1
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Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. Nature 2023; 620:651-659. [PMID: 37468627 PMCID: PMC10628994 DOI: 10.1038/s41586-023-06342-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Even among genetically identical cancer cells, resistance to therapy frequently emerges from a small subset of those cells1-7. Molecular differences in rare individual cells in the initial population enable certain cells to become resistant to therapy7-9; however, comparatively little is known about the variability in the resistance outcomes. Here we develop and apply FateMap, a framework that combines DNA barcoding with single-cell RNA sequencing, to reveal the fates of hundreds of thousands of clones exposed to anti-cancer therapies. We show that resistant clones emerging from single-cell-derived cancer cells adopt molecularly, morphologically and functionally distinct resistant types. These resistant types are largely predetermined by molecular differences between cells before drug addition and not by extrinsic factors. Changes in the dose and type of drug can switch the resistant type of an initial cell, resulting in the generation and elimination of certain resistant types. Samples from patients show evidence for the existence of these resistant types in a clinical context. We observed diversity in resistant types across several single-cell-derived cancer cell lines and cell types treated with a variety of drugs. The diversity of resistant types as a result of the variability in intrinsic cell states may be a generic feature of responses to external cues.
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Affiliation(s)
- Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Gianna T Busch
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jingxin Li
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan H Boe
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emanuelle I Grody
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Manoj Chelvanambi
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jonas Braun
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Amanpreet Kaur
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Naveen Jain
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pavithran T Ravindran
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Mellis
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karun Kiani
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mitchell E Fane
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Syeda Subia Ahmed
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Haiyin Li
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Cedric Chai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Reproductive Science, Northwestern University, Chicago, IL, USA
| | | | - Russell G Witt
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah B Johnson
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalida Wani
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Palmer MA, Nerger BA, Goodwin K, Sudhakar A, Lemke SB, Ravindran PT, Toettcher JE, Košmrlj A, Nelson CM. Stress ball morphogenesis: How the lizard builds its lung. Sci Adv 2021; 7:eabk0161. [PMID: 34936466 PMCID: PMC8694616 DOI: 10.1126/sciadv.abk0161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
The function of the lung is closely coupled to its structural anatomy, which varies greatly across vertebrates. Although architecturally simple, a complex pattern of airflow is thought to be achieved in the lizard lung due to its cavernous central lumen and honeycomb-shaped wall. We find that the wall of the lizard lung is generated from an initially smooth epithelial sheet, which is pushed through holes in a hexagonal smooth muscle meshwork by forces from fluid pressure, similar to a stress ball. Combining transcriptomics with time-lapse imaging reveals that the hexagonal meshwork self-assembles in response to circumferential and axial stresses downstream of pressure. A computational model predicts the pressure-driven changes in epithelial topology, which we probe using optogenetically driven contraction of 3D-printed engineered muscle. These results reveal the physical principles used to sculpt the unusual architecture of the lizard lung, which could be exploited as a novel strategy to engineer tissues.
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Affiliation(s)
- Michael A. Palmer
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Bryan A. Nerger
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Anvitha Sudhakar
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sandra B. Lemke
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | | | - Jared E. Toettcher
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
- Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, NJ 08544,USA
| | - Celeste M. Nelson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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3
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Hussain SS, Majumdar R, Moore GM, Narang H, Buechelmaier E, Bazil MJ, Ravindran PT, Leeman J, Li Y, Jalan M, Anderson KS, Farina A, Soni R, Mohibullah N, Hamzic E, Rong-Mullins X, Sifuentes C, Damerla RR, Viale A, Powell SN, Higginson D. Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell. Nucleic Acids Res 2021; 49:e74. [PMID: 33877327 PMCID: PMC8287935 DOI: 10.1093/nar/gkab262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.
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Affiliation(s)
- Suleman S Hussain
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Grace M Moore
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Himanshi Narang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erika S Buechelmaier
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Maximilian J Bazil
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jonathan E Leeman
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02189, USA
| | - Yi Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Anderson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Farina
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rekha Soni
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neeman Mohibullah
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edin Hamzic
- Biocomputix, Sarajevo, 71000, Bosnia and Herzegovina
| | - Xiaoqing Rong-Mullins
- Department of Biostatistics, The Ohio State University College of Public Health, Columbus, OH 43210, USA
| | | | - Rama R Damerla
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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4
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Iuliano JN, Collado JT, Gil AA, Ravindran PT, Lukacs A, Shin S, Woroniecka HA, Adamczyk K, Aramini JM, Edupuganti UR, Hall CR, Greetham GM, Sazanovich IV, Clark IP, Daryaee T, Toettcher JE, French JB, Gardner KH, Simmerling CL, Meech SR, Tonge PJ. Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. ACS Chem Biol 2020; 15:2752-2765. [PMID: 32880430 DOI: 10.1021/acschembio.0c00543] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light-oxygen-voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output domain. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding in Avena sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in a loss of the interaction between the side chain of N414 and the backbone C═O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.
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Affiliation(s)
- James N. Iuliano
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | - Agnieszka A. Gil
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Pavithran T. Ravindran
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- Department of Biophysics, Medical School, University of Pecs, Szigeti út 12, 7624 Pecs, Hungary
| | - SeungYoun Shin
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | - Katrin Adamczyk
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - James M. Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Uthama R. Edupuganti
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Ph.D. Program in Biochemistry, CUNY Graduate Center, New York, New York, United States
| | - Christopher R. Hall
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Igor V. Sazanovich
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Ian P. Clark
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, New York, 11794, United States
- Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate Center, New York, New York, United States
- Department of Chemistry and Biochemistry, City College of New York, New York, New York, United States
| | | | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, New York, 11794, United States
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5
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Gil AA, Carrasco-López C, Zhu L, Zhao EM, Ravindran PT, Wilson MZ, Goglia AG, Avalos JL, Toettcher JE. Optogenetic control of protein binding using light-switchable nanobodies. Nat Commun 2020; 11:4044. [PMID: 32792536 PMCID: PMC7426870 DOI: 10.1038/s41467-020-17836-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/13/2020] [Indexed: 12/17/2022] Open
Abstract
A growing number of optogenetic tools have been developed to reversibly control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in cells or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications including reversibly binding to endogenous intracellular targets, modulating signaling pathway activity, and controlling binding to purified protein targets in vitro. This work represents a step towards programmable photoswitchable regulation of a wide variety of target proteins.
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Affiliation(s)
- Agnieszka A Gil
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Liyuan Zhu
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | | | - Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Alexander G Goglia
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, USA.
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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6
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Ravindran PT, Wilson MZ, Jena SG, Toettcher JE. Engineering combinatorial and dynamic decoders using synthetic immediate-early genes. Commun Biol 2020; 3:436. [PMID: 32792645 PMCID: PMC7426417 DOI: 10.1038/s42003-020-01171-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Many cell- and tissue-level functions are coordinated by intracellular signaling pathways that trigger the expression of context-specific target genes. Yet the input–output relationships that link pathways to the genes they activate are incompletely understood. Mapping the pathway-decoding logic of natural target genes could also provide a basis for engineering novel signal-decoding circuits. Here we report the construction of synthetic immediate-early genes (SynIEGs), target genes of Erk signaling that implement complex, user-defined regulation and can be monitored by using live-cell biosensors to track their transcription and translation. We demonstrate the power of this approach by confirming Erk duration-sensing by FOS, elucidating how the BTG2 gene is differentially regulated by external stimuli, and designing a synthetic immediate-early gene that selectively responds to the combination of growth factor and DNA damage stimuli. SynIEGs pave the way toward engineering molecular circuits that decode signaling dynamics and combinations across a broad range of cellular contexts. Ravindran et al. report the construction of synthetic immediate-early genes (SynIEGs), target genes of the Erk signaling pathway. SynIEGs implement user-defined regulation while tracking transcription and translation. This study underscores post-transcriptional regulation in signal decoding that may be masked by analyses of RNA abundance alone.
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Affiliation(s)
- Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Department of Molecular, Cellular, and Developmental, Biology, University of California, Santa Barbara, CA, USA
| | - Siddhartha G Jena
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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7
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Abstract
Live-cell microscopy has revealed that signaling pathways carry elaborate time-varying activities. Yet, the connection between these dynamics and cellular disease has remained elusive. Recent work leverages cellular optogenetics to analyze the Ras-to-Erk transfer function in cancer cells. These analyses reveal how changes to the filtering properties of a pathway lead to the misperception of extracellular events. Overall, these studies suggest that mutations do not simply hyperactivate pathways but rather can also change their transmission properties in more subtle ways.
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Affiliation(s)
- Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Maxwell Z Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
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8
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Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell 2017; 67:757-769.e5. [PMID: 28826673 DOI: 10.1016/j.molcel.2017.07.016] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/12/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Cell signaling networks coordinate specific patterns of protein expression in response to external cues, yet the logic by which signaling pathway activity determines the eventual abundance of target proteins is complex and poorly understood. Here, we describe an approach for simultaneously controlling the Ras/Erk pathway and monitoring a target gene's transcription and protein accumulation in single live cells. We apply our approach to dissect how Erk activity is decoded by immediate early genes (IEGs). We find that IEG transcription decodes Erk dynamics through a shared band-pass filtering circuit; repeated Erk pulses transcribe IEGs more efficiently than sustained Erk inputs. However, despite highly similar transcriptional responses, each IEG exhibits dramatically different protein-level accumulation, demonstrating a high degree of post-transcriptional regulation by combinations of multiple pathways. Our results demonstrate that the Ras/Erk pathway is decoded by both dynamic filters and logic gates to shape target gene responses in a context-specific manner.
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Affiliation(s)
- Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Pavithran T Ravindran
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Wendell A Lim
- Howard Hughes Medical Institute; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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