1
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Robinson BP, Bass NR, Bhakt P, Spiliotis ET. Septin-coated microtubules promote maturation of multivesicular bodies by inhibiting their motility. J Cell Biol 2024; 223:e202308049. [PMID: 38668767 PMCID: PMC11046855 DOI: 10.1083/jcb.202308049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/06/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The microtubule cytoskeleton consists of microtubule subsets with distinct compositions of microtubule-associated proteins, which instruct the position and traffic of subcellular organelles. In the endocytic pathway, these microtubule-associated cues are poorly understood. Here, we report that in MDCK cells, endosomes with multivesicular body (MVB) and late endosome (LE) markers localize preferentially to microtubules coated with septin GTPases. Compared with early endosomes, CD63-containing MVBs/LEs are largely immotile on septin-coated microtubules. In vitro reconstitution assays revealed that the motility of isolated GFP-CD63 endosomes is directly inhibited by microtubule-associated septins. Quantification of CD63-positive endosomes containing the early endosome antigen (EEA1), the Rab7 effector and dynein adaptor RILP or Rab27a, showed that intermediary EEA1- and RILP-positive GFP-CD63 preferentially associate with septin-coated microtubules. Septin knockdown enhanced GFP-CD63 motility and decreased the percentage of CD63-positive MVBs/LEs with lysobiphosphatidic acid without impacting the fraction of EEA1-positive CD63. These results suggest that MVB maturation involves immobilization on septin-coated microtubules, which may facilitate multivesiculation and/or organelle-organelle contacts.
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Affiliation(s)
| | - Naomi R. Bass
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Priyanka Bhakt
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Elias T. Spiliotis
- Department of Biology, Drexel University, Philadelphia, PA, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
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2
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Niu S, Ma J, Li Y, Yue X, Shi K, Pan M, Song L, Tan Y, Gu L, Liu S, Chang J. PTPN23[Thr] variant reduces susceptibility and tumorigenesis in esophageal squamous cell carcinoma through dephosphorylation of EGFR. Cancer Lett 2024; 592:216936. [PMID: 38704135 DOI: 10.1016/j.canlet.2024.216936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Post-translational modifications (PTMs) have emerged as pivotal regulators of the development of cancers, including esophageal squamous cell carcinoma (ESCC). Here, we conducted a comprehensive analysis of PTM-related genetic variants associated with ESCC risk using large-scale genome-wide and exome-wide association datasets. We observed significant enrichment of PTM-related variants in the ESCC risk loci and identified five variants that were significantly associated with ESCC risk. Among them, rs6780013 in PTPN23 exhibited the highest level of significance in ESCC susceptibility in 9,728 ESCC cases and 10,977 controls (odds ratio [OR] = 0.85, 95 % confidence interval [CI] = 0.81- 0.89, P = 9.77 × 10-14). Further functional investigations revealed that PTPN23[Thr] variant binds to EGFR and modulates its phosphorylation at Thr699. PTPN23[Thr] variant substantially inhibited ESCC cell proliferation both in vitro and in vivo. Our findings underscore the critical role of PTPN23[Thr]-EGFR interaction in ESCC development, providing more insights into the pathogenesis of this cancer.
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Affiliation(s)
- Siyuan Niu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jialing Ma
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yueping Li
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xinying Yue
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ke Shi
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Miaoxin Pan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Lina Song
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yuqian Tan
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Linglong Gu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shasha Liu
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jiang Chang
- Department of Health Toxicology, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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3
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Yeon Kim S, Tang M, Lu T, Chih SY, Li W. Ferroptosis in glioma therapy: advancements in sensitizing strategies and the complex tumor-promoting roles. Brain Res 2024; 1840:149045. [PMID: 38821335 DOI: 10.1016/j.brainres.2024.149045] [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: 02/27/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Ferroptosis, an iron-dependent form of non-apoptotic regulated cell death, is induced by the accumulation of lipid peroxides on cellular membranes. Over the past decade, ferroptosis has emerged as a crucial process implicated in various physiological and pathological systems. Positioned as an alternative modality of cell death, ferroptosis holds promise for eliminating cancer cells that have developed resistance to apoptosis induced by conventional therapeutics. This has led to a growing interest in leveraging ferroptosis for cancer therapy across diverse malignancies. Gliomas are tumors arising from glial or precursor cells, with glioblastoma (GBM) being the most common malignant primary brain tumor that is associated with a dismal prognosis. This review provides a summary of recent advancements in the exploration of ferroptosis-sensitizing methods, with a specific focus on their potential application in enhancing the treatment of gliomas. In addition to summarizing the therapeutic potential, this review also discusses the intricate interplay of ferroptosis and its potential tumor-promoting roles within gliomas. Recognizing these dual roles is essential, as they could potentially complicate the therapeutic benefits of ferroptosis. Exploring strategies aimed at circumventing these tumor-promoting roles could enhance the overall therapeutic efficacy of ferroptosis in the context of glioma treatment.
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Affiliation(s)
- Soo Yeon Kim
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
| | - Miaolu Tang
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
| | - Tong Lu
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA
| | - Stephen Y Chih
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA, USA
| | - Wei Li
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, USA; Penn State Cancer Institute, Penn State College of Medicine, Hershey, PA, USA; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA.
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4
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Kuhn TM, Paulsen M, Cuylen-Haering S. Accessible high-speed image-activated cell sorting. Trends Cell Biol 2024:S0962-8924(24)00094-1. [PMID: 38789300 DOI: 10.1016/j.tcb.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
Over the past six decades, fluorescence-activated cell sorting (FACS) has become an essential technology for basic and clinical research by enabling the isolation of cells of interest in high throughput. Recent technological advancements have started a new era of flow cytometry. By combining the spatial resolution of microscopy with high-speed cell sorting, new instruments allow cell sorting based on simple image-derived parameters or sophisticated image analysis algorithms, thereby greatly expanding the scope of applications. In this review, we discuss the systems that are commercially available or have been described in enough methodological and engineering detail to allow their replication. We summarize their strengths and limitations and highlight applications that have the potential to transform various fields in basic life science research and clinical settings.
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Affiliation(s)
- Terra M Kuhn
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Malte Paulsen
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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5
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Montizaan D, Bartucci R, Reker-Smit C, de Weerd S, Åberg C, Guryev V, Spierings DCJ, Salvati A. Genome-wide forward genetic screening to identify receptors and proteins mediating nanoparticle uptake and intracellular processing. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01629-x. [PMID: 38504023 DOI: 10.1038/s41565-024-01629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/07/2024] [Indexed: 03/21/2024]
Abstract
Understanding how cells process nanoparticles is crucial to optimize nanomedicine efficacy. However, characterizing cellular pathways is challenging, especially if non-canonical mechanisms are involved. In this Article a genome-wide forward genetic screening based on insertional mutagenesis is applied to discover receptors and proteins involved in the intracellular accumulation (uptake and intracellular processing) of silica nanoparticles. The nanoparticles are covered by a human serum corona known to target the low-density lipoprotein receptor (LDLR). By sorting cells with reduced nanoparticle accumulation and deep sequencing after each sorting, 80 enriched genes are identified. We find that, as well as LDLR, the scavenger receptor SCARB1 also mediates nanoparticle accumulation. Additionally, heparan sulfate acts as a specific nanoparticle receptor, and its role varies depending on cell and nanoparticle type. Furthermore, some of the identified targets affect nanoparticle trafficking to the lysosomes. These results show the potential of genetic screening to characterize nanoparticle pathways. Additionally, they indicate that corona-coated nanoparticles are internalized via multiple receptors.
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Affiliation(s)
- Daphne Montizaan
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands
| | - Roberta Bartucci
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands
| | - Catharina Reker-Smit
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands
| | - Sander de Weerd
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands
| | - Christoffer Åberg
- Department of Pharmaceutical Analysis, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anna Salvati
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, The Netherlands.
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6
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Hatzakis N, Kaestel-Hansen J, de Sautu M, Saminathan A, Scanavachi G, Correia R, Nielsen AJ, Bleshoey S, Boomsma W, Kirchhausen T. Deep learning assisted single particle tracking for automated correlation between diffusion and function. RESEARCH SQUARE 2024:rs.3.rs-3716053. [PMID: 38352328 PMCID: PMC10862944 DOI: 10.21203/rs.3.rs-3716053/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone illustrates that besides structure, motion encodes function at the molecular and subcellular level.
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7
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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8
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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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9
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Kæstel-Hansen J, de Sautu M, Saminathan A, Scanavachi G, Da Cunha Correia RFB, Nielsen AJ, Bleshøy SV, Boomsma W, Kirchhausen T, Hatzakis NS. Deep learning assisted single particle tracking for automated correlation between diffusion and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567393. [PMID: 38014323 PMCID: PMC10680793 DOI: 10.1101/2023.11.16.567393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone indicates that besides structure, motion encodes function at the molecular and subcellular level.
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Affiliation(s)
- Jacob Kæstel-Hansen
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | - Marilina de Sautu
- Biological Chemistry and Molecular Pharmaceutics Harvard Medical School
- Laboratory of Molecular Medicine Boston Children's Hospital
| | - Anand Saminathan
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Gustavo Scanavachi
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Ricardo F Bango Da Cunha Correia
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Annette Juma Nielsen
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | - Sara Vogt Bleshøy
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
| | | | - Tom Kirchhausen
- Department of Cell Biology Harvard Medical School
- Department of Pediatrics Harvard Medical School
- Program in Cellular and Molecular Medicine Boston Children's Hospital
| | - Nikos S Hatzakis
- Department of Chemistry University of Copenhagen
- Center for 4D cellular dynamics, Department of Chemistry University of Copenhagen
- Novo Nordisk Center for Optimised Oligo Escape
- Novo Nordisk foundation Center for Protein Research
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10
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He MM, Zhu SX, Cannon JR, Christensen JK, Duggal R, Gunduz M, Hilgendorf C, Hughes A, Kekessie I, Kullmann M, Leung D, Terjung C, Wang K, Wesche F. Metabolism and Excretion of Therapeutic Peptides: Current Industry Practices, Perspectives, and Recommendations. Drug Metab Dispos 2023; 51:1436-1450. [PMID: 37591731 DOI: 10.1124/dmd.123.001437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/19/2023] Open
Abstract
Therapeutic peptides (TPeps) have expanded from the initial endogenous peptides to complex modified peptides through medicinal chemistry efforts for almost a century. Different from small molecules and large proteins, the diverse submodalities of TPeps have distinct structures and carry different absorption, distribution, metabolism, and excretion (ADME) properties. There is no distinct regulatory guidance for the industry on conducting ADME studies (what, how, and when) for TPeps. Therefore, the Peptide ADME Working Group sponsored by the Translational and ADME Sciences Leadership Group of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) was formed with the goal to develop a white paper focusing on metabolism and excretion studies to support discovery and development of TPeps. In this paper, the key learnings from an IQ industry survey and U.S. Food and Drug Administration/European Medicines Agency submission documents of TPeps approved between 2011 and 2022 are outlined in detail. In addition, a comprehensive assessment of in vitro and in vivo metabolism and excretion studies, mitigation strategies for TPep metabolism, analytical tools to conduct studies, regulatory status, and Metabolites in Safety Testing considerations are provided. Finally, an industry recommendation on conducting metabolism and excretion studies is proposed for regulatory filing of TPeps. SIGNIFICANCE STATEMENT: This white paper presents current industry practices for metabolism and excretion studies of therapeutic peptides based on an industry survey, regulatory submission documents, and expert opinions from the participants in the Peptide Absorption, Distribution, Metabolism, and Excretion Working Group of the International Consortium for Innovation and Quality in Pharmaceutical Development. The group also provides recommendations on the Metabolites in Safety Testing considerations and metabolism and excretion studies for regulatory filing of therapeutic peptides.
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Affiliation(s)
- Minxia Michelle He
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Sean Xiaochun Zhu
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Joe R Cannon
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Jesper Kammersgaard Christensen
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Ruchia Duggal
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Mithat Gunduz
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Constanze Hilgendorf
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Adam Hughes
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Ivy Kekessie
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Maximilian Kullmann
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Dennis Leung
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Carsten Terjung
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Kai Wang
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
| | - Frank Wesche
- Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana (M.M.H.); Drug Metabolism and Pharmacokinetics, Takeda Development Center Americas, Inc., Cambridge, Massachusetts (S.X.Z.); Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, Princeton, New Jersey (J.R.C.); Development ADME, Novo Nordisk A/S, Måløv, Denmark (J.K.C.); Preclinical Development ADME, Merck & Co., Boston, Massachusetts (R.D.); PK Sciences/Global Biotransformation, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts (M.G.); DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden (C.H.); Discovery Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Stevenage, United Kingdom (A.H.); Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California (I.K.); Drug Metabolism and Pharmacokinetics, Bayer AG, Wuppertal, Germany (M.K., C.T.); Small Molecule Pharmaceutical Sciences, Genentech, Inc., South San Francisco, California (D.L.); Translational PK/PD and Investigative Toxicology, Janssen Research & Development, San Diego, California (K.W.); and Department of Drug Discovery Sciences, Discovery Science Technology Group, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach a.d. Riss, Germany (F.W.)
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11
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Stossi F, Singh PK, Safari K, Marini M, Labate D, Mancini MA. High throughput microscopy and single cell phenotypic image-based analysis in toxicology and drug discovery. Biochem Pharmacol 2023; 216:115770. [PMID: 37660829 DOI: 10.1016/j.bcp.2023.115770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Measuring single cell responses to the universe of chemicals (drugs, natural products, environmental toxicants etc.) is of paramount importance to human health as phenotypic variability in sensing stimuli is a hallmark of biology that is considered during high throughput screening. One of the ways to approach this problem is via high throughput, microscopy-based assays coupled with multi-dimensional single cell analysis methods. Here, we will summarize some of the efforts in this vast and growing field, focusing on phenotypic screens (e.g., Cell Painting), single cell analytics and quality control, with particular attention to environmental toxicology and drug screening. We will discuss advantages and limitations of high throughput assays with various end points and levels of complexity.
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Affiliation(s)
- Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.
| | - Pankaj K Singh
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Kazem Safari
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Michela Marini
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Department of Mathematics, University of Houston, Houston, TX, USA
| | - Demetrio Labate
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Department of Mathematics, University of Houston, Houston, TX, USA
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
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12
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Petkidis A, Andriasyan V, Greber UF. Machine learning for cross-scale microscopy of viruses. CELL REPORTS METHODS 2023; 3:100557. [PMID: 37751685 PMCID: PMC10545915 DOI: 10.1016/j.crmeth.2023.100557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/05/2023] [Accepted: 07/20/2023] [Indexed: 09/28/2023]
Abstract
Despite advances in virological sciences and antiviral research, viruses continue to emerge, circulate, and threaten public health. We still lack a comprehensive understanding of how cells and individuals remain susceptible to infectious agents. This deficiency is in part due to the complexity of viruses, including the cell states controlling virus-host interactions. Microscopy samples distinct cellular infection stages in a multi-parametric, time-resolved manner at molecular resolution and is increasingly enhanced by machine learning and deep learning. Here we discuss how state-of-the-art artificial intelligence (AI) augments light and electron microscopy and advances virological research of cells. We describe current procedures for image denoising, object segmentation, tracking, classification, and super-resolution and showcase examples of how AI has improved the acquisition and analyses of microscopy data. The power of AI-enhanced microscopy will continue to help unravel virus infection mechanisms, develop antiviral agents, and improve viral vectors.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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13
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Wan X, Yao G, Wang K, Liu Y, Wang F, Jiang H. Transcriptomic Analysis of the Response of the Toxic Dinoflagellate Prorocentrum lima to Phosphorous Limitation. Microorganisms 2023; 11:2216. [PMID: 37764060 PMCID: PMC10535992 DOI: 10.3390/microorganisms11092216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Phosphorus (P) is a limiting macronutrient for dinoflagellate growth in the ocean. Previous studies have been focused on the physiological response of dinoflagellates to ambient P changes. However, the whole-genome's molecular mechanisms are poorly understood. In this study, RNA-Seq was utilized to compare the global gene expression patterns of a marine diarrheic shellfish poisoning (DSP) toxin-producing dinoflagellate, Prorocentrum lima, grown in inorganic P-replete and P-deficient conditions. A total of 148 unigenes were significantly up-regulated, and 30 unigenes were down-regulated under 1/4 P-limited conditions, while 2708 unigenes were significantly up-regulated, and 284 unigenes were down-regulated under 1/16 P-limited conditions. KEGG enrichment analysis of the differentially expressed genes shows that genes related to ribosomal proteins, glycolysis, fatty acid biosynthesis, phagosome formation, and ubiquitin-mediated proteolysis are found to be up-regulated, while most of the genes related to photosynthesis are down-regulated. Further analysis shows that genes encoding P transporters, organic P utilization, and endocytosis are significantly up-regulated in the P-limited cells, indicating a strong ability of P. lima to utilize dissolved inorganic P as well as intracellular organic P. These transcriptomic data are further corroborated by biochemical and physiological analyses, which reveals that under P deficiency, cellular contents of starch, lipid, and toxin increase, while photosynthetic efficiency declines. Our results indicate that has P. lima evolved diverse strategies to acclimatize to low P environments. The accumulation of carbon sources and DSP toxins could provide protection for P. lima to cope with adverse environmental conditions.
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Affiliation(s)
| | | | | | | | | | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (X.W.); (G.Y.); (K.W.); (Y.L.); (F.W.)
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14
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Wang X, Li Y, Liu A, Padilla R, Lee DM, Kim D, Mettlen M, Chen Z, Schmid SL, Danuser G. Endocytosis gated by emergent properties of membrane-clathrin interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551737. [PMID: 37577632 PMCID: PMC10418234 DOI: 10.1101/2023.08.02.551737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Clathrin-mediated endocytosis (CME), the major cellular entry pathway, starts when clathrin assembles on the plasma membrane into clathrin-coated pits (CCPs). Two populations of CCPs are detected within the same cell: 'productive' CCPs that invaginate and pinch off, forming clathrin-coated vesicles (CCVs) [1, 2], and 'abortive' CCPs [3, 4, 5] that prematurely disassemble. The mechanisms of gating between these two populations and their relations to the functions of dozens of early-acting endocytic accessory proteins (EAPs) [5, 6, 7, 8, 9] have remained elusive. Here, we use experimentally-guided modeling to integrate the clathrin machinery and membrane mechanics in a single dynamical system. We show that the split between the two populations is an emergent property of this system, in which a switch between an Open state and a Closed state follows from the competition between the chemical energy of the clathrin basket and the mechanical energy of membrane bending. In silico experiments revealed an abrupt transition between the two states that acutely depends on the strength of the clathrin basket. This critical strength is lowered by membrane-bending EAPs [10, 11, 12]. Thus, CME is poised to be shifted between abortive and productive events by small changes in membrane curvature and/or coat stability. This model clarifies the workings of a putative endocytic checkpoint whose existence was previously proposed based on statistical analyses of the lifetime distributions of CCPs [4, 13]. Overall, a mechanistic framework is established to elucidate the diverse and redundant functions of EAPs in regulating CME progression.
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15
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Schuhmacher JS, Tom Dieck S, Christoforidis S, Landerer C, Davila Gallesio J, Hersemann L, Seifert S, Schäfer R, Giner A, Toth-Petroczy A, Kalaidzidis Y, Bohnsack KE, Bohnsack MT, Schuman EM, Zerial M. The Rab5 effector FERRY links early endosomes with mRNA localization. Mol Cell 2023; 83:1839-1855.e13. [PMID: 37267905 DOI: 10.1016/j.molcel.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/06/2022] [Accepted: 05/08/2023] [Indexed: 06/04/2023]
Abstract
Localized translation is vital to polarized cells and requires precise and robust distribution of different mRNAs and ribosomes across the cell. However, the underlying molecular mechanisms are poorly understood and important players are lacking. Here, we discovered a Rab5 effector, the five-subunit endosomal Rab5 and RNA/ribosome intermediary (FERRY) complex, that recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction. FERRY displays preferential binding to certain groups of transcripts, including mRNAs encoding mitochondrial proteins. Deletion of FERRY subunits reduces the endosomal localization of transcripts in cells and has a significant impact on mRNA levels. Clinical studies show that genetic disruption of FERRY causes severe brain damage. We found that, in neurons, FERRY co-localizes with mRNA on early endosomes, and mRNA loaded FERRY-positive endosomes are in close proximity of mitochondria. FERRY thus transforms endosomes into mRNA carriers and plays a key role in regulating mRNA distribution and transport.
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Affiliation(s)
- Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Susanne Tom Dieck
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Savvas Christoforidis
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece; Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ramona Schäfer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Angelika Giner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Centre for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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16
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Cheng Y, Kang XZ, Chan P, Cheung PHH, Cheng T, Ye ZW, Chan CP, Yu CH, Jin DY. FACI is a novel clathrin adaptor protein 2-binding protein that facilitates low-density lipoprotein endocytosis. Cell Biosci 2023; 13:74. [PMID: 37072871 PMCID: PMC10114425 DOI: 10.1186/s13578-023-01023-5] [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: 12/19/2022] [Accepted: 03/27/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Cholesterol plays a vital role in multiple physiological processes. Cellular uptake of cholesterol is mediated primarily through endocytosis of low-density lipoprotein (LDL) receptor. New modifiers of this process remain to be characterized. Particularly, the role of fasting- and CREB-H-induced (FACI) protein in cholesterol homeostasis merits further investigation. METHODS Interactome profiling by proximity labeling and affinity purification - mass spectrometry was performed. Total internal reflection fluorescence microscopy and confocal immunofluorescence microscopy were used to analyze protein co-localization and interaction. Mutational analysis was carried out to define the domain and residues required for FACI localization and function. Endocytosis was traced by fluorescent cargos. LDL uptake in cultured cells and diet-induced hypercholesterolemia in mice were assessed. RESULTS FACI interacted with proteins critically involved in clathrin-mediated endocytosis, vesicle trafficking, and membrane cytoskeleton. FACI localized to clathrin-coated pits (CCP) on plasma membranes. FACI contains a conserved DxxxLI motif, which mediates its binding with the adaptor protein 2 (AP2) complex. Disruption of this motif of FACI abolished its CCP localization but didn't affect its association with plasma membrane. Cholesterol was found to facilitate FACI transport from plasma membrane to endocytic recycling compartment in a clathrin- and cytoskeleton-dependent manner. LDL endocytosis was enhanced in FACI-overexpressed AML12 cells but impaired in FACI-depleted HeLa cells. In vivo study indicated that hepatic FACI overexpression alleviated diet-induced hypercholesterolemia in mice. CONCLUSIONS FACI facilitates LDL endocytosis through its interaction with the AP2 complex.
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Affiliation(s)
- Yun Cheng
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
| | - Xiao-Zhuo Kang
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Pearl Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Pak-Hin Hinson Cheung
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Tao Cheng
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Zi-Wei Ye
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Cheng-Han Yu
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
- State Key Laboratory of Liver Research, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
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Koller A, Brunner SM, Preishuber-Pflügl J, Runge C, Ladek AM, Reitsamer HA, Trost A. Cysteinyl leukotriene receptor 1 is a potent regulator of the endosomal-lysosomal system in the ARPE-19 retinal pigment epithelial cell line. Traffic 2023; 24:177-189. [PMID: 36704929 DOI: 10.1111/tra.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023]
Abstract
The endosomal-lysosomal system is central for cell homeostasis and comprises the functions and dynamics of particular organelles including endosomes, lysosomes and autophagosomes. In previous studies, we found that the cysteinyl leukotriene receptor 1 (CysLTR1) regulates autophagy in the retinal pigment epithelial cell line ARPE-19 under basal cellular conditions. However, the underlying mechanism by which CysLTR1 regulates autophagy is unknown. Thus, in the present study, the effects of CysLTR1 inhibition on the endosomal-lysosomal system are analyzed in detail to identify the role of CysLTR1 in cell homeostasis and autophagy regulation. CysLTR1 inhibition in ARPE-19 cells by Zafirlukast, a CysLTR1 antagonist, depleted the lysosomal pool. Furthermore, CysLTR1 antagonization reduced endocytic capacity and internalization of epidermal growth factor and decreased levels of the transferrin receptor, CD71. Serum starvation abolished the effect of Zafirlukast on the autophagic flux, which identifies the endocytic regulation of serum components by CysLTR1 as an important autophagy-modulating mechanism. The role of CysLTR1 in inflammation and cell stress has been exceedingly studied, but its involvement in the endosomal-lysosomal pathway is largely unknown. This current study provides new insights into basal activity of CysLTR1 on cellular endocytosis and the subsequent impact on downstream processes like autophagy.
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Affiliation(s)
- Andreas Koller
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Susanne Maria Brunner
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Julia Preishuber-Pflügl
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Christian Runge
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Anja-Maria Ladek
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Herbert Anton Reitsamer
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Andrea Trost
- Research Program for Experimental Ophthalmology and Glaucoma Research, Department of Ophthalmology and Optometry, University Hospital of the Paracelsus Medical University, Salzburg, Austria
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18
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Joseph BB, Naslavsky N, Binti S, Conquest S, Robison L, Bai G, Homer RO, Grant BD, Caplan S, Fay DS. Conserved NIMA kinases regulate multiple steps of endocytic trafficking. PLoS Genet 2023; 19:e1010741. [PMID: 37099601 PMCID: PMC10166553 DOI: 10.1371/journal.pgen.1010741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/08/2023] [Accepted: 04/11/2023] [Indexed: 04/27/2023] Open
Abstract
Human NIMA-related kinases have primarily been studied for their roles in cell cycle progression (NEK1/2/6/7/9), checkpoint-DNA-damage control (NEK1/2/4/5/10/11), and ciliogenesis (NEK1/4/8). We previously showed that Caenorhabditis elegans NEKL-2 (NEK8/9 homolog) and NEKL-3 (NEK6/7 homolog) regulate apical clathrin-mediated endocytosis (CME) in the worm epidermis and are essential for molting. Here we show that NEKL-2 and NEKL-3 also have distinct roles in controlling endosome function and morphology. Specifically, loss of NEKL-2 led to enlarged early endosomes with long tubular extensions but showed minimal effects on other compartments. In contrast, NEKL-3 depletion caused pronounced defects in early, late, and recycling endosomes. Consistently, NEKL-2 was strongly localized to early endosomes, whereas NEKL-3 was localized to multiple endosomal compartments. Loss of NEKLs also led to variable defects in the recycling of two resident cargoes of the trans-Golgi network (TGN), MIG-14/Wntless and TGN-38/TGN38, which were missorted to lysosomes after NEKL depletion. In addition, defects were observed in the uptake of clathrin-dependent (SMA-6/Type I BMP receptor) and independent cargoes (DAF-4/Type II BMP receptor) from the basolateral surface of epidermal cells after NEKL-2 or NEKL-3 depletion. Complementary studies in human cell lines further showed that siRNA knockdown of the NEKL-3 orthologs NEK6 and NEK7 led to missorting of the mannose 6-phosphate receptor from endosomes. Moreover, in multiple human cell types, depletion of NEK6 or NEK7 disrupted both early and recycling endosomal compartments, including the presence of excess tubulation within recycling endosomes, a defect also observed after NEKL-3 depletion in worms. Thus, NIMA family kinases carry out multiple functions during endocytosis in both worms and humans, consistent with our previous observation that human NEKL-3 orthologs can rescue molting and trafficking defects in C. elegans nekl-3 mutants. Our findings suggest that trafficking defects could underlie some of the proposed roles for NEK kinases in human disease.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Naava Naslavsky
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Shaonil Binti
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sylvia Conquest
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Lexi Robison
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Rafael O. Homer
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Barth D. Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture Life Sciences, and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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19
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Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames. Mol Cell 2023; 83:994-1011.e18. [PMID: 36806354 PMCID: PMC10032668 DOI: 10.1016/j.molcel.2023.01.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
All species continuously evolve short open reading frames (sORFs) that can be templated for protein synthesis and may provide raw materials for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionarily young and had emerged de novo. We additionally identified 221 previously missed sORFs potentially translated into peptides of up to 15 amino acids-all of which are smaller than the smallest human microprotein annotated to date. To investigate the bioactivity of sORF-encoded small peptides and young microproteins, we subjected 266 candidates to a mass-spectrometry-based interactome screen with motif resolution. Based on these interactomes and additional cellular assays, we can associate several candidates with mRNA splicing, translational regulation, and endocytosis. Our work provides insights into the evolutionary origins and interaction potential of young and small proteins, thereby helping to elucidate this underexplored territory of the human proteome.
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Affiliation(s)
- Clara-L Sandmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jana F Schulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Eleonora Adami
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maike Marczenke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Annabel Christ
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nina Liebe
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Johannes Greiner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Aaron Schoenenberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Michael B Muecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Ning Liang
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Michael Gotthardt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John R Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Thomas E Willnow
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | | | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany.
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20
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Parveen S, Khamari A, Raju J, Coppolino MG, Datta S. Syntaxin 7 contributes to breast cancer cell invasion by promoting invadopodia formation. J Cell Sci 2022; 135:275829. [PMID: 35762511 DOI: 10.1242/jcs.259576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
Invasion in various cancer cells requires coordinated delivery of signaling proteins, adhesion proteins, actin-remodeling proteins and proteases to matrix-degrading structures called invadopodia. Vesicular trafficking involving SNAREs plays a crucial role in the delivery of cargo to the target membrane. Screening of 13 SNAREs from the endocytic and recycling route using a gene silencing approach coupled with functional assays identified syntaxin 7 (STX7) as an important player in MDA-MB-231 cell invasion. Total internal reflection fluorescence microscopy (TIRF-M) studies revealed that STX7 resides near invadopodia and co-traffics with MT1-MMP (also known as MMP14), indicating a possible role for this SNARE in protease trafficking. STX7 depletion reduced the number of invadopodia and their associated degradative activity. Immunoprecipitation studies revealed that STX7 forms distinct SNARE complexes with VAMP2, VAMP3, VAMP7, STX4 and SNAP23. Depletion of VAMP2, VAMP3 or STX4 abrogated invadopodia formation, phenocopying what was seen upon lack of STX7. Whereas depletion of STX4 reduced MT1-MMP level at the cell surfaces, STX7 silencing significantly reduced the invadopodia-associated MT1-MMP pool and increased the non-invadosomal pool. This study highlights STX7 as a major contributor towards the invadopodia formation during cancer cell invasion. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sameena Parveen
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal 462066, India
| | - Amrita Khamari
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal 462066, India
| | - Jyothikamala Raju
- Thazhathemalayil House, Thodupuzha East PO, Keerikode, Kerala 685585, India
| | - Marc G Coppolino
- Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Bhopal 462066, India
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21
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Endocytic trafficking of GAS6-AXL complexes is associated with sustained AKT activation. Cell Mol Life Sci 2022; 79:316. [PMID: 35622156 PMCID: PMC9135597 DOI: 10.1007/s00018-022-04312-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/27/2022] [Accepted: 04/15/2022] [Indexed: 11/18/2022]
Abstract
AXL, a TAM receptor tyrosine kinase (RTK), and its ligand growth arrest-specific 6 (GAS6) are implicated in cancer metastasis and drug resistance, and cellular entry of viruses. Given this, AXL is an attractive therapeutic target, and its inhibitors are being tested in cancer and COVID-19 clinical trials. Still, astonishingly little is known about intracellular mechanisms that control its function. Here, we characterized endocytosis of AXL, a process known to regulate intracellular functions of RTKs. Consistent with the notion that AXL is a primary receptor for GAS6, its depletion was sufficient to block GAS6 internalization. We discovered that upon receptor ligation, GAS6–AXL complexes were rapidly internalized via several endocytic pathways including both clathrin-mediated and clathrin-independent routes, among the latter the CLIC/GEEC pathway and macropinocytosis. The internalization of AXL was strictly dependent on its kinase activity. In comparison to other RTKs, AXL was endocytosed faster and the majority of the internalized receptor was not degraded but rather recycled via SNX1-positive endosomes. This trafficking pattern coincided with sustained AKT activation upon GAS6 stimulation. Specifically, reduced internalization of GAS6–AXL upon the CLIC/GEEC downregulation intensified, whereas impaired recycling due to depletion of SNX1 and SNX2 attenuated AKT signaling. Altogether, our data uncover the coupling between AXL endocytic trafficking and AKT signaling upon GAS6 stimulation. Moreover, our study provides a rationale for pharmacological inhibition of AXL in antiviral therapy as viruses utilize GAS6–AXL-triggered endocytosis to enter cells.
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22
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Francia V, Reker-Smit C, Salvati A. Mechanisms of Uptake and Membrane Curvature Generation for the Internalization of Silica Nanoparticles by Cells. NANO LETTERS 2022; 22:3118-3124. [PMID: 35377663 PMCID: PMC9011393 DOI: 10.1021/acs.nanolett.2c00537] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/29/2022] [Indexed: 06/01/2023]
Abstract
Nanosized drug carriers enter cells via active mechanisms of endocytosis but the pathways involved are often not clarified. Cells possess several mechanisms to generate membrane curvature during uptake. However, the mechanisms of membrane curvature generation for nanoparticle uptake have not been explored so far. Here, we combined different methods to characterize how silica nanoparticles with a human serum corona enter cells. In these conditions, silica nanoparticles are internalized via the LDL receptor (LDLR). We demonstrate that despite the interaction with LDLR, uptake is not clathrin-mediated, as usually observed for this receptor. Additionally, silencing the expression of different proteins involved in clathrin-independent mechanisms and several BAR-domain proteins known to generate membrane curvature strongly reduces nanoparticle uptake. Thus, nanosized objects targeted to specific receptors, such as here LDLR, can enter cells via different mechanisms than their endogenous ligands. Additionally, nanoparticles may trigger alternative mechanisms of membrane curvature generation for their internalization.
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23
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Wen Y, Xie D, Liu Z. Advances in protein analysis in single live cells: principle, instrumentation and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Gunaratne GS, Marchant JS. The ins and outs of virus trafficking through acidic Ca 2+ stores. Cell Calcium 2022; 102:102528. [PMID: 35033909 PMCID: PMC8860173 DOI: 10.1016/j.ceca.2022.102528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
Many viruses exploit host-cell Ca2+ signaling processes throughout their life cycle. This is especially relevant for viruses that translocate through the endolysosomal system, where cellular infection is keyed to the microenvironment of these acidic Ca2+ stores and Ca2+-dependent trafficking pathways. As regulators of the endolysosomal ionic milieu and trafficking dynamics, two families of endolysosomal Ca2+-permeable cation channels - two pore channels (TPCs) and transient receptor potential mucolipins (TRPMLs) - have emerged as important host-cell factors in viral entry. Here, we review: (i) current evidence implicating Ca2+ signaling in viral translocation through the endolysosomal system, (ii) the roles of these ion channels in supporting cellular infection by different viruses, and (iii) areas for future research that will help define the potential of TPC and TRPML ligands as progressible antiviral agents.
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Affiliation(s)
- Gihan S Gunaratne
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee WI 53226, USA.
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee WI 53226, USA
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25
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Paramasivam P, Stöter M, Corradi E, Dalla Costa I, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Yanez Arteta M, Nordberg P, Andersson S, Baudet ML, Bickle M, Zerial M. Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining. RNA (NEW YORK, N.Y.) 2022; 28:433-446. [PMID: 34949721 PMCID: PMC8848937 DOI: 10.1261/rna.078895.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eloina Corradi
- Department CIBIO, University of Trento, Trento 38123, Italy
| | | | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Peter Nordberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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26
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Paramasivam P, Franke C, Stöter M, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Arteta MY, Dahlén A, Bak A, Andersson S, Kalaidzidis Y, Bickle M, Zerial M. Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale. J Cell Biol 2022; 221:212896. [PMID: 34882187 PMCID: PMC8666849 DOI: 10.1083/jcb.202110137] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/09/2023] Open
Abstract
Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal compartments and capture events of mRNA escape from endosomal recycling tubules. Our results change the view of the mechanisms of endosomal escape and define quantitative parameters to guide the development of mRNA formulations toward higher efficacy and lower cytotoxicity.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christian Franke
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Annette Bak
- Advanced Drug Delivery, Pharmaceutical Science Research and Development, AstraZeneca, Boston, MA
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, Gothenburg, Sweden
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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27
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Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
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Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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28
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Feldman D, Funk L, Le A, Carlson RJ, Leiken MD, Tsai F, Soong B, Singh A, Blainey PC. Pooled genetic perturbation screens with image-based phenotypes. Nat Protoc 2022; 17:476-512. [PMID: 35022620 PMCID: PMC9654597 DOI: 10.1038/s41596-021-00653-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022]
Abstract
Discovery of the genetic components underpinning fundamental and disease-related processes is being rapidly accelerated by combining efficient, programmable genetic engineering with phenotypic readouts of high spatial, temporal and/or molecular resolution. Microscopy is a fundamental tool for studying cell biology, but its lack of high-throughput sequence readouts hinders integration in large-scale genetic screens. Optical pooled screens using in situ sequencing provide massively scalable integration of barcoded lentiviral libraries (e.g., CRISPR perturbation libraries) with high-content imaging assays, including dynamic processes in live cells. The protocol uses standard lentiviral vectors and molecular biology, providing single-cell resolution of phenotype and engineered genotype, scalability to millions of cells and accurate sequence reads sufficient to distinguish >106 perturbations. In situ amplification takes ~2 d, while sequencing can be performed in ~1.5 h per cycle. The image analysis pipeline provided enables fully parallel automated sequencing analysis using a cloud or cluster computing environment.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Luke Funk
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna Le
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - FuNien Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Brian Soong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cellular and Tissue Genomics, Genentech Inc., South San Francisco, CA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
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29
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Moreira DDP, Suzuki AM, Silva ALTE, Varella-Branco E, Meneghetti MCZ, Kobayashi GS, Fogo M, Ferrari MDFR, Cardoso RR, Lourenço NCV, Griesi-Oliveira K, Zachi EC, Bertola DR, Weinmann KDS, de Lima MA, Nader HB, Sertié AL, Passos-Bueno MR. Neuroprogenitor Cells From Patients With TBCK Encephalopathy Suggest Deregulation of Early Secretory Vesicle Transport. Front Cell Neurosci 2022; 15:803302. [PMID: 35095425 PMCID: PMC8793280 DOI: 10.3389/fncel.2021.803302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Biallelic pathogenic variants in TBCK cause encephaloneuropathy, infantile hypotonia with psychomotor retardation, and characteristic facies 3 (IHPRF3). The molecular mechanisms underlying its neuronal phenotype are largely unexplored. In this study, we reported two sisters, who harbored biallelic variants in TBCK and met diagnostic criteria for IHPRF3. We provided evidence that TBCK may play an important role in the early secretory pathway in neuroprogenitor cells (iNPC) differentiated from induced pluripotent stem cells (iPSC). Lack of functional TBCK protein in iNPC is associated with impaired endoplasmic reticulum-to-Golgi vesicle transport and autophagosome biogenesis, as well as altered cell cycle progression and severe impairment in the capacity of migration. Alteration in these processes, which are crucial for neurogenesis, neuronal migration, and cytoarchitecture organization, may represent an important causative mechanism of both neurodevelopmental and neurodegenerative phenotypes observed in IHPRF3. Whether reduced mechanistic target of rapamycin (mTOR) signaling is secondary to impaired TBCK function over other secretory transport regulators still needs further investigation.
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Affiliation(s)
- Danielle de Paula Moreira
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Angela May Suzuki
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elisa Varella-Branco
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gerson Shigeru Kobayashi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mariana Fogo
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | | | - Rafaela Regina Cardoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Naila Cristina Vilaça Lourenço
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Karina Griesi-Oliveira
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | - Elaine Cristina Zachi
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Débora Romeo Bertola
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Instituto da Criança do Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Karina de Souza Weinmann
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo Andrade de Lima
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Helena Bonciani Nader
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Andrea Laurato Sertié
- Instituto de Ensino e Pesquisa Albert Einstein, Albert Einstein Hospital, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas Sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Maria Rita Passos-Bueno,
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30
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Priya A, Datta S. Monitoring Endosomal Cargo Retrieval to the Trans-Golgi Network by Microscopic and Biochemical Approaches. Methods Mol Biol 2022; 2473:213-236. [PMID: 35819769 DOI: 10.1007/978-1-0716-2209-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The endosomal recycling pathway plays a crucial role in diverse physiologically important biological processes such as cell-to-cell signaling, nutrient uptake, immune response, and autophagy. A selective subset of these recycling cargoes, mostly transmembrane proteins, is retrieved from endosomes to the trans-Golgi network (TGN) by a retrograde transport process. Endosome-to-TGN retrograde trafficking is crucial for maintaining cellular homeostasis and signaling by preventing proteins and lipids from degradation in the lysosome. Many of the membrane sorting machinery, such as the retromer complex and sorting nexins (SNXs) are involved in endosomal retrieval and recycling of various transmembrane proteins. Recent technological advances in the resolution of light microscopy and unbiased analytical approaches in quantitative image analysis enable us to explore and understand the regulation of membrane trafficking pathways in greater detail. In this chapter, we describe quantitative imaging-based methods for analyzing the roles of proteins involved in the retrograde trafficking in retromer dependent or independent fashion, using cation-independent mannose-6-phosphate receptor (CIM6PR) as an example.
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Affiliation(s)
- Amulya Priya
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France.
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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31
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Jaimon E, Tripathi A, Khurana A, Ghosh D, Sugatha J, Datta S. Binding with heat shock cognate protein HSC70 fine-tunes the Golgi association of the small GTPase ARL5B. J Biol Chem 2021; 297:101422. [PMID: 34798070 PMCID: PMC8661063 DOI: 10.1016/j.jbc.2021.101422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
ARL5B, an ARF-like small GTPase localized to the trans-Golgi, is known for regulating endosome-Golgi trafficking and promoting the migration and invasion of breast cancer cells. Although a few interacting partners have been identified, the mechanism of the shuttling of ARL5B between the Golgi membrane and the cytosol is still obscure. Here, using GFP-binding protein (GBP) pull-down followed by mass spectrometry, we identified heat shock cognate protein (HSC70) as an additional interacting partner of ARL5B. Our pull-down and isothermal titration calorimetry (ITC)-based studies suggested that HSC70 binds to ARL5B in an ADP-dependent manner. Additionally, we showed that the N-terminal helix and the nucleotide status of ARL5B contribute to its recognition by HSC70. The confocal microscopy and cell fractionation studies in MDA-MB-231 breast cancer cells revealed that the depletion of HSC70 reduces the localization of ARL5B to the Golgi. Using in vitro reconstitution approach, we provide evidence that HSC70 fine-tunes the association of ARL5B with Golgi membrane. Finally, we demonstrated that the interaction between ARL5B and HSC70 is important for the localization of cation independent mannose-6-phosphate receptor (CIMPR) at Golgi. Collectively, we propose a mechanism by which HSC70, a constitutively expressed chaperone, modulates the Golgi association of ARL5B, which in turn has implications for the Golgi-associated functions of this GTPase.
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Affiliation(s)
- Ebsy Jaimon
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Aashutosh Tripathi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Arohi Khurana
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Dipanjana Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Jini Sugatha
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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32
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Placidi G, Campa CC. Deliver on Time or Pay the Fine: Scheduling in Membrane Trafficking. Int J Mol Sci 2021; 22:11773. [PMID: 34769203 PMCID: PMC8583995 DOI: 10.3390/ijms222111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Membrane trafficking is all about time. Automation in such a biological process is crucial to ensure management and delivery of cellular cargoes with spatiotemporal precision. Shared molecular regulators and differential engagement of trafficking components improve robustness of molecular sorting. Sequential recruitment of low affinity protein complexes ensures directionality of the process and, concomitantly, serves as a kinetic proofreading mechanism to discriminate cargoes from the whole endocytosed material. This strategy helps cells to minimize losses and operating errors in membrane trafficking, thereby matching the appealed deadline. Here, we summarize the molecular pathways of molecular sorting, focusing on their timing and efficacy. We also highlight experimental procedures and genetic approaches to robustly probe these pathways, in order to guide mechanistic studies at the interface between biochemistry and quantitative biology.
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Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
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33
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Åberg C, Piattelli V, Montizaan D, Salvati A. Sources of variability in nanoparticle uptake by cells. NANOSCALE 2021; 13:17530-17546. [PMID: 34652349 PMCID: PMC8552707 DOI: 10.1039/d1nr04690j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Understanding how nano-sized objects are taken up by cells is important for applications within medicine (nanomedicine), as well as to avoid unforeseen hazard due to nanotechnology (nanosafety). Even within the same cell population, one typically observes a large cell-to-cell variability in nanoparticle uptake, raising the question of the underlying cause(s). Here we investigate cell-to-cell variability in polystyrene nanoparticle uptake by HeLa cells, with generalisations of the results to silica nanoparticles and liposomes, as well as to A549 and primary human umbilical vein endothelial cells. We show that uptake of nanoparticles is correlated with cell size within a cell population, thereby reproducing and generalising previous reports highlighting the role of cell size in nanoparticle uptake. By repeatedly isolating (using fluorescence-activated cell sorting) the cells that take up the most and least nanoparticles, respectively, and performing RNA sequencing on these cells separately, we examine the underlying gene expression that contributes to high and low polystyrene nanoparticle accumulation in HeLa cells. We can thereby show that cell size is not the sole driver of cell-to-cell variability, but that other cellular characteristics also play a role. In contrast to cell size, these characteristics are more specific to the object (nanoparticle or protein) being taken up, but are nevertheless highly heterogeneous, complicating their detailed identification. Overall, our results highlight the complexity underlying the cellular features that determine nanoparticle uptake propensity.
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Affiliation(s)
- Christoffer Åberg
- Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Valeria Piattelli
- Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Daphne Montizaan
- Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Anna Salvati
- Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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34
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Organoids in image-based phenotypic chemical screens. Exp Mol Med 2021; 53:1495-1502. [PMID: 34663938 PMCID: PMC8569209 DOI: 10.1038/s12276-021-00641-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Image-based phenotypic screening relies on the extraction of multivariate information from cells cultured under a large variety of conditions. Technical advances in high-throughput microscopy enable screening in increasingly complex and biologically relevant model systems. To this end, organoids hold great potential for high-content screening because they recapitulate many aspects of parent tissues and can be derived from patient material. However, screening is substantially more difficult in organoids than in classical cell lines from both technical and analytical standpoints. In this review, we present an overview of studies employing organoids for screening applications. We discuss the promises and challenges of small-molecule treatments in organoids and give practical advice on designing, running, and analyzing high-content organoid-based phenotypic screens.
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35
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Simonneau C, Duschmalé M, Gavrilov A, Brandenberg N, Hoehnel S, Ceroni C, Lassalle E, Kassianidou E, Knoetgen H, Niewoehner J, Villaseñor R. Investigating receptor-mediated antibody transcytosis using blood-brain barrier organoid arrays. Fluids Barriers CNS 2021; 18:43. [PMID: 34544422 PMCID: PMC8454074 DOI: 10.1186/s12987-021-00276-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pathways that control protein transport across the blood-brain barrier (BBB) remain poorly characterized. Despite great advances in recapitulating the human BBB in vitro, current models are not suitable for systematic analysis of the molecular mechanisms of antibody transport. The gaps in our mechanistic understanding of antibody transcytosis hinder new therapeutic delivery strategy development. METHODS We applied a novel bioengineering approach to generate human BBB organoids by the self-assembly of astrocytes, pericytes and brain endothelial cells with unprecedented throughput and reproducibility using micro patterned hydrogels. We designed a semi-automated and scalable imaging assay to measure receptor-mediated transcytosis of antibodies. Finally, we developed a workflow to use CRISPR/Cas9 gene editing in BBB organoid arrays to knock out regulators of endocytosis specifically in brain endothelial cells in order to dissect the molecular mechanisms of receptor-mediated transcytosis. RESULTS BBB organoid arrays allowed the simultaneous growth of more than 3000 homogenous organoids per individual experiment in a highly reproducible manner. BBB organoid arrays showed low permeability to macromolecules and prevented transport of human non-targeting antibodies. In contrast, a monovalent antibody targeting the human transferrin receptor underwent dose- and time-dependent transcytosis in organoids. Using CRISPR/Cas9 gene editing in BBB organoid arrays, we showed that clathrin, but not caveolin, is required for transferrin receptor-dependent transcytosis. CONCLUSIONS Human BBB organoid arrays are a robust high-throughput platform that can be used to discover new mechanisms of receptor-mediated antibody transcytosis. The implementation of this platform during early stages of drug discovery can accelerate the development of new brain delivery technologies.
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Affiliation(s)
- Claire Simonneau
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Martina Duschmalé
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Alina Gavrilov
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Sylke Hoehnel
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Camilla Ceroni
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | - Evodie Lassalle
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Elena Kassianidou
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Hendrik Knoetgen
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities, Roche Innovation Center Munich, Munich, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities, Roche Innovation Center Munich, Munich, Germany
| | - Roberto Villaseñor
- Roche Pharma Research and Early Development (pRED), Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland.
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Ghosh D, Dutta A, Kashyap A, Upmanyu N, Datta S. PLP2 drives collective cell migration via ZO-1-mediated cytoskeletal remodeling at the leading edge in human colorectal cancer cells. J Cell Sci 2021; 134:271878. [PMID: 34409455 DOI: 10.1242/jcs.253468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 08/11/2021] [Indexed: 01/06/2023] Open
Abstract
Collective cell migration (CCM), in which cell-cell integrity remains preserved during movement, plays an important role in the progression of cancer. However, studies describing CCM in cancer progression are majorly focused on the effects of extracellular tissue components on moving cell plasticity. The molecular and cellular mechanisms of CCM during cancer progression remain poorly explored. Here, we report that proteolipid protein 2 (PLP2), a colonic epithelium-enriched transmembrane protein, plays a vital role in the CCM of invasive human colorectal cancer (CRC) epithelium by modulating leading-edge cell dynamics in 2D. The extracellular pool of PLP2, secreted via exosomes, was also found to contribute to the event. During CCM, the protein was found to exist in association with ZO-1 (also known as TJP1) and to be involved in the positioning of the latter at the migrating edge. PLP2-mediated positioning of ZO-1 at the leading edge further alters actin cytoskeletal organization that involves Rac1 activation. Taken together, our findings demonstrate that PLP2, via its association with ZO-1, drives CCM in CRC epithelium by modulating the leading-edge actin cytoskeleton, thereby opening up new avenues of cancer research. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Dipanjana Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.,School of Pharmacy and Research, People's University, Bhopal 462037, India
| | - Ankita Dutta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Anjali Kashyap
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Neeraj Upmanyu
- School of Pharmacy and Research, People's University, Bhopal 462037, India
| | - Sunando Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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Behrens HM, Schmidt S, Spielmann T. The newly discovered role of endocytosis in artemisinin resistance. Med Res Rev 2021; 41:2998-3022. [PMID: 34309894 DOI: 10.1002/med.21848] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/15/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022]
Abstract
Artemisinin and its derivatives (ART) are the cornerstone of malaria treatment as part of artemisinin combination therapy (ACT). However, reduced susceptibility to artemisinin as well as its partner drugs threatens the usefulness of ACTs. Single point mutations in the parasite protein Kelch13 (K13) are necessary and sufficient for the reduced sensitivity of malaria parasites to ART but several alternative mechanisms for this resistance have been proposed. Recent work found that K13 is involved in the endocytosis of host cell cytosol and indicated that this is the process responsible for resistance in parasites with mutated K13. These studies also identified a series of further proteins that act together with K13 in the same pathway, including previously suspected resistance proteins such as UBP1 and AP-2μ. Here, we give a brief overview of artemisinin resistance, present the recent evidence of the role of endocytosis in ART resistance and discuss previous hypotheses in light of this new evidence. We also give an outlook on how the new insights might affect future research.
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Affiliation(s)
- Hannah Michaela Behrens
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sabine Schmidt
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Tobias Spielmann
- Molecular Biology and Immunology Section, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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38
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Smith MP, Ferguson HR, Ferguson J, Zindy E, Kowalczyk KM, Kedward T, Bates C, Parsons J, Watson J, Chandler S, Fullwood P, Warwood S, Knight D, Clarke RB, Francavilla C. Reciprocal priming between receptor tyrosine kinases at recycling endosomes orchestrates cellular signalling outputs. EMBO J 2021; 40:e107182. [PMID: 34086370 PMCID: PMC8447605 DOI: 10.15252/embj.2020107182] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/25/2022] Open
Abstract
Integration of signalling downstream of individual receptor tyrosine kinases (RTKs) is crucial to fine-tune cellular homeostasis during development and in pathological conditions, including breast cancer. However, how signalling integration is regulated and whether the endocytic fate of single receptors controls such signalling integration remains poorly elucidated. Combining quantitative phosphoproteomics and targeted assays, we generated a detailed picture of recycling-dependent fibroblast growth factor (FGF) signalling in breast cancer cells, with a focus on distinct FGF receptors (FGFRs). We discovered reciprocal priming between FGFRs and epidermal growth factor (EGF) receptor (EGFR) that is coordinated at recycling endosomes. FGFR recycling ligands induce EGFR phosphorylation on threonine 693. This phosphorylation event alters both FGFR and EGFR trafficking and primes FGFR-mediated proliferation but not cell invasion. In turn, FGFR signalling primes EGF-mediated outputs via EGFR threonine 693 phosphorylation. This reciprocal priming between distinct families of RTKs from recycling endosomes exemplifies a novel signalling integration hub where recycling endosomes orchestrate cellular behaviour. Therefore, targeting reciprocal priming over individual receptors may improve personalized therapies in breast and other cancers.
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Affiliation(s)
- Michael P Smith
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Harriet R Ferguson
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Jennifer Ferguson
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Egor Zindy
- Division of Cell Matrix and Regenerative MedicineSchool of Biological Science, FBMHThe University of ManchesterManchesterUK
- Present address:
Center for Microscopy and Molecular ImagingUniversité Libre de Bruxelles (ULB)GosseliesBelgium
| | - Katarzyna M Kowalczyk
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Thomas Kedward
- Division of Cancer SciencesSchool of Medical ScienceFBMHThe University of ManchesterManchesterUK
| | - Christian Bates
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Joseph Parsons
- Division of Cancer SciencesSchool of Medical ScienceFBMHThe University of ManchesterManchesterUK
| | - Joanne Watson
- Division of Evolution and Genomic SciencesSchool of Biological ScienceFBMHThe University of ManchesterManchesterUK
| | - Sarah Chandler
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Paul Fullwood
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
| | - Stacey Warwood
- Bio‐MS Core Research FacilityFBMHThe University of ManchesterManchesterUK
| | - David Knight
- Bio‐MS Core Research FacilityFBMHThe University of ManchesterManchesterUK
| | - Robert B Clarke
- Division of Cancer SciencesSchool of Medical ScienceFBMHThe University of ManchesterManchesterUK
- Manchester Breast CentreManchester Cancer Research CentreManchesterUK
| | - Chiara Francavilla
- Division of Molecular and Cellular FunctionSchool of Biological ScienceFaculty of Biology Medicine and Health (FBMH)The University of ManchesterManchesterUK
- Manchester Breast CentreManchester Cancer Research CentreManchesterUK
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39
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Kostopoulou N, Bellou S, Bagli E, Markou M, Kostaras E, Hyvönen M, Kalaidzidis Y, Papadopoulos A, Chalmantzi V, Kyrkou A, Panopoulou E, Fotsis T, Murphy C. Embryonic stem cells are devoid of macropinocytosis, a trafficking pathway for activin A in differentiated cells. J Cell Sci 2021; 134:jcs246892. [PMID: 34313314 DOI: 10.1242/jcs.246892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Ligand-receptor complexes formed at the plasma membrane are internalised via various endocytic pathways that influence the ultimate signalling output by regulating the selection of interaction partners by the complex along the trafficking route. We report that, in differentiated cells, activin A-receptor complexes are internalised via clathrin-mediated endocytosis (CME) and macropinocytosis (MP), whereas in human embryonic stem cells (hESCs) internalisation occurs via CME. We further show that hESCs are devoid of MP, which becomes functional upon differentiation towards endothelial cells through mesoderm mediators. Our results reveal, for the first time, that MP is an internalisation route for activin A in differentiated cells, and that MP is not active in hESCs and is induced as cells differentiate.
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Affiliation(s)
- Nikoleta Kostopoulou
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
| | - Sofia Bellou
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- Confocal Laser Scanning Microscopy Unit, Network of Research Supporting Laboratories, University of Ioannina, Ioannina, 45110, Greece
| | - Eleni Bagli
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
| | - Maria Markou
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Ioannina, 45110, Greece
| | - Eleftherios Kostaras
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Ioannina, 45110, Greece
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Yiannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Angelos Papadopoulos
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Varvara Chalmantzi
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Athena Kyrkou
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
| | - Ekaterini Panopoulou
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Ioannina, 45110, Greece
| | - Theodore Fotsis
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Ioannina, 45110, Greece
| | - Carol Murphy
- Foundation for Research & Technology-Hellas (FORTH), Institute of Molecular Biology and Biotechnology (IMBB), Department of Biomedical Research, Ioannina, 45110, Greece
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham, A118 Aston Webb, Edgbaston, Birmingham, B15 2TT, UK
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40
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Turegano-Lopez M, Santuy A, DeFelipe J, Merchan-Perez A. Size, Shape, and Distribution of Multivesicular Bodies in the Juvenile Rat Somatosensory Cortex: A 3D Electron Microscopy Study. Cereb Cortex 2021; 30:1887-1901. [PMID: 31665237 PMCID: PMC7132939 DOI: 10.1093/cercor/bhz211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/30/2019] [Accepted: 08/16/2019] [Indexed: 12/27/2022] Open
Abstract
Multivesicular bodies (MVBs) are membrane-bound organelles that belong to the endosomal pathway. They participate in the transport, sorting, storage, recycling, degradation, and release of multiple substances. They interchange cargo with other organelles and participate in their renovation and degradation. We have used focused ion beam milling and scanning electron microscopy (FIB-SEM) to obtain stacks of serial sections from the neuropil of the somatosensory cortex of the juvenile rat. Using dedicated software, we have 3D-reconstructed 1618 MVBs. The mean density of MVBs was 0.21 per cubic micron. They were unequally distributed between dendrites (39.14%), axons (18.16%), and nonsynaptic cell processes (42.70%). About one out of five MVBs (18.16%) were docked on mitochondria, representing the process by which the endosomal pathway participates in mitochondrial maintenance. Other features of MVBs, such as the presence of tubular protrusions (6.66%) or clathrin coats (19.74%) can also be interpreted in functional terms, since both are typical of early endosomes. The sizes of MVBs follow a lognormal distribution, with differences across cortical layers and cellular compartments. The mean volume of dendritic MVBs is more than twice as large as the volume of axonic MVBs. In layer I, they are smaller, on average, than in the other layers.
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Affiliation(s)
- M Turegano-Lopez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - A Santuy
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - J DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain.,Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Avda Doctor Arce, 37, 28002 Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) ISCIII, Madrid, Spain
| | - A Merchan-Perez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) ISCIII, Madrid, Spain.,Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain
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41
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Deep probabilistic tracking of particles in fluorescence microscopy images. Med Image Anal 2021; 72:102128. [PMID: 34229189 DOI: 10.1016/j.media.2021.102128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 01/16/2023]
Abstract
Tracking of particles in temporal fluorescence microscopy image sequences is of fundamental importance to quantify dynamic processes of intracellular structures as well as virus structures. We introduce a probabilistic deep learning approach for fluorescent particle tracking, which is based on a recurrent neural network that mimics classical Bayesian filtering. Compared to previous deep learning methods for particle tracking, our approach takes into account uncertainty, both aleatoric and epistemic uncertainty. Thus, information about the reliability of the computed trajectories is determined. Manual tuning of tracking parameters is not necessary and prior knowledge about the noise statistics is not required. Short and long-term temporal dependencies of individual object dynamics are exploited for state prediction, and assigned detections are used to update the predicted states. For correspondence finding, we introduce a neural network which computes assignment probabilities jointly across multiple detections as well as determines the probabilities of missing detections. Training requires only simulated data and therefore tedious manual annotation of ground truth is not needed. We performed a quantitative performance evaluation based on synthetic and real 2D as well as 3D fluorescence microscopy images. We used image data of the Particle Tracking Challenge as well as real time-lapse fluorescence microscopy images displaying virus structures and chromatin structures. It turned out that our approach yields state-of-the-art results or improves the tracking results compared to previous methods.
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42
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Chen C, Zhao Z, Qian N, Wei S, Hu F, Min W. Multiplexed live-cell profiling with Raman probes. Nat Commun 2021; 12:3405. [PMID: 34099708 PMCID: PMC8184955 DOI: 10.1038/s41467-021-23700-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Single-cell multiparameter measurement has been increasingly recognized as a key technology toward systematic understandings of complex molecular and cellular functions in biological systems. Despite extensive efforts in analytical techniques, it is still generally challenging for existing methods to decipher a large number of phenotypes in a single living cell. Herein we devise a multiplexed Raman probe panel with sharp and mutually resolvable Raman peaks to simultaneously quantify cell surface proteins, endocytosis activities, and metabolic dynamics of an individual live cell. When coupling it to whole-cell spontaneous Raman micro-spectroscopy, we demonstrate the utility of this technique in 14-plexed live-cell profiling and phenotyping under various drug perturbations. In particular, single-cell multiparameter measurement enables powerful clustering, correlation, and network analysis with biological insights. This profiling platform is compatible with live-cell cytometry, of low instrument complexity and capable of highly multiplexed measurement in a robust and straightforward manner, thereby contributing a valuable tool for both basic single-cell biology and translation applications such as high-content cell sorting and drug discovery.
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Affiliation(s)
- Chen Chen
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Shixuan Wei
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
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43
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Subhash N, Sundaramurthy V. Advances in host-based screening for compounds with intracellular anti-mycobacterial activity. Cell Microbiol 2021; 23:e13337. [PMID: 33813790 DOI: 10.1111/cmi.13337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
Intracellular pathogens interact with host systems in intimate ways to sustain a pathogenic lifestyle. Consequently, these interactions can potentially be targets of host-directed interventions against infectious diseases. In case of tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis (Mtb), while effective anti-tubercular compounds are available, the long treatment duration and emerging drug resistance necessitate identification of new class of molecules with anti-TB activity, as well as new treatment strategies. A significant part of the effort in finding new anti-TB drugs is focused on bacterial targets in bacterial systems. However, the host environment plays a major role in pathogenesis mechanisms and must be considered actively in these efforts. On the one hand, the bacterial origin targets must be relevant and accessible in the host, while on the other hand, new host origin targets required for the bacterial survival can be targeted. Such targets are good candidates for host-directed therapeutics, a strategy gaining traction as an adjunct in TB treatment. In this review, we will summarise the screening platforms used to identify compounds with anti-tubercular activities inside different host environments and outline recent technical advances in these platforms. Finally, while the examples given are specific to mycobacteria, the methods and principles outlined are broadly applicable to most intracellular infections.
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Affiliation(s)
- Neeraja Subhash
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.,SASTRA University, Thanjavur, India
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44
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Torrino S, Tiroille V, Dolfi B, Dufies M, Hinault C, Bonesso L, Dagnino S, Uhler J, Irondelle M, Gay AS, Fleuriot L, Debayle D, Lacas-Gervais S, Cormont M, Bertero T, Bost F, Gilleron J, Clavel S. UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling. eLife 2021; 10:68348. [PMID: 33884955 PMCID: PMC8118655 DOI: 10.7554/elife.68348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022] Open
Abstract
To adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that ubiquitin domain-containing protein 1 (UBTD1) plays a crucial role in both the epidermal growth factor receptor (EGFR) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through N-acylsphingosine amidohydrolase 1 (ASAH1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1, via the ubiquitination of Sequestosome 1 (SQSTM1/p62) by RNF26 and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing a hitherto unknown function of UBTD1 in EGFR-driven human cell proliferation.
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Affiliation(s)
- Stéphanie Torrino
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France.,Université Côte d'Azur, Inserm, C3M, Team Targeting prostate cancer cell metabolism, Nice, France
| | - Victor Tiroille
- Université Côte d'Azur, Inserm, C3M, Team Targeting prostate cancer cell metabolism, Nice, France
| | - Bastien Dolfi
- Université Côte d'Azur, Inserm, C3M, Team Metabolism and cancer, Nice, France
| | - Maeva Dufies
- Biomedical Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Charlotte Hinault
- Université Côte d'Azur, Inserm, C3M, Team Targeting prostate cancer cell metabolism, Nice, France.,Biochemistry Laboratory, University Hospital, Nice, France
| | | | - Sonia Dagnino
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial CollegeLondon, London, United Kingdom
| | - Jennifer Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | | | | | | | | | | | - Mireille Cormont
- Université Côte d'Azur, Inserm, C3M, Team Cellular and Molecular Pathophysiology of Obesity and Diabetes, Nice, France
| | | | - Frederic Bost
- Université Côte d'Azur, Inserm, C3M, Team Targeting prostate cancer cell metabolism, Nice, France
| | - Jerome Gilleron
- Université Côte d'Azur, Inserm, C3M, Team Cellular and Molecular Pathophysiology of Obesity and Diabetes, Nice, France
| | - Stephan Clavel
- Université Côte d'Azur, Inserm, C3M, Team Targeting prostate cancer cell metabolism, Nice, France
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45
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Wu H, Voeltz GK. Reticulon-3 Promotes Endosome Maturation at ER Membrane Contact Sites. Dev Cell 2021; 56:52-66.e7. [PMID: 33434526 DOI: 10.1016/j.devcel.2020.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 10/22/2022]
Abstract
ER tubules form and maintain membrane contact sites (MCSs) with endosomes. How and why these ER-endosome MCSs persist as endosomes traffic and mature is poorly understood. Here we find that a member of the reticulon protein family, Reticulon-3L (Rtn3L), enriches at ER-endosome MCSs as endosomes mature. We show that this localization is due to the long divergent N-terminal cytoplasmic domain of Rtn3L. We found that Rtn3L is recruited to ER-endosome MCSs by endosomal protein Rab9a, which marks a transition stage between early and late endosomes. Rab9a utilizes an FSV region to recruit Rtn3L via its six LC3-interacting region motifs. Consistent with our localization results, depletion or deletion of RTN3 from cells results in endosome maturation and cargo sorting defects, similar to RAB9A depletion. Together our data identify a tubular ER protein that promotes endosome maturation at ER MCSs.
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Affiliation(s)
- Haoxi Wu
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA.
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46
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Maddu S, Cheeseman BL, Müller CL, Sbalzarini IF. Learning physically consistent differential equation models from data using group sparsity. Phys Rev E 2021; 103:042310. [PMID: 34005966 DOI: 10.1103/physreve.103.042310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 11/07/2022]
Abstract
We propose a statistical learning framework based on group-sparse regression that can be used to (i) enforce conservation laws, (ii) ensure model equivalence, and (iii) guarantee symmetries when learning or inferring differential-equation models from data. Directly learning interpretable mathematical models from data has emerged as a valuable modeling approach. However, in areas such as biology, high noise levels, sensor-induced correlations, and strong intersystem variability can render data-driven models nonsensical or physically inconsistent without additional constraints on the model structure. Hence, it is important to leverage prior knowledge from physical principles to learn biologically plausible and physically consistent models rather than models that simply fit the data best. We present the group iterative hard thresholding algorithm and use stability selection to infer physically consistent models with minimal parameter tuning. We show several applications from systems biology that demonstrate the benefits of enforcing priors in data-driven modeling.
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Affiliation(s)
- Suryanarayana Maddu
- Technische Universität Dresden, Faculty of Computer Science, 01069 Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
| | - Bevan L Cheeseman
- Technische Universität Dresden, Faculty of Computer Science, 01069 Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Christian L Müller
- Center for Computational Mathematics, Flatiron Institute, New York, New York 10010, USA.,Department of Statistics, LMU München, 80539 Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ivo F Sbalzarini
- Technische Universität Dresden, Faculty of Computer Science, 01069 Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany.,Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany.,Cluster of Excellence Physics of Life, TU Dresden, 01307 Dresden, Germany
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47
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Functional annotation of lncRNA in high-throughput screening. Essays Biochem 2021; 65:761-773. [PMID: 33835127 PMCID: PMC8564734 DOI: 10.1042/ebc20200061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
Recent efforts on the characterization of long non-coding RNAs (lncRNAs) revealed their functional roles in modulating diverse cellular processes. These include pluripotency maintenance, lineage commitment, carcinogenesis, and pathogenesis of various diseases. By interacting with DNA, RNA and protein, lncRNAs mediate multifaceted mechanisms to regulate transcription, RNA processing, RNA interference and translation. Of more than 173000 discovered lncRNAs, the majority remain functionally unknown. The cell type-specific expression and localization of the lncRNA also suggest potential distinct functions of lncRNAs across different cell types. This highlights the niche of identifying functional lncRNAs in different biological processes and diseases through high-throughput (HTP) screening. This review summarizes the current work performed and perspectives on HTP screening of functional lncRNAs where different technologies, platforms, cellular responses and the downstream analyses are discussed. We hope to provide a better picture in applying different technologies to facilitate functional annotation of lncRNA efficiently.
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48
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Li H, Li L, Yu L, Yang X, Shi X, Wang J, Li J, Lin S. Transcriptome profiling reveals versatile dissolved organic nitrogen utilization, mixotrophy, and N conservation in the dinoflagellate Prorocentrum shikokuense under N deficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143013. [PMID: 33203560 DOI: 10.1016/j.scitotenv.2020.143013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Harmful algal blooms formed by certain dinoflagellate species often occur when environmental nitrogen nutrients (N) are limited. However, the molecular mechanism by which dinoflagellates adapt to low N environments is poorly understood. In this study, we characterized the transcriptomic responses of Prorocentrum shikokuense to N deficiency, along with its physiological impact. Under N deficiency, P. shikokuense cultures exhibited growth inhibition, a reduction in cell size, and decreases in cellular chlorophyll a and nitrogen contents but an increase in carbon content. Accordingly, gene expression profiles indicated that carbon fixation and catabolism and fatty acid metabolism were enhanced. Transporter genes of nitrate/nitrite, ammonium, urea, and amino acids were significantly upregulated, indicating that P. shikokuense cells invest to enhance the uptake of available dissolved N. Notably, upregulated genes included those involved in endocytosis and phagosomes, evidence that P. shikokuense is a mixotrophic organism that activates phagotrophy to overcome N deficiency. Additionally, vacuolar amino acid transporters, the urea cycle, and urea hydrolysis genes were upregulated, indicating N recycling within the cells under N deficiency. Our study indicates that P. shikokuense copes with N deficiency by economizing nitrogen use and adopting multiple strategies to maximize N acquisition and reuse while maintaining carbon fixation. The remarkable low N adaptability may confer competitive advantages to P. shikokuense for forming harmful blooms in DIN-limited environments.
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Affiliation(s)
- Hongfei Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton CT06405, USA
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaohong Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton CT06405, USA..
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Blandin AF, Cruz Da Silva E, Mercier MC, Glushonkov O, Didier P, Dedieu S, Schneider C, Devy J, Etienne-Selloum N, Dontenwill M, Choulier L, Lehmann M. Gefitinib induces EGFR and α5β1 integrin co-endocytosis in glioblastoma cells. Cell Mol Life Sci 2021; 78:2949-2962. [PMID: 33151388 PMCID: PMC11073190 DOI: 10.1007/s00018-020-03686-6] [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: 03/02/2020] [Revised: 09/08/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022]
Abstract
Overexpression of EGFR drives glioblastomas (GBM) cell invasion but these tumours remain resistant to EGFR-targeted therapies such as tyrosine kinase inhibitors (TKIs). Endocytosis, an important modulator of EGFR function, is often dysregulated in glioma cells and is associated with therapy resistance. However, the impact of TKIs on EGFR endocytosis has never been examined in GBM cells. In the present study, we showed that gefitinib and other tyrosine kinase inhibitors induced EGFR accumulation in early-endosomes as a result of an increased endocytosis. Moreover, TKIs trigger early-endosome re-localization of another membrane receptor, the fibronectin receptor alpha5beta1 integrin, a promising therapeutic target in GBM that regulates physiological EGFR endocytosis and recycling in cancer cells. Super-resolution dSTORM imaging showed a close-proximity between beta1 integrin and EGFR in intracellular membrane compartments of gefitinib-treated cells, suggesting their potential interaction. Interestingly, integrin depletion delayed gefitinib-mediated EGFR endocytosis. Co-endocytosis of EGFR and alpha5beta1 integrin may alter glioma cell response to gefitinib. Using an in vitro model of glioma cell dissemination from spheroid, we showed that alpha5 integrin-depleted cells were more sensitive to TKIs than alpha5-expressing cells. This work provides evidence for the first time that EGFR TKIs can trigger massive EGFR and alpha5beta1 integrin co-endocytosis, which may modulate glioma cell invasiveness under therapeutic treatment.
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Affiliation(s)
- Anne-Florence Blandin
- Department of Oncologic Pathology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Elisabete Cruz Da Silva
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Marie-Cécile Mercier
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Oleksandr Glushonkov
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Pascal Didier
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Stéphane Dedieu
- UMR CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), Reims, France
| | - Cristophe Schneider
- UMR CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), Reims, France
| | - Jessica Devy
- UMR CNRS 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), Reims, France
| | - Nelly Etienne-Selloum
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
- Département de Pharmacie, Centre de Lutte Contre le Cancer Paul Strauss, 67000, Strasbourg, France
| | - Monique Dontenwill
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Laurence Choulier
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France
| | - Maxime Lehmann
- UMR 7021, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, CNRS, Université de Strasbourg, 67401, Illkirch, France.
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50
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Wollmann T, Rohr K. Deep Consensus Network: Aggregating predictions to improve object detection in microscopy images. Med Image Anal 2021; 70:102019. [PMID: 33730623 DOI: 10.1016/j.media.2021.102019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
Detection of cells and particles in microscopy images is a common and challenging task. In recent years, detection approaches in computer vision achieved remarkable improvements by leveraging deep learning. Microscopy images pose challenges like small and clustered objects, low signal to noise, and complex shape and appearance, for which current approaches still struggle. We introduce Deep Consensus Network, a new deep neural network for object detection in microscopy images based on object centroids. Our network is trainable end-to-end and comprises a Feature Pyramid Network-based feature extractor, a Centroid Proposal Network, and a layer for ensembling detection hypotheses over all image scales and anchors. We suggest an anchor regularization scheme that favours prior anchors over regressed locations. We also propose a novel loss function based on Normalized Mutual Information to cope with strong class imbalance, which we derive within a Bayesian framework. In addition, we introduce an improved algorithm for Non-Maximum Suppression which significantly reduces the algorithmic complexity. Experiments on synthetic data are performed to provide insights into the properties of the proposed loss function and its robustness. We also applied our method to challenging data from the TUPAC16 mitosis detection challenge and the Particle Tracking Challenge, and achieved results competitive or better than state-of-the-art.
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Affiliation(s)
- Thomas Wollmann
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University Im Neuenheimer Feld 267, Heidelberg, Germany.
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University Im Neuenheimer Feld 267, Heidelberg, Germany.
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