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Article ; Online: Bridging systems biology and tissue engineering: Unleashing the full potential of complex 3D

Cadavid, Jose L / Li, Nancy T / McGuigan, Alison P

Biophysics reviews

2024 Volume 5, Issue 2, Page(s) 21301

Abstract: Rapid advances in tissue engineering have resulted in more complex and physiologically relevant ... ...

Abstract	Rapid advances in tissue engineering have resulted in more complex and physiologically relevant 3D
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2688-4089
ISSN (online)	2688-4089
DOI	10.1063/5.0179125
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Article ; Online: Exploring New Dimensions of Tumor Heterogeneity: The Application of Single Cell Analysis to Organoid-Based 3D In Vitro Models.

Landon-Brace, Natalie / Li, Nancy T / McGuigan, Alison P

Advanced healthcare materials

2023 Volume 12, Issue 26, Page(s) e2300903

Abstract: Modeling the heterogeneity of the tumor microenvironment (TME) in vitro is essential to investigating fundamental cancer biology and developing novel treatment strategies that holistically address the factors affecting tumor progression and therapeutic ... ...

Abstract	Modeling the heterogeneity of the tumor microenvironment (TME) in vitro is essential to investigating fundamental cancer biology and developing novel treatment strategies that holistically address the factors affecting tumor progression and therapeutic response. Thus, the development of new tools for both in vitro modeling, such as patient-derived organoids (PDOs) and complex 3D in vitro models, and single cell omics analysis, such as single-cell RNA-sequencing, represents a new frontier for investigating tumor heterogeneity. Specifically, the integration of PDO-based 3D in vitro models and single cell analysis offers a unique opportunity to explore the intersecting effects of interpatient, microenvironmental, and tumor cell heterogeneity on cell phenotypes in the TME. In this review, the current use of PDOs in complex 3D in vitro models of the TME is discussed and the emerging directions in the development of these models are highlighted. Next, work that has successfully applied single cell analysis to PDO-based models is examined and important experimental considerations are identified for this approach. Finally, open questions are highlighted that may be amenable to exploration using the integration of PDO-based models and single cell analysis. Ultimately, such investigations may facilitate the identification of novel therapeutic targets for cancer that address the significant influence of tumor-TME interactions.
MeSH term(s)	Humans ; Neoplasms ; Biology ; Organoids ; Phenotype ; Single-Cell Analysis ; Tumor Microenvironment
Language	English
Publishing date	2023-08-27
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2649576-4
ISSN	2192-2659 ; 2192-2640
ISSN (online)	2192-2659
ISSN	2192-2640
DOI	10.1002/adhm.202300903
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Article ; Online: Application of CRISPR screens to investigate mammalian cell competition.

Paraskevopoulos, Michail / McGuigan, Alison P

Briefings in functional genomics

2021 Volume 20, Issue 3, Page(s) 135–147

Abstract: Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control ... ...

Abstract	Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a 'super-competitor' status and outcompete the normal epithelium to establish a precancerous field. To date, many genetic drivers of cell competition have been identified predominately through studies in Drosophila. Especially during the last couple of years, ethylmethanesulfonate-based genetic screens have been instrumental to our understanding of the molecular regulators behind some of the most common competition mechanisms in Drosophila, namely competition due to impaired ribosomal function (or anabolism) and mechanical sensitivity. Despite recent findings in Drosophila and in mammalian models of cell competition, the drivers of mammalian cell competition remain largely elusive. Since the discovery of CRISPR/Cas9, its use in functional genomics has been indispensable to uncover novel cancer vulnerabilities. We envision that CRISPR/Cas9 screens will enable systematic, genome-scale probing of mammalian cell competition to discover novel mutations that not only trigger cell competition but also identify novel molecular components that are essential for the recognition and elimination of less fit cells. In this review, we summarize recent contributions that further our understanding of the molecular mechanisms of cell competition by genetic screening in Drosophila, and provide our perspective on how similar and novel screening strategies made possible by whole-genome CRISPR/Cas9 screening can advance our understanding of mammalian cell competition in the future.
MeSH term(s)	Animals ; CRISPR-Cas Systems/genetics ; Cell Competition ; Genetic Testing ; Genome ; Mammals/genetics
Language	English
Publishing date	2021-03-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elab020
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Article ; Online: Easy and robust micropatterning using fibrinogen anchors.

Latour, Simon / McGuigan, Alison P

The Journal of cell biology

2020 Volume 220, Issue 2

Abstract: Micropatterning is a process to precisely deposit molecules, typically proteins, onto a substrate of choice with micrometer resolution. Watson et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202009063) describe an innovative yet accessible ... ...

Abstract	Micropatterning is a process to precisely deposit molecules, typically proteins, onto a substrate of choice with micrometer resolution. Watson et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202009063) describe an innovative yet accessible strategy to enable the reproducible micropatterning of virtually any protein while maintaining its biological activity.
MeSH term(s)	Fibrinogen
Chemical Substances	Fibrinogen (9001-32-5)
Language	English
Publishing date	2020-11-06
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202012105
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Article ; Online: Characterization of an

Lee, Daniel / Latour, Simon / Emblem, Michael / Clark, Hunter J / Santos, Jobette T / Jang, Jaewan / McGuigan, Alison P / Nitz, Mark

Bioconjugate chemistry

2023 Volume 34, Issue 12, Page(s) 2358–2365

Abstract: Aldehydes are attractive bioorthogonal coupling partners. The ease of manipulation of aldehydes and their orthogonality to other classes of bioorthogonal reactions have inspired the exploration of chemistries, which generate irreversible conjugates. ... ...

Abstract	Aldehydes are attractive bioorthogonal coupling partners. The ease of manipulation of aldehydes and their orthogonality to other classes of bioorthogonal reactions have inspired the exploration of chemistries, which generate irreversible conjugates. Similarly, nitrones have been shown to be potent 1,3-dipoles in bioorthogonal reactions when paired with strained alkynes. Here, we combine the reactivity of nitrones with the simplicity of aldehydes using an
MeSH term(s)	Humans ; HEK293 Cells ; Proteins/chemistry ; Nitrogen Oxides/chemistry ; Alkynes/chemistry ; Aldehydes ; Azides/chemistry ; Cycloaddition Reaction
Chemical Substances	nitrones ; Proteins ; Nitrogen Oxides ; Alkynes ; Aldehydes ; Azides
Language	English
Publishing date	2023-12-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.3c00463
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Article ; Online: Design Parameters for a Mass Cytometry Detectable HaloTag Ligand.

Potter, Nicole / Latour, Simon / Wong, Edmond C N / Winnik, Mitchell A / Jackson, Hartland W / McGuigan, Alison P / Nitz, Mark

Bioconjugate chemistry

2023 Volume 35, Issue 1, Page(s) 80–91

Abstract: Mass cytometry permits the high dimensional analysis of complex biological samples; however, some techniques are not yet integrated into the mass cytometry workflow due to reagent availability. The use of self-labeling protein systems, such as HaloTag, ... ...

Abstract	Mass cytometry permits the high dimensional analysis of complex biological samples; however, some techniques are not yet integrated into the mass cytometry workflow due to reagent availability. The use of self-labeling protein systems, such as HaloTag, are one such application. Here, we describe the design and implementation of the first mass cytometry ligands for use with HaloTag. "Click"-amenable HaloTag warheads were first conjugated onto poly(l-lysine) or poly(acrylic acid) polymers that were then functionalized with diethylenetriaminepentaacetic acid (DTPA) lutetium metal chelates. Kinetic analysis of the HaloTag labeling rates demonstrated that the structure appended to the 1-chlorohexyl warhead was key to success. A construct with a diethylene glycol spacer appended to a benzamide gave similar rates (
MeSH term(s)	Humans ; Ligands ; Kinetics ; HEK293 Cells ; Proteins ; Polymers ; Hydrolases
Chemical Substances	Ligands ; haloalkane dehalogenase (EC 3.8.1.5) ; Proteins ; Polymers ; Hydrolases (EC 3.-)
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/acs.bioconjchem.3c00434
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Article ; Online: REVOLVER: A low-cost automated protein purifier based on parallel preparative gravity column workflows.

Diep, Patrick / Cadavid, Jose L / Yakunin, Alexander F / McGuigan, Alison P / Mahadevan, Radhakrishnan

HardwareX

2022 Volume 11, Page(s) e00291

Abstract: Protein purification is a ubiquitous procedure in biochemistry and the life sciences, and represents a key step in the protein production pipeline. The need for scalable and parallel protein purification systems is driven by the demands for increasing ... ...

Abstract	Protein purification is a ubiquitous procedure in biochemistry and the life sciences, and represents a key step in the protein production pipeline. The need for scalable and parallel protein purification systems is driven by the demands for increasing the throughput of recombinant protein characterization. Therefore, automating the process to simultaneously handle multiple samples with minimal human intervention is highly desirable, yet there are only a handful of such systems that have been developed, all of which are closed source and expensive. To address this challenge, we present REVOLVER, a 3D-printed programmable protein purification system based on gravity-column workflows and controlled by Arduino boards that can be built for under $130 USD. REVOLVER takes a cell lysate sample and completes a full protein purification process with almost no human intervention and yields results indistinguishable from those obtained by an experienced biochemist when purifying a real-world protein sample. We further present and describe MULTI-VOLVER, a scalable version of the REVOLVER that allows for parallel purification of up to six samples and can be built for under $250 USD. Both systems can help accelerate protein purification and ultimately link them to bio-foundries for protein characterization and engineering.
Language	English
Publishing date	2022-03-11
Publishing country	England
Document type	Journal Article
ISSN	2468-0672
ISSN (online)	2468-0672
DOI	10.1016/j.ohx.2022.e00291
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Article ; Online: An Automation Workflow for High-Throughput Manufacturing and Analysis of Scaffold-Supported 3D Tissue Arrays.

Cao, Ruonan / Li, Nancy T / Latour, Simon / Cadavid, Jose L / Tan, Cassidy M / Forman, Ari / Jackson, Hartland W / McGuigan, Alison P

Advanced healthcare materials

2023 Volume 12, Issue 19, Page(s) e2202422

Abstract: Patient-derived organoids have emerged as a useful tool to model tumour heterogeneity. Scaling these complex culture models while enabling stratified analysis of different cellular sub-populations, however, remains a challenge. One strategy to enable ... ...

Abstract	Patient-derived organoids have emerged as a useful tool to model tumour heterogeneity. Scaling these complex culture models while enabling stratified analysis of different cellular sub-populations, however, remains a challenge. One strategy to enable higher throughput organoid cultures is the scaffold-supported platform for organoid-based tissues (SPOT). SPOT allows the generation of flat, thin, and dimensionally-defined microtissues in both 96- and 384-well plate footprints that are compatible with longitudinal image-based readouts. SPOT is currently manufactured manually, however, limiting scalability. In this study, an automation approach to engineer tumour-mimetic 3D microtissues in SPOT using a liquid handler is optimized and comparable within- and between-sample variation to standard manual manufacturing is shown. Further, a liquid handler-supported cell extraction protocol to support single-cell-based end-point analysis using high-throughput flow cytometry and multiplexed cytometry by time of flight is developed. As a proof-of-value demonstration, 3D complex tissues containing different proportions of tumour and stromal cells are generated to probe the reciprocal impact of co-culture. It is also demonstrated that primary patient-derived organoids can be incorporated into the pipeline to capture patient-level tumour heterogeneity. It is envisioned that this automated 96/384-SPOT workflow will provide opportunities for future applications in high-throughput screening for novel personalized therapeutic targets.
MeSH term(s)	Humans ; Workflow ; Coculture Techniques ; Neoplasms/pathology ; High-Throughput Screening Assays/methods ; Automation ; Organoids
Language	English
Publishing date	2023-05-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649576-4
ISSN	2192-2659 ; 2192-2640
ISSN (online)	2192-2659
ISSN	2192-2640
DOI	10.1002/adhm.202202422
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Article ; Online: Planar organization of airway epithelial cell morphology using hydrogel grooves during ciliogenesis fails to induce ciliary alignment.

Varma, Ratna / Poon, James / Liao, Zhongfa / Aitchison, J Stewart / Waddell, Thomas K / Karoubi, Golnaz / McGuigan, Alison P

Biomaterials science

2022 Volume 10, Issue 2, Page(s) 396–409

Abstract: Topographical cues are known to influence cell organization both in native tissues ... ...

Abstract	Topographical cues are known to influence cell organization both in native tissues and
MeSH term(s)	Cells, Cultured ; Cilia ; Epithelial Cells ; Epithelium ; Humans ; Hydrogels ; Induced Pluripotent Stem Cells
Chemical Substances	Hydrogels
Language	English
Publishing date	2022-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2693928-9
ISSN	2047-4849 ; 2047-4830
ISSN (online)	2047-4849
ISSN	2047-4830
DOI	10.1039/d1bm01327k
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Article ; Online: Applications of Omics Technologies for Three-Dimensional

Pieters, Vera M / Co, Ileana L / Wu, Nila C / McGuigan, Alison P

Tissue engineering. Part C, Methods

2021 Volume 27, Issue 3, Page(s) 183–199

Abstract: Omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, multiomics, and integrated modalities, have greatly contributed to our understanding of various diseases by enabling researchers to probe the ... ...

Abstract	Omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, multiomics, and integrated modalities, have greatly contributed to our understanding of various diseases by enabling researchers to probe the molecular wiring of cellular systems in a high-throughput and precise manner. With the development of tissue-engineered three-dimensional (3D)
MeSH term(s)	Epigenomics ; Genomics ; Humans ; Metabolomics ; Neoplasms ; Proteomics
Language	English
Publishing date	2021-02-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2420585-0
ISSN	1937-3392 ; 1937-3384
ISSN (online)	1937-3392
ISSN	1937-3384
DOI	10.1089/ten.TEC.2020.0300
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