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Janská L, Anandi L, Kirchberger NC, Marinkovic ZS, Schachtner LT, Guzelsoy G, Carmona-Fontaine C. The MEMIC: An ex vivo system to model the complexity of the tumor microenvironment. Dis Model Mech 2021; 14:271783. [PMID: 34407185 PMCID: PMC8382743 DOI: 10.1242/dmm.048942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 01/29/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
There is an urgent need for accurate, scalable and cost-efficient models of the tumor microenvironment. Here, we detail how to fabricate and use the metabolic microenvironment chamber (MEMIC) – a 3D-printed ex vivo model of intratumoral heterogeneity. A major driver of the cellular and molecular diversity in tumors is accessibility to the blood stream. Whereas perivascular tumor cells have direct access to oxygen and nutrients, cells further from the vasculature must survive under progressively more ischemic environments. The MEMIC simulates this differential access to nutrients, allow co-culturing any number of cell types, and it is optimized for live imaging and other microscopy-based analyses. Owing to a modular design and full experimental control, the MEMIC provides insights into the tumor microenvironment that would be difficult to obtain via other methods. As proof of principle, we show that cells sense gradual changes in metabolite concentration leading to predictable molecular and cellular spatial patterns. We propose the MEMIC as a complement to standard in vitro and in vivo experiments, diversifying the tools available to accurately model, perturb and monitor the tumor microenvironment. Editor's choice: We present how to fabricate the MEMIC, an experimental model of the tumor microenvironment, describing proof-of-principle experiments and providing image analysis tools that are helpful when using this system.
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Affiliation(s)
- Libuše Janská
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Libi Anandi
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Nell C Kirchberger
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Zoran S Marinkovic
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Logan T Schachtner
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Gizem Guzelsoy
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Carlos Carmona-Fontaine
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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Olesnicky EC, Bono JM, Bell L, Schachtner LT, Lybecker MC. The RNA-binding protein caper is required for sensory neuron development in Drosophila melanogaster. Dev Dyn 2017; 246:610-624. [PMID: 28543982 DOI: 10.1002/dvdy.24523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/18/2017] [Accepted: 05/16/2017] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Alternative splicing mediated by RNA-binding proteins (RBPs) is emerging as a fundamental mechanism for the regulation of gene expression. Alternative splicing has been shown to be a widespread phenomenon that facilitates the diversification of gene products in a tissue-specific manner. Although defects in alternative splicing are rooted in many neurological disorders, only a small fraction of splicing factors have been investigated in detail. RESULTS We find that the splicing factor Caper is required for the development of multiple different mechanosensory neuron subtypes at multiple life stages in Drosophila melanogaster. Disruption of Caper function causes defects in dendrite morphogenesis of larval dendrite arborization neurons and neuronal positioning of embryonic proprioceptors, as well as the development and maintenance of adult mechanosensory bristles. Additionally, we find that Caper dysfunction results in aberrant locomotor behavior in adult flies. Transcriptome-wide analyses further support a role for Caper in alternative isoform regulation of genes that function in neurogenesis. CONCLUSIONS Our results provide the first evidence for a fundamental and broad requirement for the highly conserved splicing factor Caper in the development and maintenance of the nervous system and provide a framework for future studies on the detailed mechanism of Caper-mediated RNA regulation. Developmental Dynamics 246:610-624, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Laura Bell
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Logan T Schachtner
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
| | - Meghan C Lybecker
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado
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Schachtner LT, Sola IE, Forand D, Antonacci S, Postovit AJ, Mortimer NT, Killian DJ, Olesnicky EC. Drosophila Shep and C. elegans SUP-26 are RNA-binding proteins that play diverse roles in nervous system development. Dev Genes Evol 2015; 225:319-30. [PMID: 26271810 DOI: 10.1007/s00427-015-0514-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 05/04/2015] [Accepted: 08/03/2015] [Indexed: 12/14/2022]
Abstract
The Caenorhabditis elegans gene sup-26 encodes a well-conserved RNA-recognition motif-containing RNA-binding protein (RBP) that functions in dendrite morphogenesis of the PVD sensory neuron. The Drosophila ortholog of sup-26, alan shepard (shep), is expressed throughout the nervous system and has been shown to regulate neuronal remodeling during metamorphosis. Here, we extend these studies to show that sup-26 and shep are required for the development of diverse cell types within the nematode and fly nervous systems during embryonic and larval stages. We ascribe roles for sup-26 in regulating dendrite number and the expression of genes involved in mechanosensation within the nematode peripheral nervous system. We also find that in Drosophila, shep regulates dendrite length and branch order of nociceptive neurons, regulates the organization of neuronal clusters of the peripheral nervous system and the organization of axons within the ventral nerve cord. Taken together, our results suggest that shep/sup-26 orthologs play diverse roles in neural development across animal species. Moreover, we discuss potential roles for shep/sup-26 orthologs in the human nervous system.
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Affiliation(s)
- Logan T Schachtner
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Ismail E Sola
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Daniel Forand
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Simona Antonacci
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903, USA
| | - Adam J Postovit
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, CO, 80208, USA.,School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903, USA.
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado at Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA.
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