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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics. Mol Cell Proteomics 2024:100800. [PMID: 38880244 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given mass-to-charge range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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2
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Pulli K, Saarimäki-Vire J, Ahonen P, Liu X, Ibrahim H, Chandra V, Santambrogio A, Wang Y, Vaaralahti K, Iivonen AP, Känsäkoski J, Tommiska J, Kemkem Y, Varjosalo M, Vuoristo S, Andoniadou CL, Otonkoski T, Raivio T. A splice site variant in MADD affects hormone expression in pancreatic β cells and pituitary gonadotropes. JCI Insight 2024; 9:e167598. [PMID: 38775154 PMCID: PMC11141940 DOI: 10.1172/jci.insight.167598] [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: 06/27/2023] [Accepted: 04/12/2024] [Indexed: 06/02/2024] Open
Abstract
MAPK activating death domain (MADD) is a multifunctional protein regulating small GTPases RAB3 and RAB27, MAPK signaling, and cell survival. Polymorphisms in the MADD locus are associated with glycemic traits, but patients with biallelic variants in MADD manifest a complex syndrome affecting nervous, endocrine, exocrine, and hematological systems. We identified a homozygous splice site variant in MADD in 2 siblings with developmental delay, diabetes, congenital hypogonadotropic hypogonadism, and growth hormone deficiency. This variant led to skipping of exon 30 and in-frame deletion of 36 amino acids. To elucidate how this mutation causes pleiotropic endocrine phenotypes, we generated relevant cellular models with deletion of MADD exon 30 (dex30). We observed reduced numbers of β cells, decreased insulin content, and increased proinsulin-to-insulin ratio in dex30 human embryonic stem cell-derived pancreatic islets. Concordantly, dex30 led to decreased insulin expression in human β cell line EndoC-βH1. Furthermore, dex30 resulted in decreased luteinizing hormone expression in mouse pituitary gonadotrope cell line LβT2 but did not affect ontogeny of stem cell-derived GnRH neurons. Protein-protein interactions of wild-type and dex30 MADD revealed changes affecting multiple signaling pathways, while the GDP/GTP exchange activity of dex30 MADD remained intact. Our results suggest MADD-specific processes regulate hormone expression in pancreatic β cells and pituitary gonadotropes.
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Affiliation(s)
- Kristiina Pulli
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Pekka Ahonen
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Xiaonan Liu
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Vikash Chandra
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Alice Santambrogio
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Yafei Wang
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Kirsi Vaaralahti
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Anna-Pauliina Iivonen
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
| | - Johanna Känsäkoski
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
- Department of Physiology, Faculty of Medicine
| | - Johanna Tommiska
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
- Department of Physiology, Faculty of Medicine
| | - Yasmine Kemkem
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sanna Vuoristo
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
- Department of Obstetrics and Gynecology; and
- HiLIFE, University of Helsinki, Helsinki, Finland
| | - Cynthia L. Andoniadou
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
- New Children’s Hospital, Helsinki University Hospital, Pediatric Research Center, Helsinki, Finland
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program (STEMM), Research Programs Unit, Faculty of Medicine, and
- Department of Physiology, Faculty of Medicine
- New Children’s Hospital, Helsinki University Hospital, Pediatric Research Center, Helsinki, Finland
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3
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Torres-Sangiao E, Happonen L, Heusel M, Palm F, Gueto-Tettay C, Malmström L, Shannon O, Malmström J. Quantification of Adaptive Immune Responses Against Protein-Binding Interfaces in the Streptococcal M1 Protein. Mol Cell Proteomics 2024; 23:100753. [PMID: 38527648 PMCID: PMC11059317 DOI: 10.1016/j.mcpro.2024.100753] [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: 04/03/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024] Open
Abstract
Bacterial or viral antigens can contain subdominant protein regions that elicit weak antibody responses upon vaccination or infection although there is accumulating evidence that antibody responses against subdominant regions can enhance the protective immune response. One proposed mechanism for subdominant protein regions is the binding of host proteins that prevent antibody production against epitopes hidden within the protein binding interfaces. Here, we used affinity purification combined with quantitative mass spectrometry (AP-MS) to examine the level of competition between antigen-specific antibodies and host-pathogen protein interaction networks using the M1 protein from Streptococcus pyogenes as a model system. As most humans have circulating antibodies against the M1 protein, we first used AP-MS to show that the M1 protein interspecies protein network formed with human plasma proteins is largely conserved in naïve mice. Immunizing mice with the M1 protein generated a time-dependent increase of anti-M1 antibodies. AP-MS analysis comparing the composition of the M1-plasma protein network from naïve and immunized mice showed significant enrichment of 292 IgG peptides associated with 56 IgG chains in the immune mice. Despite the significant increase of bound IgGs, the levels of interacting plasma proteins were not significantly reduced in the immune mice. The results indicate that the antigen-specific polyclonal IgG against the M1 protein primarily targets epitopes outside the other plasma protein binding interfaces. In conclusion, this study demonstrates that AP-MS is a promising strategy to determine the relationship between antigen-specific antibodies and host-pathogen interaction networks that could be used to define subdominant protein regions of relevance for vaccine development.
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Affiliation(s)
- Eva Torres-Sangiao
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Escherichia coli Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Clinical Microbiology Lab, University Hospital Complex of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Lotta Happonen
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Morizt Heusel
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Evosep ApS, Odense, Denmark
| | - Frida Palm
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Carlos Gueto-Tettay
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lars Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Onna Shannon
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Faculty of Odontology, Section for Oral Biology and Pathology, Malmö University, Malmö, Sweden
| | - Johan Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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4
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Hallal SM, Tűzesi Á, Sida LA, Xian E, Madani D, Muralidharan K, Shivalingam B, Buckland ME, Satgunaseelan L, Alexander KL. Glioblastoma biomarkers in urinary extracellular vesicles reveal the potential for a 'liquid gold' biopsy. Br J Cancer 2024; 130:836-851. [PMID: 38212481 PMCID: PMC10912426 DOI: 10.1038/s41416-023-02548-9] [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: 08/14/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Biomarkers that reflect glioblastoma tumour activity and treatment response are urgently needed to help guide clinical management, particularly for recurrent disease. As the urinary system is a major clearance route of circulating extracellular vesicles (EVs; 30-1000 nm nanoparticles) we explored whether sampling urinary-EVs could serve as a simple and non-invasive liquid biopsy approach for measuring glioblastoma-associated biomarkers. METHODS Fifty urine specimens (15-60 ml) were collected from 24 catheterised glioblastoma patients immediately prior to primary (n = 17) and recurrence (n = 7) surgeries, following gross total resection (n = 9), and from age/gender-matched healthy participants (n = 14). EVs isolated by differential ultracentrifugation were characterised and extracted proteomes were analysed by high-resolution data-independent acquisition liquid chromatography tandem mass spectrometry (DIA-LC-MS/MS). RESULTS Overall, 6857 proteins were confidently identified in urinary-EVs (q-value ≤ 0.01), including 94 EV marker proteins. Glioblastoma-specific proteomic signatures were determined, and putative urinary-EV biomarkers corresponding to tumour burden and recurrence were identified (FC ≥ | 2 | , adjust p-val≤0.05, AUC > 0.9). CONCLUSION In-depth DIA-LC-MS/MS characterisation of urinary-EVs substantiates urine as a viable source of glioblastoma biomarkers. The promising 'liquid gold' biomarker panels described here warrant further investigation.
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Affiliation(s)
- Susannah M Hallal
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Ágota Tűzesi
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Liam A Sida
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Elissa Xian
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Daniel Madani
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Krishna Muralidharan
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Brindha Shivalingam
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Neurosurgery Department, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Laveniya Satgunaseelan
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kimberley L Alexander
- Brain Cancer Research, Neurosurgery Department, Chris O'Brien Lifehouse, Camperdown, NSW, Australia.
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
- School of Medical Sciences, Faculty of Medicine and Health Sciences, The University of Sydney, Camperdown, NSW, Australia.
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5
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Zore G, Abdulghani M, Kodgire S, Kazi R, Shelar A, Patil R. Proteome dataset of Candida albicans (ATCC10231) opaque cell. BMC Res Notes 2024; 17:2. [PMID: 38167002 PMCID: PMC10759580 DOI: 10.1186/s13104-023-06661-z] [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: 08/04/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVES Candida albicans, a polymorphic yeast, is one of the most common, opportunistic fungal pathogens of humans. Among the different morphological forms, opaque form is one of the least-studied ones. This opaque phenotype is essential for mating and is also reported to be involved in colonizing the gastrointestinal tract. Considering the significance of the clinical and sexual reproduction of C. albicans, we have investigated the morphophysiological modulations in opaque form using a proteomic approach. DATA DESCRIPTION In the current investigation, we have used Micro-Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis to create a protein profile for opaque-specific proteins. Whole-cell proteins from C. albicans (ATCC10231) cells that had been cultured for seven days on synthetic complete dextrose (SCD) medium in both as an opaque (test) and as a white (control) form cells were extracted, digested, and identified using LC-MS/MS. This information is meant to serve the scientific community and represents the proteome profile (SWATH Spectral Libraries) of C. albicans opaque form.
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Affiliation(s)
- Gajanan Zore
- Dept. of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer, Bandersindri NH 8, Kishangarh Dist Ajmer (Rajasthan), India
| | - Mazen Abdulghani
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, 431606, MS, India.
| | - Santosh Kodgire
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, 431606, MS, India
| | - Rubina Kazi
- Division of Biochemical Sciences, CSIR-NCL, Pune-8, Pune, MS, India
| | - Amruta Shelar
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, MS, India
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, MS, India
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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8
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Hay BN, Akinlaja MO, Baker TC, Houfani AA, Stacey RG, Foster LJ. Integration of data-independent acquisition (DIA) with co-fractionation mass spectrometry (CF-MS) to enhance interactome mapping capabilities. Proteomics 2023; 23:e2200278. [PMID: 37144656 DOI: 10.1002/pmic.202200278] [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: 10/28/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Proteomics technologies are continually advancing, providing opportunities to develop stronger and more robust protein interaction networks (PINs). In part, this is due to the ever-growing number of high-throughput proteomics methods that are available. This review discusses how data-independent acquisition (DIA) and co-fractionation mass spectrometry (CF-MS) can be integrated to enhance interactome mapping abilities. Furthermore, integrating these two techniques can improve data quality and network generation through extended protein coverage, less missing data, and reduced noise. CF-DIA-MS shows promise in expanding our knowledge of interactomes, notably for non-model organisms (NMOs). CF-MS is a valuable technique on its own, but upon the integration of DIA, the potential to develop robust PINs increases, offering a unique approach for researchers to gain an in-depth understanding into the dynamics of numerous biological processes.
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Affiliation(s)
- Brenna N Hay
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mopelola O Akinlaja
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Teesha C Baker
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - R Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Sandbaumhüter F, Nezhyva M, Andrén PE, Jansson ET. Label-Free Quantitative Thermal Proteome Profiling Reveals Target Transcription Factors with Activities Modulated by MC3R Signaling. Anal Chem 2023; 95:15400-15408. [PMID: 37804223 PMCID: PMC10585664 DOI: 10.1021/acs.analchem.3c03643] [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: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Thermal proteome profiling with label-free quantitation using ion-mobility-enhanced LC-MS offers versatile data sets, providing information on protein differential expression, thermal stability, and the activities of transcription factors. We developed a multidimensional data analysis workflow for label-free quantitative thermal proteome profiling (TPP) experiments that incorporates the aspects of gene set enrichment analysis, differential protein expression analysis, and inference of transcription factor activities from LC-MS data. We applied it to study the signaling processes downstream of melanocortin 3 receptor (MC3R) activation by endogenous agonists derived from the proopiomelanocortin prohormone: ACTH, α-MSH, and γ-MSH. The obtained information was used to map signaling pathways downstream of MC3R and to deduce transcription factors responsible for cellular response to ligand treatment. Using our workflow, we identified differentially expressed proteins and investigated their thermal stability. We found in total 298 proteins with altered thermal stability, resulting from MC3R activation. Out of these, several proteins were transcription factors, indicating them as being downstream target regulators that take part in the MC3R signaling cascade. We found transcription factors CCAR2, DDX21, HMGB2, SRSF7, and TET2 to have altered thermal stability. These apparent target transcription factors within the MC3R signaling cascade play important roles in immune responses. Additionally, we inferred the activities of the transcription factors identified in our data set. This was done with Bayesian statistics using the differential expression data we obtained with label-free quantitative LC-MS. The inferred transcription factor activities were validated in our bioinformatic pipeline by the phosphorylated peptide abundances that we observed, highlighting the importance of post-translational modifications in transcription factor regulation. Our multidimensional data analysis workflow allows for a comprehensive characterization of the signaling processes downstream of MC3R activation. It provides insights into protein differential expression, thermal stability, and activities of key transcription factors. All proteomic data generated in this study are publicly available at DOI: 10.6019/PXD039945.
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Affiliation(s)
| | - Mariya Nezhyva
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
- Science
for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, 751 24 Uppsala, Sweden
| | - Erik T. Jansson
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 24 Uppsala, Sweden
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Pacheco RI, Cristo MI, Anjo SI, Silva AF, Sousa MI, Tavares RS, Sousa AP, Almeida Santos T, Moura-Ramos M, Caramelo F, Manadas B, Ramalho-Santos J, Amaral SG. New Insights on Sperm Function in Male Infertility of Unknown Origin: A Multimodal Approach. Biomolecules 2023; 13:1462. [PMID: 37892144 PMCID: PMC10605211 DOI: 10.3390/biom13101462] [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: 08/08/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The global trend of rising (male) infertility is concerning, and the unidentifiable causes in half of the cases, the so-called unknown origin male infertility (UOMI), demands a better understanding and assessment of both external/internal factors and mechanisms potentially involved. In this work, it was our aim to obtain new insight on UOMI, specifically on idiopathic (ID) and Unexplained male infertility (UMI), relying on a detailed evaluation of the male gamete, including functional, metabolic and proteomic aspects. For this purpose, 1114 semen samples, from males in couples seeking infertility treatment, were collected at the Reproductive Medicine Unit from the Centro Hospitalar e Universitário de Coimbra (CHUC), from July 2018-July 2022. Based on the couples' clinical data, seminal/hormonal analysis, and strict eligibility criteria, samples were categorized in 3 groups, control (CTRL), ID and UMI. Lifestyle factors and anxiety/depression symptoms were assessed via survey. Sperm samples were evaluated functionally, mitochondrially and using proteomics. The results of Assisted Reproduction Techniques were assessed whenever available. According to our results, ID patients presented the worst sperm functional profile, while UMI patients were similar to controls. The proteomic analysis revealed 145 differentially expressed proteins, 8 of which were specifically altered in ID and UMI samples. Acrosin (ACRO) and sperm acrosome membrane-associated protein 4 (SACA4) were downregulated in ID patients while laminin subunit beta-2 (LAMB2), mannose 6-phosphate isomerase (MPI), ATP-dependent 6-phosphofructokinase liver type (PFKAL), STAR domain-containing protein 10 (STA10), serotransferrin (TRFE) and exportin-2 (XPO2) were downregulated in UMI patients. Using random forest analysis, SACA4 and LAMB2 were identified as the sperm proteins with a higher chance of distinguishing ID and UMI patients, and their function and expression variation were in accordance with the functional results. No alterations were observed in terms of lifestyle and psychological factors among the 3 groups. These findings obtained in an experimental setting based on 3 well-defined groups of subjects, might help to validate new biomarkers for unknown origin male infertility (ID and UMI) that, in the future, can be used to improve diagnostics and treatments.
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Affiliation(s)
- Rita I. Pacheco
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Maria I. Cristo
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Sandra I. Anjo
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Andreia F. Silva
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Maria Inês Sousa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Renata S. Tavares
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ana Paula Sousa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
| | - Teresa Almeida Santos
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Mariana Moura-Ramos
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
- Center for Research in Neuropsychology and Cognitive and Behavioral Intervention, Faculty of Psychology and Educational Sciences, University of Coimbra, 3000-115 Coimbra, Portugal
- Clinical Psychology Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | | | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - João Ramalho-Santos
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Gomes Amaral
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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11
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Zore G, Abdulghani M, Kazi R, Shelar A, Patil R. Proteomic dataset of Candida albicans (ATCC 10231) Biofilm. BMC Res Notes 2023; 16:155. [PMID: 37491288 PMCID: PMC10369833 DOI: 10.1186/s13104-023-06436-6] [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: 09/09/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
OBJECTIVES The ability to form biofilm is considered as one of major virulence factors of Candida albicans, as biofilms form growth confers antifungal resistance and facilitate immune evasion. It is intriguing to understand morphophysiological modulations in the C. albicans cells growing under biofilm form growth. DATA DESCRIPTION In present study, we have profiled biofilm-specific proteins using LC-MS/MS analysis. Whole cell proteins of C. albicans cells grown under biofilm form growth (test) and planktonic (control) growth for 24 h were extracted, digested and identified using micro-Liquid Chromatography-Mass Spectrometry (LC-MS/MS). The present data represents proteomic profile (SWATH Spectral Libraries) of C. albicans biofilm intended to be useful to scientific community as it exhibits reuse potential.
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Affiliation(s)
- Gajanan Zore
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India
| | - Mazen Abdulghani
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS, 431606, India.
| | - Rubina Kazi
- Division of Biochemical Sciences, CSIR-NCL, Pune-8, Pune, MS, India
| | - Amruta Shelar
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, MS, 411007, India
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, MS, 411007, India
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12
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Wang RQ, Geng Y, Song JN, Yu HD, Bao K, Wang YR, Croué JP, Miyatake H, Ito Y, Liu YR, Chen YM. Biogenic Solution Map Based on the Definition of the Metabolic Correlation Distance between 4-Dimensional Fingerprints. Anal Chem 2023; 95:7503-7511. [PMID: 37130068 DOI: 10.1021/acs.analchem.2c05480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Accurate discrimination and classification of unknown species are the basis to predict its characteristics or applications to make correct decisions. However, for biogenic solutions that are ubiquitous in nature and our daily lives, direct determination of their similarities and disparities by their molecular compositions remains a scientific challenge. Here, we explore a standard and visualizable ontology, termed "biogenic solution map", that organizes multifarious classes of biogenic solutions into a map of hierarchical structures. To build the map, a novel 4-dimensional (4D) fingerprinting method based on data-independent acquisition data sets of untargeted metabolomics is developed, enabling accurate characterization of complex biogenic solutions. A generic parameter of metabolic correlation distance, calculated based on averaged similarities between 4D fingerprints of sample groups, is able to define "species", "genus", and "family" of each solution in the map. With the help of the "biogenic solution map", species of unknown biogenic solutions can be explicitly defined. Simultaneously, intrinsic correlations and subtle variations among biogenic solutions in the map are accurately illustrated. Moreover, it is worth mentioning that samples of the same analyte but prepared by alternative protocols may have significantly different metabolic compositions and could be classified into different "genera".
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Affiliation(s)
- Ren-Qi Wang
- School of Food and Biological Engineering, College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Ye Geng
- School of Food and Biological Engineering, College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Juan-Na Song
- School of Food and Biological Engineering, College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Huai-Dong Yu
- Gezhu Bio Co., Ltd, Beijing 100037, People's Republic of China
| | - Kai Bao
- SINTEF Digital, Oslo N-0314, Norway
| | - Yu-Ru Wang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Jean-Philippe Croué
- Institut de Chimie des Milieux et des Matériaux IC2MP UMR 7285 CNRS, Université de Poitiers, Poitiers 86000, France
| | - Hideyuki Miyatake
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 3510198, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 3510198, Japan
| | - Yan-Ru Liu
- Shaanxi Collaborative Innovation Center Medicinal Resource Industrialization, Shaanxi University of Chinese Medicine, Xianyang 712083, People's Republic of China
| | - Yong-Mei Chen
- School of Food and Biological Engineering, College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
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13
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Li B, Altelaar M, van Breukelen B. Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy. Int J Mol Sci 2023; 24:ijms24097884. [PMID: 37175590 PMCID: PMC10178578 DOI: 10.3390/ijms24097884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Many essential cellular functions are carried out by multi-protein complexes that can be characterized by their protein-protein interactions. The interactions between protein subunits are critically dependent on the strengths of their interactions and their cellular abundances, both of which span orders of magnitude. Despite many efforts devoted to the global discovery of protein complexes by integrating large-scale protein abundance and interaction features, there is still room for improvement. Here, we integrated >7000 quantitative proteomic samples with three published affinity purification/co-fractionation mass spectrometry datasets into a deep learning framework to predict protein-protein interactions (PPIs), followed by the identification of protein complexes using a two-stage clustering strategy. Our deep-learning-technique-based classifier significantly outperformed recently published machine learning prediction models and in the process captured 5010 complexes containing over 9000 unique proteins. The vast majority of proteins in our predicted complexes exhibited low or no tissue specificity, which is an indication that the observed complexes tend to be ubiquitously expressed throughout all cell types and tissues. Interestingly, our combined approach increased the model sensitivity for low abundant proteins, which amongst other things allowed us to detect the interaction of MCM10, which connects to the replicative helicase complex via the MCM6 protein. The integration of protein abundances and their interaction features using a deep learning approach provided a comprehensive map of protein-protein interactions and a unique perspective on possible novel protein complexes.
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Affiliation(s)
- Bohui Li
- Biomolecular Mass Spectrometry and Proteomics, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
- Mass Spectrometry and Proteomics Facility, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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14
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Pinto L, Macedo J, Araújo B, Anjo S, Silveira-Rosa T, Patrício P, Teixeira F, Manadas B, Rodrigues AJ, Lepore A, Salgado A, Gomes E. Glial-Restricted Precursors stimulate endogenous cytogenesis and effectively recover emotional deficits in a model of cytogenesis ablation. RESEARCH SQUARE 2023:rs.3.rs-2747462. [PMID: 37034743 PMCID: PMC10081440 DOI: 10.21203/rs.3.rs-2747462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Adult cytogenesis, the continuous generation of newly-born neurons (neurogenesis) and glial cells (gliogenesis) throughout life, is highly impaired in several neuropsychiatric disorders, such as Major Depressive Disorder (MDD), impacting negatively on cognitive and emotional domains. Despite playing a critical role in brain homeostasis, the importance of gliogenesis has been overlooked, both in healthy and diseased states. To examine the role of newly formed glia, we transplanted Glial Restricted Precursors (GRPs) into the adult hippocampal dentate gyrus (DG), or injected their secreted factors (secretome), into a previously validated transgenic GFAP-tk rat line, in which cytogenesis is transiently compromised. We explored the long-term effects of both treatments on physiological and behavioral outcomes. Grafted GRPs reversed anxiety-like and depressive-like deficits, while the secretome promoted recovery of only anxiety-like behavior. Furthermore, GRPs elicited a recovery of neurogenic and gliogenic levels in the ventral DG, highlighting the unique involvement of these cells in the regulation of brain cytogenesis. Both GRPs and their secretome induced significant alterations in the DG proteome, directly influencing proteins and pathways related to cytogenesis, regulation of neural plasticity and neuronal development. With this work, we demonstrate a valuable and specific contribution of glial progenitors to normalizing gliogenic levels, rescueing neurogenesis and, importantly, promoting recovery of emotional deficits characteristic of disorders such as MDD.
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Affiliation(s)
| | | | | | - Sandra Anjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra
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15
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Segal D, Maier S, Mastromarco GJ, Qian WW, Nabeel-Shah S, Lee H, Moore G, Lacoste J, Larsen B, Lin ZY, Selvabaskaran A, Liu K, Smibert C, Zhang Z, Greenblatt J, Peng J, Lee HO, Gingras AC, Taipale M. A central chaperone-like role for 14-3-3 proteins in human cells. Mol Cell 2023; 83:974-993.e15. [PMID: 36931259 DOI: 10.1016/j.molcel.2023.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
14-3-3 proteins are highly conserved regulatory proteins that interact with hundreds of structurally diverse clients and act as central hubs of signaling networks. However, how 14-3-3 paralogs differ in specificity and how they regulate client protein function are not known for most clients. Here, we map the interactomes of all human 14-3-3 paralogs and systematically characterize the effect of disrupting these interactions on client localization. The loss of 14-3-3 binding leads to the coalescence of a large fraction of clients into discrete foci in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Congruently, the engraftment of 14-3-3 binding motifs to nonclients can suppress their aggregation or phase separation. Finally, we show that 14-3-3s negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and inhibit its activity as a translational repressor. Our work suggests that 14-3-3s have a more prominent role as chaperone-like molecules than previously thought.
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Affiliation(s)
- Dmitri Segal
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | | | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hyunmin Lee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Gaelen Moore
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Abeeshan Selvabaskaran
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Karen Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Craig Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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16
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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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17
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Xiao W, Chen Y, Wang C. Quantitative Chemoproteomic Methods for Reactive Cysteinome Profiling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Weidi Xiao
- Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
| | - Ying Chen
- Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
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18
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NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency. Sci Data 2023; 10:24. [PMID: 36631473 PMCID: PMC9834231 DOI: 10.1038/s41597-022-01687-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 09/07/2022] [Indexed: 01/13/2023] Open
Abstract
The National Institute of Health (NIH) Library of integrated network-based cellular signatures (LINCS) program is premised on the generation of a publicly available data resource of cell-based biochemical responses or "signatures" to genetic or environmental perturbations. NeuroLINCS uses human inducible pluripotent stem cells (hiPSCs), derived from patients and healthy controls, and differentiated into motor neuron cell cultures. This multi-laboratory effort strives to establish i) robust multi-omic workflows for hiPSC and differentiated neuronal cultures, ii) public annotated data sets and iii) relevant and targetable biological pathways of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Here, we focus on the proteomics and the quality of the developed workflow of hiPSC lines from 6 individuals, though epigenomics and transcriptomics data are also publicly available. Known and commonly used markers representing 73 proteins were reproducibly quantified with consistent expression levels across all hiPSC lines. Data quality assessments, data levels and metadata of all 6 genetically diverse human iPSCs analysed by DIA-MS are parsable and available as a high-quality resource to the public.
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19
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Marote A, Santos D, Mendes-Pinheiro B, Serre-Miranda C, Anjo SI, Vieira J, Ferreira-Antunes F, Correia JS, Borges-Pereira C, Pinho AG, Campos J, Manadas B, Teixeira MR, Correia-Neves M, Pinto L, Costa PM, Roybon L, Salgado AJ. Cellular Aging Secretes: a Comparison of Bone-Marrow-Derived and Induced Mesenchymal Stem Cells and Their Secretome Over Long-Term Culture. Stem Cell Rev Rep 2023; 19:248-263. [PMID: 36152233 DOI: 10.1007/s12015-022-10453-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2022] [Indexed: 01/29/2023]
Abstract
Mesenchymal stem cells (MSCs) hold promising therapeutic potential in several clinical applications, mainly due to their paracrine activity. The implementation of future secretome-based therapeutic strategies requires the use of easily accessible MSCs sources that provide high numbers of cells with homogenous characteristics. MSCs obtained from induced pluripotent stem cells (iMSCs) have been put forward as an advantageous alternative to the gold-standard tissue sources, such as bone marrow (BM-MSCs). In this study, we aimed at comparing the secretome of BM-MSCs and iMSCs over long-term culture. For that, we performed a broad characterization of both sources regarding their identity, proteomic secretome analysis, as well as replicative senescence and associated phenotypes, including its effects on MSCs secretome composition and immunomodulatory action. Our results evidence a rejuvenated phenotype of iMSCs, which is translated into a superior proliferative capacity before the induction of replicative senescence. Despite this significant difference between iMSCs and BM-MSCs proliferation, both untargeted and targeted proteomic analysis revealed a similar secretome composition for both sources in pre-senescent and senescent states. These results suggest that shifting from the use of BM-MSCs to a more advantageous source, like iMSCs, may yield similar therapeutic effects as identified over the past years for this gold-standard MSC source.
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Affiliation(s)
- Ana Marote
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| | - Diogo Santos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bárbara Mendes-Pinheiro
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cláudia Serre-Miranda
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sandra I Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Multidisciplinary Institute of Ageing (MIA), University of Coimbra, Coimbra, Portugal
| | - Joana Vieira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal.,Cancer Genetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (HealthResearch Network), Portuguese Oncology Institute of Porto (IPO Porto) / PortoComprehensive Cancer Center, Porto, Portugal
| | - Filipa Ferreira-Antunes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana Sofia Correia
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Caroline Borges-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Andreia G Pinho
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jonas Campos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Manuel R Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal.,Cancer Genetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (HealthResearch Network), Portuguese Oncology Institute of Porto (IPO Porto) / PortoComprehensive Cancer Center, Porto, Portugal.,School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Behavioral and Molecular Lab (Bn'ML), University of Minho, Braga, Portugal
| | - Pedro M Costa
- Stemmatters, Biotecnologia e Medicina Regenerativa S.A., Guimarães, Portugal
| | - Laurent Roybon
- Stem Cell Laboratory for CNS Disease Modeling, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, Lund, Sweden.,Strategic Research Area MultiPark, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund University, Lund, Sweden
| | - António J Salgado
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
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20
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Liu P, Zhang H, Della Valle F, Orlando V. Dynamic Interactome of PRC2-EZH1 Complex Using Tandem-Affinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol 2023; 2655:101-116. [PMID: 37212992 DOI: 10.1007/978-1-0716-3143-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Polycomb repressive complex 2 (PRC2) is a well-characterized chromatin regulator of transcription programs acting through H3K27me3 deposition. In mammals, there are two main versions of PRC2 complexes: PRC2-EZH2, which is prevalent in cycling cells, and PRC2-EZH1 where EZH1 replaces EZH2 in post-mitotic tissues. Stoichiometry of PRC2 complex is dynamically modulated during cellular differentiation and various stress conditions. Therefore, unraveling unique architecture of PRC2 complexes under specific biological context through comprehensive and quantitative characterization could provide insight into the underlying mechanistic molecular mechanism in regulation of transcription process. In this chapter, we describe an efficient method which combines tandem-affinity purification (TAP) with label-free quantitative proteomics strategy for studying PRC2-EZH1 complex architecture alterations and identifying novel protein regulators in post-mitotic C2C12 skeletal muscle cells.
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Affiliation(s)
- Peng Liu
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia.
| | - Huoming Zhang
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Francesco Della Valle
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia
| | - Valerio Orlando
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, KAUST Environmental Epigenetics Research Program, Thuwal, Kingdom of Saudi Arabia.
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21
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Abdulghani M, Iram R, Chidrawar P, Bhosle K, Kazi R, Patil R, Kharat K, Zore G. Proteomic profile of Candida albicans biofilm. J Proteomics 2022; 265:104661. [PMID: 35728770 DOI: 10.1016/j.jprot.2022.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Candida albicans biofilms are characterized by structural and cellular heterogeneity that confers antifungal resistance and immune evasion. Despite this, biofilm formation remains poorly understood. In this study, we used proteomic analysis to understand biofilm formation in C. albicans related to morphophysiological and architectural features. LC-MS/MS analysis revealed that 64 proteins were significantly modulated, of which 31 were upregulated and 33 were downregulated. The results indicate that metabolism (25 proteins), gene expression (13 proteins), stress response (7 proteins), and cell wall (5 proteins) composition are modulated. The rate of oxidative phosphorylation (OxPhos) and biosynthesis of UDP-N-acetylglucosamine, vitamin B6, and thiamine increased, while the rate of methionine biosynthesis decreased. There was a significant modification of the cell wall architecture due to higher levels of Sun41, Pir1 and Csh1 and increased glycosylation of proteins. It was observed that C. albicans induces hyphal growth by upregulating the expression of genes involved in cAMP-PKA and MAPK pathways. This study is significant in that it suggests an increase in OxPhos and alteration of cell wall architecture that could be contributing to the recalcitrance of C. albicans cells growing in biofilms. Nevertheless, a deeper investigation is needed to explore it further. SIGNIFICANCE: Candida sps is included in the list of pathogens with potential drug resistance threat due to the increased frequency especially colonization of medical devices, and tissues among the patients, in recent years. Significance of our study is that we are reporting traits like modulation in cell wall composition, amino acid and vitamin biosynthesis and importantly energy generation (OxPhos) etc. These traits could be conferring antifungal resistance, host immune evasion etc. and thus survival, in addition to facilitating biofilm formation. These findings are expected to prime the further studies on devising potent strategy against biofilm growth among the patients.
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Affiliation(s)
- Mazen Abdulghani
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Rasiqua Iram
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Priti Chidrawar
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Kajal Bhosle
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Rubina Kazi
- Division of Biochemical Sciences, CSIR-NCL, Pune 8, MS, India
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MS, India
| | - Kiran Kharat
- Department of Biotechnology, Deogiri College, Aurangabad, MS, India
| | - Gajanan Zore
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India.
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22
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Peppercorn K, Kleffmann T, Jones O, Hughes S, Tate W. Secreted Amyloid Precursor Protein Alpha, a Neuroprotective Protein in the Brain Has Widespread Effects on the Transcriptome and Proteome of Human Inducible Pluripotent Stem Cell-Derived Glutamatergic Neurons Related to Memory Mechanisms. Front Neurosci 2022; 16:858524. [PMID: 35692428 PMCID: PMC9179159 DOI: 10.3389/fnins.2022.858524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Secreted amyloid precursor protein alpha (sAPPα) processed from a parent human brain protein, APP, can modulate learning and memory. It has potential for development as a therapy preventing, delaying, or even reversing Alzheimer’s disease. In this study a comprehensive analysis to understand how it affects the transcriptome and proteome of the human neuron was undertaken. Human inducible pluripotent stem cell (iPSC)-derived glutamatergic neurons in culture were exposed to 1 nM sAPPα over a time course and changes in the transcriptome and proteome were identified with RNA sequencing and Sequential Window Acquisition of All THeoretical Fragment Ion Spectra-Mass Spectrometry (SWATH-MS), respectively. A large subset (∼30%) of differentially expressed transcripts and proteins were functionally involved with the molecular biology of learning and memory, consistent with reported links of sAPPα to memory enhancement, as well as neurogenic, neurotrophic, and neuroprotective phenotypes in previous studies. Differentially regulated proteins included those encoded in previously identified Alzheimer’s risk genes, APP processing related proteins, proteins involved in synaptogenesis, neurotransmitters, receptors, synaptic vesicle proteins, cytoskeletal proteins, proteins involved in protein and organelle trafficking, and proteins important for cell signalling, transcriptional splicing, and functions of the proteasome and lysosome. We have identified a complex set of genes affected by sAPPα, which may aid further investigation into the mechanism of how this neuroprotective protein affects memory formation and how it might be used as an Alzheimer’s disease therapy.
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Affiliation(s)
- Katie Peppercorn
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Division of Health Sciences, Research Infrastructure Centre, University of Otago, Dunedin, New Zealand
| | - Owen Jones
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Stephanie Hughes
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
| | - Warren Tate
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Brain Health Research Centre, University of Otago, Dunedin, New Zealand
- *Correspondence: Warren Tate,
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23
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Kim C, Wang X, Kültz D. Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line. Life (Basel) 2022; 12:life12060787. [PMID: 35743818 PMCID: PMC9225295 DOI: 10.3390/life12060787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.
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Affiliation(s)
- Chanhee Kim
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - Dietmar Kültz
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-2991
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24
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Lombard-Banek C, Pohl KI, Kwee EJ, Elliott JT, Schiel JE. A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies. J Proteome Res 2022; 21:1229-1239. [PMID: 35404046 PMCID: PMC9087334 DOI: 10.1021/acs.jproteome.1c00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance qualifications (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multiattribute method (MAM) principles to characterize the proteome of cell therapies. Here, we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined a control strategy and highlighted some metrics to improve the reproducibility of SWATH acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells. Raw and processed data were deposited in PRIDE (PXD029780).
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Affiliation(s)
- Camille Lombard-Banek
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Bioengineering Research, Rockville, Maryland 20850, United States
| | | | - Edward J. Kwee
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
| | - John T. Elliott
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
| | - John E. Schiel
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Bioengineering Research, Rockville, Maryland 20850, United States
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25
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Torres-Sangiao E, Giddey AD, Leal Rodriguez C, Tang Z, Liu X, Soares NC. Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens. Front Med (Lausanne) 2022; 9:850374. [PMID: 35586072 PMCID: PMC9108449 DOI: 10.3389/fmed.2022.850374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
The profound effects of and distress caused by the global COVID-19 pandemic highlighted what has been known in the health sciences a long time ago: that bacteria, fungi, viruses, and parasites continue to present a major threat to human health. Infectious diseases remain the leading cause of death worldwide, with antibiotic resistance increasing exponentially due to a lack of new treatments. In addition to this, many pathogens share the common trait of having the ability to modulate, and escape from, the host immune response. The challenge in medical microbiology is to develop and apply new experimental approaches that allow for the identification of both the microbe and its drug susceptibility profile in a time-sensitive manner, as well as to elucidate their molecular mechanisms of survival and immunomodulation. Over the last three decades, proteomics has contributed to a better understanding of the underlying molecular mechanisms responsible for microbial drug resistance and pathogenicity. Proteomics has gained new momentum as a result of recent advances in mass spectrometry. Indeed, mass spectrometry-based biomedical research has been made possible thanks to technological advances in instrumentation capability and the continuous improvement of sample processing and workflows. For example, high-throughput applications such as SWATH or Trapped ion mobility enable the identification of thousands of proteins in a matter of minutes. This type of rapid, in-depth analysis, combined with other advanced, supportive applications such as data processing and artificial intelligence, presents a unique opportunity to translate knowledge-based findings into measurable impacts like new antimicrobial biomarkers and drug targets. In relation to the Research Topic “Proteomic Approaches to Unravel Mechanisms of Resistance and Immune Evasion of Bacterial Pathogens,” this review specifically seeks to highlight the synergies between the powerful fields of modern proteomics and microbiology, as well as bridging translational opportunities from biomedical research to clinical practice.
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Affiliation(s)
- Eva Torres-Sangiao
- Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, Santander, Spain
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), Santander, Spain
- *Correspondence: Eva Torres-Sangiao,
| | - Alexander Dyason Giddey
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cristina Leal Rodriguez
- Copenhagen Prospectives Studies on Asthma in Childhood, COPSAC, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Zhiheng Tang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Nelson C. Soares
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares,
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26
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14-3-3β is essential for milk composition stimulated by Leu/IGF-1 via IGF1R signaling pathway in BMECs. In Vitro Cell Dev Biol Anim 2022; 58:384-395. [PMID: 35648337 DOI: 10.1007/s11626-022-00682-x] [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: 11/29/2021] [Accepted: 03/29/2022] [Indexed: 11/05/2022]
Abstract
The cell proliferation of bovine mammary epithelial cells (BMECs) and consequent milk synthesis are regulated by multiple factors. The purpose of this study was to examine the effect of 14-3-3β on cellular proliferation and milk fat/β-casein synthesis in BMECs and reveal its underlying mechanisms. In this study, we employed gene function analysis to explore the regulatory effect and molecular mechanisms of 14-3-3β on milk synthesis and proliferation in BMECs. We found that leucine and IGF-1 enhance cell proliferation and milk synthesis in a 14-3-3β-dependent manner and only exhibiting such effect in the presence of 14-3-3β. We further determined that 14-3-3β interacts with the IGF1R self-phosphorylation site and it additionally mediated leucine and IGF-1 to stimulate the synthesis of milk through the IGF1R-AKT-mTORC1 signaling pathway. In summary, our data indicated that 14-3-3β mediates the expression of milk fat and protein stimulated by leucine and IGF-1, leading to lactogenesis through IGF1R signaling pathway in BMECs.
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27
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Anjos L, Pinto PIS, Santos S, Estêvão MD, Santa C, Manadas B, Canário AVM, Power DM. Proteome dataset of sea bass ( Dicentrarchus labrax) skin-scales exposed to fluoxetine and estradiol. Data Brief 2022; 41:107971. [PMID: 35252491 PMCID: PMC8889360 DOI: 10.1016/j.dib.2022.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Aquatic organisms such as fish are particularly at risk of exposure to pollutants. The surface of fish is the first point of contact with pollutants, but few studies have considered the impact of pollutants on the skin-scale barrier. The present proteome data are the basis of the findings discussed in the associated research article “Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol” [1]. Juvenile sea bass were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) the vehicle, coconut oil (control). The scale proteome of fish exposed to these compounds for 5 days was analysed using quantitative label-free proteomics technology SWATH-MS (sequential windowed data-independent acquisition of the total high-resolution-mass spectra). The proteome data generated was submitted to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020983. LC-MS data from pooled protein extracts from the scales of all experimental groups was acquired using information-dependent acquisition (IDA) and 1,254 proteins were identified by searching against the sea bass genome database. 715 proteins were quantified by SWATH acquisition, and 213 proteins had modified levels (p < 0.05) between the E2- or FLX-exposed fish compared to the control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.
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Affiliation(s)
- Liliana Anjos
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Patrícia I S Pinto
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Soraia Santos
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - M Dulce Estêvão
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Escola Superior de Saúde da Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Adelino V M Canário
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Shanghai Ocean University International Center for Marine Studies, Shanghai 201306, China
| | - Deborah M Power
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Shanghai Ocean University International Center for Marine Studies, Shanghai 201306, China
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28
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Spotted Fever Group Rickettsia Trigger Species-Specific Alterations in Macrophage Proteome Signatures with Different Impacts in Host Innate Inflammatory Responses. Microbiol Spectr 2021; 9:e0081421. [PMID: 34935429 PMCID: PMC8693926 DOI: 10.1128/spectrum.00814-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular details underlying differences in pathogenicity between Rickettsia species remain to be fully understood. Evidence points to macrophage permissiveness as a key mechanism in rickettsial virulence. Different studies have shown that several rickettsial species responsible for mild forms of rickettsioses can also escape macrophage-mediated killing mechanisms and establish a replicative niche within these cells. However, their manipulative capacity with respect to host cellular processes is far from being understood. A deeper understanding of the interplay between mildly pathogenic rickettsiae and macrophages and the commonalities and specificities of host responses to infection would illuminate differences in immune evasion mechanisms and pathogenicity. We used quantitative proteomics by sequential windowed data independent acquisition of the total high-resolution mass spectra with tandem mass spectrometry (SWATH-MS/MS) to profile alterations resulting from infection of THP-1 macrophages with three mildly pathogenic rickettsiae: Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in these cells. We show that all three species trigger different proteome signatures. Our results reveal a significant impact of infection on proteins categorized as type I interferon responses, which here included several components of the retinoic acid-inducible gene I (RIG-1)-like signaling pathway, mRNA splicing, and protein translation. Moreover, significant differences in protein content between infection conditions provide evidence for species-specific induced alterations. Indeed, we confirm distinct impacts on host inflammatory responses between species during infection, demonstrating that these species trigger different levels of beta interferon (IFN-β), differences in the bioavailability of the proinflammatory cytokine interleukin 1β (IL-1β), and differences in triggering of pyroptotic events. This work reveals novel aspects and exciting nuances of macrophage-Rickettsia interactions, adding additional layers of complexity between Rickettsia and host cells' constant arms race for survival. IMPORTANCE The incidence of diseases caused by Rickettsia has been increasing over the years. It has long been known that rickettsioses comprise diseases with a continuous spectrum of severity. There are highly pathogenic species causing diseases that are life threatening if untreated, others causing mild forms of the disease, and a third group for which no pathogenicity to humans has been described. These marked differences likely reflect distinct capacities for manipulation of host cell processes, with macrophage permissiveness emerging as a key virulence trait. However, what defines pathogenicity attributes among rickettsial species is far from being resolved. We demonstrate that the mildly pathogenic Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in macrophages, trigger different proteome signatures in these cells and differentially impact critical components of innate immune responses by inducing different levels of beta interferon (IFN-β) and interleukin 1β (IL-1β) and different timing of pyroptotic events during infection. Our work reveals novel nuances in rickettsia-macrophage interactions, offering new clues to understand Rickettsia pathogenicity.
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29
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Stachowicz A, Sundararaman N, Venkatraman V, Van Eyk J, Fert-Bober J. pH/Acetonitrile-Gradient Reversed-Phase Fractionation of Enriched Hyper-Citrullinated Library in Combination with LC-MS/MS Analysis for Confident Identification of Citrullinated Peptides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:107-126. [PMID: 34905169 DOI: 10.1007/978-1-0716-1936-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Citrullination, the Ca2+-driven enzymatic conversion of arginine residues to citrulline, is a posttranslational modification, implicated in several physiological and pathological processes. Several methods to detect citrullinated proteins have been developed, including color development reagent, fluorescence, phenylglyoxal, and antibody-based methods. These methods yet suffer from limitations in sensitivity, specificity, or citrullinated site determination. Mass spectrometry (MS)-based proteomic analysis has emerged as a promising method to resolve these problems. However, due to low abundance of citrullinated proteins and similar MS features to deamidation of asparagine and glutamine, confident identification of citrullinated proteome is challenging. Here, we present a systematic approach to identify a compendium of steps to enhance the number of detected citrullinated residue and implement diagnostic MS feature that allow the confidence of MS-based identifications. Our method is based on the concept of generation of hyper-citrullinated library with high-pH reversed-phase peptide fractionation that allows to enrich in low abundance citrullinated peptides and amplify the effect of charge loss upon citrullination. Application of our approach to complex global citrullino-proteome datasets demonstrates the confident assessment of citrullinated peptides, thereby enhancing the size and functional interpretation of citrullinated proteomes.
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Affiliation(s)
- Aneta Stachowicz
- Cedars-Sinai Medical Center, Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA
- Chair of Pharmacology, Jagiellonian University Medical College, Institute of Pharmacology, Krakow, Poland
| | - Niveda Sundararaman
- Cedars-Sinai Medical Center, Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Los Angeles, CA, USA
| | - Vidya Venkatraman
- Cedars-Sinai Medical Center, Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Los Angeles, CA, USA
| | - Jennifer Van Eyk
- Cedars-Sinai Medical Center, Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA
- Cedars-Sinai Medical Center, Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Los Angeles, CA, USA
| | - Justyna Fert-Bober
- Cedars-Sinai Medical Center, Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA.
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30
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Yan Y, Wang J, Dong X, Cai Y, Wang Y, Ren L, Zhang C, Tao M, Luo K, Zeng Y, Liu S. Quantitative proteomic analysis of hepatic tissue in allotetraploid hybridized from red crucian carp and common carp identified crucial proteins and pathways associated with metabolism and growth rate. Proteomics 2021; 22:e2100115. [PMID: 34713569 DOI: 10.1002/pmic.202100115] [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: 04/26/2021] [Revised: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023]
Abstract
Allotetraploid is a new species produced by distant hybridization between red crucian carp (Carassius auratus red var., abbreviated as RCC) and common carp (Cyprinus carpio L., abbreviated as CC). There is a significant difference in growth rate between allotetraploid and its parents. However, the underlying molecular mechanism is largely unknown. In this study, to find direct evidence associated with metabolism and growth rate in protein level, we performed quantitative proteomics analysis on liver tissues between allotetraploid and its parents. A total of 2502 unique proteins were identified and quantified by SWATH-MS in our proteomics profiling. Subsequently, comprehensive bioinformatics analyses including gene ontology enrichment analysis, pathway and network analysis, and protein-protein interaction analysis (PPI) were conducted based on differentially expressed proteins (DEPs) between allotetraploid and its parents. The results revealed several significant DEPs involved in metabolism pathways in liver. More specifically, the integrative analysis highlighted that the DEPs ACSBG1, OAT, and LDHBA play vital roles in metabolism pathways including "pentose phosphate pathway," "TCA cycle," and "glycolysis and gluconeogenesis." These could directly affect the growth rate in fresh water fishes by regulating the metabolism, utilization, and exchange of substance and energy. Since the liver is the central place for metabolism activity in animals, we firstly established the comprehensive and quantitative proteomics knowledge base for liver tissue from freshwater fishes, our study may serve as an irreplaceable reference for further studies regarding fishes' culture and growth.
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Affiliation(s)
- Yujie Yan
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Junting Wang
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xiaoping Dong
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yisheng Cai
- National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yude Wang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Li Ren
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Chun Zhang
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Min Tao
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Kaikun Luo
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Yong Zeng
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China.,National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- The State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, Hunan, China
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31
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Wang RQ, Ding J, Geng Y, Li YZ, Mei YW, Bao K, Yu HD, Feng YQ. CRB-SWATH: A Method for Enhancing Untargeted Precursor Ion Extraction and Automatically Constructing Their Tandem Mass Spectra from SWATH Datasets by Chromatographic Retention Behaviors. Anal Chem 2021; 93:12273-12280. [PMID: 34459594 DOI: 10.1021/acs.analchem.1c01841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequential window acquisition of all theoretical spectra (SWATH) as a typical data-independent acquisition (DIA) strategy is favorable for untargeted metabolomics. It could theoretically acquire product ions of all precursor ions, including precursor ions showing chromatographic peaks of rather poor qualities. However, existing data processing methods present limited capabilities in capturing poor-quality peaks of precursor ions. Thus, although their product ions could be acquired, their precursor ions are absent. Here, we present a new strategy, chromatographic retention behavior-SWATH (CRB-SWATH), that could unbiasedly capture poor-quality peaks and provide high resolutions of multiplexed mass spectroscopy (MS/MS) spectra in SWATH datasets. CRB-SWATH monitors CRBs of SWATH-MS signals under a series of altered elution gradients. As signals of compounds differ from noise by showing CRBs, both the precursor and fragment ions are captured, while ignoring their peak qualities. Moreover, CRB-SWATH offers good chances to resolve highly multiplexed MS/MS spectra in SWATH datasets because precursor ions coeluted in a single elution gradient often present different CRBs. In the untargeted metabolic analysis of Hela cell extracts, CRB-SWATH showed the advantage in exclusively capturing 2645 ions of poor-quality peaks (i.e., tiny peaks, discontinuous ion traces, tailing peaks, zigzag peaks, etc.), accounting for 34.4% of all the untargeted precursor ions extracted. Therein, it is noteworthy that among 2116 negative ions detected in hydrophilic interaction liquid chromatography (HILIC) mode, 1284 poor-quality ion peaks (>60%) were exclusively captured by CRB-SWATH. As CRB-SWATH automatically captures a large sum of true ion peaks of poor qualities, extracts MS/MS spectra of high purities, and provides chromatographic retention behaviors of untargeted metabolites for identification and classification, it could be a useful metabolomics tool for understanding biological phenomena better.
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Affiliation(s)
- Ren-Qi Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, People's Republic of China
| | - Jun Ding
- Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Ye Geng
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, People's Republic of China
| | - Yuan-Zheng Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, People's Republic of China
| | - Ying-Wu Mei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Kai Bao
- SINTEF Digital, 124 Blindern, Oslo 0314, Norway
| | - Huai-Dong Yu
- Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Shanghai 200335, People's Republic of China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, People's Republic of China
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32
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Kammers K, Taub MA, Mathias RA, Yanek LR, Kanchan K, Venkatraman V, Sundararaman N, Martin J, Liu S, Hoyle D, Raedschelders K, Holewinski R, Parker S, Dardov V, Faraday N, Becker DM, Cheng L, Wang ZZ, Leek JT, Van Eyk JE, Becker LC. Gene and protein expression in human megakaryocytes derived from induced pluripotent stem cells. J Thromb Haemost 2021; 19:1783-1799. [PMID: 33829634 DOI: 10.1111/jth.15334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/25/2021] [Accepted: 02/19/2021] [Indexed: 01/26/2023]
Abstract
BACKGROUND There is interest in deriving megakaryocytes (MKs) from pluripotent stem cells (iPSC) for biological studies. We previously found that genomic structural integrity and genotype concordance is maintained in iPSC-derived MKs. OBJECTIVE To establish a comprehensive dataset of genes and proteins expressed in iPSC-derived MKs. METHODS iPSCs were reprogrammed from peripheral blood mononuclear cells (MNCs) and MKs were derived from the iPSCs in 194 healthy European American and African American subjects. mRNA was isolated and gene expression measured by RNA sequencing. Protein expression was measured in 62 of the subjects using mass spectrometry. RESULTS AND CONCLUSIONS MKs expressed genes and proteins known to be important in MK and platelet function and demonstrated good agreement with previous studies in human MKs derived from CD34+ progenitor cells. The percent of cells expressing the MK markers CD41 and CD42a was consistent in biological replicates, but variable across subjects, suggesting that unidentified subject-specific factors determine differentiation of MKs from iPSCs. Gene and protein sets important in platelet function were associated with increasing expression of CD41/42a, while those related to more basic cellular functions were associated with lower CD41/42a expression. There was differential gene expression by the sex and race (but not age) of the subject. Numerous genes and proteins were highly expressed in MKs but not known to play a role in MK or platelet function; these represent excellent candidates for future study of hematopoiesis, platelet formation, and/or platelet function.
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Affiliation(s)
- Kai Kammers
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rasika A Mathias
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lisa R Yanek
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kanika Kanchan
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Niveda Sundararaman
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Joshua Martin
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Senquan Liu
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dixie Hoyle
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Koen Raedschelders
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ronald Holewinski
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Sarah Parker
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Victoria Dardov
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nauder Faraday
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Diane M Becker
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Linzhao Cheng
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zack Z Wang
- Division of Hematology and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Barbra Streisand Woman's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lewis C Becker
- The GeneSTAR Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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33
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Tian X, de Vries MP, Permentier HP, Bischoff R. The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode. Anal Chem 2021; 93:8196-8202. [PMID: 34053216 PMCID: PMC8209779 DOI: 10.1021/acs.analchem.1c00453] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Data-independent
acquisition (DIA) is an increasingly used approach
for quantitative proteomics. However, most current isotope labeling
strategies are not suitable for DIA as they lead to more complex MS2
spectra or severe ratio distortion. As a result, DIA suffers from
a lower throughput than data-dependent acquisition (DDA) due to a
lower level of multiplexing. Herein, we synthesized an isotopically
labeled acetyl-isoleucine-proline (Ac-IP) tag for multiplexed quantification
in DIA. Differentially labeled peptides have distinct precursor ions
carrying the quantitative information but identical MS2 spectra since
the isotopically labeled Ac-Ile part leaves as a neutral loss upon
collision-induced dissociation, while fragmentation of the peptide
backbone generates regular fragment ions for identification. The Ac-IP-labeled
samples can be analyzed using general DIA liquid chromatography–mass
spectrometry settings, and the data obtained can be processed with
established approaches. Relative quantification requires deconvolution
of the isotope envelope of the respective precursor ions. Suitability
of the Ac-IP tag is demonstrated with a triplex-labeled yeast proteome
spiked with bovine serum albumin that was mixed at 10:5:1 ratios,
resulting in measured ratios of 9.7:5.3:1.1.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, 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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Uchida Y, Higuchi T, Shirota M, Kagami S, Saigusa D, Koshiba S, Yasuda J, Tamiya G, Kuriyama S, Kinoshita K, Yaegashi N, Yamamoto M, Terasaki T, Sugawara J. Identification and Validation of Combination Plasma Biomarker of Afamin, Fibronectin and Sex Hormone-Binding Globulin to Predict Pre-eclampsia. Biol Pharm Bull 2021; 44:804-815. [PMID: 34078812 DOI: 10.1248/bpb.b20-01043] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of the present study was to identify a plasma protein biomarker able to predict pre-eclampsia (PE). Comprehensive quantitative proteomics using mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH-MS) was applied to plasma samples of 7 PE and 14 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE), and 11 proteins were selected as candidates potentially able to differentiate the two groups. Plasmas collected at gestational weeks 14-24 from 36 PE and 120 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE) were used to conduct selected reaction monitoring quantification analysis, optimize protein combinations and conduct internal validation, which consisted of 30 iterations of 10-fold cross-validation using multivariate logistic regression and receiver operating characteristic (ROC) analysis. The combination of afamin, fibronectin, and sex-hormone-binding globulin was selected as the best candidate. The 3-protein combination predictive model (predictive equation and cut-off value) generated using the internal validation subjects was successfully validated in another group of validation subjects (36 PE and 54 healthy (for PE subjects, plasma samples were taken before onset of PE)) and showed good predictive performance, with the area under the curve (AUC) 0.835 and odds ratio 13.43. In conclusion, we newly identified a 3-protein combination biomarker and established a predictive equation and cut-off value that can predict the onset of PE based on analysis of plasma samples collected during gestational weeks 14-24.
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Affiliation(s)
- Yasuo Uchida
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | | | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Satoshi Kagami
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Jun Yasuda
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute
| | - Gen Tamiya
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Tetsuya Terasaki
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
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35
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Geary B, Peat E, Dransfield S, Cook N, Thistlethwaite F, Graham D, Carter L, Hughes A, Krebs MG, Whetton AD. Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials. Cancers (Basel) 2021; 13:cancers13102443. [PMID: 34069985 PMCID: PMC8157875 DOI: 10.3390/cancers13102443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 12/22/2022] Open
Abstract
TARGET (tumour characterisation to guide experimental targeted therapy) is a cancer precision medicine programme focused on molecular characterisation of patients entering early phase clinical trials. Performance status (PS) measures a patient's ability to perform a variety of activities. However, the quality of present algorithms to assess PS is limited and based on qualitative clinician assessment. Plasma samples from patients enrolled into TARGET were analysed using the mass spectrometry (MS) technique: sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS. SWATH-MS was used on a discovery cohort of 55 patients to differentiate patients into either a good or poor prognosis by creation of a Wellness Score (WS) that showed stronger prediction of overall survival (p = 0.000551) compared to PS (p = 0.001). WS was then tested against a validation cohort of 77 patients showing significant (p = 0.000451) prediction of overall survival. WS in both sets had receiver operating characteristic curve area under the curve (AUC) values of 0.76 (p = 0.002) and 0.67 (p = 0.011): AUC of PS was 0.70 (p = 0.117) and 0.55 (p = 0.548). These signatures can now be evaluated further in larger patient populations to assess their utility in a clinical setting.
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Affiliation(s)
- Bethany Geary
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NQ, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
| | - Erin Peat
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Sarah Dransfield
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Natalie Cook
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Fiona Thistlethwaite
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Donna Graham
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Louise Carter
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
| | - Andrew Hughes
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
| | - Matthew G. Krebs
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M20 4BX, UK; (E.P.); (S.D.); (N.C.); (D.G.)
- Correspondence: (M.G.K.); (A.D.W.); Tel.: +44-(0)161-275-6267 (A.D.W.)
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NQ, UK;
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (F.T.); (L.C.); (A.H.)
- Manchester National Institute for Health Research Biomedical Research Centre, Manchester M13 9WL, UK
- Correspondence: (M.G.K.); (A.D.W.); Tel.: +44-(0)161-275-6267 (A.D.W.)
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36
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De Marchi T, Pyl PT, Sjöström M, Klasson S, Sartor H, Tran L, Pekar G, Malmström J, Malmström L, Niméus E. Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance. J Proteome Res 2021; 20:2983-3001. [PMID: 33855848 PMCID: PMC8155562 DOI: 10.1021/acs.jproteome.1c00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 12/21/2022]
Abstract
Proteogenomic approaches have enabled the generat̲ion of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here, we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Furthermore, we confirm previously detected enrichments of molecular pathways associated with estrogen receptor-dependent activity and provide novel evidence of epithelial-to-mesenchymal activity in mammography-detected spiculated tumors. Several transcript-protein pairs displayed radically different abundances depending on the overall clinical properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant tumor subgroups, which in turn alter both cancer biology and the abundance of biomarker candidates and drug targets.
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Affiliation(s)
- Tommaso De Marchi
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Paul Theodor Pyl
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Martin Sjöström
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Stina Klasson
- Department
Plastic and Reconstructive Surgery, Skåne
University Hospital, Inga Marie Nilssons gata 47, Malmö SE-20502, Sweden
| | - Hanna Sartor
- Division
of Diagnostic Radiology, Department of Translational Medicine, Skåne University Hospital, Entrégatan 7, Lund SE-22185, Sweden
| | - Lena Tran
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
| | - Gyula Pekar
- Division
of Oncology and Pathology, Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund SE-22185, Sweden
| | - Johan Malmström
- Division
of Infection Medicine, Department of Clinical Sciences Lund, Faculty
of Medicine, Lund University, Klinikgatan 32, Lund SE-22184, Sweden
| | - Lars Malmström
- S3IT, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
- Institute
for Computational Science, University of
Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Emma Niméus
- Division
of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, Lund SE-223 62, Sweden
- Department
of Surgery, Skåne University Hospital, Lund 222 42, Sweden
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37
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Bakochi A, Mohanty T, Pyl PT, Gueto-Tettay CA, Malmström L, Linder A, Malmström J. Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis. eLife 2021; 10:64159. [PMID: 33821792 PMCID: PMC8043743 DOI: 10.7554/elife.64159] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/04/2021] [Indexed: 12/21/2022] Open
Abstract
Meningitis is a potentially life-threatening infection characterized by the inflammation of the leptomeningeal membranes. Many different viral and bacterial pathogens can cause meningitis, with differences in mortality rates, risk of developing neurological sequelae, and treatment options. Here, we constructed a compendium of digital cerebrospinal fluid (CSF) proteome maps to define pathogen-specific host response patterns in meningitis. The results revealed a drastic and pathogen-type specific influx of tissue-, cell-, and plasma proteins in the CSF, where, in particular, a large increase of neutrophil-derived proteins in the CSF correlated with acute bacterial meningitis. Additionally, both acute bacterial and viral meningitis result in marked reduction of brain-enriched proteins. Generation of a multiprotein LASSO regression model resulted in an 18-protein panel of cell- and tissue-associated proteins capable of classifying acute bacterial meningitis and viral meningitis. The same protein panel also enabled classification of tick-borne encephalitis, a subgroup of viral meningitis, with high sensitivity and specificity. The work provides insights into pathogen-specific host response patterns in CSF from different disease etiologies to support future classification of pathogen type based on host response patterns in meningitis.
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Affiliation(s)
- Anahita Bakochi
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Tirthankar Mohanty
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Paul Theodor Pyl
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Biomedical Center, Lund University, Lund, Sweden
| | | | - Lars Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Adam Linder
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
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Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. Nat Commun 2021; 12:1597. [PMID: 33712617 PMCID: PMC7954794 DOI: 10.1038/s41467-021-21873-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) between modular binding domains and their target peptide motifs are thought to largely depend on the intrinsic binding specificities of the domains. The large family of SRC Homology 3 (SH3) domains contribute to cellular processes via their ability to support such PPIs. While the intrinsic binding specificities of SH3 domains have been studied in vitro, whether each domain is necessary and sufficient to define PPI specificity in vivo is largely unknown. Here, by combining deletion, mutation, swapping and shuffling of SH3 domains and measurements of their impact on protein interactions in yeast, we find that most SH3s do not dictate PPI specificity independently from their host protein in vivo. We show that the identity of the host protein and the position of the SH3 domains within their host are critical for PPI specificity, for cellular functions and for key biophysical processes such as phase separation. Our work demonstrates the importance of the interplay between a modular PPI domain such as SH3 and its host protein in establishing specificity to wire PPI networks. These findings will aid understanding how protein networks are rewired during evolution and in the context of mutation-driven diseases such as cancer. The SRC Homology 3 (SH3) domains mediate protein–protein interactions (PPIs). Here, the authors assess the SH3-mediated PPIs in yeast, and show that the identity of the protein itself and the position of the SH3 both affect the interaction specificity and thus the PPI-dependent cellular functions.
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Novais EJ, Choi H, Madhu V, Suyama K, Anjo SI, Manadas B, Shapiro IM, Salgado AJ, Risbud MV. Hypoxia and Hypoxia-Inducible Factor-1α Regulate Endoplasmic Reticulum Stress in Nucleus Pulposus Cells: Implications of Endoplasmic Reticulum Stress for Extracellular Matrix Secretion. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:487-502. [PMID: 33307037 PMCID: PMC7927276 DOI: 10.1016/j.ajpath.2020.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022]
Abstract
Endoplasmic reticulum (ER) stress is shown to promote nucleus pulposus (NP) cell apoptosis and intervertebral disc degeneration. However, little is known about ER stress regulation by the hypoxic disc microenvironment and its contribution to extracellular matrix homeostasis. NP cells were cultured under hypoxia (1% partial pressure of oxygen) to assess ER stress status, and gain-of-function and loss-of-function approaches were used to assess the role of hypoxia-inducible factor (HIF)-1α in this pathway. In addition, the contribution of ER stress induction on the NP cell secretome was assessed by a nontargeted quantitative proteomic analysis by sequential windowed data independent acquisition of the total high-resolution mass spectra-mass spectrometry. NP cells exhibited a lower ER stress burden under hypoxia. Knockdown of HIF-1α increased C/EBP homologous protein, protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor 6 (ATF6) levels, whereas HIF-1α stabilization decreased the expression of ER stress markers Ddit3, Hsp5a, Atf6, and Eif2a. Interestingly, ER stress inducers tunicamycin and thapsigargin induced HIF-1α activity under hypoxia while promoting the unfolded protein response. NP cell secretome analysis demonstrated an impact of ER stress induction on extracellular matrix secretion, with decreases in collagens and cell adhesion-related proteins. Moreover, analysis of transcriptomic data of NP tissues from aged mice and degenerated human discs showed higher levels of unfolded protein response markers and decreased levels of matrix components. Our study shows, for the first time, that hypoxia and HIF-1α attenuate ER stress responses in NP cells, and ER stress promotes inefficient extracellular matrix secretion under hypoxia.
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Affiliation(s)
- Emanuel J Novais
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania; Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal; Life and Health Sciences Research Institute/Biomaterials, Biodegradables and Biomimetics (ICVS/3B's) - PT Government Associate Laboratory, Braga, Portugal
| | - Hyowon Choi
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vedavathi Madhu
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kaori Suyama
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Department of Anatomy and Cellular Biology, Tokai University School of Medicine, Isehara, Japan
| | - Sandra I Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Irving M Shapiro
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - António J Salgado
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal; Life and Health Sciences Research Institute/Biomaterials, Biodegradables and Biomimetics (ICVS/3B's) - PT Government Associate Laboratory, Braga, Portugal
| | - Makarand V Risbud
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania.
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Mao Y, Chen P, Ke M, Chen X, Ji S, Chen W, Tian R. Fully Integrated and Multiplexed Sample Preparation Technology for Sensitive Interactome Profiling. Anal Chem 2021; 93:3026-3034. [DOI: 10.1021/acs.analchem.0c05076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Peizhong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, SAR 999077, China
| | - Mi Ke
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shanping Ji
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
- SUSTech Academy for Advanced Interdisciplinary Studies, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
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Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics. Nat Commun 2021; 12:71. [PMID: 33397984 PMCID: PMC7782698 DOI: 10.1038/s41467-020-20367-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/27/2020] [Indexed: 02/02/2023] Open
Abstract
Signaling complexes are often organized in a spatiotemporal manner and on a minute timescale. Proximity labeling based on engineered ascorbate peroxidase APEX2 pioneered in situ capture of spatiotemporal membrane protein complexes in living cells, but its application to cytosolic proteins remains limited due to the high labeling background. Here, we develop proximity labeling probes with increased labeling selectivity. These probes, in combination with label-free quantitative proteomics, allow exploring cytosolic protein assemblies such as phosphotyrosine-mediated protein complexes formed in response to minute-scale EGF stimulation. As proof-of-concept, we systematically profile the spatiotemporal interactome of the EGFR signaling component STS1. For STS1 core complexes, our proximity proteomics approach shows comparable performance to affinity purification-mass spectrometry-based temporal interactome profiling, while also capturing additional—especially endosomally-located—protein complexes. In summary, we provide a generic approach for exploring the interactome of mobile cytosolic proteins in living cells at a temporal resolution of minutes. APEX-based proximity labeling allows capturing protein interaction dynamics but its high labeling background limits its utility for cytosolic proteins. Here, the authors develop more selective proximity labeling probes, enabling the APEX-based characterization of time-resolved cytosolic protein interactomes.
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42
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Cardoso JMS, Anjo SI, Manadas B, Silva H, Abrantes I, Nakamura K, Fonseca L. Virulence Biomarkers of Bursaphelenchus xylophilus: A Proteomic Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:822289. [PMID: 35211137 PMCID: PMC8861294 DOI: 10.3389/fpls.2021.822289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/28/2021] [Indexed: 05/19/2023]
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, one of the most serious forest pests worldwide, is considered the causal agent of the pine wilt disease (PWD). The main host species belong to the genus Pinus, and a variation in the susceptibility of several pine species to PWN infection is well-known. It is also recognized that there is variation in the virulence among B. xylophilus isolates. In the present study, we applied a quantitative mass spectrometry-based proteomics approach to perform a deep characterization of proteomic changes across two B. xylophilus isolates with different virulence from different hosts and geographical origins. A total of 1,456 proteins were quantified and compared in the two isolates secretomes, and a total of 2,741 proteins were quantified and compared in the nematode proteomes in pine tree extract and fungus stimuli conditions. From the proteomic analyses, a group of proteins was selected and identified as potential virulence biomarkers and shed light on putative most pathogenic proteins of this plant-parasitic nematode. Proteomic data are available via ProteomeXchange with identifier PXD029377.
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Affiliation(s)
- Joana M. S. Cardoso
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
- *Correspondence: Joana M. S. Cardoso,
| | - Sandra I. Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Hugo Silva
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Katsunori Nakamura
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Japan
| | - Luís Fonseca
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
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Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol 2021; 17:e8792. [PMID: 33434350 PMCID: PMC7803364 DOI: 10.15252/msb.20188792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
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Wei JP, Wen W, Dai Y, Qin LX, Wen YQ, Duan DD, Xu SJ. Drinking water temperature affects cognitive function and progression of Alzheimer's disease in a mouse model. Acta Pharmacol Sin 2021; 42:45-54. [PMID: 32451415 PMCID: PMC7921420 DOI: 10.1038/s41401-020-0407-5] [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: 09/01/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
Lifestyle factors may affect mental health and play a critical role in the development of neurodegenerative diseases including Alzheimer's disease (AD). However, whether the temperatures of daily beverages have any impact on cognitive function and AD development has never been studied. In this study, we investigated the effects of daily drinking water temperatures on cognitive function and AD development and progression in mice and the underlying mechanisms. Cognitive function of mice was assessed using passive avoidance test, open field test, and Morris water maze. Wild-type Kunming mice receiving intragastric water (IW, 10 mL/kg, 2 times/day) at 0 °C for consecutive 15 days displayed significant cognitive defects accompanied by significant decrease in gain of body weight, gastric emptying rate, pepsin activity, and an increase in the energy charge in the cortex when compared with mice receiving the same amount of IW at 25 °C (a temperature mimicking most common drinking habits in human), suggesting the altered neuroenergetics may cause cognitive decline. Similarly, in the transgenic APPwse/PS1De9 familial AD mice and their age- and gender-matched wild-type C57BL/6 mice, receiving IW at 0 °C, but not at 25 °C, for 35 days caused a significant time-dependent decrease in body weight and cognitive function, accompanied by a decreased expression of PI3K, Akt, the glutamate/GABA ratio, as well as neuropathy with significant amyloid lesion in the cortex and hippocampus. All of these changes were significantly aggravated in the APPwse/PS1De9 mice than in the control C57BL/6 mice. These data demonstrate that daily beverage at 0 °C may alter brain insulin-mediated neuroenergetics, glutamate/GABA ratio, cause cognitive decline and neuropathy, and promote AD progression.
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Affiliation(s)
- Jiang-Ping Wei
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wen Wen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yuan Dai
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Li-Xia Qin
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yue-Qiang Wen
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Dayue Darrel Duan
- Center for Phenomics of Traditional Chinese Medicine and the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China.
| | - Shi-Jun Xu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Institute of Material Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Silva H, Anjo SI, Manadas B, Abrantes I, Fonseca L, Cardoso JMS. Comparative Analysis of Bursaphelenchus xylophilus Secretome Under Pinus pinaster and P. pinea Stimuli. FRONTIERS IN PLANT SCIENCE 2021; 12:668064. [PMID: 34046053 PMCID: PMC8144518 DOI: 10.3389/fpls.2021.668064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 05/19/2023]
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, the pine wilt disease's (PWD) causal agent, is a migratory endoparasitic nematode skilled to feed on pine tissues and on fungi that colonize the trees. In order to study B. xylophilus secretomes under the stimulus of pine species with different susceptibilities to disease, nematodes were exposed to aqueous pine extracts from Pinus pinaster (high-susceptible host) and P. pinea (low-susceptible host). Sequential windowed acquisition of all theoretical mass spectra (SWATH-MS) was used to determine relative changes in protein amounts between B. xylophilus secretions, and a total of 776 secreted proteins were quantified in both secretomes. From these, 22 proteins were found increased in the B. xylophilus secretome under the P. pinaster stimulus and 501 proteins increased under the P. pinea stimulus. Functional analyses of the 22 proteins found increased in the P. pinaster stimulus showed that proteins with peptidase, hydrolase, and antioxidant activities were the most represented. On the other hand, gene ontology (GO) enrichment analysis of the 501 proteins increased under the P. pinea stimulus revealed an enrichment of proteins with binding activity. The differences detected in the secretomes highlighted the diverse responses from the nematode to overcome host defenses with different susceptibilities and provide new clues on the mechanism behind the pathogenicity of this plant-parasitic nematode. Proteomic data are available via ProteomeXchange with identifier PXD024011.
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Affiliation(s)
- Hugo Silva
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Sandra I. Anjo
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Luís Fonseca
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Joana M. S. Cardoso
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
- *Correspondence: Joana M. S. Cardoso,
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Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Syst 2020; 11:589-607.e8. [PMID: 33333029 PMCID: PMC8034988 DOI: 10.1016/j.cels.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex formation, which in turn constitutes the basis for protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes. In this study, we extend co-fractionation and mass spectrometric data analysis to perform quantitative, network-based studies of proteome organization, via the size-exclusion chromatography algorithmic toolkit (SECAT). This framework explicitly accounts for the dynamic nature and rewiring of protein complexes across multiple cell states and samples, thus, elucidating molecular mechanisms that are differentially implemented across different experimental settings. Systematic analysis of multiple datasets shows that SECAT represents a highly scalable and effective methodology to assess condition/state-specific protein-network state. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven CT, USA; Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York NY, USA; Department of Biomedical Informatics, Columbia University, New York NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York NY, USA; J.P. Sulzberger Columbia Genome Center, Columbia University, New York NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA.
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Li J, Zhan X. Mass spectrometry-based proteomics analyses of post-translational modifications and proteoforms in human pituitary adenomas. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140584. [PMID: 33321259 DOI: 10.1016/j.bbapap.2020.140584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Pituitary adenoma (PA) is a common intracranial neoplasm, which affects the hypothalamus-pituitary-target organ axis systems, and is hazardous to human health. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, nitration, and sumoylation, are vitally important in the PA pathogenesis. The large-scale analysis of PTMs could provide a global view of molecular mechanisms for PA. Proteoforms, which are used to define various protein structural and functional forms originated from the same gene, are the future direction of proteomics research. The global studies of different proteoforms and PTMs of hypophyseal hormones such as growth hormone (GH) and prolactin (PRL) and the proportion change of different GH proteoforms or PRL proteoforms in human pituitary tissue could provide new insights into the clinical value of pituitary hormones in PAs. Multiple quantitative proteomics methods, including mass spectrometry (MS)-based label-free and stable isotope-labeled strategies in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides increase the feasibility for researchers to study PA proteomes. This article reviews the research status of PTMs and proteoforms in PAs, including the enrichment method, technical limitation, quantitative proteomics strategies, and the future perspectives, to achieve the goals of in-depth understanding its molecular pathogenesis, and discovering effective biomarkers and clinical therapeutic targets for predictive, preventive, and personalized treatment of PA patients.
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Affiliation(s)
- Jiajia Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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Wright MT, Plate L. Revealing functional insights into ER proteostasis through proteomics and interactomics. Exp Cell Res 2020; 399:112417. [PMID: 33301765 DOI: 10.1016/j.yexcr.2020.112417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 12/16/2022]
Abstract
The endoplasmic reticulum (ER), responsible for processing approximately one-third of the human proteome including most secreted and membrane proteins, plays a pivotal role in protein homeostasis (proteostasis). Dysregulation of ER proteostasis has been implicated in a number of disease states. As such, continued efforts are directed at elucidating mechanisms of ER protein quality control which are mediated by transient and dynamic protein-protein interactions with molecular chaperones, co-chaperones, protein folding and trafficking factors that take place in and around the ER. Technological advances in mass spectrometry have played a pivotal role in characterizing and understanding these protein-protein interactions that dictate protein quality control mechanisms. Here, we highlight the recent progress from mass spectrometry-based investigation of ER protein quality control in revealing the topological arrangement of the proteostasis network, stress response mechanisms that adjust the ER proteostasis capacity, and disease specific changes in proteostasis network engagement. We close by providing a brief outlook on underexplored areas of ER proteostasis where mass spectrometry is a tool uniquely primed to further expand our understanding of the regulation and coordination of protein quality control processes in diverse diseases.
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Affiliation(s)
- Madison T Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Tian X, de Vries MP, Permentier HP, Bischoff R. A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes. Anal Chem 2020; 92:16149-16157. [PMID: 33256395 PMCID: PMC7745205 DOI: 10.1021/acs.analchem.0c03858] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Quantifying proteins based on peptide-coupled
reporter ions is
a multiplexed quantitative strategy in proteomics that alleviates
the problem of ratio distortion caused by peptide cofragmentation,
as commonly observed in other reporter-ion-based approaches, such
as TMT and iTRAQ. Data-independent acquisition (DIA) is an attractive
alternative to data-dependent acquisition (DDA) due to its better
reproducibility. While multiplexed labeling is widely used in DDA,
it is rarely used in DIA, presumably because current approaches lead
to more complex MS2 spectra, severe ratio distortion, or to a reduction
in quantification accuracy and precision. Herein, we present a versatile
acetyl-alanine-glycine (Ac-AG) tag that conceals quantitative information
in isobarically labeled peptides and reveals it upon tandem MS in
the form of peptide-coupled reporter ions. Since the peptide-coupled
reporter ion is precursor-specific while fragment ions of the peptide
backbone originating from different labeling channels are identical,
the Ac-AG tag is compatible with both DDA and DIA. By isolating the
monoisotopic peak of the precursor ion in DDA, intensities of the
peptide-coupled reporter ions represent the relative ratios between
constituent samples, whereas in DIA, the ratio can be inferred after
deconvoluting the peptide-coupled reporter ion isotopes. The proteome
quantification capability of the Ac-AG tag was demonstrated by triplex
labeling of a yeast proteome spiked with bovine serum albumin (BSA)
over a 10-fold dynamic range. Within this complex proteomics background,
BSA spiked at 1:5:10 ratios was detected at ratios of 1.00:4.87:10.13
in DDA and 1.16:5.20:9.64 in DIA.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hjalmar P Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 16, 9713 AV Groningen, The Netherlands
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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