Dennis Clegg
· ProfessorVerifiedUniversity of California, Santa Barbara · Neuroscience
Active 1981–2025
About
Dennis O. Clegg is a Professor at the University of California, Santa Barbara, affiliated with the Center for Stem Cell Biology and Engineering, the Molecular, Cellular, and Developmental Biology (MCDB) department, and the Neuroscience program. His research focuses on stem cell biology and engineering, as indicated by his role as Co-Director of the Laboratory for Stem Cell Biology and Engineering. He is involved in advancing understanding and development in these fields through his leadership and research activities at UCSB.
Research topics
- Biology
- Genetics
- Medicine
- Surgery
- Ophthalmology
- Internal medicine
- Computational biology
- Evolutionary biology
- Cell biology
- Molecular biology
- Biochemistry
Selected publications
bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-22
preprintOpen accessABSTRACT Vitronectin is a prominent constituent of the extracelluar matrix (ECM) that plays a key role in inflammation by regulating cell adhesion, migration, and complement activation. Together with other inflammatory biomarkers, lipids, and hydroxyapatite, an ECM component, vitronectin, accumulates in abnormal deposits and drusen associated with age-related macular degeneration (AMD). Using an engineered polypeptide (VnHX) containing the hexmopexin-like domain (HX) of vitronectin, we found that the HX domain directly promotes hydroxyapatite (HAP) accumulation. Next, we screened humanized single-chain variable fragments (scFvs) against vitronectin that inhibit the interaction between VnHX and HAP, leveraging the binding of VnHX to HAP. We then tested these scFvs for their ability to block Vn-containg deposits secreted by stem cell-derived retinal pigment epithelium (RPE). In this in vitro drusen model, treatment with the anti-vitronectin antibodies decreased vitronectin accumulation. Furthermore, the antibody treatment led to decreased accumulation of C5b-9 and clusterin, indicating alterations in the complement pathway and cellular stress. These results support that vitronectin has a functional role drusen accumulation and possibly in AMD progression. Vitronectin would be a novel, promising therapeutic target for AMD.
Biomedicines · 2025-08-07
articleOpen accessObjective: Retinal capillary dropout, characterized by acellular capillaries or “ghost vessels,” is an early pathological sign of diabetic retinopathy (DR) that remains undetectable through standard clinical imaging techniques until visible morphological changes, such as microaneurysms or hemorrhages, occur. This study aims to develop a non-destructive artificial intelligence (AI)-based method using fluorescein angiography (FA) images to detect early-stage, silent retinal capillary dropout. Methods: We utilized 94 FA images and corresponding destructive retinal capillary density measurements obtained through retinal trypsin digestion from 51 Nile rats. Early capillary dropout was defined as having an acellular capillary density of ≥18 counts per mm2. A DenseNet based deep learning model was trained to classify images into early capillary dropout or normal. A Bayesian framework incorporating diabetes duration was used to enhance model predictions. RNA sequencing was conducted on retinal vasculature to identify molecular markers associated with capillary early dropout. Results: The AI-based FA imaging model demonstrated an accuracy of 80.85%, sensitivity of 84.21%, specificity of 75.68%, and an AUC of 0.86. Integration of diabetes duration into a Bayesian predictive framework further improved the model’s performance (AUC = 0.90). Transcriptomic analysis identified 43 genes significantly upregulated in retinal tissues preceding capillary dropout. Notably, inflammatory markers such as Bcl2a1, Birc5, and Il20rb were among these genes, indicating that inflammation might play a critical role in early DR pathogenesis. Conclusions: This study demonstrates that AI-enhanced FA imaging can predict silent retinal capillary dropout before conventional clinical signs of DR emerge. Combining AI predictions with diabetes duration data significantly improves diagnostic performance. The identified gene markers further highlight inflammation as a potential driver in early DR, offering novel insights and potential therapeutic targets for preventing DR progression.
2025-01-22
reportSenior authorVision impairments affect over 2.2 billion people worldwide. The most physiologically accurate human retina models are Retinal Organoids (ROs) — stem cell-derived structures containing the major cell types found in the human retina. However, the current protocol for deriving ROs from stem cells is h
Journal of Extracellular Biology · 2024-09-01 · 5 citations
articleOpen accessAbstract Retinal pigment epithelial (RPE) cells are exclusive to the retina, critically multifunctional in maintaining the visual functions and health of photoreceptors and the retina. Despite their vital functions throughout lifetime, RPE cells lack regenerative capacity, rendering them vulnerable which can lead to degenerative retinal diseases. With advancements in stem cell technology enabling the differentiation of functional cells from pluripotent stem cells and leveraging the robust autocrine and paracrine functions of RPE cells, extracellular vesicles (EVs) secreted by RPE cells hold significant therapeutic potential in supplementing RPE cell activity. While previous research has primarily focused on the trophic factors secreted by RPE cells, there is a lack of studies investigating miRNA, which serves as a master regulator of gene expression. Profiling and defining the functional role of miRNA contained within RPE‐secreted EVs is critical as it constitutes a necessary step in identifying the optimal phenotype of the EV‐secreting cell and understanding the biological cargo of EVs to develop EV‐based therapeutics. In this study, we present a comprehensive profile of miRNA in small extracellular vesicles (sEVs) secreted during RPE maturation following differentiation from human embryonic stem cells (hESCs); early ‐ stage hESC‐RPE (20–21 days in culture), mid ‐ stage hESC‐RPE (30–31 days in culture) and late ‐ stage hESC‐RPE (60–61 days in culture). This exploration is essential for ongoing efforts to develop and optimize EV‐based intraocular therapeutics utilizing RPE‐secreted EVs, which may significantly impact the function of dysfunctional RPE cells in retinal diseases.
bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-13 · 4 citations
preprintOpen accessABSTRACT Dysfunction of the retinal pigment epithelium (RPE) is a common shared pathology in major degenerative retinal diseases despite variations in the primary etiologies of each disease. Due to their demanding and indispensable functional roles throughout the lifetime, RPE cells are vulnerable to genetic predisposition, external stress, and aging processes. Building upon recent advancements in stem cell technology for differentiating healthy RPE cells and recognizing the significant roles of small extracellular vesicles (sEV) in cellular paracrine and autocrine actions, we investigated the hypothesis that the RPE-secreted sEV alone can restore essential RPE functions and rescue photoreceptors in RPE dysfunction-driven retinal degeneration. Our findings support the rationale for developing intravitreal treatment of sEV. We demonstrate that intravitreally delivered sEV effectively penetrate the full thickness of the retina. Xenogenic intraocular administration of human-derived EVs did not induce acute immune reactions in rodents. sEV derived from human embryonic stem cell (hESC)-derived fully differentiated RPE cells, but not sEV-depleted conditioned cell culture media (CCM minus sEV), rescued photoreceptors and their function in a Royal College of Surgeons (RCS) rat model. This model is characterized by photoreceptor death and retinal degeneration resulting from a mutation in the MerTK gene in RPE cells. From the bulk RNA sequencing study, we identified 447 differently expressed genes in the retina after hESC-RPE-sEV treatment compared with the untreated control. Furthermore, 394 out of 447 genes (88%) showed a reversal in expression toward the healthy state in Long-Evans (LE) rats after treatment compared to the diseased state. Particularly, detrimental alterations in gene expression in RCS rats, including essential RPE functions such as phototransduction, vitamin A metabolism, and lipid metabolism were partially reversed. Defective photoreceptor outer segment engulfment due to intrinsic MerTK mutation was partially ameliorated. These findings suggest that RPE-secreted sEV may play a functional role similar to that of RPE cells. Our study justifies further exploration to fully unlock future therapeutic interventions with sEV in a broad array of degenerative retinal diseases.
Investigative Ophthalmology & Visual Science · 2024-03-11 · 11 citations
articleOpen accessPurpose: Isolating extracellular vesicles (EVs) with high yield, replicable purity, and characterization remains a bottleneck in the development of EV therapeutics. To address these challenges, the current study aims to establish the necessary framework for preclinical and clinical studies in the development of stem cell-derived intraocular EV therapeutics. Methods: Small EVs (sEVs) were separated from the conditioned cell culture medium (CCM) of the human embryogenic stem cell-derived fully polarized retinal pigment epithelium (hESC-RPE-sEV) by a commercially available microfluidic tangential flow filtration (TFF) device ExoDisc (ED) or differential ultracentrifugation (dUC). The scaling and concentration capabilities and purity of recovered sEVs were assessed. Size, number, and surface markers of sEVs were determined by orthogonal approaches using multiple devices. Results: ED yielded higher numbers of sEVs, ranging from three to eight times higher depending on the measurement device, compared to dUC using the same 5 mL of CCM input. Within the same setting, the purity of ED-recovered hESC-RPE-sEVs was higher than that for dUC-recovered sEVs. ED yielded a higher concentration of particles, which is strongly correlated with the input volume, up to 10 mL (r = 0.98, P = 0.016). Meanwhile, comprehensive characterization profiles of EV surface markers between ED- and dUC-recovered hESC-RPE-sEVs were compatible. Conclusions: Our study supports TFF as a valuable strategy for separating sEVs for the development of intraocular EV therapeutics. However, there is a growing need for diverse devices to optimize TFF for use in EV preparation. Using orthogonal approaches in EV characterization remains ideal for reliably characterizing heterogeneous EV.
Cells · 2024
Senior authorCorresponding- Biology
- Cell biology
- Molecular biology
The chromatin-associated protein WDR5 has been widely studied due to its role in histone modification and its potential as a pharmacological target for the treatment of cancer. In humans, the protein with highest sequence homology to WDR5 is encoded by the retrogene WDR5B, which remains unexplored. Here, we used CRISPR-Cas9 genome editing to generate WDR5B knockout and WDR5B-FLAG knock-in cell lines for further characterization. In contrast to WDR5, WDR5B exhibits low expression in pluripotent cells and is upregulated upon neural differentiation. Loss or shRNA depletion of WDR5B impairs cell growth and increases the fraction of non-viable cells in proliferating retinal pigment epithelial (RPE) cultures. CUT&RUN chromatin profiling in RPE and neural progenitors indicates minimal WDR5B enrichment at established WDR5 binding sites. These results suggest that WDR5 and WDR5B exhibit several divergent biological properties despite sharing a high degree of sequence homology.
bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-31 · 2 citations
preprintOpen accessAbstract Retinal pigment epithelium (RPE) cells are exclusive to the retina, critically multifunctional in maintaining the visual functions and health of photoreceptors and the retina. Despite their vital functions throughout lifetime, RPE cells lack regenerative capacity, rendering them vulnerable and central to degenerative retinal diseases. With advancements in stem cell technology enabling the differentiation of functional cells from pluripotent stem cells and leveraging the robust autocrine and paracrine functions of RPE cells, extracellular vesicles (EVs) secreted by RPE cells hold significant therapeutic potential in supplementing RPE cell activity. While previous research has primarily focused on the trophic factors secreted by RPE cells, there is a lack of studies investigating miRNA, which serves as a master regulator of gene expression. Profiling and defining the functional role of miRNA contained within RPE-secreted EVs is critical as it constitutes a necessary step in identifying the optimal phenotype of the EV secreting cell and understanding biological cargo of EVs to develop EV-based therapeutics. In this study, we present a comprehensive profile of miRNA in small extracellular vesicles (sEV) secreted during RPE maturation following differentiation from human embryonic stem cells (hESCs). This exploration is essential for ongoing efforts to develop and optimize EV-based intraocular therapeutics utilizing RPE-secreted EVs, which may significantly impact the function of dysfunctional RPE cells.
bioRxiv (Cold Spring Harbor Laboratory) · 2024-06-03 · 1 citations
preprintOpen accessHypertrophy Cardiomyopathy (HCM) is the most prevalent hereditary cardiovascular disease - affecting >1:500 individuals. Advanced forms of HCM clinically present with hypercontractility, hypertrophy and fibrosis. Several single-point mutations in b-myosin heavy chain (MYH7) have been associated with HCM and increased contractility at the organ level. Different MYH7 mutations have resulted in increased, decreased, or unchanged force production at the molecular level. Yet, how these molecular kinetics link to cell and tissue pathogenesis remains unclear. The Hippo Pathway, specifically its effector molecule YAP, has been demonstrated to be reactivated in pathological hypertrophic growth. We hypothesized that changes in force production (intrinsically or extrinsically) directly alter the homeostatic mechano-signaling of the Hippo pathway through changes in stresses on the nucleus. Using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we asked whether homeostatic mechanical signaling through the canonical growth regulator, YAP, is altered 1) by changes in the biomechanics of HCM mutant cardiomyocytes and 2) by alterations in the mechanical environment. We use genetically edited hiPSC-CM with point mutations in MYH7 associated with HCM, and their matched controls, combined with micropatterned traction force microscopy substrates to confirm the hypercontractile phenotype in MYH7 mutants. We next modulate contractility in healthy and disease hiPSC-CMs by treatment with positive and negative inotropic drugs and demonstrate a correlative relationship between contractility and YAP activity. We further demonstrate the activation of YAP in both HCM mutants and healthy hiPSC-CMs treated with contractility modulators is through enhanced nuclear deformation. We conclude that the overactivation of YAP, possibly initiated and driven by hypercontractility, correlates with excessive CCN2 secretion (connective tissue growth factor), enhancing cardiac fibroblast/myofibroblast transition and production of known hypertrophic signaling molecule TGFβ. Our study suggests YAP being an indirect player in the initiation of hypertrophic growth and fibrosis in HCM. Our results provide new insights into HCM progression and bring forth a testbed for therapeutic options in treating HCM.
Establishment of Transgene‐Free Porcine Induced Pluripotent Stem Cells
Current Protocols · 2024-05-01 · 3 citations
articleOpen accessAlthough protocols to generate authentic transgene-free mouse and human induced pluripotent stem cells (iPSCs) are now well established, standard methods for reprogramming porcine somatic cells still suffer from low efficiency and transgene retention. The Basic Protocol describes reprogramming procedures to establish transgene-free porcine iPSCs (PiPSCs) from porcine fibroblasts. This method uses episomal plasmids encoding POU5F1, SOX2, NANOG, KLF4, SV40LT, c-MYC, LIN28A, and microRNA-302/367, combined with an optimized medium, to establish PiPSC lines. Support protocols describe the establishment and characterization of clonal PiPSC lines, as well as the preparation of feeder cells and EBNA1 mRNA. This optimized, step-by-step approach tailored to this species enables the efficient derivation of PiPSCs in ∼4 weeks. The establishment of transgene-free PiPSCs provides a new and valuable model for studies of larger mammalian species' development, disease, and regenerative biology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Reprogramming of porcine fibroblasts with episomal plasmids Support Protocol 1: Preparation of mouse embryonic fibroblasts for feeder layer Support Protocol 2: Preparation of in vitro-transcribed EBNA1 mRNA Support Protocol 3: Establishment of clonal porcine induced pluripotent stem cell (PiPSC) lines Support Protocol 4: PiPSC characterization: Genomic DNA PCR and RT-PCR Support Protocol 5: PiPSC characterization: Immunostaining.
Recent grants
NIH · $1.1M · 2003
Frequent coauthors
- 44 shared
Mark S. Humayun
Southern California Eye Institute
- 35 shared
David R. Hinton
University of Southern California
- 24 shared
Sherry T. Hikita
University of California, Santa Barbara
- 23 shared
Danhong Zhu
Putian University
- 23 shared
Biju B. Thomas
University of Southern California
- 22 shared
Lincoln V. Johnson
Menlo School
- 21 shared
Britney O. Pennington
University of California, Santa Barbara
- 17 shared
James A. Thomson
Morgridge Institute for Research
Labs
Not provided
Education
B.S., Biochemistry
UC Davis
Ph.D., Biochemistry
UC Berkeley
Awards & honors
- UCSB Distinguished Teaching Award in the Physical Sciences
- Pacific Coast Business Times Champions in Health Care Award
- National Eye Institute Audacious Goals award
- Frontiers of Vision Research Lecturer at the National Eye In…
- Keynote Lecturer at the Stem Cells World Congress
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