Yuyan Cheng, Ph.D.

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Assistant Professor of Ophthalmology
Department: Ophthalmology

Contact information
FM Kirby Center, Steller Chance 3rd Floor
Philadelphia, PA 19104
Ph.D (Biochemistry and Molecular Biology)
University of Miami, 2016.
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Description of Research Expertise

Research Interests

Research Details

Neurons, among the longest living cells in the human body, undergo various stresses from normal aging to disease states. The central vision of our lab is to understand how neurons age, respond to degenerative insult and injury, and, critically, how they fail to self-repair. By dissecting the molecular and cellular events shaping neuronal functions after acute or chronic damage, we aim to inform potential therapeutics for neurodegenerative diseases and, more broadly, neural repair.

Our primary approach integrates single-cell genomics and spatial transcriptomics with CRISPR-based genetic tools to profile and perturb neurons, including their cell-cell interactions with the environment during health and disease. Focusing on retinal and optic nerve degenerative disorders, our ultimate goal is to translate genomic findings to gene and cell therapies that can restore lost visual functions in human patients.

Selected Publications

Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X; PsychENCODE Consortium‡; Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M; PsychENCODE Consortium.: Single-cell genomics and regulatory networks for 388 human brains. Science 384: eadi5199, May 2024.

Wamsley B, Bicks L, Cheng Y, Kawaguchi R, Quintero D, Margolis M, Grundman J, Liu J, Xiao S, Hawken N, Mazariegos S, Geschwind DH.: Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics. Science 384: eadh2602, May 2024.

Kumar A, Karuppagounder SS, Chen Y, Corona C, Kawaguchi R, Cheng Y, Balkaya M, Sagdullaev BT, Wen Z, Stuart C, Cho S, Ming GL, Tuvikene J, Timmusk T, Geschwind DH, Ratan RR.: 2-Deoxyglucose drives plasticity via an adaptive ER stress-ATF4 pathway and elicits stroke recovery and Alzheimer's resilience. Neuron 111: 2831-2846, Sep 2023.

Rexach EJ, Cheng Y, Chen L, Polioudakis D, Lin, LC, Mitri V, Elkins A, Yin A, Calini D, Kawaguchi R, Ou J, Huang J, Williams C, Seeley W, Trojanowski JQ, Lee E, Vinters H, Malhotra D, Geschwind DH. : Disease-specific selective vulnerability and neuroimmune pathways in dementia revealed by single cell genomics. bioRxiv 2023.09. 29.560245, Sep 2023.

Kumar A, Karuppagounder SS, Chen Y, Corona C, Kawaguchi R, Cheng Y, Balkaya M, Sagdullaev BT, Wen Z, Coppola G, Stuart C, Cho S, Ming G, Tuvikene J, Timmusk T, Geschwind DH, Ratan RR. : The Intermittent Fasting Mimetic, 2-deoxyglucose, Reprograms Brain Derived Neurotrophic Factor (BDNF) transcription via an Adaptive ER Stress-ATF4 Pathway and Improves Outcomes in Alzheimer’s and Stroke Models. Neuron 111(2831-2846), 2023.

Cheah M, Cheng Y*, Petrova V, Cimpean A, Jendelova P, Swarup V, Woolf CJ, Geschwind DH, Fawcett JW. : Integrin-driven Axon Regeneration in the Spinal Cord Activates a Distinctive CNS Regeneration Program. Journal of Neuroscience 43 (4775-4794), 2023 Notes: *co-first author. Featured as a cover story.

Tian F, Cheng Y*, Zhou S, Wang Q, Monavarfeshani A, Gao K, Jiang W, Kawaguchi R, Wang Q, Tang M, Donahue R, Meng H, Zhang Y, Jacobi A, Yan W, Yin J, Cai X, Yang Z, Hegarty S, Stanicka J, Dmitriev P, Taub D, Zhu J, Woolf CJ, Sanes JR, Geschwind DH, He Z.: Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells. Neuron 110: 2607-2624, Aug 2022 Notes: *co-first author; Featured as a cover story and highlighted in Neuron 2022;110:2516-2519.

Cheng Y, Yin Y, Zhang A, Bernstein AM, Kawaguchi R, Gao K, Potter K, Gilbert HY, Ao Y, Ou J, Fricano-Kugler CJ, Goldberg JL, He Z, Woolf CJ, Sofroniew MV, Benowitz LI, Geschwind DH.: Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice. Nat Commun 13: 4418, Jul 2022.

Cheng Y, Pardo M, Armini RS, Martinez A, Mouhsine H, Zagury JF, Jope RS, Beurel E.: Stress-induced neuroinflammation is mediated by GSK3-dependent TLR4 signaling that promotes susceptibility to depression-like behavior. Brain Behav Immun 2016.

Cheng Y, Desse S, Martinez A, Worthen RJ, Jope RS, Beurel E.: TNFα disrupts blood brain barrier integrity to maintain prolonged depressive-like behavior in mice. Brain Behav Immun 2018.

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Last updated: 06/28/2024
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