Publications

Hamann CA, Kjar A, Kim H, Simmons AJ, Brien HJ, Quartey CI, Walton BL, Lau KS, Lippmann ES, Brunger JM. (2025). Induced neural progenitor specification from human pluripotent stem cells by a refined synthetic Notch platform. ACS Synthetic Biology, 14(5), 1482-1495. https://doi.org/10.1021/acssynbio.4c00742

Spetz MR, Kim H, Chavarria D, Conger DJ, Shattuck-Brandt R, Shekharan SR, Shostak A, Ligocki AP, Brien HJ, Embalabala RJ, Mobley BC, Schrag MS, Lippmann ES, Brunger JM. (2025). Amyloid-β-regulated gene circuits for programmable Alzheimer’s disease therapy. bioRxiv (pre-print). https://doi.org/10.1101/2025.03.12.642808

Walton B, Shattuck-Brandt R, Hamann CA, Tung VW, Colazo JM, Brand DD, Hasty KA, Duvall CL, Brunger JM. (2025). A programmable arthritis-specific receptor for guided articular cartilage regenerative medicine. Osteoarthritis and Cartilage, 33(2), 231-240. https://doi.org/10.1016/j.joca.2024.12.002

Brien, H. J., Lee, J. C., Sharma, J., Hamann, C. A., Spetz, M. R., Lippmann, E. S., & Brunger, J. M. (2024). Templated Pluripotent Stem Cell Differentiation via Substratum-Guided Artificial Signaling. ACS biomaterials science & engineering, 10(10), 6465–6482. https://doi.org/10.1021/acsbiomaterials.4c00885

Shi, S., Hamann, C. A., Lee, J. C., & Brunger, J. M. (2024). Use of CRISPRoff and synthetic Notch to modulate and relay endogenous gene expression programs in engineered cells. Frontiers in bioengineering and biotechnology, 12, 1346810. https://doi.org/10.3389/fbioe.2024.1346810

DeJulius, C. R., Walton, B. L., Colazo, J. M., Francini, N., Brunger, J. M., & Duvall, C. L. (2024). Engineering approaches for RNA-based and cell-based osteoarthritis therapies. Nature Reviews Rheumatology, 20(2), 81-100. https://doi.org/10.1038/s41584-023-01067-4

Gil M, Hamann CA, Brunger JM, Gama V. (2024). Engineering a CRISPRoff platform to modulate expression of myeloid cell leukemia (MCL-1) in committed oligodendrocyte neural precursor cells. Bio-protocols. 14(1):e4913. https://doi.org/10.21769/BioProtoc.4913

Lee JC, Brien HJ, Walton BL, Eidman ZM, Toda S, Lim WA, Brunger JM. Instructional materials that control cellular activity through synthetic Notch receptors. Biomaterials. 2023 Jun;297:122099. doi: 10.1016/j.biomaterials.2023.122099.

Lee, J. C., Walton, B. L., Hamann, C. A., & Brunger, J. M. (2020). Synthetic regulation of multicellular systems for regenerative engineering. Current Opinion in Biomedical Engineering, 16, 42-51. https://doi.org/10.1016/j.cobme.2020.100252

Other Publications

Kim H, Kjar A, Embalabala RJ, Brunger JM, Lippmann ES. Precision targeting of C3+ reactive astrocyte subpopulations with endogenous ADAR in an iPSC-derived model. bioRxiv (pre-print). 2025.06.11.659213; doi: https://doi.org/10.1101/2025.06.11.659213. 

Yamada T, Trentesaux C, Brunger JM, Xiao Y, Stevens AJ, Martyn I, Kasparek P, Shroff NP, Aguilar A, Bruneau BG, Boffelli D, Klein OD, Lim WA. Synthetic organizer cells guide development via spatial and biochemical instructions. Cell. 2025 Feb6;188(3):778-795.e18. doi: 10.1016/j.cell.2024.11.017.

Kjar A, Haschert MR, Zepeda JC, Simmons AJ, Yates A, Chavarria D, Fernandez M, Robertson G, Abdulrahman A, Kim H, Marguerite NT, Moen RK, Drake LE, Curry CW, O’Grady BJ, Gama V, Lau KS, Grueter B, Brunger JM, Lippmann ES. Biofunctionalized gelatin hydrogels support development and maturation of iPSC-derived cortical organoids. Cell Reports. 2024 Nov 26;43(11):114874. doi: 10.1016/j.celrep.2024.114874.

Bezold, M. G., Dollinger, B. R., DeJulius, C. R., Keech, M. C., Hanna, A. R., Kittel, A. R., Yu, F., Gupta, M. K., D’Arcy, R., Brunger, J. M., & Duvall, C. L. (2025). Shear-thinning hydrogel for allograft cell transplantation and externally controlled transgene expression. Biomaterials, 314, 122812. https://doi.org/10.1016/j.biomaterials.2024.122812

Libke ML, Cunningham DJ, Furman BD, Yi JS, Brunger JM, Kraus VB, Guilak F, McNulty AL, *Olson SA. Mode of injury and level of synovitis alter inflammatory chondrocyte gene expression and associated pathways. Scientific Reports. 2024 Nov 21;14(1):28917. doi: 10.1038/s41598-024-71964-5.

Scanzello, C. R., Hasty, K. A., Chung, C. B., Griffin, T. M., Willet, N. J., Krug, H., Chu, Q., Ewart, D., Jerban, S., Baker, J. F., Duvall, C. L., Brunger, J. M., Burdick, J. A., Spindler, K. P., & Drissi, H. (2024). Teaming up to overcome challenges toward translation of new therapeutics for osteoarthritis. Journal of Orthopaedic Research®, 42(12), 2659-2672. https://doi.org/10.1002/jor.25944

Fletcher, R. B., Stokes, L. D., Kelly, I. B., 3rd, Henderson, K. M., Vallecillo-Viejo, I. C., Colazo, J. M., Wong, B. V., Yu, F., d’Arcy, R., Struthers, M. N., Evans, B. C., Ayers, J., Castanon, M., Weirich, M. J., Reilly, S. K., Patel, S. S., Ivanova, Y. I., Silvera Batista, C. A., Weiss, S. M., Gersbach, C. A., Brunger, J. M., Duvall, C. L. (2023). Nonviral In Vivo Delivery of CRISPR-Cas9 Using Protein-Agnostic, High-Loading Porous Silicon and Polymer Nanoparticles. ACS nano, 17(17), 16412–16431. https://doi.org/10.1021/acsnano.2c12261

Kim, H., Leng, K., Park, J., Sorets, A. G., Kim, S., Shostak, A., Embalabala, R. J., Mlouk, K., Katdare, K. A., Rose, I. V., Sturgeon, S. M., Neal, E. H., Ao, Y., Wang, S., Sofroniew, M. V., Brunger, J. M., McMahon, D. G., Schrag, M. S., Kampmann, M., . . . Lippmann, E. S. (2022). Reactive astrocytes transduce inflammation in a blood-brain barrier model through a TNF-STAT3 signaling axis and secretion of alpha 1-antichymotrypsin. Nature Communications, 13(1), 1-18. https://doi.org/10.1038/s41467-022-34412-4

Shi, Y., Kim, H., Hamann, C. A., Rhea, E. M., Brunger, J. M., & Lippmann, E. S. (2022). Nuclear receptor ligand screening in an iPSC-derived in vitro blood-brain barrier model identifies new contributors to leptin transport. Fluids and barriers of the CNS, 19(1), 77. https://doi.org/10.1186/s12987-022-00375-3

Huynh NP, Gloss CC, Lorentz J, Tang R, Brunger JM, McAlinden A, Zhang B, Guilak F. Long non-coding RNA GRASLND enhances chondrogenesis via suppression of interferon type II signaling pathway. Elife 2020, 9.

Toda S, Brunger JM, Lim WA: Synthetic development: learning to program multicellular self-organization. Curr Opin Syst Biol 2019, 14:41–49.

Pferdehirt L, Ross AK, Brunger JM, Guilak F. A Synthetic Gene Circuit for Self-Regulating Delivery of Biologic Drugs in Engineered Tissues. Tissue Eng Part A 2019, 25:809–820.

Huynh NPT, Brunger JM, Gloss CC, Moutos FT, Gersbach CA, Guilak F. Genetic Engineering of Mesenchymal Stem Cells for Differential Matrix Deposition  on 3D Woven Scaffolds. Tissue Eng Part A 2018, 24:1531–1544.

Brunger JM, Zutshi A, Willard VP, Gersbach CA, Guilak F. CRISPR/Cas9 Editing of Murine Induced Pluripotent Stem Cells for Engineering Inflammation-Resistant Tissues. Arthritis Rheumatol 2017, 69:1111–1121.

Brunger JM, Zutshi A, Willard VP, Gersbach CA, Guilak F. Genome Engineering of Stem Cells for Autonomously Regulated, Closed-Loop Delivery of Biologic Drugs. Stem Cell Reports 2017, 333:1307–1311.

Farhang N, Brunger JM, Stover JD, Thakore PI, Lawrence B, Guilak F, Gersbach CA, Setton LA, Bowles RD. CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments. Tissue Eng Part A 2017, doi:10.1089/ten.TEA.2016.0441.

Adkar SS, Brunger JM, Willard VP, Wu C-L, Gersbach CA, Guilak F. Genome Engineering for Personalized Arthritis Therapeutics. Trends Mol Med 2017, 23:917–931.

Diekman BO, Thakore PI, O’Connor SK, Willard VP, Brunger JM, Christoforou N, Leong KW, Gersbach CA, Guilak F. Knockdown of the cell cycle inhibitor p21 enhances cartilage formation by induced pluripotent stem cells. Tissue Eng Part A 2015, 21:1261–74.

Glass KA, Link JM, Brunger JM, Moutos FT, Gersbach CA, Guilak F. Tissue-engineered cartilage with inducible and tunable immunomodulatory properties. Biomaterials 2014, 35:5921–5931.

Brunger JM, Huynh NPT, Guenther CM, Perez-Pinera P, Moutos FT, Sanchez-Adams J, Gersbach CA, Guilak F. Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage. Proc Natl Acad Sci 2014, 111:E798–E806.

Francisco AT, Mancino RJ, Bowles RD, Brunger JM, Tainter DM, Chen Y-T, Richardson WJ, Guilak F, Setton LA. Injectable laminin-functionalized hydrogel for nucleus pulposus regeneration. Biomaterials 2013, 34:7381–7388.

Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods 2013, 10:239–242.

Abrahamsson CK, Yang F, Park H, Brunger JM, Valonen PK, Langer R, Welter JF, Caplan AI, Guilak F, Freed LE. Chondrogenesis and mineralization during in vitro culture of human mesenchymal stem cells on three-dimensional woven scaffolds. Tissue Eng Part A 2010, 16:3709–18.