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Tharp KM, Park S, Timblin GA, Richards AL, Berg JA, Twells NM, Riley NM, Peltan EL, Shon DJ, Stevenson E, Tsui K, Palomba F, Lefebvre AEYT, Soens RW, Ayad NM, Hoeve-Scott JT, Healy K, Digman M, Dillin A, Bertozzi CR, Swaney DL, Mahal LK, Cantor JR, Paszek MJ, Weaver VM. The microenvironment dictates glycocalyx construction and immune surveillance. Res Sq 2023:rs.3.rs-3164966. [PMID: 37645943 PMCID: PMC10462183 DOI: 10.21203/rs.3.rs-3164966/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Efforts to identify anti-cancer therapeutics and understand tumor-immune interactions are built with in vitro models that do not match the microenvironmental characteristics of human tissues. Using in vitro models which mimic the physical properties of healthy or cancerous tissues and a physiologically relevant culture medium, we demonstrate that the chemical and physical properties of the microenvironment regulate the composition and topology of the glycocalyx. Remarkably, we find that cancer and age-related changes in the physical properties of the microenvironment are sufficient to adjust immune surveillance via the topology of the glycocalyx, a previously unknown phenomenon observable only with a physiologically relevant culture medium.
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Affiliation(s)
- Kevin M. Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14850, USA
| | - Greg A. Timblin
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alicia L. Richards
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jordan A. Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas M. Twells
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nicholas M. Riley
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Egan L. Peltan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford CA USA 94305
- Sarafan ChEM-H, Stanford University, Stanford, CA USA 94305
| | - D. Judy Shon
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kimberly Tsui
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94597, USA
| | - Francesco Palomba
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, CA 92697, USA
| | | | - Ross W. Soens
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nadia M.E. Ayad
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Johanna ten Hoeve-Scott
- UCLA Metabolomics Center, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Kevin Healy
- Department of Chemical and Systems Biology, Sarafan ChEM-H and Howard Hughes Medical Institute, Stanford University, Stanford, CA USA 94305
| | - Michelle Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, CA 92697, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94597, USA
| | - Carolyn R. Bertozzi
- Department of Chemical and Systems Biology, Sarafan ChEM-H and Howard Hughes Medical Institute, Stanford University, Stanford, CA USA 94305
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jason R. Cantor
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry and Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J. Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA 94143, USA
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Rossiter NJ, Huggler KS, Adelmann CH, Keys HR, Soens RW, Sabatini DM, Cantor JR. CRISPR screens in physiologic medium reveal conditionally essential genes in human cells. Cell Metab 2021; 33:1248-1263.e9. [PMID: 33651980 PMCID: PMC8172426 DOI: 10.1016/j.cmet.2021.02.005] [Citation(s) in RCA: 57] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/04/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022]
Abstract
Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly reflect metabolite availability in human blood. Here, we performed CRISPR-based screens in traditional versus human plasma-like medium (HPLM). Sets of conditionally essential genes in human cancer cell lines span several cellular processes and vary with both natural cell-intrinsic diversity and the combination of basal and serum components that comprise typical media. Notably, we traced the causes for each of three conditional CRISPR phenotypes to the availability of metabolites uniquely defined in HPLM versus conventional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions.
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Affiliation(s)
| | - Kimberly S Huggler
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Charles H Adelmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ross W Soens
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jason R Cantor
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA.
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Rasmussen DM, Soens RW, Davie TJ, Vaneerd CK, Bhattacharyya B, May JF. The structure of DcrB, a lipoprotein from Salmonella enterica, reveals flexibility in the N-terminal segment of the Mog1p/PsbP-like fold. J Struct Biol 2018; 204:513-518. [PMID: 30339832 PMCID: PMC9976613 DOI: 10.1016/j.jsb.2018.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/08/2018] [Accepted: 10/15/2018] [Indexed: 01/01/2023]
Abstract
DcrB is an 18 kDa lipoprotein that contains a single domain of unknown function. DcrB is found within Enterobacteriaceae, a family of Gram-negative bacteria which includes pathogens that can cause food-borne illness and hospital-acquired infections. In Salmonella enterica serovar Typhimurium, DcrB is up-regulated by conditions that promote the production of known virulence factors. We determined the structure of a truncated form of DcrB from Salmonella to 1.92 Å resolution by X-ray crystallography. This truncated form, DcrBΔ37, contains the entire domain of unknown function but lacks the lipoprotein signal sequence (residues 1-20) as well as residues 21-37. The DcrBΔ37 monomer contains the Mog1p/PsbP-like fold, which is found in functionally diverse proteins in mammals, yeast, plants, and cyanobacteria. Interestingly, DcrBΔ37 crystallized as a domain-swapped homodimer in which the N-terminal β-hairpin extends from one protomer to interact with the core of the second protomer. This domain-swapping indicates that the N-terminal portion of the Mog1p/PsbP-like fold likely has conformational flexibility. Overall, our results provide the first example of an enterobacterial protein that contains the Mog1p/PsbP-like fold and expands knowledge of the structural and phylogenetic diversity of Mog1p/PsbP-like proteins.
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Affiliation(s)
- Damien M Rasmussen
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States
| | - Ross W Soens
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States
| | - Timothy J Davie
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States
| | - Cody K Vaneerd
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States
| | - Basudeb Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States
| | - John F May
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, United States.
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