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Aksoylu IS, Martin P, Robert F, Szkop KJ, Redmond NE, Bhattacharyya S, Wang J, Chen S, Beauchamp RL, Nobeli I, Pelletier J, Larsson O, Ramesh V. Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations. Mol Autism 2023; 14:39. [PMID: 37880800 PMCID: PMC10601155 DOI: 10.1186/s13229-023-00572-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND.
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Affiliation(s)
- Inci S Aksoylu
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Pauline Martin
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Francis Robert
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Nicholas E Redmond
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Srirupa Bhattacharyya
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Jennifer Wang
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Shan Chen
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Roberta L Beauchamp
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences,, Birkbeck, University of London, London, WC1E 7HX, UK
| | - Jerry Pelletier
- Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, PQ, H3G1Y6, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 77, Stockholm, Sweden.
| | - Vijaya Ramesh
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA.
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Okebiorun M, Oberbeck C, Waite C, Clark S, Miller D, Barney Smith EH, Cornell KA, Browning J. Selective Optical Imaging for Detection of Bacterial Biofilms in Tissues. J Imaging 2023; 9:160. [PMID: 37623692 PMCID: PMC10455256 DOI: 10.3390/jimaging9080160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
SIGNIFICANCE The development of an imaging technique to accurately identify biofilm regions on tissues and in wounds is crucial for the implementation of precise surface-based treatments, leading to better patient outcomes and reduced chances of infection. AIM The goal of this study was to develop an imaging technique that relies on selective trypan blue (TB) staining of dead cells, necrotic tissues, and bacterial biofilms, to identify biofilm regions on tissues and wounds. APPROACH The study explored combinations of ambient multi-colored LED lights to obtain maximum differentiation between stained biofilm regions and the underlying chicken tissue or glass substrate during image acquisition. The TB imaging results were then visually and statistically compared to fluorescence images using a shape similarity measure. RESULTS The comparisons between the proposed TB staining method and the fluorescence standard used to detect biofilms on tissues and glass substrates showed up to 97 percent similarity, suggesting that the TB staining method is a promising technique for identifying biofilm regions. CONCLUSIONS The TB staining method demonstrates significant potential as an effective imaging technique for the identification of fluorescing and non-fluorescing biofilms on tissues and in wounds. This approach could lead to improved precision in surface-based treatments and better patient outcomes.
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Affiliation(s)
- Michael Okebiorun
- Biomedical Engineering Program, Boise State University, Boise, ID 83725, USA;
| | - Cody Oberbeck
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA or (E.H.B.S.)
| | - Cameron Waite
- Department of Mechanical and Biomedical Engineering, Boise State University, Boise, ID 83725, USA
| | - Samuel Clark
- Department of Mathematics, Boise State University, Boise, ID 83725, USA
| | - Dalton Miller
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA (K.A.C.)
| | - Elisa H. Barney Smith
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA or (E.H.B.S.)
- Autonomous Systems and Software Program, Luleå Tekniska Universitet, 97187 Luleå, Sweden
| | - Kenneth A. Cornell
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA (K.A.C.)
| | - Jim Browning
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA or (E.H.B.S.)
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Babakhanova G, Zimmerman SM, Pierce LT, Sarkar S, Schaub NJ, Simon CG. Quantitative, traceable determination of cell viability using absorbance microscopy. PLoS One 2022; 17:e0262119. [PMID: 35045103 PMCID: PMC8769294 DOI: 10.1371/journal.pone.0262119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/18/2021] [Indexed: 01/22/2023] Open
Abstract
Cell viability, an essential measurement for cell therapy products, lacks traceability. One of the most common cell viability tests is trypan blue dye exclusion where blue-stained cells are counted via brightfield imaging. Typically, live and dead cells are classified based on their pixel intensities which may vary arbitrarily making it difficult to compare results. Herein, a traceable absorbance microscopy method to determine the intracellular uptake of trypan blue is demonstrated. The intensity pixels of the brightfield images are converted to absorbance images which are used to calculate moles of trypan blue per cell. Trypan blue cell viability measurements, where trypan blue content in each cell is quantified, enable traceable live-dead classifications. To implement the absorbance microscopy method, we developed an open-source AbsorbanceQ application that generates quantitative absorbance images. The validation of absorbance microscopy is demonstrated using neutral density filters. Results from four different microscopes demonstrate a mean absolute deviation of 3% from the expected optical density values. When assessing trypan blue-stained Jurkat cells, the difference in intracellular uptake of trypan blue in heat-shock-killed cells using two different microscopes is 3.8%. Cells killed with formaldehyde take up ~50% less trypan blue as compared to the heat-shock-killed cells, suggesting that the killing mechanism affects trypan blue uptake. In a test mixture of approximately 50% live and 50% dead cells, 53% of cells were identified as dead (±6% standard deviation). Finally, to mimic batches of low-viability cells that may be encountered during a cell manufacturing process, viability was assessed for cells that were 1) overgrown in the cell culture incubator for five days or 2) incubated in DPBS at room temperature for five days. Instead of making live-dead classifications using arbitrary intensity values, absorbance imaging yields traceable units of moles that can be compared, which is useful for assuring quality for biomanufacturing processes.
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Affiliation(s)
- Greta Babakhanova
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Stephen M. Zimmerman
- Energy and Environment Division, Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Laura T. Pierce
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Sumona Sarkar
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Nicholas J. Schaub
- National Center for the Advancement of Translational Sciences, National Institutes of Health, Bethesda, MD, United States of America
| | - Carl G. Simon
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
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