Zhiquan Liu

All Publications

• Precise Correction of the Pde6b-L659P Mutation Causing Retinal Degeneration with Minimum Bystander Editing by Advanced Genome Editing Tools. Research (Washington, D.C.) Liu, Z., Chen, S., Sun, Y. 2025; 8: 0770

  Abstract

  Recently developed base editing (BE), prime editing (PE), and click editing (CE) technologies enable precise and efficient genome editing with minimal risk of double-strand breaks and associated toxicity. However, their effectiveness in correcting real disease-causing mutations has not been systematically compared. Here, we aim to evaluate the potential of BE, PE, and CE technologies in rescuing the retinal degeneration-causing Pde6b (c.1976T>C, p.L659P) mutation. This site is prone to bystander effects, making it an ideal model for comparing the editing outcomes of these 3 novel technologies, particularly their editing precision. We optimized BE, PE, and CE systems in vitro using Pde6b-L659P cell models and compared their editing via deep sequencing. BE and PE had similar efficiency, but PE was the most precise, minimizing bystander edits. CE had lower efficiency and higher indel rates, needing further optimization. Using the optimal PE system for in vivo electroporation in Pde6b-L659P mice, we achieved 12.4% targeted repair with high precision, partially rescuing retinal degeneration. This study demonstrates proof of concept for the precise correction of the Pde6b-L659P mutation causing retinal degeneration using BE, PE, and CE tools. The findings offer valuable insights into the future optimization of precision gene editing techniques and their potential translational applications.

  View details for DOI 10.34133/research.0770

  View details for PubMedID 40607323

  View details for PubMedCentralID PMC12220932

• Efficient Rescue of Retinal Degeneration in Pde6a Mice by Engineered Base Editing and Prime Editing. Advanced science (Weinheim, Baden-Wurttemberg, Germany) Liu, Z., Chen, S., Davis, A. E., Lo, C. H., Wang, Q., Li, T., Ning, K., Zhang, Q., Zhao, J., Wang, S., Sun, Y. 2024: e2405628

  Abstract

  Retinitis pigmentosa (RP) is a complex spectrum of inherited retinal diseases marked by the gradual loss of photoreceptor cells, ultimately leading to blindness. Among these, mutations in PDE6A, responsible for encoding a cGMP-specific phosphodiesterase, stand out as pivotal in autosomal recessive RP (RP43). Unfortunately, no effective therapy currently exists for this specific form of RP. However, recent advancements in genome editing, such as base editing (BE) and prime editing (PE), offer a promising avenue for precise and efficient gene therapy. Here, it is illustrated that the engineered BE and PE systems, particularly PE, exhibit high efficiency in rescuing a target point mutation with minimal bystander effects in an RP mouse model carrying the Pde6a (c.2009A > G, p.D670G) mutation. The optimized BE and PE systems are first screened in N2a cells and subsequently assessed in electroporated mouse retinas. Notably, the optimal PE system, delivered via dual adeno-associated virus (AAV), precisely corrects the pathogenic mutation with average 9.4% efficiency, with no detectable bystander editing. This correction restores PDE6A protein expression, preserved photoreceptors, and rescued retinal function in Pde6a mice. Therefore, this study offers a proof-of-concept demonstration for the treatment of Pde6a-related retinal degeneration using BE and PE systems.

  View details for DOI 10.1002/advs.202405628

  View details for PubMedID 39297417

• Matrine Reduces Intraocular Pressure in Corticosteroid-Induced Ocular Hypertensive Mouse Eyes. Investigative ophthalmology & visual science Zhang, Q., Liu, Z., Chen, S., Wang, Q., Lo, C. H., Ning, K., Zhao, J., Shen, Y., Liton, P. B., Sun, Y. 2025; 66 (11): 18

  Abstract

  This study investigates the potential of matrine, a quinolizidine alkaloid, in regulating intraocular pressure (IOP) in normal and corticosteroid-induced ocular hypertension (OHT) mice.Wild-type C57BL/6 mice were randomly divided into normal and OHT groups. The OHT mouse model was established by periocular conjunctival fornix injections of dexamethasone-21-acetate (DEX). IOP was measured at 0.0, 0.5, 1.0, 3.0, and 6.0 hours after matrine treatment in both groups. Aqueous humor (AH) outflow facility was measured using our previously described/validated perfusion system. Anterior segment-optical coherence tomography was used to evaluate morphological changes in the anterior chamber following matrine treatment. Hematoxylin and eosin staining and immunofluorescence staining were used to investigate structural changes.Matrine treatment (50-200 µg/g) decreased the IOP in normal mice in a dose-dependent manner. AH outflow facility in normal mice elevated at 0.5 hours after matrine treatment (100 and 200 µg/g). Additionally, 100 µg/g matrine treatment increased the angle opening distance in the anterior chamber. In DEX-induced OHT mice, matrine (100 and 200 µg/g) reduced the elevated IOP and increased the AH outflow facility. Furthermore, 100 µg/g matrine treatment increased the angle opening distance compared with that of PBS-treated controls. However, matrine (100 µg/g) did not induce significant changes in trabecular meshwork gross morphology or the expression of cell contractility and extracellular matrix markers in OHT mice at 0.5 hours after treatment.Matrine decreased the IOP in the DEX-induced OHT mouse model, highlighting its potential as a therapeutic agent for managing glaucoma, particularly in corticosteroid-associated secondary cases.

  View details for DOI 10.1167/iovs.66.11.18

  View details for PubMedID 40772663

• Pathophysiology of intraoperative floppy iris syndrome: An unsettled debate. Survey of ophthalmology Shen, Y., Frauches, R., Zhao, J., Lo, C. H., Ning, K., Chen, S., Liu, Z., Zhang, F., Sun, Y. 2025

  Abstract

  Intraoperative floppy iris syndrome (IFIS)--characterized by iris blowing, prolapse, and progressive miosis during phacoemulsification surgery--poses significant challenges for eye surgeons. Despite being described almost 2 decades ago, its pathophysiology remains unclear. Initially, IFIS was thought to be a result of sympathetic signal blockage in the iris dilator muscle, since α-blockers such as tamsulosin were found to be a strong predisposing factor; however, many IFIS cases occur even in patients who discontinued α-blockers prior to cataract surgery. Several potential mechanisms through which α-blockers induces chronic changes in the iris - iris dilator atrophy, drug-melanin interaction, and loss of vascular tone - have been proposed as possible mechanisms. We address the prevailing theories on α-receptor-dependent mechanisms for IFIS and the current prophylactic measures undertaken to prevent IFIS-associated intraocular complications.

  View details for DOI 10.1016/j.survophthal.2025.06.002

  View details for PubMedID 40472999

• Gene therapy for ocular hypertension using hfCas13d-mediated mRNA targeting. PNAS nexus Chen, S., Liu, Z., Lo, C. H., Wang, Q., Ning, K., Zhang, Q., Zhao, J., Shen, Y., Sun, Y. 2025; 4 (6): pgaf168

  Abstract

  Glaucoma is a major global cause of irreversible vision loss. It is marked by elevated intraocular pressure (IOP) and the loss of retinal ganglion cells (RGC). While there are medical and surgical therapies for glaucoma aiming to reduce aqueous humor production or enhance its drainage, these treatments are often inadequate for effectively managing the disease. In this study, we developed a targeted therapy for glaucoma by knocking down two genes associated with aqueous humor production (aquaporin 1 [AQP1] and carbonic anhydrase type 2 [CA2]) using Cas13 RNA editing systems. We demonstrate that hfCas13d-mediated knockdown of AQP1 and CA2 significantly lowers IOP in wild-type mice and in a corticosteroid-induced glaucoma mouse model. We show that the lowered IOP results from decreasing aqueous production without affecting the outflow facility; this treatment also significantly promotes RGC survival as compared with untreated control groups. Therefore, CRISPR-Cas-based gene editing may be an effective treatment to lower IOP for glaucomatous optic neuropathy.

  View details for DOI 10.1093/pnasnexus/pgaf168

  View details for PubMedID 40575705

  View details for PubMedCentralID PMC12199245

• Precise Correction of the <i>Pde6b</i>-L659P Mutation Causing Retinal Degeneration via Base and Prime Editing Liu, Z., Chen, S., Zhao, J., Sun, Y. CELL PRESS. 2025

  View details for Web of Science ID 001521604300026

• Effect of Brimonidine on Retinal Ganglion Cell Function by in vivo Calcium Imaging of Optic Nerve Crush in Mice. Experimental eye research Li, T., Kowal, T. J., Zhao, J., Li, L., Wang, Q., Ning, K., Lo, C. H., Liu, Z., Shen, Y., Yu, J., Jin, H., Sun, Y. 2025: 110355

  Abstract

  Brimonidine has shown neuroprotective effects in animal studies, but clinical trials failed to demonstrate effective endpoints. Here, we used a newly developed in vivo calcium imaging method to measure RGC function of brimonidine in mice optic nerve crush (ONC) models. To transduce RGCs in vivo, wild-type C57Bl/6j mice were treated with intravitreal AAV2-mSncg-jGCaMP7s, a live-cell Ca2+ tracer. RGCs are defined as 10 subtypes according to different responses to UV light. Mice were treated with topical brimonidine or placebo three times daily for two weeks after ONC. The calcium signals of live-cell RGCs were measured with the Heidelberg cSLO system. Ganglion cell complex (GCC) thickness and IOP were examined at different timepoints after treatment. RGCs were counted after RBPMS immunostaining. Live calcium imaging showed ONC significantly decreased RGC number at 14 days post-ONC compared to controls. The topical brimonidine administration changed calcium signal responses of RGC to UV light in ONC mice. It showed brimonidine partly prevented the decrease of survival ON-RGCs percent after ONC. Single RGC analysis showed a lower conversion percent of ON-RGCs to OFF-RGCs with brimonidine administration after ONC. However, no significant differences in RGC survival, IOP or GCC thickness were noted between eyes treated with brimonidine or placebo. In the acute ONC mice model, in vivo calcium imaging revealed that brimonidine maintained the Ca2+ activation of ON-RGCs to UV stimulation, inhibiting the conversion of survival ON-RGCs to OFF-RGCs. This indicates that ON-RGCs may be more resilient to acute optic nerve injury based on the calcium imaging method.

  View details for DOI 10.1016/j.exer.2025.110355

  View details for PubMedID 40127747

• dCasMINI-mediated therapy rescues photoreceptors degeneration in a mouse model of retinitis pigmentosa. Science advances Wang, Q., Xu, X., Chen, S., Lu, R., Li, L., Lo, C. H., Liu, Z., Ning, K., Li, T., Kowal, T. J., Wang, B., Hartnett, M. E., Wang, S., Qi, L. S., Sun, Y. 2024; 10 (51): eadn7540

  Abstract

  Retinitis pigmentosa (RP) is characterized by degeneration of rod and cone photoreceptors that progresses to irreversible blindness. Now, there are no mutation-agnostic approaches to treat RP. Here, we utilized a single adeno-associated virus (AAV)-based CRISPR activation system to activate phosphodiesterase 6B (Pde6b) to mitigate the severe degeneration in Pde6anmf363 mice. We demonstrate that transcriptional activation of Pde6b can rescue the loss of Pde6a, with preservation of retinal structure, restoration of electroretinography responses, and improvement of visual function as assessed by optokinetic response and looming-induced escape behaviors. These findings demonstrate the therapeutic potential of a dCasMINI-mediated activation strategy that provides a mutation-independent treatment for retinal degeneration. This study offers a promising therapeutic approach for RP and potentially other forms of genetic diseases.

  View details for DOI 10.1126/sciadv.adn7540

  View details for PubMedID 39693439

  View details for PubMedCentralID PMC11654696

• All-in-one AAV-mediated Nrl gene inactivation rescues retinal degeneration in Pde6a mice. JCI insight Liu, Z., Chen, S., Lo, C. H., Wang, Q., Sun, Y. 2024

  Abstract

  Retinitis pigmentosa (RP) is a complex group of inherited retinal diseases characterized by progressive death of photoreceptor cells and eventual blindness. Pde6a, which encodes a cGMP-specific phosphodiesterase, is a crucial pathogenic gene for autosomal recessive RP (RP43); there is no effective therapy for this form of RP. The compact CRISPR/SaCas9 system, which can be packaged into a single adeno-associated virus, holds promise for simplifying effective gene therapy. Here, we demonstrated that all-in-one AAV-SaCas9-mediated Nrl gene inactivation can efficiently prevent retinal degeneration in a RP mouse model with Pde6anmf363/nmf363 mutation. We screened single guide RNAs (sgRNAs) capable of efficiently editing mouse Nrl gene in N2a cells and then achieved effective gene editing by using a single AAV to co-deliver SaCas9 and an optimal Nrl-sg2 into the mouse retina. Excitingly, in vivo inactivation of Nrl improved photoreceptor cell survival and rescued retinal function in treated Pde6a deficient mice. Thus, we showed that a practical, gene-independent method, AAV-SaCas9-mediated Nrl inactivation, holds promise for future therapeutic applications in patients with RP.

  View details for DOI 10.1172/jci.insight.178159

  View details for PubMedID 39499900

• Defective Neurogenesis in Lowe Syndrome is Caused by Mitochondria Loss and Cilia-related Sonic Hedgehog Defects. bioRxiv : the preprint server for biology Lo, C. H., Chen, S., Zhao, J., Liu, Z., Wang, B., Wang, Q., Kowal, T. J., Sun, Y. 2024

  Abstract

  Human brain development is a complex process that requires intricate coordination of multiple cellular and developmental events. Dysfunction of lipid metabolism can lead to neurodevelopmental disorders. Lowe syndrome (LS) is a recessive X-linked disorder associated with proximal tubular renal disease, congenital cataracts and glaucoma, and central nervous system developmental delays. Mutations in OCRL, which encodes an inositol polyphosphate 5-phosphatase, lead to the development of LS. The cellular mechanism responsible for neuronal dysfunction in LS is unknown. Here we show depletion of mitochondrial DNA and decrease in mitochondrial activities result in neuronal differentiation defects. Increased astrocytes, which are secondary responders to neurodegeneration, are observed in neuronal (iN) cells differentiated from Lowe patient-derived iPSCs and an LS mouse model. Inactivation of cilia-related sonic hedgehog signaling, which organizes the pattern of cellular neuronal differentiation, is observed in an OCRL knockout, iN cells differentiated from Lowe patient-derived iPSCs, and an LS mouse model. Taken together, our findings indicate that mitochondrial dysfunction and impairment of the ciliary sonic hedgehog signaling pathway represent a novel pathogenic mechanism underlying the disrupted neuronal differentiation observed in LS.

  View details for DOI 10.1101/2024.11.01.621496

  View details for PubMedID 39553960

  View details for PubMedCentralID PMC11565974

• Primary cilia formation requires the Leigh syndrome-associated mitochondrial protein NDUFAF2. The Journal of clinical investigation Lo, C. H., Liu, Z., Chen, S., Lin, F., Berneshawi, A. R., Yu, C. Q., Koo, E. B., Kowal, T. J., Ning, K., Hu, Y., Wang, W. J., Liao, Y. J., Sun, Y. 2024; 134 (13)

  Abstract

  Mitochondria-related neurodegenerative diseases have been implicated in the disruption of primary cilia function. Mutation in an intrinsic mitochondrial complex I component NDUFAF2 has been identified in Leigh syndrome, a severe inherited mitochondriopathy. Mutations in ARMC9, which encodes a basal body protein, cause Joubert syndrome, a ciliopathy with defects in the brain, kidney, and eye. Here, we report a mechanistic link between mitochondria metabolism and primary cilia signaling. We discovered that loss of NDUFAF2 caused both mitochondrial and ciliary defects in vitro and in vivo and identified NDUFAF2 as a binding partner for ARMC9. We also found that NDUFAF2 was both necessary and sufficient for cilia formation and that exogenous expression of NDUFAF2 rescued the ciliary and mitochondrial defects observed in cells from patients with known ARMC9 deficiency. NAD+ supplementation restored mitochondrial and ciliary dysfunction in ARMC9-deficient cells and zebrafish and ameliorated the ocular motility and motor deficits of a patient with ARMC9 deficiency. The present results provide a compelling mechanistic link, supported by evidence from human studies, between primary cilia and mitochondrial signaling. Importantly, our findings have significant implications for the development of therapeutic approaches targeting ciliopathies.

  View details for DOI 10.1172/JCI175560

  View details for PubMedID 38949024

• Gene Therapy for Glaucoma using CRISPR/Cas13d in mice Chen, S., Liu, Z., Lo, C., Sun, Y. ASSOC RESEARCH VISION OPHTHALMOLOGY INC. 2024

  View details for Web of Science ID 001313316200302

• Employing plasmid-based CRISPR-hyperdCas12, CasRx, and prime editing systems for in vivo gene manipulation in the mouse retina Li, L., Hamed, L., Liu, Z., Deng, B., Sun, Y., Wang, S. ASSOC RESEARCH VISION OPHTHALMOLOGY INC. 2024

  View details for Web of Science ID 001313316207295

• Efficient prevention of retinal degeneration in <i>Pde6a</i> mice by all-inone AAV-mediated <i>Nrl</i> gene editing Liu, Z., Chen, S., Lo, C., Wang, Q., Sun, Y. ASSOC RESEARCH VISION OPHTHALMOLOGY INC. 2024

  View details for Web of Science ID 001312227704183

• Base editing correction of OCRL in Lowe syndrome: ABE-mediated functional rescue in patient-derived fibroblasts. Human molecular genetics Chen, S., Lo, C. H., Liu, Z., Wang, Q., Ning, K., Li, T., Sun, Y. 2024

  Abstract

  Lowe syndrome, a rare X-linked multisystem disorder presenting with major abnormalities in the eyes, kidneys, and central nervous system, is caused by mutations in OCRL gene (NG_008638.1). Encoding an inositol polyphosphate 5-phosphatase, OCRL catalyzes the hydrolysis of PI(4,5)P2 into PI4P. There are no effective targeted treatments for Lowe syndrome. Here, we demonstrate a novel gene therapy for Lowe syndrome in patient fibroblasts using an adenine base editor (ABE) that can efficiently correct pathogenic point mutations. We show that ABE8e-NG-based correction of a disease-causing mutation in a Lowe patient-derived fibroblast line containing R844X mutation in OCRL gene, restores OCRL expression at mRNA and protein levels. It also restores cellular abnormalities that are hallmarks of OCRL dysfunction, including defects in ciliogenesis, microtubule anchoring, α-actinin distribution, and F-actin network. The study indicates that ABE-mediated gene therapy is a feasible treatment for Lowe syndrome, laying the foundation for therapeutic application of ABE in the currently incurable disease.

  View details for DOI 10.1093/hmg/ddae045

  View details for PubMedID 38557732