1
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Renner TM, Akache B, Stuible M, Rohani N, Cepero-Donates Y, Deschatelets L, Dudani R, Harrison BA, Baardsnes J, Koyuturk I, Hill JJ, Hemraz UD, Régnier S, Lenferink AEG, Durocher Y, McCluskie MJ. Tuning the immune response: sulfated archaeal glycolipid archaeosomes as an effective vaccine adjuvant for induction of humoral and cell-mediated immunity towards the SARS-CoV-2 Omicron variant of concern. Front Immunol 2023; 14:1182556. [PMID: 37122746 PMCID: PMC10140330 DOI: 10.3389/fimmu.2023.1182556] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Liposomes composed of sulfated lactosyl archaeol (SLA) have been shown to be a safe and effective vaccine adjuvant with a multitude of antigens in preclinical studies. In particular, SLA-adjuvanted SARS-CoV-2 subunit vaccines based on trimeric spike protein antigens were shown to be immunogenic and efficacious in mice and hamsters. With the continued emergence of SARS-CoV-2 variants, we sought to evaluate next-generation vaccine formulations with an updated antigenic identity. This was of particular interest for the widespread Omicron variant, given the abundance of mutations and structural changes observed within its spike protein compared to other variants. An updated version of our resistin-trimerized SmT1 corresponding to the B.1.1.529 variant was successfully generated in our Chinese Hamster Ovary (CHO) cell-based antigen production platform and characterized, revealing some differences in protein profile and ACE2 binding affinity as compared to reference strain-based SmT1. We next evaluated this Omicron-based spike antigen for its immunogenicity and ability to generate robust antigen-specific immune responses when paired with SLA liposomes or AddaS03 (a mimetic of the AS03 oil-in-water emulsion adjuvant system found in commercialized SARS-CoV-2 protein vaccines). Immunization of mice with vaccine formulations containing this updated antigen with either adjuvant stimulated neutralizing antibody responses favouring Omicron over the reference strain. Cell-mediated responses, which play an important role in the neutralization of intracellular infections, were induced to a much higher degree with the SLA adjuvant relative to the AddaS03-adjuvanted formulations. As such, updated vaccines that are better capable of targeting towards SARS-CoV-2 variants can be generated through an optimized combination of antigen and adjuvant components.
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Affiliation(s)
- Tyler M. Renner
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Bassel Akache
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Matthew Stuible
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | - Nazanin Rohani
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | | | - Lise Deschatelets
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Renu Dudani
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Blair A. Harrison
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Jason Baardsnes
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | - Izel Koyuturk
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | - Jennifer J. Hill
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Usha D. Hemraz
- National Research Council Canada, Aquatic and Crop Resource Development, Montreal, QC, Canada
| | - Sophie Régnier
- National Research Council Canada, Aquatic and Crop Resource Development, Montreal, QC, Canada
| | - Anne E. G. Lenferink
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | - Yves Durocher
- National Research Council Canada, Human Health Therapeutics, Montreal, QC, Canada
| | - Michael J. McCluskie
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON, Canada
- *Correspondence: Michael J. McCluskie,
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2
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Sulea T, Baardsnes J, Stuible M, Rohani N, Tran A, Parat M, Cepero Donates Y, Duchesne M, Plante P, Kour G, Durocher Y. Structure-based dual affinity optimization of a SARS-CoV-1/2 cross-reactive single-domain antibody. PLoS One 2022; 17:e0266250. [PMID: 35353868 PMCID: PMC8967028 DOI: 10.1371/journal.pone.0266250] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
The SARS coronavirus 2 (SARS-CoV-2) spike (S) protein binding to the human ACE2 receptor is the molecular event that initiates viral entry into host cells and leads to infection and virus replication. There is a need for agents blocking viral entry into host cells that are cross-reactive with emerging virus variants. VHH-72 is an anti-SARS-CoV-1 single-domain antibody that also exhibits cross-specificity with SARS-CoV-2 but with decreased binding affinity. Here we applied a structure-based approach to affinity-mature VHH-72 for the SARS-CoV-2 spike protein while retaining the original affinity for SARS-CoV-1. This was achieved by employing the computational platform ADAPT in a constrained dual-affinity optimization mode as a means of broadening specificity. Select mutants designed by ADAPT were formatted as fusions with a human IgG1-Fc fragment. These mutants demonstrated improved binding to the SARS-CoV-2 spike protein due to decreased dissociation rates. Functional testing for virus neutralization revealed improvements relative to the parental VHH72-Fc up to 10-fold using a SARS-CoV-2 pseudotyped lentivirus and 20-fold against the SARS-CoV-2 authentic live virus (Wuhan variant). Binding and neutralization improvements were maintained for some other SARS-CoV-2 variants currently in circulation. These improved VHH-72 mutants are predicted to establish novel interactions with the S antigen. They will be useful, alone or as fusions with other functional modules, in the global quest for treatments of COVID-19 infections.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail:
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Pierre Plante
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Guneet Kour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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3
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Hao L, Rohani N, Zhao RT, Pulver EM, Mak H, Kelada OJ, Ko H, Fleming HE, Gertler FB, Bhatia SN. Microenvironment-triggered multimodal precision diagnostics. Nat Mater 2021; 20:1440-1448. [PMID: 34267368 DOI: 10.1038/s41563-021-01042-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/26/2021] [Indexed: 05/24/2023]
Abstract
Therapeutic outcomes in oncology may be aided by precision diagnostics that offer early detection, localization and the opportunity to monitor response to therapy. Here, we report a multimodal nanosensor engineered to target tumours through acidosis, respond to proteases in the microenvironment to release urinary reporters and (optionally) carry positron emission tomography probes to enable localization of primary and metastatic cancers in mouse models of colorectal cancer. We present a paradigm wherein this multimodal sensor can be employed longitudinally to assess burden of disease non-invasively, including tumour progression and response to chemotherapy. Specifically, we showed that acidosis-mediated tumour insertion enhanced on-target release of matrix metalloproteinase-responsive reporters in urine. Subsequent on-demand loading of the radiotracer 64Cu allowed pH-dependent tumour visualization, enabling enriched microenvironmental characterization when compared with the conventional metabolic tracer 18F-fluorodeoxyglucose. Through tailored target specificities, this modular platform has the capacity to be engineered as a pan-cancer test that may guide treatment decisions for numerous tumour types.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nazanin Rohani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emilia M Pulver
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Howard Mak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Ludwig Center at Massachusetts Institute of Technology's Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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4
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Sulea T, Rohani N, Baardsnes J, Corbeil CR, Deprez C, Cepero-Donates Y, Robert A, Schrag JD, Parat M, Duchesne M, Jaramillo ML, Purisima EO, Zwaagstra JC. Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment. MAbs 2021; 12:1682866. [PMID: 31777319 PMCID: PMC6927761 DOI: 10.1080/19420862.2019.1682866] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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] [Indexed: 01/26/2023] Open
Abstract
Recent development of monoclonal antibodies as mainstream anticancer agents demands further optimization of their safety for use in humans. Potent targeting and/or effector activities on normal tissues is an obvious toxicity concern. Optimization of specific tumor targeting could be achieved by taking advantage of the extracellular acidity of solid tumors relative to normal tissues. Here, we applied a structure-based computational approach to engineer anti-human epidermal growth factor receptor 2 (Her2) antibodies with selective binding in the acidic tumor microenvironment. We used an affinity maturation platform in which dual-pH histidine-scanning mutagenesis was implemented for pH selectivity optimization. Testing of a small set of designs for binding to the recombinant Her2 ectodomain led to the identification of antigen-binding fragment (Fab) variants with the desired pH-dependent binding behavior. Binding selectivity toward acidic pH was improved by as much as 25-fold relative to the parental bH1-Fab. In vitro experiments on cells expressing intact Her2 confirmed that designed variants formatted as IgG1/k full-size antibodies have high affinity and inhibit the growth of tumor spheroids at a level comparable to that of the benchmark anti-Her2 antibody trastuzumab (Herceptin®) at acidic pH, whereas these effects were significantly reduced at physiological pH. In contrast, both Herceptin and the parental bH1 antibody exhibited strong cell binding and growth inhibition irrespective of pH. This work demonstrates the feasibility of computational optimization of antibodies for selective targeting of the acidic environment such as that found in many solid tumors.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christopher R Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Maria L Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - John C Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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5
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Coughlin S, Bahaadini S, Rohani N, Zevin M, Patane O, Harandi M, Jackson C, Noroozi V, Allen S, Areeda J, Coughlin M, Ruiz P, Berry C, Crowston K, Katsaggelos A, Lundgren A, Østerlund C, Smith J, Trouille L, Kalogera V. Classifying the unknown: Discovering novel gravitational-wave detector glitches using similarity learning. Int J Clin Exp Med 2019. [DOI: 10.1103/physrevd.99.082002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Cancer Res 2019; 79:1952-1966. [PMID: 30755444 PMCID: PMC6467770 DOI: 10.1158/0008-5472.can-18-1604] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [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: 05/25/2018] [Revised: 09/19/2018] [Accepted: 02/06/2019] [Indexed: 01/07/2023]
Abstract
Acidosis is a fundamental feature of the tumor microenvironment, which directly regulates tumor cell invasion by affecting immune cell function, clonal cell evolution, and drug resistance. Despite the important association of tumor microenvironment acidosis with tumor cell invasion, relatively little is known regarding which areas within a tumor are acidic and how acidosis influences gene expression to promote invasion. Here, we injected a labeled pH-responsive peptide to mark acidic regions within tumors. Surprisingly, acidic regions were not restricted to hypoxic areas and overlapped with highly proliferative, invasive regions at the tumor-stroma interface, which were marked by increased expression of matrix metalloproteinases and degradation of the basement membrane. RNA-seq analysis of cells exposed to low pH conditions revealed a general rewiring of the transcriptome that involved RNA splicing and enriched for targets of RNA binding proteins with specificity for AU-rich motifs. Alternative splicing of Mena and CD44, which play important isoform-specific roles in metastasis and drug resistance, respectively, was sensitive to histone acetylation status. Strikingly, this program of alternative splicing was reversed in vitro and in vivo through neutralization experiments that mitigated acidic conditions. These findings highlight a previously underappreciated role for localized acidification of tumor microenvironment in the expression of an alternative splicing-dependent tumor invasion program. SIGNIFICANCE: This study expands our understanding of acidosis within the tumor microenvironment and indicates that acidosis induces potentially therapeutically actionable changes to alternative splicing.
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Affiliation(s)
- Nazanin Rohani
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Maria S Alexis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
| | - Konstantin Krismer
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts
| | - Mira N Moufarrej
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Anthony R Soltis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Department of Biology, MIT, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | | | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Cambridge, Massachusetts
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
- Department of Biology, MIT, Cambridge, Massachusetts
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7
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Premaraj TS, Rohani N, Covey D, Premaraj S. In vitro evaluation of surface properties of Pro Seal ® and Opal ® Seal TM in preventing white spot lesions. Orthod Craniofac Res 2018. [PMID: 28643906 DOI: 10.1111/ocr.12181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 11/28/2022]
Abstract
OBJECTIVES To evaluate the surface properties of two commercially available sealants (Pro Seal® (PS) and Opal® SealTM (OS)) in terms of fluoride(F) release, biofilm formation of Streptococcus mutans and Lactobacillus and the ability to resist acid penetration. SETTING University of Nebraska Medical Center. MATERIAL & METHODS Discs of similar diameter and thickness were made from OS and PS. Discs were soaked in double-distilled water, and F released was measured with fluoride meter daily for 14 consecutive days, then at 21 and 28 days. Biofilm formation was evaluated with Streptococcus mutans and Lactobacilli grown on sealant discs using confocal microscopy. Extracted human teeth (n=8) with sealant-coated buccal surfaces and untreated lingual surfaces were exposed to 0.1M lactic acid(pH=4.5) to test the acid penetration. After 1-4 weeks of exposure, teeth were subjected to microhardness testing and SEM microscopy. RESULTS PS released significantly higher levels of F than OS. PS showed more S. mutans adherence than OS, whereas Lactobacillus did not show any differences in adherence. Both sealants protected enamel surfaces, showing statistically significant difference in the depth of acid penetration compared to their unsealed control sides. CONCLUSION F release was adequate to aid in remineralization, although clinically it would not likely aid in preventing demineralization as there was no prolonged release of F by both sealants tested. S. mutans adherence to OS surface was less compared to PS surface, which could be of relevance in biofilm formation and white spot lesions. Both sealants protected enamel surfaces from acid penetration.
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Affiliation(s)
- T S Premaraj
- College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, USA
| | - N Rohani
- College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, USA
| | - D Covey
- College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, USA
| | - S Premaraj
- College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, USA
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8
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Zevin M, Coughlin S, Bahaadini S, Besler E, Rohani N, Allen S, Cabero M, Crowston K, Katsaggelos AK, Larson SL, Lee TK, Lintott C, Littenberg TB, Lundgren A, Østerlund C, Smith JR, Trouille L, Kalogera V. Gravity Spy: integrating advanced LIGO detector characterization, machine learning, and citizen science. Class Quantum Gravity 2017; 34:064003. [PMID: 29722360 PMCID: PMC5927381 DOI: 10.1088/1361-6382/aa5cea] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
With the first direct detection of gravitational waves, the advanced laser interferometer gravitational-wave observatory (LIGO) has initiated a new field of astronomy by providing an alternative means of sensing the universe. The extreme sensitivity required to make such detections is achieved through exquisite isolation of all sensitive components of LIGO from non-gravitational-wave disturbances. Nonetheless, LIGO is still susceptible to a variety of instrumental and environmental sources of noise that contaminate the data. Of particular concern are noise features known as glitches, which are transient and non-Gaussian in their nature, and occur at a high enough rate so that accidental coincidence between the two LIGO detectors is non-negligible. Glitches come in a wide range of time-frequency-amplitude morphologies, with new morphologies appearing as the detector evolves. Since they can obscure or mimic true gravitational-wave signals, a robust characterization of glitches is paramount in the effort to achieve the gravitational-wave detection rates that are predicted by the design sensitivity of LIGO. This proves a daunting task for members of the LIGO Scientific Collaboration alone due to the sheer amount of data. In this paper we describe an innovative project that combines crowdsourcing with machine learning to aid in the challenging task of categorizing all of the glitches recorded by the LIGO detectors. Through the Zooniverse platform, we engage and recruit volunteers from the public to categorize images of time-frequency representations of glitches into pre-identified morphological classes and to discover new classes that appear as the detectors evolve. In addition, machine learning algorithms are used to categorize images after being trained on human-classified examples of the morphological classes. Leveraging the strengths of both classification methods, we create a combined method with the aim of improving the efficiency and accuracy of each individual classifier. The resulting classification and characterization should help LIGO scientists to identify causes of glitches and subsequently eliminate them from the data or the detector entirely, thereby improving the rate and accuracy of gravitational-wave observations. We demonstrate these methods using a small subset of data from LIGO's first observing run.
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Affiliation(s)
- M Zevin
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
| | - S Coughlin
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
| | - S Bahaadini
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - E Besler
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - N Rohani
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - S Allen
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - M Cabero
- Max-Planck-Institut für Gravitationsphysik, Callinstrasse 38, D-30167 Hannover, Germany
| | - K Crowston
- School of Information Studies, Syracuse University, Syracuse, NY 13210, United States of America
| | - A K Katsaggelos
- Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60201, United States of America
| | - S L Larson
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - T K Lee
- Department of Communication, University of Utah, Salt Lake City, UT 84112, United States of America
| | - C Lintott
- Department of Physics, University of Oxford, Oxford, United Kingdom
| | - T B Littenberg
- NASA/Marshall Space Flight Center, Huntsville, AL 35812, United States of America
| | - A Lundgren
- Max-Planck-Institut für Gravitationsphysik, Callinstrasse 38, D-30167 Hannover, Germany
| | - C Østerlund
- School of Information Studies, Syracuse University, Syracuse, NY 13210, United States of America
| | - J R Smith
- Department of Physics, California State University Fullerton, Fullerton, CA 92831, United States of America
| | - L Trouille
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
- Adler Planetarium, Chicago, IL 60605, United States of America
| | - V Kalogera
- Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) and Deptartment of Physics and Astronomy, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, United States of America
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9
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Oudin MJ, Hughes SK, Rohani N, Moufarrej MN, Jones JG, Condeelis JS, Lauffenburger DA, Gertler FB. Characterization of the expression of the pro-metastatic Mena(INV) isoform during breast tumor progression. Clin Exp Metastasis 2015; 33:249-61. [PMID: 26680363 DOI: 10.1007/s10585-015-9775-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 08/24/2015] [Accepted: 12/07/2015] [Indexed: 01/16/2023]
Abstract
Several functionally distinct isoforms of the actin regulatory Mena are produced by alternative splicing during tumor progression. Forced expression of the Mena(INV) isoform drives invasion, intravasation and metastasis. However, the abundance and distribution of endogenously expressed Mena(INV) within primary tumors during progression remain unknown, as most studies to date have only assessed relative mRNA levels from dissociated tumor samples. We have developed a Mena(INV) isoform-specific monoclonal antibody and used it to examine Mena(INV) expression patterns in mouse mammary and human breast tumors. Mena(INV) expression increases during tumor progression and to examine the relationship between Mena(INV) expression and markers for epithelial or mesenchymal status, stemness, stromal cell types and hypoxic regions. Further, while Mena(INV) robustly expressed in vascularized areas of the tumor, it is not confined to cells adjacent to blood vessels. Altogether, these data demonstrate the specificity and utility of the anti-Mena(INV)-isoform specific antibody, and provide the first description of endogenous Mena(INV) protein expression in mouse and human tumors.
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Affiliation(s)
- Madeleine J Oudin
- Koch Institute for Integrative Cancer Research, MIT, 76-317, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
| | - Shannon K Hughes
- Koch Institute for Integrative Cancer Research, MIT, 76-317, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
| | - Nazanin Rohani
- Koch Institute for Integrative Cancer Research, MIT, 76-317, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Mira N Moufarrej
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
| | - Joan G Jones
- Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - John S Condeelis
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Douglas A Lauffenburger
- Koch Institute for Integrative Cancer Research, MIT, 76-317, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, MIT, 76-317, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.,Department of Biology, MIT, Cambridge, MA, 02139, USA
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10
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Abstract
The physical separation of the embryonic regions that give rise to the tissues and organs of multicellular organisms is a fundamental aspect of morphogenesis. Pioneer experiments by Holtfreter had shown that embryonic cells can sort based on "tissue affinities," which have long been considered to rely on differences in cell-cell adhesion. However, vertebrate embryonic tissues also express a variety of cell surface cues, in particular ephrins and Eph receptors, and there is now firm evidence that these molecules are systematically used to induce local repulsion at contacts between different cell types, efficiently preventing mixing of adjacent cell populations.
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Affiliation(s)
| | - Rudolf Winklbauer
- Dpt. of Cell and Systems Biology; University of Toronto; Toronto, Canada
| | - Nazanin Rohani
- Dpt. of Biology; McGill University; Montreal, Quebec, Canada
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Maghzal N, Kayali HA, Rohani N, Kajava AV, Fagotto F. EpCAM controls actomyosin contractility and cell adhesion by direct inhibition of PKC. Dev Cell 2013; 27:263-77. [PMID: 24183651 DOI: 10.1016/j.devcel.2013.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 07/03/2013] [Accepted: 10/07/2013] [Indexed: 01/06/2023]
Abstract
Epithelial cell adhesion molecule (EpCAM) is a cell-surface protein highly expressed in embryonic tissues and in malignant carcinomas. We report that EpCAM acts as a potent inhibitor of novel protein kinase C (nPKC) in both embryos and cancer cells. We observed dramatic effects of loss of EpCAM on amphibian embryonic tissues, which include sequentially strong overstimulation of PKC activity and of the Erk pathway, leading to exacerbated myosin contractility, loss of cadherin-mediated adhesion, tissue dissociation, and, ultimately, cell death. We show that PKC inhibition is caused by a short segment of the EpCAM cytoplasmic tail. This motif resembles the pseudosubstrate inhibitory domains of PKCs and binds nPKCs with high affinity. A bioinformatics search reveals the existence of similar motifs in other plasma membrane proteins, most of which are cell-cell adhesion molecules. Thus, direct inhibition of PKC by EpCAM represents a general mode of regulation of signal transduction by cell-surface proteins.
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Affiliation(s)
- Nadim Maghzal
- Department of Biology, McGill University, Montreal, H3A1B1 Quebec, Canada
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Fagotto F, Rohani N, Touret AS, Li R. A molecular base for cell sorting at embryonic boundaries: contact inhibition of cadherin adhesion by ephrin/ Eph-dependent contractility. Dev Cell 2013; 27:72-87. [PMID: 24094740 DOI: 10.1016/j.devcel.2013.09.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 06/26/2013] [Accepted: 09/04/2013] [Indexed: 12/20/2022]
Abstract
The mechanism responsible for subdividing the embryo into individual tissues is a fundamental, yet still poorly understood, question in developmental biology. Various general hypotheses have been proposed, involving differences in cell adhesion, contractility, or contact-mediated repulsion. However, the key parameter in tissue separation, i.e., the regulation of cadherin-based adhesion at the boundary, has not yet been investigated. We show that cadherin clustering is specifically inhibited at the vertebrate notochord-presomitic mesoderm boundary, preventing formation of adhesive bonds between cells of the two different types. This local regulation depends on differentially expressed ephrins and Eph receptors, which increase cell contractility and generate a membrane blebbing-like behavior along the boundary. Inhibiting myosin activity is sufficient to induce cadherin clustering and formation of stable contacts across the boundary, causing notochord and presomitic tissues to fuse. Local inhibition of cadherin adhesion explains how sharp separation can be achieved in response to cell-cell contact signals.
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Affiliation(s)
- François Fagotto
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada.
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Rohani N, Canty L, Luu O, Fagotto F, Winklbauer R. EphrinB/EphB signaling controls embryonic germ layer separation by contact-induced cell detachment. PLoS Biol 2011; 9:e1000597. [PMID: 21390298 PMCID: PMC3046958 DOI: 10.1371/journal.pbio.1000597] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [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: 06/25/2010] [Accepted: 01/18/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The primordial organization of the metazoan body is achieved during gastrulation by the establishment of the germ layers. Adhesion differences between ectoderm, mesoderm, and endoderm cells could in principle be sufficient to maintain germ layer integrity and prevent intermixing. However, in organisms as diverse as fly, fish, or amphibian, the ectoderm-mesoderm boundary not only keeps these germ layers separated, but the ectoderm also serves as substratum for mesoderm migration, and the boundary must be compatible with repeated cell attachment and detachment. PRINCIPAL FINDINGS We show that localized detachment resulting from contact-induced signals at the boundary is at the core of ectoderm-mesoderm segregation. Cells alternate between adhesion and detachment, and detachment requires ephrinB/EphB signaling. Multiple ephrinB ligands and EphB receptors are expressed on each side of the boundary, and tissue separation depends on forward signaling across the boundary in both directions, involving partially redundant ligands and receptors and activation of Rac and RhoA. CONCLUSION This mechanism differs from a simple differential adhesion process of germ layer formation. Instead, it involves localized responses to signals exchanged at the tissue boundary and an attachment/detachment cycle which allows for cell migration across a cellular substratum.
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Affiliation(s)
- Nazanin Rohani
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Laura Canty
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Olivia Luu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - François Fagotto
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Rudolf Winklbauer
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
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