1
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Puumala E, Sychantha D, Lach E, Reeves S, Nabeela S, Fogal M, Nigam A, Johnson JW, Aspuru-Guzik A, Shapiro RS, Uppuluri P, Kalyaanamoorthy S, Magolan J, Whitesell L, Robbins N, Wright GD, Cowen LE. Allosteric inhibition of tRNA synthetase Gln4 by N-pyrimidinyl-β-thiophenylacrylamides exerts highly selective antifungal activity. Cell Chem Biol 2024; 31:760-775.e17. [PMID: 38402621 PMCID: PMC11031294 DOI: 10.1016/j.chembiol.2024.01.010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/19/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Candida species are among the most prevalent causes of systemic fungal infections, which account for ∼1.5 million annual fatalities. Here, we build on a compound screen that identified the molecule N-pyrimidinyl-β-thiophenylacrylamide (NP-BTA), which strongly inhibits Candida albicans growth. NP-BTA was hypothesized to target C. albicans glutaminyl-tRNA synthetase, Gln4. Here, we confirmed through in vitro amino-acylation assays NP-BTA is a potent inhibitor of Gln4, and we defined how NP-BTA arrests Gln4's transferase activity using co-crystallography. This analysis also uncovered Met496 as a critical residue for the compound's species-selective target engagement and potency. Structure-activity relationship (SAR) studies demonstrated the NP-BTA scaffold is subject to oxidative and non-oxidative metabolism, making it unsuitable for systemic administration. In a mouse dermatomycosis model, however, topical application of the compound provided significant therapeutic benefit. This work expands the repertoire of antifungal protein synthesis target mechanisms and provides a path to develop Gln4 inhibitors.
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Affiliation(s)
- Emily Puumala
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Sychantha
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Elizabeth Lach
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shawn Reeves
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sunna Nabeela
- Division of Infectious Diseases, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA
| | - Meea Fogal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - AkshatKumar Nigam
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jarrod W Johnson
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto Toronto, ON M5S 3H6, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada; Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4, Canada; Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada; Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada; Acceleration Consortium, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Priya Uppuluri
- Division of Infectious Diseases, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | | | - Jakob Magolan
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Maroc L, Shaker H, Shapiro RS. Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces ( Candida) glabrata via a novel CRISPR activation system. mSphere 2024; 9:e0076123. [PMID: 38265239 PMCID: PMC10900893 DOI: 10.1128/msphere.00761-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
The overexpression of genes frequently arises in Nakaseomyces (formerly Candida) glabrata via gain-of-function mutations, gene duplication, or aneuploidies, with important consequences on pathogenesis traits and antifungal drug resistance. This highlights the need to develop specific genetic tools to mimic and study genetic amplification in this important fungal pathogen. Here, we report the development, validation, and applications of the first clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) system in N. glabrata for targeted genetic overexpression. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in N. glabrata, and further assess optimal guide RNA targeting for robust overexpression. We demonstrate the applications of CRISPRa to overexpress genes involved in fungal pathogenesis and drug resistance and detect corresponding phenotypic alterations in these key traits, including the characterization of novel phenotypes. Finally, we capture strain variation using our CRISPRa system in two commonly used N. glabrata genetic backgrounds. Together, this tool will expand our capacity for functional genetic overexpression in this pathogen, with numerous possibilities for future applications.IMPORTANCENakaseomyces (formerly Candida) glabrata is an important fungal pathogen that is now the second leading cause of candidiasis infections. A common strategy that this pathogen employs to resist antifungal treatment is through the upregulation of gene expression, but we have limited tools available to study this phenomenon. Here, we develop, optimize, and apply the use of CRISPRa as a means to overexpress genes in N. glabrata. We demonstrate the utility of this system to overexpress key genes involved in antifungal susceptibility, stress tolerance, and biofilm growth. This tool will be an important contribution to our ability to study the biology of this important fungal pathogen.
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Affiliation(s)
- Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Hajer Shaker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
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3
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Librais GMN, Jiang Y, Razzaq I, Brandl CJ, Shapiro RS, Lajoie P. Evolutionary diversity of the control of the azole response by Tra1 across yeast species. G3 (Bethesda) 2024; 14:jkad250. [PMID: 37889998 PMCID: PMC10849324 DOI: 10.1093/g3journal/jkad250] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/16/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
Tra1 is an essential coactivator protein of the yeast SAGA and NuA4 acetyltransferase complexes that regulate gene expression through multiple mechanisms including the acetylation of histone proteins. Tra1 is a pseudokinase of the PIKK family characterized by a C-terminal PI3K domain with no known kinase activity. However, mutations of specific arginine residues to glutamine in the PI3K domains (an allele termed tra1Q3) result in reduced growth and increased sensitivity to multiple stresses. In the opportunistic fungal pathogen Candida albicans, the tra1Q3 allele reduces pathogenicity and increases sensitivity to the echinocandin antifungal drug caspofungin, which disrupts the fungal cell wall. Here, we found that compromised Tra1 function, in contrast to what is seen with caspofungin, increases tolerance to the azole class of antifungal drugs, which inhibits ergosterol synthesis. In C. albicans, tra1Q3 increases the expression of genes linked to azole resistance, such as ERG11 and CDR1. CDR1 encodes a multidrug ABC transporter associated with efflux of multiple xenobiotics, including azoles. Consequently, cells carrying tra1Q3 show reduced intracellular accumulation of fluconazole. In contrast, a tra1Q3 Saccharomyces cerevisiae strain displayed opposite phenotypes: decreased tolerance to azole, decreased expression of the efflux pump PDR5, and increased intracellular accumulation of fluconazole. Therefore, our data provide evidence that Tra1 differentially regulates the antifungal response across yeast species.
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Affiliation(s)
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Iqra Razzaq
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
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4
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Shapiro RS. Unearthing the story of the first antifungal drugs. Nat Rev Microbiol 2023; 21:631. [PMID: 37700051 DOI: 10.1038/s41579-023-00937-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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Shapiro RS, Gerstein AC. Powering up antifungal treatment: using small molecules to unlock the potential of existing therapies. mBio 2023; 14:e0107323. [PMID: 37530533 PMCID: PMC10470729 DOI: 10.1128/mbio.01073-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/22/2023] [Indexed: 08/03/2023] Open
Abstract
Fungal pathogens are increasingly appreciated as a significant infectious disease challenge. Compared to bacteria, fungal cells are more closely related to human cells, and few classes of antifungal drugs are available. Combination therapy offers a potential solution to reduce the likelihood of resistance acquisition and extend the lifespan of existing antifungals. There has been recent interest in combining first-line drugs with small-molecule adjuvants. In a recent article, Alabi et al. identified 1,4-benzodiazepines as promising molecules to enhance azole activity in pathogenic Candida spp. (P. E. Alabi, C. Gautier, T. P. Murphy, X. Gu, M. Lepas, V. Aimanianda, J. K. Sello, I. V. Ene, 2023, mBio https://doi.org/10.1128/mbio.00479-23). These molecules have no antifungal activity on their own but exhibited significant potentiation of fluconazole in azole-susceptible and -resistant isolates. Additionally, the 1,4-benzodiazepines increased the fungicidal activity of azoles that are typically fungistatic to Candida spp., inhibited filamentation (a virulence-associated trait), and accordingly increased host survival in Galleria mellonella. This research thus provides another encouraging step on the critical pathway toward reducing mortality due to antimicrobial resistance.
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Affiliation(s)
- Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Aleeza C. Gerstein
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
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6
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Rathie B, Theelen B, Laurence M, Shapiro RS. Antimicrobial Susceptibility Testing for Three Malassezia Species. Microbiol Spectr 2023; 11:e0507622. [PMID: 37310217 PMCID: PMC10433853 DOI: 10.1128/spectrum.05076-22] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
The Malassezia genus comprises lipid-dependent yeasts that have long been associated with common skin diseases, and have recently been linked with Crohn's disease and certain cancers. Understanding Malassezia susceptibility to diverse antimicrobial agents is crucial for identifying effective antifungal therapies. Here, we tested the efficacy of isavuconazole, itraconazole, terbinafine, and artemisinin against three Malassezia species: M. restricta, M. slooffiae, and M. sympodialis. Using broth microdilution, we found antifungal properties for the two previously unstudied antimicrobials: isavuconazole and artemisinin. Overall, all Malassezia species were particularly susceptible to itraconazole, with a MIC range from 0.007 to 0.110 μg/mL. IMPORTANCE The Malassezia genus is known to be involved in a variety of skin conditions and has recently been associated with diseases such as Crohn's disease, pancreatic ductal carcinoma, and breast cancer. This work was completed to assess susceptibility to a variety of antimicrobial drugs on three Malassezia species, in particular Malassezia restricta, which is an abundant Malassezia species both on human skin and internal organs and has been implicated in Crohn's disease. We tested two previously unstudied drugs and developed a new testing method to overcome current limitations for measuring growth inhibition of slow-growing Malassezia strains.
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Affiliation(s)
- Brooke Rathie
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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7
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Iyer KR, Li SC, Revie NM, Lou JW, Duncan D, Fallah S, Sanchez H, Skulska I, Ušaj MM, Safizadeh H, Larsen B, Wong C, Aman A, Kiyota T, Yoshimura M, Kimura H, Hirano H, Yoshida M, Osada H, Gingras AC, Andes DR, Shapiro RS, Robbins N, Mazhab-Jafari MT, Whitesell L, Yashiroda Y, Boone C, Cowen LE. Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad-spectrum activity. Cell Chem Biol 2023; 30:795-810.e8. [PMID: 37369212 PMCID: PMC11016341 DOI: 10.1016/j.chembiol.2023.06.005] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 04/17/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
Rising drug resistance among pathogenic fungi, paired with a limited antifungal arsenal, poses an increasing threat to human health. To identify antifungal compounds, we screened the RIKEN natural product depository against representative isolates of four major human fungal pathogens. This screen identified NPD6433, a triazenyl indole with broad-spectrum activity against all screening strains, as well as the filamentous mold Aspergillus fumigatus. Mechanistic studies indicated that NPD6433 targets the enoyl reductase domain of fatty acid synthase 1 (Fas1), covalently inhibiting its flavin mononucleotide-dependent NADPH-oxidation activity and arresting essential fatty acid biosynthesis. Robust Fas1 inhibition kills Candida albicans, while sublethal inhibition impairs diverse virulence traits. At well-tolerated exposures, NPD6433 extended the lifespan of nematodes infected with azole-resistant C. albicans. Overall, identification of NPD6433 provides a tool with which to explore lipid homeostasis as a therapeutic target in pathogenic fungi and reveals a mechanism by which Fas1 function can be inhibited.
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Affiliation(s)
- Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sheena C Li
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Dustin Duncan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sara Fallah
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Iwona Skulska
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Mojca Mattiazzi Ušaj
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada
| | - Hamid Safizadeh
- Department of Computer Science and Engineering and Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Brett Larsen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Cassandra Wong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mami Yoshimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiromi Kimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | | | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA; Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada; RIKEN Center for Sustainable Resource Science, Wako, Japan.
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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8
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La Bella AA, Andersen MJ, Gervais NC, Molina JJ, Molesan A, Stuckey PV, Wensing L, Nobile CJ, Shapiro RS, Santiago-Tirado FH, Flores-Mireles AL. The catheterized bladder environment promotes Efg1- and Als1-dependent Candida albicans infection. Sci Adv 2023; 9:eade7689. [PMID: 36867691 PMCID: PMC9984171 DOI: 10.1126/sciadv.ade7689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Catheter-associated urinary tract infections (CAUTIs) account for 40% of hospital-acquired infections (HAIs). As 20 to 50% of hospitalized patients receive catheters, CAUTIs are one of the most common HAIs, resulting in increased morbidity, mortality, and health care costs. Candida albicans is the second most common CAUTI uropathogen, yet relative to its bacterial counterparts, little is known about how fungal CAUTIs are established. Here, we show that the catheterized bladder environment induces Efg1- and fibrinogen (Fg)-dependent biofilm formation that results in CAUTI. In addition, we identify the adhesin Als1 as the critical fungal factor for C. albicans Fg-urine biofilm formation. Furthermore, we show that in the catheterized bladder, a dynamic and open system, both filamentation and attachment are required, but each by themselves are not sufficient for infection. Our study unveils the mechanisms required for fungal CAUTI establishment, which may aid in the development of future therapies to prevent these infections.
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Affiliation(s)
- Alyssa Ann La Bella
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Nicholas C. Gervais
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | - Alex Molesan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Peter V. Stuckey
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA, USA
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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9
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Gervais NC, La Bella AA, Wensing LF, Sharma J, Acquaviva V, Best M, Cadena López RO, Fogal M, Uthayakumar D, Chavez A, Santiago-Tirado F, Flores-Mireles AL, Shapiro RS. Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans. G3 (Bethesda) 2023; 13:jkac301. [PMID: 36450451 PMCID: PMC9911074 DOI: 10.1093/g3journal/jkac301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/02/2021] [Accepted: 11/04/2022] [Indexed: 12/02/2022]
Abstract
For the fungal pathogen Candida albicans, genetic overexpression readily occurs via a diversity of genomic alterations, such as aneuploidy and gain-of-function mutations, with important consequences for host adaptation, virulence, and evolution of antifungal drug resistance. Given the important role of overexpression on C. albicans biology, it is critical to develop and harness tools that enable the analysis of genes expressed at high levels in the fungal cell. Here, we describe the development, optimization, and application of a novel, single-plasmid-based CRISPR activation (CRISPRa) platform for targeted genetic overexpression in C. albicans, which employs a guide RNA to target an activator complex to the promoter region of a gene of interest, thus driving transcriptional expression of that gene. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in C. albicans, and we assess optimal guide RNA targeting for robust and constitutive overexpression. We further demonstrate the specificity of the system via RNA sequencing. We highlight the application of CRISPR activation to overexpress genes involved in pathogenesis and drug susceptibility, and contribute toward the identification of novel phenotypes. Consequently, this tool will facilitate a broad range of applications for the study of C. albicans genetic overexpression.
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Affiliation(s)
- Nicholas C Gervais
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Alyssa A La Bella
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lauren F Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Victoria Acquaviva
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Madison Best
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | | | - Meea Fogal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
- Present address: Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Ana L Flores-Mireles
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
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10
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Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda) 2022; 12:jkac224. [PMID: 36179219 PMCID: PMC9635647 DOI: 10.1093/g3journal/jkac224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/12/2022] [Indexed: 01/13/2023]
Abstract
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.
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Affiliation(s)
- Nicola T Case
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Iuliana V Ene
- Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK
| | | | - Aleeza C Gerstein
- Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Neil A R Gow
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Iliyan D Iliev
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Bruce S Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | | | - Aaron P Mitchell
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Donald C Sheppard
- McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Eva E Stukenbrock
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA
| | | | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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11
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Cochrane RR, Shrestha A, Severo de Almeida MM, Agyare-Tabbi M, Brumwell SL, Hamadache S, Meaney JS, Nucifora DP, Say HH, Sharma J, Soltysiak MPM, Tong C, Van Belois K, Walker EJL, Lachance MA, Gloor GB, Edgell DR, Shapiro RS, Karas BJ. Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi. Biodes Res 2022; 2022:9802168. [PMID: 37850145 PMCID: PMC10521675 DOI: 10.34133/2022/9802168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/28/2022] [Indexed: 10/19/2023] Open
Abstract
Fungi are nature's recyclers, allowing for ecological nutrient cycling and, in turn, the continuation of life on Earth. Some fungi inhabit the human microbiome where they can provide health benefits, while others are opportunistic pathogens that can cause disease. Yeasts, members of the fungal kingdom, have been domesticated by humans for the production of beer, bread, and, recently, medicine and chemicals. Still, the great untapped potential exists within the diverse fungal kingdom. However, many yeasts are intractable, preventing their use in biotechnology or in the development of novel treatments for pathogenic fungi. Therefore, as a first step for the domestication of new fungi, an efficient DNA delivery method needs to be developed. Here, we report the creation of superior conjugative plasmids and demonstrate their transfer via conjugation from bacteria to 7 diverse yeast species including the emerging pathogen Candida auris. To create our superior plasmids, derivatives of the 57 kb conjugative plasmid pTA-Mob 2.0 were built using designed gene deletions and insertions, as well as some unintentional mutations. Specifically, a cluster mutation in the promoter of the conjugative gene traJ had the most significant effect on improving conjugation to yeasts. In addition, we created Golden Gate assembly-compatible plasmid derivatives that allow for the generation of custom plasmids to enable the rapid insertion of designer genetic cassettes. Finally, we demonstrated that designer conjugative plasmids harboring engineered restriction endonucleases can be used as a novel antifungal agent, with important applications for the development of next-generation antifungal therapeutics.
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Affiliation(s)
- Ryan R. Cochrane
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Arina Shrestha
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Mariana M. Severo de Almeida
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Michelle Agyare-Tabbi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Stephanie L. Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Samir Hamadache
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Jordyn S. Meaney
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Daniel P. Nucifora
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Henry Heng Say
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | | | - Cheryl Tong
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Katherine Van Belois
- Department of Biology, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Emma J. L. Walker
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Marc-André Lachance
- Department of Biology, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Gregory B. Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - David R. Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Bogumil J. Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada, N6A 5C1
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12
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Sharma J, Shapiro RS. Mucin modulates microbial morphogenesis. Nat Chem Biol 2022; 18:684-686. [PMID: 35668190 DOI: 10.1038/s41589-022-01053-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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13
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Revie NM, Iyer KR, Maxson ME, Zhang J, Yan S, Fernandes CM, Meyer KJ, Chen X, Skulska I, Fogal M, Sanchez H, Hossain S, Li S, Yashiroda Y, Hirano H, Yoshida M, Osada H, Boone C, Shapiro RS, Andes DR, Wright GD, Nodwell JR, Del Poeta M, Burke MD, Whitesell L, Robbins N, Cowen LE. Targeting fungal membrane homeostasis with imidazopyrazoindoles impairs azole resistance and biofilm formation. Nat Commun 2022; 13:3634. [PMID: 35752611 PMCID: PMC9233667 DOI: 10.1038/s41467-022-31308-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 08/09/2021] [Accepted: 06/14/2022] [Indexed: 11/23/2022] Open
Abstract
Fungal infections cause more than 1.5 million deaths annually. With an increase in immune-deficient susceptible populations and the emergence of antifungal drug resistance, there is an urgent need for novel strategies to combat these life-threatening infections. Here, we use a combinatorial screening approach to identify an imidazopyrazoindole, NPD827, that synergizes with fluconazole against azole-sensitive and -resistant isolates of Candida albicans. NPD827 interacts with sterols, resulting in profound effects on fungal membrane homeostasis and induction of membrane-associated stress responses. The compound impairs virulence in a Caenorhabditis elegans model of candidiasis, blocks C. albicans filamentation in vitro, and prevents biofilm formation in a rat model of catheter infection by C. albicans. Collectively, this work identifies an imidazopyrazoindole scaffold with a non-protein-targeted mode of action that re-sensitizes the leading human fungal pathogen, C. albicans, to azole antifungals.
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Affiliation(s)
- Nicole M Revie
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michelle E Maxson
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jiabao Zhang
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Su Yan
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Caroline M Fernandes
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Kirsten J Meyer
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Xuefei Chen
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Iwona Skulska
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Meea Fogal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Saif Hossain
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sheena Li
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Hirano
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON, Canada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Gerard D Wright
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
- Division of Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
- Veteran Administration Medical Center, Northport, NY, USA
| | - Martin D Burke
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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14
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Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X. High-content CRISPR screening. Nat Rev Methods Primers 2022; 2:9. [PMID: 37214176 PMCID: PMC10200264 DOI: 10.1038/s43586-022-00098-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development - with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen.
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Affiliation(s)
- Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florence Chardon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Matthew B. Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Keith A. Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thomas M. Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Geoff Stanley
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Mathew Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
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15
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Wensing L, Shapiro RS. Design and Generation of a CRISPR Interference System for Genetic Repression and Essential Gene Analysis in the Fungal Pathogen Candida albicans. Methods Mol Biol 2022; 2377:69-88. [PMID: 34709611 DOI: 10.1007/978-1-0716-1720-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Studying life-threatening fungal pathogens such as Candida albicans is of critical importance, yet progress can be hindered by challenges associated with manipulating these pathogens genetically. CRISPR-based technologies have significantly improved our ability to manipulate the genomes of countless organisms, including fungal pathogens such as C. albicans. CRISPR interference (CRISPRi) is a modified variation of CRISPR technology that enables the targeted genetic repression of specific genes of interest and can be used as a technique for studying essential genes. We recently developed tools to enable CRISPRi in C. albicans and the repression of essential genes in this fungus. Here, we describe a protocol for CRISPRi in C. albicans, including the design of the single-guide RNAs (sgRNAs) for targeting essential genes, the high-efficiency cloning of sgRNAs into C. albicans-optimized CRISPRi plasmids, transformation into fungal strains, and testing to monitor the repression capabilities of these constructs. Together, this protocol will illuminate efficient strategies for targeted genetic repression of essential genes in C. albicans using a novel CRISPRi platform.
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Affiliation(s)
- Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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16
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Gervais NC, Halder V, Shapiro RS. A data library of Candida albicans functional genomic screens. FEMS Yeast Res 2021; 21:6433625. [PMID: 34864983 DOI: 10.1093/femsyr/foab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/30/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Functional genomic screening of genetic mutant libraries enables the characterization of gene function in diverse organisms. For the fungal pathogen Candida albicans, several genetic mutant libraries have been generated and screened for diverse phenotypes, including tolerance to environmental stressors and antifungal drugs, and pathogenic traits such as cellular morphogenesis, biofilm formation and host-pathogen interactions. Here, we compile and organize C. albicans functional genomic screening data from ∼400 screens, to generate a data library of genetic mutant strains analyzed under diverse conditions. For quantitative screening data, we normalized these results to enable quantitative and comparative analysis of different genes across different phenotypes. Together, this provides a unique C. albicans genetic database, summarizing abundant phenotypic data from functional genomic screens in this critical fungal pathogen.
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Affiliation(s)
- Nicholas C Gervais
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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17
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Uthayakumar D, Sharma J, Wensing L, Shapiro RS. CRISPR-Based Genetic Manipulation of Candida Species: Historical Perspectives and Current Approaches. Front Genome Ed 2021; 2:606281. [PMID: 34713231 PMCID: PMC8525362 DOI: 10.3389/fgeed.2020.606281] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022] Open
Abstract
The Candida genus encompasses a diverse group of ascomycete fungi that have captured the attention of the scientific community, due to both their role in pathogenesis and emerging applications in biotechnology; the development of gene editing tools such as CRISPR, to analyze fungal genetics and perform functional genomic studies in these organisms, is essential to fully understand and exploit this genus, to further advance antifungal drug discovery and industrial value. However, genetic manipulation of Candida species has been met with several distinctive barriers to progress, such as unconventional codon usage in some species, as well as the absence of a complete sexual cycle in its diploid members. Despite these challenges, the last few decades have witnessed an expansion of the Candida genetic toolbox, allowing for diverse genome editing applications that range from introducing a single point mutation to generating large-scale mutant libraries for functional genomic studies. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is among the most recent of these advancements, bringing unparalleled versatility and precision to genetic manipulation of Candida species. Since its initial applications in Candida albicans, CRISPR-Cas9 platforms are rapidly evolving to permit efficient gene editing in other members of the genus. The technology has proven useful in elucidating the pathogenesis and host-pathogen interactions of medically relevant Candida species, and has led to novel insights on antifungal drug susceptibility and resistance, as well as innovative treatment strategies. CRISPR-Cas9 tools have also been exploited to uncover potential applications of Candida species in industrial contexts. This review is intended to provide a historical overview of genetic approaches used to study the Candida genus and to discuss the state of the art of CRISPR-based genetic manipulation of Candida species, highlighting its contributions to deciphering the biology of this genus, as well as providing perspectives for the future of Candida genetics.
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Affiliation(s)
- Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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18
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Razzaq I, Berg MD, Jiang Y, Genereaux J, Uthayakumar D, Kim GH, Agyare-Tabbi M, Halder V, Brandl CJ, Lajoie P, Shapiro RS. The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis. Genetics 2021; 219:iyab131. [PMID: 34849885 PMCID: PMC8633099 DOI: 10.1093/genetics/iyab131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/29/2021] [Accepted: 08/02/2021] [Indexed: 11/14/2022] Open
Abstract
Candida albicans is the most common cause of death from fungal infections. The emergence of resistant strains reducing the efficacy of first-line therapy with echinocandins, such as caspofungin calls for the identification of alternative therapeutic strategies. Tra1 is an essential component of the SAGA and NuA4 transcriptional co-activator complexes. As a PIKK family member, Tra1 is characterized by a C-terminal phosphoinositide 3-kinase domain. In Saccharomyces cerevisiae, the assembly and function of SAGA and NuA4 are compromised by a Tra1 variant (Tra1Q3) with three arginine residues in the putative ATP-binding cleft changed to glutamine. Whole transcriptome analysis of the S. cerevisiae tra1Q3 strain highlights Tra1's role in global transcription, stress response, and cell wall integrity. As a result, tra1Q3 increases susceptibility to multiple stressors, including caspofungin. Moreover, the same tra1Q3 allele in the pathogenic yeast C. albicans causes similar phenotypes, suggesting that Tra1 broadly mediates the antifungal response across yeast species. Transcriptional profiling in C. albicans identified 68 genes that were differentially expressed when the tra1Q3 strain was treated with caspofungin, as compared to gene expression changes induced by either tra1Q3 or caspofungin alone. Included in this set were genes involved in cell wall maintenance, adhesion, and filamentous growth. Indeed, the tra1Q3 allele reduces filamentation and other pathogenesis traits in C. albicans. Thus, Tra1 emerges as a promising therapeutic target for fungal infections.
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Affiliation(s)
- Iqra Razzaq
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Grace H Kim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Michelle Agyare-Tabbi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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19
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Abstract
Candida albicans is an opportunistic fungal pathogen and a model organism to study fungal pathogenesis. It exists as a harmless commensal organism and member of the healthy human microbiome, but can cause life-threatening mucosal and systemic infections. A model host to study C. albicans infection and pathogenesis is the nematode Caenorhabditis elegans. C. elegans is frequently used as a model host to study microbial-host interactions because it can be infected by many human pathogens and there are also close morphological resemblances between the intestinal cells of C. elegans and mammals, where C. albicans infections can occur. This article outlines a detailed methodology for exploiting C. elegans as a host to study C. albicans infection, including a C. elegans egg preparation protocol and an agar-based C. elegans killing protocol to monitor fungal virulence. These protocols can additionally be used to study C. albicans genetic mutants in order to further our understanding of the genes involved in pathogenesis and virulence in C. albicans and the mechanisms of host-microbe interactions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Caenorhabditis elegans eggs Support Protocol 1: Freezing and recovering Caenorhabditis elegans Support Protocol 2: Making superfood agar and OP50 plates Basic Protocol 2: Caenorhabditis elegans/Candida albicans agar killing assay Support Protocol 3: Constructing a worm pick.
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Affiliation(s)
- Grace H Kim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sierra Rosiana
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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20
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Halder V, McDonnell B, Uthayakumar D, Usher J, Shapiro RS. Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility and host interactions. FEMS Microbiol Rev 2021; 45:fuaa055. [PMID: 33145589 DOI: 10.1093/femsre/fuaa055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
Genetic interaction (GI) analysis is a powerful genetic strategy that analyzes the fitness and phenotypes of single- and double-gene mutant cells in order to dissect the epistatic interactions between genes, categorize genes into biological pathways, and characterize genes of unknown function. GI analysis has been extensively employed in model organisms for foundational, systems-level assessment of the epistatic interactions between genes. More recently, GI analysis has been applied to microbial pathogens and has been instrumental for the study of clinically important infectious organisms. Here, we review recent advances in systems-level GI analysis of diverse microbial pathogens, including bacterial and fungal species. We focus on important applications of GI analysis across pathogens, including GI analysis as a means to decipher complex genetic networks regulating microbial virulence, antimicrobial drug resistance and host-pathogen dynamics, and GI analysis as an approach to uncover novel targets for combination antimicrobial therapeutics. Together, this review bridges our understanding of GI analysis and complex genetic networks, with applications to diverse microbial pathogens, to further our understanding of virulence, the use of antimicrobial therapeutics and host-pathogen interactions. .
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Brianna McDonnell
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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21
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Rosiana S, Zhang L, Kim GH, Revtovich AV, Uthayakumar D, Sukumaran A, Geddes-McAlister J, Kirienko NV, Shapiro RS. Comprehensive genetic analysis of adhesin proteins and their role in virulence of Candida albicans. Genetics 2021; 217:iyab003. [PMID: 33724419 PMCID: PMC8045720 DOI: 10.1093/genetics/iyab003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022] Open
Abstract
Candida albicans is a microbial fungus that exists as a commensal member of the human microbiome and an opportunistic pathogen. Cell surface-associated adhesin proteins play a crucial role in C. albicans' ability to undergo cellular morphogenesis, develop robust biofilms, colonize, and cause infection in a host. However, a comprehensive analysis of the role and relationships between these adhesins has not been explored. We previously established a CRISPR-based platform for efficient generation of single- and double-gene deletions in C. albicans, which was used to construct a library of 144 mutants, comprising 12 unique adhesin genes deleted singly, and every possible combination of double deletions. Here, we exploit this adhesin mutant library to explore the role of adhesin proteins in C. albicans virulence. We perform a comprehensive, high-throughput screen of this library, using Caenorhabditis elegans as a simplified model host system, which identified mutants critical for virulence and significant genetic interactions. We perform follow-up analysis to assess the ability of high- and low-virulence strains to undergo cellular morphogenesis and form biofilms in vitro, as well as to colonize the C. elegans host. We further perform genetic interaction analysis to identify novel significant negative genetic interactions between adhesin mutants, whereby combinatorial perturbation of these genes significantly impairs virulence, more than expected based on virulence of the single mutant constituent strains. Together, this study yields important new insight into the role of adhesins, singly and in combinations, in mediating diverse facets of virulence of this critical fungal pathogen.
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Affiliation(s)
- Sierra Rosiana
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | - Liyang Zhang
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Grace H Kim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | | | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
| | | | | | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON NIG 2W1, Canada
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22
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Horianopoulos LC, Gluck-Thaler E, Benoit Gelber I, Cowen LE, Geddes-McAlister J, Landry CR, Schwartz IS, Scott JA, Sellam A, Sheppard DC, Spribille T, Subramaniam R, Walker AK, Harris SD, Shapiro RS, Gerstein AC. The Canadian Fungal Research Network: current challenges and future opportunities. Can J Microbiol 2020; 67:13-22. [PMID: 32717148 DOI: 10.1139/cjm-2020-0263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungi critically impact the health and function of global ecosystems and economies. In Canada, fungal researchers often work within silos defined by subdiscipline and institutional type, complicating the collaborations necessary to understand the impacts fungi have on the environment, economy, and plant and animal health. Here, we announce the establishment of the Canadian Fungal Research Network (CanFunNet, https://fungalresearch.ca), whose mission is to strengthen and promote fungal research in Canada by facilitating dialogue among scientists. We summarize the challenges and opportunities for Canadian fungal research that were discussed at CanFunNet's inaugural meeting in 2019, and identify 4 priorities for our community: (i) increasing collaboration among scientists, (ii) studying diversity in the context of ecological disturbance, (iii) preserving culture collections in the absence of sustained funding, and (iv) leveraging diverse expertise to attract trainees. We have gathered additional information to support our recommendations, including a survey identifying underrepresentation of fungal-related courses at Canadian universities, a list of Canadian fungaria and culture collections, and a case study of a human fungal pathogen outbreak. We anticipate that these discussions will help prioritize fungal research in Canada, and we welcome all researchers to join this nationwide effort to enhance knowledge dissemination and funding advocacy.
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Affiliation(s)
- Linda C Horianopoulos
- Department of Microbiology and Immunology, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Emile Gluck-Thaler
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Isabelle Benoit Gelber
- Centre for Structural and Functional Genomics, Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, QC H4B 1R6, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, 474-570 Gordon Street, Guelph, ON N1G 1Y2, Canada
| | - Christian R Landry
- Département de biologie and Département de biochimie, microbiologie et bio-informatique, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, 8440 112 Street NW, Edmonton, AB T6G 2R7, Canada
| | - James A Scott
- Dalla Lana School of Public Health, University of Toronto, 223 College Street, Toronto, ON, M5T 1R4, Canada
| | - Adnane Sellam
- Department of Microbiology, Infectious Disease and Immunology, Montreal Heart Institute, Université de Montréal, 5000, rue Bélanger, Montréal, QC H1T 1C8, Canada
| | - Donald C Sheppard
- Department of Microbiology and Immunology, McGill University, 3775, rue University, Room 511, Montréal, QC H3A 2B4.,McGill Interdisciplinary Initiative in Infection and Immunity, 3666 McTavish Street, 2nd Floor, Montréal, QC H3Y 1Y2, Canada
| | - Toby Spribille
- Department of Biological Sciences, University of Alberta, 11335 Saskatchewan Drive NW, Edmonton, AB T6G 2H5, Canada
| | - Rajagopal Subramaniam
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Allison K Walker
- Department of Biology, Acadia University, 33 Westwood Avenue, Room 302, Wolfville, NS B4P 2R6, Canada
| | - Steven D Harris
- Department of Biological Sciences, University of Manitoba, Biological Sciences Building, Winnipeg, MB R3T 2N2, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, 474-570 Gordon Street, Guelph, ON N1G 1Y2, Canada
| | - Aleeza C Gerstein
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB R3T 2N2, Canada.,Department of Statistics, University of Manitoba, 318 Machray Hall, Winnipeg, MB R3T 2N2, Canada
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23
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Mei Y, Jiang T, Zou Y, Wang Y, Zhou J, Li J, Liu L, Tan J, Wei L, Li J, Dai H, Peng Y, Zhang L, Lopez-Ribot JL, Shapiro RS, Chen C, Liu NN, Wang H. FDA Approved Drug Library Screening Identifies Robenidine as a Repositionable Antifungal. Front Microbiol 2020; 11:996. [PMID: 32582050 PMCID: PMC7283467 DOI: 10.3389/fmicb.2020.00996] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Due to the increasing prevalence of pathogenic fungal infections, the emergence of antifungal resistant clinical isolates worldwide, and the limited arsenal of available antifungals, developing new antifungal strategies is imperative. In this study, we screened a library of 1068 FDA-approved drugs to identify hits that exhibit broad-spectrum antifungal activity. Robenidine, an anticoccidial agent which has been widely used to treat coccidian infections of poultry and rabbits, was identified in this screen. Physiological concentration of robenidine (8 μM) was able to significantly inhibit yeast cell growth, filamentation and biofilm formation of Candida albicans – the most extensively studied human fungal pathogen. Moreover, we observed a broad-spectrum antifungal activity of this compound against fluconazole resistant clinical isolates of C. albicans, as well as a wide range of other clinically relevant fungal pathogens. Intriguingly, robenidine-treated C. albicans cells were hypersensitive to diverse cell wall stressors, and analysis of the cell wall structure by transmission electron microscopy (TEM) showed that the cell wall was severely damaged by robenidine, implying that this compound may target the cell wall integrity signaling pathway. Indeed, upon robenidine treatment, we found a dose dependent increase in the phosphorylation of the cell wall integrity marker Mkc1, which was decreased after prolonged exposure. Finally, we provide evidence by RNA-seq and qPCR that Rlm1, the downstream transcription factor of Mkc1, may represent a potential target of robenidine. Therefore, our data suggest that robenidine, a FDA approved anti-coccidiosis drug, displays a promising and broadly effective antifungal strategy, and represents a potentially repositionable candidate for the treatment of fungal infections.
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Affiliation(s)
- Yikun Mei
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tong Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zou
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Wang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyang Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Liu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingcong Tan
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luqi Wei
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanqin Dai
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jose L Lopez-Ribot
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Changbin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Ning-Ning Liu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Thomson GJ, Hernon C, Austriaco N, Shapiro RS, Belenky P, Bennett RJ. Metabolism-induced oxidative stress and DNA damage selectively trigger genome instability in polyploid fungal cells. EMBO J 2019; 38:e101597. [PMID: 31448850 PMCID: PMC6769381 DOI: 10.15252/embj.2019101597] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 01/21/2019] [Revised: 06/30/2019] [Accepted: 08/01/2019] [Indexed: 01/04/2023] Open
Abstract
Understanding how cellular activities impact genome stability is critical to multiple biological processes including tumorigenesis and reproductive biology. The fungal pathogen Candida albicans displays striking genome dynamics during its parasexual cycle as tetraploid cells, but not diploid cells, exhibit genome instability and reduce their ploidy when grown on a glucose-rich "pre-sporulation" medium. Here, we reveal that C. albicans tetraploid cells are metabolically hyperactive on this medium with higher rates of fermentation and oxidative respiration relative to diploid cells. This heightened metabolism results in elevated levels of reactive oxygen species (ROS), activation of the ROS-responsive transcription factor Cap1, and the formation of DNA double-strand breaks. Genetic or chemical suppression of ROS levels suppresses each of these phenotypes and also protects against genome instability. These studies reveal how endogenous metabolic processes can generate sufficient ROS to trigger genome instability in polyploid C. albicans cells. We also discuss potential parallels with metabolism-induced instability in cancer cells and speculate that ROS-induced DNA damage could have facilitated ploidy cycling prior to a conventional meiosis in eukaryotes.
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Affiliation(s)
- Gregory J Thomson
- Molecular Microbiology and Immunology DepartmentBrown UniversityProvidenceRIUSA
| | - Claire Hernon
- Molecular Microbiology and Immunology DepartmentBrown UniversityProvidenceRIUSA
| | | | - Rebecca S Shapiro
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - Peter Belenky
- Molecular Microbiology and Immunology DepartmentBrown UniversityProvidenceRIUSA
| | - Richard J Bennett
- Molecular Microbiology and Immunology DepartmentBrown UniversityProvidenceRIUSA
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25
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Abstract
Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR-Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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26
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Halder V, Porter CBM, Chavez A, Shapiro RS. Author Correction: Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nat Protoc 2019; 14:2595. [PMID: 30976123 DOI: 10.1038/s41596-019-0157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The version of this paper originally published contained reference errors. The sentence "To dissect complex genetic interactions in C. albicans, a CRISPR-Cas9-based Gene Drive Array (GDA) was developed" incorrectly cited ref. 13, and should have cited ref. 14. In addition, the reference included as ref. 13 in the original paper was incorrect, and should have been the following: Shapiro, R. S., Chavez, A. & Collins, J. J. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat. Rev. Microbiol. 16, 333-339 (2018). This reference should have been cited after the sentence "Recent innovations in CRISPR-Cas9-based genome editing have facilitated such genetic interaction analyses." The original reference 13 (Gerami-Nejad, M., Zacchi, L. F., McClellan, M., Matter, K. & Berman, J. Shuttle vectors for facile gap repair cloning and integration into a neutral locus in Candida albicans. Microbiology 159, 565-579 (2013)) should have been cited later in the paper, and is now in the reference list as ref. 27. As a result, original references 27-33 have been renumbered in the reference list and in the text. These changes have been made in the PDF and HTML versions of the protocol.
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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27
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Halder V, Porter CBM, Chavez A, Shapiro RS. Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nat Protoc 2019; 14:955-975. [PMID: 30737491 DOI: 10.1038/s41596-018-0122-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
The study of fungal pathogens is of immediate importance, yet progress is hindered by the technical challenges of genetic manipulation. For Candida species, their inability to maintain plasmids, unusual codon usage, and inefficient homologous recombination are among the obstacles limiting efficient genetic manipulation. New advances in genomic biotechnologies-particularly CRISPR-based tools-have revolutionized genome editing for many fungal species. Here, we present a protocol for CRISPR-Cas9-based manipulation in Candida albicans using a modified gene-drive-based strategy that takes ~1 month to complete. We detail the generation of Candida-optimized Cas9-based plasmids for gene deletion, an efficient transformation protocol using C. albicans haploids, and an optimized mating strategy to generate homozygous single- and double-gene diploid mutants. We further describe protocols for quantifying cell growth and analysis pipelines to calculate fitness and genetic interaction scores for genetic mutants. This protocol overcomes previous limitations associated with genetic manipulation in C. albicans and advances researchers' ability to perform genetic analysis in this pathogen; the protocol also has broad applicability to other mating-competent microorganisms.
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Affiliation(s)
- Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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28
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Sharma J, Rosiana S, Razzaq I, Shapiro RS. Linking Cellular Morphogenesis with Antifungal Treatment and Susceptibility in Candida Pathogens. J Fungi (Basel) 2019; 5:E17. [PMID: 30795580 PMCID: PMC6463059 DOI: 10.3390/jof5010017] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
Fungal infections are a growing public health concern, and an increasingly important cause of human mortality, with Candida species being amongst the most frequently encountered of these opportunistic fungal pathogens. Several Candida species are polymorphic, and able to transition between distinct morphological states, including yeast, hyphal, and pseudohyphal forms. While not all Candida pathogens are polymorphic, the ability to undergo morphogenesis is linked with the virulence of many of these pathogens. There are also many connections between Candida morphogenesis and antifungal drug treatment and susceptibility. Here, we review how Candida morphogenesis-a key virulence trait-is linked with antifungal drugs and antifungal drug resistance. We highlight how antifungal therapeutics are able to modulate morphogenesis in both sensitive and drug-resistant Candida strains, the shared signaling pathways that mediate both morphogenesis and the cellular response to antifungal drugs and drug resistance, and the connection between Candida morphology, drug resistance, and biofilm growth. We further review the development of anti-virulence drugs, and targeting Candida morphogenesis as a novel therapeutic strategy to target fungal pathogens. Together, this review highlights important connections between fungal morphogenesis, virulence, and susceptibility to antifungals.
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Affiliation(s)
- Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Sierra Rosiana
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Iqra Razzaq
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Wensing L, Sharma J, Uthayakumar D, Proteau Y, Chavez A, Shapiro RS. A CRISPR Interference Platform for Efficient Genetic Repression in Candida albicans. mSphere 2019; 4:e00002-19. [PMID: 30760609 PMCID: PMC6374589 DOI: 10.1128/msphere.00002-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 01/04/2019] [Accepted: 01/18/2019] [Indexed: 12/26/2022] Open
Abstract
Fungal pathogens are emerging as an important cause of human disease, and Candida albicans is among the most common causative agents of fungal infections. Studying this fungal pathogen is of the utmost importance and necessitates the development of molecular technologies to perform comprehensive genetic and functional genomic analysis. Here, we designed and developed a novel clustered regularly interspaced short palindromic repeat interference (CRISPRi) system for targeted genetic repression in C. albicans We engineered a nuclease-dead Cas9 (dCas9) construct that, paired with a guide RNA targeted to the promoter of an endogenous gene, is capable of targeting that gene for transcriptional repression. We further optimized a favorable promoter locus to achieve repression and demonstrated that fusion of dCas9 to an Mxi1 repressor domain was able to further enhance transcriptional repression. Finally, we demonstrated the application of this CRISPRi system through genetic repression of the essential molecular chaperone HSP90 This is the first demonstration of a functional CRISPRi repression system in C. albicans, and this valuable technology will enable many future applications in this critical fungal pathogen.IMPORTANCE Fungal pathogens are an increasingly important cause of human disease and mortality, and Candida albicans is among the most common causes of fungal disease. Studying this important fungal pathogen requires a comprehensive genetic toolkit to establish how different genetic factors play roles in the biology and virulence of this pathogen. Here, we developed a CRISPR-based genetic regulation platform to achieve targeted repression of C. albicans genes. This CRISPR interference (CRISPRi) technology exploits a nuclease-dead Cas9 protein (dCas9) fused to transcriptional repressors. The dCas9 fusion proteins pair with a guide RNA to target genetic promoter regions and to repress expression from these genes. We demonstrated the functionality of this system for repression in C. albicans and show that we can apply this technology to repress essential genes. Taking the results together, this work presents a new technology for efficient genetic repression in C. albicans, with important applications for genetic analysis in this fungal pathogen.
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Affiliation(s)
- Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Yannic Proteau
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Polvi EJ, Veri AO, Liu Z, Hossain S, Hyde S, Kim SH, Tebbji F, Sellam A, Todd RT, Xie JL, Lin ZY, Wong CJ, Shapiro RS, Whiteway M, Robbins N, Gingras AC, Selmecki A, Cowen LE. Functional divergence of a global regulatory complex governing fungal filamentation. PLoS Genet 2019; 15:e1007901. [PMID: 30615616 PMCID: PMC6336345 DOI: 10.1371/journal.pgen.1007901] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 07/27/2018] [Revised: 01/17/2019] [Accepted: 12/16/2018] [Indexed: 01/17/2023] Open
Abstract
Morphogenetic transitions are prevalent in the fungal kingdom. For a leading human fungal pathogen, Candida albicans, the capacity to transition between yeast and filaments is key for virulence. For the model yeast Saccharomyces cerevisiae, filamentation enables nutrient acquisition. A recent functional genomic screen in S. cerevisiae identified Mfg1 as a regulator of morphogenesis that acts in complex with Flo8 and Mss11 to mediate transcriptional responses crucial for filamentation. In C. albicans, Mfg1 also interacts physically with Flo8 and Mss11 and is critical for filamentation in response to diverse cues, but the mechanisms through which it regulates morphogenesis remained elusive. Here, we explored the consequences of perturbation of Mfg1, Flo8, and Mss11 on C. albicans morphogenesis, and identified functional divergence of complex members. We observed that C. albicans Mss11 was dispensable for filamentation, and that overexpression of FLO8 caused constitutive filamentation even in the absence of Mfg1. Harnessing transcriptional profiling and chromatin immunoprecipitation coupled to microarray analysis, we identified divergence between transcriptional targets of Flo8 and Mfg1 in C. albicans. We also established that Flo8 and Mfg1 cooperatively bind to promoters of key regulators of filamentation, including TEC1, for which overexpression was sufficient to restore filamentation in the absence of Flo8 or Mfg1. To further explore the circuitry through which Mfg1 regulates morphogenesis, we employed a novel strategy to select for mutations that restore filamentation in the absence of Mfg1. Whole genome sequencing of filamentation-competent mutants revealed chromosome 6 amplification as a conserved adaptive mechanism. A key determinant of the chromosome 6 amplification is FLO8, as deletion of one allele blocked morphogenesis, and chromosome 6 was not amplified in evolved lineages for which FLO8 was re-located to a different chromosome. Thus, this work highlights rewiring of key morphogenetic regulators over evolutionary time and aneuploidy as an adaptive mechanism driving fungal morphogenesis. Fungal infections pose a severe burden to human health worldwide. Candida albicans is a leading cause of systemic fungal infections, with mortality rates approaching 40%. One of the key virulence traits of this fungus is its ability to transition between yeast and filamentous forms in response to diverse host-relevant cues. The model yeast Saccharomyces cerevisiae is also capable of filamentous growth in certain conditions, and previous work has identified a key transcriptional complex required for filamentation in both species. However, here we discover that the circuitry governed by this complex in C. albicans is largely distinct from that in the non-pathogenic S. cerevisiae. We also employ a novel selection strategy to perform experimental evolution, identifying chromosome triplication as a mechanism to restore filamentation in a non-filamentous mutant. This work reveals unique circuitry governing a key virulence trait in a leading fungal pathogen, identifying potential therapeutic targets to combat these life-threatening infections.
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Affiliation(s)
- Elizabeth J. Polvi
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Amanda O. Veri
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Saif Hossain
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Sabrina Hyde
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Faiza Tebbji
- Infectious Disease Research Centre, Université Laval, Quebec, Canada
| | - Adnane Sellam
- Infectious Disease Research Centre, Université Laval, Quebec, Canada
| | - Robert T. Todd
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Jinglin L. Xie
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Cassandra J. Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Rebecca S. Shapiro
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | | | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- * E-mail:
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Geddes-McAlister J, Shapiro RS. New pathogens, new tricks: emerging, drug-resistant fungal pathogens and future prospects for antifungal therapeutics. Ann N Y Acad Sci 2018; 1435:57-78. [DOI: 10.1111/nyas.13739] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/19/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jennifer Geddes-McAlister
- Department of Molecular and Cellular Biology; University of Guelph; Guelph Ontario Canada
- Department of Proteomics and Signal Transduction; Max Planck Institute of Biochemistry; Munich Germany
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology; University of Guelph; Guelph Ontario Canada
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Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM. Precise Cas9 targeting enables genomic mutation prevention. Proc Natl Acad Sci U S A 2018; 115:3669-3673. [PMID: 29555762 PMCID: PMC5889643 DOI: 10.1073/pnas.1718148115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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] [Indexed: 12/26/2022] Open
Abstract
Here, we present a generalized method of guide RNA "tuning" that enables Cas9 to discriminate between two target sites that differ by a single-nucleotide polymorphism. We employ our methodology to generate an in vivo mutation prevention system in which Cas9 actively restricts the occurrence of undesired gain-of-function mutations within a population of engineered organisms. We further demonstrate that the system is scalable to a multitude of targets and that the general tuning and prevention concepts are portable across engineered Cas9 variants and Cas9 orthologs. Finally, we show that the mutation prevention system maintains robust activity even when placed within the complex environment of the mouse gastrointestinal tract.
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Affiliation(s)
- Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Benjamin W Pruitt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - Marcelle Tuttle
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - Rebecca S Shapiro
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ryan J Cecchi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - Jordan Winston
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - Brian M Turczyk
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - Michael Tung
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02115;
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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Veri AO, Miao Z, Shapiro RS, Tebbji F, O’Meara TR, Kim SH, Colazo J, Tan K, Vyas VK, Whiteway M, Robbins N, Wong KH, Cowen LE. Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space. PLoS Genet 2018; 14:e1007270. [PMID: 29590106 PMCID: PMC5873724 DOI: 10.1371/journal.pgen.1007270] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 10/30/2017] [Accepted: 02/22/2018] [Indexed: 12/24/2022] Open
Abstract
The capacity to respond to temperature fluctuations is critical for microorganisms to survive within mammalian hosts, and temperature modulates virulence traits of diverse pathogens. One key temperature-dependent virulence trait of the fungal pathogen Candida albicans is its ability to transition from yeast to filamentous growth, which is induced by environmental cues at host physiological temperature. A key regulator of temperature-dependent morphogenesis is the molecular chaperone Hsp90, which has complex functional relationships with the transcription factor Hsf1. Although Hsf1 controls global transcriptional remodeling in response to heat shock, its impact on morphogenesis remains unknown. Here, we establish an intriguing paradigm whereby overexpression or depletion of C. albicans HSF1 induces morphogenesis in the absence of external cues. HSF1 depletion compromises Hsp90 function, thereby driving filamentation. HSF1 overexpression does not impact Hsp90 function, but rather induces a dose-dependent expansion of Hsf1 direct targets that drives overexpression of positive regulators of filamentation, including Brg1 and Ume6, thereby bypassing the requirement for elevated temperature during morphogenesis. This work provides new insight into Hsf1-mediated environmentally contingent transcriptional control, implicates Hsf1 in regulation of a key virulence trait, and highlights fascinating biology whereby either overexpression or depletion of a single cellular regulator induces a profound developmental transition. For human pathogens, the capacity to respond to elevated temperature is required for survival, with elevated temperature in the form of fever as a conserved host response to defend against infection. One of the leading fungal pathogens of humans in Candida albicans, which is capable of growing in both a yeast and filamentous state. The ability to transition between these forms is a key virulence trait, and one that is highly temperature-dependent. A pivotal regulator of filamentous growth is the temperature-responsive molecular chaperone Hsp90, which has complex relationships with the transcription factor Hsf1. Although Hsf1 regulates changes in gene expression in response to heat shock, its impact on morphogenesis remains unknown. Here, we uncover an intriguing phenomenon whereby overexpression or depletion of C. albicans HSF1 induces morphogenesis. We observe that HSF1 depletion compromises Hsp90 function, thereby driving filamentation. In contrast, HSF1 overexpression induces a dose-dependent expansion of its transcriptional targets that drives overexpression of positive regulators of filamentous growth. This work illuminates novel mechanisms through which tuning the levels of an environmentally contingent transcription factor drives a key developmental program.
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Affiliation(s)
- Amanda O. Veri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Faiza Tebbji
- Infectious Disease Research Centre, Université Laval, Quebec City, Quebec, Canada
| | - Teresa R. O’Meara
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Juan Colazo
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Valmik K. Vyas
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, Quebec, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat Microbiol 2018; 3:73-82. [PMID: 29062088 PMCID: PMC5832965 DOI: 10.1038/s41564-017-0043-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [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: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022]
Abstract
Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'gene drive array' platform to facilitate efficient genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different gene drive disabling a gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We generate double-gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how genetic networks shift under diverse conditions. This platform transforms our ability to perform genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Alejandro Chavez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, 10032, NY, USA
| | - Caroline B M Porter
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meagan Hamblin
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christian S Kaas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Expression Technologies 2, Novo Nordisk A/S, Maaloev, 2760, Denmark
| | - James E DiCarlo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | - Xiaoli Xu
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | | | | | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Shapiro RS, Konhauser KO. Hematite-coated microfossils: primary ecological fingerprint or taphonomic oddity of the Paleoproterozoic? Geobiology 2015; 13:209-24. [PMID: 25639940 DOI: 10.1111/gbi.12127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 01/05/2015] [Indexed: 05/22/2023]
Abstract
Microfossils belonging to the 1.88-billion-year-old 'Gunflint-biota' are preserved as carbonaceous and hematitic filaments and spheres that are believed to represent ancient chemolithoautotrophic Fe(II) oxidizing bacteria that grew above a chemocline where ferruginous seawater upwelled into shallow, oxygenated waters. This 'biological' model posits that hematite formed during burial from dewatering of the precursor ferric oxyhydroxides that encrusted Fe(II)-oxidizing bacteria. Here, we present an alternate 'taphonomic' model in which iron-rich groundwaters discharged into buried stromatolites; thus, the mineralization reactions are more informative of diagenetic processes than they are for primary marine conditions. We sampled centimeter-scale columnar stromatolites from both the lower and upper stromatolite horizons of the Biwabik and Gunflint formations, across a range of metamorphic gradients including unaltered to prehnite-pumpellyite taconite, supergene altered ore, and amphibolite-pyroxene grade contact-metamorphic zones. Fossils are rare to very rare and comprise curved filaments that exist in clusters with similar orientations. The filaments from throughout the Biwabik are similar to well-preserved carbonaceous Gunflintia from Ontario. Spheres of Huroniospora are also found in both formations. Microfossils from the least altered sections are preserved as carbon. Prehnite-pumpellyite samples are composed of either carbon or hematite (Fe2 O3 ). Within the contact aureole, filaments are densely coated by magnetite (Fe3 O4 ); the highest grade samples are secondarily oxidized to martite. The consistency in stromatolite microstructure and lithofacies throughout the metamorphic grades suggests they formed under similar environmental conditions. Post-depositional alteration led to replacement of the carbon by iron oxide. The facies association, filament distribution, and lack of branching and attached spherical cells argue against Gunflintia being a direct analogue to common marine, chemolithoautotrophic Fe(II)-oxidizing bacteria. Instead, we propose that the presence of hematite-coated microfossils is a reflection of taphonomic processes and does not necessarily reflect the byproduct of an original microbial ecosystem.
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Affiliation(s)
- R S Shapiro
- Geological and Environmental Sciences Department, CSU Chico, Chico, CA, USA
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Affiliation(s)
- Rebecca S. Shapiro
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Institute of Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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Gambaro K, Quinn MCJ, Cáceres-Gorriti KY, Shapiro RS, Provencher D, Rahimi K, Mes-Masson AM, Tonin PN. Low levels of IGFBP7 expression in high-grade serous ovarian carcinoma is associated with patient outcome. BMC Cancer 2015; 15:135. [PMID: 25886299 PMCID: PMC4381406 DOI: 10.1186/s12885-015-1138-8] [Citation(s) in RCA: 16] [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: 10/01/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insulin-like growth factor binding protein 7 (IGFBP7) has been suggested to act as a tumour suppressor gene in various human cancers, yet its role in epithelial ovarian cancer (EOC) has not yet been investigated. We previously observed that IGFBP7 was one of several genes found significantly upregulated in an EOC cell line model rendered non-tumourigenic as consequence of genetic manipulation. The aim of the present study was to investigate the role of IGFBP7 in high-grade serous ovarian carcinomas (HGSC), the most common type of EOC. METHODS We analysed IGFBP7 gene expression in 11 normal ovarian surface epithelial cells (NOSE), 79 high-grade serous ovarian carcinomas (HGSC), and seven EOC cell lines using a custom gene expression array platform. IGFBP7 mRNA expression profiles were also extracted from publicly available databases. Protein expression was assessed by immunohistochemistry of 175 HGSC and 10 normal fallopian tube samples using tissue microarray and related to disease outcome. We used EOC cells to investigate possible mechanisms of gene inactivation and describe various in vitro growth effects of exposing EOC cell lines to human recombinant IGFBP7 protein and conditioned media. RESULTS All HGSCs exhibited IGFBP7 expression levels that were significantly (p = 0.001) lower than the mean of the expression value of NOSE samples and that of a whole ovary sample. IGFBP7 gene and protein expression were lower in tumourigenic EOC cell lines relative to a non-tumourigenic EOC cell line. None of the EOC cell lines harboured a somatic mutation in IGFBP7, although loss of heterozygosity (LOH) of the IGFBP7 locus and epigenetic methylation silencing of the IGFBP7 promoter was observed in two of the cell lines exhibiting loss of gene/protein expression. In vitro functional assays revealed an alteration of the EOC cell migration capacity. Protein expression analysis of HGSC samples revealed that the large majority of tumour cores (72.6%) showed low or absence of IGFBP7 staining and revealed a significant correlation between IGFBP7 protein expression and a prolonged overall survival (p = 0.044). CONCLUSION The low levels of IGFPB7 in HGSC relative to normal tissues, and association with survival are consistent with a purported role in tumour suppressor pathways.
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Affiliation(s)
- Karen Gambaro
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Michael C J Quinn
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Katia Y Cáceres-Gorriti
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada.
| | - Rebecca S Shapiro
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada.
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada. .,Department of Obstetric-Gynecology, Université de Montréal, Montreal, H2L 4M1, Canada.
| | - Kurosh Rahimi
- Department of Pathology, Université de Montréal, Montreal, H3C 3J7, Canada.
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montreal, H2X 0B9, Canada. .,Department of Medicine, Université de Montréal, Montreal, H3C 3J7, Canada.
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, H4A 3J1, Canada. .,Department of Medicine, McGill University, Montreal, H3G 1A4, Canada. .,Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Site Glen Pavillion Block E, Cancer Research Program E026217 (cubicle E), Montreal, Quebec, H4A 3J1, Canada.
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Abstract
Intravenous and subcutaneous immunoglobulins (IVIg and SCIg, respectively) are increasingly used in clinical practice, not only as replacement therapy but also for immunomodulation. Physicians have learned that primary immunodeficiency (PID) patients are susceptible to recurrent respiratory tract infections even when appropriately treated with immunoglobulin (Ig) therapy. Further investigation will establish whether a combined therapeutic approach including Ig dose optimization will prevent progressive lung disease in PID. The wear-off effects observed with IVIg can be minimized by adjusting the dosing regimen. It is also possible to avoid the cyclic wear-off following transition to SCIg administration. Consideration of benefit versus risk with Ig therapy includes evaluating the potential occurrence of thromboembolic and haemolytic events, which may be more frequent when Ig is administered in high doses and in the presence of pre-existing risk factors. The ability to select an administration method from IVIg, SCIg or hyaluronidase-facilitated SCIg infusions provides patient choice and alternatives if one or other administration route is not suitable for a patient. The evolution in indications, applications, and understanding of Ig therapy described here has reinforced the need for robust methods to prioritize Ig use.
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Affiliation(s)
- R S Shapiro
- Midwest Immunology Clinic, Plymouth, MA, USA
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Abstract
Immunoglobulin (Ig) replacement therapy has been the mainstay of primary immunodeficiencies (PID) treatment for more than 30 years and has substantially changed the lives of patients. This review focuses on aspects of Ig use in clinical practice in addition to discussing prioritizing future Ig use. Despite Ig therapy, PID patients continue to be predisposed to recurrent, subclinical respiratory tract infections, which may lead to chronic lung disease. Research has shown that one of the underlying reasons for this deterioration in lung function is the differential distribution and concentration of Ig isotypes in the airway lumen. Further to this, the relationship between Ig dose and infection outcome is explored, expanding on end-of-cycle loss of efficacy (wear-off) particularly with intravenous immunoglobulin (IVIg), how this can confound the determination of optimal IgG dose and how our aim of treatment should be to improve clinical outcome. This review goes on to discuss the safety of Ig replacement therapy, which is generally well tolerated by most patients, compares the rates of systemic adverse reactions between IVIg and SCIg and highlights the advantages of SCIg administration in this respect, including the use of pre-infused subcutaneous recombinant human hyaluronidase to aid subcutaneous infusion volumes. The growing demand for Ig replacement therapy is challenging physicians; here we show the development of prioritization algorithms to assist in identifying those who will benefit most from this clinically valuable therapy.
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Affiliation(s)
- R S Shapiro
- Midwest Immunology Clinic, Plymouth, MA, USA
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40
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Siering PL, Wolfe GV, Wilson MS, Yip AN, Carey CM, Wardman CD, Shapiro RS, Stedman KM, Kyle J, Yuan T, Van Nostrand JD, He Z, Zhou J. Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem. Geobiology 2013; 11:356-376. [PMID: 23679065 DOI: 10.1111/gbi.12041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/12/2013] [Indexed: 06/02/2023]
Abstract
Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 °C, but temperatures reach 93 °C locally. We extracted DNA from water and sediments collected from warm (52 °C) and hot (73-83 °C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle.
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Affiliation(s)
- P L Siering
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA.
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Shapiro RS, Ryan O, Boone C, Cowen LE. Regulatory circuitry governing morphogenesis in Saccharomyces cerevisiae and Candida albicans. Cell Cycle 2012; 11:4294-5. [PMID: 23095675 PMCID: PMC3552904 DOI: 10.4161/cc.22608] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Abstract
Temperature is a critical and ubiquitous environmental signal that governs the development and virulence of diverse microbial species, including viruses, archaea, bacteria, fungi, and parasites. Microbial survival is contingent upon initiating appropriate responses to the cellular stress induced by severe environmental temperature change. In the case of microbial pathogens, development and virulence are often coupled to sensing host physiological temperatures. As such, microbes have developed diverse molecular strategies to sense fluctuations in temperature, and nearly all cellular molecules, including proteins, lipids, RNA, and DNA, can act as thermosensors that detect changes in environmental temperature and initiate relevant cellular responses. The myriad of molecular mechanisms by which microbes sense and respond to temperature reveals an elegant repertoire of strategies to orchestrate cellular signaling, developmental programs, and virulence with spatial and temporal environmental cues.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Shapiro RS, Zaas AK, Betancourt-Quiroz M, Perfect JR, Cowen LE. The Hsp90 co-chaperone Sgt1 governs Candida albicans morphogenesis and drug resistance. PLoS One 2012; 7:e44734. [PMID: 22970302 PMCID: PMC3435277 DOI: 10.1371/journal.pone.0044734] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [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: 06/22/2012] [Accepted: 08/07/2012] [Indexed: 12/30/2022] Open
Abstract
The molecular chaperone Hsp90 orchestrates regulatory circuitry governing fungal morphogenesis, biofilm development, drug resistance, and virulence. Hsp90 functions in concert with co-chaperones to regulate stability and activation of client proteins, many of which are signal transducers. Here, we characterize the first Hsp90 co-chaperone in the leading human fungal pathogen, Candida albicans. We demonstrate that Sgt1 physically interacts with Hsp90, and that it governs C. albicans morphogenesis and drug resistance. Genetic depletion of Sgt1 phenocopies depletion of Hsp90, inducing yeast to filament morphogenesis and invasive growth. Sgt1 governs these traits by bridging two morphogenetic regulators: Hsp90 and the adenylyl cyclase of the cAMP-PKA signaling cascade, Cyr1. Sgt1 physically interacts with Cyr1, and depletion of either Sgt1 or Hsp90 activates cAMP-PKA signaling, revealing the elusive link between Hsp90 and the PKA signaling cascade. Sgt1 also mediates tolerance and resistance to the two most widely deployed classes of antifungal drugs, azoles and echinocandins. Depletion of Sgt1 abrogates basal tolerance and acquired resistance to azoles, which target the cell membrane. Depletion of Sgt1 also abrogates tolerance and resistance to echinocandins, which target the cell wall, and renders echinocandins fungicidal. Though Sgt1 and Hsp90 have a conserved impact on drug resistance, the underlying mechanisms are distinct. Depletion of Hsp90 destabilizes the client protein calcineurin, thereby blocking crucial responses to drug-induced stress; in contrast, depletion of Sgt1 does not destabilize calcineurin, but blocks calcineurin activation in response to drug-induced stress. Sgt1 influences not only morphogenesis and drug resistance, but also virulence, as genetic depletion of C. albicans Sgt1 leads to reduced kidney fungal burden in a murine model of systemic infection. Thus, our characterization of the first Hsp90 co-chaperone in a fungal pathogen establishes C. albicans Sgt1 as a global regulator of morphogenesis and drug resistance, providing a new target for treatment of life-threatening fungal infections.
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Affiliation(s)
- Rebecca S. Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Aimee K. Zaas
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marisol Betancourt-Quiroz
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - John R. Perfect
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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44
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Abstract
Temperature change is a ubiquitous environmental signal, which exerts powerful control over the development and virulence of microbial pathogens. For Candida albicans, the leading fungal pathogen of humans, temperature influences mating, phenotypic switching, resistance to antifungal drugs and the morphogenetic transition from yeast to filamentous growth. C. albicans morphogenesis is profoundly influenced by temperature, and most filament-inducing cues depend on a concurrent increase in temperature to 37°C before morphogenesis can occur, although the molecular mechanisms underpinning this temperature-dependent developmental transition remain largely unknown. We established that the thermally responsive molecular chaperone Hsp90 orchestrates temperature-dependent morphogenesis, via previously uncharacterized cellular circuitry, comprised of the cyclin-dependent kinase Pho85, the cyclin Pcl1 and the transcriptional regulator Hms1. Here we elaborate on Hsp90's pleiotropic effects on temperature-dependent morphogenetic circuitry, and highlight how changes in protein form and function in response to stress complements the diverse repertoire of mechanisms of microbial temperature sensing.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE. Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry. PLoS Genet 2012; 8:e1002562. [PMID: 22438817 PMCID: PMC3305360 DOI: 10.1371/journal.pgen.1002562] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [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: 08/17/2011] [Accepted: 01/13/2012] [Indexed: 11/18/2022] Open
Abstract
The molecular chaperone Hsp90 regulates the folding of diverse signal transducers in all eukaryotes, profoundly affecting cellular circuitry. In fungi, Hsp90 influences development, drug resistance, and evolution. Hsp90 interacts with ∼10% of the proteome in the model yeast Saccharomyces cerevisiae, while only two interactions have been identified in Candida albicans, the leading fungal pathogen of humans. Utilizing a chemical genomic approach, we mapped the C. albicans Hsp90 interaction network under diverse stress conditions. The chaperone network is environmentally contingent, and most of the 226 genetic interactors are important for growth only under specific conditions, suggesting that they operate downstream of Hsp90, as with the MAPK Hog1. Few interactors are important for growth in many environments, and these are poised to operate upstream of Hsp90, as with the protein kinase CK2 and the transcription factor Ahr1. We establish environmental contingency in the first chaperone network of a fungal pathogen, novel effectors upstream and downstream of Hsp90, and network rewiring over evolutionary time. Hsp90 is an essential and conserved molecular chaperone in eukaryotes that assists with folding diverse proteins, especially regulators of cellular signaling. By activating signaling in response to environmental cues, Hsp90 has a profound impact on myriad aspects of biology. In fungi, Hsp90 influences development, drug resistance, and evolution. In the model yeast Saccharomyces cerevisiae, Hsp90 interacts with ∼10% of proteins. In the leading human fungal pathogen, Candida albicans, only two interactions have been identified. We conducted a chemical genetic screen to elucidate the C. albicans Hsp90 interaction network under diverse stress conditions. The majority of the 226 genetic interactors are important for growth under specific conditions, suggesting that they act downstream of Hsp90 and that the network is environmentally contingent. For example, the kinase Hog1 depends upon Hsp90 for activation. Only a few interactors are important for growth in many conditions, suggesting that they act upstream of Hsp90. For example, the protein kinase CK2 regulates function of the Hsp90 chaperone machine and the transcription factor Ahr1 governs HSP90 expression. Thus, we identify novel effectors upstream and downstream of Hsp90, and establish the first chaperone network of a fungal pathogen, with evidence for environmental contingency and network rewiring over evolutionary time.
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Affiliation(s)
- Stephanie Diezmann
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Shapiro RS, Sellam A, Tebbji F, Whiteway M, Nantel A, Cowen LE. Pho85, Pcl1, and Hms1 signaling governs Candida albicans morphogenesis induced by high temperature or Hsp90 compromise. Curr Biol 2012; 22:461-70. [PMID: 22365851 DOI: 10.1016/j.cub.2012.01.062] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 01/13/2012] [Accepted: 01/30/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Temperature exerts powerful control over development and virulence of diverse pathogens. In the leading human fungal pathogen, Candida albicans, temperature governs morphogenesis, a key virulence trait. Many cues that induce the yeast to filament transition are contingent on a minimum of 37°C, whereas further elevation to 39°C serves as an independent inducer. The molecular chaperone Hsp90 is a key regulator of C. albicans temperature-dependent morphogenesis. Compromise of Hsp90 function genetically, pharmacologically, or by elevated temperature induces filamentation in a manner that depends on protein kinase A signaling but is independent of the terminal transcription factor, Efg1. RESULTS Here, we establish that despite morphological and regulatory differences, inhibition of Hsp90 induces a transcriptional profile similar to that induced by other filamentation cues and does so independently of Efg1. Further, we identify Hms1 as a transcriptional regulator required for morphogenesis induced by elevated temperature or Hsp90 compromise. Hms1 functions downstream of the cyclin Pcl1 and the cyclin-dependent kinase Pho85, both of which are required for temperature-dependent filamentation. Upon Hsp90 inhibition, Hms1 binds to DNA elements involved in filamentous growth, including UME6 and RBT5, and regulates their expression, providing a mechanism through which Pho85, Pcl1, and Hms1 govern morphogenesis. Consistent with the importance of morphogenetic flexibility for virulence, deletion of C. albicans HMS1 attenuates virulence in a metazoan model of infection. CONCLUSIONS Thus, we establish a new mechanism through which Hsp90 orchestrates C. albicans morphogenesis, and define novel regulatory circuitry governing a temperature-dependent developmental program, with broad implications for temperature sensing and virulence of microbial pathogens.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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47
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Abstract
The molecular chaperone Hsp90 regulates morphogenesis of the leading human fungal pathogen Candida albicans. Hsp90 inhibition induces filaments with a delay in mitotic exit mediated by the checkpoint protein Bub2. Hsp90 depletion destabilizes the cyclin-dependent kinase Cdc28, providing a link between Hsp90, cell cycle regulation, and morphogenesis. The trimorphic fungus Candida albicans is the leading cause of systemic candidiasis, a disease with poor prognosis affecting immunocompromised individuals. The capacity of C. albicans to transition between morphological states is a key determinant of its ability to cause life-threatening infection. Recently the molecular chaperone heat shock protein 90 (Hsp90) was implicated as a major regulator of temperature-dependent C. albicans morphogenesis; compromising Hsp90 function induces filamentation and relieves repression of Ras1–protein kinase A (PKA) signaling, although the mechanism involved remains unknown. Here we demonstrate that filaments generated by compromise of Hsp90 function are neither pseudohyphae nor hyphae but closely resemble filaments formed in response to cell cycle arrest. Closer examination revealed that these filaments exhibit a delay in mitotic exit mediated by the checkpoint protein Bub2. Furthermore, Hsp90 inhibition also led to a distinct morphology with defects in cytokinesis. We found that the cyclin-dependent kinase Cdc28 was destabilized in response to depletion of Hsp90 and that Cdc28 physically interacts with Hsp90, implicating this major cell cycle regulator as a novel Hsp90 client protein in C. albicans. Taken together, our results suggest that Hsp90 is instrumental in the regulation of cell division during yeast-form growth in C. albicans and exerts its major effects during late cell cycle events.
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Affiliation(s)
- Heather Senn
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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48
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Abstract
Hsp90 is environmentally contingent molecular chaperone that influences the form and function of diverse signal transducers. Here we discuss our recent findings that Hsp90 regulates the morphogenetic transition from yeast to filamentous forms required for virulence of the most prevalent fungal pathogen of humans, Candida albicans, and does so via cAMP-PKA signalling. This transition is normally regulated by environmental cues that are contingent upon elevated temperature to relieve Hsp90-mediated repression of the morphogenetic program. Intriguingly, Hsp90 inhibition induces filamentation independent of the canonical PKA transcription factor Efg1, in striking similarity to a select set of morphogenetic stimuli. Further investigation will determine the downstream transcription factors through which Hsp90 regulates morphogenesis and the precise mechanism of Hsp90's interaction with the cAMP-PKA pathway. C. albicans is one of many fungal species that undergo a morphological transition in a temperature-dependent manner, thus Hsp90's capacity to govern this key developmental program may provide insight into morphogenesis of diverse organisms.
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Affiliation(s)
- R S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Abstract
Immunoglobulin (Ig) administration via the subcutaneous (s.c.) route has become increasingly popular in recent years. The method does not require venous access, is associated with few systemic side effects and has been reported to improve patients' quality of life. One current limitation to its use is the large volumes which need to be administered. Due to the inability of tissue to accept such large volumes, frequent administration at multiple sites is necessary. Most studies conducted to date have investigated the use of subcutaneous immunoglobulin (SCIg) in patients treated previously with the intravenous (i.v.) formulation. New data now support the use of s.c. administration in previously untreated patients with primary immunodeficiencies. SCIg treatment may further be beneficial in the treatment of autoimmune neurological conditions, such as multi-focal motor neuropathy; however, controlled trials directly comparing the s.c. and i.v. routes are still to be performed for this indication. New developments may further improve and facilitate the s.c. administration route. For example, hyaluronidase-facilitated administration increases the bioavailability of SCIg, and may allow for the administration of larger volumes at a single site. Alternatively, more concentrated formulations may reduce the volume required for administration, and a rapid-push technique may allow for shorter administration times. As these developments translate into clinical practice, more physicians and patients may choose the s.c. administration route in the future.
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Affiliation(s)
- S Misbah
- John Radcliffe Hospital, Oxford, UK.
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Shapiro RS, Uppuluri P, Zaas AK, Collins C, Senn H, Perfect JR, Heitman J, Cowen LE. Hsp90 orchestrates temperature-dependent Candida albicans morphogenesis via Ras1-PKA signaling. Curr Biol 2009; 19:621-9. [PMID: 19327993 DOI: 10.1016/j.cub.2009.03.017] [Citation(s) in RCA: 227] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 03/02/2009] [Accepted: 03/03/2009] [Indexed: 02/02/2023]
Abstract
BACKGROUND Hsp90 is an environmentally contingent molecular chaperone that influences the form and function of diverse regulators of cellular signaling. Hsp90 potentiates the evolution of fungal drug resistance by enabling crucial cellular stress responses. Here we demonstrate that in the leading fungal pathogen of humans, Candida albicans, Hsp90 governs cellular circuitry required not only for drug resistance but also for the key morphogenetic transition from yeast to filamentous growth that is crucial for virulence. This transition is normally regulated by environmental cues, such as exposure to serum, that are contingent upon elevated temperature to induce morphogenesis. The basis for this temperature dependence has remained enigmatic. RESULTS We show that compromising Hsp90 function pharmacologically or genetically induces a transition from yeast to filamentous growth in the absence of external cues. Elevated temperature relieves Hsp90-mediated repression of the morphogenetic program. Hsp90 regulates morphogenetic circuitry by repressing Ras1-PKA signaling. Modest Hsp90 compromise enhances the phenotypic effects of activated Ras1 signaling whereas deletion of positive regulators of the Ras1-PKA cascade blocks the morphogenetic response to Hsp90 inhibition. Consistent with the requirement for morphogenetic flexibility for virulence, depletion of C. albicans Hsp90 attenuates virulence in a murine model of systemic disease. CONCLUSIONS Hsp90 governs the integration of environmental cues with cellular signaling to orchestrate fungal morphogenesis and virulence, suggesting new therapeutic strategies for life-threatening infectious disease. Hsp90's capacity to govern a key developmental program in response to temperature change provides a new mechanism that complements the elegant repertoire that organisms utilize to sense temperature.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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