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Shannon Sirk

Assistant Professor, Department of Bioengineering
Affiliate Professor, Microbiology

Research Description

Engineering Better Biotherapeutics

Biotherapeutic drugs have revolutionized the treatment of many diseases, leading to dramatically improved health outcomes for countless people (and pets). Historically, progress in this area has centered on protein-based drugs, most notably therapeutic monoclonal antibodies and their derivatives. In recent years, the scope of biotherapeutic development has broadened from protein-based engineering to engineering the cells themselves to serve as living therapeutics.

Our research aims to capitalize and expand on the progress and promise across the spectrum of biotherapeutic advances to address unmet needs in human health, animal health, and the environment.

Engineering living therapeutics: The human body is a complex ecosystem supporting symbiotic relationships with thousands of microbial species. By some estimates, human commensal microbial cells outnumber human cells by a factor of ten. Such symbiotic microorganisms are integral to the health and metabolism of not only humans, but also animals, insects, and plants. Commensal microbes are already perfectly suited for safe and effective colonization of various physiological niches; what remains is to engineer them to function as robust biochemical factories capable of on-site, on-demand production and delivery of therapeutic cargo. Our efforts in this area focus on genomic and metabolic engineering to direct and optimize expression and secretion of therapeutic payloads from key human commensal species in the gut and respiratory tract.

Engineering biotherapeutic cargo: In addition to engineering the microbial chassis, we also engineer the therapeutic cargo being delivered. To accommodate efficient bacterial expression, we use small antibody fragments. Compared to full-length antibodies from which they are derived, antibody fragments are much smaller, less complex, and easier for bacteria to produce and secrete. However, small fragments lack some of the functions inherent in full-length antibodies, including long serum half-life. Our efforts in this area focus on protein engineering approaches to enhance serum half-life and optimize bacterial secretion of our therapeutic payloads.



A.B. Biology, Occidental College, 2001
Ph.D. Molecular and Medical Pharmacology, University of California Los Angeles, 2009
Postdoc, Scripps Research Institute, La Jolla, 2010-2014
Postdoc, Stanford University, 2014-2017

Additional Campus Affiliations

Associate Director, Microbial Systems Initiative
Associate Member, Cancer Center at Illinois
Affiliate, Personalized Nutrition Initiative
Affiliate, Carl R. Woese Institute for Genomic Biology, Microbiome Metabolic Engineering Theme
Assistant Professor, Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine


Highlighted Publications

Short FcRn-binding peptides enable salvage and transcytosis of scFv antibody fragments, Kelly VW, and Sirk SJ. ACS Chemical Biology 17 (2), 404-413 (2022)
Living Therapeutics: The Next Frontier of Precision Medicine, Kelly VW, Liang BK, and Sirk SJ. ACS Synthetic Biology 9 (12), 3184-3201 (2020)
A metabolic pathway for activation of dietary glucosinolates by a human gut symbiont
Liou CS*, Sirk SJ*, Diaz CAC*, Klein AP, Fischer CR, Higginbottom SK, Erez A, Donia MS, Sonnenburg JL, and Sattely ES *Equal contribution. Cell 180, 717-28 (2020)
Directed evolution of targeted recombinases for genome engineering, Sirk SJ, Methods in Molecular Biology 1867, 89-102 (2018)
Genome-editing technologies: principles and applications, Gaj T, Sirk SJ, Shui S, and Liu J. Cold Spring Harbor Perspectives in Biology 12, a023754 (2016)
Protein delivery using Cys2–His2 zinc-finger domains, Gaj T, Liu J, Anderson KE, Sirk SJ, and Barbas CF. ACS Chemical Biology 9, 1662-7 (2014)
Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign, Gaj T, Sirk SJ, Tingle R, Mercer AC, Wallen MA, and Barbas CF. Journal of the American Chemical Society 136, 5047-56 (2014)
Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants,  Sirk SJ, Gaj T, Jonsson A, Mercer AC, and Barbas CF. Nucleic Acids Research 42, 4755-66 (2014)
Cell-penetrating peptide-mediated delivery of TALEN proteins via bioconjugation for genome engineering, Liu J, Gaj T, Patterson JT, Sirk SJ, and Barbas CF. PLOS ONE 9, e85755 (2014)
Expanding the scope of site‐specific recombinases for genetic and metabolic engineering, Gaj T, Sirk SJ, and Barbas CF. Biotechnology & Bioengineering 111, 1-15 (2014)
Regulation of endogenous human gene expression by ligand-inducible TALE transcription factors, Mercer AC, Gaj T, Sirk SJ, Lamb BM, and Barbas CF. ACS Synthetic Biology 3, 723-30 (2014)
Antibody conjugation approach enhances breadth and potency of neutralization of anti-HIV-1 antibodies and CD4-IgG, Gavrilyuk J, Ban H, Uehara H, Sirk SJ, Saye-Francisco K, Cuevas A, Zablowsky E, Oza A, Seaman MS, Burton DR, and Barbas CF. Journal of Virology 87, 4985-93 (2013)
A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells, Gaj T, Mercer AC, Sirk SJ, Smith HL, and Barbas CF. Nucleic Acids Research 41, 3937-46 (2013)
Targeted gene knockout by direct delivery of zinc-finger nuclease proteins, Gaj T, Guo J, Kato Y, Sirk SJ, and Barbas CF. Nature Methods 9, 805-7 (2012)
ImmunoPET using engineered antibody fragments: fluorine-18 labeled diabodies for same-day imaging, Olafsen T, Sirk SJ, Olma S, Shen CKF, and Wu AM. Tumor Biology 33, 669-77 (2012)
Microfluidic-based 18F-Labeling of biomolecules for immuno–positron emission tomography, Liu K, Lepin EJ, Wang MW, Guo F, Lin WY, Chen YC, Sirk SJ, Olma S, Phelps ME, Zhao XZ, Tseng HR, van Dam RM, Wu AM, and Shen CKF. Molecular Imaging 10, 168-76 (2011)
ImmunoPET imaging of B-cell lymphoma using 124I-anti-CD20 scFv dimers (diabodies), Olafsen T, Sirk SJ, Betting DJ, Kenanova VE, Bauer KB, Ladno W, Raubitschek AA, Timmerman JM, and Wu AM. Protein Engineering, Design & Selection 23, 243-249 (2010)
Cys-diabody quantum dot conjugates (immunoQdots) for cancer marker detection, Barat B, Sirk SJ, McCabe KE, Li J, Lepin EJ, Remenyi R, Koh AL, Olafsen T, Gambhir SS, Weiss S, and Wu AM. Bioconjugate Chemistry 20, 1474-81 (2009)
Site-specific, thiol-mediated conjugation of fluorescent probes to cysteine-modified diabodies targeting CD20 or HER2, Sirk SJ, Olafsen T, Barat B, Bauer KB, and Wu AM. Bioconjugate Chemistry 19, 2527-34 (2008)
Measurement of amphotericin B concentration by resonant Raman spectroscopy – a novel technique that may be useful for non-invasive monitoring, La Via WV, Lambert JL, Pelletier MJ, Morookian JM, Sirk SJ, Mickiene D, Walsh TJ, and Borchert MS. Medical Mycology 44, 169-74 (2006)
Measurement of aqueous glucose in a model anterior chamber using Raman spectroscopy, Lambert JL, Morookian JM, Sirk SJ, and Borchert MS. Journal of Raman Spectroscopy 33, 524-29 (2002)

Recent Publications

Kelly, V. W., & Sirk, S. J. (2022). Short FcRn-Binding Peptides Enable Salvage and Transcytosis of scFv Antibody Fragments. ACS chemical biology, 17(2), 404-413.

Kelly, V. W., Liang, B. K., & Sirk, S. J. (2020). Living Therapeutics: The Next Frontier of Precision Medicine. ACS synthetic biology, 9(12), 3184-3201.

Liou, C. S., Sirk, S. J., Diaz, C. A. C., Klein, A. P., Fischer, C. R., Higginbottom, S. K., Erez, A., Donia, M. S., Sonnenburg, J. L., & Sattely, E. S. (2020). A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont. Cell, 180(4), 717-728.e19.

Sirk, S. J. (2018). Directed evolution of targeted recombinases for genome engineering. In Methods in Molecular Biology (pp. 89-102). (Methods in Molecular Biology; Vol. 1867). Humana Press Inc..

Gaj, T., Sirk, S. J., Shui, S. L., & Liu, J. (2016). Genome-editing technologies: Principles and applications. Cold Spring Harbor Perspectives in Biology, 8(12), Article a023754.

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