51
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Pereira RS, Kumar R, Cais A, Paulini L, Kahler A, Bravo J, Minciacchi VR, Krack T, Kowarz E, Zanetti C, Godavarthy PS, Hoeller F, Llavona P, Stark T, Tascher G, Nowak D, Meduri E, Huntly BJP, Münch C, Pampaloni F, Marschalek R, Krause DS. Distinct and targetable role of calcium-sensing receptor in leukaemia. Nat Commun 2023; 14:6242. [PMID: 37802982 PMCID: PMC10558580 DOI: 10.1038/s41467-023-41770-0] [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: 09/30/2022] [Accepted: 09/12/2023] [Indexed: 10/08/2023] Open
Abstract
Haematopoietic stem cells (HSC) reside in the bone marrow microenvironment (BMM), where they respond to extracellular calcium [eCa2+] via the G-protein coupled calcium-sensing receptor (CaSR). Here we show that a calcium gradient exists in this BMM, and that [eCa2+] and response to [eCa2+] differ between leukaemias. CaSR influences the location of MLL-AF9+ acute myeloid leukaemia (AML) cells within this niche and differentially impacts MLL-AF9+ AML versus BCR-ABL1+ leukaemias. Deficiency of CaSR reduces AML leukaemic stem cells (LSC) 6.5-fold. CaSR interacts with filamin A, a crosslinker of actin filaments, affects stemness-associated factors and modulates pERK, β-catenin and c-MYC signaling and intracellular levels of [Ca2+] in MLL-AF9+ AML cells. Combination treatment of cytarabine plus CaSR-inhibition in various models may be superior to cytarabine alone. Our studies suggest CaSR to be a differential and targetable factor in leukaemia progression influencing self-renewal of AML LSC via [eCa2+] cues from the BMM.
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Affiliation(s)
- Raquel S Pereira
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Rahul Kumar
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Alessia Cais
- Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara Paulini
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Alisa Kahler
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Jimena Bravo
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Valentina R Minciacchi
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Theresa Krack
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Eric Kowarz
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Costanza Zanetti
- University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Fabian Hoeller
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Pablo Llavona
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Tabea Stark
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Eshwar Meduri
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Francesco Pampaloni
- Buchmann Institute for Molecular Life Sciences (BMLS, CEF-MC), Goethe University, Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany.
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.
- Institute of General Pharmacology and Toxicology, Goethe-University, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Frankfurt Cancer Institute, Frankfurt, Germany.
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52
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Boykov IN, Montgomery MM, Hagen JT, Aruleba RT, McLaughlin KL, Coalson HS, Nelson MA, Pereyra AS, Ellis JM, Zeczycki TN, Vohra NA, Tan SF, Cabot MC, Fisher-Wellman KH. Pan-tissue mitochondrial phenotyping reveals lower OXPHOS expression and function across cancer types. Sci Rep 2023; 13:16742. [PMID: 37798427 PMCID: PMC10556099 DOI: 10.1038/s41598-023-43963-5] [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: 07/03/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023] Open
Abstract
Targeting mitochondrial oxidative phosphorylation (OXPHOS) to treat cancer has been hampered due to serious side-effects potentially arising from the inability to discriminate between non-cancerous and cancerous mitochondria. Herein, comprehensive mitochondrial phenotyping was leveraged to define both the composition and function of OXPHOS across various murine cancers and compared to both matched normal tissues and other organs. When compared to both matched normal tissues, as well as high OXPHOS reliant organs like heart, intrinsic expression of the OXPHOS complexes, as well as OXPHOS flux were discovered to be consistently lower across distinct cancer types. Assuming intrinsic OXPHOS expression/function predicts OXPHOS reliance in vivo, these data suggest that pharmacologic blockade of mitochondrial OXPHOS likely compromises bioenergetic homeostasis in healthy oxidative organs prior to impacting tumor mitochondrial flux in a clinically meaningful way. Although these data caution against the use of indiscriminate mitochondrial inhibitors for cancer treatment, considerable heterogeneity was observed across cancer types with respect to both mitochondrial proteome composition and substrate-specific flux, highlighting the possibility for targeting discrete mitochondrial proteins or pathways unique to a given cancer type.
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Affiliation(s)
- Ilya N Boykov
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - McLane M Montgomery
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - James T Hagen
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Raphael T Aruleba
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Kelsey L McLaughlin
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Hannah S Coalson
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Margaret A Nelson
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Andrea S Pereyra
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Jessica M Ellis
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Nasreen A Vohra
- Department of Surgery, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Myles C Cabot
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA.
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA.
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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53
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Webber CJ, Murphy CN, Rondón-Ortiz AN, van der Spek SJF, Kelly EX, Lampl NM, Chiesa G, Khalil AS, Emili A, Wolozin B. Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways. Hum Mol Genet 2023; 32:2966-2980. [PMID: 37522762 PMCID: PMC10549787 DOI: 10.1093/hmg/ddad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023] Open
Abstract
Aggregation of TAR DNA-binding protein 43 kDa (TDP-43) is thought to drive the pathophysiology of amyotrophic lateral sclerosis and some frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and can form insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.
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Affiliation(s)
- Chelsea J Webber
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Caroline N Murphy
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Alejandro N Rondón-Ortiz
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Sophie J F van der Spek
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Elena X Kelly
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Noah M Lampl
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
| | - Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
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54
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Zumsteg J, Hirschler A, Carapito C, Maurer L, Villette C, Heintz D, Dahl C, El Nayal A, Sangal V, Mahmoud H, Van Dorsselaer A, Ismail W. Mechanistic insights into sulfur source-driven physiological responses and metabolic reorganization in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8. Appl Environ Microbiol 2023; 89:e0082623. [PMID: 37655899 PMCID: PMC10537767 DOI: 10.1128/aem.00826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Comparative proteomics and untargeted metabolomics were combined to study the physiological and metabolic adaptations of Rhodococcus qingshengii IGTS8 under biodesulfurization conditions. After growth in a chemically defined medium with either dibenzothiophene (DBT) or MgSO4 as the sulfur source, many differentially produced proteins and metabolites associated with several metabolic and physiological processes were detected including the metabolism of carbohydrates, amino acids, lipids, nucleotides, vitamins, protein synthesis, transcriptional regulation, cell envelope biogenesis, and cell division. Increased production of the redox cofactor mycofactocin and associated proteins was one of the most striking adaptations under biodesulfurization conditions. While most central metabolic enzymes were less abundant in the presence of DBT, a key enzyme of the glyoxylate shunt, isocitrate lyase, was up to 26-fold more abundant. Several C1 metabolism and oligotrophy-related enzymes were significantly more abundant in the biodesulfurizing culture. R. qingshengii IGTS8 exhibited oligotrophic growth in liquid and solid media under carbon starvation. Moreover, the oligotrophic growth was faster on the solid medium in the presence of DBT compared to MgSO4 cultures. In the DBT culture, the cell envelope and phospholipids were remodeled, with lower levels of phosphatidylethanolamine and unsaturated and short-chain fatty acids being the most prominent changes. Biodesulfurization increased the biosynthesis of osmoprotectants (ectoine and mannosylglycerate) as well as glutamate and induced the stringent response. Our findings reveal highly diverse and overlapping stress responses that could protect the biodesulfurizing culture not only from the associated sulfate limitation but also from chemical, oxidative, and osmotic stress, allowing efficient resource management. IMPORTANCE Despite decades of research, a commercially viable bioprocess for fuel desulfurization has not been developed yet. This is mainly due to lack of knowledge of the physiology and metabolism of fuel-biodesulfurizing bacteria. Being a stressful condition, biodesulfurization could provoke several stress responses that are not understood. This is particularly important because a thorough understanding of the microbial stress response is essential for the development of environmentally friendly and industrially efficient microbial biocatalysts. Our comparative systems biology studies provide a mechanistic understanding of the biology of biodesulfurization, which is crucial for informed developments through the rational design of recombinant biodesulfurizers and optimization of the bioprocess conditions. Our findings enhance the understanding of the physiology, metabolism, and stress response not only in biodesulfurizing bacteria but also in rhodococci, a precious group of biotechnologically important bacteria.
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Affiliation(s)
- Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Loïc Maurer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Département mécanique, ICube Laboratoire des sciences de l’ingénieur, de l’informatique et de l’imagerie, UNISTRA/CNRS/ENGEES/INSA, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ashraf El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Huda Mahmoud
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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55
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Pleiko K, Haugas M, Parfejevs V, Pantelejevs T, Parisini E, Teesalu T, Riekstina U. Targeting triple-negative breast cancer cells with a β1-integrin binding aptamer. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:871-884. [PMID: 37680989 PMCID: PMC10481362 DOI: 10.1016/j.omtn.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
Targeted therapies have increased the treatment options for triple-negative breast cancer patients. However, the paucity of targetable biomarkers and tumor heterogeneity have limited the ability of precision-guided interventions to live up to their full potential. As affinity-targeting ligands, aptamers show high selectivity toward target molecules. Compared with antibodies, aptamers have lower molecular weight, increased stability during transportation, reduced immunogenicity, and increased tissue uptake. Recently, we reported discovery of the GreenB1 aptamer, which is internalized in cultured triple-negative MDA-MB-231 human breast cancer cells. We show that the GreenB1 aptamer specifically targets β1-integrin, a protein linked previously to breast cancer cell invasiveness and migration. Aptamer binds to β1-integrin with low nanomolar affinity. Our findings suggest potential applications for GreenB1-guided precision agents for diagnosis and therapy of cancers overexpressing β1-integrin.
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Affiliation(s)
- Karlis Pleiko
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Maarja Haugas
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Vadims Parfejevs
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Tambet Teesalu
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Una Riekstina
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
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56
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Zhang L, Wirth M, Patra U, Stroh J, Isaakidis K, Rieger L, Kossatz S, Milanovic M, Zang C, Demel U, Keiten‐Schmitz J, Wagner K, Steiger K, Rad R, Bassermann F, Müller S, Keller U, Schick M. Actionable loss of SLF2 drives B-cell lymphomagenesis and impairs the DNA damage response. EMBO Mol Med 2023; 15:e16431. [PMID: 37485814 PMCID: PMC10493575 DOI: 10.15252/emmm.202216431] [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: 06/10/2022] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
The DNA damage response (DDR) acts as a barrier to malignant transformation and is often impaired during tumorigenesis. Exploiting the impaired DDR can be a promising therapeutic strategy; however, the mechanisms of inactivation and corresponding biomarkers are incompletely understood. Starting from an unbiased screening approach, we identified the SMC5-SMC6 Complex Localization Factor 2 (SLF2) as a regulator of the DDR and biomarker for a B-cell lymphoma (BCL) patient subgroup with an adverse prognosis. SLF2-deficiency leads to loss of DDR factors including Claspin (CLSPN) and consequently impairs CHK1 activation. In line with this mechanism, genetic deletion of Slf2 drives lymphomagenesis in vivo. Tumor cells lacking SLF2 are characterized by a high level of DNA damage, which leads to alterations of the post-translational SUMOylation pathway as a safeguard. The resulting co-dependency confers synthetic lethality to a clinically applicable SUMOylation inhibitor (SUMOi), and inhibitors of the DDR pathway act highly synergistic with SUMOi. Together, our results identify SLF2 as a DDR regulator and reveal co-targeting of the DDR and SUMOylation as a promising strategy for treating aggressive lymphoma.
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Affiliation(s)
- Le Zhang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Matthias Wirth
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Upayan Patra
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Jacob Stroh
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
| | - Konstandina Isaakidis
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Leonie Rieger
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
| | - Susanne Kossatz
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
- Nuclear Medicine, Klinikum rechts der IsarTechnical University of MunichMunichGermany
| | - Maja Milanovic
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Chuanbing Zang
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Uta Demel
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
- Clinician Scientist ProgramBerlin Institute of Health (BIH)BerlinGermany
| | - Jan Keiten‐Schmitz
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Kristina Wagner
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Katja Steiger
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Comparative Experimental Pathology, Institute of PathologyTechnical University of MunichMunichGermany
| | - Roland Rad
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
- Institute of Molecular Oncology and Functional Genomics, TUM School of MedicineTechnische Universität MünchenMunichGermany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Medicine III, Klinikum rechts der IsarTechnical University of MunichMunichGermany
- Center for Translational Cancer Research (TranslaTUM)Technische Universität MünchenMunichGermany
| | - Stefan Müller
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Institute of Biochemistry IIGoethe University Frankfurt, Medical SchoolFrankfurtGermany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
| | - Markus Schick
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin FranklinCharité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ)HeidelbergGermany
- Max‐Delbrück‐Center for Molecular MedicineBerlinGermany
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57
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Handin N, Yuan D, Ölander M, Wegler C, Karlsson C, Jansson-Löfmark R, Hjelmesæth J, Åsberg A, Lauschke VM, Artursson P. Proteome deconvolution of liver biopsies reveals hepatic cell composition as an important marker of fibrosis. Comput Struct Biotechnol J 2023; 21:4361-4369. [PMID: 37711184 PMCID: PMC10498185 DOI: 10.1016/j.csbj.2023.08.037] [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: 04/04/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Human liver tissue is composed of heterogeneous mixtures of different cell types and their cellular stoichiometry can provide information on hepatic physiology and disease progression. Deconvolution algorithms for the identification of cell types and their proportions have recently been developed for transcriptomic data. However, no method for the deconvolution of bulk proteomics data has been presented to date. Here, we show that proteomes, which usually contain less data than transcriptomes, can provide useful information for cell type deconvolution using different algorithms. We demonstrate that proteomes from defined mixtures of cell lines, isolated primary liver cells, and human liver biopsies can be deconvoluted with high accuracy. In contrast to transcriptome-based deconvolution, liver tissue proteomes also provided information about extracellular compartments. Using deconvolution of proteomics data from liver biopsies of 56 patients undergoing Roux-en-Y gastric bypass surgery we show that proportions of immune and stellate cells correlate with inflammatory markers and altered composition of extracellular matrix proteins characteristic of early-stage fibrosis. Our results thus demonstrate that proteome deconvolution can be used as a molecular microscope for investigations of the composition of cell types, extracellular compartments, and for exploring cell-type specific pathological events. We anticipate that these findings will allow the refinement of retrospective analyses of the growing number of proteome datasets from various liver disease states and pave the way for AI-supported clinical and preclinical diagnostics.
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Affiliation(s)
- Niklas Handin
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden
| | - Di Yuan
- Department of Information Technology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Magnus Ölander
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden
| | - Christine Wegler
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden
| | - Cecilia Karlsson
- Late-stage Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, SE- 41345, Sweden
| | - Rasmus Jansson-Löfmark
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg SE-43153, Sweden
| | - Jøran Hjelmesæth
- Morbid Obesity Centre, Department of Medi cine, Vestfold Hospital Trust, NO-3103 Tønsberg, Norway
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Institute of Clinical Medicine, University of Oslo, NO-0318 Oslo, Norway
| | - Anders Åsberg
- Department of Pharmacy, University of Oslo, NO-0316 Oslo, Norway
- Department of Transplanation Medicin, Oslo University Hospital-Rikshospitalet, NO-0424 Oslo, Norway
| | - Volker M. Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Per Artursson
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden
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Färber B, Lapshyna O, Künstner A, Kohl M, Sauer T, Bichmann K, Heckelmann B, Watzelt J, Honselmann K, Bolm L, ten Winkel M, Busch H, Ungefroren H, Keck T, Gemoll T, Wellner UF, Braun R. Molecular profiling and specific targeting of gemcitabine-resistant subclones in heterogeneous pancreatic cancer cell populations. Front Oncol 2023; 13:1230382. [PMID: 37719017 PMCID: PMC10502231 DOI: 10.3389/fonc.2023.1230382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Purpose Chemotherapy is pivotal in the multimodal treatment of pancreatic ductal adenocarcinoma (PDAC). Technical advances unveiled a high degree of inter- and intratumoral heterogeneity. We hypothesized that intratumoral heterogeneity (ITH) impacts response to gemcitabine treatment and demands specific targeting of resistant subclones. Methods Using single cell-derived cell lines (SCDCLs) from the classical cell line BxPC3 and the basal-like cell line Panc-1, we addressed the effect of ITH on response to gemcitabine treatment. Results Individual SCDCLs of both parental tumor cell populations showed considerable heterogeneity in response to gemcitabine. Unsupervised PCA including the 1,000 most variably expressed genes showed a clustering of the SCDCLs according to their respective sensitivity to gemcitabine treatment for BxPC3, while this was less clear for Panc-1. In BxPC3 SCDCLs, enriched signaling pathways EMT, TNF signaling via NfKB, and IL2STAT5 signaling correlated with more resistant behavior to gemcitabine. In Panc-1 SCDCLs MYC targets V1 and V2 as well as E2F targets were associated with stronger resistance. We used recursive feature elimination for Feature Selection in order to compute sets of proteins that showed strong association with the response to gemcitabine. The optimal protein set calculated for Panc-1 comprised fewer proteins in comparison to the protein set determined for BxPC3. Based on molecular profiles, we could show that the gemcitabine-resistant SCDCLs of both BxPC3 and Panc-1 are more sensitive to the BET inhibitor JQ1 compared to the respective gemcitabine-sensitive SCDCLs. Conclusion Our model system of SCDCLs identified gemcitabine-resistant subclones and provides evidence for the critical role of ITH for treatment response in PDAC. We exploited molecular differences as the basis for differential response and used these for more targeted therapy of resistant subclones.
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Affiliation(s)
- Benedikt Färber
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Olga Lapshyna
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Michael Kohl
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Kira Bichmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Benjamin Heckelmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Jessica Watzelt
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Kim Honselmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Louisa Bolm
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Meike ten Winkel
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Hendrik Ungefroren
- First Department of Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tobias Keck
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Ulrich F. Wellner
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Rüdiger Braun
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
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Wang YY, Lin YH, Wu VC, Lin YH, Huang CY, Ku WC, Sun CY. Decreased Klotho Expression Causes Accelerated Decline of Male Fecundity through Oxidative Injury in Murine Testis. Antioxidants (Basel) 2023; 12:1671. [PMID: 37759974 PMCID: PMC10526093 DOI: 10.3390/antiox12091671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Oxidative stress is the etiology for 30-80% of male patients affected by infertility, which is a major health problem worldwide. Klotho protein is an aging suppressor that functions as a humoral factor modulating various cellular processes including antioxidation and anti-inflammation, and its dysregulation leads to human pathologies. Male mice lacking Klotho are sterile, and decreased Klotho levels in the serum are observed in men suffering from infertility with lower sperm counts. However, the mechanism by which Klotho maintains healthy male fertility remains unclear. Klotho haplodeficiency (Kl+/-) accelerates fertility reduction by impairing sperm quality and spermatogenesis in Kl+/- mice. Testicular proteomic analysis revealed that loss of Klotho predominantly disturbed oxidation and the glutathione-related pathway. We further focused on the glutathione-S-transferase (GST) family which counteracts oxidative stress in most cell types and closely relates with fertility. Several GST proteins, including GSTP1, GSTO2, and GSTK1, were significantly downregulated, which subsequently resulted in increased levels of the lipid peroxidation product 4-hydroxynonenal and apoptosis in murine testis with low or no expression of Klotho. Taken together, the loss of one Kl allele accelerates male fecundity loss because diminished antioxidant capability induces oxidative injury in mice. This is the first study that highlights a connection between Klotho and GST proteins.
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Affiliation(s)
- Ya-Yun Wang
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan; (Y.-Y.W.); (Y.-H.L.)
| | - Ying-Hung Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan; (Y.-Y.W.); (Y.-H.L.)
| | - Vin-Cent Wu
- Taiwan Consortium for Acute Kidney Injury and Renal Diseases (CAKs), Taipei 100, Taiwan;
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yu-Hua Lin
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 242, Taiwan;
- Division of Urology, Department of Surgery, Cardinal Tien Hospital, New Taipei City 231, Taiwan
| | - Chia-Yen Huang
- Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei 106, Taiwan;
- School of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Wei-Chi Ku
- School of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Chiao-Yin Sun
- Division of Nephrology, Department of Internal Medicine, Keelung Chang Gung Memorial Hospital, Keelung 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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60
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Neely BA, Ellisor DL, Davis WC. Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin ( Tursiops truncatus). Genes (Basel) 2023; 14:1696. [PMID: 37761836 PMCID: PMC10531373 DOI: 10.3390/genes14091696] [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: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins. Since the identification of larger proteins with more identified peptides implies reduced database fragmentation and improved gene annotation accuracy, we propose the metric NP10, which attempts to capture this quality improvement. The NP10 metric is calculated by first stratifying proteomic results by identifying the top decile (or 10th 10-quantile) of identified proteins based on the number of peptides per protein and then returns the median molecular weight of the resulting proteins. When using the 2016 versus 2012 Tursiops truncatus genome annotation to search this proteomic data set, there was a 21% improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which showed a 33% improvement in NP10. These results demonstrate that proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets across species to facilitate the evaluation of new de novo and existing genome.
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Affiliation(s)
- Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, 331 Fort Johnson Road, Charleston, SC 29412, USA; (D.L.E.); (W.C.D.)
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61
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Wang C, Ulryck N, Herzel L, Pythoud N, Kleiber N, Guérineau V, Jactel V, Moritz C, Bohnsack M, Carapito C, Touboul D, Bohnsack K, Graille M. N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing. Nucleic Acids Res 2023; 51:7496-7519. [PMID: 37283053 PMCID: PMC10415138 DOI: 10.1093/nar/gkad487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last 'orphan' modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Lydia Herzel
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Nicole Kleiber
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, École polytechnique, ENSTA, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Chloé Moritz
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI, FR2048 Strasbourg, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
- Laboratoire de Chimie Moléculaire (LCM), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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Abellon-Ruiz J, Jana K, Silale A, Frey AM, Baslé A, Trost M, Kleinekathöfer U, van den Berg B. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides. Nat Commun 2023; 14:4714. [PMID: 37543597 PMCID: PMC10404256 DOI: 10.1038/s41467-023-40427-2] [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: 11/25/2022] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
Vitamin B12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B12 outer membrane transporters together with a conserved array of surface-exposed B12-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B12 with high affinities. Closing of the BtuG lid following B12 capture causes destabilisation of the bound B12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.
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Affiliation(s)
- Javier Abellon-Ruiz
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kalyanashis Jana
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew M Frey
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthias Trost
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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63
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Beaumal C, Beck A, Hernandez-Alba O, Carapito C. Advanced mass spectrometry workflows for accurate quantification of trace-level host cell proteins in drug products: Benefits of FAIMS separation and gas-phase fractionation DIA. Proteomics 2023; 23:e2300172. [PMID: 37148167 DOI: 10.1002/pmic.202300172] [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: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies (mAb) production relies on multiple purification steps before release as a drug product (DP). A few host cell proteins (HCPs) may co-purify with the mAb. Their monitoring is crucial due to the considerable risk they represent for mAb stability, integrity, and efficacy and their potential immunogenicity. Enzyme-linked immunosorbent assays (ELISA) commonly used for global HCP monitoring present limitations in terms of identification and quantification of individual HCPs. Therefore, liquid chromatography tandem mass spectrometry (LC-MS/MS) has emerged as a promising alternative. Challenging DP samples show an extreme dynamic range requiring high performing methods to detect and reliably quantify trace-level HCPs. Here, we investigated the benefits of adding high-field asymmetric ion mobility spectrometry (FAIMS) separation and gas phase fractionation (GPF) prior to data independent acquisition (DIA). FAIMS LC-MS/MS analysis allowed the identification of 221 HCPs among which 158 were reliably quantified for a global amount of 880 ng/mg of NIST mAb Reference Material. Our methods have also been successfully applied to two FDA/EMA approved DPs and allowed digging deeper into the HCP landscape with the identification and quantification of a few tens of HCPs with sensitivity down to the sub-ng/mg of mAb level.
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Affiliation(s)
- Corentin Beaumal
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Alain Beck
- IRPF, Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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Ukkola I, Nummela P, Heiskanen A, Holm M, Zafar S, Kero M, Haglund C, Satomaa T, Kytölä S, Ristimäki A. N-Glycomic Profiling of Microsatellite Unstable Colorectal Cancer. Cancers (Basel) 2023; 15:3571. [PMID: 37509233 PMCID: PMC10376987 DOI: 10.3390/cancers15143571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Aberrant glycosylation affects cancer progression and immune evasion. Approximately 15% of colorectal cancers (CRCs) demonstrate microsatellite instability (MSI) and display major differences in outcomes and therapeutic responses, as compared to corresponding microsatellite stable (MSS) tumors. We compared the N-glycan profiles of stage II and IV MSI CRC tumors, further subdivided into BRAFV600E wild-type and mutated subgroups (n = 10 in each subgroup), with each other and with those of paired non-neoplastic mucosal samples using mass spectrometry. Further, the N-glycans of BRAFV600E wild-type stage II MSI tumors were compared to corresponding MSS tumors (n = 9). Multiple differences in N-glycan profiles were identified between the MSI CRCs and control tissues, as well as between the stage II MSI and MSS samples. The MSI CRC tumors showed a lower relative abundance of high-mannose N-glycans than did the control tissues or the MSS CRCs. Among MSI CRC subgroups, acidic N-glycans showed tumor stage and BRAF mutation status-dependent variation. Specifically, the large, sulfated/phosphorylated, and putative terminal N-acetylhexosamine-containing acidic N-glycans differed between the MSI CRC subgroups, showing opposite changes in stages II and IV, when comparing BRAF mutated and wild-type tumors. Our results show that molecular subgroups of CRC exhibit characteristic glycan profiles that may explain certain carcinogenic properties of MSI tumors.
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Affiliation(s)
- Iiris Ukkola
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | - Pirjo Nummela
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | | | - Matilda Holm
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Sadia Zafar
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
| | - Mia Kero
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Caj Haglund
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Department of Surgery, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Tero Satomaa
- Glykos Finland Co., Ltd., 00790 Helsinki, Finland
| | - Soili Kytölä
- HUSLAB, Department of Genetics, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Ari Ristimäki
- HUSLAB, Department of Pathology, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, Helsinki University Hospital and University of Helsinki, 00014 Helsinki, Finland
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66
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Baijal K, Abramchuk I, Herrera CM, Stephen Trent M, Lavallée-Adam M, Downey M. Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.546892. [PMID: 37461725 PMCID: PMC10350021 DOI: 10.1101/2023.07.06.546892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (∆ppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and ∆ppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks. From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in ∆ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in ∆ppk cells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that ∆ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
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Affiliation(s)
- Kanchi Baijal
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Iryna Abramchuk
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carmen M. Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular & Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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67
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Potts M, Fletcher-Etherington A, Nightingale K, Mescia F, Bergamaschi L, Calero-Nieto FJ, Antrobus R, Williamson J, Parsons H, Huttlin EL, Kingston N, Göttgens B, Bradley JR, Lehner PJ, Matheson NJ, Smith KGC, Wills MR, Lyons PA, Weekes MP. Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity. Cell Rep 2023; 42:112613. [PMID: 37302069 PMCID: PMC10243220 DOI: 10.1016/j.celrep.2023.112613] [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: 11/15/2022] [Revised: 03/29/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
Certain serum proteins, including C-reactive protein (CRP) and D-dimer, have prognostic value in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, these factors are non-specific, providing limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations that drive the pathogenesis of severe COVID-19. To identify cellular phenotypes associated with disease, we performed a comprehensive, unbiased analysis of total and plasma-membrane PBMC proteomes from 40 unvaccinated individuals with SARS-CoV-2, spanning the whole disease spectrum. Combined with RNA sequencing (RNA-seq) and flow cytometry from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing that immune-cell dysregulation progresses with increasing disease. The cell-surface proteins CEACAMs1, 6, and 8, CD177, CD63, and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3+CD4+CEACAM1/6/8+CD177+CD63+CD89+ and CD16+CEACAM1/6/8+ mononuclear cells. Utilization of these markers may facilitate real-time patient assessment by flow cytometry and identify immune populations that could be targeted to ameliorate immunopathology.
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Affiliation(s)
- Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alice Fletcher-Etherington
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Federica Mescia
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Laura Bergamaschi
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - James Williamson
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Harriet Parsons
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
| | - Berthold Göttgens
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 OAW, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Paul J Lehner
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Nicholas J Matheson
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; NHS Blood and Transplant, Cambridge CB2 0PT, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mark R Wills
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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68
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Ramírez CR, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-wide FPOP Data by FragPipe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543263. [PMID: 37333157 PMCID: PMC10274679 DOI: 10.1101/2023.06.01.543263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Monitoring protein structure before and after perturbations can give insights into the role and function of proteins. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry (MS) allows monitoring of structural rearrangements by exposing proteins to OH radicals that oxidize solvent accessible residues, indicating protein regions undergoing movement. Some of the benefits of FPOP include high throughput and lack of scrambling due to label irreversibility. However, the challenges of processing FPOP data have thus far limited its proteome-scale uses. Here, we present a computational workflow for fast and sensitive analysis of FPOP datasets. Our workflow combines the speed of MSFragger search with a unique hybrid search method to restrict the large search space of FPOP modifications. Together, these features enable more than 10-fold faster FPOP searches that identify 50% more modified peptide spectra than previous methods. We hope this new workflow will increase the accessibility of FPOP to enable more protein structure and function relationships to be explored.
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Affiliation(s)
| | - Jessica Arlett Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, USA
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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69
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Murashov AK, Pak ES, Mar J, O’Brien K, Fisher-Wellman K, Bhat KM. Paternal Western diet causes transgenerational increase in food consumption in Drosophila with parallel alterations in the offspring brain proteome and microRNAs. FASEB J 2023; 37:e22966. [PMID: 37227156 PMCID: PMC10234493 DOI: 10.1096/fj.202300239rr] [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: 02/09/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Several lines of evidence indicate that ancestral diet might play an important role in determining offspring's metabolic traits. However, it is not yet clear whether ancestral diet can affect offspring's food choices and feeding behavior. In the current study, taking advantage of Drosophila model system, we demonstrate that paternal Western diet (WD) increases offspring food consumption up to the fourth generation. Paternal WD also induced alterations in F1 offspring brain proteome. Using enrichment analyses of pathways for upregulated and downregulated proteins, we found that upregulated proteins had significant enrichments in terms related to translation and translation factors, whereas downregulated proteins displayed enrichments in small molecule metabolic processes, TCA cycles, and electron transport chain (ETC). Using MIENTURNET miRNA prediction tool, dme-miR-10-3p was identified as the top conserved miRNA predicted to target proteins regulated by ancestral diet. RNAi-based knockdown of miR-10 in the brain significantly increased food consumption, implicating miR-10 as a potential factor in programming feeding behavior. Together, these findings suggest that ancestral nutrition may influence offspring feeding behavior through alterations in miRNAs.
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Affiliation(s)
- Alexander K. Murashov
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Elena S. Pak
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Jordan Mar
- Department of Molecular Medicine, University of South Florida, Tampa, FL
| | - Kevin O’Brien
- Department of Biostatistics, College of Allied Health Sciences, East Carolina University, Greenville, NC
| | - Kelsey Fisher-Wellman
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL
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70
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Moran JJ, Bernstein HC, Mobberley JM, Thompson AM, Kim YM, Dana KL, Cory AB, Courtney S, Renslow RS, Fredrickson JK, Kreuzer HW, Lipton MS. Daylight-driven carbon exchange through a vertically structured microbial community. Front Microbiol 2023; 14:1139213. [PMID: 37303779 PMCID: PMC10251406 DOI: 10.3389/fmicb.2023.1139213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Interactions between autotrophs and heterotrophs are central to carbon (C) exchange across trophic levels in essentially all ecosystems and metabolite exchange is a frequent mechanism for distributing C within spatially structured ecosystems. Yet, despite the importance of C exchange, the timescales at which fixed C is transferred in microbial communities is poorly understood. We employed a stable isotope tracer combined with spatially resolved isotope analysis to quantify photoautotrophic uptake of bicarbonate and track subsequent exchanges across a vertical depth gradient in a stratified microbial mat over a light-driven diel cycle. We observed that C mobility, both across the vertical strata and between taxa, was highest during periods of active photoautotrophy. Parallel experiments with 13C-labeled organic substrates (acetate and glucose) showed comparably less exchange of C within the mat. Metabolite analysis showed rapid incorporation of 13C into molecules that can both comprise a portion of the extracellular polymeric substances in the system and serve to transport C between photoautotrophs and heterotrophs. Stable isotope proteomic analysis revealed rapid C exchange between cyanobacterial and associated heterotrophic community members during the day with decreased exchange at night. We observed strong diel control on the spatial exchange of freshly fixed C within tightly interacting mat communities suggesting a rapid redistribution, both spatially and taxonomically, primarily during daylight periods.
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Affiliation(s)
- James J. Moran
- Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Hans C. Bernstein
- Pacific Northwest National Laboratory, Richland, WA, United States
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
- ARC – The Arctic Centre for Sustainable Energy, UiT The Arctic University of Norway, Tromsø, Norway
| | | | | | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karl L. Dana
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Steph Courtney
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ryan S. Renslow
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Helen W. Kreuzer
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Mary S. Lipton
- Pacific Northwest National Laboratory, Richland, WA, United States
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71
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González A, Covarrubias-Pinto A, Bhaskara RM, Glogger M, Kuncha SK, Xavier A, Seemann E, Misra M, Hoffmann ME, Bräuning B, Balakrishnan A, Qualmann B, Dötsch V, Schulman BA, Kessels MM, Hübner CA, Heilemann M, Hummer G, Dikić I. Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature 2023:10.1038/s41586-023-06089-2. [PMID: 37225996 DOI: 10.1038/s41586-023-06089-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/14/2023] [Indexed: 05/26/2023]
Abstract
The endoplasmic reticulum (ER) undergoes continuous remodelling via a selective autophagy pathway, known as ER-phagy1. ER-phagy receptors have a central role in this process2, but the regulatory mechanism remains largely unknown. Here we report that ubiquitination of the ER-phagy receptor FAM134B within its reticulon homology domain (RHD) promotes receptor clustering and binding to lipidated LC3B, thereby stimulating ER-phagy. Molecular dynamics (MD) simulations showed how ubiquitination perturbs the RHD structure in model bilayers and enhances membrane curvature induction. Ubiquitin molecules on RHDs mediate interactions between neighbouring RHDs to form dense receptor clusters that facilitate the large-scale remodelling of lipid bilayers. Membrane remodelling was reconstituted in vitro with liposomes and ubiquitinated FAM134B. Using super-resolution microscopy, we discovered FAM134B nanoclusters and microclusters in cells. Quantitative image analysis revealed a ubiquitin-mediated increase in FAM134B oligomerization and cluster size. We found that the E3 ligase AMFR, within multimeric ER-phagy receptor clusters, catalyses FAM134B ubiquitination and regulates the dynamic flux of ER-phagy. Our results show that ubiquitination enhances RHD functions via receptor clustering, facilitates ER-phagy and controls ER remodelling in response to cellular demands.
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Affiliation(s)
- Alexis González
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Marius Glogger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Santosh K Kuncha
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Audrey Xavier
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Eric Seemann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Mohit Misra
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ashwin Balakrishnan
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Michael M Kessels
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, Friedrich Schiller University, Jena, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikić
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany.
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72
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Foronda H, Fu Y, Covarrubias-Pinto A, Bocker HT, González A, Seemann E, Franzka P, Bock A, Bhaskara RM, Liebmann L, Hoffmann ME, Katona I, Koch N, Weis J, Kurth I, Gleeson JG, Reggiori F, Hummer G, Kessels MM, Qualmann B, Mari M, Dikić I, Hübner CA. Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 2023:10.1038/s41586-023-06090-9. [PMID: 37225994 DOI: 10.1038/s41586-023-06090-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/17/2023] [Indexed: 05/26/2023]
Abstract
Membrane-shaping proteins characterized by reticulon homology domains play an important part in the dynamic remodelling of the endoplasmic reticulum (ER). An example of such a protein is FAM134B, which can bind LC3 proteins and mediate the degradation of ER sheets through selective autophagy (ER-phagy)1. Mutations in FAM134B result in a neurodegenerative disorder in humans that mainly affects sensory and autonomic neurons2. Here we report that ARL6IP1, another ER-shaping protein that contains a reticulon homology domain and is associated with sensory loss3, interacts with FAM134B and participates in the formation of heteromeric multi-protein clusters required for ER-phagy. Moreover, ubiquitination of ARL6IP1 promotes this process. Accordingly, disruption of Arl6ip1 in mice causes an expansion of ER sheets in sensory neurons that degenerate over time. Primary cells obtained from Arl6ip1-deficient mice or from patients display incomplete budding of ER membranes and severe impairment of ER-phagy flux. Therefore, we propose that the clustering of ubiquitinated ER-shaping proteins facilitates the dynamic remodelling of the ER during ER-phagy and is important for neuronal maintenance.
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Affiliation(s)
- Hector Foronda
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Yangxue Fu
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | | | - Hartmut T Bocker
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Blink AG, Jena, Germany
| | - Alexis González
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Eric Seemann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Patricia Franzka
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Andrea Bock
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Lutz Liebmann
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marina E Hoffmann
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany
| | - Istvan Katona
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Nicole Koch
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Joseph G Gleeson
- Department of Neurosciences, Rady Children's Institute for Genomic Medicine Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael M Kessels
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Britta Qualmann
- Institute for Biochemistry I, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Ivan Dikić
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
- Center for Rare Diseases, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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73
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Hammarén MM, Luukinen H, Sillanpää A, Remans K, Lapouge K, Custódio T, Löw C, Myllymäki H, Montonen T, Seeger M, Robertson J, Nyman TA, Savijoki K, Parikka M. In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies. mSystems 2023:e0107322. [PMID: 37184670 DOI: 10.1128/msystems.01073-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifier PXD033425 and PXD039416, respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined are a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm-surface-binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection.
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Affiliation(s)
- Milka Marjut Hammarén
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hanna Luukinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alina Sillanpää
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tânia Custódio
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Henna Myllymäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Toni Montonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markus Seeger
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Joseph Robertson
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Kirsi Savijoki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mataleena Parikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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74
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Ito G, Tatara Y, Itoh K, Yamada M, Yamashita T, Sakamoto K, Nozaki T, Ishida K, Wake Y, Kaneko T, Fukuda T, Sugano E, Tomita H, Ozaki T. Novel dicarbonyl metabolic pathway via mitochondrial ES1 possessing glyoxalase III activity. BBA ADVANCES 2023; 3:100092. [PMID: 37250100 PMCID: PMC10209487 DOI: 10.1016/j.bbadva.2023.100092] [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] [Indexed: 05/31/2023] Open
Abstract
Glycation, caused by reactive dicarbonyls, plays a role in various diseases by forming advanced glycation end products. In live cells, reactive dicarbonyls such as glyoxal (GO) and methylglyoxal (MGO) are produced during cell metabolism, and these should be removed consistently. However, the dicarbonyl metabolic system in the mitochondria remains unclear. It has been speculated that the mammalian mitochondrial protein ES1 is a homolog of bacterial elbB possessing glyoxalase III (GLO3) activity. Therefore, in this study, to investigate ES1 functions and GLO3 activity, we generated ES1-knockout (KO) mice and recombinant mouse ES1 protein and investigated the biochemical and histological analyses. In the mitochondrial fraction obtained from ES1-KO mouse brains, the GO metabolism and cytochrome c oxidase activity were significantly lower than those in the mitochondrial fraction obtained from wildtype (WT) mouse brains. However, the morphological features of the mitochondria did not change noticeably in the ES1-KO mouse brains compared with those in the WT mouse brains. The mitochondrial proteome analysis showed that the MGO degradation III pathway and oxidative phosphorylation-related proteins were increased. These should be the response to the reduced GO metabolism caused by ES1 deletion to compensate for the dicarbonyl metabolism and damaged cytochrome c oxidase by elevated GO. Recombinant mouse ES1 protein exhibited catalytic activity of converting GO to glycolic acid. These results indicate that ES1 possesses GLO3 activity and modulates the metabolism of GO in the mitochondria. To our knowledge, this is the first study to show a novel metabolic pathway for reactive dicarbonyls in mitochondria.
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Affiliation(s)
- Ginga Ito
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifuchou, Hirosaki, Aomori 036-8562, Japan
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifuchou, Hirosaki, Aomori 036-8562, Japan
| | - Miwa Yamada
- Department of Biological Chemistry, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Tetsuro Yamashita
- Department of Biological Chemistry, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Kimitoshi Sakamoto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Takayuki Nozaki
- Technical Support Center for Life Science Research, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Kinji Ishida
- Technical Support Center for Life Science Research, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Yui Wake
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Takehito Kaneko
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Tomokazu Fukuda
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Eriko Sugano
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Hiroshi Tomita
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
| | - Taku Ozaki
- Department of Biological Science, Graduate School of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
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75
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Neyroud D, Laitano O, Dasgupta A, Lopez C, Schmitt RE, Schneider JZ, Hammers DW, Sweeney HL, Walter GA, Doles J, Judge SM, Judge AR. Blocking muscle wasting via deletion of the muscle-specific E3 ligase MuRF1 impedes pancreatic tumor growth. Commun Biol 2023; 6:519. [PMID: 37179425 PMCID: PMC10183033 DOI: 10.1038/s42003-023-04902-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Cancer-induced muscle wasting reduces quality of life, complicates or precludes cancer treatments, and predicts early mortality. Herein, we investigate the requirement of the muscle-specific E3 ubiquitin ligase, MuRF1, for muscle wasting induced by pancreatic cancer. Murine pancreatic cancer (KPC) cells, or saline, were injected into the pancreas of WT and MuRF1-/- mice, and tissues analyzed throughout tumor progression. KPC tumors induces progressive wasting of skeletal muscle and systemic metabolic reprogramming in WT mice, but not MuRF1-/- mice. KPC tumors from MuRF1-/- mice also grow slower, and show an accumulation of metabolites normally depleted by rapidly growing tumors. Mechanistically, MuRF1 is necessary for the KPC-induced increases in cytoskeletal and muscle contractile protein ubiquitination, and the depression of proteins that support protein synthesis. Together, these data demonstrate that MuRF1 is required for KPC-induced skeletal muscle wasting, whose deletion reprograms the systemic and tumor metabolome and delays tumor growth.
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Affiliation(s)
- Daria Neyroud
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
- Institute of Sports Sciences, University of Lausanne, Lausanne, Switzerland
| | - Orlando Laitano
- Myology Institute, University of Florida, Gainesville, FL, USA
- Department of Applied Physiology & Kinesiology, University of Florida, Gainesville, FL, USA
| | - Aneesha Dasgupta
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Christopher Lopez
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Rebecca E Schmitt
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jessica Z Schneider
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - David W Hammers
- Myology Institute, University of Florida, Gainesville, FL, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - H Lee Sweeney
- Myology Institute, University of Florida, Gainesville, FL, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Glenn A Walter
- Myology Institute, University of Florida, Gainesville, FL, USA
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
| | - Jason Doles
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Sarah M Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Andrew R Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA.
- Myology Institute, University of Florida, Gainesville, FL, USA.
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76
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Chen M, Zhu P, Wan Q, Ruan X, Wu P, Hao Y, Zhang Z, Sun J, Nie W, Chen S. High-Coverage Four-Dimensional Data-Independent Acquisition Proteomics and Phosphoproteomics Enabled by Deep Learning-Driven Multidimensional Predictions. Anal Chem 2023; 95:7495-7502. [PMID: 37126374 DOI: 10.1021/acs.analchem.2c05414] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Four-dimensional (4D) data-independent acquisition (DIA)-based proteomics is a promising technology. However, its full performance is restricted by the time-consuming building and limited coverage of a project-specific experimental library. Herein, we developed a versatile multifunctional deep learning model Deep4D based on self-attention that could predict the collisional cross section, retention time, fragment ion intensity, and charge state with high accuracies for both the unmodified and phosphorylated peptides and thus established the complete workflows for high-coverage 4D DIA proteomics and phosphoproteomics based on multidimensional predictions. A 4D predicted library containing ∼2 million peptides was established that could realize experimental library-free DIA analysis, and 33% more proteins were identified than using an experimental library of single-shot measurement in the example of HeLa cells. These results show the great values of the convenient high-coverage 4D DIA proteomics methods.
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Affiliation(s)
- Moran Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Pujia Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Xianqin Ruan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Pengfei Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanhong Hao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhourui Zhang
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Jian Sun
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Wenjing Nie
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
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77
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Verathamjamras C, Chantaraamporn J, Sornprachum T, Mutapat P, Chokchaichamnankit D, Mingkwan K, Luevisadpibul V, Srisomsap C, Chutipongtanate S, Svasti J, Champattanachai V. Label-free quantitative proteomics reveals aberrant expression levels of LRG, C9, FN, A1AT and AGP1 in the plasma of patients with colorectal cancer. Clin Proteomics 2023; 20:15. [PMID: 37024778 PMCID: PMC10077704 DOI: 10.1186/s12014-023-09407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the major causes of cancer-related death worldwide. Although commercial biomarkers of CRC are currently available, they are still lacking in terms of sensitivity and specificity; thus, searching for reliable blood-based biomarkers are important for the primary screening of CRC. METHODS Plasma samples of patients with non-metastatic (NM) and metastatic (M) CRC and healthy controls were fractionated using MARS-14 immunoaffinity chromatography. The flow-through and elute fractions representing low- and high-abundant proteins, respectively, were analyzed by label-free quantitative proteomics mass spectrometry. The functional analysis of the proteins with greater than 1.5-fold differential expression level between the CRC and the healthy control groups were analyzed for their biological processes and molecular functions. In addition, the levels of plasma proteins showing large alterations in CRC patients were confirmed by immunoblotting using two independent cohorts. Moreover, receiver operating characteristic (ROC) curve analysis was performed for individual and combinations of biomarker candidates so as to evaluate the diagnostic performance of biomarker candidates. RESULTS From 163 refined identifications, five proteins were up-regulated and two proteins were down-regulated in NM-CRC while eight proteins were up-regulated and three proteins were down-regulated in M-CRC, respectively. Altered plasma proteins in NM-CRC were mainly involved in complement activation, while those in M-CRC were clustered in acute-phase response, complement activation, and inflammatory response. Results from the study- and validation-cohorts indicate that the levels of leucine-rich alpha-2-glycoprotein-1(LRG), complement component C9 (C9), alpha-1-acid glycoprotein 1 (AGP1), and alpha-1-antitrypsin (A1AT) were statistically increased, while fibronectin (FN) level was statistically decreased in CRC patients compared to healthy controls, with most alterations found in a metastatic stage-dependent manner. ROC analysis revealed that FN exhibited the best diagnostic performance to discriminate CRC patients and healthy controls while AGP1 showed the best discrimination between the disease stages in both cohorts. The combined biomarker candidates, FN + A1AT + AGP1, exhibited perfect discriminatory power to discriminate between the CRC population and healthy controls whereas LRG + A1AT + AGP1 was likely to be the best panel to discriminate the metastatic stages in both cohorts. CONCLUSIONS This study identified and quantified distinct plasma proteome profiles of CRC patients. Selected CRC biomarker candidates including FN, LRG, C9, A1AT, and AGP1 may be further applied for screening larger cohorts including disease groups from other types of cancer or other diseases.
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Affiliation(s)
| | | | | | - Photsathorn Mutapat
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Kanokwan Mingkwan
- Division of Surgery, Sapphasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Virat Luevisadpibul
- Division of Information and Technology, Ubonrak Thonburi Hospital, Ubon Ratchathani, Thailand
| | | | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
- Applied Biological Science Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Voraratt Champattanachai
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand.
- Applied Biological Science Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.
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78
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Gombos S, Miras M, Howe V, Xi L, Pottier M, Kazemein Jasemi NS, Schladt M, Ejike JO, Neumann U, Hänsch S, Kuttig F, Zhang Z, Dickmanns M, Xu P, Stefan T, Baumeister W, Frommer WB, Simon R, Schulze WX. A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution. THE NEW PHYTOLOGIST 2023; 238:637-653. [PMID: 36636779 DOI: 10.1111/nph.18730] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large-scale systematic localization, defining a high-confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD-localized. Callose-degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium-like proteins, which also diversified into PD-localized and non-PD-localized members on distinct phylogenetic clades. Our high-confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large-scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.
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Affiliation(s)
- Sven Gombos
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Manuel Miras
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Vicky Howe
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Mathieu Pottier
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Neda S Kazemein Jasemi
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Moritz Schladt
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - J Obinna Ejike
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Sebastian Hänsch
- Center for Advanced Imaging, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Franziska Kuttig
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Marcel Dickmanns
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Peng Xu
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Thorsten Stefan
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Wolf B Frommer
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
- Institute for Transformative Biomolecules, Nagoya University, Nagoya, 464-0813, Japan
| | - Rüdiger Simon
- Department of Developmental Genetics, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593, Stuttgart, Germany
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79
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Nieddu V, Melocchi V, Battistini C, Franciosa G, Lupia M, Stellato C, Bertalot G, Olsen JV, Colombo N, Bianchi F, Cavallaro U. Matrix Gla Protein drives stemness and tumor initiation in ovarian cancer. Cell Death Dis 2023; 14:220. [PMID: 36977707 PMCID: PMC10050398 DOI: 10.1038/s41419-023-05760-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023]
Abstract
Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking, and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpopulation of neoplastic cells, termed ovarian cancer stem cells (OCSC), that are endowed with self-renewing and tumor-initiating properties. This implies that interfering with OCSC function should offer novel therapeutic perspectives to defeat OC progression. To this aim, a better understanding of the molecular and functional makeup of OCSC in clinically relevant model systems is essential. We have profiled the transcriptome of OCSC vs. their bulk cell counterpart from a panel of patient-derived OC cell cultures. This revealed that Matrix Gla Protein (MGP), classically known as a calcification-preventing factor in cartilage and blood vessels, is markedly enriched in OCSC. Functional assays showed that MGP confers several stemness-associated traits to OC cells, including a transcriptional reprogramming. Patient-derived organotypic cultures pointed to the peritoneal microenvironment as a major inducer of MGP expression in OC cells. Furthermore, MGP was found to be necessary and sufficient for tumor initiation in OC mouse models, by shortening tumor latency and increasing dramatically the frequency of tumor-initiating cells. Mechanistically, MGP-driven OC stemness was mediated by the stimulation of Hedgehog signaling, in particular through the induction of the Hedgehog effector GLI1, thus highlighting a novel MGP/Hedgehog pathway axis in OCSC. Finally, MGP expression was found to correlate with poor prognosis in OC patients, and was increased in tumor tissue after chemotherapy, supporting the clinical relevance of our findings. Thus, MGP is a novel driver in OCSC pathophysiology, with a major role in stemness and in tumor initiation.
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Affiliation(s)
- V Nieddu
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCSS, Milan, Italy
| | - V Melocchi
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - C Battistini
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCSS, Milan, Italy
| | - G Franciosa
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - M Lupia
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCSS, Milan, Italy
| | - C Stellato
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCSS, Milan, Italy
| | - G Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, Trento, Italy
- Centre for Medical Sciences - CISMed, University of Trento, Trento, Italy
| | - J V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - N Colombo
- Division of Gynecologic Oncology, European Institute of Oncology IRCSS, Milan, Italy
- University of Milan-Bicocca, Milan, Italy
| | - F Bianchi
- Cancer Biomarkers Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - U Cavallaro
- Unit of Gynaecological Oncology Research, European Institute of Oncology IRCSS, Milan, Italy.
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80
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Chandler KB, Pavan CH, Cotto Aparicio HG, Sackstein R. Enrichment and nLC-MS/MS Analysis of Head and Neck Cancer Mucinome Glycoproteins. J Proteome Res 2023; 22:1231-1244. [PMID: 36971183 DOI: 10.1021/acs.jproteome.2c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Mucin-domain glycoproteins expressed on cancer cell surfaces play central roles in cell adhesion, cancer progression, stem cell renewal, and immune evasion. Despite abundant evidence that mucin-domain glycoproteins are critical to the pathobiology of head and neck squamous cell carcinoma (HNSCC), our knowledge of the composition of that mucinome is grossly incomplete. Here, we utilized a catalytically inactive point mutant of the enzyme StcE (StcEE447D) to capture mucin-domain glycoproteins in head and neck cancer cell line lysates followed by their characterization using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), in-gel digestion, nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), and enrichment analyses. We demonstrate the feasibility of this workflow for the study of mucin-domain glycoproteins in HNSCC, identify a set of mucin-domain glycoproteins common to multiple HNSCC cell lines, and report a subset of mucin-domain glycoproteins that are uniquely expressed in HSC-3 cells, a cell line derived from a highly aggressive metastatic tongue squamous cell carcinoma. This effort represents the first attempt to identify mucin-domain glycoproteins in HNSCC in an untargeted, unbiased analysis, paving the way for a more comprehensive characterization of the mucinome components that mediate aggressive tumor cell phenotypes. Data associated with this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029420.
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81
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Kou YQ, Yang YP, Pan ZJ, Du SS, Yuan WN, He K, Nie B. Prognostic-Related Biomarkers in Pancreatic Ductal Adenocarcinoma Correlating with Immune Infiltrates Based on Proteomics. Med Sci Monit 2023; 29:e938785. [PMID: 36905103 PMCID: PMC10015732 DOI: 10.12659/msm.938785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) accounts for 85% of pancreatic carcinoma cases. Patients with PDAC have a poor prognosis. The lack of reliable prognostic biomarkers makes treatment challenging for patients with PDAC. Using a bioinformatics database, we sought to identify prognostic biomarkers for PDAC. MATERIAL AND METHODS Using proteomic analysis of the Clinical Proteomics Tumor Analysis Consortium (CPTAC) database, we were able to identify core differential proteins between early and advanced pancreatic ductal adenocarcinoma tissue, and then we used survival analysis, Cox regression analysis, and area under the ROC curves to screen for more significant differential proteins. Additionally, the Kaplan-Meier plotter database was utilized to determine the relationship between prognosis and immune infiltration in PDAC. RESULTS We identified 378 differential proteins in early (n=78) and advanced stages (n=47) of PDAC (P<0.05). PLG, COPS5, FYN, ITGB3, IRF3, and SPTA1 served as independent prognostic factors of patients with PDAC. Patients with higher COPS5 expression had shorter overall survival (OS) and recurrence-free survival, and those with higher PLG, ITGB3, and SPTA1, and lower FYN and IRF3 expression had shorter OS. More importantly, COPS5, IRF3 were negatively associated with macrophages and NK cells, but PLG, FYN, ITGB3, and SPTA1 were positively related to the expression of CD8+ T cells and B cells. COPS5 affected the prognosis of PDAC patients by acting on B cells, CD8+ T cells, macrophages, and NK cells immune infiltration, while PLG, FYN, ITGB3, IRF3, and SPTA1 affected PDAC patient prognosis through some immune cells. CONCLUSIONS PLG, COPS5, FYN, IRF3, ITGB3 and SPTA1 could be potential immunotherapeutic targets and valuable prognostic biomarkers of PDAC.
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Affiliation(s)
- Yan-Qi Kou
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Yu-Ping Yang
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Zhao-Jie Pan
- Department of Gastrointestinal Endoscopy, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Shen-Shen Du
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Wei-Nan Yuan
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Kun He
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
| | - Biao Nie
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China (mainland)
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82
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Hessmann S, Chery C, Anne-Sophie S, Gervais A, Carapito C. Host Cell Protein Quantification Workflow Using Optimized Standards combined with Data-Independent Acquisition Mass Spectrometry. J Pharm Anal 2023. [DOI: 10.1016/j.jpha.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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83
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El-Mansi S, Robinson CL, Kostelnik KB, McCormack JJ, Mitchell TP, Lobato-Márquez D, Rajeeve V, Cutillas P, Cutler DF, Mostowy S, Nightingale TD. Proximity proteomics identifies septins and PAK2 as decisive regulators of actomyosin-mediated expulsion of von Willebrand factor. Blood 2023; 141:930-944. [PMID: 36564030 PMCID: PMC10023740 DOI: 10.1182/blood.2022017419] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/07/2022] [Accepted: 11/27/2022] [Indexed: 12/25/2022] Open
Abstract
In response to tissue injury, within seconds the ultra-large glycoprotein von Willebrand factor (VWF) is released from endothelial storage organelles (Weibel-Palade bodies) into the lumen of the blood vasculature, where it leads to the recruitment of platelets. The marked size of VWF multimers represents an unprecedented burden on the secretory machinery of endothelial cells (ECs). ECs have evolved mechanisms to overcome this, most notably an actomyosin ring that forms, contracts, and squeezes out its unwieldy cargo. Inhibiting the formation or function of these structures represents a novel therapeutic target for thrombotic pathologies, although characterizing proteins associated with such a dynamic process has been challenging. We have combined APEX2 proximity labeling with an innovative dual loss-of-function screen to identify proteins associated with actomyosin ring function. We show that p21 activated kinase 2 (PAK2) recruits septin hetero-oligomers, a molecular interaction that forms a ring around exocytic sites. This cascade of events controls actomyosin ring function, aiding efficient exocytic release. Genetic or pharmacological inhibition of PAK2 or septins led to inefficient release of VWF and a failure to form platelet-catching strings. This new molecular mechanism offers additional therapeutic targets for the control of thrombotic disease and is highly relevant to other secretory systems that employ exocytic actomyosin machinery.
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Affiliation(s)
- Sammy El-Mansi
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christopher L. Robinson
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Katja B. Kostelnik
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jessica J. McCormack
- MRC Laboratory of Molecular Cell Biology, University College London, London, United Kingdom
| | - Tom P. Mitchell
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Damián Lobato-Márquez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vinothini Rajeeve
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro Cutillas
- Cell Signalling & Proteomics Group, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Daniel F. Cutler
- MRC Laboratory of Molecular Cell Biology, University College London, London, United Kingdom
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Thomas D. Nightingale
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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84
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Neyroud D, Laitano O, Daguspta A, Lopez C, Schmitt RE, Schneider JZ, Hammers DW, Sweeney HL, Walter GA, Doles J, Judge SM, Judge AR. Blocking muscle wasting via deletion of the muscle-specific E3 ubiquitin ligase MuRF1 impedes pancreatic tumor growth. RESEARCH SQUARE 2023:rs.3.rs-2524562. [PMID: 36798266 PMCID: PMC9934780 DOI: 10.21203/rs.3.rs-2524562/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Cancer-induced muscle wasting reduces quality of life, complicates or precludes cancer treatments, and predicts early mortality. Herein, we investigated the requirement of the muscle-specific E3 ubiquitin ligase, MuRF1, for muscle wasting induced by pancreatic cancer. Murine pancreatic cancer (KPC) cells, or saline, were injected into the pancreas of WT and MuRF1-/- mice, and tissues analyzed throughout tumor progression. KPC tumors induced progressive wasting of skeletal muscle and systemic metabolic reprogramming in WT mice, but not MuRF1-/- mice. KPC tumors from MuRF1-/- mice also grew slower, and showed an accumulation of metabolites normally depleted by rapidly growing tumors. Mechanistically, MuRF1 was necessary for the KPC-induced increases in cytoskeletal and muscle contractile protein ubiquitination, and the depression of proteins that support protein synthesis. Together, these data demonstrate that MuRF1 is required for KPC-induced skeletal muscle wasting, whose deletion reprograms the systemic and tumor metabolome and delays tumor growth.
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Affiliation(s)
- Daria Neyroud
- Department of Physical Therapy, University of Florida, Gainesville, USA
- Myology Institute, University of Florida, Gainesville, USA
- Institute of Sports Sciences, University of Lausanne, Lausanne, Switzerland
| | - Orlando Laitano
- Myology Institute, University of Florida, Gainesville, USA
- Department of Applied Physiology & Kinesiology, University of Florida, Gainesville, USA
| | - Aneesha Daguspta
- Department of Anatomy, Cell Biology and Physiology, Indiana university school of medicine, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Christopher Lopez
- Department of Physical Therapy, University of Florida, Gainesville, USA
- Myology Institute, University of Florida, Gainesville, USA
| | - Rebecca E. Schmitt
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jessica Z. Schneider
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - David W. Hammers
- Myology Institute, University of Florida, Gainesville, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, USA
| | - H. Lee Sweeney
- Myology Institute, University of Florida, Gainesville, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, USA
| | - Glenn A Walter
- Myology Institute, University of Florida, Gainesville, USA
- Department of Physiology and Aging, University of Florida, Gainesville, USA
| | - Jason Doles
- Department of Anatomy, Cell Biology and Physiology, Indiana university school of medicine, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Sarah M. Judge
- Department of Physical Therapy, University of Florida, Gainesville, USA
- Myology Institute, University of Florida, Gainesville, USA
| | - Andrew R Judge
- Department of Physical Therapy, University of Florida, Gainesville, USA
- Myology Institute, University of Florida, Gainesville, USA
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85
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Borzou P, Ghaisari J, Izadi I, Eshraghi Y, Gheisari Y. A novel strategy for dynamic modeling of genome-scale interaction networks. Bioinformatics 2023; 39:7056637. [PMID: 36825834 PMCID: PMC9969830 DOI: 10.1093/bioinformatics/btad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/26/2023] [Indexed: 02/25/2023] Open
Abstract
MOTIVATION The recent availability of omics data allows the construction of holistic maps of interactions between numerous role-playing biomolecules. However, these networks are often static, ignoring the dynamic behavior of biological processes. On the other hand, dynamic models are commonly constructed on small scales. Hence, the construction of large-scale dynamic models that can quantitatively predict the time-course cellular behaviors remains a big challenge. RESULTS In this study, a pipeline is proposed for the automatic construction of large-scale dynamic models. The pipeline uses a list of biomolecules and their time-course trajectories in a given phenomenon as input. First, the interaction network of the biomolecules is constructed. To state the underlying molecular events of each interaction, it is translated into a map of biochemical reactions. Next, to define the kinetics of the reactions, an ordinary differential equation (ODE) is generated for each involved biomolecule. Finally, the parameters of the ODE system are estimated by a novel large-scale parameter approximation method. The high performance of the pipeline is demonstrated by modeling the response of a colorectal cancer cell line to different chemotherapy regimens. In conclusion, Systematic Protein Association Dynamic ANalyzer constructs genome-scale dynamic models, filling the gap between large-scale static and small-scale dynamic modeling strategies. This simulation approach allows for holistic quantitative predictions which are critical for the simulation of therapeutic interventions in precision medicine. AVAILABILITY AND IMPLEMENTATION Detailed information about the constructed large-scale model of colorectal cancer is available in supplementary data. The SPADAN toolbox source code is also available on GitHub (https://github.com/PooyaBorzou/SPADAN). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pooya Borzou
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Jafar Ghaisari
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Iman Izadi
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Yasin Eshraghi
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan 81746-73476, Iran
| | - Yousof Gheisari
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan 81746-73476, Iran
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86
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Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. J Proteome Res 2023; 22:615-624. [PMID: 36648445 PMCID: PMC10166710 DOI: 10.1021/acs.jproteome.2c00624] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. Many of the tools include machine-learning modeling to extract the most information from data sets and build robust statistical models to compute the probabilities that derived information is correct. Here we present the latest information on the many TPP tools, and how TPP can be deployed on various platforms from personal Windows laptops to Linux clusters and expansive cloud computing environments. We describe tutorials on how to use TPP in a variety of ways and describe synergistic projects that leverage TPP. We conclude with plans for continued development of TPP.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | | | | | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jimmy K Eng
- Proteomics Resource, University of Washington, Seattle, Washington 98195, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
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87
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Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. J Proteome Res 2023; 22:287-301. [PMID: 36626722 PMCID: PMC9903322 DOI: 10.1021/acs.jproteome.2c00637] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 01/11/2023]
Abstract
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.
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Affiliation(s)
- Eric W. Deutsch
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R. Jones
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Pierre-Alain Binz
- Clinical
Chemistry Service, Lausanne University Hospital, 1011 976 Lausanne, Switzerland
| | - Henry Lam
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, P. R. China.
| | - Joshua Klein
- Program for
Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Wout Bittremieux
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Department
of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
| | - Yasset Perez-Riverol
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David L. Tabb
- SA MRC
Centre for TB Research, DST/NRF Centre of Excellence for Biomedical
TB Research, Division of Molecular Biology and Human Genetics, Faculty
of Medicine and Health Sciences, Stellenbosch
University, Cape Town 7602, South Africa
| | - Mathias Walzer
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sylvie Ricard-Blum
- Univ.
Lyon, Université Lyon 1, ICBMS, UMR 5246, 69622 Villeurbanne, France
| | - Henning Hermjakob
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Bioinformatics
and Scientific Data, Leibniz Institute of
Plant Biochemistry, 06120 Halle, Germany
- German
Centre for Integrative Biodiversity Research (iDiv), 04103 Halle-Jena-Leipzig, Germany
| | - Tytus D. Mak
- Mass Spectrometry
Data Center, National Institute of Standards
and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United
States
| | - Shin Kawano
- Database
Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- Faculty
of Contemporary Society, Toyama University
of International Studies, Toyama 930-1292, Japan
- School
of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Luis Mendoza
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Tim Van Den Bossche
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Nuno Bandeira
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Jeremy Carver
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Benjamin Pullman
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Zhi Sun
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Nils Hoffmann
- Institute
for Bio- and Geosciences (IBG-5), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
| | - Jim Shofstahl
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Yunping Zhu
- National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, #38, Life Science Park, Changping District, Beijing 102206, China
| | - Luana Licata
- Fondazione
Human Technopole, 20157 Milan, Italy
- Department
of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Federica Quaglia
- Institute
of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), 70126 Bari, Italy
- Department
of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | | | - Sandra E. Orchard
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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88
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Arab I, Fondrie WE, Laukens K, Bittremieux W. Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. J Proteome Res 2023; 22:585-593. [PMID: 36688569 DOI: 10.1021/acs.jproteome.2c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A key analysis task in mass spectrometry proteomics is matching the acquired tandem mass spectra to their originating peptides by sequence database searching or spectral library searching. Machine learning is an increasingly popular postprocessing approach to maximize the number of confident spectrum identifications that can be obtained at a given false discovery rate threshold. Here, we have integrated semisupervised machine learning in the ANN-SoLo tool, an efficient spectral library search engine that is optimized for open modification searching to identify peptides with any type of post-translational modification. We show that machine learning rescoring boosts the number of spectra that can be identified for both standard searching and open searching, and we provide insights into relevant spectrum characteristics harnessed by the machine learning model. The semisupervised machine learning functionality has now been fully integrated into ANN-SoLo, which is available as open source under the permissive Apache 2.0 license on GitHub at https://github.com/bittremieux/ANN-SoLo.
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Affiliation(s)
- Issar Arab
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium.,Biomedical Informatics Network Antwerpen (biomina), 2020 Antwerp, Belgium
| | | | - Kris Laukens
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium.,Biomedical Informatics Network Antwerpen (biomina), 2020 Antwerp, Belgium
| | - Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium.,Biomedical Informatics Network Antwerpen (biomina), 2020 Antwerp, Belgium
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89
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Kreft IC, Huisman EJ, Cnossen MH, van Alphen FPJ, van der Zwaan C, van Leeuwen K, van Spaendonk R, Porcelijn L, Veen CSB, van den Biggelaar M, de Haas M, Meijer AB, Hoogendijk AJ. Proteomic landscapes of inherited platelet disorders with different etiologies. JOURNAL OF THROMBOSIS AND HAEMOSTASIS : JTH 2023; 21:359-372.e3. [PMID: 36700500 DOI: 10.1016/j.jtha.2022.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Inherited platelet disorders (IPDs) are a heterogeneous group of rare diseases that are caused by the defects in early megakaryopoiesis, proplatelet formation, and/or mature platelet function. Although genomic sequencing is increasingly used to identify genetic variants underlying IPD, this technique does not disclose resulting molecular changes that impact platelet function. Proteins are the functional units that shape platelet function; however, insights into how variants that cause IPDs impact platelet proteomes are limited. OBJECTIVES The objective of this study was to profile the platelet proteomics signatures of IPDs. METHODS We performed unbiased label-free quantitative mass spectrometry (MS)-based proteome profiling on platelets of 34 patients with IPDs with variants in 13 ISTH TIER1 genes that affect different stages of platelet development. RESULTS In line with the phenotypical heterogeneity between IPDs, proteomes were diverse between IPDs. We observed extensive proteomic alterations in patients with a GFI1B variant and for genetic variants in genes encoding proteins that impact cytoskeletal processes (MYH9, TUBB1, and WAS). Using the diversity between IPDs, we clustered protein dynamics, revealing disrupted protein-protein complexes. This analysis furthermore grouped proteins with similar cellular function and location, classifying mitochondrial protein constituents and identifying both known and putative novel alpha granule associated proteins. CONCLUSIONS With this study, we demonstrate a MS-based proteomics perspective to IPDs. By integrating the effects of IPDs that impact different aspects of platelet function, we dissected the biological contexts of protein alterations to gain further insights into the biology of platelet (dys)function.
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Affiliation(s)
- Iris C Kreft
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Elise J Huisman
- Department of Pediatric Hematology, Erasmus MC Sophia Children's Hospital, University Medical Center Rotterdam, The Netherlands; Unit of Transfusion Medicine, Sanquin Blood Supply, Amsterdam, The Netherlands
| | - Marjon H Cnossen
- Department of Pediatric Hematology, Erasmus MC Sophia Children's Hospital, University Medical Center Rotterdam, The Netherlands
| | | | - Carmen van der Zwaan
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Karin van Leeuwen
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands
| | - Rosalina van Spaendonk
- Department of Immunohematology Diagnostic, Sanquin Diagnostic Services, Amsterdam, The Netherlands; Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Leendert Porcelijn
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Caroline S B Veen
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Maartje van den Biggelaar
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands; Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Masja de Haas
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands; Center for Clinical Transfusion Research, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexander B Meijer
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands; Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Arie J Hoogendijk
- Department of Molecular Hematology, Sanquin Research, Amsterdam, The Netherlands.
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90
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Zhong Y, Yang F, Su T, Wu X, Zheng W, Zhang L, Liang G, Wang L, Wang L, Wang S, Yang H. Proteome and phosphoproteome profiling of non-small cell lung cancer cell line A549 treated with TRAIL. Proteomics 2023; 23:e2200248. [PMID: 36222260 DOI: 10.1002/pmic.202200248] [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: 06/10/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is recognized for its promising therapeutic effects against cancer. However, mechanisms underlying the effect of TRAIL on protein expression, signal transduction, and apoptosis induction remain unclear. We surmised that a systematic analysis of the proteome and phosphoproteome associated with TRAIL signaling may help elucidate the mechanisms involved and facilitate the development of therapeutics. Therefore, we investigated the proteome and phosphoproteome of non-small cell lung cancer cell line A549 treated with TRAIL. Our results indicated that 126 proteins and 1684 phosphosites were markedly differentially expressed between the phosphate-buffered saline- and TRAIL-treated groups. The expression at protein and phosphosite levels were not completely consistent. Gene ontology functional analysis revealed that metal ion (zinc) binding was highly affected by TRAIL treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that almost all pathways that involved differentially expressed phosphosites were associated with apoptosis. We also identified an important kinase, AKT1, and its series of substrates in TRAIL signaling. The results of this study may provide guidance for future research on tumor therapy using TRAIL.
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Affiliation(s)
- Yi Zhong
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Fen Yang
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiyu Wu
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Zheng
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Zhang
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ge Liang
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lian Wang
- Chengdu Centre for Disease Control and Prevention, Chengdu, China
| | - Lijun Wang
- Department of Ophthalmology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Shisheng Wang
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- Proteomics-Metabolomics Platform of Core Facilities, Key Lab of Transplant Engineering and Immunology, MOH, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
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Sánchez-Martín P, Kriegenburg F, Alves L, Adam J, Elsaesser J, Babic R, Mancilla H, Licheva M, Tascher G, Münch C, Eimer S, Kraft C. ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy. J Cell Sci 2023; 136:jcs260546. [PMID: 36644903 PMCID: PMC10022743 DOI: 10.1242/jcs.260546] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
Autophagy is a catabolic process during which cytosolic material is enwrapped in a newly formed double-membrane structure called the autophagosome, and subsequently targeted for degradation in the lytic compartment of the cell. The fusion of autophagosomes with the lytic compartment is a tightly regulated step and involves membrane-bound SNARE proteins. These play a crucial role as they promote lipid mixing and fusion of the opposing membranes. Among the SNARE proteins implicated in autophagy, the essential SNARE protein YKT6 is the only SNARE protein that is evolutionarily conserved from yeast to humans. Here, we show that alterations in YKT6 function, in both mammalian cells and nematodes, produce early and late autophagy defects that result in reduced survival. Moreover, mammalian autophagosomal YKT6 is phospho-regulated by the ULK1 kinase, preventing premature bundling with the lysosomal SNARE proteins and thereby inhibiting autophagosome-lysosome fusion. Together, our findings reveal that timely regulation of the YKT6 phosphorylation status is crucial throughout autophagy progression and cell survival.
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Affiliation(s)
- Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Ludovico Alves
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Julius Adam
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jana Elsaesser
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Riccardo Babic
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hector Mancilla
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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92
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Drakos SG, Badolia R, Makaju A, Kyriakopoulos CP, Wever-Pinzon O, Tracy CM, Bakhtina A, Bia R, Parnell T, Taleb I, Ramadurai DKA, Navankasattusas S, Dranow E, Hanff TC, Tseliou E, Shankar TS, Visker J, Hamouche R, Stauder EL, Caine WT, Alharethi R, Selzman CH, Franklin S. Distinct Transcriptomic and Proteomic Profile Specifies Patients Who Have Heart Failure With Potential of Myocardial Recovery on Mechanical Unloading and Circulatory Support. Circulation 2023; 147:409-424. [PMID: 36448446 PMCID: PMC10062458 DOI: 10.1161/circulationaha.121.056600] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Extensive evidence from single-center studies indicates that a subset of patients with chronic advanced heart failure (HF) undergoing left ventricular assist device (LVAD) support show significantly improved heart function and reverse structural remodeling (ie, termed "responders"). Furthermore, we recently published a multicenter prospective study, RESTAGE-HF (Remission from Stage D Heart Failure), demonstrating that LVAD support combined with standard HF medications induced remarkable cardiac structural and functional improvement, leading to high rates of LVAD weaning and excellent long-term outcomes. This intriguing phenomenon provides great translational and clinical promise, although the underlying molecular mechanisms driving this recovery are largely unknown. METHODS To identify changes in signaling pathways operative in the normal and failing human heart and to molecularly characterize patients who respond favorably to LVAD unloading, we performed global RNA sequencing and phosphopeptide profiling of left ventricular tissue from 93 patients with HF undergoing LVAD implantation (25 responders and 68 nonresponders) and 12 nonfailing donor hearts. Patients were prospectively monitored through echocardiography to characterize their myocardial structure and function and identify responders and nonresponders. RESULTS These analyses identified 1341 transcripts and 288 phosphopeptides that are differentially regulated in cardiac tissue from nonfailing control samples and patients with HF. In addition, these unbiased molecular profiles identified a unique signature of 29 transcripts and 93 phosphopeptides in patients with HF that distinguished responders after LVAD unloading. Further analyses of these macromolecules highlighted differential regulation in 2 key pathways: cell cycle regulation and extracellular matrix/focal adhesions. CONCLUSIONS This is the first study to characterize changes in the nonfailing and failing human heart by integrating multiple -omics platforms to identify molecular indices defining patients capable of myocardial recovery. These findings may guide patient selection for advanced HF therapies and identify new HF therapeutic targets.
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Affiliation(s)
- Stavros G. Drakos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Rachit Badolia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Aman Makaju
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Christos P. Kyriakopoulos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Omar Wever-Pinzon
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Christopher M. Tracy
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Anna Bakhtina
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Ryan Bia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Timothy Parnell
- Bioinformatics Core, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States
| | - Iosif Taleb
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Dinesh K. A. Ramadurai
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Sutip Navankasattusas
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth Dranow
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thomas C. Hanff
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Eleni Tseliou
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thirupura S. Shankar
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Joseph Visker
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Rana Hamouche
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth L. Stauder
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - William T. Caine
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Rami Alharethi
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Craig H. Selzman
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
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93
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Praus F, Künstner A, Sauer T, Kohl M, Kern K, Deichmann S, Végvári Á, Keck T, Busch H, Habermann JK, Gemoll T. Panomics reveals patient individuality as the major driver of colorectal cancer progression. J Transl Med 2023; 21:41. [PMID: 36691026 PMCID: PMC9869555 DOI: 10.1186/s12967-022-03855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/26/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aimed to integrate genomic, transcriptomic, and proteomic analyses to identify significant differences in expression during CRC progression using a unique set of paired patient samples while considering tumour heterogeneity. METHODS We analysed fresh-frozen tissue samples prepared under strict cryogenic conditions of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from the same patients. Somatic mutations of known cancer-related genes were analysed using Illumina's TruSeq Amplicon Cancer Panel; the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC‒MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated based on differential expression results. RESULTS Although panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumour and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with patient-specific transcriptomes and proteomes. CONCLUSION Our research results highlight the importance of inter- and intra-tumour heterogeneity as well as individual, patient-paired evaluations for clinical studies. In addition to changes among groups reflecting CRC progression, we identified significant expression differences between normal colon mucosa, primary tumour, and liver metastasis samples from individuals, which might accelerate implementation of precision oncology in the future.
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Affiliation(s)
- Friederike Praus
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Michael Kohl
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Katharina Kern
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Steffen Deichmann
- Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Ákos Végvári
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
- Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Tobias Keck
- Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Oncology Pathology, Karolinska Institutet, 171 64, Solna, Sweden
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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Mashini AG, Oakley CA, Beepat SS, Peng L, Grossman AR, Weis VM, Davy SK. The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum. Microorganisms 2023; 11:292. [PMID: 36838257 PMCID: PMC9967746 DOI: 10.3390/microorganisms11020292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.
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Affiliation(s)
| | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Sandeep S. Beepat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
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95
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Chakraborty A, Halder B, Mondal S, Barrett A, Zhi W, Csanyi G, Sabbatini ME. NADPH oxidase 1 in chronic pancreatitis-activated pancreatic stellate cells facilitates the progression of pancreatic cancer. Am J Cancer Res 2023; 13:118-142. [PMID: 36777508 PMCID: PMC9906081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/12/2022] [Indexed: 02/14/2023] Open
Abstract
Patients suffering from chronic pancreatitis (CP) have a higher risk of pancreatic ductal adenocarcinoma (PDAC) compared to the general population. For instance, the presence of an activated pancreatic stellate cell (PaSC)-rich stroma in CP has facilitated the progression of non-invasive pancreatic intraepithelial neoplasia (PanIN) lesions to invasive PDAC. We have previously found that in a mouse model of CP, NADPH oxidase 1 (Nox1) in activated PaSCs forms fibrotic tissue and up-regulates both matrix metalloproteinase (MMP) 9 and the transcription factor Twist1. Yet, the role and mechanism of Nox1 in activated PaSCs from mice with CP (CP-activated PaSCs) in the progression of PDAC is unknown. For that, we tested the ability of Nox1 in CP-activated PaSCs to facilitate the growth of pancreatic cancer cells, and the mechanisms involved in these effects by identifying proteins in the secretome of CP-activated PaSCs whose production were Nox1-dependent. We found that, in vitro, Nox1 evoked a pro-invasive and cancer-promoting phenotype in CP-activated PaSCs via Twist1/MMP-9 expression, causing changes in the extracellular matrix composition. In vivo, Nox1 in CP-activated PaSCs facilitated tumor growth and stromal expansion. Using mass spectrometry, we identified proteins protecting from endoplasmic reticulum, oxidative and metabolic stresses in the secretome of CP-activated PaSCs whose production was Nox1-dependent, including peroxiredoxins (Prdx1 and Prdx4), and thioredoxin reductase 1. In conclusion, inhibiting the Nox1 signaling in activated PaSCs from patients with CP at early stages can reduce the reorganization of extracellular matrix, and the protection of neoplastic cells from cellular stresses, ameliorating the progression of PDAC.
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Affiliation(s)
- Ananya Chakraborty
- Department of Biological Sciences, Augusta UniversityAugusta, Georgia, USA
| | - Bithika Halder
- Department of Biological Sciences, Augusta UniversityAugusta, Georgia, USA
| | - Souravi Mondal
- Department of Biological Sciences, Augusta UniversityAugusta, Georgia, USA
| | - Amanda Barrett
- Department of Surgical Pathology, Medical College of Georgia, Augusta UniversityAugusta, Georgia, USA
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, Georgia, USA
| | - Gabor Csanyi
- Department of Pharmacology and Toxicology, and Vascular Biology Center, Medical College of Georgia, Augusta UniversityAugusta, Georgia, USA
| | - Maria E Sabbatini
- Department of Biological Sciences, Augusta UniversityAugusta, Georgia, USA
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Huebbers JW, Mantz M, Panstruga R, Huesgen PF. Proteomics dataset on detached and purified Arabidopsis thaliana rosette leaf trichomes. Data Brief 2023; 46:108897. [PMID: 36817732 PMCID: PMC9936375 DOI: 10.1016/j.dib.2023.108897] [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: 11/09/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Trichomes are highly specialized uni- or multicellular outgrowths of epidermal cells of plant organs that, in the case of leaves, contribute to plant resistance against abiotic and biotic stress. The model plant Arabidopsis thaliana features single-celled non-glandular rosette leaf trichomes that are dispensable under laboratory conditions. Trichomes have therefore become a successful model to identify plant genes involved in cellular differentiation and cell wall development. We have recently devised an improved method for the enrichment of plant leaf trichomes that relies on the biochemical weakening of the trichome-leaf junctions and a magnetic stirrer-based mechanical stimulus for trichome release followed by density gradient purification of trichomes. Here we provide detailed information on a label-free quantitative (LFQ) shotgun proteomics dataset collected at four stages while applying this protocol to isolate trichomes from rosette leaves of A. thaliana, from (i) whole seedlings before enrichment, from (ii) trichome-depleted material after separation, from (iii) detached trichomes, and from (iv) enriched trichomes after sucrose density gradient centrifugation. Proteins were extracted, digested with trypsin and the resulting peptides identified by nanoflow-chromatography coupled to tandem mass spectrometry. This dataset informs on proteins and biochemical processes present and/or enriched in A. thaliana rosette leaf trichomes, complementing recent large-scale proteome maps. The data further enables comparative analysis with trichome proteomic data from other plant species, may be reanalyzed using different software packages or search settings, and may serve as a reference benchmark for future method refinement.
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Affiliation(s)
- Jan W. Huebbers
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, Aachen 52056, Germany
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, Jülich 52425,Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, Aachen 52056, Germany
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, Jülich 52425,Germany,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) Medical Faculty and University Hospital, University of Cologne, Cologne, Germany,Department for Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany,Corresponding author at: Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, Jülich 52425, Germany.
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Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver J, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman B, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss M, Zhu Y, Ishihama Y, Vizcaíno J. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res 2023; 51:D1539-D1548. [PMID: 36370099 PMCID: PMC9825490 DOI: 10.1093/nar/gkac1040] [Citation(s) in RCA: 170] [Impact Index Per Article: 170.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Luis Mendoza
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chakradhar Bandla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Selvakumar Kamatchinathan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- School of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | | | | | - Yunping Zhu
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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98
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Yokoyama M, Fujita T, Kadonosawa Y, Tatara Y, Motooka D, Ikawa M, Fujii H, Yokoayama Y. Development of transgenic mice overexpressing mouse carbonyl reductase 1. Mol Biol Rep 2023; 50:531-540. [PMID: 36352178 DOI: 10.1007/s11033-022-07994-x] [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: 05/06/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Carbonyl reductase 1 (CBR1) is a nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase with broad substrate specificity. CBR1 catalyzes the reduction of numerous carbonyl compounds, including quinones, prostaglandins, menadione, and multiple xenobiotics, while also participating in various cellular processes, such as carcinogenesis, apoptosis, signal transduction, and drug resistance. In this study, we aimed to generate transgenic mice overexpressing mouse Cbr1 (mCbr1), characterize the mCbr1 expression in different organs, and identify changes in protein expression patterns. METHODS AND RESULTS To facilitate a deeper understanding of the functions of CBR1, we generated transgenic mice overexpressing CBR1 throughout the body. These transgenic mice overexpress 3xFLAG-tagged mCbr1 (3xFLAG-mCbr1) under the CAG promoter. Two lines of transgenic mice were generated, one with 3xFLAG-mCbr1 expression in multiple tissues, and the other, with specific expression of 3xFLAG-mCbr1 in the heart. Pathway and network analysis using transgenic mouse hearts identified 73 proteins with levels of expression correlating with mCbr1 overexpression. The expression of voltage-gated anion channels, which may be directly related to calcium ion-related myocardial contraction, was also upregulated. CONCLUSION mCbr1 transgenic mice may be useful for further in vivo analyses of the molecular mechanisms regulated by Cbr1; such analyses will provide a better understanding of its effects on carcinogenesis and cardiotoxicity of certain cancer drugs.
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Affiliation(s)
- Minako Yokoyama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yuka Kadonosawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Masahito Ikawa
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan
| | - Yoshihito Yokoayama
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, 036-8562, Hirosaki, Aomori, Japan.
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99
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Vávra J, Sergunin A, Stráňava M, Kádek A, Shimizu T, Man P, Martínková M. Hydrogen/Deuterium Exchange Mass Spectrometry of Heme-Based Oxygen Sensor Proteins. Methods Mol Biol 2023; 2648:99-122. [PMID: 37039988 DOI: 10.1007/978-1-0716-3080-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Hydrogen/deuterium exchange (HDX) is a well-established analytical technique that enables monitoring of protein dynamics and interactions by probing the isotope exchange of backbone amides. It has virtually no limitations in terms of protein size, flexibility, or reaction conditions and can thus be performed in solution at different pH values and temperatures under controlled redox conditions. Thanks to its coupling with mass spectrometry (MS), it is also straightforward to perform and has relatively high throughput, making it an excellent complement to the high-resolution methods of structural biology. Given the recent expansion of artificial intelligence-aided protein structure modeling, there is considerable demand for techniques allowing fast and unambiguous validation of in silico predictions; HDX-MS is well-placed to meet this demand. Here we present a protocol for HDX-MS and illustrate its use in characterizing the dynamics and structural changes of a dimeric heme-containing oxygen sensor protein as it responds to changes in its coordination and redox state. This allowed us to propose a mechanism by which the signal (oxygen binding to the heme iron in the sensing domain) is transduced to the protein's functional domain.
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Affiliation(s)
- Jakub Vávra
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Artur Sergunin
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Stráňava
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alan Kádek
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., BIOCEV, Vestec, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Man
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic.
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., BIOCEV, Vestec, Czech Republic.
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic.
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100
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Rabl M, Clark C, Dayon L, Bowman GL, Popp J. Blood plasma protein profiles of neuropsychiatric symptoms and related cognitive decline in older people. J Neurochem 2023; 164:242-254. [PMID: 36281546 DOI: 10.1111/jnc.15715] [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] [Received: 06/08/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 01/31/2023]
Abstract
Neuropsychiatric symptoms (NPS) severely affect patients and their caregivers, and are associated with worse long-term outcomes. This study tested the hypothesis that altered protein levels in blood plasma could serve as biomarkers of NPS; and that altered protein levels are associated with persisting NPS and cognitive decline over time. We performed a cross-sectional and longitudinal study in older subjects with cognitive impairment and cognitively unimpaired in a memory clinic setting. NPS were recorded through the Neuropsychiatric Inventory Questionnaire (NPI-Q) while cognitive and functional impairment was assessed using the clinical dementia rating sum of boxes (CDR-SoB) score at baseline and follow-up visits. Shotgun proteomic analysis based on liquid chromatography-mass spectrometry was conducted in blood plasma samples, identifying 420 proteins. The presence of Alzheimer's Disease (AD) pathology was determined by cerebrospinal fluid biomarkers. Eighty-five subjects with a mean age of 70 (±7.4) years, 62% female and 54% with mild cognitive impairment or mild dementia were included. We found 15 plasma proteins with altered baseline levels in participants with NPS (NPI-Q score > 0). Adding those 15 proteins to a reference model based on clinical data (age, CDR-SoB) significantly improved the prediction of NPS (from receiver operating characteristic area under the curve [AUC] 0.75 to AUC 0.91, p = 0.004) with a specificity of 89% and a sensitivity of 74%. The identified proteins additionally predicted both persisting NPS and cognitive decline at follow-up visits. The observed associations were independent of the presence of AD pathology. Using proteomics, we identified a panel of specific blood proteins associated with current and future NPS, and related cognitive decline in older people. These findings show the potential of untargeted proteomics to identify blood-based biomarkers of pathological alterations relevant for NPS and related clinical disease progression.
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Affiliation(s)
- Miriam Rabl
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,University of Lausanne, Lausanne, Switzerland
| | - Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland.,Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gene L Bowman
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zurich, Zurich, Switzerland.,Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
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