Publications

Ageing promotes microglial accumulation of slow-degrading synaptic proteins

Guldner IH, Wagner VP, Moran-Losada P, Shi SM,Hevler JF, Chen K, Meese BT, Ghoochani A, Pulido E, Oh HSE, Guen YL, Lu N, WongPS, To N, Garceau D, Guo Z, Luo J, Bertozzi CR, Lundberg E, Abu-Remaileh M,Sasner M, Keller A, Yang AC, Cheung TH, Wyss-Coray T.
Nature. 2026; 650: 930–941.

RBFOX2-dependent alternative splicing of Numb regulates Notch signaling during muscle stem cell activation

Lin K, Liu J, Tse EHY, Yin Y, Chan ITC, Dong A, Ngan LP, Cheung TH.
Stem Cell Reports. 2026; 21(1): 102745.

MYOD represses gene expression from non-E-box motifs

Nicoletti C, Massenet J, Pintado-Urbanc AP, Connor LJ, Nicolau M, Sundar S, Xu M, Schmitt A, Zhang W, Fang Z, Chan TCI, Wang YX, Tapscott SJ, Cheung TH, Simon MD, Caputo L, Puri PL.
Genes & Development. 2025. doi: 10.1101/gad.352708.125.

Synaptic proteins that aggregate and degrade slower with aging accumulate in microglia

Guldner IH, Wagner VP, Moran-Losada P, Shi SM, Chen K, Meese BT, Oh H, Le Guen Y, Lu N, Wong PS, To NS, Garceau D, Guo Z, Luo J, Sasner M, Keller A, Yang AC, Cheung TH, Wyss-Coray T.
bioRxiv. 2025. doi: https://doi.org/10.1101/2025.05.20.654652

Autophagy in adult stem cell homeostasis, aging, and disease therapy

Zhao K, Chan ITC, Tse EHY, Xie Z, Cheung TH, Zeng YA.
Cell Regeneration. 2025; 14: 14.

Detection of Cellular Senescence on Murine Muscle Tissue Sections by Senescence-Associated β-Galactosidase Staining

Zhang W, Cheung TH.
In: Turksen, K. (eds) Methods in Molecular Biology, vol 2939. 2025. Humana, New York, NY.

Glycocalyx dysregulation impairs blood–brain barrier in ageing and disease

Shi SM, Suh RJ, Shon DJ, Garcia FJ, Buff JK, Atkins M, Li L, Lu N, Sun B, Luo J, To NS, Cheung TH, McNerney MW, Heiman M, Bertozzi CR, Wyss-Coray T.
Nature. 2025; 639: 985-994.

E-box independent chromatin recruitment turns MYOD into a transcriptional repressor

Nicoletti C, Massenet J, Pintado-Urbanc AP, Connor LJ, Nicolau M, Sundar S, Xu M, Schmitt A, Zhang W, Fang Z, Chan TCI, Tapscott SJ, Cheung TH, Simon MD, Caputo L, Puri PL.
bioRxiv. 2024. doi: https://doi.org/10.1101/2024.12.05.627024

Setdb1 protects genome integrity in murine muscle stem cells to allow for regenerative myogenesis and inflammation

Garcia P, Jarassier W, Brun C, Giordani L, Agostini F, Kung WH, Peccate C, Ravent J, Fall S, Petit V, Cheung TH, Ait-Si-Ali S, Le Grand F.
Developmental Cell. 2024; 59(17): 2375-2392. e8.

Muscle stem cell niche dynamics during muscle homeostasis and regeneration.

Yin Y, He GJ, Hu S, Tse EHY, Cheung TH.
Current Topics in Developmental Biology. 2024; 158: 151-177.

Niche inflammatory signals control periodical mammary regeneration and protect stem cells from cytotoxic stress

Liu C, Xu Y, Yang G, Tao Y, Chang J, Wang S, Cheung TH, Chen J, Zeng YA.
Cell Stem Cell. 2024; 31(1): 89-105.

Protocol for low-input proteomic analysis of in situ fixed adult murine muscle stem cells

Zhang W, Zeng W, Wong PS, Cheung TH.
STAR Protocols. 2023; 4 (4): 102750.

ATAC-seq protocol for the profiling of chromatin accessibility of in situ fixed quiescent and activated muscle stem cells

Dong A, Chan ITC, Cheung TH.
STAR Protocols. 2023; 4(3):102376.

Restoration of CPEB4 Prevents Muscle Stem Cell Senescence During Aging.

Zeng W, Zhang W, Tse EHY, Liu J, Dong A, Lam KSW, Luan S, Kung WH, Chan TC, Cheung TH.
Developmental Cell. 2023;58:1-16.

Polycomb Ezh1 maintains murine muscle stem cell quiescence through non-canonical regulation of Notch signaling

Feng X, Wang AH, Juan AH, Ko KD, Jiang K, Riparini G, Ciuffoli V, Kaba A, Lopez C, Naz F, Jarnik M, Aliberti E, Hu S, Segalés J, Khateb M, Acevedo-Luna N, Randazzo D, Cheung TH, Muñoz-Cánoves P, Dell’Orso A, Sartorelli V.
Developmental Cell. 2023 Jun;58(12):1052-1070.e10.

Setdb1 safeguards genome integrity in muscle stem cells to allow for regenerative myogenesis and inflammation

Garcia P, Jarassier W, Brun C, Giordani L, Agostini F, Kung WH, Peccate C, Ravent J, Fall S, Petit V, Cheung TH, Ait-Si-Ali S, Le Grand F.
bioRxiv. 2023. doi: https://doi.org/10.1101/2023.06.08.544190

Visualization of RNA Transcripts in Muscle Stem Cells Using Single-Molecule Fluorescence In Situ Hybridization

Yue L, Cheung TH.
In: Asakura, A. (eds) Skeletal Muscle Stem Cells. Methods in Molecular Biology, vol 2640. 2023. Humana, New York, NY.

Single-Cell Transcriptomic Analysis of Mononuclear Cell Populations in Skeletal Muscle

He GJ, Galvis J, Cheung TH, Le Grand F.
In: Asakura, A. (eds) Skeletal Muscle Stem Cells. Methods in Molecular Biology, vol 2640. 2023. Humana, New York, NY.

Activation of Wnt/β-catenin signaling by Zeb1 in endothelial progenitors induces vascular quiescence entry

Yu QC, Geng A, Preusch CB, Chen Y, Peng G, Xu Y, Jia Y, Miao Y, Xue H, Gao D, Bao L, Pan W, Chen J, Carcia KC, Cheung TH, Zeng YA.
Cell Reports. 2022;41(8):111694.

Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

Dong A, Liu J, Lin K, Zeng W, So WK, Hu S, Cheung TH.
iScience. 2022; 25(9):104954.

CPEB1 directs muscle stem cell activation by reprogramming the translational landscape.

Zeng W, Yue L, Lam KSW, Zhang W, So WK, Tse EHY, Cheung TH.
Nature Communications 2022; 13(1):947.

Deciphering the chromatin organization and dynamics for muscle stem cell function.

Dong A, Cheung TH.
Current Opinion in Cell Biology. 2021;73:124-132.

Nuclear receptors NHR-49 and NHR-79 promote peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans.

Zeng L, Li X, Preusch CB, He GJ, Xu N, Cheung TH, Qu J, Mak HY.
PLOS Genetics. 2021;17(7):e1009635.

Stem cell quiescence: the challenging path to activation.

Urbán N, Cheung TH.
Development. 2021;148(3):dev165084.

A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression.

Dong A, Preusch CB, So WK, Lin K, Luan S, Yi R, Wong JW, Wu Z, Cheung TH.
Proceedings of the National Academy of Sciences. 2020;117(51):32464-32475.

Protocol for Isolation and Characterization of In Situ Fixed Quiescent Muscle Stem Cells.

Yue L, Cheung TH.
STAR Protocol. 2020;1(3):100128.

Dek Modulates Global Intron Retention during Muscle Stem Cells Quiescence Exit.

Yue L, Wan R, Luan S, Zeng W, Cheung TH.
Developmental Cell. 2020;53(6):661-676.e6.

IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer's Disease.

Lau SF, Chen C, Fu WY, Qu JY, Cheung TH, Fu AKY, Ip NY.
Cell Report. 2020;31(3):107530.

High-contrast, fast chemical imaging by coherent Raman scattering using a self-synchronized two-colour fibre laser.

Kong C, Pilger C, Hachmeister H, Wei X, Cheung TH, Lai CSW, Lee NP, Tsia KK, Wong KKY, Huser T.
Light: Science & Application. 2020; 9:25.

α2-Chimaerin is essential for neural stem cell homeostasis in mouse adult neurogenesis.

Su YT, Lau SF, Ip JP, Cheung TH, Fu AK, Ip NY.
Proceedings of the National Academy of Sciences. 2019; 116(27); 13651-13660.

YY1 regulates skeletal muscle regeneration through controlling metabolic reprogramming of satellite cells.

Chen F, Zhou J, Li Y, Zhao Y, Yuan J, Cao Y, Wang L, Zhang Z, Zhang B, Wang CC, Cheung TH, Wu Z, Wong CC, Sun H, Wang H.
EMBO J. 2019; 38(10):e99727.

High-Dimensional Single-Cell Cartography Reveals Novel Skeletal Muscle-Resident Cell Populations.

Giordani L, He GJ, Negroni E, Sakai H, Law JYC, Siu MM, Wan R, Corneau A, Tajbakhsh S, Cheung TH, Le Grand F.
Molecular Cell. 2019; 74(3):609-621.e6.

Hormones induce the formation of luminal-derived basal cells in the mammary gland.

Song W, Wang R, Jiang W, Yin Q, Peng G, Yang R, Yu QC, Chen J, Li J, Cheung TH, Jing N, Zeng YA.
Cell Research. 2019; 29(3):206-220.

Impaired Notch Signaling Leads to a Decrease in p53 Activity and Mitotic Catastrophe in Aged Muscle Stem Cells.

Liu L, Charville GW, Cheung TH, Yoo B, Santos PJ, Schroeder M and Rando TA.
Cell Stem Cell. 2018; 23(4):544-556.e4.

Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies.

van der Wal E, Herrero-Hernandez P, Wan R, Broeders M, In 't Groen SLM, van Gestel TJM, van IJcken WFJ, Cheung TH, van der Ploeg AT, Schaaf GJ, Pijnappel WWMP.
Stem Cell Reports. 2018; 10(6):1975-1990.

p110α of PI3K is necessary and sufficient for quiescence exit in adult muscle satellite cells.

Wang G, Zhu H, Situ C, Han L, Yu Y, Cheung TH, Liu K, Wu Z.
EMBO J. 2018; 37(8):e98239.

Molecular Regulation of Cellular Quiescence: A Perspective from Adult Stem Cells and Its Niches.

So WK, Cheung TH.
Methods in Molecular Biology. 2018; 1686:1-25.

Compact fs ytterbium fiber laser at 1010 nm for biomedical applications.

Kong C, Pilger C, Hachmeister H, Wei X, Cheung TH, Lai CSW, Huser T, Tsia KK, Wong KKY.
Biomed Optics Express. 2017; 8(11):4921-4932.

Anemoside A3 ameliorates experimental autoimmune encephalomyelitis by modulating T helper 17 cell response.

Ip FCF, Ng YP, Or TCT, Sun P, Fu G, Li JYH, Ye WC, Cheung TH, Ip NY.
PLoS One. 2017; 12(7):e0182069.

A Molecular Switch Regulating Cell Fate Choice between Muscle Progenitor Cells and Brown Adipocytes.

An Y, Wang G, Diao Y, Long Y, Fu X, Weng M, Zhou L, Sun K, Cheung TH, Ip NY, Sun H, Wang H, Wu Z.
Developmental Cell. 2017; 41(4):382-391.e5.

Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis.

Mueller AA, van Velthoven CT, Fukumoto KD, Cheung TH, Rando TA.
Nature. 2016; 540(7632):276-279.

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

Stunnenberg HG, Hirst M.
Cell. 2016; 167(5):1145-1149.

STAT3 Regulates Self-Renewal of Adult Muscle Satellite Cells during Injury-Induced Muscle Regeneration.

Zhu H, Xiao F, Wang G, Wei X, Jiang L, Chen Y, Zhu L, Wang H, Diao Y, Wang H, Ip NY, Cheung TH, Wu Z.
Cell Report. 2016; 16(8):2102-2115.

IL-33 ameliorates Alzheimer's disease-like pathology and cognitive decline.

Fu AK, Hung KW, Yuen MY, Zhou X, Mak DS, Chan IC, Cheung TH, Zhang B, Fu WY, Liew FY, Ip NY.
Proceedings of the National Academy of Sciences. 2016; 113(19):E2705-13.

Ex Vivo Expansion and In Vivo Self-Renewal of Human Muscle Stem Cells.

Charville GW, Cheung TH, Yoo B, Santos PJ, Lee GK, Shrager JB, Rando TA.
Stem Cell Reports. 2015; 5(4):621-32.

Isolation of skeletal muscle stem cells by fluorescence-activated cell sorting.

Liu L, Cheung TH, Charville GW, Rando TA.
Nature Protocols. 2015; 10(10):1612-24.

Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging.

Liu L, Cheung TH, Charville GW, Hurgo BM, Leavitt T, Shih J, Brunet A, Rando TA.
Cell Report. 2013; 4(1):189-204.

Molecular regulation of stem cell quiescence.

Cheung TH, Rando TA.
Nature Reviews Molecular Cell Biology. 2013; 14(6):329-40.

Notch signaling is necessary to maintain quiescence in adult muscle stem cells.

Bjornson CR, Cheung TH, Liu L, Tripathi PV, Steeper KM, Rando TA.
Stem Cells. 2012; 30(2):232-42.

All's well that ends well: alternative polyadenylation and its implications for stem cell biology.

Mueller AA, Cheung TH, Rando TA.
Current Opinion in Cell Biology. 2013; 25(2):222-32.

Alternative polyadenylation mediates microRNA regulation of muscle stem cell function.

Boutet SC, Cheung TH, Quach NL, Liu L, Prescott SL, Edalati A, Iori K, Rando TA.
Cell Stem Cell. 2012; 10(3):327-36.

Maintenance of muscle stem-cell quiescence by microRNA-489.

Cheung TH, Quach NL, Charville GW, Liu L, Park L, Edalati A, Yoo B, Hoang P, Rando TA.
Nature. 2012; 482(7386):524-8.

Remodeling the cardiac transcriptional landscape with diet.

Luczak ED, Barthel KK, Stauffer BL, Konhilas JP, Cheung TH, Leinwand LA.
Physiological Genomics. 2011; 43(12):772-80.

Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2.

Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR 3rd, Han M.
Molecular Cell. 2007; 28(4):598-613.

Identifying pattern-defined regulatory islands in mammalian genomes.

Cheung TH, Barthel KK, Kwan YL, Liu X.
Proceedings of the National Academy of Sciences. 2007; 104(24):10116-21.

Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT.

Cheung TH, Kwan YL, Hamady M, Liu X.
Genome Biology. 2006; 7(10):R97.

Global gene expression analysis of ERK5 and ERK1/2 signaling reveals a role for HIF-1 in ERK5-mediated responses.

Schweppe RE, Cheung TH, Ahn NG.
Journal of Biological Chemistry. 2006; 281(30):20993-21003.

A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program.

Knuesel M, Cheung HT, Hamady M, Barthel KK, Liu X.
Molecular & Cellular Proteomics. 2005; 4(10):1626-36.

Does protein structure influence trypsin miscleavage? Using structural properties to predict the behavior of related proteins.

Hamady M, Cheung TH, Tufo H, Knight R.
IEEE Engineering in Medicine and Biology Magazine. 2005; 24(3):58-66.

Key challenges in proteomics and proteoinformatics. Progress in proteins.

Hamady M, Cheung TH, Resing K, Cios KJ, Knight R.
IEEE Engineering in Medicine and Biology Magazine. 2005; 24(3):34-40.

Control of cell cycle-dependent degradation of c-Ski proto-oncoprotein by Cdc34.

Macdonald M, Wan Y, Wang W, Roberts E, Cheung TH, Erickson R, Knuesel MT, Liu X.
Oncogene. 2004; 23(33):5643-53.

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.

Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG.
Analytical Chemistry. 2004; 76(13):3556-68.