1
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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2
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Abstract
Treatment resistance leads to cancer patient mortality. Therapeutic approaches that employ synthetic lethality to target mutational vulnerabilities in key tumor cell signaling pathways have proven effective in overcoming therapeutic resistance in some cancers. Yet, tumors are organs composed of malignant cells residing within a cellular and noncellular stroma. Tumor evolution and resistance to anticancer treatment are mediated through a dynamic and reciprocal dialogue with the tumor microenvironment (TME). Accordingly, expanding tumor cell synthetic lethality to encompass contextual synthetic lethality has the potential to eradicate tumors by targeting critical TME circuits that promote tumor progression and therapeutic resistance. In this Review, we summarize current knowledge about the TME and discuss its role in treatment. We outline the concept of tumor cell-specific synthetic lethality and describe therapeutic approaches to expand this paradigm to leverage TME synthetic lethality to improve cancer therapy.
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Affiliation(s)
| | | | - Zena Werb
- Department of Anatomy
- Helen Diller Family Comprehensive Cancer Center
| | - Valerie M. Weaver
- Department of Surgery
- Helen Diller Family Comprehensive Cancer Center
- Center for Bioengineering and Tissue Regeneration, and
- Radiation Oncology, Department of Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California, USA
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3
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Metcalf KJ, Kimmel BR, Sykora DJ, Modica JA, Parker KA, Berens E, Dai R, Dravid VP, Werb Z, Mrksich M. Synthetic Tuning of Domain Stoichiometry in Nanobody-Enzyme Megamolecules. Bioconjug Chem 2020; 32:143-152. [PMID: 33301672 DOI: 10.1021/acs.bioconjchem.0c00578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This paper presents a method to synthetically tune atomically precise megamolecule nanobody-enzyme conjugates for prodrug cancer therapy. Previous efforts to create heterobifunctional protein conjugates suffered from heterogeneity in domain stoichiometry, which in part led to the failure of antibody-enzyme conjugates in clinical trials. We used the megamolecule approach to synthesize anti-HER2 nanobody-cytosine deaminase conjugates with tunable numbers of nanobody and enzyme domains in a single, covalent molecule. Linking two nanobody domains to one enzyme domain improved avidity to a human cancer cell line by 4-fold but did not increase cytotoxicity significantly due to lowered enzyme activity. In contrast, a megamolecule composed of one nanobody and two enzyme domains resulted in an 8-fold improvement in the catalytic efficiency and increased the cytotoxic effect by over 5-fold in spheroid culture, indicating that the multimeric structure allowed for an increase in local drug activation. Our work demonstrates that the megamolecule strategy can be used to study structure-function relationships of protein conjugate therapeutics with synthetic control of protein domain stoichiometry.
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Affiliation(s)
- Kevin J Metcalf
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Blaise R Kimmel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel J Sykora
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Kelly A Parker
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric Berens
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Raymond Dai
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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4
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Winkler J, Abisoye-Ogunniyan A, Metcalf KJ, Werb Z. Concepts of extracellular matrix remodelling in tumour progression and metastasis. Nat Commun 2020; 11:5120. [PMID: 33037194 PMCID: PMC7547708 DOI: 10.1038/s41467-020-18794-x] [Citation(s) in RCA: 839] [Impact Index Per Article: 209.8] [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: 01/24/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Tissues are dynamically shaped by bidirectional communication between resident cells and the extracellular matrix (ECM) through cell-matrix interactions and ECM remodelling. Tumours leverage ECM remodelling to create a microenvironment that promotes tumourigenesis and metastasis. In this review, we focus on how tumour and tumour-associated stromal cells deposit, biochemically and biophysically modify, and degrade tumour-associated ECM. These tumour-driven changes support tumour growth, increase migration of tumour cells, and remodel the ECM in distant organs to allow for metastatic progression. A better understanding of the underlying mechanisms of tumourigenic ECM remodelling is crucial for developing therapeutic treatments for patients. Tumors are more than cancer cells — the extracellular matrix is a protein structure that organizes all tissues and is altered in cancer. Here, the authors review recent progress in understanding how the cancer cells and tumor-associated stroma cells remodel the extracellular matrix to drive tumor growth and metastasis.
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Affiliation(s)
- Juliane Winkler
- Department of Anatomy, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94143, USA.
| | - Abisola Abisoye-Ogunniyan
- Department of Anatomy, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94143, USA
| | - Kevin J Metcalf
- Department of Anatomy, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94143, USA
| | - Zena Werb
- Department of Anatomy, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94143, USA
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5
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Abbasi AJ, Abisoye-Ogunniyan A, Alanizi AA, Alazzeh A, Atamaniuc E, Awni L, Berens EB, Bouwman M, Diadhiou CM, Gonzalez H, Hagerling C, Hinrichs JH, Liu SY, Metcalf KJ, Nanjaraj A, Owyong M, Qureshi S, Robles I, Salari K, Shamardani K, Verbeek T, Winkler J, Xu Z. Our mentor Zena Werb (1945–2020). Neoplasia 2020. [DOI: 10.1016/j.neo.2020.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Zhou S, Metcalf KJ, Bugga P, Grant J, Mrksich M. Photoactivatable Reaction for Covalent Nanoscale Patterning of Multiple Proteins. ACS Appl Mater Interfaces 2018; 10:40452-40459. [PMID: 30379516 PMCID: PMC6640637 DOI: 10.1021/acsami.8b16736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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] [Indexed: 06/08/2023]
Abstract
This article describes a photochemical approach for independently patterning multiple proteins to an inert substrate, particularly for studies of cell adhesion. A photoactivatable chloropyrimidine ligand was employed for covalent immobilization of SnapTag fusion proteins on self-assembled monolayers of alkanethiolates on gold. A two-step procedure was used: first, patterned UV illumination of the surface activated protein capture ligands, and second, incubation with a SnapTag fusion protein bound to the surface in illuminated regions. Two different fluorescent proteins were patterned in registry with features of 400 nm in size over a 1 mm2 area. An example is given wherein an anti-carcinoembryonic antigen (anti-CEA) scFv antibody was patterned to direct the selective attachment of a human cancer cell line that express the CEA antigen. This method enables the preparation of surfaces with control over the density and activity of independently patterned proteins.
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Affiliation(s)
- Shengwang Zhou
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, People’s
Republic of China
- Department of Biomedical Engineering,
Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United
States
| | - Kevin J. Metcalf
- Department of Biomedical Engineering,
Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United
States
| | - Pradeep Bugga
- Department of Chemistry, Northwestern
University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jennifer Grant
- Department of Chemistry, Northwestern
University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, People’s
Republic of China
- Department of Biomedical Engineering,
Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United
States
- Department of Chemistry, Northwestern
University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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7
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Abstract
In this investigation, we report evidence for energy transfer in new protein-based megamolecules with tunable distances between donor and acceptor fluorescent proteins. The megamolecules used in this work are monodisperse oligomers, with molecular weights of ∼100-300 kDa and lengths of ∼5-20 nm, and are precisely defined structures of fusion protein building blocks and covalent cross-linkers. Such structures are promising because the study of energy transfer in protein complexes is usually difficult in this long length regime due to synthetic limitations. We incorporated fluorescent proteins into the megamolecule structure and varied the separation distance between donor and acceptor by changing the length of the cross-linker in dimer conjugates and inserting nonfluorescent spacer proteins to create oligomers. Two-photon absorption measurements demonstrated strong coupling between donor and acceptor dipoles in the megamolecules. For the dimer systems, no effect of the cross-linker length on energy transfer efficiency was observed with the steady-state fluorescence investigation. However, for the same dimer conjugates, energy transfer rates decreased upon increasing cross-linker length, as evaluated by fluorescence up-conversion. Molecular dynamics simulations were used to rationalize the results, providing quantitative agreement between measured and calculated energy transfer lengths for steady-state results, and showing that the differences between the time-resolved and steady-state measurements arise from the long time scale for large-scale fluctuations in the megamolecule structure. Our results show an increase in energy transfer length with increasing megamolecule size. This is evidence for long-range energy transfer in large protein megamolecules.
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Affiliation(s)
- Elijah L. Taylor
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kevin J. Metcalf
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Benedetta Carlotti
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Cheng-Tsung Lai
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A. Modica
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Burns ML, Malott TM, Metcalf KJ, Puguh A, Chan JR, Shusta EV. Pro-region engineering for improved yeast display and secretion of brain derived neurotrophic factor. Biotechnol J 2015; 11:425-36. [PMID: 26580314 DOI: 10.1002/biot.201500360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 06/09/2015] [Revised: 08/21/2015] [Accepted: 10/19/2015] [Indexed: 11/11/2022]
Abstract
Brain derived neurotrophic factor (BDNF) is a promising therapeutic candidate for a variety of neurological diseases. However, it is difficult to produce as a recombinant protein. In its native mammalian context, BDNF is first produced as a pro-protein with subsequent proteolytic removal of the pro-region to yield mature BDNF protein. Therefore, in an attempt to improve yeast as a host for heterologous BDNF production, the BDNF pro-region was first evaluated for its effects on BDNF surface display and secretion. Addition of the wild-type pro-region to yeast BDNF production constructs improved BDNF folding both as a surface-displayed and secreted protein in terms of binding its natural receptors TrkB and p75, but titers remained low. Looking to further enhance the chaperone-like functions provided by the pro-region, two rounds of directed evolution were performed, yielding mutated pro-regions that further improved the display and secretion properties of BDNF. Subsequent optimization of the protease recognition site was used to control whether the produced protein was in pro- or mature BDNF forms. Taken together, we have demonstrated an effective strategy for improving BDNF compatibility with yeast protein engineering and secretion platforms.
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Affiliation(s)
- Michael L Burns
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Thomas M Malott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin J Metcalf
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Arthya Puguh
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonah R Chan
- Department of Neurology, Program in Neuroscience, University of California, San Francisco, San Francisco, California, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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9
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Azam A, Li C, Metcalf KJ, Tullman-Ercek D. Type III secretion as a generalizable strategy for the production of full-length biopolymer-forming proteins. Biotechnol Bioeng 2015; 113:2313-20. [PMID: 25993982 DOI: 10.1002/bit.25656] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/29/2015] [Accepted: 05/11/2015] [Indexed: 12/29/2022]
Abstract
Biopolymer-forming proteins are integral in the development of customizable biomaterials, but recombinant expression of these proteins is challenging. In particular, biopolymer-forming proteins have repetitive, glycine-rich domains and, like many heterologously expressed proteins, are prone to incomplete translation, aggregation, and proteolytic degradation in the production host. This necessitates tailored purification processes to isolate each full-length protein of interest from the truncated forms as well as other contaminating proteins; owing to the repetitive nature of these proteins, the truncated polypeptides can have very similar chemistry to the full-length form and are difficult to separate from the full-length protein. We hypothesized that bacterial expression and secretion would be a promising alternative option for biomaterials-forming proteins, simplifying isolation of the full-length target protein. By using a selective secretion system, truncated forms of the protein are not secreted and thus are not found in the culture harvest. We show that a synthetically upregulated type III secretion system leads to a general increase in secretion titer for each protein that we tested. Moreover, we observe a substantial enhancement in the homogeneity of full-length forms of pro-resilin, tropo-elastin crosslinking domains, and silk proteins produced in this manner, as compared with proteins purified from the cytosol. Secretion via the type III apparatus limits co-purification of truncated forms of the target protein and increases protein purity without extensive purification steps. Demonstrating the utility of such a system, we introduce several modifications to resilin-based peptides and use an un-optimized, single-column process to purify these proteins. The resulting materials are of sufficiently high quantity and yield for the production of antimicrobial hydrogels with highly reproducible rheological properties. The ease of this process and its applicability to an array of engineered biomaterial-forming peptides lend support for the application of bacterial expression and secretion for other proteins that are traditionally difficult to express and isolate from the bacterial cytoplasm. Biotechnol. Bioeng. 2016;113: 2313-2320. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Anum Azam
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California
| | - Cheng Li
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California
| | - Kevin J Metcalf
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720
| | - Danielle Tullman-Ercek
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California. .,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720.
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