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Gätjen D, Wieczorek M, Listek M, Tomszak F, Nölle V, Hanack K, Droste M. A switchable secrete-and-capture system enables efficient selection of Pichia pastoris clones producing high yields of Fab fragments. J Immunol Methods 2022; 511:113383. [PMID: 36356896 DOI: 10.1016/j.jim.2022.113383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Pichia pastoris (syn. Komagataella phaffii) represents a commonly used expression system in the biotech industry. High clonal variation of transformants, however, typically results in a broad range of specific productivities for secreted proteins. To isolate rare clones with exceedingly high product titers, an extensive number of clones need to be screened. In contrast to high-throughput screenings of P. pastoris clones in microtiter plates, secrete-and-capture methodologies have the potential to efficiently isolate high-producer clones among millions of cells through fluorescence-activated cell sorting (FACS). Here, we describe a novel approach for the non-covalent binding of fragment antigen-binding (Fab) proteins to the cell surface for the isolation of high-producing clones. Eight different single-chain variable fragment (scFv)-based capture matrices specific for the constant part of the Fabs were fused to the Saccharomyces cerevisiae alpha-agglutinin (SAG1) anchor protein for surface display in P. pastoris. By encoding the capture matrix on an episomal plasmid harboring inherently unstable autonomously replicating sequences (ARS), this secrete-and-capture system offers a switchable scFv display. Efficient plasmid clearance upon removal of selective pressure enabled the direct use of isolated clones for subsequent Fab production. Flow-sorted clones (n = 276) displaying high amounts of Fabs showed a significant increase in median Fab titers detected in the cell-free supernatant (CFS) compared to unsorted clones (n = 276) when cells were cultivated in microtiter plates (factor in the range of ∼21-49). Fab titers of clones exhibiting the highest product titer observed for each of the two approaches were increased by up to 8-fold for the sorted clone. Improved Fab yields of sorted cells vs. unsorted cells were confirmed in an upscaled shake flask cultivation of selected candidates (factor in the range of ∼2-3). Hence, the developed display-based selection method proved to be a valuable tool for efficient clone screening in the early stages of our bioprocess development.
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Affiliation(s)
- Dominic Gätjen
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany; Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
| | - Marek Wieczorek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Martin Listek
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
| | - Florian Tomszak
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Volker Nölle
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
| | - Miriam Droste
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany.
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Fluorescence-activated cell sorting-mediated directed evolution of Wickerhamomyces ciferrii for enhanced production of tetraacetyl phytosphingosine. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-021-1017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Varela JN, Yadav VG. A Pichia biosensor for high-throughput analyses of compounds that can influence mosquito behavior. Microbiologyopen 2021; 10:e1139. [PMID: 33264511 PMCID: PMC7851572 DOI: 10.1002/mbo3.1139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
Mosquitoes utilize their sense of smell to locate prey and feed on their blood. Repellents interfere with the biochemical cascades that detect odors. Consequently, repellants are highly effective and resource-efficient alternatives for controlling the spread of mosquito-borne illnesses. Unfortunately, the discovery of repellents is slow, laborious, and error-prone. To this end, we have taken a giant stride toward improving the speed and accuracy of repellant discovery by constructing a prototypical whole-cell biosensor for accurate detection of mosquito behavior-modifying compounds such as repellants. As a proof-of-concept, we genetically engineered Pichia pastoris to express the olfactory receptor co-receptor (Orco) of Anopheles gambiae mosquitoes. This transmembrane protein behaves like a cationic channel upon activation by stimulatory odorants. When the engineered Pichia cells are cultured in calcium-containing Hank's buffer, induction of the medium with a stimulatory odorant results in an influx of calcium ions into the cells, and the stimulatory effect is quantifiable using the calcium-sequestering fluorescent dye, fluo-4-acetoxymethyl ester. Moreover, the stimulatory effect can be titrated by adjusting either the concentration of calcium ions in the medium or the level of induction of the stimulatory odorant. Subsequent exposure of the activated Pichia cells to a repellant molecule inhibits the stimulatory effect and quenches the fluorescent signal, also in a titratable manner. Significantly, the modular architecture of the biosensor allows easy and efficient expansion of its detection range by co-expressing Orco with other olfactory receptors. The high-throughput assay is also compatible with robotic screening infrastructure, and our development represents a paradigm change for the discovery of mosquito repellants.
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Affiliation(s)
- Julia Nogueira Varela
- Department of Chemical and Biological Engineering & School of Biomedical EngineeringThe University of British ColumbiaVancouverBCCanada
| | - Vikramaditya G. Yadav
- Department of Chemical and Biological Engineering & School of Biomedical EngineeringThe University of British ColumbiaVancouverBCCanada
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4
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Chen Z, Chen JJ, Fan R. Single-Cell Protein Secretion Detection and Profiling. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:431-449. [PMID: 30978293 DOI: 10.1146/annurev-anchem-061318-115055] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Secreted proteins play important roles in mediating various biological processes such as cell-cell communication, differentiation, migration, and homeostasis at the population or tissue level. Here, we review bioanalytical technologies and devices for detecting protein secretions from single cells. We begin by discussing conventional approaches followed by detailing the latest advances in microengineered systems for detecting single-cell protein secretions with an emphasis on multiplex measurement. These platforms include droplet microfluidics, micro-/nanowell-based assays, and microchamber-based assays, among which the advantages and limitations are compared. Microscale systems also enable the tracking of protein secretion dynamics in single cells, further empowering the study of the cell-cell communication network. Looking forward, we discuss the remaining challenges and future opportunities that will transform basic research of cellular secretion functions at the systems level and the clinical applications for immune monitoring and cancer treatment.
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Affiliation(s)
- Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Jonathan J Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA;
- Yale Cancer Center, Yale Stem Cell Center, Human and Translational Immunology Program, Yale School of Medicine, New Haven, Connecticut 06520, USA
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5
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Abstract
Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.
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6
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Fang Y, Chu TH, Ackerman ME, Griswold KE. Going native: Direct high throughput screening of secreted full-length IgG antibodies against cell membrane proteins. MAbs 2017; 9:1253-1261. [PMID: 28933630 PMCID: PMC5680790 DOI: 10.1080/19420862.2017.1381812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Gel microdroplet – fluorescence activated cell sorting (GMD-FACS) is an innovative high throughput screening platform for recombinant protein libraries, and we show here that GMD-FACS can overcome many of the limitations associated with conventional screening methods for antibody libraries. For example, phage and cell surface display benefit from exceptionally high throughput, but generally require high quality, soluble antigen target and necessitate the use of anchored antibody fragments. In contrast, the GMD-FACS assay can screen for soluble, secreted, full-length IgGs at rates of several thousand clones per second, and the technique enables direct screening against membrane protein targets in their native cellular context. In proof-of-concept experiments, rare anti-EGFR antibody clones were efficiently enriched from a 10,000-fold excess of anti-CCR5 clones in just three days. Looking forward, GMD-FACS has the potential to contribute to antibody discovery and engineering for difficult targets, such as ion channels and G protein-coupled receptors.
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Affiliation(s)
- Yongliang Fang
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA
| | - Thach H Chu
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA
| | - Margaret E Ackerman
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA.,b Department of Microbiology and Immunology , Dartmouth , Hanover , NH , USA
| | - Karl E Griswold
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA.,c Immunology & Cancer Immunotherapy Program, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center , Lebanon , NH , USA.,d Department of Biological Sciences , Dartmouth , Hanover , NH.,e Department of Chemistry , Dartmouth , Hanover , NH , USA
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7
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Matthews CB, Wright C, Kuo A, Colant N, Westoby M, Love JC. Reexamining opportunities for therapeutic protein production in eukaryotic microorganisms. Biotechnol Bioeng 2017; 114:2432-2444. [DOI: 10.1002/bit.26378] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/19/2017] [Accepted: 07/03/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Catherine B. Matthews
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - Angel Kuo
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Noelle Colant
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - J. Christopher Love
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
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8
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Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization. SENSORS 2016; 16:232. [PMID: 26891303 PMCID: PMC4801608 DOI: 10.3390/s16020232] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput).
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Looser V, Bruhlmann B, Bumbak F, Stenger C, Costa M, Camattari A, Fotiadis D, Kovar K. Cultivation strategies to enhance productivity of Pichia pastoris: A review. Biotechnol Adv 2015; 33:1177-93. [DOI: 10.1016/j.biotechadv.2015.05.008] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
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Castellarnau M, Szeto GL, Su HW, Tokatlian T, Love JC, Irvine DJ, Voldman J. Stochastic particle barcoding for single-cell tracking and multiparametric analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:489-98. [PMID: 25180800 PMCID: PMC4303509 DOI: 10.1002/smll.201401369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 07/29/2014] [Indexed: 05/04/2023]
Abstract
This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.
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Affiliation(s)
- Marc Castellarnau
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Gregory L. Szeto
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Hao-Wei Su
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Talar Tokatlian
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - J. Christopher Love
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Darrell J. Irvine
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
| | - Joel Voldman
- Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge MA 02139, USA
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11
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Torres A, Hill AS, Love JC. Nanowell-based immunoassays for measuring single-cell secretion: characterization of transport and surface binding. Anal Chem 2014; 86:11562-9. [PMID: 25347613 PMCID: PMC4255675 DOI: 10.1021/ac4030297] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/27/2014] [Indexed: 12/17/2022]
Abstract
Arrays of subnanoliter wells (nanowells) provide a useful system to isolate single cells and analyze their secreted proteins. Two general approaches have emerged: one that uses open arrays and local capture of secreted proteins, and a second (called microengraving) that relies on closed arrays to capture secreted proteins on a solid substrate, which is subsequently removed from the array. However, the design and operating parameters for efficient capture from these two approaches to analyze single-cell secretion have not been extensively considered. Using numerical simulations, we analyzed the operational envelope for both open and closed formats, as a function of the spatial distribution of capture ligands, their affinities for the protein, and the rates of single-cell secretion. Based on these analyses, we present a modified approach to capture secreted proteins in-well for highly active secreting cells. This simple method for in-well detection should facilitate rapid identification of cell lines with high specific productivities.
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Affiliation(s)
- Alexis
J. Torres
- Department of Chemical Engineering, Department of Biological
Engineering, and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Abby S. Hill
- Department of Chemical Engineering, Department of Biological
Engineering, and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - J. Christopher Love
- Department of Chemical Engineering, Department of Biological
Engineering, and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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12
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Zepeda AB, Figueroa CA, Abdalla DSP, Maranhão AQ, Ulloa PH, Pessoa A, Farías JG. Biomarkers to evaluate the effects of temperature and methanol on recombinant Pichia pastoris. Braz J Microbiol 2014; 45:475-83. [PMID: 25242930 PMCID: PMC4166271 DOI: 10.1590/s1517-83822014000200014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Pichia pastoris is methylotrophic yeast used as an efficient expression system for heterologous protein production. In order to evaluate the effects of temperature (10 and 30 °C) and methanol (1 and 3% (v/v)) on genetically-modified Pichia pastoris, different biomarkers were evaluated: Heat stress (HSF-1 and Hsp70), oxidative stress (OGG1 and TBARS) and antioxidant (GLR). Three yeast cultures were performed: 3X = 3% methanol-10 °C, 4X = 3% methanol-30 °C, and 5X = 1% methanol-10°C. The expression level of HIF-1α, HSF-1, HSP-70 and HSP-90 biomarkers were measured by Western blot and in situ detection was performed by immunocytochemistry. Ours results show that at 3% methanol −30 °C there is an increase of mitochondrial OGG1 (mtOGG1), Glutathione Reductase (GLR) and TBARS. In addition, there was a cytosolic expression of HSF-1 and HSP-70, which indicates a deprotection against nucleolar fragmentation (apoptosis). On the other hand, at 3% methanol −10 °C and 1% and at methanol −10 °C conditions there was nuclear expression of OGG1, lower levels of TBARS and lower expression of GLR, cytosolic expression of HSF-1 and nuclear expression HSP-70. In conclusion, our results suggest that 3% methanol-30 °C is a condition that induces a strong oxidative stress and risk factors of apoptosis in modified-genetically P. pastoris.
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Affiliation(s)
- Andrea B Zepeda
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile. ; Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carolina A Figueroa
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile. ; Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Dulcineia S P Abdalla
- Departamento de Análises Clínicas e Toxicológicas Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andrea Q Maranhão
- Departamento de Biología Celular Instituto de Ciências Biológicas Universidade de Brasilia BrasíliaDF Brazil Departamento de Biología Celular, Instituto de Ciências Biológicas, Universidade de Brasilia, Brasília, DF, Brazil
| | - Patricio H Ulloa
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
| | - Adalberto Pessoa
- Departamento de Tecnologia Bioquímico-Farmacêutica Faculdade de Ciências Farmacêuticas Universidade de São Paulo São PauloSP Brazil Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jorge G Farías
- Departamento de Ingeniería Química Facultad de Ingeniería, Ciencias y Administración Universidad de La Frontera Temuco Chile Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
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13
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Adalsteinsson VA, Tahirova N, Tallapragada N, Yao X, Campion L, Angelini A, Douce TB, Huang C, Bowman B, Williamson CA, Kwon DS, Wittrup KD, Love JC. Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines. Integr Biol (Camb) 2014; 5:1272-81. [PMID: 23995780 DOI: 10.1039/c3ib40059j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is an inflammatory disease of tissue that is largely influenced by the interactions between multiple cell types, secreted factors, and signal transduction pathways. While single-cell sequencing continues to refine our understanding of the clonotypic heterogeneity within tumors, the complex interplay between genetic variations and non-genetic factors ultimately affects therapeutic outcome. Much has been learned through bulk studies of secreted factors in the tumor microenvironment, but the secretory behavior of single cells has been largely uncharacterized. Here we directly profiled the secretions of ELR+ CXC chemokines from thousands of single colorectal tumor and stromal cells, using an array of subnanoliter wells and a technique called microengraving to characterize both the rates of secretion of several factors at once and the numbers of cells secreting each chemokine. The ELR+ CXC chemokines are highly redundant, pro-angiogenic cytokines that signal via the CXCR1 and CXCR2 receptors, influencing tumor growth and progression. We find that human primary colorectal tumor and stromal cells exhibit polyfunctional heterogeneity in the combinations and magnitudes of secretions for these chemokines. In cell lines, we observe similar variance: phenotypes observed in bulk can be largely absent among the majority of single cells, and discordances exist between secretory states measured and gene expression for these chemokines among single cells. Together, these measures suggest secretory states among tumor cells are complex and can evolve dynamically. Most importantly, this study reveals new insight into the intratumoral phenotypic heterogeneity of human primary tumors.
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Affiliation(s)
- Viktor A Adalsteinsson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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14
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Gierahn TM, Loginov D, Love JC. Crossword: a fully automated algorithm for the segmentation and quality control of protein microarray images. J Proteome Res 2014; 13:362-71. [PMID: 24417579 PMCID: PMC3979532 DOI: 10.1021/pr401167h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological assays formatted as microarrays have become a critical tool for the generation of the comprehensive data sets required for systems-level understanding of biological processes. Manual annotation of data extracted from images of microarrays, however, remains a significant bottleneck, particularly for protein microarrays due to the sensitivity of this technology to weak artifact signal. In order to automate the extraction and curation of data from protein microarrays, we describe an algorithm called Crossword that logically combines information from multiple approaches to fully automate microarray segmentation. Automated artifact removal is also accomplished by segregating structured pixels from the background noise using iterative clustering and pixel connectivity. Correlation of the location of structured pixels across image channels is used to identify and remove artifact pixels from the image prior to data extraction. This component improves the accuracy of data sets while reducing the requirement for time-consuming visual inspection of the data. Crossword enables a fully automated protocol that is robust to significant spatial and intensity aberrations. Overall, the average amount of user intervention is reduced by an order of magnitude and the data quality is increased through artifact removal and reduced user variability. The increase in throughput should aid the further implementation of microarray technologies in clinical studies.
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Affiliation(s)
- Todd M Gierahn
- Department of Chemical Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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15
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Gasser B, Prielhofer R, Marx H, Maurer M, Nocon J, Steiger M, Puxbaum V, Sauer M, Mattanovich D. Pichia pastoris: protein production host and model organism for biomedical research. Future Microbiol 2013; 8:191-208. [DOI: 10.2217/fmb.12.133] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pichia pastoris is the most frequently used yeast system for heterologous protein production today. The last few years have seen several products based on this platform reach approval as biopharmaceutical drugs. Successful glycoengineering to humanize N-glycans is further fuelling this development. However, detailed understanding of the yeast’s physiology, genetics and regulation has only developed rapidly in the last few years since published genome sequences have become available. An expanding toolbox of genetic elements and strains for the improvement of protein production is being generated, including promoters, gene copy-number enhancement, gene knockout and high-throughput methods. Protein folding and secretion have been identified as significant bottlenecks in yeast expression systems, pinpointing a major target for strain optimization. At the same time, it has become obvious that P. pastoris, as an evolutionarily more ‘ancient’ yeast, may in some cases be a better model for human cell biology and disease than Saccharomyces cerevisiae.
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Affiliation(s)
- Brigitte Gasser
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Roland Prielhofer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Hans Marx
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Michael Maurer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
- University of Applied Sciences FH-Campus Vienna, School of Bioengineering, 1190 Vienna, Austria
| | - Justyna Nocon
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Matthias Steiger
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Verena Puxbaum
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Michael Sauer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Diethard Mattanovich
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
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Markely LRA, Wang DIC. High-throughput analysis of intraclonal variability of glycoprotein sialylation. Biotechnol Prog 2011; 28:591-4. [DOI: 10.1002/btpr.738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 09/24/2011] [Indexed: 01/01/2023]
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