Publications

PUBLISHED & PENDING

Lad H (co-first author), Esteban E.M. (co-first author), Tiper Y, Mahoudeau A (co-third author), Xie Y (co-third author), Tendrel B, Allenbach Y, Benveniste O (co-senior author), Gilbert P.M. (co-senior author) (2024) Distinct pathogenic influences of anti-HMGCR+ and anti-SRP+ immune-mediated necrotizing myopathy autoantibodies on engineered muscle function. BioRxiv, doi.org/10.1101/2024.08.26.609771

Jacques E. (co-first author), Garcia P. (co-first author), Mercier O., Hu Y., Degletagne C., Ravent J., Fall S., Almeida M.P., Wheeler A.R., Angers S., Gilbert P.M. (co-senior author), Le Grand F. (co-senior author) (2024) Integrating in silico predictions with an engineered tissue assay identifies Perlecan as an age-perturbed re-quiescence cue for muscle stem cells. BioRxiv, doi.org/10.1101/2024.07.22.604619

Gulati N. (co-first author), Davoudi S. (co-first author), Xu B. (co-first author), Rjaibi S.T. (co-second author), Jacques E. (co-second author), Pham J., Fard A., McGuigan A.P. (co-senior author), Gilbert P.M. (co-senior author) (2024) mini-MEndR: A miniaturized 96-well predictive assay to evaluate muscle stem cell mediated repair. BMC Methods, doi.org/10.1186/s44330-024-00005-4

Rjaibi S., Jacques E., Ni C., Cu B., Kouthouridis S., Sitole J., Lad H., Gulati N., Li N.T., Ahn H., Ginsberg H., Zhang B., Le Grand F., Gilbert P.M. (co-senior author) and McGuigan A.P. (co-senior author) (2024) A cryopreservation strategy for myoblast storage in paper-based scaffolds for inter-laboratory studies of skeletal muscle health. Advanced Materials Interfaces: doi.org/10.1002/admi.202400382

Nguyen J. and Gilbert P.M. (2024) Decoding the forces that shape muscle stem cell function. Current Topics in Developmental Biology. Editors: M. Rudnicki & J. Dilworth.

Nguyen C.T., Chávez-Madero C. (co-second author), Jacques E. (co-second author), Musgrave B., Yin T., Saraci K., Gilbert P.M., Stewart B.A. (2024) Electron microscopic analysis of the influence of iPSC-derived motor neurons on bioengineered human skeletal muscle tissues. Cell & Tissue Research: doi.org/10.1007/s00441-024-03864-z

Nguyen J., Wang L., Lei W., Hu Y., Gulati N., Chavez-Madero C., Brandt M., Betz T., Gilbert P.M. (2024) Culture substrate stiffness impacts human myoblast contractility-dependent proliferation and nuclear wrinkling. Journal of Cell Science: doi.org/10.1242/jcs.261666

Gilbert P.M., Hofmann S., Ng H-H., Vankelecom H., Wells J.M. (2024) Organoids in endocrine and metabolic research: current and emerging applications. Nature Reviews Endocrinology: doi.org/10.1038/s41574-023-00933-1

Kajabadi N., Low M., Jacques E. (co-third author), Lad H. (co-third author), Tung L.W., Babaeijandaghi F., Gamu D., Zelada D., Wong C.K., Chang C., Yi L., Wosczyna M.N., Rando T.A., Henríquez J.P., Gibson W.T., Gilbert P.M., Rossi F.M.V. (2023) Beta-catenin activation in mesenchymal progenitors leads to muscle mass loss. Developmental Cell, 58(6): 489-505.

Rosenstein A.H., Nguyen M., Al-Attar R., Serra D., Gulati N., Yin T., Gilbert P.M., Garton M. (2023) A Flexible Transgene Integration ‘Landing-Pad’ Toolkit in Human Induced Pluripotent Stem Cells Enables Facile Cellular Engineering, Gene Zygosity Control, and Parallel Transgene Integration. BioRxiv: doi.org/10.1101/2023.03.03.531057

Hofemeier A.D., Muenker T.M., Herkenrath F., Ristau M., Brandt M., Shahriyari M., Tiburcy M., Zimmerman W.H., Lenz C., Mamchaoui K., Bigot A., Gilbert P.M., Betz T. (2022) Dystrophin is a mechanical tension sensor. BioRxiv: doi.org/10.1101/2022.12.23.521750

Jacques E., Kuang Y., Kann A.P., Le Grand F., Krauss R.S., Gilbert P.M. (2022) The mini-IDLE 3D biomimetic culture assay enables interrogation of mechanisms governing muscle stem cell quiescence and niche repopulation. eLife, https://elifesciences.org/articles/81738. Learn more here.

Prochazka L., Michaels Y.S., Lau C., Jones R.D., Siu M., Ting Y., Wu D., Jang E., Vázquez-Cantú M., Gilbert P.M., Kaul H., Benenson Y., Zandstra P.W. (2022) Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells. Molecular Systems Biology, 18: e10886.

Pieters V.M., Rjaibi S.T., Singh K., Li N.T., Khan S.T., Nunes S.S., Dal Cin A., Gilbert P.M.*, McGuigan A.P.* (2022) A three-dimensional human adipocyte model of fatty acid-induced obesity. Biofabrication, 14: 045009.

Kann A.P., Hung M., Wang W., Nguyen J, Gilbert P.M., Wu W., Krauss R.S. (2022) An injury-responsive Rac-to-Rho GPTase switch drives activation of muscle stem cells through rapid cytoskeletal remodeling. Cell Stem Cell, 29(6): 933-947.

Moyle L.A., Davoudi S., Gilbert P.M. (2022) Innovation in culture systems to study muscle complexity. Experimental Cell Research, 411(1): 112966.

Davoudi S. (co-first author), Xu B. (co-first author), Jacques E. (co-second author), Cadavid J.L. (co-second author), McFee M., Chin C.-Y., Meysami A., Ebrahimi M., Bakooshli M.A., Tung K., Ahn H., Ginsberg H.J., McGuigan A.P. (co-senior author), Gilbert P.M. (co-senior author) (2021) MEndR: An in vitro functional assay to predict in vivo muscle stem cell mediated repair. Advanced Functional Materials, 32(2): 2106548.

Nguyen C.T., Ebrahimi M., Gilbert P.M., Stewart B.A. (2021) Electrophysiological analysis of healthy and dystrophic 3D bioengineered skeletal muscle tissues. American Journal of Physiology - Cell Physiology, 321(4): 749-759.

Ebrahimi M. (co-first author), Lad H. (co-first author), Fusto A., Tiper Y., Datye A., Nguyen CT., Jacques E., Moyle L.A., Nguyen T., Musgrave B., Chavez-Madero C., Bigot A., Chen C., Turner S., Stewart B.A., Pegoraro E., Vitiello L., Gilbert P.M. (2021) De novo revertant fiber formation and therapy testing in a 3D culture model of Duchenne muscular dystrophy skeletal muscle. Acta Biomaterialia, 132: 227-244.

Lad H., Musgrave B., Ebrahimi M., Gilbert P.M. (2021) Assessing functional metrics of skeletal muscle health in human skeletal muscle microtissues. Journal of Visual Experimentation, DOI: 10.3791/62307.

Girardi F., Taleb A., Ebrahimi M., Datye A., Gamage D. G., Peccate C., Giordani L., Millay D. P., Gilbert P. M., Cadot B., Le Grand F. (2021) TGFβ signaling curbs cell fusion and muscle regeneration. Nature Communications, 12(1): 750.

Hofemeier A. D., Limon T., Muenker T. M., Wallmeyer B., Jurado A., Afshar M. E., Ebrahimi M., Tsukanov R., Oleksiievets N., Enderlein J., Gilbert P. M., Betz T. (2021) Global and local tension measurements in biomimetic skeletal muscle tissues reveals early mechanical homeostasis. eLife, 10: e60145.

Lad, H., Saumur, T. M., Herridge, M. S., Dos Santos, C. C., Mathur, S., Batt, J., Gilbert, P. M. (2020) Intensive Care Unit-Acquired Weakness: Not just Another Muscle Atrophying Condition. International Journal of Molecular Sciences, 21(21): 7840.

Moyle, M. A., Cheng, R. Y., Liu, H., Davoudi, S., Ferreira, S. A., Nissar, A. A., Sun, Y., Gentleman, E., Simmons, C. A., Gilbert, P. M. (2020). Three-dimensional niche stiffness synergizes with Wnt7a to modulate the extent of satellite cell symmetric self-renewal divisions. Molecular Biology of the Cell, 31(16): 1651-1821.

Moyle, M. A., Jacques, E., Gilbert, P. M. (2020). Engineering the next generation of human skeletal muscle models: from cellular complexity to disease modelling. Current Opinion in Biomedical Engineering, 16: 9-18.

Thavandiran, N., Hale, C., Blit, P., Sandberg, M. L.., McElvain, M. E., Gagliardi, M., Sun, B., Witty, A., Graham, G., Do, V. T. H, Bakooshli, M. A., Le, H., Ostblom, J., McEwen, S., Chau, E., Prowse, A., Fernandes, I., Norman, A., Gilbert, P. M., Keller, G., Tagari, P., Xu, H., Radisic, M., Zandstra, P. W. (2020). Functional arrays of human pluripotent stem cell-derived cardiac microtissues. Scientific Reports, 10: 6919.

Afshar, M. E. (co-first author), Abraha, H. Y. (co-first author), Bakooshli, M. A. (co-first author), Davoudi, S., Thavandiran, N., Tung, K., Ahn, H., Ginsberg, H. J., Zandstra, P. W., Gilbert, P. M. (2020). A 96-well culture platform enables longitudinal analyses of engineered human skeletal muscle microtissue strength. Scientific Reports, 10: 6918.

Fusto, A., Moyle, L. A., Gilbert, P. M., Pegoraro, E. (2019). Cored in the act: the use of models to understand core myopathies. Disease Models & Mechanisms, 12(12): dmm041368.

Nixon, A. M. L., Duque, A., Yelle, N., McLaughlin, M., Davoudi, S., Pedley, N. M., Haynes, J., Brown, K. R., Pan, J., Hart, T., Gilbert, P. M., Singh, S. K., O’Brien, C. A., Sidhu. S., Moffat, J. (2019). A rapid in vitro methodology for simultaneous target discovery and antibody generation against functional cell subpopulations. Scientific Reports, 9: 842.

Bakooshli, M. A., Lippmann, E. S., Mulcahy, B., Iyer, N., Nguyen, C. T., Tung, Kayee, T., Stewart, B. A., van den Dorpel, H., Fuehrmann, T., Shoichet, M., Bigot, A., Pegoraro, E., Ahn, H., Ginsberg, H., Zhen, M., Ashton, R. S., Gilbert, P. M. (2019) A 3D culture model of innervated human skeletal muscle enables studies of the adult neuromuscular junction and disease modeling. eLife, 8: e44530.

Davoudi, S., Chin, C-Y,, Cooke, M. J., Tam, R,Y., Shoichet, M. S., Gilbert, P. M. (2018) Muscle stem cell intramuscular delivery within hyaluronin methylcellulose improves engraftment efficiency and dispersion. Biomaterials, 173: 34-46.

Li, E. W., McKee-Muir, O. C., Gilbert, P. M. (2018) Cellular biomechanics in skeletal muscle regeneration. In: Myogenesis in Development and Disease, Sassoon D (Ed.) Amsterdam, Netherlands: Elsevier.

Safaee, H., Bakooshli, M. A., Davoudi, S., Cheng, R. Y., Martowirogo, A. J., Li, E. W., Simmons, C. A., Gilbert, P. M. (2017) Tethered Jagged-1 synergizes with culture substrate stiffness to modulate Notch-induced myogenic progenitor differentiation. Cellular and Molecular Bioengineering, 10(5): 501-513.

Davoudi, S., Gilbert, P. M. (2017). Optimization of satellite cell culture through biomaterials. In: Methods in Molecular Biology, E. Perdiguero and D. Cornelison (Ed.), New York, NY: Springer, 1556: 329-341.

Gilbert, P. M.*, Weaver, V. M.* (*Co-corresponding authors; 2016). Cellular adaptation to biomechanical stress across length scales in tissue homeostasis and disease. Seminars in Cell and Developmental Biology, 67: 141-152.

Nissar, A. A., Martowirogo, A., Gilbert, P. M. (2016). Targeting the stem cell niche with regenerative biomaterials. Current Opinion in Solid State and Materials Science, 20(4): 180-192.

Morrissey-Scoot, J. D., Cheng, R., Davoudi, S., Gilbert, P. M. (2016). Biomechanical origins of muscle stem cell signal transduction. Journal of Molecular Biology, 428(7): 1441-54.

Gomez-Aristizabal, A., Sharma, A., Bakooshli, M. A., Kapoor, M., Gilbert, P. M., Viswanathan, S., Gandhi, R. (2016). Stage-specific differences in secretory profile of mesenchymal stromal cells subjected to early- vs late- OA synovial fluid. Osteoarthritis and Cartilage, 5: 737-741.

Bakooshli, M. A., Gilbert, P. M. (2015). Muscling in on the third dimension. eLife, 4: e06430.

Magnusson, K. E. G., Jalden, J., Gilbert, P. M., Blau, H. M. (2015). Global linking of tracks using Viterbi algorithm. IEEE Transactions on Medical Imaging, 34(4): 911-929.

Cosgrove, B. D., Gilbert, P. M.*, Porpiglia, E., Mourkioti, F., Lee, S. P., Corbel, S. Y., Llewellyn, M. E., Delp, S. P., Blau, H. M.* (*Co-corresponding authors; 2014). Rejuvenation of the muscle stem cell population restores strength to injured aged muscles. Nature Medicine, 20: 255-64.

Mouw, J. K., Yui, Y., Damiano, L., O Bainer, R., Lakins, J. N., Acerbi, I., Ou, G., Wijekoon, A. C., Levental, K. R., Gilbert, P. M., Hwang, E. S., Chen, Y-Y., Weaver, V. M. (2014). Tissue mechanics modulate microRNA-dependent PTEN expression to regulate malignant progression. Nature Medicine, 20: 360-367.

Gilbert, P. M., Corbel, S., Doyonnas, R., Havenstrite, K., Magnusson, K.E.G., Blau, H. M. (2012). A single cell bioengineering approach to elucidate mechanisms of adult stem cell self-renewal. Integrative Biology, 4(4):360-367.

Sengupta, D., Gilbert, P. M., Johnson, K. L., Blau, H. M., Heilshorn, S. C. (2012). Protein-engineered biomaterials to generate human skeletal muscle mimics. Advanced Healthcare Materials, 1(6):785-789.

Gibbs, K. D. Jr., Gilbert, P. M., Blau, H. M., Weissman, I. L., Nolan, G. P., Majeti, R. (2011). Single cell analysis of phosphor-signaling networks reveals G-SCF drives human hematopoietic stem cells into cell cycle. Blood, 117(16):4226-33.

Gilbert, P. M., Blau, H. M. (2011). Engineering a stem cell house into a home. Stem cell research and therapy, 2(1): 1-9.

Gilbert, P. M.*, Havenstrite, K.*, Magnusson, K. E. G., Sacco, A., Leonardi, N., Nguyen, N., Kraft, P., Thrun, S., Lutolf, M., & Blau, H. M. (*Equal Contribution; 2010). Substrate elasticity regulates skeletal muscle stem cell self-renewal in culture. Science, 329(5995): 1078-81.

Gilbert, P. M.*, Mouw, J. K.*, Unger, M. A., Lakins, J. N., Gbegnon, M. K., Clemmer, V. B., Benezra, M., Licht, J. D., Boudreau, N. J., Tsai, K. K. C., Welm, A. L., Feldman, M. D., Weber, B. L., & Weaver, V. M. (*Equal contribution; 2010). HOXA9 regulates BRCA1 expression to modulate human breast tumor phenotype. Journal of Clinical Investigation, 120(5):1535-50.

Lutolf, M., Gilbert, P. M., & Blau, H. M. (2009). Designing biomaterials to direct stem cell fate. Nature, 462: 433-441.

Blau, H. M., Sacco, A., & Gilbert, P. M. (2009). Skeletal muscle stem cells. In: Essentials of Stem Cell Biology.  R. Lanza et al (Eds.) San Diego, California: Academic Press Inc: 249-257.

Cosgrove, B. D., Sacco, A., Gilbert, P. M., & Blau, H. M. (2009). A home away from home: Challenges and opportunities in engineering in vitro muscle satellite cell niches. Differentiation, 78(203):  185-94.

Blau, H. M., Sacco, A., & Gilbert, P. M. (2008). Stem cell self-renewal. Stem Cell Encyclopedia.  SAGE Publishing.

Geng, J., Shin, M. E., Gilbert, P. M., Collins, R. N., & Burd, C. G. (2005). Saccharomyces cerevisiae Rab-GDI displacement factor ortholog Yip3p forms distinct complexes with the Ypt1 Rab GTPase and the reticulon Rtn1p. Eukaryotic Cell, 4(7): 1166-1174.

Weaver, V. M. & Gilbert, P. (2004). Watch thy neighbor: cancer is a communal affair. Journal of Cell Science, 117(Pt8): 1287-1290.

Calero, M., Chen, C. Z., Zhu, W., Winand, N., Havas, K. A., Gilbert, P. M., Burd, C. G., & Collins, R. N. (2003). Dual prenylation is required for Rab protein localization and function. Molecular Biology of the Cell, 14(5): 1852-1867.

Shin, M. E., Ogburn, K. D., Varban, O. A., Gilbert, P. M., & Burd, C. G. (2001). FYVE domain targets Pib1 ubiquitin ligase to endosome and vacuolar membranes. Journal of Biological Chemistry, 276(44): 41388-41393.

Gilbert, P. M., & Burd, C. G. (2001). GDP dissociation inhibitor domain II required for Rab GTPase recycling. Journal of Biological Chemistry, 267(11): 8014-8020.

BIORXIV PREPRINTS

Nguyen C.T., Chávez-Madero C. (co-second author), Jacques E. (co-second author), Musgrave B., Yin T., Saraci K., Gilbert P.M., Stewart B.A. (2023) Electron microscopic analysis of the influence of iPSC-derived motor neurons on bioengineered human skeletal muscle tissues.

Nguyen J., Wang L., Lei W., Hu Y., Gulati N., Chavez-Madero C., Brandt M., Betz T., Gilbert P.M. (2023) Culture substrate stiffness impacts human myoblast contractility-dependent proliferation and nuclear wrinkling.

Jacques E., Kuang Y., Kann A.P., Krauss R.S., Gilbert P.M. (2022) Rescue of aged muscle stem cell quiescence defects by AKT inhibition revealed with a 3D biomimetic culture assay.

Pieters V.M., Rjaibi S.T., Singh K., Li N.T., Khan S.T., Nunes S.S., Dal Cin A., Gilbert P.M.*, McGuigan A.P.* (2022) A three-dimensional human adipocyte model of fatty acid-induced obesity.

Prochazka L., Michaels Y.S., Lau C., Siu M., Yin T., Wu D., Jang E., Jones R.D., Vasquez-Cantu M., Gilbert P.M., Kaul H., Benenson Y., Zandstra P.W. (2021) Discrete-to-analog signal conversion in human pluripotent stem cells.

Nguyen C.T., Ebrahimi M., Gilbert P.M., Stewart B.A. (2020) Electrophysiological analysis of healthy and dystrophic 3D bioengineered skeletal muscle tissues.

Thavandiran, N., Hale, C., Blit, P., Sandberg, M. L., McElvain, M. E., Gagliardi, M., Sun, Bo., Witty, A., Graham, G., Mcintosh, M., Bakooshli, M. A., Le, H., Ostblom, J., McEwen, S., Chau, E., Prowse, A., Fernandes, I., Gilbert, P. M., Keller, G., Tagari, P., Xu, H., Radisic, M., Zandstra, P. W. (2019). Functional Arrays of Human Pluripotent Stem Cell-Derived Cardiac Microtissues.

Afshar, M. E., Abraha, H. Y., Bakooshli, M. A., Davoudi, S., Thavandiran, N., Tung, K., Ahn, H., Ginsberg, H., Zandstra, P. W., & Gilbert, P. M. (2019). A 96-well culture platform enables longitudinal analyses of engineered human skeletal muscle microtissue strength.

Davoudi, S., Chin, C-Y., Mumtaz, A., Cooke, M. C., Tam, R. Y., Shoichet, M. S., & Gilbert, P. M. (2018). Muscle stem cell intramuscular delivery within hyaluronin methylcellulose improves engraftment efficiency and dispersion.

Bakooshli, M. A., Lippman, E. S., Mulcahy, B., Iyer, N., Nguyen, C. T., Tung, K., Stewart, B. A., van den Dorpel, H., Fuehrmann, T., Shoichet, M. S., Bigot, A., Pegoraro, E., Ahn, H., Ginsberg, H., Zhen, M., Ashton, R. S., & Gilbert, P. M. (2018). A three-dimensional culture model of innervated human skeletal muscle enables studies of the adult neuromuscular junction and disease modeling.