Dr. Clayton Santiago's research focuses on the molecular and gene regulatory networks that govern retinal development, disease, and regeneration. During his postdoctoral training at Johns Hopkins University, he generated large-scale transcriptomic and epigenomic datasets to map cell-state transitions from retinal progenitors to mature retinal cell types, identifying how transcription factors such as the NFI family coordinate mitotic exit and cell fate specification. Beyond basic development, his work has led to the development of a novel biotechnological framework that leverages cell-specific alternative splicing to achieve precise transgene expression. This system has demonstrated significant translational potential, including rescuing defects in retinal degeneration models.
In parallel, Dr. Santiago has played a key role in developing and characterizing preclinical models of proliferative vitreoretinopathy (PVR), where he applied single-cell RNA sequencing and chromatin accessibility profiling to uncover conserved transcriptional networks that drive retinal scarring. Building on this foundation, his current research program focuses on modulating pathways underlying retinal fibrosis. Using an integrated approach that combines single-cell multiomics, spatial transcriptomics, and long-read sequencing, he investigates both extrinsic signaling cues and intrinsic transcriptional regulators that govern injury responses. His long-term goal is to translate these mechanistic insights into targeted, next-generation therapies and to integrate refined splicing-based delivery systems to prevent vision loss and restore retinal function in blinding diseases.
- Postdoc, Johns Hopkins University, 2025
- PhD, Biomedical Sciences, University of Florida, 2018
- MSc, Biological Sciences, Villanova University, 2012
- BSc, Biotechnology, Manipal University, 2010
Education & Training
McNerney C, Santiago CP, Eldred K, Reh T, Glass I, Lord N, Hernandez A, Blackshaw S & Johnston Jr RJ. (2026). DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids. Genes & Development 40 (1-2), 70-93. https://doi.org/10.1101/gad.352924.125
Liu YV*, Santiago CP*, Sogunro A, Konar GJ, Hu M, McNally MM, Lu Y, Li Z, Agakishiev D, Hadyniak SE, Hussey KA, Creamer TJ, Orzolek LD, Teng, D, Qian J, Johnston Jr RJ, Blackshaw S & Singh MS. (2023). Single-cell transcriptome analysis of xenotransplanted human retinal organoids defines two migratory cell populations of nonretinal origin. Stem Cell Reports 18(5):1138-1154. https://doi.org/10.1016/j.stemcr.2023.04.004 *Authors contributed equally to this work.
Santiago CP*, Gimmen MY*, Lu Y, McNally MM, Duncan LH, Creamer TJ, Orzolek LD, Blackshaw S & Singh MS. (2023). Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of retinal detachment-related proliferative vitreoretinopathy. Ophthalmology Science 23;3(4):100335. https://doi.org/10.1016/j.xops.2023.100335 *Authors contributed equally to this work.
Ling JP*, Bygrave AM*, Santiago CP*, Carmen-Orozco RP, Trinh VT, Yu M, Li Y, Liu Y, Bowden KD, Duncan LH, Han J, Taneja K, Dongmo R, Babola TA, Parker P, Jiang L, Leavey PJ, Smith JJ, Vistein R, Gimmen MY, Dubner B, Helmenstine E, Teodorescu P, Karantanos T, Ghiaur G, Kanold PO, Bergles D, Langmead B, Sun S, Nielsen KJ, Peachey N, Singh MS, Dalton WB, Rajaii F, Huganir RL & Blackshaw S. (2022). Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature communications, 13 (1), 5773. https://doi.org/10.1038/s41467-022-33523-2 *Authors contributed equally to this work.
Lyu P*, Hoang T*, Santiago CP*, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, & Blackshaw S. (2021). Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina. Cell reports, 37(7),109994. https://doi.org/10.1016/j.celrep.2021.109994 *Authors contributed equally to this work.
- Retinal development
- Retinal degeneration
- Regeneration
- Gene therapy
- Single cell and spatial transcriptomics
- Epigenetics