Cellular Innovation by Rational Design and Evolution

Living cells use circuits of interacting molecules to process signals, remember information, and interact in complex ways with their environments. Our laboratory is interested in creating artificial cellular systems that exceed the design and functional repertoire of nature. Through building these synthetic systems de novo, we are uncovering the design principles of natural cellular circuits and how they carry out specific biological functions. To address the most pressing human diseases, we also use these systems to program useful cellular behaviors in a broader quest to develop next-generation cellular therapeutics.

Our unique approach is to develop, and then creatively integrate, advanced forms of rational design and laboratory evolution to address problems at different levels of cellular organization. First, we develop synthetic biology frameworks to engineer and study the molecular circuits that control gene regulation in eukaryotes. We have made fundamental discoveries involving transcription circuits and epigenetic regulatory systems, and translated these discoveries into platforms for programming therapeutic human cells for personalized medicine. Second, we deepen and expand the functional repertoire of synthetic networks by creating new biomolecule components through advanced continuous evolution methods. To this end, we invented an open-source, automated continuous culture platform called eVOLVER that enables hundreds of microbial populations to be propagated in individually-controlled conditions over long time-scales. We are deploying eVOLVER to enable fundamental eco-evolutionary studies of cellular systems, and to evolve proteins with new and biomedically-useful functions at unprecedented scale.

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Design and Modular Assembly of Synthetic Intramembrane Proteolysis Receptors for Custom Gene Regulation in Therapeutic Cells
Iowis Zhu, Raymond Liu, Axel Hyrenius-Wittsten, Dan I. Piraner, Josef Alavi, Divya V. Israni, Ahmad S. Khalil and Kole T. Roybal
bioRxiv, doi: 10.1101/2021.05.21.445218

Here to Stay: Writing Lasting Epigenetic Memories (Preview)
Hagar F. Moussa*, James F. Angstman* and Ahmad S. Khalil
Cell, 184: 2281-2283 (2021)

Clinically-Driven Design of Synthetic Gene Regulatory Programs in Human Cells
Divya V. Israni*, Hui-Shan Li*, Keith A. Gagnon, Jeffry D. Sander, Kole T. Roybal, J. Keith Joung, Wilson W. Wong and Ahmad S. Khalil
bioRxiv, doi: 10.1101/2021.02.22.432371

Engineering Clinically-Approved Drug Gated CAR Circuits
Hui-Shan Li*, Nicole M. Wong*, Elliot Tague, John T. Ngo, Ahmad S. Khalil and Wilson W. Wong
bioRxiv, doi: 10.1101/2020.12.14.419812

Transcriptional Kinetic Synergy: A Complex Landscape Revealed by Integrating Modelling and Synthetic Biology
Rosa Martinez-Corral, Minhee Park, Kelly Biette, Dhana Friedrich, Clarrissa Scholes, Ahmad S. Khalil, Jeremy Gunawardena and Angela H. DePace
bioRxiv, doi: 10.1101/2020.08.31.276261

Environmental Fluctuations Reshape an Unexpected Diversity-Disturbance Relationship in a Microbial Community
Christopher P. Mancuso, Hyunseok Lee, Clare I. Abreu, Jeff Gore and Ahmad S. Khalil
eLife, 10: e67175 (2021)

A Code of Ethics for Gene Drive Research
George J. Annas, Chase L. Beisel, Kendell Clement, Andrea Crisanti, Stacy Francis, Marco Galardini, Roberto Galizi, Julian Grünewald, Greta Immobile, Ahmad S. Khalil, Ruth Müller, Vikram Pattanayak, Karl Petri, Ligi Paul, Luca Pinello, Alekos Simoni, Chrysanthi Taxiarchi and J. Keith Joung
CRISPR J, 4: 19-24 (2021)

Automated Continuous Evolution of Proteins In Vivo
Ziwei Zhong*, Brandon G. Wong*, Arjun Ravikumar, Garri A. Arzumanyan, Ahmad S. Khalil and Chang C. Liu
ACS Synthetic Biology, 9: 1270-1276 (2020)

Barcoded Microbial System for High-Resolution Object Provenance
Jason Qian*, Zhi-xiang Lu*, Christopher P. Mancuso*, Han-Ying Jhuang*, Rocío del Carmen Barajas-Ornelas*, Sarah A. Boswell*, Fernando H. Ramírez-Guadiana, Victoria Jones, Akhila Sonti, Kole Sedlack, Lior Artzi, Giyoung Jung, Mohammad Arammash, Mary E. Pettit, Michael Melfi, Lorena Lyon, Siân V. Owen, Michael Baym, Ahmad S. Khalil, Pamela A. Silver, David Z. Rudner and Michael Springer
Science, 368: 1135-1140 (2020)

Protein Assembly Systems in Natural and Synthetic Biology
Giulio Chiesa*, Szilvia Kiriakov and Ahmad S. Khalil
BMC Biology, 28: 35 (2020)

Designing Automated, High-Throughput Continuous Cell Growth Experiments Using eVOLVER
Zachary J. Heins, Christopher P. Mancuso, Szilvia Kiriakov, Brandon G. Wong, Caleb J. Bashor and Ahmad S. Khalil
Journal of Visualized Experiments, 147: e59652 (2019)

Complex Signal Processing in Synthetic Gene Circuits Using Cooperative Regulatory Assemblies
Caleb J. Bashor*, Nikit Patel*, Sandeep Choubey, Ali Beyzavi, Jane Kondev, James J. Collins and Ahmad S. Khalil
Science, 364: 593-597 (2019)

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