About

Professor Karl Wahlin leads the Wahlin Lab at UC San Diego, focusing on stem cells and retinal regeneration. His research leverages advances in stem cell culturing and differentiation to explore human retinal development in vitro. The lab utilizes human pluripotent stem cells (PSCs) grown as three-dimensional "mini-retinas" or as dissociated two-dimensional monolayers to investigate retinal biology. By employing gene editing techniques such as CRISPR-Cas9, the lab engineers cells to express cell type-specific fluorescent protein reporters, enabling detailed study of retinal cells from the earliest neural retina stages through to final differentiation. The overarching goal of this research is to develop transplantable retinal tissue, create models for eye development, and establish "disease-in-a-dish" systems to study retinal degenerative diseases.

Research topics

• Biology
• Computer Science
• Neuroscience
• Artificial Intelligence
• Cell biology
• Pathology
• Immunology
• Virology
• Cognitive science
• Psychology
• Medicine
• Genetics

Selected publications

• Age-Driven Lipid Remodeling Activates Lysosome-Mediated Plasma Membrane Repair

  Research Square · 2026-01-20

  preprintOpen access
  PublisherOA PDFDOI

• Peptide display on small extracellular vesicles directs tissue-specific tropism and delivery of gene editing machinery

  Biomaterials · 2026-05-15

  articleOpen access

  Small extracellular vesicles (EVs) deliver nucleic acid and protein therapeutics that promote tissue repair, however, there are few approaches to direct the tropism of EVs to specific tissues. Here, we address this challenge by engineering EVs to display a peptide library on the surface of EVs that is linked to barcoded guide RNA payloads (gRNAs). We show how these EVs can be administered systemically into mouse models and the cellular uptake of these gRNA-bearing EVs assessed by recovery of the small RNAs followed by PCR amplification and barcode sequencing. Since the design of the peptide library was linked to specific barcodes encoded on the same plasmid, subsequent sequencing of barcode sequences recovered from tissues revealed profiles of EV uptake associated with the display of specific peptide sequences on the surface of EVs. Therefore, candidate peptide motifs were cloned for validation using in vivo and in vitro readouts. In addition to the barcode-based tissue profiling, gRNA-laded EVs mediated functional gene editing in the Cre-loxP R26 LSL-tdTomato reporter mouse model in vivo. These studies demonstrated how EV display linked with barcoded gRNA payloads can address barriers to EV-based delivery of gene editing therapies.

  PublisherDOI

• A Cross-Species Hydroquinone Model Replicates Smoking-Related Corneal Endothelial Oxidative Injury and Enables Therapeutic Screening of FGF10

  Investigative Ophthalmology & Visual Science · 2026-03-06

  articleOpen access

  Purpose: To establish an in vitro model of smoking-associated oxidative injury to the corneal endothelium and evaluate an injury-mitigating factor. Methods: Primary human and porcine corneal endothelial cells (CEnCs) were exposed to hydroquinone (HQ; 0-150 µM, 48 hours). Outcomes included viability (ATP-based assay), reactive oxygen species (ROS), and apoptosis (TUNEL). Bulk RNA sequencing (RNA-seq) profiled HQ (Nrf2 and Hippo-Yap pathways) and HQ ± fibroblast growth factor 10 (FGF10) responses under moderate stress (cadherin/Wnt programs). FGF10 dose-response (1-100 ng/mL) identified 30 ng/mL for subsequent HQ ± FGF10 studies. Western blotting provided protein validation. Results: HQ caused dose-dependent loss of viability with increased ROS and apoptosis (EC50: 191.2 µM human; 151.2 µM porcine). RNA-seq showed induction of Nrf2 antioxidant/detoxification genes with attenuation of Hippo-Yap signaling. At 150 µM HQ, total Yap decreased and the pYap/Yap ratio increased, consistent with Yap inactivation. FGF10 improved viability across doses (1-100 ng/mL; plateau 30-100 ng/mL) and required cotreatment during HQ exposure. Using 30 ng/mL, FGF10 improved viability across HQ doses, reduced ROS at 100 to 150 µM, and decreased apoptosis at 50 to 100 µM. At 50 µM HQ, FGF10 increased cadherin/Wnt-related transcripts, while N-cadherin protein decreased and β-catenin remained stable, consistent with junctional remodeling rather than full endothelial-mesenchymal transition. Key injury and rescue phenotypes were consistent across species. Conclusions: Our study supports HQ as a translatable in vitro model of smoking-related oxidative stress in CEnCs. FGF10 shows injury-mitigating and pro-regenerative effects, supporting further preclinical evaluation to preserve endothelial integrity and potentially lessen reliance on transplantation in corneal endothelial dystrophies.

  PublisherOA PDFDOI

• Morphological and Molecular Defects in Human Three-Dimensional Retinal Organoid Model of X-Linked Juvenile Retinoschisis.

  2025-01-17

  article

  Summary X-linked juvenile retinoschisis (XLRS), linked to mutations in the RS1 gene, is a degenerative retinopathy with a retinal splitting phenotype. We generated human induced pluripotent stem cells (hiPSCs) from patients to study XLRS in a 3D retinal organoid in vitro differentiation system. This model recapitulates key features of XLRS including retinal splitting, defective retinoschisin production, outer-segment defects, abnormal paxillin turnover, and impaired ER-Golgi transportation. RS1 mutation also affects the development of photoreceptor sensory cilia and results in altered expression of other retinopathy-associated genes. CRISPR/Cas9 correction of the disease-associated C625T mutation normalizes the splitting phenotype, outer-segment defects, paxillin dynamics, ciliary marker expression, and transcriptome profiles. Likewise, mutating RS1 in control hiPSCs produces the disease-associated phenotypes. Finally, we show that the C625T mutation can be repaired precisely and efficiently using a base-editing approach. Taken together, our data establish 3D organoids as a valid disease model.

• Altered Fhod3 expression involved in progressive high-frequency hearing loss via dysregulation of actin polymerization stoichiometry in the cuticular plate

  PLoS Genetics · 2024-03-18 · 2 citations

  articleOpen accessCorresponding

  Age-related hearing loss (ARHL) is a common sensory impairment with complex underlying mechanisms. In our previous study, we performed a meta-analysis of genome-wide association studies (GWAS) in mice and identified a novel locus on chromosome 18 associated with ARHL specifically linked to a 32 kHz tone burst stimulus. Consequently, we investigated the role of Formin Homology 2 Domain Containing 3 (Fhod3), a newly discovered candidate gene for ARHL based on the GWAS results. We observed Fhod3 expression in auditory hair cells (HCs) primarily localized at the cuticular plate (CP). To understand the functional implications of Fhod3 in the cochlea, we generated Fhod3 overexpression mice (Pax2-Cre+/-; Fhod3Tg/+) (TG) and HC-specific conditional knockout mice (Atoh1-Cre+/-; Fhod3fl/fl) (KO). Audiological assessments in TG mice demonstrated progressive high-frequency hearing loss, characterized by predominant loss of outer hair cells, and a decreased phalloidin intensities of CP. Ultrastructural analysis revealed loss of the shortest row of stereocilia in the basal turn of the cochlea, and alterations in the cuticular plate surrounding stereocilia rootlets. Importantly, the hearing and HC phenotype in TG mice phenocopied that of the KO mice. These findings suggest that balanced expression of Fhod3 is critical for proper CP and stereocilia structure and function. Further investigation of Fhod3 related hearing impairment mechanisms may lend new insight towards the myriad mechanisms underlying ARHL, which in turn could facilitate the development of therapeutic strategies for ARHL.

  PublisherOA PDFDOI

• Loss of GTF2I promotes neuronal apoptosis and synaptic reduction in human cellular models of neurodevelopment

  Cell Reports · 2024-02-27 · 8 citations

  articleOpen access

  Individuals with Williams syndrome (WS), a neurodevelopmental disorder caused by hemizygous loss of 26-28 genes at 7q11.23, characteristically portray a hypersocial phenotype. Copy-number variations and mutations in one of these genes, GTF2I, are associated with altered sociality and are proposed to underlie hypersociality in WS. However, the contribution of GTF2I to human neurodevelopment remains poorly understood. Here, human cellular models of neurodevelopment, including neural progenitors, neurons, and three-dimensional cortical organoids, are differentiated from CRISPR-Cas9-edited GTF2I-knockout (GTF2I-KO) pluripotent stem cells to investigate the role of GTF2I in human neurodevelopment. GTF2I-KO progenitors exhibit increased proliferation and cell-cycle alterations. Cortical organoids and neurons demonstrate increased cell death and synaptic dysregulation, including synaptic structural dysfunction and decreased electrophysiological activity on a multielectrode array. Our findings suggest that changes in synaptic circuit integrity may be a prominent mediator of the link between alterations in GTF2I and variation in the phenotypic expression of human sociality.

  PublisherOA PDFDOI

• Greater Outflow Facility Increase After Targeted Trabecular Bypass in Angiographically Determined Low-Flow Regions

  Ophthalmology Glaucoma · 2023-06-20 · 24 citations

  articleOpen access

  PURPOSE: To investigate the impact of trabecular bypass surgery targeted to angiographically determined high- vs. low-aqueous humor outflow areas on outflow facility (C) and intraocular pressure (IOP). DESIGN: Ex vivo comparative study. SUBJECTS: Postmortem ex vivo porcine and human eyes. METHODS: Porcine (n = 14) and human (n = 13) whole globes were acquired. In both species, anterior segments were dissected, mounted onto a perfusion chamber, and perfused using Dulbecco's phosphate buffered solution containing glucose in a constant flow paradigm to achieve a stable baseline. Fluorescein was perfused into the anterior chamber and used to identify baseline segmental high- and low-flow regions of the conventional outflow pathways. The anterior segments were divided into 2 groups, and a 5 mm needle goniotomy was performed in either a high- or low-flow area. Subsequently, C and IOP were quantitatively reassessed and compared between surgery in baseline "high-flow" and "low-flow" region eyes followed by indocyanine green angiography. MAIN OUTCOME MEASURES: Outflow facility. RESULTS: In all eyes, high- and low-flow segments could be identified. Performing a 5-mm goniotomy increased outflow facility to a variable extent depending on baseline flow status. In the porcine high-flow group, C increased from 0.31 ± 0.09 to 0.39 ± 0.09 μL/mmHg/min (P = 0.12). In the porcine low-flow group, C increased from 0.29 ± 0.03 to 0.56 ± 0.10 μL/mmHg/min (P < 0.001). In the human high-flow group, C increased from 0.38 ± 0.20 to 0.41 ± 0.20 μL/mmHg/min (P = 0.02). In the human low-flow group, C increased from 0.25 ± 0.11 to 0.32 ± 0.11 μL/mmHg/min (<0.001). There was statistically significant greater increase in C for eyes where surgery was targeted to baseline low-flow regions in both porcine (0.07 ± 0.09 vs. 0.27 ± 0.13, P = 0.007 μL/mmHg/min, high vs low flow) and human eyes (0.03 ± 0.03 vs. 0.07 ± 0.02, P = 0.03 μL/mmHg/min, high vs. low flow). CONCLUSIONS: Targeting surgery to low-flow areas of the trabecular meshwork yields higher overall facility increase and IOP reduction compared to surgery in high-flow areas. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

  PublisherDOI

• Mechanical Disruption of the Inner Limiting Membrane In Vivo Enhances Targeting to the Inner Retina

  Investigative Ophthalmology & Visual Science · 2023-12-20 · 11 citations

  articleOpen access

  Purpose: To evaluate the effects of mechanical disruption of the inner limiting membrane (ILM) on the ability to target interventions to the inner neurosensory retina in a rodent model. Our study used an animal model to gain insight into the normal physiology of the ILM and advances our understanding of the effects of mechanical ILM removal on the viral transduction of retinal ganglion cells and retinal ganglion cell transplantation. Methods: The ILM in the in vivo rat eye was disrupted using mechanical forces applied to the vitreoretinal interface. Immunohistology and electron microscopy were used to verify the removal of the ILM in retina flatmounts and sections. To assess the degree to which ILM disruption enhanced transvitreal access to the retina, in vivo studies involving intravitreal injections of adeno-associated virus (AAV) to transduce retinal ganglion cells (RGCs) and ex vivo studies involving co-culture of human stem cell-derived RGCs (hRGCs) on retinal explants were performed. RGC transduction efficiency and transplanted hRGC integration with retinal explants were evaluated by immunohistology of the retinas. Results: Mechanical disruption of the ILM in the rodent eye was sufficient to remove the ILM from targeted retinal areas while preserving the underlying retinal nerve fiber layer and RGCs. Removal of the ILM enhanced the transduction efficiency of intravitreally delivered AAV threefold (1380.0 ± 290.1 vs. 442.0 ± 249.3 cells/mm2; N = 6; P = 0.034). Removal of the ILM was also sufficient to promote integration of transplanted RGCs within the inner retina. Conclusions: The ILM is a barrier to transvitreally delivered agents including viral vectors and cells. Mechanical removal of the ILM is sufficient to enhance access to the inner retina, improve viral transduction efficiencies of RGCs, and enhance cellular integration of transplanted RGCs with the retina.

  PublisherOA PDFDOI

• Altered Fhod3 Expression Involved in Progressive High-Frequency Hearing Loss via Dysregulation of Actin Polymerization Stoichiometry in The Cuticular Plate

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-07-25 · 6 citations

  preprintOpen access

  Age-related hearing loss (ARHL) is a common sensory impairment with comlex underlying mechanisms. In our previous study, we performed a meta-analysis of genome-wide association studies (GWAS) in mice and identified a novel locus on chromosome 18 associated with ARHL specifically linked to a 32 kHz tone burst stimulus. Consequently, we investigated the role of Formin Homology 2 Domain Containing 3 (Fhod3), a newly discovered candidate gene for ARHL based on the GWAS results. We observed Fhod3 expression in auditory hair cells (HCs) and primarily localized at the cuticular plate (CP). To understand the functional implications of Fhod3 in the cochlea, we generated Fhod3 overexpression mice (Pax2-Cre+/-; Fhod3Tg/+) (TG) and HC-specific conditional knockout mice (Atoh1-Cre+/-; Fhod3fl/fl) (KO). Audiological assessments in TG mice demonstrated progressive high-frequency hearing loss, characterized by predominant loss of outer HCs and decrease phalloidin intensities of CP. Ultrastructural analysis revealed shortened stereocilia in the basal turn cochlea. Importantly, the hearing and HC phenotype in TG mice were replicated in KO mice. These findings indicate that Fhod3 plays a critical role in regulating actin dynamics in CP and stereocilia. Further investigation of Fhod3-related hearing impairment mechanisms may facilitate the development of therapeutic strategies for ARHL in humans.

  PublisherOA PDFDOI

• First Organoid Intelligence (OI) workshop to form an OI community

  Frontiers in Artificial Intelligence · 2023 · 52 citations

  • Computer Science
  • Artificial Intelligence
  • Computer Science

  The brain is arguably the most powerful computation system known. It is extremely efficient in processing large amounts of information and can discern signals from noise, adapt, and filter faulty information all while running on only 20 watts of power. The human brain's processing efficiency, progressive learning, and plasticity are unmatched by any computer system. Recent advances in stem cell technology have elevated the field of cell culture to higher levels of complexity, such as the development of three-dimensional (3D) brain organoids that recapitulate human brain functionality better than traditional monolayer cell systems. Organoid Intelligence (OI) aims to harness the innate biological capabilities of brain organoids for biocomputing and synthetic intelligence by interfacing them with computer technology. With the latest strides in stem cell technology, bioengineering, and machine learning, we can explore the ability of brain organoids to compute, and store given information (input), execute a task (output), and study how this affects the structural and functional connections in the organoids themselves. Furthermore, understanding how learning generates and changes patterns of connectivity in organoids can shed light on the early stages of cognition in the human brain. Investigating and understanding these concepts is an enormous, multidisciplinary endeavor that necessitates the engagement of both the scientific community and the public. Thus, on Feb 22-24 of 2022, the Johns Hopkins University held the first Organoid Intelligence Workshop to form an OI Community and to lay out the groundwork for the establishment of OI as a new scientific discipline. The potential of OI to revolutionize computing, neurological research, and drug development was discussed, along with a vision and roadmap for its development over the coming decade.

  PublisherOA PDFDOI

Recent grants

• Pluripotent Stem Cell Derived 3D Retinas for Studies of Early Onset Retinal Degeneration

  NIH · $2.4M · 2020–2026

• NIH Grant R00EY024648

  NIH · $778k · 2020

• NIH Grant K99EY024648

  NIH · $180k · 2016

Frequent coauthors

• Donald J. Zack

  Johns Hopkins University

  148 shared

• Jesper Lagergren

  Karolinska Institutet

  127 shared

• Cynthia Berlinicke

  Johns Hopkins University

  49 shared

• Srinivas R. Sripathi

  Retina Foundation of the Southwest

  41 shared

• Julien Maruotti

  37 shared

• Jiang Qian

  Johns Hopkins Medicine

  35 shared

• John Maret‐Ouda

  Karolinska Institutet

  34 shared

• Fredrik Mattsson

  Stockholm University

  34 shared

Education

• Ph.D., Neuroscience

  Johns Hopkins School of Medicine

  2009

Awards & honors

• Bright Focus Foundation (2018)
• Carolyn K. McGillvray Award for Macular Degeneration (2018)
• NIH Pathway to Independence Award (K99/R00) (2015 - 2019)