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Fernandes SA, Angelidaki DD, Nüchel J, Pan J, Gollwitzer P, Elkis Y, Artoni F, Wilhelm S, Kovacevic-Sarmiento M, Demetriades C. Spatial and functional separation of mTORC1 signalling in response to different amino acid sources. Nat Cell Biol 2024:10.1038/s41556-024-01523-7. [PMID: 39385049 DOI: 10.1038/s41556-024-01523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 10/11/2024]
Abstract
Amino acid (AA) availability is a robust determinant of cell growth through controlling mechanistic/mammalian target of rapamycin complex 1 (mTORC1) activity. According to the predominant model in the field, AA sufficiency drives the recruitment and activation of mTORC1 on the lysosomal surface by the heterodimeric Rag GTPases, from where it coordinates the majority of cellular processes. Importantly, however, the teleonomy of the proposed lysosomal regulation of mTORC1 and where mTORC1 acts on its effector proteins remain enigmatic. Here, by using multiple pharmacological and genetic means to perturb the lysosomal AA-sensing and protein recycling machineries, we describe the spatial separation of mTORC1 regulation and downstream functions in mammalian cells, with lysosomal and non-lysosomal mTORC1 phosphorylating distinct substrates in response to different AA sources. Moreover, we reveal that a fraction of mTOR localizes at lysosomes owing to basal lysosomal proteolysis that locally supplies new AAs, even in cells grown in the presence of extracellular nutrients, whereas cytoplasmic mTORC1 is regulated by exogenous AAs. Overall, our study substantially expands our knowledge about the topology of mTORC1 regulation by AAs and hints at the existence of distinct, Rag- and lysosome-independent mechanisms that control its activity at other subcellular locations. Given the importance of mTORC1 signalling and AA sensing for human ageing and disease, our findings will probably pave the way towards the identification of function-specific mTORC1 regulators and thus highlight more effective targets for drug discovery against conditions with dysregulated mTORC1 activity in the future.
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Affiliation(s)
- Stephanie A Fernandes
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Graduate School of Ageing Research, Cologne, Germany
| | | | - Julian Nüchel
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jiyoung Pan
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Graduate School of Ageing Research, Cologne, Germany
| | | | - Yoav Elkis
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Filippo Artoni
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Graduate School of Ageing Research, Cologne, Germany
| | - Sabine Wilhelm
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Constantinos Demetriades
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Graduate School of Ageing Research, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
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2
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Boyang H, Yangyanqiu W, Wenting R, Chenxin Y, Jian C, Zhanbo Q, Yanjun Y, Qiang Y, Shuwen H. Application and progress of highcontent imaging in molecular biology. Biotechnol J 2023; 18:e2300170. [PMID: 37639283 DOI: 10.1002/biot.202300170] [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: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Humans have adopted many different methods to explore matter imaging, among which high content imaging (HCI) could conduct automated imaging analysis of cells while maintaining its structural and functional integrity. Meanwhile, as one of the most important research tools for diagnosing human diseases, HCI is widely used in the frontier of medical research, and its future application has attracted researchers' great interests. Here, the meaning of HCI was briefly explained, the history of optical imaging and the birth of HCI were described, and the experimental methods of HCI were described. Furthermore, the directions of the application of HCI were highlighted in five aspects: protein localization changes, gene identification, chemical and genetic analysis, microbiology, and drug discovery. Most importantly, some challenges and future directions of HCI were discussed, and the application and optimization of HCI were expected to be further explored.
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Affiliation(s)
- Hu Boyang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Wang Yangyanqiu
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Rui Wenting
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Chenxin
- Shulan International Medical School, Zhejiang Shuren University, Hangzhou, China
| | - Chu Jian
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Qu Zhanbo
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Yao Yanjun
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Qiang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Han Shuwen
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, China
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3
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Lamont EI, Lee M, Burgdorf D, Ibsen C, McQualter J, Sarhan R, Thompson O, Schulze SR. Mocs1 ( Molybdenum cofactor synthesis 1) may contribute to lifespan extension in Drosophila. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000517. [PMID: 35098048 PMCID: PMC8790633 DOI: 10.17912/micropub.biology.000517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
While evaluating the effect on lifespan of decreased ribosomal protein (Rp) expression in Drosophila, we discovered a potential function in the same process for the Molybdenum cofactor synthesis 1 (Mocs1) gene. We utilized the UAS-GAL4 inducible system, by crossing tissue-specific GAL4 drivers to the Harvard Drosophila Transgenic RNAi Project (TrIP) responder lines for Rp gene knockdown. We also employed a negative control that knocked down a gene unrelated to Drosophila (GAL4). Relative to the genetic background in which no driven transgenes were present, lifespan was significantly lengthened in females, both for Rp knockdown and the negative GAL4 control. We reasoned that the Mocs1 gene, located immediately downstream of the integration site on the third chromosome where all the TrIP responders are targeted might be responsible for the lifespan effects observed, due to the potential for upregulation using the UAS-GAL4 system. We repeated the lifespan experiment using an enhancer trap in the same location as the TrIP transgenes, and found that lifespan was significantly lengthened in females that possessed both the driver and responder, relative to controls, implicating Mocs1 in the biology of aging.
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Affiliation(s)
- Eleanor I. Lamont
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Michael Lee
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - David Burgdorf
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Camille Ibsen
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Jazmyne McQualter
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Ryan Sarhan
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Olivia Thompson
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Sandra R Schulze
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA,
Correspondence to: Sandra R Schulze ()
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Kim MJ, O'Connor MB. Drosophila Activin signaling promotes muscle growth through InR/TORC1-dependent and -independent processes. Development 2021; 148:dev190868. [PMID: 33234715 PMCID: PMC7823159 DOI: 10.1242/dev.190868] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022]
Abstract
The Myostatin/Activin branch of the TGF-β superfamily acts as a negative regulator of vertebrate skeletal muscle size, in part, through downregulation of insulin/insulin-like growth factor 1 (IGF-1) signaling. Surprisingly, recent studies in Drosophila indicate that motoneuron-derived Activin signaling acts as a positive regulator of muscle size. Here we demonstrate that Drosophila Activin signaling promotes the growth of muscle cells along all three axes: width, thickness and length. Activin signaling positively regulates the insulin receptor (InR)/TORC1 pathway and the level of Myosin heavy chain (Mhc), an essential sarcomeric protein, via increased Pdk1 and Akt1 expression. Enhancing InR/TORC1 signaling in the muscle of Activin pathway mutants restores Mhc levels close to those of the wild type, but only increases muscle width. In contrast, hyperactivation of the Activin pathway in muscles increases overall larval body and muscle fiber length, even when Mhc levels are lowered by suppression of TORC1. Together, these results indicate that the Drosophila Activin pathway regulates larval muscle geometry and body size via promoting InR/TORC1-dependent Mhc production and the differential assembly of sarcomeric components into either pre-existing or new sarcomeric units depending on the balance of InR/TORC1 and Activin signals.
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Affiliation(s)
- Myung-Jun Kim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael B O'Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Parniewska MM, Stocker H. The Splicing Factor SF2 Is Critical for Hyperproliferation and Survival in a TORC1-Dependent Model of Early Tumorigenesis in Drosophila. Int J Mol Sci 2020; 21:ijms21124465. [PMID: 32599686 PMCID: PMC7352841 DOI: 10.3390/ijms21124465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 01/05/2023] Open
Abstract
The Target of Rapamycin complex 1 (TORC1) is an evolutionarily conserved kinase complex coordinating cellular growth with nutritional conditions and growth factor signaling, and its activity is elevated in many cancer types. The use of TORC1 inhibitors as anticancer drugs is, however, limited by unwanted side-effects and development of resistance. We therefore attempted to identify limiting modulators or downstream effectors of TORC1 that could serve as therapeutic targets. Drosophila epithelial tissues that lack the tumor suppressor Pten hyperproliferate upon nutrient restriction in a TORC1-dependent manner. We probed candidates of the TORC1 signaling network for factors limiting the overgrowth of Pten mutant tissues. The serine/arginine-rich splicing factor 2 (SF2) was identified as the most limiting factor: SF2 knockdown drives Pten mutant cells into apoptosis, while not affecting control tissue. SF2 acts downstream of or in parallel to TORC1 but is not required for the activation of the TORC1 target S6K. Transcriptomics analysis revealed transcripts with alternatively used exons regulated by SF2 in the tumor context, including p53. SF2 may therefore represent a highly specific therapeutic target for tumors with hyperactive TORC1 signaling.
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6
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Venugopal P, Veyssière H, Couderc JL, Richard G, Vachias C, Mirouse V. Multiple functions of the scaffold protein Discs large 5 in the control of growth, cell polarity and cell adhesion in Drosophila melanogaster. BMC DEVELOPMENTAL BIOLOGY 2020; 20:10. [PMID: 32552730 PMCID: PMC7301484 DOI: 10.1186/s12861-020-00218-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/28/2020] [Indexed: 12/24/2022]
Abstract
Background Scaffold proteins support a variety of key processes during animal development. Mutant mouse for the MAGUK protein Discs large 5 (Dlg5) presents a general growth impairment and moderate morphogenetic defects. Results Here, we generated null mutants for Drosophila Dlg5 and show that it owns similar functions in growth and epithelial architecture. Dlg5 is required for growth at a cell autonomous level in several tissues and at the organism level, affecting cell size and proliferation. Our results are consistent with Dlg5 modulating hippo pathway in the wing disc, including the impact on cell size, a defect that is reproduced by the loss of yorkie. However, other observations indicate that Dlg5 regulates growth by at least another way that may involve Myc protein but nor PI3K neither TOR pathways. Moreover, epithelia cells mutant for Dlg5 also show a reduction of apical domain determinants, though not sufficient to induce a complete loss of cell polarity. Dlg5 is also essential, in the same cells, for the presence at Adherens junctions of N-Cadherin, but not E-Cadherin. Genetic analyses indicate that junction and polarity defects are independent. Conclusions Together our data show that Dlg5 own several conserved functions that are independent of each other in regulating growth, cell polarity and cell adhesion. Moreover, they reveal a differential regulation of E-cadherin and N-cadherin apical localization.
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Affiliation(s)
- Parvathy Venugopal
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France.,present address : School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala, 690525, India
| | - Hugo Veyssière
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France.,present address : University Clermont Auvergne, INSERM U1240, Centre de Lutte Contre le Cancer Jean PERRIN, 58 rue Montalembert, 63011, Clermont-Ferrand, France
| | - Jean-Louis Couderc
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Graziella Richard
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Caroline Vachias
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Vincent Mirouse
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France.
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7
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Roy D, Kahler DJ, Yun C, Hubbard EJA. Functional Interactions Between rsks-1/S6K, glp-1/Notch, and Regulators of Caenorhabditis elegans Fertility and Germline Stem Cell Maintenance. G3 (BETHESDA, MD.) 2018; 8:3293-3309. [PMID: 30126834 PMCID: PMC6169383 DOI: 10.1534/g3.118.200511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
Abstract
The proper accumulation and maintenance of stem cells is critical for organ development and homeostasis. The Notch signaling pathway maintains stem cells in diverse organisms and organ systems. In Caenorhabditis elegans, GLP-1/Notch activity prevents germline stem cell (GSC) differentiation. Other signaling mechanisms also influence the maintenance of GSCs, including the highly-conserved TOR substrate ribosomal protein S6 kinase (S6K). Although C. elegans bearing either a null mutation in rsks-1/S6K or a reduction-of-function (rf) mutation in glp-1/Notch produce half the normal number of adult germline progenitors, virtually all these single mutant animals are fertile. However, glp-1(rf) rsks-1(null) double mutant animals are all sterile, and in about half of their gonads, all GSCs differentiate, a distinctive phenotype associated with a significant reduction or loss of GLP-1 signaling. How rsks-1/S6K promotes GSC fate is unknown. Here, we determine that rsks-1/S6K acts germline-autonomously to maintain GSCs, and that it does not act through Cyclin-E or MAP kinase in this role. We found that interfering with translation also enhances glp-1(rf), but that regulation through rsks-1 cannot fully account for this effect. In a genome-scale RNAi screen for genes that act similarly to rsks-1/S6K, we identified 56 RNAi enhancers of glp-1(rf) sterility, many of which were previously not known to interact functionally with Notch. Further investigation revealed at least six candidates that, by genetic criteria, act linearly with rsks-1/S6K. These include genes encoding translation-related proteins, cacn-1/Cactin, an RNA exosome component, and a Hedgehog-related ligand. We found that additional Hedgehog-related ligands may share functional relationships with glp-1/Notch and rsks-1/S6K in maintaining germline progenitors.
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Affiliation(s)
- Debasmita Roy
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016
| | - David J Kahler
- NYU High Throughput Biology Laboratory, NYU Langone Health, New York, NY 10016
| | - Chi Yun
- NYU High Throughput Biology Laboratory, NYU Langone Health, New York, NY 10016
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York, NY 10016
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8
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Muñoz-Soriano V, Belacortu Y, Sanz FJ, Solana-Manrique C, Dillon L, Suay-Corredera C, Ruiz-Romero M, Corominas M, Paricio N. Cbt modulates Foxo activation by positively regulating insulin signaling in Drosophila embryos. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30034-8. [PMID: 30055320 DOI: 10.1016/j.bbagrm.2018.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 01/05/2023]
Abstract
In late Drosophila embryos, the epidermis exhibits a dorsal hole as a consequence of germ band retraction. It is sealed during dorsal closure (DC), a morphogenetic process in which the two lateral epidermal layers converge towards the dorsal midline and fuse. We previously demonstrated the involvement of the Cbt transcription factor in Drosophila DC. However its molecular role in the process remained obscure. In this study, we used genomic approaches to identify genes regulated by Cbt as well as its direct targets during late embryogenesis. Our results reveal a complex transcriptional circuit downstream of Cbt and evidence that it is functionally related with the Insulin/insulin-like growth factor signaling pathway. In this context, Cbt may act as a positive regulator of the pathway, leading to the repression of Foxo activity. Our results also suggest that the DC defects observed in cbt embryos could be partially due to Foxo overactivation and that a regulatory feedback loop between Foxo and Cbt may be operating in the DC context.
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Affiliation(s)
- Verónica Muñoz-Soriano
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Yaiza Belacortu
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Francisco José Sanz
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Cristina Solana-Manrique
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Luke Dillon
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Carmen Suay-Corredera
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Marina Ruiz-Romero
- Departament de Genètica, Facultat de Biologia, and Institut de Biomedicina (IBUB) de la Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Corominas
- Departament de Genètica, Facultat de Biologia, and Institut de Biomedicina (IBUB) de la Universitat de Barcelona, Barcelona, Spain
| | - Nuria Paricio
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain.
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9
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Park D, Kang M, Choi JW, Paik SM, Ko J, Lee S, Lee Y, Son K, Ha J, Choi M, Park W, Kim HY, Jeon NL. Microstructure guided multi-scale liquid patterning on an open surface. LAB ON A CHIP 2018; 18:2013-2022. [PMID: 29873341 DOI: 10.1039/c7lc01288h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Liquid patterning is a quintessential aspect in cell-based screening. While there are a variety of methods to handle microliquids utilizing surface treatments, complex microfluidic systems, and automated dispensing, most of the stated methods are both expensive and difficult to implement. Here, we present a fast multi-scale microliquid-patterning method on an open surface using embossed microstructures without surface modification. Arrays of micropillars can trap microliquids when a bulk drop is swept by an elastic sweeper on polystyrene (PS) substrates. The patterning mechanism on a basic form of a 2 × 2 rectangular array of circular pillars is analyzed theoretically and verified with experiments. Nanoliter-to-microliter volumes of liquids are patterned into various shapes by arranging the pillars based on the analysis. Furthermore, an array of geometrically modified pillars can capture approximately 8000 droplets on a large substrate (55 mm × 55 mm) in one step. Given the simplistic method of wipe patterning, the proposed platform can be utilized in both manual benchtop and automated settings. We will provide proof of concept experiments of single colony isolation using nanoliter-scale liquid patterning and of human angiogenic vessel formation using sequential patterning of microliter-scale liquids.
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Affiliation(s)
- Dohyun Park
- Division of WCU (World Class University) Multiscale Mechanical Design, Seoul National University, Seoul, 08826, Republic of Korea
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10
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Spatial Activation of TORC1 Is Regulated by Hedgehog and E2F1 Signaling in the Drosophila Eye. Dev Cell 2017; 42:363-375.e4. [PMID: 28829944 DOI: 10.1016/j.devcel.2017.07.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 06/17/2017] [Accepted: 07/23/2017] [Indexed: 01/20/2023]
Abstract
Target of rapamycin complex 1 (TORC1) regulates cell growth in response to nutrients and growth factors. Although TORC1 signaling has been thoroughly studied at the cellular level, the regulation of TORC1 in multicellular tissues and organs has remained elusive. Here we found that TORC1 is selectively activated in the second mitotic wave (SMW), the terminal synchronous cell division, of the developing Drosophila eye. We demonstrated that Hedgehog (Hh) signaling regulates TORC1 through E2F1 and the cyclin D/Cdk4 complex in the SMW, and this regulation is independent from insulin and amino acid signaling pathways. TORC1 is necessary for the proper G1/S transition of the cells, and the activation of TORC1 rescues the cell-cycle defect of Hh signaling-deficient cells in the SMW. Based on this evolutionarily conserved regulation of TORC1 by Hh signaling, we propose that Hh-dependent developmental signaling pathways spatially regulate TORC1 activity in multicellular organisms.
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11
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Abstract
WNK (With-No-Lysine (K)) kinases are serine-threonine kinases characterized by an atypical placement of a catalytic lysine within the kinase domain. Mutations in human WNK1 or WNK4 cause an autosomal dominant syndrome of hypertension and hyperkalemia, reflecting the fact that WNK kinases are critical regulators of renal ion transport processes. Here, the role of WNKs in the regulation of ion transport processes in vertebrate and invertebrate renal function, cellular and organismal osmoregulation, and cell migration and cerebral edema will be reviewed, along with emerging literature demonstrating roles for WNKs in cardiovascular and neural development, Wnt signaling, and cancer. Conserved roles for these kinases across phyla are emphasized.
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Affiliation(s)
| | - Andreas Jenny
- Albert Einstein College of Medicine, New York, NY, United States.
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12
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Bunched and Madm Function Downstream of Tuberous Sclerosis Complex to Regulate the Growth of Intestinal Stem Cells in Drosophila. Stem Cell Rev Rep 2016; 11:813-25. [PMID: 26323255 PMCID: PMC4653243 DOI: 10.1007/s12015-015-9617-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Drosophila adult midgut contains intestinal stem cells that support homeostasis and repair. We show here that the leucine zipper protein Bunched and the adaptor protein Madm are novel regulators of intestinal stem cells. MARCM mutant clonal analysis and cell type specific RNAi revealed that Bunched and Madm were required within intestinal stem cells for proliferation. Transgenic expression of a tagged Bunched showed a cytoplasmic localization in midgut precursors, and the addition of a nuclear localization signal to Bunched reduced its function to cooperate with Madm to increase intestinal stem cell proliferation. Furthermore, the elevated cell growth and 4EBP phosphorylation phenotypes induced by loss of Tuberous Sclerosis Complex or overexpression of Rheb were suppressed by the loss of Bunched or Madm. Therefore, while the mammalian homolog of Bunched, TSC-22, is able to regulate transcription and suppress cancer cell proliferation, our data suggest the model that Bunched and Madm functionally interact with the TOR pathway in the cytoplasm to regulate the growth and subsequent division of intestinal stem cells.
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13
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Mattiazzi Usaj M, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol 2016; 26:598-611. [PMID: 27118708 DOI: 10.1016/j.tcb.2016.03.008] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022]
Abstract
High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.
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Affiliation(s)
| | - Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada.
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14
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Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N. Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal 2015; 8:rs9. [PMID: 26350902 PMCID: PMC4642709 DOI: 10.1126/scisignal.aab3729] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The tuberous sclerosis complex (TSC) family of tumor suppressors, TSC1 and TSC2, function together in an evolutionarily conserved protein complex that is a point of convergence for major cell signaling pathways that regulate mTOR complex 1 (mTORC1). Mutation or aberrant inhibition of the TSC complex is common in various human tumor syndromes and cancers. The discovery of novel therapeutic strategies to selectively target cells with functional loss of this complex is therefore of clinical relevance to patients with nonmalignant TSC and those with sporadic cancers. We developed a CRISPR-based method to generate homogeneous mutant Drosophila cell lines. By combining TSC1 or TSC2 mutant cell lines with RNAi screens against all kinases and phosphatases, we identified synthetic interactions with TSC1 and TSC2. Individual knockdown of three candidate genes (mRNA-cap, Pitslre, and CycT; orthologs of RNGTT, CDK11, and CCNT1 in humans) reduced the population growth rate of Drosophila cells lacking either TSC1 or TSC2 but not that of wild-type cells. Moreover, individual knockdown of these three genes had similar growth-inhibiting effects in mammalian TSC2-deficient cell lines, including human tumor-derived cells, illustrating the power of this cross-species screening strategy to identify potential drug targets.
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Affiliation(s)
| | - Alexander J Valvezan
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Colleen Kelley
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Richelle Sopko
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Roesel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shuailiang Lin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Buckner
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rong Tao
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bahar Yilmazel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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15
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Parkhitko AA, Favorova OO, Khabibullin DI, Anisimov VN, Henske EP. Kinase mTOR: regulation and role in maintenance of cellular homeostasis, tumor development, and aging. BIOCHEMISTRY (MOSCOW) 2015; 79:88-101. [PMID: 24794724 DOI: 10.1134/s0006297914020023] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Serine/threonine protein kinase mTOR regulates the maintenance of cellular homeostasis by coordinating transcription, translation, metabolism, and autophagy with availability of amino acids, growth factors, ATP, and oxygen. The mTOR kinase is a component of two protein complexes, mTORC1 and mTORC2, which are different in their composition and regulate different cellular processes. An uncontrolled activation of the mTOR kinase is observed in cells of the majority of tumors, as well as in diabetes and neurodegenerative and some other diseases. At present, inhibitors of the kinase complex mTORC1 are undergoing clinical trials. This review focuses on different aspects of the regulation of the mTORC1 and mTORC2 complexes, on their role in the regulation of protein synthesis, metabolism, and autophagy, as well as on using mTOR inhibitors for treatment of tumors and slowing of aging.
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Affiliation(s)
- A A Parkhitko
- Department of Genetics, Harvard Medical School, Boston, 02155, USA.
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16
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A large-scale in vivo RNAi screen to identify genes involved in Notch-mediated follicle cell differentiation and cell cycle switches. Sci Rep 2015. [PMID: 26205122 PMCID: PMC4513280 DOI: 10.1038/srep12328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During Drosophila oogenesis, follicle cells sequentially undergo three distinct cell-cycle programs: the mitotic cycle, endocycle, and gene amplification. Notch signaling plays a central role in regulating follicle-cell differentiation and cell-cycle switches; its activation is essential for the mitotic cycle/endocycle (M/E) switch. Cut, a linker between Notch signaling and cell-cycle regulators, is specifically downregulated by Notch during the endocycle stage. To determine how signaling pathways coordinate during the M/E switch and to identify novel genes involved in follicle cell differentiation, we performed an in vivo RNAi screen through induced knockdown of gene expression and examination of Cut expression in follicle cells. We screened 2205 RNAi lines and found 33 genes regulating Cut expression during the M/E switch. These genes were confirmed with the staining of two other Notch signaling downstream factors, Hindsight and Broad, and validated with multiple independent RNAi lines. We applied gene ontology software to find enriched biological meaning and compared our results with other publications to find conserved genes across tissues. Specifically, we found earlier endocycle entry in anterior follicle cells than those in the posterior, identified that the insulin-PI3K pathway participates in the precise M/E switch, and suggested Nejire as a cofactor of Notch signaling during oogenesis.
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17
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A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation. PLoS One 2015; 10:e0116096. [PMID: 25790369 PMCID: PMC4366019 DOI: 10.1371/journal.pone.0116096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/04/2014] [Indexed: 11/19/2022] Open
Abstract
mTOR complex1, the major regulator of mRNA translation in all eukaryotic cells, is strongly activated in most cancers. We performed a genome-wide RNAi screen in a human cancer cell line, seeking genes that regulate S6 phosphorylation, readout of mTORC1 activity. Applying a stringent selection, we retrieved nearly 600 genes wherein at least two RNAis gave significant reduction in S6-P. This cohort contains known regulators of mTOR complex 1 and is significantly enriched in genes whose depletion affects the proliferation/viability of the large set of cancer cell lines in the Achilles database in a manner paralleling that caused by mTOR depletion. We next examined the effect of RNAi pools directed at 534 of these gene products on S6-P in TSC1 null mouse embryo fibroblasts. 76 RNAis reduced S6 phosphorylation significantly in 2 or 3 replicates. Surprisingly, among this cohort of genes the only elements previously associated with the maintenance of mTORC1 activity are two subunits of the vacuolar ATPase and the CUL4 subunit DDB1. RNAi against a second set of 84 targets reduced S6-P in only one of three replicates. However, an indication that this group also bears attention is the presence of rpS6KB1 itself, Rac1 and MAP4K3, a protein kinase that supports amino acid signaling to rpS6KB1. The finding that S6 phosphorylation requires a previously unidentified, functionally diverse cohort of genes that participate in fundamental cellular processes such as mRNA translation, RNA processing, DNA repair and metabolism suggests the operation of feedback pathways in the regulation of mTORC1 operating through novel mechanisms.
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18
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Protein Microarrays with Novel Microfluidic Methods: Current Advances. MICROARRAYS 2014; 3:180-202. [PMID: 27600343 PMCID: PMC4996363 DOI: 10.3390/microarrays3030180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 01/08/2023]
Abstract
Microfluidic-based micromosaic technology has allowed the pattering of recognition elements in restricted micrometer scale areas with high precision. This controlled patterning enabled the development of highly multiplexed arrays multiple analyte detection. This arraying technology was first introduced in the beginning of 2001 and holds tremendous potential to revolutionize microarray development and analyte detection. Later, several microfluidic methods were developed for microarray application. In this review we discuss these novel methods and approaches which leverage the property of microfluidic technologies to significantly improve various physical aspects of microarray technology, such as enhanced imprinting homogeneity, stability of the immobilized biomolecules, decreasing assay times, and reduction of the costs and of the bulky instrumentation.
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19
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Singh S, Carpenter AE, Genovesio A. Increasing the Content of High-Content Screening: An Overview. ACTA ACUST UNITED AC 2014; 19:640-50. [PMID: 24710339 PMCID: PMC4230961 DOI: 10.1177/1087057114528537] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/31/2013] [Indexed: 01/17/2023]
Abstract
Target-based high-throughput screening (HTS) has recently been critiqued for its relatively poor yield compared to phenotypic screening approaches. One type of phenotypic screening, image-based high-content screening (HCS), has been seen as particularly promising. In this article, we assess whether HCS is as high content as it can be. We analyze HCS publications and find that although the number of HCS experiments published each year continues to grow steadily, the information content lags behind. We find that a majority of high-content screens published so far (60−80%) made use of only one or two image-based features measured from each sample and disregarded the distribution of those features among each cell population. We discuss several potential explanations, focusing on the hypothesis that data analysis traditions are to blame. This includes practical problems related to managing large and multidimensional HCS data sets as well as the adoption of assay quality statistics from HTS to HCS. Both may have led to the simplification or systematic rejection of assays carrying complex and valuable phenotypic information. We predict that advanced data analysis methods that enable full multiparametric data to be harvested for entire cell populations will enable HCS to finally reach its potential.
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Affiliation(s)
- Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Auguste Genovesio
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA École Normale Supérieure, 45, Rue d'Ulm, 75005 Paris
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20
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Panchaud N, Péli-Gulli MP, De Virgilio C. SEACing the GAP that nEGOCiates TORC1 activation: evolutionary conservation of Rag GTPase regulation. Cell Cycle 2013; 12:2948-52. [PMID: 23974112 PMCID: PMC3875668 DOI: 10.4161/cc.26000] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The target of rapamycin complex 1 (TORC1) regulates eukaryotic cell growth in response to a variety of input signals. In S. cerevisiae, amino acids activate TORC1 through the Rag guanosine triphosphatase (GTPase) heterodimer composed of Gtr1 and Gtr2 found together with Ego1 and Ego3 in the EGO complex (EGOC). The GTPase activity of Gtr1 is regulated by the SEA complex (SEAC). Specifically, SEACIT, a SEAC subcomplex containing Iml1, Npr2, and Npr3 functions as a GTPase activator (GAP) for Gtr1 to decrease the activity of TORC1 and, consequently, growth, after amino acid deprivation. Here, we present genetic epistasis data, which show that SEACAT, the other SEAC subcomplex, containing Seh1, Sea2–4, and Sec13, antagonizes the GAP function of SEACIT. Orthologs of EGOC (Ragulator), SEACIT (GATOR1), and SEACAT (GATOR2) are present in higher eukaryotes, highlighting the remarkable conservation, from yeast to man, of Rag GTPase and TORC1 regulation.
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Affiliation(s)
- Nicolas Panchaud
- Department of Biology; Division of Biochemistry; University of Fribourg; Fribourg, Switzerland
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21
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Short B. Stem cells get a cholesterol test. J Biophys Biochem Cytol 2013. [PMCID: PMC3664718 DOI: 10.1083/jcb.2015if] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Study reveals that dietary cholesterol regulates Hedgehog signaling and stem cell proliferation in flies.
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22
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Hartman TR, Strochlic TI, Ji Y, Zinshteyn D, O'Reilly AM. Diet controls Drosophila follicle stem cell proliferation via Hedgehog sequestration and release. ACTA ACUST UNITED AC 2013; 201:741-57. [PMID: 23690177 PMCID: PMC3664720 DOI: 10.1083/jcb.201212094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dietary cholesterol levels control follicle stem cell proliferation in the Drosophila ovary via regulation of Hedgehog protein localization. A healthy diet improves adult stem cell function and delays diseases such as cancer, heart disease, and neurodegeneration. Defining molecular mechanisms by which nutrients dictate stem cell behavior is a key step toward understanding the role of diet in tissue homeostasis. In this paper, we elucidate the mechanism by which dietary cholesterol controls epithelial follicle stem cell (FSC) proliferation in the fly ovary. In nutrient-restricted flies, the transmembrane protein Boi sequesters Hedgehog (Hh) ligand at the surface of Hh-producing cells within the ovary, limiting FSC proliferation. Upon feeding, dietary cholesterol stimulates S6 kinase–mediated phosphorylation of the Boi cytoplasmic domain, triggering Hh release and FSC proliferation. This mechanism enables a rapid, tissue-specific response to nutritional changes, tailoring stem cell divisions and egg production to environmental conditions sufficient for progeny survival. If conserved in other systems, this mechanism will likely have important implications for studies on molecular control of stem cell function, in which the benefits of low calorie and low cholesterol diets are beginning to emerge.
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Affiliation(s)
- Tiffiney R Hartman
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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23
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Quidville V, Alsafadi S, Goubar A, Commo F, Scott V, Pioche-Durieu C, Girault I, Baconnais S, Le Cam E, Lazar V, Delaloge S, Saghatchian M, Pautier P, Morice P, Dessen P, Vagner S, André F. Targeting the deregulated spliceosome core machinery in cancer cells triggers mTOR blockade and autophagy. Cancer Res 2013; 73:2247-58. [PMID: 23358685 DOI: 10.1158/0008-5472.can-12-2501] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The spliceosome is a large ribonucleoprotein complex that guides pre-mRNA splicing in eukaryotic cells. Here, we determine whether the spliceosome could constitute an attractive therapeutic target in cancer. Analysis of gene expression arrays from lung, breast, and ovarian cancers datasets revealed that several genes encoding components of the core spliceosome composed of a heteroheptameric Sm complex were overexpressed in malignant disease as compared with benign lesions and could also define a subset of highly aggressive breast cancers. siRNA-mediated depletion of SmE (SNRPE) or SmD1 (SNRPD1) led to a marked reduction of cell viability in breast, lung, and melanoma cancer cell lines, whereas it had little effect on the survival of the nonmalignant MCF-10A breast epithelial cells. SNRPE or SNRPD1 depletion did not lead to apoptotic cell death but autophagy, another form of cell death. Indeed, induction of autophagy was revealed by cytoplasmic accumulation of autophagic vacuoles and by an increase in both LC3 (MAP1LC3A) protein conversion and the amount of acidic autophagic vacuoles. Knockdown of SNRPE dramatically decreased mTOR mRNA and protein levels and was accompanied by a deregulation of the mTOR pathway, which, in part, explains the SNRPE-dependent induction of autophagy. These findings provide a rational to develop new therapeutic agents targeting spliceosome core components in oncology.
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Affiliation(s)
- Virginie Quidville
- Institut National de la Santé et de la Recherche Médicale (INSERM) U981, Paris, France
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24
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Ueda E, Geyer FL, Nedashkivska V, Levkin PA. DropletMicroarray: facile formation of arrays of microdroplets and hydrogel micropads for cell screening applications. LAB ON A CHIP 2012; 12:5218-24. [PMID: 23114283 DOI: 10.1039/c2lc40921f] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We describe a one-step method for creating thousands of isolated pico- to microliter-sized droplets with defined geometry and volume. Arrays of droplets are instantly formed as liquid moves along a superhydrophilic-superhydrophobic patterned surface. Bioactive molecules, nonadherent cells, or microorganisms can be trapped in the fully isolated microdroplets for high-throughput screening, or in hydrogel micropads for screening in 3D microenvironments.
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Affiliation(s)
- Erica Ueda
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany
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25
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Claerhout S, Dutta B, Bossuyt W, Zhang F, Nguyen-Charles C, Dennison JB, Yu Q, Yu S, Balázsi G, Lu Y, Mills GB. Abortive autophagy induces endoplasmic reticulum stress and cell death in cancer cells. PLoS One 2012; 7:e39400. [PMID: 22745748 PMCID: PMC3383753 DOI: 10.1371/journal.pone.0039400] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 05/21/2012] [Indexed: 11/19/2022] Open
Abstract
Autophagic cell death or abortive autophagy has been proposed to eliminate damaged as well as cancer cells, but there remains a critical gap in our knowledge in how this process is regulated. The goal of this study was to identify modulators of the autophagic cell death pathway and elucidate their effects on cellular signaling and function. The result of our siRNA library screenings show that an intact coatomer complex I (COPI) is obligatory for productive autophagy. Depletion of COPI complex members decreased cell survival and impaired productive autophagy which preceded endoplasmic reticulum stress. Further, abortive autophagy provoked by COPI depletion significantly altered growth factor signaling in multiple cancer cell lines. Finally, we show that COPI complex members are overexpressed in an array of cancer cell lines and several types of cancer tissues as compared to normal cell lines or tissues. In cancer tissues, overexpression of COPI members is associated with poor prognosis. Our results demonstrate that the coatomer complex is essential for productive autophagy and cellular survival, and thus inhibition of COPI members may promote cell death of cancer cells when apoptosis is compromised.
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Affiliation(s)
- Sofie Claerhout
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
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26
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TOR is required for the retrograde regulation of synaptic homeostasis at the Drosophila neuromuscular junction. Neuron 2012; 74:166-78. [PMID: 22500638 DOI: 10.1016/j.neuron.2012.01.030] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2012] [Indexed: 11/22/2022]
Abstract
Homeostatic mechanisms operate to stabilize synaptic function; however, we know little about how they are regulated. Exploiting Drosophila genetics, we have uncovered a critical role for the target of rapamycin (TOR) in the regulation of synaptic homeostasis at the Drosophila larval neuromuscular junction. Loss of postsynaptic TOR disrupts a retrograde compensatory enhancement in neurotransmitter release that is normally triggered by a reduction in postsynaptic glutamate receptor activity. Moreover, postsynaptic overexpression of TOR or a phosphomimetic form of S6 ribosomal protein kinase, a common target of TOR, can trigger a strong retrograde increase in neurotransmitter release. Interestingly, heterozygosity for eIF4E, a critical component of the cap-binding protein complex, blocks the retrograde signal in all these cases. Our findings suggest that cap-dependent translation under the control of TOR plays a critical role in establishing the activity dependent homeostatic response at the NMJ.
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27
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Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root DE, Garraway LA, Sabatini DM. MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma. Sci Signal 2012; 5:rs4. [PMID: 22589389 DOI: 10.1126/scisignal.2002612] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cell microarrays are a promising tool for performing large-scale functional genomic screening in mammalian cells at reasonable cost, but owing to technical limitations they have been restricted for use with a narrow range of cell lines and short-term assays. Here, we describe MicroSCALE (Microarrays of Spatially Confined Adhesive Lentiviral Features), a cell microarray-based platform that enables application of this technology to a wide range of cell types and longer-term assays. We used MicroSCALE to uncover kinases that when overexpressed partially desensitized B-RAFV600E-mutant melanoma cells to inhibitors of the mitogen-activated protein kinase kinase kinase (MAPKKK) RAF, the MAPKKs MEK1 and 2 (MEK1/2, mitogen-activated protein kinase kinase 1 and 2), mTOR (mammalian target of rapamycin), or PI3K (phosphatidylinositol 3-kinase). These screens indicated that cells treated with inhibitors acting through common mechanisms were affected by a similar profile of overexpressed proteins. In contrast, screens involving inhibitors acting through distinct mechanisms yielded unique profiles, a finding that has potential relevance for small-molecule target identification and combination drugging studies. Further, by integrating large-scale functional screening results with cancer cell line gene expression and pharmacological sensitivity data, we validated the nuclear factor κB pathway as a potential mediator of resistance to MAPK pathway inhibitors. The MicroSCALE platform described here may enable new classes of large-scale, resource-efficient screens that were not previously feasible, including those involving combinations of cell lines, perturbations, and assay outputs or those involving limited numbers of cells and limited or expensive reagents.
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Affiliation(s)
- Kris C Wood
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
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28
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Mohr SE, Perrimon N. RNAi screening: new approaches, understandings, and organisms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:145-58. [PMID: 21953743 DOI: 10.1002/wrna.110] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
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Affiliation(s)
- Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA, USA
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29
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Lin J, Hackam DJ. Worms, flies and four-legged friends: the applicability of biological models to the understanding of intestinal inflammatory diseases. Dis Model Mech 2011; 4:447-56. [PMID: 21669933 PMCID: PMC3124049 DOI: 10.1242/dmm.007252] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Diseases of intestinal inflammation, including Crohn's disease, ulcerative colitis and necrotizing enterocolitis, cause substantial acute and chronic disability in a large proportion of the population. Crohn's disease and ulcerative colitis, which are collectively referred to as inflammatory bowel disease (IBD), lead to recurrent episodes of intestinal dysfunction and systemic illness, whereas necrotizing enterocolitis is characterized by the development of dramatic and all too often fatal intestinal necrosis in infants. To determine the molecular underpinnings of these disorders, investigators have explored a variety of animal models that vary widely in their complexity. These experimental systems include the invertebrate nematode Caenorhabditis elegans, the more complex invertebrate Drosophila melanogaster, and vertebrate systems including mice, rats and other mammals. This review explores the experimental models that are used to mimic and evaluate the pathogenic mechanisms leading to these diseases of intestinal inflammation. We then highlight, as an example, how the use of different experimental models that focus on the role of Toll-like receptor 4 (TLR4) signaling in the gut has revealed important distinctions between the pathogenesis of IBD and necrotizing enterocolitis. Specifically, TLR4-mediated signaling plays a protective role in the development of Crohn's disease and ulcerative colitis, whereas this signaling pathway plays a causative role in the development of necrotizing enterocolitis in the newborn small intestine by adversely affecting intestinal injury and repair mechanisms.
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Affiliation(s)
- Joyce Lin
- Division of Pediatric Surgery, Children's Hospital of Pittsburgh, Pittsburgh, PA 15213, USA
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