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Pereira BA, Ritchie S, Chambers CR, Gordon KA, Magenau A, Murphy KJ, Nobis M, Tyma VM, Liew YF, Lucas MC, Naeini MM, Barkauskas DS, Chacon-Fajardo D, Howell AE, Parker AL, Warren SC, Reed DA, Lee V, Metcalf XL, Lee YK, O’Regan LP, Zhu J, Trpceski M, Fontaine ARM, Stoehr J, Rouet R, Lin X, Chitty JL, Porazinski S, Wu SZ, Filipe EC, Cadell AL, Holliday H, Yang J, Papanicolaou M, Lyons RJ, Zaratzian A, Tayao M, Da Silva A, Vennin C, Yin J, Dew AB, McMillan PJ, Goldstein LD, Deveson IW, Croucher DR, Samuel MS, Sim HW, Batten M, Chantrill L, Grimmond SM, Gill AJ, Samra J, Jeffry Evans TR, Sasaki T, Phan TG, Swarbrick A, Sansom OJ, Morton JP, Pajic M, Parker BL, Herrmann D, Cox TR, Timpson P. Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response. SCIENCE ADVANCES 2024; 10:eadl1197. [PMID: 38959305 PMCID: PMC11221519 DOI: 10.1126/sciadv.adl1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by increasing fibrosis, which can enhance tumor progression and spread. Here, we undertook an unbiased temporal assessment of the matrisome of the highly metastatic KPC (Pdx1-Cre, LSL-KrasG12D/+, LSL-Trp53R172H/+) and poorly metastatic KPflC (Pdx1-Cre, LSL-KrasG12D/+, Trp53fl/+) genetically engineered mouse models of pancreatic cancer using mass spectrometry proteomics. Our assessment at early-, mid-, and late-stage disease reveals an increased abundance of nidogen-2 (NID2) in the KPC model compared to KPflC, with further validation showing that NID2 is primarily expressed by cancer-associated fibroblasts (CAFs). Using biomechanical assessments, second harmonic generation imaging, and birefringence analysis, we show that NID2 reduction by CRISPR interference (CRISPRi) in CAFs reduces stiffness and matrix remodeling in three-dimensional models, leading to impaired cancer cell invasion. Intravital imaging revealed improved vascular patency in live NID2-depleted tumors, with enhanced response to gemcitabine/Abraxane. In orthotopic models, NID2 CRISPRi tumors had less liver metastasis and increased survival, highlighting NID2 as a potential PDAC cotarget.
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Affiliation(s)
- Brooke A. Pereira
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Shona Ritchie
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Cecilia R. Chambers
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Katie A. Gordon
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Astrid Magenau
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Kendelle J. Murphy
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Max Nobis
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Intravital Imaging Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Victoria M. Tyma
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Ying Fei Liew
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Morghan C. Lucas
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marjan M. Naeini
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Deborah S. Barkauskas
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- ACRF INCITe Intravital Imaging Centre, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Diego Chacon-Fajardo
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Anna E. Howell
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Amelia L. Parker
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Sean C. Warren
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Daniel A. Reed
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Victoria Lee
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Xanthe L. Metcalf
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Young Kyung Lee
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Luke P. O’Regan
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Jessie Zhu
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Michael Trpceski
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Angela R. M. Fontaine
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- ACRF INCITe Intravital Imaging Centre, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Janett Stoehr
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Romain Rouet
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Immune Biotherapies Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Xufeng Lin
- Data Science Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Jessica L. Chitty
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Sean Porazinski
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Sunny Z. Wu
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Genentech Inc., South San Francisco, CA, USA
| | - Elysse C. Filipe
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Antonia L. Cadell
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Holly Holliday
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Jessica Yang
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Michael Papanicolaou
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Ruth J. Lyons
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Anaiis Zaratzian
- Histopathology Platform, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael Tayao
- Histopathology Platform, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Andrew Da Silva
- Histopathology Platform, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Claire Vennin
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| | - Julia Yin
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Alysha B. Dew
- Centre for Advanced Histology & Microscopy, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
| | - Paul J. McMillan
- Centre for Advanced Histology & Microscopy, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Biological Optical Microscopy Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Leonard D. Goldstein
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Data Science Platform, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Ira W. Deveson
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - David R. Croucher
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Michael S. Samuel
- Centre for Cancer Biology, An Alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
- Basil Hetzel Institute for Translational Health Research, Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - Hao-Wen Sim
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, New South Wales, Australia
- Department of Medical Oncology, Chris O’Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Marcel Batten
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Lorraine Chantrill
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- Department of Medical Oncology, Illawarra Shoalhaven Local Health District, Wollongong, New South Wales, Australia
| | - Sean M. Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Anthony J. Gill
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Jaswinder Samra
- Department of Surgery, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Thomas R. Jeffry Evans
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Takako Sasaki
- Department of Biochemistry, Faculty of Medicine, Oita University, Oita, Japan
| | - Tri G. Phan
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Precision Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jennifer P. Morton
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Marina Pajic
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- Translational Oncology Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Benjamin L. Parker
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - David Herrmann
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Thomas R. Cox
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
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2
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Kaag Rasmussen M, Møllgård K, Bork PAR, Weikop P, Esmail T, Drici L, Wewer Albrechtsen NJ, Carlsen JF, Huynh NPT, Ghitani N, Mann M, Goldman SA, Mori Y, Chesler AT, Nedergaard M. Trigeminal ganglion neurons are directly activated by influx of CSF solutes in a migraine model. Science 2024; 385:80-86. [PMID: 38963846 DOI: 10.1126/science.adl0544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/01/2024] [Indexed: 07/06/2024]
Abstract
Classical migraine patients experience aura, which is transient neurological deficits associated with cortical spreading depression (CSD), preceding headache attacks. It is not currently understood how a pathological event in cortex can affect peripheral sensory neurons. In this study, we show that cerebrospinal fluid (CSF) flows into the trigeminal ganglion, establishing nonsynaptic signaling between brain and trigeminal cells. After CSD, ~11% of the CSF proteome is altered, with up-regulation of proteins that directly activate receptors in the trigeminal ganglion. CSF collected from animals exposed to CSD activates trigeminal neurons in naïve mice in part by CSF-borne calcitonin gene-related peptide (CGRP). We identify a communication pathway between the central and peripheral nervous system that might explain the relationship between migrainous aura and headache.
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Affiliation(s)
- Martin Kaag Rasmussen
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter A R Bork
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pia Weikop
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Tina Esmail
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lylia Drici
- NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolai J Wewer Albrechtsen
- NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department for Clinical Biochemistry, University Hospital Copenhagen - Bispebjerg, Copenhagen, 2400 Copenhagen, Denmark
| | - Jonathan Frederik Carlsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Radiology, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Nguyen P T Huynh
- Center for Translational Neuromedicine, Division of Glial Disease and Therapeutics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Sana Biotechnology, Cambridge, MA 02139, USA
| | - Nima Ghitani
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD 20892, USA
| | - Matthias Mann
- NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Center for Translational Neuromedicine, Division of Glial Disease and Therapeutics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Sana Biotechnology, Cambridge, MA 02139, USA
| | - Yuki Mori
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexander T Chesler
- National Center for Complementary and Integrative Health (NCCIH), Bethesda, MD 20892, USA
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Center for Translational Neuromedicine, Division of Glial Disease and Therapeutics, University of Rochester Medical Center, Rochester, NY 14642, USA
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3
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Pfister K, Young V, Frankel B, Silva Barbosa A, Burton J, Bons J, Zhang B, Chiba T, Uhlean R, Goetzman E, Schilling B, Sims-Lucas S. Succinylation of Park7 activates a protective metabolic response to acute kidney injury. Am J Physiol Renal Physiol 2024; 327:F128-F136. [PMID: 38695076 DOI: 10.1152/ajprenal.00062.2024] [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: 02/26/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024] Open
Abstract
Acute kidney injury (AKI) is extremely prevalent among hospitalizations and presents a significant risk for the development of chronic kidney disease and increased mortality. Ischemia caused by shock, trauma, and transplant are common causes of AKI. To attenuate ischemic AKI therapeutically, we need a better understanding of the physiological and cellular mechanisms underlying damage. Instances of ischemia are most damaging in proximal tubule epithelial cells (PTECs) where hypoxic signaling cascades, and perhaps more rapidly, posttranslational modifications (PTMs), act in concert to change cellular metabolism. Here, we focus on the effects of the understudied PTM, lysine succinylation. We have previously shown a protective effect of protein hypersuccinylation on PTECs after depletion of the desuccinylase sirtuin5. General trends in the results suggested that hypersuccinylation led to upregulation of peroxisomal activity and was protective against kidney injury. Included in the list of changes was the Parkinson's-related deglycase Park7. There is little known about any links between peroxisome activity and Park7. In this study, we show in vitro and in vivo that Park7 has a crucial role in protection from AKI and upregulated peroxisome activity. These data in combination with published results of Park7's protective role in cardiovascular damage and chronic kidney disease lead us to hypothesize that succinylation of Park7 may ameliorate oxidative damage resulting from AKI and prevent disease progression. This novel mechanism provides a potential therapeutic mechanism that can be targeted.NEW & NOTEWORTHY Succinylation is an understudied posttranslational modification that has been shown to increase peroxisomal activity. Furthermore, increased peroxisomal activity has been shown to reduce oxidative stress and protect proximal tubules after acute kidney injury. Analysis of mass spectrometry succinylomic and proteomic data reveals a novel role for Parkinson's related Park7 in mediating Nrf2 antioxidant response after kidney injury. This novel protection pathway provides new insights for kidney injury prevention and development of novel therapeutics.
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Affiliation(s)
- Katherine Pfister
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Victoria Young
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Brendon Frankel
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Anne Silva Barbosa
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Jordan Burton
- Buck Institute for Research on Aging, Novato, California, United States
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California, United States
| | - Bob Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Takuto Chiba
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Rebecca Uhlean
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Eric Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States
| | - Sunder Sims-Lucas
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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4
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Strongin Z, Raymond Marchand L, Deleage C, Pampena MB, Cardenas MA, Beusch CM, Hoang TN, Urban EA, Gourves M, Nguyen K, Tharp GK, Lapp S, Rahmberg AR, Harper J, Del Rio Estrada PM, Gonzalez-Navarro M, Torres-Ruiz F, Luna-Villalobos YA, Avila-Rios S, Reyes-Teran G, Sekaly R, Silvestri G, Kulpa DA, Saez-Cirion A, Brenchley JM, Bosinger SE, Gordon DE, Betts MR, Kissick HT, Paiardini M. Distinct SIV-specific CD8 + T cells in the lymph node exhibit simultaneous effector and stem-like profiles and are associated with limited SIV persistence. Nat Immunol 2024; 25:1245-1256. [PMID: 38886592 DOI: 10.1038/s41590-024-01875-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024]
Abstract
Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Laurence Raymond Marchand
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Christian Michel Beusch
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elizabeth A Urban
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Mael Gourves
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey Lapp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Perla M Del Rio Estrada
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio Gonzalez-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Comision Coordinadora de los Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Mexico City, Mexico
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Asier Saez-Cirion
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David Ezra Gordon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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5
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Akalu YT, Patel RS, Taft J, Canas-Arranz R, Richardson A, Buta S, Martin-Fernandez M, Sazeides C, Pearl RL, Mainkar G, Kurland AP, Geltman R, Rosberger H, Kang DD, Kurian AA, Kaur K, Altman J, Dong Y, Johnson JR, Zhangi L, Lim JK, Albrecht RA, García-Sastre A, Rosenberg BR, Bogunovic D. Broad-spectrum RNA antiviral inspired by ISG15 -/- deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600468. [PMID: 38979204 PMCID: PMC11230275 DOI: 10.1101/2024.06.24.600468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Type I interferons (IFN-I) are cytokines with potent antiviral and inflammatory capacities. IFN-I signaling drives the expression of hundreds of IFN-I stimulated genes (ISGs), whose aggregate function results in the control of viral infection. A few of these ISGs are tasked with negatively regulating the IFN-I response to prevent overt inflammation. ISG15 is a negative regulator whose absence leads to persistent, low-grade elevation of ISG expression and concurrent, self-resolving mild autoinflammation. The limited breadth and low-grade persistence of ISGs expressed in ISG15 deficiency are sufficient to confer broad-spectrum antiviral resistance. Inspired by ISG15 deficiency, we have identified a nominal collection of 10 ISGs that recapitulate the broad antiviral potential of the IFN-I system. The expression of the 10 ISG collection in an IFN-I non-responsive cell line increased cellular resistance to Zika, Vesicular Stomatitis, Influenza A (IAV), and SARS-CoV-2 viruses. A deliverable prophylactic formulation of this syndicate of 10 ISGs significantly inhibited IAV PR8 replication in vivo in mice and protected hamsters against a lethal SARS-CoV-2 challenge, suggesting its potential as a broad-spectrum antiviral against many current and future emerging viral pathogens. One-Sentence Summary Human inborn error of immunity-guided discovery and development of a broad-spectrum RNA antiviral therapy.
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6
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Patel SK, Bons J, Rose JP, Chappel JR, Beres RL, Watson MA, Webster C, Burton JB, Bruderer R, Desprez PY, Reiter L, Campisi J, Baker ES, Schilling B. Exosomes Released from Senescent Cells and Circulatory Exosomes Isolated from Human Plasma Reveal Aging-associated Proteomic and Lipid Signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.22.600215. [PMID: 38979258 PMCID: PMC11230204 DOI: 10.1101/2024.06.22.600215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Senescence emerged as a significant mechanism of aging and age-related diseases, offering an attractive target for clinical interventions. Senescent cells release a senescence-associated secretory phenotype (SASP), including exosomes that may act as signal transducers between distal tissues, propagating secondary or bystander senescence and signaling throughout the body. However, the composition of exosome SASP remains underexplored, presenting an opportunity for novel unbiased discovery. Here, we present a detailed proteomic and lipidomic analysis of exosome SASP using mass spectrometry from human plasma from young and older individuals and from tissue culture of senescent primary human lung fibroblasts. We identified ~1,300 exosome proteins released by senescent fibroblasts induced by three different senescence inducers causing most exosome proteins to be differentially regulated with senescence. In parallel, a human plasma cohort from young and old individuals revealed over 1,350 exosome proteins and 171 plasma exosome proteins were regulated when comparing old vs young individuals. Of the age-regulated plasma exosome proteins, we observed 52 exosome SASP factors that were also regulated in exosomes from the senescent fibroblasts, including serine protease inhibitors (SERPINs), Prothrombin, Coagulation factor V, Plasminogen, and Reelin. In addition, 247 lipids were identified with high confidence in all exosome samples. Following the senescence inducers, a majority of the identified phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin species increased significantly indicating cellular membrane changes. The most notable categories of significantly changed proteins were related to extracellular matrix remodeling and inflammation, both potentially detrimental pathways that can damage surrounding tissues and even induce secondary or bystander senescence. Our findings reveal mechanistic insights and potential senescence biomarkers, enabling a better approach to surveilling the senescence burden in the aging population and offering promising therapeutic targets for interventions.
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7
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Zhang R, Bons J, Rose JP, Schilling B, Verdin E. Protocol for mass spectrometric profiling of lysine malonylation by lysine acetyltransferase in CRISPRi K562 cell lines. STAR Protoc 2024; 5:103074. [PMID: 38771695 PMCID: PMC11135037 DOI: 10.1016/j.xpro.2024.103074] [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: 12/12/2023] [Revised: 03/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024] Open
Abstract
Lysine malonylation is a protein posttranslational modification. We present a protocol to generate stable gene-knockdown K562 cell lines through lentiviral infection of a CRISPR interference (CRISPRi) system followed by lysine malonylation measurement using mass spectrometry (MS). We detail guide RNA (gRNA) vector cloning, lentiviral infection, cell line purification, protein digestion, malonyl-lysine enrichment, desalting, and MS acquisition and analysis. For complete details on the use and execution of this protocol, please refer to Zhang et al.1 and Bons et al.2.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob P Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
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8
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Santos Guedes de Sa K, Silva J, Bayarri-Olmos R, Brinda R, Alec Rath Constable R, Colom Diaz PA, Kwon DI, Rodrigues G, Wenxue L, Baker C, Bhattacharjee B, Wood J, Tabacof L, Liu Y, Putrino D, Horvath TL, Iwasaki A. A causal link between autoantibodies and neurological symptoms in long COVID. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309100. [PMID: 38947091 PMCID: PMC11213106 DOI: 10.1101/2024.06.18.24309100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Acute SARS-CoV-2 infection triggers the generation of diverse and functional autoantibodies (AABs), even after mild cases. Persistently elevated autoantibodies have been found in some individuals with long COVID (LC). Using a >21,000 human protein array, we identified diverse AAB targets in LC patients that correlated with their symptoms. Elevated AABs to proteins in the nervous system were found in LC patients with neurocognitive and neurological symptoms. Purified Immunoglobulin G (IgG) samples from these individuals reacted with human pons tissue and were cross-reactive with mouse sciatic nerves, spinal cord, and meninges. Antibody reactivity to sciatic nerves and meninges correlated with patient-reported headache and disorientation. Passive transfer of IgG from patients to mice led to increased sensitivity and pain, mirroring patient-reported symptoms. Similarly, mice injected with IgG showed loss of balance and coordination, reflecting donor-reported dizziness. Our findings suggest that targeting AABs could benefit some LC patients.
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Affiliation(s)
- Keyla Santos Guedes de Sa
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Rafael Bayarri-Olmos
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Ryan Brinda
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Robert Alec Rath Constable
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Patricia A. Colom Diaz
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Dong-il Kwon
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gisele Rodrigues
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Li Wenxue
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Christopher Baker
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Bornali Bhattacharjee
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Jamie Wood
- Cohen Center for Recovery from Complex Chronic Illness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Tabacof
- Cohen Center for Recovery from Complex Chronic Illness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yansheng Liu
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - David Putrino
- Cohen Center for Recovery from Complex Chronic Illness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tamas L. Horvath
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, Center for Infection and Immunity, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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9
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Baker C, Bruderer R, Abbott J, Arthur JSC, Brenes AJ. Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples. J Proteome Res 2024; 23:1926-1936. [PMID: 38691771 PMCID: PMC11165578 DOI: 10.1021/acs.jproteome.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Data-independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spectronaut, we show that the default search parameters can be easily optimized to minimize the occurrence of false positives across different samples. Using an immunological infection model system to demonstrate the impact of adjusting search settings, we analyzed Mus musculus macrophages and compared their proteome to macrophages spiked withCandida albicans. This experimental system enabled the identification of "false positives" as Candida albicans peptides and proteins should not be present in the Mus musculus-only samples. We show that adjusting the search parameters reduced "false positive" identifications by 89% at the peptide and protein level, thereby considerably increasing the quality of the data. We also show that these optimized parameters incurred a moderate cost, only reducing the overall number of "true positive" identifications across each biological replicate by <6.7% at both the peptide and protein level. We believe the value of our updated search parameters extends beyond a two-organism analysis and would be of great value to any DIA experiment analyzing heterogeneous populations of cell types or tissues.
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Affiliation(s)
- Christa
P. Baker
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | | | - James Abbott
- Data
Analysis Group, Division of Computational Biology, School of Life
Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - J. Simon C. Arthur
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Alejandro J. Brenes
- Division
of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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10
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Yu S, Qin X, Li Z. Multicomponent qualitative and quantitative analysis of Farfarae Flos in serum using UHPLC-Q TOF-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1240:124145. [PMID: 38744158 DOI: 10.1016/j.jchromb.2024.124145] [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: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
Farfarae Flos is a traditional herb widely employed for treating coughs, bronchitis, and asthmatic disorders. In the current study, we utilized SWATH and IDA data acquisition modes in combination with multiple data processing techniques to identify Farfarae Flos metabolites in mice serum. A total of 56 compounds were characterized, including 31 phenolic acids, 13 flavonoids, 11 sesquiterpenoids and 1 alkaloid. Further quantitative analysis was conducted on 12 absorbed metabolites, utilizing a newly developed and rigorously validated analytical method. Our approach demonstrated an acceptable level of specificity, accuracy, precision, and stability. When applied to compare the serum of mice treated with FF, all 12 metabolites showed the highest concentration at 0.5 h. Overall, this study presented a novel strategy for unraveling the active compounds of FF via serum pharmacochemistry analysis, which made a foundation for exploring the pharmacodynamic material basis of FF.
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Affiliation(s)
- Shuting Yu
- Institute of Taihang Materia Medica, Shanxi University of Chinese Medicine, Jinzhong 030619, China; Experimental Management Center, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhenyu Li
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China.
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11
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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [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: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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12
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Wong JPH, Blazev R, Ng YK, Goodman CA, Montgomery MK, Watt KI, Carl CS, Watt MJ, Voldstedlund CT, Richter EA, Crouch PJ, Steyn FJ, Ngo ST, Parker BL. Characterization of the skeletal muscle arginine methylome in health and disease reveals remodeling in amyotrophic lateral sclerosis. FASEB J 2024; 38:e23647. [PMID: 38787599 DOI: 10.1096/fj.202400045r] [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: 01/08/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Arginine methylation is a protein posttranslational modification important for the development of skeletal muscle mass and function. Despite this, our understanding of the regulation of arginine methylation under settings of health and disease remains largely undefined. Here, we investigated the regulation of arginine methylation in skeletal muscles in response to exercise and hypertrophic growth, and in diseases involving metabolic dysfunction and atrophy. We report a limited regulation of arginine methylation under physiological settings that promote muscle health, such as during growth and acute exercise, nor in disease models of insulin resistance. In contrast, we saw a significant remodeling of asymmetric dimethylation in models of atrophy characterized by the loss of innervation, including in muscle biopsies from patients with myotrophic lateral sclerosis (ALS). Mass spectrometry-based quantification of the proteome and asymmetric arginine dimethylome of skeletal muscle from individuals with ALS revealed the largest compendium of protein changes with the identification of 793 regulated proteins, and novel site-specific changes in asymmetric dimethyl arginine (aDMA) of key sarcomeric and cytoskeletal proteins. Finally, we show that in vivo overexpression of PRMT1 and aDMA resulted in increased fatigue resistance and functional recovery in mice. Our study provides evidence for asymmetric dimethylation as a regulator of muscle pathophysiology and presents a valuable proteomics resource and rationale for numerous methylated and nonmethylated proteins, including PRMT1, to be pursued for therapeutic development in ALS.
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Affiliation(s)
- Julian P H Wong
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yaan-Kit Ng
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig A Goodman
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Magdalene K Montgomery
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin I Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Victoria, Australia
- The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Peter J Crouch
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Shyuan T Ngo
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Parker
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
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13
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Yang Y, Cheng Y, Lu Z, Ye H, Du G, Li Z. Comparative proteomic and metabolomic analyses reveal stress responses of hemp to salinity. PLANT CELL REPORTS 2024; 43:154. [PMID: 38809335 DOI: 10.1007/s00299-024-03237-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
KEY MESSAGE Integrated omics analyses outline the cellular and metabolic events of hemp plants in response to salt stress and highlight several photosynthesis and energy metabolism related pathways as key regulatory points. Soil salinity affects many physiological processes of plants and leads to crop yield losses worldwide. For hemp, a crop that is valued for multiple aspects, such as its medical compounds, fibre, and seed, a comprehensive understanding of its salt stress responses is a prerequisite for resistance breeding and tailoring its agronomic performance to suit certain industrial applications. Here, we first observed the phenotype of salt-stressed hemp plants and found that under NaCl treatment, hemp plants displayed pronounced growth defects, as indicated by the significantly reduced average height, number of leaves, and chlorophyll content. Next, we conducted comparative proteomics and metabolomics to dissect the complex salt-stress response mechanisms. A total of 314 proteins and 649 metabolites were identified to be differentially behaving upon NaCl treatment. Functional classification and enrichment analysis unravelled that many differential proteins were proteases associated with photosynthesis. Through metabolic pathway enrichment, several energy-related pathways were found to be altered, such as the biosynthesis and degradation of branched-chain amino acids, and our network analysis showed that many ribosomal proteins were involved in these metabolic adaptations. Taken together, for hemp plants, influences on chloroplast function probably represent a major toxic effect of salinity, and modulating several energy-producing pathways possibly through translational regulation is presumably a key protective mechanism against the negative impacts. Our data and analyses provide insights into our understanding of hemp's stress biology and may lay a foundation for future functional genomics studies.
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Affiliation(s)
- Yang Yang
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Yu Cheng
- School of Agriculture, Yunnan University, Kunming, 650091, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650091, China
| | - Zhenhua Lu
- School of Agriculture, Yunnan University, Kunming, 650091, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650091, China
| | - Hailong Ye
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Zheng Li
- School of Agriculture, Yunnan University, Kunming, 650091, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650091, China.
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14
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Onfray C, Chevolleau S, Moinard E, Girard O, Mahadik K, Allsop R, Georgolopoulos G, Lavigne R, Renoult O, Aksoy I, Lemaitre E, Hulin P, Ouimette JF, Fréour T, Pecqueur C, Pineau C, Pasque V, Rougeulle C, David L. Unraveling hallmark suitability for staging pre- and post-implantation stem cell models. Cell Rep 2024; 43:114232. [PMID: 38761378 DOI: 10.1016/j.celrep.2024.114232] [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: 07/11/2023] [Revised: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
The advent of novel 2D and 3D models for human development, including trophoblast stem cells and blastoids, has expanded opportunities for investigating early developmental events, gradually illuminating the enigmatic realm of human development. While these innovations have ushered in new prospects, it has become essential to establish well-defined benchmarks for the cell sources of these models. We aimed to propose a comprehensive characterization of pluripotent and trophoblastic stem cell models by employing a combination of transcriptomic, proteomic, epigenetic, and metabolic approaches. Our findings reveal that extended pluripotent stem cells share many characteristics with primed pluripotent stem cells, with the exception of metabolic activity. Furthermore, our research demonstrates that DNA hypomethylation and high metabolic activity define trophoblast stem cells. These results underscore the necessity of considering multiple hallmarks of pluripotency rather than relying on a single criterion. Multiplying hallmarks alleviate stage-matching bias.
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Affiliation(s)
- Constance Onfray
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Simon Chevolleau
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Eva Moinard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Océane Girard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Kasturi Mahadik
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Ryan Allsop
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Grigorios Georgolopoulos
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Régis Lavigne
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Ophélie Renoult
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Irene Aksoy
- University Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Elsa Lemaitre
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | - Philippe Hulin
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | | | - Thomas Fréour
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Department of Obstetrics, Gynecology and Reproductive Medicine, Dexeus University Hospital, 08028 Barcelona, Spain; CHU Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Claire Pecqueur
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Charles Pineau
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Claire Rougeulle
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France.
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15
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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16
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Costanzo M, Cevenini A, Kollipara L, Caterino M, Bianco S, Pirozzi F, Scerra G, D'Agostino M, Pavone LM, Sickmann A, Ruoppolo M. Methylmalonic acidemia triggers lysosomal-autophagy dysfunctions. Cell Biosci 2024; 14:63. [PMID: 38760822 PMCID: PMC11102240 DOI: 10.1186/s13578-024-01245-1] [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: 11/21/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Methylmalonic acidemia (MMA) is a rare inborn error of propionate metabolism caused by deficiency of the mitochondrial methylmalonyl-CoA mutase (MUT) enzyme. As matter of fact, MMA patients manifest impairment of the primary metabolic network with profound damages that involve several cell components, many of which have not been discovered yet. We employed cellular models and patients-derived fibroblasts to refine and uncover new pathologic mechanisms connected with MUT deficiency through the combination of multi-proteomics and bioinformatics approaches. RESULTS Our data show that MUT deficiency is connected with profound proteome dysregulations, revealing molecular actors involved in lysosome and autophagy functioning. To elucidate the effects of defective MUT on lysosomal and autophagy regulation, we analyzed the morphology and functionality of MMA-lysosomes that showed deep alterations, thus corroborating omics data. Lysosomes of MMA cells present as enlarged vacuoles with low degradative capabilities. Notwithstanding, treatment with an anti-propionigenic drug is capable of totally rescuing lysosomal morphology and functional activity in MUT-deficient cells. These results indicate a strict connection between MUT deficiency and lysosomal-autophagy dysfunction, providing promising therapeutic perspectives for MMA. CONCLUSIONS Defective homeostatic mechanisms in the regulation of autophagy and lysosome functions have been demonstrated in MUT-deficient cells. Our data prove that MMA triggers such dysfunctions impacting on autophagosome-lysosome fusion and lysosomal activity.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy.
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
| | - Armando Cevenini
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | | | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Sabrina Bianco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Francesca Pirozzi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Gianluca Scerra
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Massimo D'Agostino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy.
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
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17
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Müller F, Jansen J, Offensperger F, Eichbichler D, Stengel F, Scheffner M. Cobalamins Function as Allosteric Activators of an Angelman Syndrome-Associated UBE3A/E6AP Variant. Chembiochem 2024; 25:e202400184. [PMID: 38573110 DOI: 10.1002/cbic.202400184] [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: 02/29/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024]
Abstract
Genetic aberrations of the maternal UBE3A allele, which encodes the E3 ubiquitin ligase E6AP, are the cause of Angelman syndrome (AS), an imprinting disorder. In most cases, the maternal UBE3A allele is not expressed. Yet, approximately 10 percent of AS individuals harbor distinct point mutations in the maternal allele resulting in the expression of full-length E6AP variants that frequently display compromised ligase activity. In a high-throughput screen, we identified cyanocobalamin, a vitamin B12-derivative, and several alloxazine derivatives as activators of the AS-linked E6AP-F583S variant. Furthermore, we show by cross-linking coupled to mass spectrometry that cobalamins affect the structural dynamics of E6AP-F583S and apply limited proteolysis coupled to mass spectrometry to obtain information about the regions of E6AP that are involved in, or are affected by binding cobalamins and alloxazine derivatives. Our data suggest that dietary supplementation with vitamin B12 can be beneficial for AS individuals.
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Affiliation(s)
- Franziska Müller
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Jasmin Jansen
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Fabian Offensperger
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Daniela Eichbichler
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457, Konstanz, Germany
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18
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Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568149. [PMID: 38045259 PMCID: PMC10690147 DOI: 10.1101/2023.11.21.568149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology was benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We applied this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detected 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of novel phosphorylation events relevant to mitochondrial and brain biology.
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19
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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20
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Deinhardt-Emmer S, Deshpande S, Kitazawa K, Herman AB, Bons J, Rose JP, Kumar PA, Anerillas C, Neri F, Ciotlos S, Perez K, Köse-Vogel N, Häder A, Abdelmohsen K, Löffler B, Gorospe M, Desprez PY, Melov S, Furman D, Schilling B, Campisi J. Role of the Senescence-Associated Factor Dipeptidyl Peptidase 4 in the Pathogenesis of SARS-CoV-2 Infection. Aging Dis 2024; 15:1398-1415. [PMID: 37728586 PMCID: PMC11081172 DOI: 10.14336/ad.2023.0812] [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: 03/28/2023] [Accepted: 08/12/2023] [Indexed: 09/21/2023] Open
Abstract
During cellular senescence, persistent growth arrest and changes in protein expression programs are accompanied by a senescence-associated secretory phenotype (SASP). In this study, we detected the upregulation of the SASP-related protein dipeptidyl peptidase 4 (DDP4) in human primary lung cells rendered senescent by exposure to ionizing radiation. DPP4 is an exopeptidase that plays a crucial role in the cleavage of various proteins, resulting in the loss of N-terminal dipeptides and proinflammatory effects. Interestingly, our data revealed an association between severe coronavirus disease 2019 (COVID-19) and DDP4, namely that DPP4 levels increased in the plasma of patients with COVID-19 and were correlated with age and disease progression. Although we could not determine the direct effect of DDP4 on viral replication, mechanistic studies in cell culture revealed a negative impact on the expression of the tight junction protein zonula occludens-1 (ZO-1), which contributes to epithelial barrier function. Mass spectrometry analysis indicated that DPP4 overexpressing cells exhibited a decrease in ZO-1 and increased expression of pro-inflammatory cytokines and chemokines. By investigating the effect of DPP4 on the barrier function of human primary cells, we detected an increase in ZO-1 using DPP4 inhibitors. These results provide an important contribution to our understanding of DPP4 in the context of senescence, suggesting that DPP4 plays a major role as part of the SASP. Our results provide evidence that cellular senescence, a hallmark of aging, has an important impact on respiratory infections.
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Affiliation(s)
- Stefanie Deinhardt-Emmer
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | | | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Allison B. Herman
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Francesco Neri
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Serban Ciotlos
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Kevin Perez
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Nilay Köse-Vogel
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Antje Häder
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - David Furman
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Buck Artificial Intelligence Platform, Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
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21
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Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res 2024; 23:1768-1778. [PMID: 38580319 PMCID: PMC11077481 DOI: 10.1021/acs.jproteome.4c00009] [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: 01/04/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.
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Affiliation(s)
- Annie Ha
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Amanda Khoo
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Shahbaz Khan
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Matthew Waas
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Danny Vesprini
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Stanley K. Liu
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Oliver John Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Paul C. Boutros
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Urology, University of California, Los
Angeles, Los Angeles, California 90095, United States
- Institute
for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Stem Cell Research Center, University of California, Los
Angeles, California 90095, United States
- Broad
Stem Cell Research Center, University of
California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90024, United States
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Thomas Kislinger
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
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22
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Bortel P, Piga I, Koenig C, Gerner C, Martinez-Val A, Olsen JV. Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics. Mol Cell Proteomics 2024; 23:100754. [PMID: 38548019 PMCID: PMC11087715 DOI: 10.1016/j.mcpro.2024.100754] [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: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
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Affiliation(s)
- Patricia Bortel
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Ilaria Piga
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claire Koenig
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ana Martinez-Val
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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23
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Numa K, Patel SK, Zhang ZA, Burton JB, Matsumoto A, Hughes JWB, Sotozono C, Schilling B, Desprez PY, Campisi J, Kitazawa K. Senescent characteristics of human corneal endothelial cells upon ultraviolet-A exposure. Aging (Albany NY) 2024; 16:6673-6693. [PMID: 38683123 PMCID: PMC11087119 DOI: 10.18632/aging.205761] [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: 12/20/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
PURPOSE The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A. METHODS We assessed cell morphology, senescence-associated β-galactosidase (SA-β-gal) activity, cell proliferation and expression of senescence markers (p16 and p21) in hCEnCs exposed to UV-A radiation, and senescent hCEnCs induced by ionizing radiation (IR) were used as positive controls. We performed RNA sequencing and proteomics analyses to compare gene and protein expression profiles between UV-A- and IR-induced senescent hCEnCs, and we also compared the results to non-senescent hCEnCs. RESULTS Cells exposed to 5 J/cm2 of UV-A or to IR exhibited typical senescent phenotypes, including enlargement, increased SA-β-gal activity, decreased cell proliferation and elevated expression of p16 and p21. RNA-Seq analysis revealed that 83.9% of the genes significantly upregulated and 82.6% of the genes significantly downregulated in UV-A-induced senescent hCEnCs overlapped with the genes regulated in IR-induced senescent hCEnCs. Proteomics also revealed that 93.8% of the proteins significantly upregulated in UV-A-induced senescent hCEnCs overlapped with those induced by IR. In proteomics analyses, senescent hCEnCs induced by UV-A exhibited elevated expression levels of several factors part of the senescence-associated secretory phenotype. CONCLUSIONS In this study, where senescence was induced by UV-A, a more physiological stress for hCEnCs compared to IR, we determined that UV-A modulated the expression of many genes and proteins typically altered upon IR treatment, a more conventional method of senescence induction, even though UV-A also modulated specific pathways unrelated to IR.
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Affiliation(s)
- Kohsaku Numa
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | - Sandip Kumar Patel
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | | | | | - Akifumi Matsumoto
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | | | - Chie Sotozono
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | | | - Pierre-Yves Desprez
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- California Pacific Medical Center, Research Institute, San Francisco, CA 94107, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
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24
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Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C CDH1 governs mitotic protein stability and cell cycle entry. Nat Commun 2024; 15:3220. [PMID: 38622115 PMCID: PMC11018817 DOI: 10.1038/s41467-024-47427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Induced oncoproteins degradation provides an attractive anti-cancer modality. Activation of anaphase-promoting complex (APC/CCDH1) prevents cell-cycle entry by targeting crucial mitotic proteins for degradation. Phosphorylation of its co-activator CDH1 modulates the E3 ligase activity, but little is known about its regulation after phosphorylation and how to effectively harness APC/CCDH1 activity to treat cancer. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1)-catalyzed phosphorylation-dependent cis-trans prolyl isomerization drives tumor malignancy. However, the mechanisms controlling its protein turnover remain elusive. Through proteomic screens and structural characterizations, we identify a reciprocal antagonism of PIN1-APC/CCDH1 mediated by domain-oriented phosphorylation-dependent dual interactions as a fundamental mechanism governing mitotic protein stability and cell-cycle entry. Remarkably, combined PIN1 and cyclin-dependent protein kinases (CDKs) inhibition creates a positive feedback loop of PIN1 inhibition and APC/CCDH1 activation to irreversibly degrade PIN1 and other crucial mitotic proteins, which force permanent cell-cycle exit and trigger anti-tumor immunity, translating into synergistic efficacy against triple-negative breast cancer.
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Affiliation(s)
- Shizhong Ke
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Lin Wang
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02215, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
| | - Abhishek Thavamani
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nami Kim
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nandita M Naik
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Huaxiu Sui
- Key Laboratory of Functional and Clinical Translational Medicine, Fujian Province University, Xiamen Medical College, Xiamen, 361023, China
| | - Wei Tang
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Chenxi Qiu
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Kazuhiro Koikawa
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Felipe Batalini
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Medicine, Division of Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Emily Stern Gatof
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Daniela Arango Isaza
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jaymin M Patel
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Xiaodong Wang
- Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - John G Clohessy
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT, 06516, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
| | - Xiao Zhen Zhou
- Departments of Pathology and Laboratory Medicine, Biochemistry, and Oncology, and Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Cancer Research Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Department of Medicine and Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Kun Ping Lu
- Departments of Biochemistry and Oncology, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 3K7, Canada.
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25
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Ng YK, Blazev R, McNamara JW, Dutt M, Molendijk J, Porrello ER, Elliott DA, Parker BL. Affinity Purification-Mass Spectrometry and Single Fiber Physiology/Proteomics Reveals Mechanistic Insights of C18ORF25. J Proteome Res 2024; 23:1285-1297. [PMID: 38480473 DOI: 10.1021/acs.jproteome.3c00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
C18ORF25 was recently shown to be phosphorylated at S67 by AMP-activated protein kinase (AMPK) in the skeletal muscle, following acute exercise in humans. Phosphorylation was shown to improve the ex vivo skeletal muscle contractile function in mice, but our understanding of the molecular mechanisms is incomplete. Here, we profiled the interactome of C18ORF25 in mouse myotubes using affinity purification coupled to mass spectrometry. This analysis included an investigation of AMPK-dependent and S67-dependent protein/protein interactions. Several nucleocytoplasmic and contractile-associated proteins were identified, which revealed a subset of GTPases that associate with C18ORF25 in an AMPK- and S67 phosphorylation-dependent manner. We confirmed that C18ORF25 is localized to the nucleus and the contractile apparatus in the skeletal muscle. Mice lacking C18Orf25 display defects in calcium handling specifically in fast-twitch muscle fibers. To investigate these mechanisms, we developed an integrated single fiber physiology and single fiber proteomic platform. The approach enabled a detailed assessment of various steps in the excitation-contraction pathway including SR calcium handling and force generation, followed by paired single fiber proteomic analysis. This enabled us to identify >700 protein/phenotype associations and 36 fiber-type specific differences, following loss of C18Orf25. Taken together, our data provide unique insights into the function of C18ORF25 and its role in skeletal muscle physiology.
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Affiliation(s)
- Yaan-Kit Ng
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ronnie Blazev
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - James W McNamara
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
| | - Mriga Dutt
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Jeffrey Molendijk
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
| | - Enzo R Porrello
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - David A Elliott
- Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, 3052 VIC, Australia
- Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, 3052 VIC, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, 3052 VIC, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3052 VIC, Australia
- Centre for Muscle Research, The University of Melbourne, Parkville, 3052 VIC, Australia
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26
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Picciani M, Gabriel W, Giurcoiu VG, Shouman O, Hamood F, Lautenbacher L, Jensen CB, Müller J, Kalhor M, Soleymaniniya A, Kuster B, The M, Wilhelm M. Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit. Proteomics 2024; 24:e2300112. [PMID: 37672792 DOI: 10.1002/pmic.202300112] [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: 06/14/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Machine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting the adoption of state-of-the-art ML/DL models in proteomics analysis pipelines. We demonstrate its ability to reproduce and even improve our results from previously published rescoring analyses on two distinct use cases. Oktoberfest is freely available on GitHub (https://github.com/wilhelm-lab/oktoberfest) and can easily be installed locally through the cross-platform PyPI Python package.
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Affiliation(s)
- Mario Picciani
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wassim Gabriel
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Victor-George Giurcoiu
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Omar Shouman
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Firas Hamood
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ludwig Lautenbacher
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Cecilia Bang Jensen
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mostafa Kalhor
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Armin Soleymaniniya
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias Wilhelm
- Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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27
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Hu Z, Chen PH, Li W, Krone M, Zheng S, Saarbach J, Velasco IU, Hines J, Liu Y, Crews CM. EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling. SCIENCE ADVANCES 2024; 10:eadj7251. [PMID: 38536914 PMCID: PMC10971414 DOI: 10.1126/sciadv.adj7251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 02/22/2024] [Indexed: 04/05/2024]
Abstract
We recently developed a heterobifunctional approach [phosphorylation targeting chimeras (PhosTACs)] to achieve the targeted protein dephosphorylation (TPDephos). Here, we envisioned combining the inhibitory effects of receptor tyrosine kinase inhibitors (RTKIs) and the active dephosphorylation by phosphatases to achieve dual inhibition of kinases. We report an example of tyrosine phosphatase-based TPDephos and the effective epidermal growth factor receptor (EGFR) tyrosine dephosphorylation. We also used phosphoproteomic approaches to study the signaling transductions affected by PhosTAC-related molecules at the proteome-wide level. This work demonstrated the differential signaling pathways inhibited by PhosTAC compared with the TKI, gefitinib. Moreover, a covalent PhosTAC selective for mutated EGFR was developed and showed its inhibitory potential for dysregulated EGFR. Last, EGFR PhosTACs, consistent with EGFR dephosphorylation profiles, induced apoptosis and inhibited cancer cell viability during prolonged PhosTAC treatment. PhosTACs showcased their potential of modulating RTKs activity, expanding the scope of bifunctional molecule utility.
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Affiliation(s)
- Zhenyi Hu
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Po-Han Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Mackenzie Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Sijin Zheng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Jacques Saarbach
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ines Urquizo Velasco
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - John Hines
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
- Department of Pharmacology, Yale University, New Haven, CT 06511, USA
- Yale University School of Medicine, New Haven, CT 06511, USA
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28
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Peng Z, Li J, Jiang X, Wan C. sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome. Brief Bioinform 2024; 25:bbae147. [PMID: 38600664 PMCID: PMC11006793 DOI: 10.1093/bib/bbae147] [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: 12/05/2023] [Revised: 02/25/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72 000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.
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Affiliation(s)
- Zhao Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, People’s Republic of China
| | - Jiaqiang Li
- School of Computer Science, and Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University, Wuhan 430079, Hubei, People’s Republic of China
| | - Xingpeng Jiang
- School of Computer Science, and Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University, Wuhan 430079, Hubei, People’s Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, People’s Republic of China
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29
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Luan Y, Hu J, Wang Q, Wang X, Li W, Qu R, Yang C, Rajendran BK, Zhou H, Liu P, Zhang N, Shi Y, Liu Y, Tang W, Lu J, Wu D. Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitis. Cell Rep 2024; 43:113934. [PMID: 38461416 PMCID: PMC11064424 DOI: 10.1016/j.celrep.2024.113934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Neutrophils are important innate immune cells with plasticity, heterogenicity, and functional ambivalency. While bone marrow is often regarded as the primary source of neutrophil production, the roles of extramedullary production in regulating neutrophil plasticity and heterogenicity in autoimmune diseases remain poorly understood. Here, we report that the lack of wingless-type MMTV integration site family member 5 (WNT5) unleashes anti-inflammatory protection against colitis in mice, accompanied by reduced colonic CD8+ T cell activation and enhanced splenic extramedullary myelopoiesis. In addition, colitis upregulates WNT5 expression in splenic stromal cells. The ablation of WNT5 leads to increased splenic production of hematopoietic niche factors, as well as elevated numbers of splenic neutrophils with heightened CD8+ T cell suppressive capability, in part due to elevated CD101 expression and attenuated pro-inflammatory activities. Thus, our study reveals a mechanism by which neutrophil plasticity and heterogenicity are regulated in colitis through WNT5 and highlights the role of splenic neutrophil production in shaping inflammatory outcomes.
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Affiliation(s)
- Yi Luan
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Jiajia Hu
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Qijun Wang
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Xujun Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | - Rihao Qu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chuan Yang
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Barani Kumar Rajendran
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Hongyue Zhou
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Peng Liu
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA
| | - Ningning Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Yu Shi
- School of Management, Yale University, New Haven, CT 06511, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, West Haven, CT 06516, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Wenwen Tang
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA.
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
| | - Dianqing Wu
- Department of Pharmacology, Vascular Biology and Therapeutic Program, Yale School of Medicine, New Haven, CT 06519, USA.
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30
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Chen M, Zhang L, Yao Z, Cao X, Ma Q, Chen S, Zhang X, Zhao S. Integrated Transcriptome and Proteome Analysis Reveals That Cell Wall Activity Affects Phelipanche aegyptiaca Parasitism. PLANTS (BASEL, SWITZERLAND) 2024; 13:869. [PMID: 38592861 PMCID: PMC10974318 DOI: 10.3390/plants13060869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Phelipanche aegyptiaca can infect many crops, causing large agricultural production losses. It is important to study the parasitism mechanism of P. aegyptiaca to control its harm. In this experiment, the P. aegyptiaca HY13M and TE9M from Tacheng Prefecture and Hami City in Xinjiang, respectively, were used to analyze the parasitical mechanism of P. aegyptiaca by means of transcriptome and proteome analyses. The parasitic capacity of TE9M was significantly stronger than that of HY13M in Citrullus lanatus. The results showed that the DEGs and DEPs were prominently enriched in the cell wall metabolism pathways, including "cell wall organization or biogenesis", "cell wall organization", and "cell wall". Moreover, the functions of the pectinesterase enzyme gene (TR138070_c0_g), which is involved in the cell wall metabolism of P. aegyptiaca in its parasitism, were studied by means HIGS. The number and weight of P. aegyptiaca were significantly reduced when TR138070_c0_g1, which encodes a cell-wall-degrading protease, was silenced, indicating that it positively regulates P. aegyptiaca parasitism. Thus, these results suggest that the cell wall metabolism pathway is involved in P. aegyptiaca differentiation of the parasitic ability and that the TR138070_c0_g1 gene plays an important role in P. aegyptiaca's parasitism.
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Affiliation(s)
- Meixiu Chen
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Lu Zhang
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Zhaoqun Yao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Xiaolei Cao
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Qianqian Ma
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Siyu Chen
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Xuekun Zhang
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
| | - Sifeng Zhao
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi University, Shihezi 832003, China; (M.C.); (L.Z.)
- Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China; (Z.Y.); (X.C.); (Q.M.); (S.C.)
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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [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: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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32
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Creus-Muncunill J, Haure-Mirande JV, Mattei D, Bons J, Ramirez AV, Hamilton BW, Corwin C, Chowdhury S, Schilling B, Ellerby LM, Ehrlich ME. TYROBP/DAP12 knockout in Huntington's disease Q175 mice cell-autonomously decreases microglial expression of disease-associated genes and non-cell-autonomously mitigates astrogliosis and motor deterioration. J Neuroinflammation 2024; 21:66. [PMID: 38459557 PMCID: PMC10924371 DOI: 10.1186/s12974-024-03052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG trinucleotide repeat in the Huntingtin gene (HTT). Immune activation is abundant in the striatum of HD patients. Detection of active microglia at presymptomatic stages suggests that microgliosis is a key early driver of neuronal dysfunction and degeneration. Recent studies showed that deletion of Tyrobp, a microglial protein, ameliorates neuronal dysfunction in Alzheimer's disease amyloidopathy and tauopathy mouse models while decreasing components of the complement subnetwork. OBJECTIVE While TYROBP/DAP12-mediated microglial activation is detrimental for some diseases such as peripheral nerve injury, it is beneficial for other diseases. We sought to determine whether the TYROBP network is implicated in HD and whether Tyrobp deletion impacts HD striatal function and transcriptomics. METHODS To test the hypothesis that Tyrobp deficiency would be beneficial in an HD model, we placed the Q175 HD mouse model on a Tyrobp-null background. We characterized these mice with a combination of behavioral testing, immunohistochemistry, transcriptomic and proteomic profiling. Further, we evaluated the gene signature in isolated Q175 striatal microglia, with and without Tyrobp. RESULTS Comprehensive analysis of publicly available human HD transcriptomic data revealed that the TYROBP network is overactivated in the HD putamen. The Q175 mice showed morphologic microglial activation, reduced levels of post-synaptic density-95 protein and motor deficits at 6 and 9 months of age, all of which were ameliorated on the Tyrobp-null background. Gene expression analysis revealed that lack of Tyrobp in the Q175 model does not prevent the decrease in the expression of striatal neuronal genes but reduces pro-inflammatory pathways that are specifically active in HD human brain, including genes identified as detrimental in neurodegenerative diseases, e.g. C1q and members of the Ccr5 signaling pathway. Integration of transcriptomic and proteomic data revealed that astrogliosis and complement system pathway were reduced after Tyrobp deletion, which was further validated by immunofluorescence analysis. CONCLUSIONS Our data provide molecular and functional support demonstrating that Tyrobp deletion prevents many of the abnormalities in the HD Q175 mouse model, suggesting that the Tyrobp pathway is a potential therapeutic candidate for Huntington's disease.
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Affiliation(s)
| | | | - Daniele Mattei
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Angie V Ramirez
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - B Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sarah Chowdhury
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | | | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA.
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33
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Burton JB, Silva-Barbosa A, Bons J, Rose J, Pfister K, Simona F, Gandhi T, Reiter L, Bernhardt O, Hunter CL, Goetzman ES, Sims-Lucas S, Schilling B. Substantial downregulation of mitochondrial and peroxisomal proteins during acute kidney injury revealed by data-independent acquisition proteomics. Proteomics 2024; 24:e2300162. [PMID: 37775337 DOI: 10.1002/pmic.202300162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 10/01/2023]
Abstract
Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the susceptibility for recurrent AKI or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury, and the contralateral kidneys remained uninjured to enable comparison and assess injury-induced changes in the kidney proteome. A ZenoTOF 7600 mass spectrometer was optimized for data-independent acquisition (DIA) to achieve comprehensive protein identification and quantification. Short microflow gradients and the generation of a deep kidney-specific spectral library allowed for high-throughput, comprehensive protein quantification. Upon AKI, the kidney proteome was completely remodeled, and over half of the 3945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins that function in fatty acid oxidation, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured kidneys exhibited severely damaged tissues and injury markers. The comprehensive and sensitive kidney-specific DIA-MS assays feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome, and will serve as useful tools for developing novel therapeutics to remediate kidney function.
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Affiliation(s)
- Jordan B Burton
- Buck Institute for Research on Aging, Novato, California, USA
| | - Anne Silva-Barbosa
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, California, USA
| | - Katherine Pfister
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | | | | | | | - Eric S Goetzman
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sunder Sims-Lucas
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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White MEH, Sinn LR, Jones DM, de Folter J, Aulakh SK, Wang Z, Flynn HR, Krüger L, Tober-Lau P, Demichev V, Kurth F, Mülleder M, Blanchard V, Messner CB, Ralser M. Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics. Nat Biomed Eng 2024; 8:233-247. [PMID: 37474612 DOI: 10.1038/s41551-023-01067-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.
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Affiliation(s)
- Matthew E H White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ludwig R Sinn
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - D Marc Jones
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Joost de Folter
- Software Engineering and Artificial Intelligence Technology Platform, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Ziyue Wang
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lynn Krüger
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Critical Care Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Mülleder
- Core Facility High-throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Véronique Blanchard
- Institute of Diagnostic Laboratory Medicine, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Precision Proteomic Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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35
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Garralda E, Beaulieu ME, Moreno V, Casacuberta-Serra S, Martínez-Martín S, Foradada L, Alonso G, Massó-Vallés D, López-Estévez S, Jauset T, Corral de la Fuente E, Doger B, Hernández T, Perez-Lopez R, Arqués O, Castillo Cano V, Morales J, Whitfield JR, Niewel M, Soucek L, Calvo E. MYC targeting by OMO-103 in solid tumors: a phase 1 trial. Nat Med 2024; 30:762-771. [PMID: 38321218 PMCID: PMC10957469 DOI: 10.1038/s41591-024-02805-1] [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: 02/07/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Among the 'most wanted' targets in cancer therapy is the oncogene MYC, which coordinates key transcriptional programs in tumor development and maintenance. It has, however, long been considered undruggable. OMO-103 is a MYC inhibitor consisting of a 91-amino acid miniprotein. Here we present results from a phase 1 study of OMO-103 in advanced solid tumors, established to examine safety and tolerability as primary outcomes and pharmacokinetics, recommended phase 2 dose and preliminary signs of activity as secondary ones. A classical 3 + 3 design was used for dose escalation of weekly intravenous, single-agent OMO-103 administration in 21-day cycles, encompassing six dose levels (DLs). A total of 22 patients were enrolled, with treatment maintained until disease progression. The most common adverse events were grade 1 infusion-related reactions, occurring in ten patients. One dose-limiting toxicity occurred at DL5. Pharmacokinetics showed nonlinearity, with tissue saturation signs at DL5 and a terminal half-life in serum of 40 h. Of the 19 patients evaluable for response, 12 reached the predefined 9-week time point for assessment of drug antitumor activity, eight of those showing stable disease by computed tomography. One patient defined as stable disease by response evaluation criteria in solid tumors showed a 49% reduction in total tumor volume at best response. Transcriptomic analysis supported target engagement in tumor biopsies. In addition, we identified soluble factors that are potential pharmacodynamic and predictive response markers. Based on all these data, the recommended phase 2 dose was determined as DL5 (6.48 mg kg-1).ClinicalTrials.gov identifier: NCT04808362 .
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Affiliation(s)
| | | | - Víctor Moreno
- START Madrid-FJD-Hospital Fundación Jiménez Díaz, Madrid, Spain
| | | | | | | | - Guzman Alonso
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | | | - Bernard Doger
- START Madrid-FJD-Hospital Fundación Jiménez Díaz, Madrid, Spain
| | | | | | - Oriol Arqués
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | | | - Laura Soucek
- Vall d'Hebron Institute of Oncology, Barcelona, Spain.
- Peptomyc S.L., Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Emiliano Calvo
- START Madrid-CIOCC-Centro Integral Oncológico Clara Campal, Madrid, Spain
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36
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Schurman CA, Kaya S, Dole N, Luna NMM, Castillo N, Potter R, Rose JP, Bons J, King CD, Burton JB, Schilling B, Melov S, Tang S, Schaible E, Alliston T. Aging impairs the osteocytic regulation of collagen integrity and bone quality. Bone Res 2024; 12:13. [PMID: 38409111 PMCID: PMC10897167 DOI: 10.1038/s41413-023-00303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024] Open
Abstract
Poor bone quality is a major factor in skeletal fragility in elderly individuals. The molecular mechanisms that establish and maintain bone quality, independent of bone mass, are unknown but are thought to be primarily determined by osteocytes. We hypothesize that the age-related decline in bone quality results from the suppression of osteocyte perilacunar/canalicular remodeling (PLR), which maintains bone material properties. We examined bones from young and aged mice with osteocyte-intrinsic repression of TGFβ signaling (TβRIIocy-/-) that suppresses PLR. The control aged bone displayed decreased TGFβ signaling and PLR, but aging did not worsen the existing PLR suppression in male TβRIIocy-/- bone. This relationship impacted the behavior of collagen material at the nanoscale and tissue scale in macromechanical tests. The effects of age on bone mass, density, and mineral material behavior were independent of osteocytic TGFβ. We determined that the decline in bone quality with age arises from the loss of osteocyte function and the loss of TGFβ-dependent maintenance of collagen integrity.
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Affiliation(s)
- Charles A Schurman
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Serra Kaya
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Neha Dole
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Nadja M Maldonado Luna
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
| | - Natalia Castillo
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Ryan Potter
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Jacob P Rose
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jordan B Burton
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Simon Tang
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Eric Schaible
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA.
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA.
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37
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Phung TK, Berndsen K, Shastry R, Phan TLCHB, Muqit MMK, Alessi DR, Nirujogi RS. CURTAIN-A unique web-based tool for exploration and sharing of MS-based proteomics data. Proc Natl Acad Sci U S A 2024; 121:e2312676121. [PMID: 38324566 PMCID: PMC10873628 DOI: 10.1073/pnas.2312676121] [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: 07/26/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024] Open
Abstract
To facilitate analysis and sharing of mass spectrometry (MS)-based proteomics data, we created online tools called CURTAIN (https://curtain.proteo.info) and CURTAIN-PTM (https://curtainptm.proteo.info) with an accompanying series of video tutorials (https://www.youtube.com/@CURTAIN-me6hl). These are designed to enable non-MS experts to interactively peruse volcano plots and deconvolute primary experimental data so that replicates can be visualized in bar charts or violin plots and exported in publication-ready format. They also allow assessment of overall experimental quality by correlation matrix and profile plot analysis. After making a selection of protein "hits", the user can analyze known domain structure, AlphaFold predicted structure, reported interactors, relative expression as well as disease links. CURTAIN-PTM permits analysis of all identified PTM sites on protein(s) of interest with selected databases. CURTAIN-PTM also links with the Kinase Library to predict upstream kinases that may phosphorylate sites of interest. We provide examples of the utility of CURTAIN and CURTAIN-PTM in analyzing how targeted degradation of the PPM1H Rab phosphatase that counteracts the Parkinson's LRRK2 kinase impacts cellular protein levels and phosphorylation sites. We also reanalyzed a ubiquitylation dataset, characterizing the PINK1-Parkin pathway activation in primary neurons, revealing data of interest not highlighted previously. CURTAIN and CURTAIN-PTM are free to use and open source, enabling researchers to share and maximize the impact of their proteomics data. We advocate that MS data published in volcano plot format be reported containing a shareable CURTAIN weblink, thereby allowing readers to better analyze and exploit the data.
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Affiliation(s)
- Toan K. Phung
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Kerryn Berndsen
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Rosamund Shastry
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Tran L. C. H. B. Phan
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Miratul M. K. Muqit
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Raja S. Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
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Silva Barbosa AC, Pfister KE, Chiba T, Bons J, Rose JP, Burton JB, King CD, O'Broin A, Young V, Zhang B, Sivakama B, Schmidt AV, Uhlean R, Oda A, Schilling B, Goetzman ES, Sims-Lucas S. Dicarboxylic Acid Dietary Supplementation Protects against AKI. J Am Soc Nephrol 2024; 35:135-148. [PMID: 38044490 PMCID: PMC10843194 DOI: 10.1681/asn.0000000000000266] [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: 03/17/2023] [Accepted: 10/20/2023] [Indexed: 12/05/2023] Open
Abstract
SIGNIFICANCE STATEMENT In this study, we demonstrate that a common, low-cost compound known as octanedioic acid (DC 8 ) can protect mice from kidney damage typically caused by ischemia-reperfusion injury or the chemotherapy drug cisplatin. This compound seems to enhance peroxisomal activity, which is responsible for breaking down fats, without adversely affecting mitochondrial function. DC 8 is not only affordable and easy to administer but also effective. These encouraging findings suggest that DC 8 could potentially be used to assist patients who are at risk of experiencing this type of kidney damage. BACKGROUND Proximal tubules are rich in peroxisomes, which are damaged during AKI. Previous studies demonstrated that increasing peroxisomal fatty acid oxidation (FAO) is renoprotective, but no therapy has emerged to leverage this mechanism. METHODS Mice were fed with either a control diet or a diet enriched with dicarboxylic acids, which are peroxisome-specific FAO substrates, then subjected to either ischemia-reperfusion injury-AKI or cisplatin-AKI models. Biochemical, histologic, genetic, and proteomic analyses were performed. RESULTS Both octanedioic acid (DC 8 ) and dodecanedioic acid (DC 12 ) prevented the rise of AKI markers in mice that were exposed to renal injury. Proteomics analysis demonstrated that DC 8 preserved the peroxisomal and mitochondrial proteomes while inducing extensive remodeling of the lysine succinylome. This latter finding indicates that DC 8 is chain shortened to the anaplerotic substrate succinate and that peroxisomal FAO was increased by DC 8 . CONCLUSIONS DC 8 supplementation protects kidney mitochondria and peroxisomes and increases peroxisomal FAO, thereby protecting against AKI.
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Affiliation(s)
- Anne C. Silva Barbosa
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Katherine E. Pfister
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Takuto Chiba
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, California
| | | | | | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, California
| | - Victoria Young
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bob Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bharathi Sivakama
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexandra V. Schmidt
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rebecca Uhlean
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Akira Oda
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Eric S. Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sunder Sims-Lucas
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
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Lou R, Shui W. Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023. Mol Cell Proteomics 2024; 23:100712. [PMID: 38182042 PMCID: PMC10847697 DOI: 10.1016/j.mcpro.2024.100712] [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: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate, and reproducible quantitative proteomics. This review provides a comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools. DIA acquisition schemes are categorized based on the design of precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, and parallel accumulation-serial fragmentation-enhanced DIA methods. For DIA data analysis, major strategies are classified into spectrum reconstruction, sequence-based search, library-based search, de novo sequencing, and sequencing-independent approaches. A wide array of software tools implementing these strategies are reviewed, with details on their overall workflows and scoring approaches at different steps. The generation and optimization of spectral libraries, which are critical resources for DIA analysis, are also discussed. Publicly available benchmark datasets covering global proteomics and phosphoproteomics are summarized to facilitate performance evaluation of various software tools and analysis workflows. Continued advances and synergistic developments of versatile components in DIA workflows are expected to further enhance the power of DIA-based proteomics.
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Affiliation(s)
- Ronghui Lou
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Mylopotamitaki D, Weiss M, Fewlass H, Zavala EI, Rougier H, Sümer AP, Hajdinjak M, Smith GM, Ruebens K, Sinet-Mathiot V, Pederzani S, Essel E, Harking FS, Xia H, Hansen J, Kirchner A, Lauer T, Stahlschmidt M, Hein M, Talamo S, Wacker L, Meller H, Dietl H, Orschiedt J, Olsen JV, Zeberg H, Prüfer K, Krause J, Meyer M, Welker F, McPherron SP, Schüler T, Hublin JJ. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 2024; 626:341-346. [PMID: 38297117 PMCID: PMC10849966 DOI: 10.1038/s41586-023-06923-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany.
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Elena Irene Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Karen Ruebens
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Bordeaux, France
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Huan Xia
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Jakob Hansen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - André Kirchner
- Department of Soil Protection and Soil Survey, State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Michael Hein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Ecology, Leuphana University, Lüneburg, Germany
- Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, Leipzig, Germany
| | - Sahra Talamo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Bologna University, Bologna, Italy
| | - Lukas Wacker
- Ion Beam Physics, ETH Zurich, Zurich, Switzerland
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Ding H, Shi Z, Lin H, Sun Y, Zhang L, Liu F, Wang X, Zhang Z, Zhang G. Serum proteomics identifies novel diagnostic biomarkers for asthma in preschool children. J Thorac Dis 2024; 16:65-80. [PMID: 38410598 PMCID: PMC10894366 DOI: 10.21037/jtd-23-974] [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: 06/19/2023] [Accepted: 11/17/2023] [Indexed: 02/28/2024]
Abstract
Background Asthma is characterized by airway hyperresponsiveness, reversible airway obstruction, and chronic airway inflammation. It is the most common chronic disease in childhood. However, the diagnosis of childhood asthma remains challenging, and there is an urgent need to develop new diagnostic methods. Methods To identify biomarkers of asthma in children, we adopted the Orbitrap-based data-independent acquisition (DIA) mass spectrometry proteomics method to analyze the serum proteomic signatures of children with acute asthma and convalescent children. Results We identified 747 proteins in 46 serum samples and 50 differentially expressed proteins (DEPs) that distinguished between asthmatic and healthy children. Next, functional enrichment analysis of the DEPs was conducted, it was indicated that the DEPs were significantly enriched in immune-related and function terms and pathways. Furthermore, we performed statistical analysis and identified MMP14, ABHD12B, PCYOX1, LTBP1, CFHR4, APOA1, IGHG4, ANG and IGFALS proteins as the diagnostic biomarker candidates. Ultimately, a promising asthma diagnostic model for preschool children based on IGFALS was built and evaluated. The area under the curve (AUC) of the IGFALS model was 0.959. Conclusions In this study, the DIA proteome strategy was used and the largest number of proteins of asthmatic children serum proteomics was identified. The proteomics results showed that the DEPs play the central role of the inflammation-immune mechanism in asthma pathogenesis, suggesting that these proteins may be used in asthma diagnosis, prognosis, or therapy, and suggested biomarkers for asthma of preschool children. In conclusion, our results provide insight into the pathophysiology of asthma. We believe that the diagnostic model will facilitate clinical decision-making regarding asthma in preschool children.
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Affiliation(s)
| | | | - Haibo Lin
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuan Sun
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Lu Zhang
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Feiyan Liu
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xuelin Wang
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhihong Zhang
- Department of Pediatrics, Children’s Hospital, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
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Liao X, Li W, Zhou H, Rajendran BK, Li A, Ren J, Luan Y, Calderwood DA, Turk B, Tang W, Liu Y, Wu D. The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8 + T cells. Nat Commun 2024; 15:603. [PMID: 38242867 PMCID: PMC10798966 DOI: 10.1038/s41467-024-44885-0] [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: 10/21/2022] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
CD8+ T cells play an important role in anti-tumor immunity. Better understanding of their regulation could advance cancer immunotherapies. Here we identify, via stepwise CRISPR-based screening, that CUL5 is a negative regulator of the core signaling pathways of CD8+ T cells. Knocking out CUL5 in mouse CD8+ T cells significantly improves their tumor growth inhibiting ability, with significant proteomic alterations that broadly enhance TCR and cytokine signaling and their effector functions. Chemical inhibition of neddylation required by CUL5 activation, also enhances CD8 effector activities with CUL5 validated as a major target. Mechanistically, CUL5, which is upregulated by TCR stimulation, interacts with the SOCS-box-containing protein PCMTD2 and inhibits TCR and IL2 signaling. Additionally, CTLA4 is markedly upregulated by CUL5 knockout, and its inactivation further enhances the anti-tumor effect of CUL5 KO. These results together reveal a negative regulatory mechanism for CD8+ T cells and have strong translational implications in cancer immunotherapy.
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Affiliation(s)
- Xiaofeng Liao
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Hongyue Zhou
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Barani Kumar Rajendran
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Ao Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jingjing Ren
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yi Luan
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Benjamin Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wenwen Tang
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Research Institute, Yale University School of Medicine, West Haven, CT, 06516, USA.
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Dianqing Wu
- Vascular Biology and Therapeutic Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, 06520, USA.
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43
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Augustine TN, Buthelezi S, Pather K, Xulu KR, Stoychev S. Secretomics reveals hormone-therapy of breast cancer may induce survival by facilitating hypercoagulation and immunomodulation in vitro. Sci Rep 2024; 14:1486. [PMID: 38233507 PMCID: PMC10794708 DOI: 10.1038/s41598-023-49755-1] [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: 07/07/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Tumour cell haematogenous dissemination is predicated on molecular changes that enhance their capacity for invasion and preparation of the pre-metastatic niche. It is increasingly evident that platelets play an essential role in this transformation. The systemic nature of signalling molecules and extravascular factors that participate in mediating platelet-tumour cell interactions led to the development of an in vitro co-culture using whole blood and breast tumour cells, allowing us to decipher the impact of hormone-therapy on tumour cells and associated changes in the plasma proteome. Using mass spectrometry, we determined dysregulation of proteins associated with maintaining an invasive tumour phenotype. Tumour changes in genes associated with EMT and survival were documented. This is postulated to be induced via tumour cell interactions with the coagulatory and immune systems. Results highlight tumour cell adaptability to both treatment and blood resulting in a pro-tumorigenic response and a hypercoagulatory state. We illustrate that the breast cancer cell secretome can be altered by hormone-therapy, subject to the tumour subphenotype and linked to platelet activation. More sophisticated co-culture systems are required to recapitulate these interactions to better understand tumorigenesis. Moreover, deeper plasma profiling, using abundant protein depleted and/or vesicle enriched strategies, will likely reveal additional secretory proteins related to tumour cell-platelet interactions.
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Affiliation(s)
- Tanya N Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Sindisiwe Buthelezi
- Department of Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Kyrtania Pather
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kutlwano R Xulu
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stoyan Stoychev
- Department of Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa.
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44
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Saumer P, Scheffner M, Marx A, Stengel F. Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2. Nucleic Acids Res 2024; 52:101-113. [PMID: 37994785 PMCID: PMC10783519 DOI: 10.1093/nar/gkad1113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Post-translational modifications (PTMs) of histones have fundamental effects on chromatin structure and function. While the impact of PTMs on the function of core histones are increasingly well understood, this is much less the case for modifications of linker histone H1, which is at least in part due to a lack of proper tools. In this work, we establish the assembly of intact chromatosomes containing site-specifically ubiquitylated and acetylated linker histone H1.2 variants obtained by a combination of chemical biology approaches. We then use these complexes in a tailored affinity enrichment mass spectrometry workflow to identify and comprehensively characterize chromatosome-specific cellular interactomes and the impact of site-specific linker histone modifications on a proteome-wide scale. We validate and benchmark our approach by western-blotting and by confirming the involvement of chromatin-bound H1.2 in the recruitment of proteins involved in DNA double-strand break repair using an in vitro ligation assay. We relate our data to previous work and in particular compare it to data on modification-specific interaction partners of free H1. Taken together, our data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions beyond DNA compaction and constitutes an important resource for future investigations of histone epigenetic modifications.
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Affiliation(s)
- Philip Saumer
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
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Wilson KA, Bar S, Dammer EB, Carrera EM, Hodge BA, Hilsabeck TAU, Bons J, Brownridge GW, Beck JN, Rose J, Granath-Panelo M, Nelson CS, Qi G, Gerencser AA, Lan J, Afenjar A, Chawla G, Brem RB, Campeau PM, Bellen HJ, Schilling B, Seyfried NT, Ellerby LM, Kapahi P. OXR1 maintains the retromer to delay brain aging under dietary restriction. Nat Commun 2024; 15:467. [PMID: 38212606 PMCID: PMC10784588 DOI: 10.1038/s41467-023-44343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Dietary restriction (DR) delays aging, but the mechanism remains unclear. We identified polymorphisms in mtd, the fly homolog of OXR1, which influenced lifespan and mtd expression in response to DR. Knockdown in adulthood inhibited DR-mediated lifespan extension in female flies. We found that mtd/OXR1 expression declines with age and it interacts with the retromer, which regulates trafficking of proteins and lipids. Loss of mtd/OXR1 destabilized the retromer, causing improper protein trafficking and endolysosomal defects. Overexpression of retromer genes or pharmacological restabilization with R55 rescued lifespan and neurodegeneration in mtd-deficient flies and endolysosomal defects in fibroblasts from patients with lethal loss-of-function of OXR1 variants. Multi-omic analyses in flies and humans showed that decreased Mtd/OXR1 is associated with aging and neurological diseases. mtd/OXR1 overexpression rescued age-related visual decline and tauopathy in a fly model. Hence, OXR1 plays a conserved role in preserving retromer function and is critical for neuronal health and longevity.
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Affiliation(s)
- Kenneth A Wilson
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sudipta Bar
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Brian A Hodge
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Tyler A U Hilsabeck
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jennifer N Beck
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | | | - Grace Qi
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jianfeng Lan
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Guanxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, The Afilliated Hospital of Guilin Medican University, Guilin, 541001, Guanxi, China
| | - Alexandra Afenjar
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire, Paris, 75012, France
- Département de Génétique et Embryologie Médicale, CRMR des Malformations et Maladies Congénitales du Cervelet, GRC ConCer-LD, Sorbonne Universités, Hôpital Trousseau, Paris, 75012, France
| | - Geetanjali Chawla
- RNA Biology Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institute of Eminence, NH91, Tehsil Dadri, G. B. Nagar, 201314, Uttar Pradesh, India
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC, H3T 1J4, Canada
| | - Hugo J Bellen
- Departments of Molecular and Human Genetics and Neuroscience, Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
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46
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Moutin EB, Bons J, Giavara G, Lourenco F, Pan D, Burton JB, Shah S, Colombé M, Gascard P, Tlsty T, Schilling B, Winton DJ. Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon. Cell Mol Gastroenterol Hepatol 2024; 17:639-656. [PMID: 38199279 PMCID: PMC10905044 DOI: 10.1016/j.jcmgh.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is both a consequence and a mediator of disease progression. Despite previous characterization of epithelial and stromal remodeling during inflammatory bowel disease, a complete understanding of its impact on disease progression is lacking. METHODS A comprehensive proteomic pipeline using data-independent acquisition was applied to decellularized colon samples from the Muc2 knockout (Muc2KO) mouse model of colitis for an in-depth characterization of extracellular matrix remodeling. Unique proteomic profiles of the matrisomal landscape were extracted from prepathologic and overt colitis. Integration of proteomics and transcriptomics data sets extracted from the same murine model produced network maps describing the orchestrating role of matrisomal proteins in tissue remodeling during the progression of colitis. RESULTS The in-depth proteomic workflow used here allowed the addition of 34 proteins to the known colon matrisomal signature. Protein signatures of prepathologic and pathologic colitic states were extracted, differentiating the 2 states by expression of small leucine-rich proteoglycans. We outlined the role of this class and other matrisomal proteins in tissue remodeling during colitis, as well as the potential for coordinated regulation of cell types by matrisomal ligands. CONCLUSIONS Our work highlights a central role for matrisomal proteins in tissue remodeling during colitis and defines orchestrating nodes that can be exploited in the selection of therapeutic targets.
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Affiliation(s)
- Elisa B Moutin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Giada Giavara
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Filipe Lourenco
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Deng Pan
- Department of Pathology, University of California, San Francisco, California
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, California
| | - Mathilde Colombé
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Philippe Gascard
- Department of Pathology, University of California, San Francisco, California
| | - Thea Tlsty
- Department of Pathology, University of California, San Francisco, California
| | | | - Douglas J Winton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom.
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47
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Xu A, Tang LC, Jovanovic M, Regev O. Uncovering Distinct Peptide Charging Behaviors in Electrospray Ionization Mass Spectrometry Using a Large-Scale Dataset. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:90-99. [PMID: 38095561 PMCID: PMC10767741 DOI: 10.1021/jasms.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Electrospray ionization is a powerful and prevalent technique used to ionize analytes in mass spectrometry. The distribution of charges that an analyte receives (charge state distribution, CSD) is an important consideration for interpreting mass spectra. However, due to an incomplete understanding of the ionization mechanism, the analyte properties that influence CSDs are not fully understood. Here, we employ a machine learning-based approach and analyze CSDs of hundreds of thousands of peptides. Interestingly, half of the peptides exhibit charges that differ from what one would naively expect (the number of basic sites). We find that these peptides can be classified into two regimes (undercharging and overcharging) and that these two regimes display markedly different charging characteristics. Notably, peptides in the overcharging regime show minimal dependence on basic site count, and more generally, the two regimes exhibit distinct sequence determinants. These findings highlight the rich ionization behavior of peptides and the potential of CSDs for enhancing peptide identification.
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Affiliation(s)
- Allyn
M. Xu
- Department
of Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Lauren C. Tang
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Marko Jovanovic
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Oded Regev
- Computer
Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
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48
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Rice SJ, Belani CP. Design of experiments approach for systematic optimization of a single-shot diaPASEF plasma proteomics workflow applicable for high-throughput. Proteomics Clin Appl 2024; 18:e2300006. [PMID: 37650339 DOI: 10.1002/prca.202300006] [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: 01/20/2023] [Revised: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
PURPOSE Plasma is an abundant source of protein biomarkers. Mass spectrometry (MS) is an effective means to measure a large number of proteins in a single run. The recent development of data-independent acquisition with parallel accumulation and serial fragmentation (diaPASEF) on a trapped ion mobility spectrometer (TIMS) affords deep proteomic coverage with short liquid chromatography gradients. In this work, we utilized a process optimization approach, design of experiments (DoE), to maximize precursor identification for a plasma proteomic diaPASEF workflow. EXPERIMENTAL DESIGN A partial factorial design was used to screen 11 sample preparation factors and six diaPASEF MS acquisition factors. Selected factors were optimized using the response surface method. RESULTS Three important sample preparation factors and the two important MS acquisition factors were identified in the screening experiments and were selected for separate optimization experiments. The optimal parameters were compared to our standard plasma proteomics workflows using either a 1-h or overnight trypsin digestion. The optimized method outperformed the 1-h digestion, and it was similar in performance to the overnight digestion, however, the optimized method could be completed in a day. CONCLUSION AND CLINICAL RELEVANCE We have used DoE to report an optimized plasma proteomics workflow for diaPASEF, however, established methods are already highly optimized, and resources may be better spent on running samples than comprehensive optimization.
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Affiliation(s)
- Shawn J Rice
- Penn State Cancer Institute, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Chandra P Belani
- Penn State Cancer Institute, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
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Tshilenge KT, Bons J, Aguirre CG, Geronimo-Olvera C, Shah S, Rose J, Gerencser AA, Mak SK, Ehrlich ME, Bragg DC, Schilling B, Ellerby LM. Proteomic analysis of X-linked dystonia parkinsonism disease striatal neurons reveals altered RNA metabolism and splicing. Neurobiol Dis 2024; 190:106367. [PMID: 38042508 PMCID: PMC11103251 DOI: 10.1016/j.nbd.2023.106367] [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: 09/22/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a rare neurodegenerative disease endemic to the Philippines. The genetic cause for XDP is an insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within intron 32 of TATA-binding protein associated factor 1 (TAF1) that causes an alteration of TAF1 splicing, partial intron retention, and decreased transcription. Although TAF1 is expressed in all organs, medium spiny neurons (MSNs) within the striatum are one of the cell types most affected in XDP. To define how mutations in the TAF1 gene lead to MSN vulnerability, we carried out a proteomic analysis of human XDP patient-derived neural stem cells (NSCs) and MSNs derived from induced pluripotent stem cells. NSCs and MSNs were grown in parallel and subjected to quantitative proteomic analysis in data-independent acquisition mode on the Orbitrap Eclipse Tribrid mass spectrometer. Subsequent functional enrichment analysis demonstrated that neurodegenerative disease-related pathways, such as Huntington's disease, spinocerebellar ataxia, cellular senescence, mitochondrial function and RNA binding metabolism, were highly represented. We used weighted coexpression network analysis (WGCNA) of the NSC and MSN proteomic data set to uncover disease-driving network modules. Three of the modules significantly correlated with XDP genotype when compared to the non-affected control and were enriched for DNA helicase and nuclear chromatin assembly, mitochondrial disassembly, RNA location and mRNA processing. Consistent with aberrant mRNA processing, we found splicing and intron retention of TAF1 intron 32 in XDP MSN. We also identified TAF1 as one of the top enriched transcription factors, along with YY1, ATF2, USF1 and MYC. Notably, YY1 has been implicated in genetic forms of dystonia. Overall, our proteomic data set constitutes a valuable resource to understand mechanisms relevant to TAF1 dysregulation and to identify new therapeutic targets for XDP.
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Affiliation(s)
| | - Joanna Bons
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Carlos Galicia Aguirre
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - Samah Shah
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Jacob Rose
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Akos A Gerencser
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Sally K Mak
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA, USA
| | - Birgit Schilling
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
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50
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Souchet B, Michaïl A, Heuillet M, Dupuy-Gayral A, Haudebourg E, Pech C, Berthemy AA, Autelitano F, Billoir B, Domoto-Reilly K, Fowler C, Grabowski T, Jayadev S, Masters CL, Braudeau J. Multiomics Blood-Based Biomarkers Predict Alzheimer's Predementia with High Specificity in a Multicentric Cohort Study. J Prev Alzheimers Dis 2024; 11:567-581. [PMID: 38706273 PMCID: PMC11061038 DOI: 10.14283/jpad.2024.34] [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: 11/21/2023] [Accepted: 01/06/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND The primary criteria for diagnosing mild cognitive impairment (MCI) due to Alzheimer's Disease (AD) or probable mild AD dementia rely partly on cognitive assessments and the presence of amyloid plaques. Although these criteria exhibit high sensitivity in predicting AD among cognitively impaired patients, their specificity remains limited. Notably, up to 25% of non-demented patients with amyloid plaques may be misdiagnosed with MCI due to AD, when in fact they suffer from a different brain disorder. The introduction of anti-amyloid antibodies complicates this scenario. Physicians must prioritize which amyloid-positive MCI patients receive these treatments, as not all are suitable candidates. Specifically, those with non-AD amyloid pathologies are not primary targets for amyloid-modifying therapies. Consequently, there is an escalating medical necessity for highly specific blood biomarkers that can accurately detect pre-dementia AD, thus optimizing amyloid antibody prescription. OBJECTIVES The objective of this study was to evaluate a predictive model based on peripheral biomarkers to identify MCI and mild dementia patients who will develop AD dementia symptoms in cognitively impaired population with high specificity. DESIGN Peripheral biomarkers were identified in a gene transfer-based animal model of AD and then validated during a retrospective multi-center clinical study. SETTING Participants from 7 retrospective cohorts (US, EU and Australia). PARTICIPANTS This study followed 345 cognitively impaired individuals over up to 13 years, including 193 with MCI and 152 with mild dementia, starting from their initial visits. The final diagnoses, established during their last assessments, classified 249 participants as AD patients and 96 as having non-AD brain disorders, based on the specific diagnostic criteria for each disorder subtype. Amyloid status, assessed at baseline, was available for 82.9% of the participants, with 61.9% testing positive for amyloid. Both amyloid-positive and negative individuals were represented in each clinical group. Some of the AD patients had co-morbidities such as metabolic disorders, chronic diseases, or cardiovascular pathologies. MEASUREMENTS We developed targeted mass spectrometry assays for 81 blood-based biomarkers, encompassing 45 proteins and 36 metabolites previously identified in AAV-AD rats. METHODS We analyzed blood samples from study participants for the 81 biomarkers. The B-HEALED test, a machine learning-based diagnostic tool, was developed to differentiate AD patients, including 123 with Prodromal AD and 126 with mild AD dementia, from 96 individuals with non-AD brain disorders. The model was trained using 70% of the data, selecting relevant biomarkers, calibrating the algorithm, and establishing cutoff values. The remaining 30% served as an external test dataset for blind validation of the predictive accuracy. RESULTS Integrating a combination of 19 blood biomarkers and participant age, the B-HEALED model successfully distinguished participants that will develop AD dementia symptoms (82 with Prodromal AD and 83 with AD dementia) from non-AD subjects (71 individuals) with a specificity of 93.0% and sensitivity of 65.4% (AUROC=81.9%, p<0.001) during internal validation. When the amyloid status (derived from CSF or PET scans) and the B-HEALED model were applied in association, with individuals being categorized as AD if they tested positive in both tests, we achieved 100% specificity and 52.8% sensitivity. This performance was consistent in blind external validation, underscoring the model's reliability on independent datasets. CONCLUSIONS The B-HEALED test, utilizing multiomics blood-based biomarkers, demonstrates high predictive specificity in identifying AD patients within the cognitively impaired population, minimizing false positives. When used alongside amyloid screening, it effectively identifies a nearly pure prodromal AD cohort. These results bear significant implications for refining clinical trial inclusion criteria, facilitating drug development and validation, and accurately identifying patients who will benefit the most from disease-modifying AD treatments.
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Affiliation(s)
- B Souchet
- Jérôme Braudeau, AgenT, 4 rue Pierre Fontaine, 91000 Evry-Courcouronnes, France. e-mail address: , Telephone: +33 6 11 10 26 95
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