(1):15.

2018   Xu Q, Cao S, Rajapakse S, Matsubara JA. Understanding AMD by analogy: systematic review of lipid-related common pathogenic mechanisms in AMD, AD, AS and GN. Lipids Health Dis. 2018 Jan 4;17(1):3.

Book Chapters

2011   JA Matsubara and JD Boyd. Overview of the Central Visual Pathways. Adler’s 11th edition of Physiology of the Eye.

2011   JD Boyd and JA Matsubara. Projections to and Processing in Extrastriate Visual Cortex. Adler’s 11 th edition of Physiology of the Eye.

2010   Dengler M, Saatchi K, Dailey JP, Matsubara J, Mikelberg FS, Hafeli UO, Yeung SN. Targeted Delivery of Magnetic Cobalt Nanoparticles to the Eye Following Systemic Administration. 8 th International Conference on the Scientific and Clinical Applications of Magnetic Carriers. Ed Hafeli, Schutt and Zhorowski